based microbial monitor: Topics by Science.gov

Sample records for based microbial monitor

Impact of an indigenous microbial enhanced oil recovery field trial on microbial community structure in a high pour-point oil reservoir.

PubMed

Zhang, Fan; She, Yue-Hui; Li, Hua-Min; Zhang, Xiao-Tao; Shu, Fu-Chang; Wang, Zheng-Liang; Yu, Long-Jiang; Hou, Du-Jie

2012-08-01

Based on preliminary investigation of microbial populations in a high pour-point oil reservoir, an indigenous microbial enhanced oil recovery (MEOR) field trial was carried out. The purpose of the study is to reveal the impact of the indigenous MEOR process on microbial community structure in the oil reservoir using 16Sr DNA clone library technique. The detailed monitoring results showed significant response of microbial communities during the field trial and large discrepancies of stimulated microorganisms in the laboratory and in the natural oil reservoir. More specifically, after nutrients injection, the original dominant populations of Petrobacter and Alishewanella in the production wells almost disappeared. The expected desirable population of Pseudomonas aeruginosa, determined by enrichment experiments in laboratory, was stimulated successfully in two wells of the five monitored wells. Unexpectedly, another potential population of Pseudomonas pseudoalcaligenes which were not detected in the enrichment culture in laboratory was stimulated in the other three monitored production wells. In this study, monitoring of microbial community displayed a comprehensive alteration of microbial populations during the field trial to remedy the deficiency of culture-dependent monitoring methods. The results would help to develop and apply more MEOR processes.
Inflight Microbial Monitoring - An Alternative Method to Culture Based Detection Currently Used on the International Space Station

NASA Technical Reports Server (NTRS)

Khodadad, Christina L.; Birmele, Michele N.; Hummerick, Mary E.; Roman, Monsi; Smith, David J.

2015-01-01

Microorganisms including potential human pathogens have been detected on the International Space Station (ISS). The potential to introduce new microorganisms occurs with every exchange of crew or addition of equipment or supplies. Current microbial monitoring methods require enrichment of microorganisms and a 48-hour incubation time resulting in an increase in microbial load, detecting a limited number of unidentified microorganisms. An expedient, low-cost, in-flight method of microbial detection, identification, and enumeration is warranted.
Microbial monitoring of spacecraft and associated environments

NASA Technical Reports Server (NTRS)

La Duc, M. T.; Kern, R.; Venkateswaran, K.

2004-01-01

Rapid microbial monitoring technologies are invaluable in assessing contamination of spacecraft and associated environments. Universal and widespread elements of microbial structure and chemistry are logical targets for assessing microbial burden. Several biomarkers such as ATP, LPS, and DNA (ribosomal or spore-specific), were targeted to quantify either total bioburden or specific types of microbial contamination. The findings of these assays were compared with conventional, culture-dependent methods. This review evaluates the applicability and efficacy of some of these methods in monitoring the microbial burden of spacecraft and associated environments. Samples were collected from the surfaces of spacecraft, from surfaces of assembly facilities, and from drinking water reservoirs aboard the International Space Station (ISS). Culture-dependent techniques found species of Bacillus to be dominant on these surfaces. In contrast, rapid, culture-independent techniques revealed the presence of many Gram-positive and Gram-negative microorganisms, as well as actinomycetes and fungi. These included both cultivable and noncultivable microbes, findings further confirmed by DNA-based microbial detection techniques. Although the ISS drinking water was devoid of cultivable microbes, molecular-based techniques retrieved DNA sequences of numerous opportunistic pathogens. Each of the methods tested in this study has its advantages, and by coupling two or more of these techniques even more reliable information as to microbial burden is rapidly obtained. Copyright 2004 Springer-Verlag.
Expansion of Microbial Monitoring Capabilities on the International Space Station (ISS)

NASA Technical Reports Server (NTRS)

Khodadad, Christina L.; Oubre, Cherie; Castro, Victoria; Flint, Stephanie; Melendez, Orlando; Ott, C. Mark; Roman, Monsi

2017-01-01

Microbial monitoring is one of the tools that the National Aeronautics and Space Administration (NASA) uses on the International Space Station (ISS) to help maintain crew health and safety. In combination with regular housekeeping and disinfection when needed, microbial monitoring provides important information to the crew about the quality of the environment. Rotation of astronauts, equipment, and cargo on the ISS can affect the microbial load in the air, surfaces, and water. The current ISS microbial monitoring methods are focused on culture-based enumeration during flight and require a significant amount of crew time as well as long incubation periods of up to 5 days there by proliferating potential pathogens. In addition, the samples require return to Earth for complete identification of the microorganisms cultivated. Although the current approach assess the quality of the ISS environment, molecular technology offers faster turn-around of information particularly beneficial in an off-nominal situation. In 2011, subject matter experts from industry and academia recommended implementation of molecular-based technologies such as quantitative real-time polymerase chain reaction (qPCR) for evaluation to replace current, culture-based technologies. The RAZOR EX (BioFire Defense, Inc, Salt Lake City, UT) a ruggedized, compact, COTS (commercial off the shelf) qPCR instrument was tested, evaluated and selected in the 2 X 2015 JSC rapid flight hardware demonstration initiative as part of the Water Monitoring Suite. RAZOR EX was launched to ISS on SpaceX-9 in July 2016 to evaluate the precision and accuracy of the hardware by testing various concentrations of DNA in microgravity compared to ground controls. Flight testing was completed between September 2016 and March 2017. Data presented will detail the hardware performance of flight testing results compared to ground controls. Future goals include additional operational ground-based testing and assay development to determine if this technology can meet spaceflight microbial monitoring requirements.
Rapid detection of microbial cell abundance in aquatic systems

DOE PAGES

Rocha, Andrea M.; Yuan, Quan; Close, Dan M.; ...

2016-06-01

The detection and quantification of naturally occurring microbial cellular densities is an essential component of environmental systems monitoring. While there are a number of commonly utilized approaches for monitoring microbial abundance, capacitance-based biosensors represent a promising approach because of their low-cost and label-free detection of microbial cells, but are not as well characterized as more traditional methods. Here, we investigate the applicability of enhanced alternating current electrokinetics (ACEK) capacitive sensing as a new application for rapidly detecting and quantifying microbial cellular densities in cultured and environmentally sourced aquatic samples. ACEK capacitive sensor performance was evaluated using two distinct and dynamicmore » systems the Great Australian Bight and groundwater from the Oak Ridge Reservation in Oak Ridge, TN. Results demonstrate that ACEK capacitance-based sensing can accurately determine microbial cell counts throughout cellular concentrations typically encountered in naturally occurring microbial communities (10 3 – 10 6 cells/mL). A linear relationship was observed between cellular density and capacitance change correlations, allowing a simple linear curve fitting equation to be used for determining microbial abundances in unknown samples. As a result, this work provides a foundation for understanding the limits of capacitance-based sensing in natural environmental samples and supports future efforts focusing on evaluating the robustness ACEK capacitance-based within aquatic environments.« less
Rapid detection of microbial cell abundance in aquatic systems

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

Rocha, Andrea M.; Yuan, Quan; Close, Dan M.

The detection and quantification of naturally occurring microbial cellular densities is an essential component of environmental systems monitoring. While there are a number of commonly utilized approaches for monitoring microbial abundance, capacitance-based biosensors represent a promising approach because of their low-cost and label-free detection of microbial cells, but are not as well characterized as more traditional methods. Here, we investigate the applicability of enhanced alternating current electrokinetics (ACEK) capacitive sensing as a new application for rapidly detecting and quantifying microbial cellular densities in cultured and environmentally sourced aquatic samples. ACEK capacitive sensor performance was evaluated using two distinct and dynamicmore » systems the Great Australian Bight and groundwater from the Oak Ridge Reservation in Oak Ridge, TN. Results demonstrate that ACEK capacitance-based sensing can accurately determine microbial cell counts throughout cellular concentrations typically encountered in naturally occurring microbial communities (10 3 – 10 6 cells/mL). A linear relationship was observed between cellular density and capacitance change correlations, allowing a simple linear curve fitting equation to be used for determining microbial abundances in unknown samples. As a result, this work provides a foundation for understanding the limits of capacitance-based sensing in natural environmental samples and supports future efforts focusing on evaluating the robustness ACEK capacitance-based within aquatic environments.« less
Monitoring minimization of grade B environments based on risk assessment using three-dimensional airflow measurements and computer simulation.

PubMed

Katayama, Hirohito; Higo, Takashi; Tokunaga, Yuji; Katoh, Shigeo; Hiyama, Yukio; Morikawa, Kaoru

2008-01-01

A practical, risk-based monitoring approach using the combined data collected from actual experiments and computer simulations was developed for the qualification of an EU GMP Annex 1 Grade B, ISO Class 7 area. This approach can locate and minimize the representative number of sampling points used for microbial contamination risk assessment. We conducted a case study on an aseptic clean room, newly constructed and specifically designed for the use of a restricted access barrier system (RABS). Hotspots were located using three-dimensional airflow analysis based on a previously published empirical measurement method, the three-dimensional airflow analysis. Local mean age of air (LMAA) values were calculated based on computer simulations. Comparable results were found using actual measurements and simulations, demonstrating the potential usefulness of such tools in estimating contamination risks based on the airflow characteristics of a clean room. Intensive microbial monitoring and particle monitoring at the Grade B environmental qualification stage, as well as three-dimensional airflow analysis, were also conducted to reveal contamination hotspots. We found representative hotspots were located at perforated panels covering the air exhausts where the major piston airflows collect in the Grade B room, as well as at any locations within the room that were identified as having stagnant air. However, we also found that the floor surface air around the exit airway of the RABS EU GMP Annex 1 Grade A, ISO Class 5 area was always remarkably clean, possibly due to the immediate sweep of the piston airflow, which prevents dispersed human microbes from falling in a Stokes-type manner on settling plates placed on the floor around the Grade A exit airway. In addition, this airflow is expected to be clean with a significantly low LMAA. Based on these observed results, we propose a simplified daily monitoring program to monitor microbial contamination in Grade B environments. To locate hotspots we propose using a combination of computer simulation, actual airflow measurements, and intensive environmental monitoring at the qualification stage. Thereafter, instead of particle or microbial air monitoring, we recommend the use of microbial surface monitoring at the main air exhaust. These measures would be sufficient to assure the efficiency of the monitoring program, as well as to minimize the number of surface sampling points used in environments surrounding a RABS.
Development and application of the microbial fate and transport module for the Agricultural Policy/Environmental eXtender (APEX) model

NASA Astrophysics Data System (ADS)

Hong, E.; Park, Y.; Muirhead, R.; Jeong, J.; Pachepsky, Y. A.

2017-12-01

Pathogenic microorganisms in recreational and irrigation waters remain the subject of concern. Water quality models are used to estimate microbial quality of water sources, to evaluate microbial contamination-related risks, to guide the microbial water quality monitoring, and to evaluate the effect of agricultural management on the microbial water quality. The Agricultural Policy/Environmental eXtender (APEX) is the watershed-scale water quality model that includes highly detailed representation of agricultural management. The APEX currently does not have microbial fate and transport simulation capabilities. The objective of this work was to develop the first APEX microbial fate and transport module that could use the APEX conceptual model of manure removal together with recently introduced conceptualizations of the in-stream microbial fate and transport. The module utilizes manure erosion rates found in the APEX. Bacteria survival in soil-manure mixing layer was simulated with the two-stage survival model. Individual survival patterns were simulated for each manure application date. Simulated in-stream microbial fate and transport processes included the reach-scale passive release of bacteria with resuspended bottom sediment during high flow events, the transport of bacteria from bottom sediment due to the hyporheic exchange during low flow periods, the deposition with settling sediment, and the two-stage survival. Default parameter values were available from recently published databases. The APEX model with the newly developed microbial fate and transport module was applied to simulate seven years of monitoring data for the Toenepi watershed in New Zealand. Based on calibration and testing results, the APEX with the microbe module reproduced well the monitored pattern of E. coli concentrations at the watershed outlet. The APEX with the microbial fate and transport module will be utilized for predicting microbial quality of water under various agricultural practices, evaluating monitoring protocols, and supporting the selection of management practices based on regulations that rely on fecal indicator bacteria concentrations.
Evaluating Monitoring Strategies to Detect Precipitation-Induced Microbial Contamination Events in Karstic Springs Used for Drinking Water

PubMed Central

Besmer, Michael D.; Hammes, Frederik; Sigrist, Jürg A.; Ort, Christoph

2017-01-01

Monitoring of microbial drinking water quality is a key component for ensuring safety and understanding risk, but conventional monitoring strategies are typically based on low sampling frequencies (e.g., quarterly or monthly). This is of concern because many drinking water sources, such as karstic springs are often subject to changes in bacterial concentrations on much shorter time scales (e.g., hours to days), for example after precipitation events. Microbial contamination events are crucial from a risk assessment perspective and should therefore be targeted by monitoring strategies to establish both the frequency of their occurrence and the magnitude of bacterial peak concentrations. In this study we used monitoring data from two specific karstic springs. We assessed the performance of conventional monitoring based on historical records and tested a number of alternative strategies based on a high-resolution data set of bacterial concentrations in spring water collected with online flow cytometry (FCM). We quantified the effect of increasing sampling frequency and found that for the specific case studied, at least bi-weekly sampling would be needed to detect precipitation events with a probability of >90%. We then proposed an optimized monitoring strategy with three targeted samples per event, triggered by precipitation measurements. This approach is more effective and efficient than simply increasing overall sampling frequency. It would enable the water utility to (1) analyze any relevant event and (2) limit median underestimation of peak concentrations to approximately 10%. We conclude with a generalized perspective on sampling optimization and argue that the assessment of short-term dynamics causing microbial peak loads initially requires increased sampling/analysis efforts, but can be optimized subsequently to account for limited resources. This offers water utilities and public health authorities systematic ways to evaluate and optimize their current monitoring strategies. PMID:29213255
Evaluating Monitoring Strategies to Detect Precipitation-Induced Microbial Contamination Events in Karstic Springs Used for Drinking Water.

PubMed

Besmer, Michael D; Hammes, Frederik; Sigrist, Jürg A; Ort, Christoph

2017-01-01

Monitoring of microbial drinking water quality is a key component for ensuring safety and understanding risk, but conventional monitoring strategies are typically based on low sampling frequencies (e.g., quarterly or monthly). This is of concern because many drinking water sources, such as karstic springs are often subject to changes in bacterial concentrations on much shorter time scales (e.g., hours to days), for example after precipitation events. Microbial contamination events are crucial from a risk assessment perspective and should therefore be targeted by monitoring strategies to establish both the frequency of their occurrence and the magnitude of bacterial peak concentrations. In this study we used monitoring data from two specific karstic springs. We assessed the performance of conventional monitoring based on historical records and tested a number of alternative strategies based on a high-resolution data set of bacterial concentrations in spring water collected with online flow cytometry (FCM). We quantified the effect of increasing sampling frequency and found that for the specific case studied, at least bi-weekly sampling would be needed to detect precipitation events with a probability of >90%. We then proposed an optimized monitoring strategy with three targeted samples per event, triggered by precipitation measurements. This approach is more effective and efficient than simply increasing overall sampling frequency. It would enable the water utility to (1) analyze any relevant event and (2) limit median underestimation of peak concentrations to approximately 10%. We conclude with a generalized perspective on sampling optimization and argue that the assessment of short-term dynamics causing microbial peak loads initially requires increased sampling/analysis efforts, but can be optimized subsequently to account for limited resources. This offers water utilities and public health authorities systematic ways to evaluate and optimize their current monitoring strategies.
Microbial Monitoring of Common Opportunistic Pathogens by Comparing Multiple Real-Time PCR Platforms for Potential Space Applications

NASA Technical Reports Server (NTRS)

Oubre, Cherie M.; Birmele, Michele N.; Castro, Victoria A.; Venkateswaran, Kasthuri J.; Vaishampayan, Parag A.; Jones, Kathy U.; Singhal, Adesh; Johnston, Angela S.; Roman, Monserrate C.; Ozbolt, Tamra A.;

2013-01-01

Because the International Space Station is a closed environment with rotations of astronauts and equipment that each introduce their own microbial flora, it is necessary to monitor the air, surfaces, and water for microbial contamination. Current microbial monitoring includes labor- and time-intensive methods to enumerate total bacterial and fungal cells, with limited characterization, during in-flight testing. Although this culture-based method is sufficient for monitoring the International Space Station, on future long-duration missions more detailed characterization will need to be performed during flight, as sample return and ground characterization may not be available. At a workshop held in 2011 at NASA's Johnson Space Center to discuss alternative methodologies and technologies suitable for microbial monitoring for these long-term exploration missions, molecular-based methodologies such as polymerase chain reaction (PCR) were recommended. In response, a multi-center (Marshall Space Flight Center, Johnson Space Center, Jet Propulsion Laboratory, and Kennedy Space Center) collaborative research effort was initiated to explore novel commercial-off-the-shelf hardware options for space flight environmental monitoring. The goal was to evaluate quantitative or semi-quantitative PCR approaches for low-cost in-flight rapid identification of microorganisms that could affect crew safety. The initial phase of this project identified commercially available platforms that could be minimally modified to perform nominally in microgravity. This phase was followed by proof-of-concept testing of the highest qualifying candidates with a universally available challenge organism, Salmonella enterica. The analysis identified two technologies that were able to perform sample-to-answer testing with initial cell sample concentrations between 50 and 400 cells. In addition, the commercial systems were evaluated for initial flight safety and readiness.

Development and evaluation of the microbial fate and transport module for the Agricultural Policy/Environmental eXtender (APEX) model

NASA Astrophysics Data System (ADS)

Hong, Eun-Mi; Park, Yongeun; Muirhead, Richard; Pachepsky, Yakov

2017-04-01

Pathogenic microorganisms in recreational and irrigation waters remain the subject of concern. Water quality models are used to estimate microbial quality of water sources, to evaluate microbial contamination-related risks, to guide the microbial water quality monitoring, and to evaluate the effect of agricultural management on the microbial water quality. The Agricultural Policy/Environmental eXtender (APEX) is the watershed-scale water quality model that includes highly detailed representation of agricultural management. The APEX currently does not have microbial fate and transport simulation capabilities. The objective of this work was to develop the first APEX microbial fate and transport module that could use the APEX conceptual model of manure removal together with recently introduced conceptualizations of the in-stream microbial fate and transport. The module utilizes manure erosion rates found in the APEX. The total number of removed bacteria was set to the concentrations of bacteria in soil-manure mixing layer and eroded manure amount. Bacteria survival in soil-manure mixing layer was simulated with the two-stage survival model. Individual survival patterns were simulated for each manure application date. Simulated in-stream microbial fate and transport processes included the reach-scale passive release of bacteria with resuspended bottom sediment during high flow events, the transport of bacteria from bottom sediment due to the hyporheic exchange during low flow periods, the deposition with settling sediment, and the two-stage survival. Default parameter values were available from recently published databases. The APEX model with the newly developed microbial fate and transport module was applied to simulate seven years of monitoring data for the Toenepi watershed in New Zealand. The stream network of the watershed ran through grazing lands with the daily bovine waste deposition. Based on calibration and testing results, the APEX with the microbe module reproduced well the monitored pattern of E. coli concentrations at the watershed outlet. The APEX with the microbial fate and transport module will be utilized for predicting microbial quality of water under various agricultural practices (grazing, cropping, and manure application), evaluating monitoring protocols, and supporting the selection of management practices based on regulations that rely on fecal indicator bacteria concentrations. Future development should include modeling contributions of wildlife, manure weathering, and weather effects on manure-borne microorganism survival and release.
Urinary catheter-associated microbiota change in accordance with treatment and infection status.

PubMed

Bossa, Laetitia; Kline, Kimberly; McDougald, Diane; Lee, Bonsan Bonne; Rice, Scott A

2017-01-01

The use of long-term catheterisation to manage insensate bladders, often associated with spinal cord injury (SCI), increases the risk of microbial colonisation and infection of the urinary tract. Urinary tract infection (UTI) is typically diagnosed and treated based on the culturing of organisms from the urine, although this approach overlooks low titer, slow growing and non-traditional pathogens. Here, we present an investigation of the urinary tract microbiome in catheterised SCI individuals, using T-RFLP and metagenomic sequencing of the microbial community. We monitored three neurogenic patients over a period of 12 months, who were part of a larger study investigating the efficacy of probiotics in controlling UTIs, to determine how their urinary tract microbial community composition changed over time and in relation to probiotic treatment regimens. Bacterial biofilms adherent to urinary catheters were examined as a proxy for bladder microbes. The microbial community composition of the urinary tract differed significantly between individuals. Probiotic therapy resulted in a significant change in the microbial community associated with the catheters. The community also changed as a consequence of UTI and this shift in community composition preceded the clinical diagnosis of infection. Changes in the microbiota due to probiotic treatment or infection were transient, resolving to microbial communities similar to their pre-treatment communities, suggesting that the native community was highly resilient. Based on these results, we propose that monitoring a patient's microbial community can be used to track the health of chronically catheterized patients and thus, can be used as part of a health-status monitoring program.
Urinary catheter-associated microbiota change in accordance with treatment and infection status

PubMed Central

Bossa, Laetitia; Kline, Kimberly; Lee, Bonsan Bonne

2017-01-01

The use of long-term catheterisation to manage insensate bladders, often associated with spinal cord injury (SCI), increases the risk of microbial colonisation and infection of the urinary tract. Urinary tract infection (UTI) is typically diagnosed and treated based on the culturing of organisms from the urine, although this approach overlooks low titer, slow growing and non-traditional pathogens. Here, we present an investigation of the urinary tract microbiome in catheterised SCI individuals, using T-RFLP and metagenomic sequencing of the microbial community. We monitored three neurogenic patients over a period of 12 months, who were part of a larger study investigating the efficacy of probiotics in controlling UTIs, to determine how their urinary tract microbial community composition changed over time and in relation to probiotic treatment regimens. Bacterial biofilms adherent to urinary catheters were examined as a proxy for bladder microbes. The microbial community composition of the urinary tract differed significantly between individuals. Probiotic therapy resulted in a significant change in the microbial community associated with the catheters. The community also changed as a consequence of UTI and this shift in community composition preceded the clinical diagnosis of infection. Changes in the microbiota due to probiotic treatment or infection were transient, resolving to microbial communities similar to their pre-treatment communities, suggesting that the native community was highly resilient. Based on these results, we propose that monitoring a patient’s microbial community can be used to track the health of chronically catheterized patients and thus, can be used as part of a health-status monitoring program. PMID:28628622
Environmental monitoring: data trending using a frequency model.

PubMed

Caputo, Ross A; Huffman, Anne

2004-01-01

Environmental monitoring programs for the oversight of classified environments have used traditional statistical control charts to monitor trends in microbial recovery for classified environments. These methodologies work well for environments that yield measurable microbial recoveries. However, today successful increased control of microbial content yields numerous instances where microbial recovery in a sample is generally zero. As a result, traditional control chart methods cannot be used appropriately. Two methods to monitor the performance of a classified environment where microbial recovery is zero are presented. Both methods use the frequency between non-zero microbial recovery as an event. Therefore, the frequency of events is monitored rather than the microbial recovery count. Both methods are shown to be appropriate for use in the described instances.
The microbiome as engineering tool: Manufacturing and trading between microorganisms.

PubMed

De Vrieze, Jo; Christiaens, Marlies E R; Verstraete, Willy

2017-10-25

The integration of microbial technologies within the framework of the water-energy nexus has been taking place for over a century, but these mixed microbial communities are considered hard to deal with 'black boxes'. Process steering is mainly based on avoiding process failure by monitoring conventional parameters, e.g., pH and temperature, which often leads to operation far below the intrinsic potential. Mixed microbial communities do not reflect a randomised individual mix, but an interacting microbiological entity. Advance monitoring to obtain effective engineering of the microbiome is achievable, and even crucial to obtain the desired performance and products. This can be achieved via a top-down or bottom-up approach. The top-down strategy is reflected in the microbial resource management concept that considers the microbial community as a well-structured network. This network can be monitored by means of molecular techniques that will allow the development of accurate and quick decision tools. In contrast, the bottom-up approach makes use of synthetic cultures that can be composed starting from defined axenic cultures, based on the requirements of the process under consideration. The success of both approaches depends on real-time monitoring and control. Of particular importance is the necessity to identify and characterise the key players in the process. These key players not only relate with the establishment of functional conversions, but also with the interaction between partner bacteria. This emphasises the importance of molecular (screening) techniques to obtain structural and functional insights, minimise energy input, and maximise product output by means of integrated microbiome processes. Copyright © 2017 Elsevier B.V. All rights reserved.
Microbial Monitoring of Pathogens by Comparing Multiple Real-Time PCR Platforms for Potential Space Applications

NASA Technical Reports Server (NTRS)

Birmele, Michele

2012-01-01

The International Space Station (ISS) is a closed environment wih rotations of crew and equipment each introducing their own microbial flora making it necessary to monitor the air, surfaces, and water for microbial contamination. Current microbial monitoring includes labor and time intensive methods to enumerate total bacterial and fungal cells with limited characterization during in-flight testing. Although this culture-based method has been sufficient for monitoring the ISS, future long duration missions will need to perform more comprehensive characterization in-flight, since sample return and ground characterization may not be available. A workshop was held in 2011 at the Johnson Space Center to discuss alternative methodologies and technologies suitable for microbial monitoring for these longterm exploration missions where molecular-based methodologies, such as polymerase chain reaction (PCR), were recommended. In response, a multi-center (Marshall Space Flight Center, Johnson Space Center, Jet Propulsion Laboratory, and Kennedy Space Center) collaborative research effort was initiated to explore novel commercial-off-the-shelf hardware options for spaceflight environmental monitoring. The goal was to evaluate quantitative/semi-quantitative PCR approaches to space applications for low cost in-flight rapid identification of microorganisms affecting crew safety. The initial phase of this project identified commercially available platforms that could be minimally modified to perform nominally in microgravity followed by proof-of-concept testing on the highest qualifying candidates with a universally available test organism, Salmonella enterica. The platforms evaluated during proof-of-concept testing included the iCubate 2.0(TradeMark) (iCubate, Huntsville, AL), RAZOR EX (BioFire Diagnostics; Salt Lake City, Utah) and SmartCycler(TradeMark) (Cepheid; Sunnyvale, CA). The analysis identified two potential technologies (iCubate 2.0 and RAZOR EX) that were able to perform sample-to-answer testing with cell sample concentrations between SO to 400 cells. In addition, the commercial systems were evaluated for initial flight safety and readiness, sample concentration needs were reviewed, and a competitive procurement of commercially available platforms was initiated.
Quantitative microbial faecal source tracking with sampling guided by hydrological catchment dynamics.

PubMed

Reischer, G H; Haider, J M; Sommer, R; Stadler, H; Keiblinger, K M; Hornek, R; Zerobin, W; Mach, R L; Farnleitner, A H

2008-10-01

The impairment of water quality by faecal pollution is a global public health concern. Microbial source tracking methods help to identify faecal sources but the few recent quantitative microbial source tracking applications disregarded catchment hydrology and pollution dynamics. This quantitative microbial source tracking study, conducted in a large karstic spring catchment potentially influenced by humans and ruminant animals, was based on a tiered sampling approach: a 31-month water quality monitoring (Monitoring) covering seasonal hydrological dynamics and an investigation of flood events (Events) as periods of the strongest pollution. The detection of a ruminant-specific and a human-specific faecal Bacteroidetes marker by quantitative real-time PCR was complemented by standard microbiological and on-line hydrological parameters. Both quantitative microbial source tracking markers were detected in spring water during Monitoring and Events, with preponderance of the ruminant-specific marker. Applying multiparametric analysis of all data allowed linking the ruminant-specific marker to general faecal pollution indicators, especially during Events. Up to 80% of the variation of faecal indicator levels during Events could be explained by ruminant-specific marker levels proving the dominance of ruminant faecal sources in the catchment. Furthermore, soil was ruled out as a source of quantitative microbial source tracking markers. This study demonstrates the applicability of quantitative microbial source tracking methods and highlights the prerequisite of considering hydrological catchment dynamics in source tracking study design.
Monitoring microbial metabolites using an inductively coupled resonance circuit

NASA Astrophysics Data System (ADS)

Karnaushenko, Daniil; Baraban, Larysa; Ye, Dan; Uguz, Ilke; Mendes, Rafael G.; Rümmeli, Mark H.; de Visser, J. Arjan G. M.; Schmidt, Oliver G.; Cuniberti, Gianaurelio; Makarov, Denys

2015-08-01

We present a new approach to monitor microbial population dynamics in emulsion droplets via changes in metabolite composition, using an inductively coupled LC resonance circuit. The signal measured by such resonance detector provides information on the magnetic field interaction with the bacterial culture, which is complementary to the information accessible by other detection means, based on electric field interaction, i.e. capacitive or resistive, as well as optical techniques. Several charge-related factors, including pH and ammonia concentrations, were identified as possible contributors to the characteristic of resonance detector profile. The setup enables probing the ionic byproducts of microbial metabolic activity at later stages of cell growth, where conventional optical detection methods have no discriminating power.
PCR Based Microbial Monitor for Analysis of Recycled Water Aboard the ISSA: Issues and Prospects

NASA Technical Reports Server (NTRS)

Cassell, Gail H.; Lefkowitz, Elliot J.; Glass, John I.

1995-01-01

The monitoring of spacecraft life support systems for the presence of health threatening microorganisms is paramount for crew well being and successful completion of missions. Development of technology to monitor spacecraft recycled water based on detection and identification of the genetic material of contaminating microorganisms and viruses would be a substantial improvement over current NASA plans to monitor recycled water samples that call for the use of conventional microbiology techniques which are slow, insensitive, and labor intensive. The union of the molecular biology techniques of DNA probe hybridization and polymerase chain reaction (PCR) offers a powerful method for the detection, identification, and quantification of microorganisms and viruses. This technology is theoretically capable of assaying samples in as little as two hours with specificity and sensitivity unmatched by any other method. A major advance in probe-hybridization/PCR has come about in a technology called TaqMan(TM), which was invented by Perkin Elmer. Instrumentation using TaqMan concepts is evolving towards devices that could meet NASA's needs of size, low power use, and simplicity of operation. The chemistry and molecular biology needed to utilize these probe-hybridization/PCR instruments must evolve in parallel with the hardware. The following issues of chemistry and biology must be addressed in developing a monitor: Early in the development of a PCR-based microbial monitor it will be necessary to decide how many and which organisms does the system need the capacity to detect. We propose a set of 17 different tests that would detect groups of bacteria and fungus, as well as specific eukaryotic parasites and viruses; In order to use the great sensitivity of PCR it will be necessary to concentrate water samples using filtration. If a lower limit of detection of 1 microorganism per 100 ml is required then the microbes in a 100 ml sample must be concentrated into a volume that can be added to a PCR assay; There are not likely to be contaminants in ISSA recycled water that would inhibit PCR resulting in false-negative results; The TaqMan PCR product detection system is the most promising method for developing a rapid, highly automated gene-based microbial monitoring system. The method is inherently quantitative. NASA and other government agencies have invested in other technologies that, although potentially could lead to revolutionary advances, are not likely to mature in the next 5 years into working systems; PCR-based methods cannot distinguish between DNA or RNA of a viable microorganism and that of a non-viable organism. This may or may not be an important issue with reclaimed water on the ISSA. The recycling system probably damages the capacity of the genetic material of any bacteria or viruses killed during processing to serve as a template in a PCR desinged to amplify a large segment of DNA (less than 650 base pairs). If necessary, vital dye staining could be used in addition to PCR, to enumerate the viable cells in a water sample; The quality control methods have been developed to insure that PCR's are working properly, and that reactions are not contaminated with PCR carryover products which could lead to the generation of false-positive results; and The sequences of the small rRNA subunit gene for a large number of microorganisms are known, and they consititue the best database for rational development of the oligonucleotide reagents that give PCR its great specificity. From those gene sequences, sets of oligonucleotide primers for PCR and Taqman detection that could be used in a NASA microbial monitor were constructed using computer based methods. In addition to space utilization, a microbial monitior will have tremendous terrestrial applications. Analysis of patient samples for microbial pathogens, testing industrial effluent for biofouling bacteria, and detection biological warfare agents on the battlefield are but a few of the diverse potential uses for this technology. Once fully developed, gene-based microbial monitors will become the fundamental tool in every lab that tests for microbial contaminants, and serve as a powerful weapon in mankind's war with the germ world.

Microbial Monitoring of Surface Water in South Africa: An Overview

PubMed Central

Luyt, Catherine D.; Tandlich, Roman; Muller, Wilhelmine J.; Wilhelmi, Brendan S.

2012-01-01

Infrastructural problems force South African households to supplement their drinking water consumption from water resources of inadequate microbial quality. Microbial water quality monitoring is currently based on the Colilert®18 system which leads to rapidly available results. Using Escherichia coli as the indicator microorganism limits the influence of environmental sources on the reported results. The current system allows for understanding of long-term trends of microbial surface water quality and the related public health risks. However, rates of false positive for the Colilert®18-derived concentrations have been reported to range from 7.4% to 36.4%. At the same time, rates of false negative results vary from 3.5% to 12.5%; and the Colilert medium has been reported to provide for cultivation of only 56.8% of relevant strains. Identification of unknown sources of faecal contamination is not currently feasible. Based on literature review, calibration of the antibiotic-resistance spectra of Escherichia coli or the bifidobacterial tracking ratio should be investigated locally for potential implementation into the existing monitoring system. The current system could be too costly to implement in certain areas of South Africa where the modified H2S strip test might be used as a surrogate for the Colilert®18. PMID:23066390
Dynamic monitoring of horizontal gene transfer in soil

NASA Astrophysics Data System (ADS)

Cheng, H. Y.; Masiello, C. A.; Silberg, J. J.; Bennett, G. N.

2015-12-01

Soil microbial gene expression underlies microbial behaviors (phenotypes) central to many aspects of C, N, and H2O cycling. However, continuous monitoring of microbial gene expression in soils is challenging because genetically-encoded reporter proteins widely used in the lab are difficult to deploy in soil matrices: for example, green fluorescent protein cannot be easily visualized in soils, even in the lab. To address this problem we have developed a reporter protein that releases small volatile gases. Here, we applied this gas reporter in a proof-of-concept soil experiment, monitoring horizontal gene transfer, a microbial activity that alters microbial genotypes and phenotypes. Horizontal gene transfer is central to bacterial evolution and adaptation and is relevant to problems such as the spread of antibiotic resistance, increasing metal tolerance in superfund sites, and bioremediation capability of bacterial consortia. This process is likely to be impacted by a number of matrix properties not well-represented in the petri dish, such as microscale variations in water, nutrients, and O2, making petri-dish experiments a poor proxy for environmental processes. We built a conjugation system using synthetic biology to demonstrate the use of gas-reporting biosensors in safe, lab-based biogeochemistry experiments, and here we report the use of these sensors to monitor horizontal gene transfer in soils. Our system is based on the F-plasmid conjugation in Escherichia coli. We have found that the gas signal reports on the number of cells that acquire F-plasmids (transconjugants) in a loamy Alfisol collected from Kellogg Biological Station. We will report how a gas signal generated by transconjugants varies with the number of F-plasmid donor and acceptor cells seeded in a soil, soil moisture, and soil O2 levels.
Overview of Microbial Monitoring Technologies Considered for Use Inside Long Duration Spaceflights and Planetary Habitats

NASA Astrophysics Data System (ADS)

Roman, M. C.; Ott, C. M.

2015-03-01

NASA has been looking at microbial monitoring technologies that could be used in long duration missions. This presentation will provide an overview of the microbial monitoring technologies that are been considered for use inside spacecrafts and planetary habitats.
Monitoring microbial metabolites using an inductively coupled resonance circuit

PubMed Central

Karnaushenko, Daniil; Baraban, Larysa; Ye, Dan; Uguz, Ilke; Mendes, Rafael G.; Rümmeli, Mark H.; de Visser, J. Arjan G. M.; Schmidt, Oliver G.; Cuniberti, Gianaurelio; Makarov, Denys

2015-01-01

We present a new approach to monitor microbial population dynamics in emulsion droplets via changes in metabolite composition, using an inductively coupled LC resonance circuit. The signal measured by such resonance detector provides information on the magnetic field interaction with the bacterial culture, which is complementary to the information accessible by other detection means, based on electric field interaction, i.e. capacitive or resistive, as well as optical techniques. Several charge-related factors, including pH and ammonia concentrations, were identified as possible contributors to the characteristic of resonance detector profile. The setup enables probing the ionic byproducts of microbial metabolic activity at later stages of cell growth, where conventional optical detection methods have no discriminating power. PMID:26264183
Revision of Viable Environmental Monitoring in a Development Pilot Plant Based on Quality Risk Assessment: A Case Study.

PubMed

Ziegler, Ildikó; Borbély-Jakab, Judit; Sugó, Lilla; Kovács, Réka J

2017-01-01

In this case study, the principles of quality risk management were applied to review sampling points and monitoring frequencies in the hormonal tableting unit of a formulation development pilot plant. In the cleanroom area, premises of different functions are located. Therefore a general method was established for risk evaluation based on the Hazard Analysis and Critical Control Points (HACCP) method to evaluate these premises (i.e., production area itself and ancillary clean areas) from the point of view of microbial load and state in order to observe whether the existing monitoring program met the emerged advanced monitoring practice. LAY ABSTRACT: In pharmaceutical production, cleanrooms are needed for the manufacturing of final dosage forms of drugs-intended for human or veterinary use-in order to protect the patient's weakened body from further infections. Cleanrooms are premises with a controlled level of contamination that is specified by the number of particles per cubic meter at a specified particle size or number of microorganisms (i.e. microbial count) per surface area. To ensure a low microbial count over time, microorganisms are detected and counted by environmental monitoring methods regularly. It is reasonable to find the easily infected places by risk analysis to make sure the obtained results really represent the state of the whole room. This paper presents a risk analysis method for the optimization of environmental monitoring and verification of the suitability of the method. © PDA, Inc. 2017.
Toxicity assessment using different bioassays and microbial biosensors.

PubMed

Hassan, Sedky H A; Van Ginkel, Steven W; Hussein, Mohamed A M; Abskharon, Romany; Oh, Sang-Eun

2016-01-01

Toxicity assessment of water streams, wastewater, and contaminated sediments, is a very important part of environmental pollution monitoring. Evaluation of biological effects using a rapid, sensitive and cost effective method can indicate specific information on ecotoxicity assessment. Recently, different biological assays for toxicity assessment based on higher and lower organisms such as fish, invertebrates, plants and algal cells, and microbial bioassays have been used. This review focuses on microbial biosensors as an analytical device for environmental, food, and biomedical applications. Different techniques which are commonly used in microbial biosensing include amperometry, potentiometry, conductometry, voltammetry, microbial fuel cells, fluorescence, bioluminescence, and colorimetry. Examples of the use of different microbial biosensors in assessing a variety of environments are summarized. Copyright © 2016 Elsevier Ltd. All rights reserved.
DEVELOPMENT OF MICROBIAL METAGENOMIC MARKERS FOR ENVIRONMENTAL MONITORING AND RISK ASSESSMENT

EPA Science Inventory

The microbiological water quality standards established by EPA depend on culturing fecal indicator bacteria to predict the risks associated with water usage. For decades this has been the favored approach to microbiological monitoring in spite of the fact that culture-based meth...
Multiparametric monitoring of microbial faecal pollution reveals the dominance of human contamination along the whole Danube River

PubMed Central

Kirschner, A.K.T.; Reischer, G.H.; Jakwerth, S.; Savio, D.; Ixenmaier, S.; Toth, E.; Sommer, R.; Mach, R.L.; Linke, R.; Eiler, A.; Kolarevic, S.; Farnleitner, A.H.

2017-01-01

The microbial faecal pollution of rivers has wide-ranging impacts on a variety of human activities that rely on appropriate river water quality. Thus, detailed knowledge of the extent and origin of microbial faecal pollution is crucial for watershed management activities to maintain safe water use. In this study, the microbial faecal pollution levels were monitored by standard faecal indicator bacteria (SFIB) along a 2580 km stretch of the Danube, the world's most international river, as well as the Danube's most important tributaries. To track the origin of faecal pollution, host-associated Bacteroidetes genetic faecal marker qPCR assays for different host groups were applied in concert with SFIB. The spatial resolution analysis was followed by a time resolution analysis of faecal pollution patterns over 1 year at three selected sites. In this way, a comprehensive faecal pollution map of the total length of the Danube was created, combining substantiated information on both the extent and origin of microbial faecal pollution. Within the environmental data matrix for the river, microbial faecal pollution constituted an independent component and did not cluster with any other measured environmental parameters. Generally, midstream samples representatively depicted the microbial pollution levels at the respective river sites. However, at a few, somewhat unexpected sites, high pollution levels occurred in the lateral zones of the river while the midstream zone had good water quality. Human faecal pollution was demonstrated as the primary pollution source along the whole river, while animal faecal pollution was of minor importance. This study demonstrates that the application of host-associated genetic microbial source tracking markers in concert with the traditional concept of microbial faecal pollution monitoring based on SFIB significantly enhances the knowledge of the extent and origin of microbial faecal pollution patterns in large rivers. It constitutes a powerful tool to guide target-oriented water quality management in large river basins. PMID:28806705
Multiparametric monitoring of microbial faecal pollution reveals the dominance of human contamination along the whole Danube River.

PubMed

Kirschner, A K T; Reischer, G H; Jakwerth, S; Savio, D; Ixenmaier, S; Toth, E; Sommer, R; Mach, R L; Linke, R; Eiler, A; Kolarevic, S; Farnleitner, A H

2017-11-01

The microbial faecal pollution of rivers has wide-ranging impacts on a variety of human activities that rely on appropriate river water quality. Thus, detailed knowledge of the extent and origin of microbial faecal pollution is crucial for watershed management activities to maintain safe water use. In this study, the microbial faecal pollution levels were monitored by standard faecal indicator bacteria (SFIB) along a 2580 km stretch of the Danube, the world's most international river, as well as the Danube's most important tributaries. To track the origin of faecal pollution, host-associated Bacteroidetes genetic faecal marker qPCR assays for different host groups were applied in concert with SFIB. The spatial resolution analysis was followed by a time resolution analysis of faecal pollution patterns over 1 year at three selected sites. In this way, a comprehensive faecal pollution map of the total length of the Danube was created, combining substantiated information on both the extent and origin of microbial faecal pollution. Within the environmental data matrix for the river, microbial faecal pollution constituted an independent component and did not cluster with any other measured environmental parameters. Generally, midstream samples representatively depicted the microbial pollution levels at the respective river sites. However, at a few, somewhat unexpected sites, high pollution levels occurred in the lateral zones of the river while the midstream zone had good water quality. Human faecal pollution was demonstrated as the primary pollution source along the whole river, while animal faecal pollution was of minor importance. This study demonstrates that the application of host-associated genetic microbial source tracking markers in concert with the traditional concept of microbial faecal pollution monitoring based on SFIB significantly enhances the knowledge of the extent and origin of microbial faecal pollution patterns in large rivers. It constitutes a powerful tool to guide target-oriented water quality management in large river basins. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.
Microbial fuel cell-based biosensor for toxic carbon monoxide monitoring.

PubMed

Zhou, Shaofeng; Huang, Shaobin; Li, Yi; Zhao, Nannan; Li, Han; Angelidaki, Irini; Zhang, Yifeng

2018-08-15

This study presents an innovative microbial fuel cell-based biosensor for carbon monoxide (CO) monitoring. The hypothesis for the function of the biosensor is that CO inhibits bacterial activity in the anode and thereby reduces electricity production. A mature electrochemically active biofilm on the anode was exposed to CO gas at varied concentrations. A proportional linear relationship (R 2 = 0.987) between CO concentration and voltage drop (0.8 to 24 mV) in the range of 10% and 70% of CO concentration was observed. Notably, no further decrease of voltage output was observed by with further increasing CO concentration over 70%. Besides, the response time of the biosensor was 1 h. The compact design and simple operation of the biosensor makes it easy to be integrated in existing CO-based industrial facilities either as a forewarning sensor for CO toxicity or even as an individual on-line monitoring device. Copyright © 2018 Elsevier B.V. All rights reserved.
Development and evaluation of the bacterial fate and transport module for the Agricultural Policy/Environmental eXtender (APEX) model.

PubMed

Hong, Eun-Mi; Park, Yongeun; Muirhead, Richard; Jeong, Jaehak; Pachepsky, Yakov A

2018-02-15

The Agricultural Policy/Environmental eXtender (APEX) is a watershed-scale water quality model that includes detailed representation of agricultural management. The objective of this work was to develop a process-based model for simulating the fate and transport of manure-borne bacteria on land and in streams with the APEX model. The bacteria model utilizes manure erosion rates to estimate the amount of edge-of-field bacteria export. Bacteria survival in manure is simulated as a two-stage process separately for each manure application event. In-stream microbial fate and transport processes include bacteria release from streambeds due to sediment resuspension during high flow events, active release from the streambed sediment during low flow periods, bacteria settling with sediment, and survival. Default parameter values were selected from published databases and evaluated based on field observations. The APEX model with the newly developed microbial fate and transport module was applied to simulate fate and transport of the fecal indicator bacterium Escherichia coli in the Toenepi watershed, New Zealand that was monitored for seven years. The stream network of the watershed ran through grazing lands with daily bovine waste deposition. Results show that the APEX with the bacteria module reproduced well the monitored pattern of E. coli concentrations at the watershed outlet. The APEX with the microbial fate and transport module will be utilized for predicting microbial quality of water as affected by various agricultural practices, evaluating monitoring protocols, and supporting the selection of management practices based on regulations that rely on fecal indicator bacteria concentrations. Published by Elsevier B.V.
Microbial Monitoring of Crewed Habitats in Space—Current Status and Future Perspectives

PubMed Central

Yamaguchi, Nobuyasu; Roberts, Michael; Castro, Sarah; Oubre, Cherie; Makimura, Koichi; Leys, Natalie; Grohmann, Elisabeth; Sugita, Takashi; Ichijo, Tomoaki; Nasu, Masao

2014-01-01

Previous space research conducted during short-term flight experiments and long-term environmental monitoring on board orbiting space stations suggests that the relationship between humans and microbes is altered in the crewed habitat in space. Both human physiology and microbial communities adapt to spaceflight. Microbial monitoring is critical to crew safety in long-duration space habitation and the sustained operation of life support systems on space transit vehicles, space stations, and surface habitats. To address this critical need, space agencies including NASA (National Aeronautics and Space Administration), ESA (European Space Agency), and JAXA (Japan Aerospace Exploration Agency) are working together to develop and implement specific measures to monitor, control, and counteract biological contamination in closed-environment systems. In this review, the current status of microbial monitoring conducted in the International Space Station (ISS) as well as the results of recent microbial spaceflight experiments have been summarized and future perspectives are discussed. PMID:25130885
Micron2 Lab: Microfluidic Microbiology Lab Project

NASA Technical Reports Server (NTRS)

Burton, Aaron; Botkin, Douglas; Castro, Sarah; Crucian, Brian

2015-01-01

Microbial monitoring during spaceflight is crucial to maintain crew health and ensure water purifications systems are functioning properly. Current protocols for in-flight enumeration of bacteria in potable water systems require culture based methods. In this project, we aim to develop a flight- and microgravity-compatible flow cytometer capable of counting total microbial counts in the water supply and differentiating live from dead bacteria.
Surface, Water and Air Biocharacterization - A Comprehensive Characterization of Microorganisms and Allergens in Spacecraft Environment

NASA Technical Reports Server (NTRS)

Pierson, Duane L.; Ott, C. Mark; Cruz, Patricia; Buttner, Mark P.

2009-01-01

A Comprehensive Characterization of Microorganisms and Allergens in Spacecraft (SWAB) will use advanced molecular techniques to comprehensively evaluate microbes on board the space station, including pathogens (organisms that may cause disease). It also will track changes in the microbial community as spacecraft visit the station and new station modules are added. This study will allow an assessment of the risk of microbes to the crew and the spacecraft. Research Summary: Previous microbial analysis of spacecraft only identify microorganisms that will grow in culture, omitting greater than 90% of all microorganisms including pathogens such as Legionella (the bacterium which causes Legionnaires' disease) and Cryptosporidium (a parasite common in contaminated water) The incidence of potent allergens, such as dust mites, has never been systematically studied in spacecraft environments and microbial toxins have not been previously monitored. This study will use modern molecular techniques to identify microorganisms and allergens. Direct sampling of the ISS allows identification of the microbial communities present, and determination of whether these change or mutate over time. SWAB complements the nominal ISS environmental monitoring by providing a comparison of analyses from current media-based and advanced molecular-based technologies.
Fiber optic evanescent wave (FOEW) microbial sensor for dental application

NASA Astrophysics Data System (ADS)

Kishen, Anil; John, M. S.; Chen, Jun-Wei; Lim, Chu S.; Hu, Xiao; Asundi, Anand K.

2001-10-01

In this work a new approach based on the fiber Optic Evanescent Wave (FOEW) Spectroscopy is developed for the effective determination of dental caries activity in human saliva. The biosensor design utilized the exponentially decaying wave that extends to the lower index region of the optical fiber's core-cladding interface. In order to achieve this, a short length of the cladding is removed and the fiber core surface is coated with a porous glass medium using sol-gel technique. The acidogenic profile resulting from the Streptococcus mutans activity in the human saliva is monitored using an indicator, which was encapsulated within the porous coating. These investigations display the potential benefits of FOEW based microbial sensor to monitor caries activity in human saliva.
Microbial Monitoring Challenges and Needs for Mars Applications

NASA Technical Reports Server (NTRS)

Roman, M. C.; Ott, C. M.; Castro, V. A.; Birmele, M. N.; Roberts, M. S.; Venkateswaran, K. J.; Jan, D. L.

2012-01-01

The monitoring of microorganisms will be an important part of a mission to Mars. Microbial monitoring equipment will be needed to look for the presence of microorganisms on the planet, to confirm that planetary protection measures are working, to monitor the health of plants, bioreactors and humans living in a habitat and to monitor the performance of the life support systems that will keep them alive during their stay on Mars. Coordinating the different microbial monitoring needs during the early days of mission planning, can provide NASA with equipment that could meet more than one need while also providing complementary analysis options, which can enhance the research capabilities. The early coordination between the different NASA groups that will need microbial monitoring equipment on the surface of Mars, could also make the mission more affordable, as development of the needed equipment could be potentially cost shared.
Electrodic voltages in the presence of dissolved sulfide: Implications for monitoring natural microbial activity

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

Slater, L.; Ntarlagiannis, D.; Yee, N.

2008-10-01

There is growing interest in the development of new monitoring strategies for obtaining spatially extensive data diagnostic of microbial processes occurring in the earth. Open-circuit potentials arising from variable redox conditions in the fluid local-to-electrode surfaces (electrodic potentials) were recorded for a pair of silver-silver chloride electrodes in a column experiment, whereby a natural wetland soil containing a known community of sulfate reducers was continuously fed with a sulfate-rich nutrient medium. Measurements were made between five electrodes equally spaced along the column and a reference electrode placed on the column inflow. The presence of a sulfate reducing microbial population, coupledmore » with observations of decreasing sulfate levels, formation of black precipitate (likely iron sulfide),elevated solid phase sulfide, and a characteristic sulfurous smell, suggest microbial-driven sulfate reduction (sulfide generation) in our column. Based on the known sensitivity of a silver electrode to dissolved sulfide concentration, we interpret the electrodic potentials approaching 700 mV recorded in this experiment as an indicator of the bisulfide (HS-) concentration gradients in the column. The measurement of the spatial and temporal variation in these electrodic potentials provides a simple and rapid method for monitoring patterns of relative HS- concentration that are indicative of the activity of sulfate-reducing bacteria. Our measurements have implications both for the autonomous monitoring of anaerobic microbial processes in the subsurface and the performance of self-potential electrodes, where it is critical to isolate, and perhaps quantify, electrochemical interfaces contributing to observed potentials.« less
Monitoring and modeling of microbial and biological water quality

USDA-ARS?s Scientific Manuscript database

Microbial and biological water quality informs on the health of water systems and their suitability for uses in irrigation, recreation, aquaculture, and other activities. Indicators of microbial and biological water quality demonstrate high spatial and temporal variability. Therefore, monitoring str...
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.
Bioluminescence ATP Monitoring for the Routine Assessment of Food Contact Surface Cleanliness in a University Canteen

PubMed Central

Osimani, Andrea; Garofalo, Cristiana; Clementi, Francesca; Tavoletti, Stefano; Aquilanti, Lucia

2014-01-01

ATP bioluminescence monitoring and traditional microbiological analyses (viable counting of total mesophilic aerobes, coliforms and Escherichia coli) were used to evaluate the effectiveness of Sanitation Standard Operating Procedures (SSOP) at a university canteen which uses a HACCP-based approach. To that end, 10 cleaning control points (CPs), including food contact surfaces at risk of contamination from product residues or microbial growth, were analysed during an 8-month monitoring period. Arbitrary acceptability limits were set for both microbial loads and ATP bioluminescence readings. A highly significant correlation (r = 0.99) between the means of ATP bioluminescence readings and the viable counts of total mesophilic aerobes was seen, thus revealing a strong association of these parameters with the level of surface contamination. Among CPs, the raw meat and multi-purpose chopping boards showed the highest criticalities. Although ATP bioluminescence technology cannot substitute traditional microbiological analyses for the determination of microbial load on food contact surfaces, it has proved to be a powerful tool for the real time monitoring of surface cleanliness at mass catering plants, for verify the correct application of SSOP, and hence for their implementation/revision in the case of poor hygiene. PMID:25329534

Bioluminescence ATP monitoring for the routine assessment of food contact surface cleanliness in a university canteen.

PubMed

Osimani, Andrea; Garofalo, Cristiana; Clementi, Francesca; Tavoletti, Stefano; Aquilanti, Lucia

2014-10-17

ATP bioluminescence monitoring and traditional microbiological analyses (viable counting of total mesophilic aerobes, coliforms and Escherichia coli) were used to evaluate the effectiveness of Sanitation Standard Operating Procedures (SSOP) at a university canteen which uses a HACCP-based approach. To that end, 10 cleaning control points (CPs), including food contact surfaces at risk of contamination from product residues or microbial growth, were analysed during an 8-month monitoring period. Arbitrary acceptability limits were set for both microbial loads and ATP bioluminescence readings. A highly significant correlation (r = 0.99) between the means of ATP bioluminescence readings and the viable counts of total mesophilic aerobes was seen, thus revealing a strong association of these parameters with the level of surface contamination. Among CPs, the raw meat and multi-purpose chopping boards showed the highest criticalities. Although ATP bioluminescence technology cannot substitute traditional microbiological analyses for the determination of microbial load on food contact surfaces, it has proved to be a powerful tool for the real time monitoring of surface cleanliness at mass catering plants, for verify the correct application of SSOP, and hence for their implementation/revision in the case of poor hygiene.
21 CFR 866.2560 - Microbial growth monitor.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Microbial growth monitor. 866.2560 Section 866.2560 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Microbiology Devices § 866.2560 Microbial growth...
21 CFR 866.2560 - Microbial growth monitor.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Microbial growth monitor. 866.2560 Section 866.2560 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Microbiology Devices § 866.2560 Microbial growth...
21 CFR 866.2560 - Microbial growth monitor.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Microbial growth monitor. 866.2560 Section 866.2560 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Microbiology Devices § 866.2560 Microbial growth...
Proceedings of the NASA Microbiology Workshop

NASA Technical Reports Server (NTRS)

Roman, M. C.; Jan, D. L.

2012-01-01

Long-term spaceflight is characterized by extraordinary challenges to maintain the life-supporting instrumentation free from microbial contamination and the crew healthy. The methodology currently employed for microbial monitoring in space stations or short spaceflights within the orbit of Earth have been instrumental in safeguarding the success of the missions, but suffers certain shortcomings that are critical for long spaceflights. This workshop addressed current practices and methodologies for microbial monitoring in space systems, and identified and discussed promising alternative methodologies and cutting-edge technologies for pursuit in the microbial monitoring that hold promise for supporting future NASA long-duration space missions.
Monitoring of microbial cell viability using nanostructured electrodes modified with Graphene/Alumina nanocomposite.

PubMed

Hassan, Rabeay Y A; Mekawy, Moataz M; Ramnani, Pankaj; Mulchandani, Ashok

2017-05-15

Microbial infections are rapidly increasing; however most of the existing microbiological and molecular detection methods are time consuming and/or cannot differentiate between the viable and dead cells which may overestimate the risk of infections. Therefore, a bioelectrochemical sensing platform with a high potential to the microbial-electrode interactions was designed based on decorated graphene oxide (GO) sheet with alumina (Al 2 O 3 ) nanocrystals. GO-Al 2 O 3 nanocomposite was synthesized using self-assembly of GO and Al 2 O 3 and characterized using the scanning electron microscopy (SEM), transmission electron microscopy (TEM), x-ray diffraction (XRD), Raman-spectroscopy, electrochemical impedance spectroscopy (EIS) and cyclic voltammetry (CV). Enhancement of electrocatalytic activity of the composite-modified electrode was demonstrated. Thus, using the GO-Al 2 O 3 nanocomposite modified electrode, the cell viability was determined by monitoring the bioelectrochemical response of the living microbial cells (bacteria and yeast) upon stimulation with carbon source. The bioelectrochemical assay was optimized to obtain high sensitivity and the method was applied to monitor cell viability and screen susceptibility of metabolically active cells (E. coli, B. subtilis, Enterococcus, P. aeruginosa and Salmonella typhi) to antibiotics such as ampicillin and kanamycin. Therefore, the developed assay is suitable for cell proliferation and cytotoxicity testing. Copyright © 2017 Elsevier B.V. All rights reserved.
Real-time monitoring of a microbial electrolysis cell using an electrical equivalent circuit model.

PubMed

Hussain, S A; Perrier, M; Tartakovsky, B

2018-04-01

Efforts in developing microbial electrolysis cells (MECs) resulted in several novel approaches for wastewater treatment and bioelectrosynthesis. Practical implementation of these approaches necessitates the development of an adequate system for real-time (on-line) monitoring and diagnostics of MEC performance. This study describes a simple MEC equivalent electrical circuit (EEC) model and a parameter estimation procedure, which enable such real-time monitoring. The proposed approach involves MEC voltage and current measurements during its operation with periodic power supply connection/disconnection (on/off operation) followed by parameter estimation using either numerical or analytical solution of the model. The proposed monitoring approach is demonstrated using a membraneless MEC with flow-through porous electrodes. Laboratory tests showed that changes in the influent carbon source concentration and composition significantly affect MEC total internal resistance and capacitance estimated by the model. Fast response of these EEC model parameters to changes in operating conditions enables the development of a model-based approach for real-time monitoring and fault detection.
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.
Microbial Monitoring of Common Opportunistic Pathogens by Comparing Multiple Real-time PCR Platforms for Potential Space Applications

NASA Technical Reports Server (NTRS)

Roman, Monserrate C.; Jones, Kathy U.; Oubre, Cherie M.; Castro, Victoria; Ott, Mark C.; Birmele, Michele; Venkateswaran, Kasthuri J.; Vaishampayan, Parag A.

2013-01-01

Current methods for microbial detection: a) Labor & time intensive cultivation-based approaches that can fail to detect or characterize all cells present. b) Requires collection of samples on orbit and transportation back to ground for analysis. Disadvantages to current detection methods: a) Unable to perform quick and reliable detection on orbit. b) Lengthy sampling intervals. c) No microbe identification.
Online flow cytometry reveals microbial dynamics influenced by concurrent natural and operational events in groundwater used for drinking water treatment.

PubMed

Besmer, Michael D; Epting, Jannis; Page, Rebecca M; Sigrist, Jürg A; Huggenberger, Peter; Hammes, Frederik

2016-12-07

Detailed measurements of physical, chemical and biological dynamics in groundwater are key to understanding the important processes in place and their influence on water quality - particularly when used for drinking water. Measuring temporal bacterial dynamics at high frequency is challenging due to the limitations in automation of sampling and detection of the conventional, cultivation-based microbial methods. In this study, fully automated online flow cytometry was applied in a groundwater system for the first time in order to monitor microbial dynamics in a groundwater extraction well. Measurements of bacterial concentrations every 15 minutes during 14 days revealed both aperiodic and periodic dynamics that could not be detected previously, resulting in total cell concentration (TCC) fluctuations between 120 and 280 cells μL -1 . The aperiodic dynamic was linked to river water contamination following precipitation events, while the (diurnal) periodic dynamic was attributed to changes in hydrological conditions as a consequence of intermittent groundwater extraction. Based on the high number of measurements, the two patterns could be disentangled and quantified separately. This study i) increases the understanding of system performance, ii) helps to optimize monitoring strategies, and iii) opens the possibility for more sophisticated (quantitative) microbial risk assessment of drinking water treatment systems.
Online flow cytometry reveals microbial dynamics influenced by concurrent natural and operational events in groundwater used for drinking water treatment

PubMed Central

Besmer, Michael D.; Epting, Jannis; Page, Rebecca M.; Sigrist, Jürg A.; Huggenberger, Peter; Hammes, Frederik

2016-01-01

Detailed measurements of physical, chemical and biological dynamics in groundwater are key to understanding the important processes in place and their influence on water quality – particularly when used for drinking water. Measuring temporal bacterial dynamics at high frequency is challenging due to the limitations in automation of sampling and detection of the conventional, cultivation-based microbial methods. In this study, fully automated online flow cytometry was applied in a groundwater system for the first time in order to monitor microbial dynamics in a groundwater extraction well. Measurements of bacterial concentrations every 15 minutes during 14 days revealed both aperiodic and periodic dynamics that could not be detected previously, resulting in total cell concentration (TCC) fluctuations between 120 and 280 cells μL−1. The aperiodic dynamic was linked to river water contamination following precipitation events, while the (diurnal) periodic dynamic was attributed to changes in hydrological conditions as a consequence of intermittent groundwater extraction. Based on the high number of measurements, the two patterns could be disentangled and quantified separately. This study i) increases the understanding of system performance, ii) helps to optimize monitoring strategies, and iii) opens the possibility for more sophisticated (quantitative) microbial risk assessment of drinking water treatment systems. PMID:27924920
MURMoT. Design and Application of Microbial Uranium Reduction Monitoring Tools

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

Loeffler, Frank E.

2014-12-31

Uranium (U) contamination in the subsurface is a major remediation challenge at many DOE sites. Traditional site remedies present enormous costs to DOE; hence, enhanced bioremediation technologies (i.e., biostimulation and bioaugmentation) combined with monitoring efforts are being considered as cost-effective corrective actions to address subsurface contamination. This research effort improved understanding of the microbial U reduction process and developed new tools for monitoring microbial activities. Application of these tools will promote science-based site management decisions that achieve contaminant detoxification, plume control, and long-term stewardship in the most efficient manner. The overarching hypothesis was that the design, validation and application ofmore » a suite of new molecular and biogeochemical tools advance process understanding, and improve environmental monitoring regimes to assess and predict in situ U immobilization. Accomplishments: This project (i) advanced nucleic acid-based approaches to elucidate the presence, abundance, dynamics, spatial distribution, and activity of metal- and radionuclide-detoxifying bacteria; (ii) developed proteomics workflows for detection of metal reduction biomarker proteins in laboratory cultures and contaminated site groundwater; (iii) developed and demonstrated the utility of U isotopic fractionation using high precision mass spectrometry to quantify U(VI) reduction for a range of reduction mechanisms and environmental conditions; and (iv) validated the new tools using field samples from U-contaminated IFRC sites, and demonstrated their prognostic and diagnostic capabilities in guiding decision making for environmental remediation and long-term site stewardship.« less
Detection and Composition of Bacterial Communities in Waters using RNA-based Methods

EPA Science Inventory

In recent years, microbial water quality assessments have shifted from solely relying on pure culture-based methods to monitoring bacterial groups of interest using molecular assays such as PCR and qPCR. Furthermore, coupling next generation sequencing technologies with ribosomal...
Polythiophene biosensor for rapid detection of microbial particles in water.

PubMed

Plante, Marie-Pier; Bérubé, Eve; Bissonnette, Luc; Bergeron, Michel G; Leclerc, Mario

2013-06-12

Most microbial particles have a negatively charged surface and in this work, we describe a water quality monitoring application of a cationic polythiophene derivative (AH-35) for the rapid assessment of microbial contamination of water. Using E. coli as a prototype microbial particle, we demonstrate that the AH-35 polymer can provide a qualitative assessment of water if exposed to more than 500 CFU/mL, thereby paving the way to a new family of biosensors potentially useful for monitoring drinking water distribution systems.
Microbiological Monitoring for the Constellation Program: Current Requirements and Future Considerations

NASA Technical Reports Server (NTRS)

Ott, C. Mark

2007-01-01

Microbiological requirements for spaceflight are based on assessments of infectious disease risk which could impact crew health or mission success. The determination of risk from infectious disease is composed of several factors including (1) crew susceptibility, (2) crew exposure to the infectious disease agent, (3) the concentration of the infectious agent, and (4) the characteristics of the infectious agent. As a result of the Health Stabilization Program, stringent monitoring, and cleaning protocols, in-flight environmental microbial monitoring is not necessary for short-duration spaceflights. However, risk factors change for long-duration missions, as exemplified by the presence of medically significant organisms in the environments of both the Mir and International Space Station (ISS). Based upon this historical evidence, requirements for short duration usage aboard the Orion Crew Exploration Vehicle and Lunar Lander Vehicle will not require in-flight monitoring; however, as mission duration increases with a Lunar Outpost, an ability to detect microbial hazard will be necessary. The nature of the detection requirements will depend on the maturity of technology in a rapidly evolving marketplace. Regardless, the hardware will still need to maximize information to discipline experts and the crew, while minimizing the size, mass, power consumption, and crew time usage. The refinement of these monitors will be a major goal in our efforts to travel successfully to Mars.
Application of Nucleic Acid-Based Tools for Monitoring Monitored Natural Attenuation (MNA), Biostimulation and Bioaugmentation at Chlorinated Solvent Sites

DTIC Science & Technology

2010-12-01

K. M. Ritalahti, and J. M. Tiedje. 2003. Diversity of Dechlorinating Bacteria, p. 53-87. In M. M. Häggblom and I. D. Bossert (eds.), Dehalogenation ...Anaerobic Microbial Dehalogenation . Annu. Rev. Microbiol. 58:43-73. Smits, T. H.M., C. Devenoges, K. Szynalski, J. Maillard, and C. Holliger. 2004
Bio-analytical applications of microbial fuel cell-based biosensors for onsite water quality monitoring.

PubMed

ElMekawy, A; Hegab, H M; Pant, D; Saint, C P

2018-01-01

Globally, sustainable provision of high-quality safe water is a major challenge of the 21st century. Various chemical and biological monitoring analytics are presently utilized to guarantee the availability of high-quality water. However, these techniques still face some challenges including high costs, complex design and onsite and online limitations. The recent technology of using microbial fuel cell (MFC)-based biosensors holds outstanding potential for the rapid and real-time monitoring of water source quality. MFCs have the advantages of simplicity in design and efficiency for onsite sensing. Even though some sensing applications of MFCs were previously studied, e.g. biochemical oxygen demand sensor, recently numerous research groups around the world have presented new practical applications of this technique, which combine multidisciplinary scientific knowledge in materials science, microbiology and electrochemistry fields. This review presents the most updated research on the utilization of MFCs as potential biosensors for monitoring water quality and considers the range of potentially toxic analytes that have so far been detected using this methodology. The advantages of MFCs over established technology are also considered as well as future work required to establish their routine use. © 2017 The Society for Applied Microbiology.
Surface, Water, and Air Biocharacterization (SWAB) Flight Experiment

NASA Technical Reports Server (NTRS)

Castro, V. A.; Ott, C. M.; Pierson, D. L.

2012-01-01

The determination of risk from infectious disease during spaceflight missions is composed of several factors including both the concentration and characteristics of the microorganisms to which the crew are exposed. Thus, having a good understanding of the microbial ecology aboard spacecraft provides the necessary information to mitigate health risks to the crew. While preventive measures are taken to minimize the presence of pathogens on spacecraft, medically significant organisms have been isolated from both the Mir and International Space Station (ISS). Historically, the method for isolation and identification of microorganisms from spacecraft environmental samples depended upon their growth on culture media. Unfortunately, only a fraction of the organisms may grow on a specific culture medium, potentially omitting those microorganisms whose nutritional and physical requirements for growth are not met. To address this bias in our understanding of the ISS environment, the Surface, Water, and Air Biocharacterization (SWAB) Flight Experiment was designed to investigate and develop monitoring technology to provide better microbial characterization. For the SWAB flight experiment, we hypothesized that environmental analysis using non-culture-based technologies would reveal microorganisms, allergens, and microbial toxins not previously reported in spacecraft, allowing for a more complete health assessment. Key findings during this experiment included: a) Generally, advanced molecular techniques were able to reveal a few organisms not recovered using culture-based methods; however, there is no indication that current monitoring is "missing" any medically significant bacteria or fungi. b) Molecular techniques have tremendous potential for microbial monitoring, however, sample preparation and data analysis present challenges for spaceflight hardware. c) Analytical results indicate that some molecular techniques, such as denaturing gradient gel electrophoresis (DGGE), can be much less sensitive than culture-based methods. d) More sensitive molecular techniques, such as quantitative polymerase chain reaction (QPCR), were able to identify viral DNA from ISS environments, suggesting potential transfer of the organism between crewmembers. In addition, the hardware selected for this experiment represented advances for next-generation sample collection. The advanced nature of this collection hardware was noted, when the Sartorius MD8 Air Port air sampler from the SWAB experiment remained on board ISS at the request of JAXA investigators, who intend to use it in completion of their microbial ecology experiment.
Final Intrinsic Remediation Engineering Evaluation/Cost Analysis for the FT-002 Site, Plattsburg Air Force Base, New York

DTIC Science & Technology

1995-04-01

including the BTEX compounds (e.g., Jamison et al., 1975; Atlas , 1981, 1984, 1988; Gibson, 1984; Reinhard et al., 1984; Young, 1984; Bartha , 1986; Wilson...1981, Microbial degradation of petroleum hydrocarbons - an environmental perspective: Microbiological Reviews, vol. 45, no. 1, p. 180-209. Atlas , R.M...sand aquifer: Ground Water Monitoring Review, Winter, 1987, p. 64-71. Bartha , R., 1986, Biotechnology of petroleum pollutant biodegradation: Microbial
Using NMR-based metabolomics to monitor the biochemical composition of agricultural soils: a pilot study

USDA-ARS?s Scientific Manuscript database

NMR-based metabolomics plays a major role studying complex living systems. However, very few studies describe the application of this technique to the evaluation of soil metabolome. Here, we introduce a protocol for analyzing the biochemical compounds from agricultural soils where the microbial comm...

QUO VADIS SOURCE TRACKING? TOWARDS A STRATEGIC FRAMEWORK FOR ENVIRONMENTAL MONITORING OF FECAL POLLUTION

EPA Science Inventory

Advances in microbial source tracking (MST) have largely been driven by the need to comply with water quality standards based on traditional indicator bacteria. Recently, a number of PCR-based, culture- and library-independent methods have been gaining popularity among source tra...
Pyrosequencing for Microbial Identification and Characterization

PubMed Central

Cummings, Patrick J.; Ahmed, Ray; Durocher, Jeffrey A.; Jessen, Adam; Vardi, Tamar; Obom, Kristina M.

2013-01-01

Pyrosequencing is a versatile technique that facilitates microbial genome sequencing that can be used to identify bacterial species, discriminate bacterial strains and detect genetic mutations that confer resistance to anti-microbial agents. The advantages of pyrosequencing for microbiology applications include rapid and reliable high-throughput screening and accurate identification of microbes and microbial genome mutations. Pyrosequencing involves sequencing of DNA by synthesizing the complementary strand a single base at a time, while determining the specific nucleotide being incorporated during the synthesis reaction. The reaction occurs on immobilized single stranded template DNA where the four deoxyribonucleotides (dNTP) are added sequentially and the unincorporated dNTPs are enzymatically degraded before addition of the next dNTP to the synthesis reaction. Detection of the specific base incorporated into the template is monitored by generation of chemiluminescent signals. The order of dNTPs that produce the chemiluminescent signals determines the DNA sequence of the template. The real-time sequencing capability of pyrosequencing technology enables rapid microbial identification in a single assay. In addition, the pyrosequencing instrument, can analyze the full genetic diversity of anti-microbial drug resistance, including typing of SNPs, point mutations, insertions, and deletions, as well as quantification of multiple gene copies that may occur in some anti-microbial resistance patterns. PMID:23995536
Pyrosequencing for microbial identification and characterization.

PubMed

Cummings, Patrick J; Ahmed, Ray; Durocher, Jeffrey A; Jessen, Adam; Vardi, Tamar; Obom, Kristina M

2013-08-22

Pyrosequencing is a versatile technique that facilitates microbial genome sequencing that can be used to identify bacterial species, discriminate bacterial strains and detect genetic mutations that confer resistance to anti-microbial agents. The advantages of pyrosequencing for microbiology applications include rapid and reliable high-throughput screening and accurate identification of microbes and microbial genome mutations. Pyrosequencing involves sequencing of DNA by synthesizing the complementary strand a single base at a time, while determining the specific nucleotide being incorporated during the synthesis reaction. The reaction occurs on immobilized single stranded template DNA where the four deoxyribonucleotides (dNTP) are added sequentially and the unincorporated dNTPs are enzymatically degraded before addition of the next dNTP to the synthesis reaction. Detection of the specific base incorporated into the template is monitored by generation of chemiluminescent signals. The order of dNTPs that produce the chemiluminescent signals determines the DNA sequence of the template. The real-time sequencing capability of pyrosequencing technology enables rapid microbial identification in a single assay. In addition, the pyrosequencing instrument, can analyze the full genetic diversity of anti-microbial drug resistance, including typing of SNPs, point mutations, insertions, and deletions, as well as quantification of multiple gene copies that may occur in some anti-microbial resistance patterns.
Urinary metabolic insights into host-gut microbial interactions in healthy and IBD children

PubMed Central

Martin, Francois-Pierre; Su, Ming-Ming; Xie, Guo-Xiang; Guiraud, Seu Ping; Kussmann, Martin; Godin, Jean-Philippe; Jia, Wei; Nydegger, Andreas

2017-01-01

AIM To identify metabolic signatures in urine samples from healthy and inflammatory bowel disease (IBD) children. METHODS We applied liquid chromatography and gas chromatography coupled to targeted mass spectrometry (MS)-based metabolite profiling to identify and quantify bile acids and host-gut microbial metabolites in urine samples collected from 21 pediatric IBD patients monitored three times over one year (baseline, 6 and 12 mo), and 27 age- and gender-matched healthy children. RESULTS urinary metabolic profiles of IBD children differ significantly from healthy controls. Such metabolic differences encompass central energy metabolism, amino acids, bile acids and gut microbial metabolites. In particular, levels of pyroglutamic acid, glutamic acid, glycine and cysteine, were significantly higher in IBD children in the course of the study. This suggests that glutathione cannot be optimally synthesized and replenished. Whilst alterations of the enterohepatic circulation of bile acids in pediatric IBD patients is known, we show here that non-invasive urinary bile acid profiling can assess those altered hepatic and intestinal barrier dysfunctions. CONCLUSION The present study shows how non-invasive sampling of urine followed by targeted MS-based metabonomic analysis can elucidate and monitor the metabolic status of children with different GI health/disease status. PMID:28611517
Airborne bacterial contaminations in typical Chinese wet market with live poultry trade.

PubMed

Gao, Xin-Lei; Shao, Ming-Fei; Luo, Yi; Dong, Yu-Fang; Ouyang, Feng; Dong, Wen-Yi; Li, Ji

2016-12-01

Chinese wet markets with live poultry trade have been considered as major sources of pathogen dissemination, and sites for horizontal transfer of bacterial and viral pathogens. In this study, the pathogenic bacteria and antibiotic resistant genes (ARGs) in air samples collected at a typical Chinese wet market had been analysis and quantified. Corynebacterium minutissimum and other pathogenic bacteria accounted for 0.81-8.02% of the whole microbial community in different air samples. The four ARGs quantified in this study showed a comparable relative concentration (copies/ng_DNA) with municipal wastewater. Poultry manures were demonstrated to be important microbial contamination source in wet market, which was supported by both microbial composition based source tracking and the quantification of airborne microbial density. A series of Firmicutes and Bacteroidetes indicators of poultry area contamination were successfully screened, which will be useful for the more convenient monitoring of airborne poultry area contamination. Our results indicate bioaerosols acted as important route for the transmissions of pathogens and ARGs. Continued surveillance of airborne microbial contamination is required in poultry trade wet market. Urban live poultry markets are important sources of pathogen dissemination, and sites for horizontal transfer of viral and bacterial pathogens. In the present field-study, pathogenic bacteria and antibiotic resistance genes were focused to provide quantitative information on the levels of microbial contaminations at the indoor air of wet markets. Results demonstrated that poultry manures were important microbial contamination source in wet market, and in the meanwhile bioaerosols were identified as important route for the transmissions of microbial contaminants. A series of Firmicutes and Bacteroidetes indicators of poultry area contamination were successfully screened, which will be useful for the more convenient monitoring of airborne poultry area contamination. Copyright © 2016 Elsevier B.V. All rights reserved.
Early Results and Spaceflight Implications of the SWAB Flight Experiment

NASA Technical Reports Server (NTRS)

Ott, C. Mark; Pierson, Duane L.

2007-01-01

Microbial monitoring of spacecraft environments provides key information in the assessment of infectious disease risk to the crew. Monitoring aboard the Mir space station and International Space Station (ISS) has provided a tremendous informational baseline to aid in determining the types and concentrations of microorganisms during a mission. Still, current microbial monitoring hardware utilizes culture-based methodology which may not detect many medically significant organisms, such as Legionella pneumophila. We hypothesize that evaluation of the ISS environment using non-culture-based technologies would reveal microorganisms not previously reported in spacecraft, allowing for a more complete health assessment. To achieve this goal, a spaceflight experiment, operationally designated as SWAB, was designed to evaluate the DNA from environmental samples collected from ISS and vehicles destined for ISS. Results from initial samples indicate that the sample collection and return procedures were successful. Analysis of these samples using denaturing gradient gel electrophoresis and targeted PCR primers for fungal contaminants is underway. The current results of SWAB and their implication for in-flight molecular analysis of environmental samples will be discussed.
Field Analysis of Microbial Contamination Using Three Molecular Methods in Parallel

NASA Technical Reports Server (NTRS)

Morris, H.; Stimpson, E.; Schenk, A.; Kish, A.; Damon, M.; Monaco, L.; Wainwright, N.; Steele, A.

2010-01-01

Advanced technologies with the capability of detecting microbial contamination remain an integral tool for the next stage of space agency proposed exploration missions. To maintain a clean, operational spacecraft environment with minimal potential for forward contamination, such technology is a necessity, particularly, the ability to analyze samples near the point of collection and in real-time both for conducting biological scientific experiments and for performing routine monitoring operations. Multiple molecular methods for detecting microbial contamination are available, but many are either too large or not validated for use on spacecraft. Two methods, the adenosine- triphosphate (ATP) and Limulus Amebocyte Lysate (LAL) assays have been approved by the NASA Planetary Protection Office for the assessment of microbial contamination on spacecraft surfaces. We present the first parallel field analysis of microbial contamination pre- and post-cleaning using these two methods as well as universal primer-based polymerase chain reaction (PCR).
Monitoring of microbial communities in anaerobic digestion sludge for biogas optimisation.

PubMed

Lim, Jun Wei; Ge, Tianshu; Tong, Yen Wah

2018-01-01

This study characterised and compared the microbial communities of anaerobic digestion (AD) sludge using three different methods - (1) Clone library; (2) Pyrosequencing; and (3) Terminal restriction fragment length polymorphism (T-RFLP). Although high-throughput sequencing techniques are becoming increasingly popular and affordable, the reliance of such techniques for frequent monitoring of microbial communities may be a financial burden for some. Furthermore, the depth of microbial analysis revealed by high-throughput sequencing may not be required for monitoring purposes. This study aims to develop a rapid, reliable and economical approach for the monitoring of microbial communities in AD sludge. A combined approach where genetic information of sequences from clone library was used to assign phylogeny to T-RFs determined experimentally was developed in this study. In order to assess the effectiveness of the combined approach, microbial communities determined by the combined approach was compared to that characterised by pyrosequencing. Results showed that both pyrosequencing and clone library methods determined the dominant bacteria phyla to be Proteobacteria, Firmicutes, Bacteroidetes, and Thermotogae. Both methods also found that sludge A and B were predominantly dominated by acetogenic methanogens followed by hydrogenotrophic methanogens. The number of OTUs detected by T-RFLP was significantly lesser than that detected by the clone library. In this study, T-RFLP analysis identified majority of the dominant species of the archaeal consortia. However, many of the more highly diverse bacteria consortia were missed. Nevertheless, the combined approach developed in this study where clone sequences from the clone library were used to assign phylogeny to T-RFs determined experimentally managed to accurately predict the same dominant microbial groups for both sludge A and sludge B, as compared to the pyrosequencing results. Results showed that the combined approach of clone library and T-RFLP accurately predicted the dominant microbial groups and thus is a reliable and more economical way to monitor the evolution of microbial systems in AD sludge. Copyright © 2017 Elsevier Ltd. All rights reserved.
How Much Will It Cost To Monitor Microbial Drinking Water Quality in Sub-Saharan Africa?

PubMed Central

2017-01-01

Microbial water quality monitoring is crucial for managing water resources and protecting public health. However, institutional testing activities in sub-Saharan Africa are currently limited. Because the economics of water quality testing are poorly understood, the extent to which cost may be a barrier to monitoring in different settings is unclear. This study used cost data from 18 African monitoring institutions (piped water suppliers and health surveillance agencies in six countries) and estimates of water supply type coverage from 15 countries to assess the annual financial requirements for microbial water testing at both national and regional levels, using World Health Organization recommendations for sampling frequency. We found that a microbial water quality test costs 21.0 ± 11.3 USD, on average, including consumables, equipment, labor, and logistics, which is higher than previously calculated. Our annual cost estimates for microbial monitoring of piped supplies and improved point sources ranged between 8 000 USD for Equatorial Guinea and 1.9 million USD for Ethiopia, depending primarily on the population served but also on the distribution of piped water system sizes. A comparison with current national water and sanitation budgets showed that the cost of implementing prescribed testing levels represents a relatively modest proportion of existing budgets (<2%). At the regional level, we estimated that monitoring the microbial quality of all improved water sources in sub-Saharan Africa would cost 16.0 million USD per year, which is minimal in comparison to the projected annual capital costs of achieving Sustainable Development Goal 6.1 of safe water for all (14.8 billion USD). PMID:28459563
How Much Will It Cost To Monitor Microbial Drinking Water Quality in Sub-Saharan Africa?

PubMed

Delaire, Caroline; Peletz, Rachel; Kumpel, Emily; Kisiangani, Joyce; Bain, Robert; Khush, Ranjiv

2017-06-06

Microbial water quality monitoring is crucial for managing water resources and protecting public health. However, institutional testing activities in sub-Saharan Africa are currently limited. Because the economics of water quality testing are poorly understood, the extent to which cost may be a barrier to monitoring in different settings is unclear. This study used cost data from 18 African monitoring institutions (piped water suppliers and health surveillance agencies in six countries) and estimates of water supply type coverage from 15 countries to assess the annual financial requirements for microbial water testing at both national and regional levels, using World Health Organization recommendations for sampling frequency. We found that a microbial water quality test costs 21.0 ± 11.3 USD, on average, including consumables, equipment, labor, and logistics, which is higher than previously calculated. Our annual cost estimates for microbial monitoring of piped supplies and improved point sources ranged between 8 000 USD for Equatorial Guinea and 1.9 million USD for Ethiopia, depending primarily on the population served but also on the distribution of piped water system sizes. A comparison with current national water and sanitation budgets showed that the cost of implementing prescribed testing levels represents a relatively modest proportion of existing budgets (<2%). At the regional level, we estimated that monitoring the microbial quality of all improved water sources in sub-Saharan Africa would cost 16.0 million USD per year, which is minimal in comparison to the projected annual capital costs of achieving Sustainable Development Goal 6.1 of safe water for all (14.8 billion USD).
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.
CHARACTERIZATION OF PRECURSOR 165 RRNA FOR AEROMONAS HYDROPHILA

EPA Science Inventory

Current strategies for monitoring drinking water quality involve culture-based methods to detect the presence of microbial indicators. However, these methods are insensitive when the organisms have undergone physiological changes such as injury and starvation that can occur in h...
High-Resolution Microbial Community Succession of Microbially Induced Concrete Corrosion in Working Sanitary Manholes

PubMed Central

Ling, Alison L.; Robertson, Charles E.; Harris, J. Kirk; Frank, Daniel N.; Kotter, Cassandra V.; Stevens, Mark J.; Pace, Norman R.; Hernandez, Mark T.

2015-01-01

Microbially-induced concrete corrosion in headspaces threatens wastewater infrastructure worldwide. Models for predicting corrosion rates in sewer pipe networks rely largely on information from culture-based investigations. In this study, the succession of microbes associated with corroding concrete was characterized over a one-year monitoring campaign using rRNA sequence-based phylogenetic methods. New concrete specimens were exposed in two highly corrosive manholes (high concentrations of hydrogen sulfide and carbon dioxide gas) on the Colorado Front Range for up to a year. Community succession on corroding surfaces was assessed using Illumina MiSeq sequencing of 16S bacterial rRNA amplicons and Sanger sequencing of 16S universal rRNA clones. Microbial communities associated with corrosion fronts presented distinct succession patterns which converged to markedly low α-diversity levels (< 10 taxa) in conjunction with decreasing pH. The microbial community succession pattern observed in this study agreed with culture-based models that implicate acidophilic sulfur-oxidizer Acidithiobacillus spp. in advanced communities, with two notable exceptions. Early communities exposed to alkaline surface pH presented relatively high α-diversity, including heterotrophic, nitrogen-fixing, and sulfur-oxidizing genera, and one community exposed to neutral surface pH presented a diverse transition community comprised of less than 20% sulfur-oxidizers. PMID:25748024
High-resolution microbial community succession of microbially induced concrete corrosion in working sanitary manholes.

PubMed

Ling, Alison L; Robertson, Charles E; Harris, J Kirk; Frank, Daniel N; Kotter, Cassandra V; Stevens, Mark J; Pace, Norman R; Hernandez, Mark T

2015-01-01

Microbially-induced concrete corrosion in headspaces threatens wastewater infrastructure worldwide. Models for predicting corrosion rates in sewer pipe networks rely largely on information from culture-based investigations. In this study, the succession of microbes associated with corroding concrete was characterized over a one-year monitoring campaign using rRNA sequence-based phylogenetic methods. New concrete specimens were exposed in two highly corrosive manholes (high concentrations of hydrogen sulfide and carbon dioxide gas) on the Colorado Front Range for up to a year. Community succession on corroding surfaces was assessed using Illumina MiSeq sequencing of 16S bacterial rRNA amplicons and Sanger sequencing of 16S universal rRNA clones. Microbial communities associated with corrosion fronts presented distinct succession patterns which converged to markedly low α-diversity levels (< 10 taxa) in conjunction with decreasing pH. The microbial community succession pattern observed in this study agreed with culture-based models that implicate acidophilic sulfur-oxidizer Acidithiobacillus spp. in advanced communities, with two notable exceptions. Early communities exposed to alkaline surface pH presented relatively high α-diversity, including heterotrophic, nitrogen-fixing, and sulfur-oxidizing genera, and one community exposed to neutral surface pH presented a diverse transition community comprised of less than 20% sulfur-oxidizers.
Tilapia fish microbial spoilage monitored by a single optical gas sensor.

PubMed

Semeano, Ana T S; Maffei, Daniele F; Palma, Susana; Li, Rosamaria W C; Franco, Bernadette D G M; Roque, Ana C A; Gruber, Jonas

2018-07-01

As consumption of fish and fish-based foods increases, non-destructive monitoring of fish freshness also becomes more prominent. Fish products are very perishable and prone to microbiological growth, not always easily detected by organoleptic evaluation. The analysis of the headspace of fish specimens through gas sensing is an interesting approach to monitor fish freshness. Here we report a gas sensing method for monitoring Tilapia fish spoilage based on the application of a single gas sensitive gel material coupled to an optical electronic nose. The optical signals of the sensor and the extent of bacterial growth were followed over time, and results indicated good correlation between the two determinations, which suggests the potential application of this simple and low cost system for Tilapia fish freshness monitoring.
Rapid and quantitative detection of the microbial spoilage in chicken meat by diffuse reflectance spectroscopy (600-1100 nm).

PubMed

Lin, M; Al-Holy, M; Mousavi-Hesary, M; Al-Qadiri, H; Cavinato, A G; Rasco, B A

2004-01-01

To evaluate the feasibility of visible and short-wavelength near-infrared (SW-NIR) diffuse reflectance spectroscopy (600-1100 nm) to quantify the microbial loads in chicken meat and to develop a rapid methodology for monitoring the onset of spoilage. Twenty-four prepackaged fresh chicken breast muscle samples were prepared and stored at 21 degrees C for 24 h. Visible and SW-NIR was used to detect and quantify the microbial loads in chicken breast muscle at time intervals of 0, 2, 4, 6, 8, 10, 12 and 24 h. Spectra were collected in the diffuse reflectance mode (600-1100 nm). Total aerobic plate count (APC) of each sample was determined by the spread plate method at 32 degrees C for 48 h. Principal component analysis (PCA) and partial least squares (PLS) based prediction models were developed. PCA analysis showed clear segregation of samples held 8 h or longer compared with 0-h control. An optimum PLS model required eight latent variables for chicken muscle (R = 0.91, SEP = 0.48 log CFU g(-1)). Visible and SW-NIR combined with PCA is capable of perceiving the change of the microbial loads in chicken muscle once the APC increases slightly above 1 log cycle. Accurate quantification of the bacterial loads in chicken muscle can be calculated from the PLS-based prediction method. Visible and SW-NIR spectroscopy is a technique with a considerable potential for monitoring food safety and food spoilage. Visible and SW-NIR can acquire a metabolic snapshot and quantify the microbial loads of food samples rapidly, accurately, and noninvasively. This method would allow for more expeditious applications of quality control in food industries.
TEMPORAL VARIABILITY OF MICROBIAL INDICATORS OF FECAL CONTAMINATION OF MARINE AND FRESHWATER BEACHES

EPA Science Inventory

Monitoring methods for microbial indicators of fecal contamination are an integral component for protecting the health of swimmers exposed to potentially contaminated bathing beach waters. The design of monitoring systems which will accurately characterize the quality of water is...
Development of microbial genome-probing microarrays using digital multiple displacement amplification of uncultivated microbial single cells.

PubMed

Chang, Ho-Won; Sung, Youlboong; Kim, Kyoung-Ho; Nam, Young-Do; Roh, Seong Woon; Kim, Min-Soo; Jeon, Che Ok; Bae, Jin-Woo

2008-08-15

A crucial problem in the use of previously developed genome-probing microarrays (GPM) has been the inability to use uncultivated bacterial genomes to take advantage of the high sensitivity and specificity of GPM in microbial detection and monitoring. We show here a method, digital multiple displacement amplification (MDA), to amplify and analyze various genomes obtained from single uncultivated bacterial cells. We used 15 genomes from key microbes involved in dichloromethane (DCM)-dechlorinating enrichment as microarray probes to uncover the bacterial population dynamics of samples without PCR amplification. Genomic DNA amplified from single cells originating from uncultured bacteria with 80.3-99.4% similarity to 16S rRNA genes of cultivated bacteria. The digital MDA-GPM method successfully monitored the dynamics of DCM-dechlorinating communities from different phases of enrichment status. Without a priori knowledge of microbial diversity, the digital MDA-GPM method could be designed to monitor most microbial populations in a given environmental sample.
Hydrogel-Based Fluorescent Dual pH and Oxygen Sensors Loaded in 96-Well Plates for High-Throughput Cell Metabolism Studies.

PubMed

Wu, Shanshan; Wu, Siying; Yi, Zheyuan; Zeng, Fei; Wu, Weizhen; Qiao, Yuan; Zhao, Xingzhong; Cheng, Xing; Tian, Yanqing

2018-02-13

In this study, we developed fluorescent dual pH and oxygen sensors loaded in multi-well plates for in-situ and high-throughput monitoring of oxygen respiration and extracellular acidification during microbial cell growth for understanding metabolism. Biocompatible PHEMA-co-PAM materials were used as the hydrogel matrix. A polymerizable oxygen probe (OS2) derived from PtTFPP and a polymerizable pH probe (S2) derived from fluorescein were chemically conjugated into the matrix to solve the problem of the probe leaching from the matrix. Gels were allowed to cure directly on the bottom of 96-well plates at room-temperature via redox polymerization. The influence of matrix's composition on the sensing behaviors was investigated to optimize hydrogels with enough robustness for repeatable use with good sensitivity. Responses of the dual sensing hydrogels to dissolved oxygen (DO) and pH were studied. These dual oxygen-pH sensing plates were successfully used for microbial cell-based screening assays, which are based on the measurement of fluorescence intensity changes induced by cellular oxygen consumption and pH changes during microbial growth. This method may provide a real-time monitoring of cellular respiration, acidification, and a rapid kinetic assessment of multiple samples for cell viability as well as high-throughput drug screening. All of these assays can be carried out by a conventional plate reader.
WATER QUALITY MONITORING FOR PUBLIC HEALTH AND ENVIRONMENTAL PROTECTION

EPA Science Inventory

The applicability of using microbial population measures as indicators of aquatic condition has a rich history based primarily to study factors that affect the sanitary and ecological condition of fresh water streams. These studies are generally conducted by collecting water site...

CHARACTERIZATION OF PRECURSOR FOR 16S rRNA FOR AEROMONAS HYDROPHILA

EPA Science Inventory

Current strategies for monitoring drinking water quality involve culture-based methods to detect the presence of microbial indicators. However, these methods are insensitive when the organisms have undergone physiological changes such as injury and starvation that can occur in h...
Cleanrooms and tissue banking how happy I could be with either GMP or GTP?

PubMed

Klykens, J; Pirnay, J-P; Verbeken, G; Giet, O; Baudoux, E; Jashari, R; Vanderkelen, A; Ectors, N

2013-12-01

The regulatory framework of tissue banking introduces a number of requirements for monitoring cleanrooms for processing tissue or cell grafts. Although a number of requirements were clearly defined, some requirements are open for interpretation. This study aims to contribute to the interpretation of GMP or GTP guidelines for tissue banking. Based on the experience of the participating centers, the results of the monitoring program were evaluated to determine the feasibility of a cleanroom in tissue banking and the monitoring program. Also the microbial efficacy of a laminar airflow cabinet and an incubator in a cleanroom environment was evaluated. This study indicated that a monitoring program of a cleanroom at rest in combination with (final) product testing is a feasible approach. Although no statistical significance (0.90 < p < 0.95) was found there is a strong indication that a Grade D environment is not the ideal background environment for a Grade A obtained through a laminar airflow cabinet. The microbial contamination of an incubator in a cleanroom is limited but requires closed containers for tissue and cell products.
Monitoring of Microbial Loads During Long Duration Missions as a Risk Reduction Tool

NASA Technical Reports Server (NTRS)

Roman, Monsi C.

2011-01-01

Humans have been exploring space for more than 40 years. For all those years microorganisms have accompanied, first un-manned spacecraft/cargo and later manned vessels. Microorganisms are everywhere on Earth, could easily adapt to new environments and/or can rapidly mutate to survive in very harsh conditions. Their presence in spacecraft and cargo have caused a few inconveniences over the years of humans spaceflight, ranging from crew health, life support systems challenges and material degradation. The sterilization of spacecraft that will host humans in long duration mission would be a costly operation that will not provide a long-term solution to the microbial colonization of the vessels. As soon as a human is exposed to the spacecraft, during the mission, microorganisms will start to populate the new environment. As the hum an presence in space increases in length, the risk from the microbial load, to hardware and crew will also increase. Mitigation of this risk includes several different strategies that will include minimizing the microbial load (in numbers and diversity) and monitoring. This presentation will provide a list of the risk mitigation strategies that should be implemented during ground processing, and during the mission. It will also discuss the areas that should be discussed before an effective in-flight microbial monitoring regimen is implemented. Microbial monitoring technologies will also be presented.
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.
WATERBORNE DISEASES AND MICROBIAL QUALITY MONITORING FOR RECREATIONAL WATER BODIES USING REGULATORY METHODS

EPA Science Inventory

This chapter will provide the reader with a historical perspective of microbial water quality and monitoring of recreational waters, with special attention to marine environments. It will review the regulations that are currently in effect in the United States and discuss critic...
Development and Use of Integrated Microarray-Based Genomic Technologies for Assessing Microbial Community Composition and Dynamics

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

Zhou, J.; Wu, L.; Gentry, T.

2006-04-05

To effectively monitor microbial populations involved in various important processes, a 50-mer-based oligonucleotide microarray was developed based on known genes and pathways involved in: biodegradation, metal resistance and reduction, denitrification, nitrification, nitrogen fixation, methane oxidation, methanogenesis, carbon polymer decomposition, and sulfate reduction. This array contains approximately 2000 unique and group-specific probes with <85% similarity to their non-target sequences. Based on artificial probes, our results showed that at hybridization conditions of 50 C and 50% formamide, the 50-mer microarray hybridization can differentiate sequences having <88% similarity. Specificity tests with representative pure cultures indicated that the designed probes on the arrays appearedmore » to be specific to their corresponding target genes. Detection limits were about 5-10ng genomic DNA in the absence of background DNA, and 50-100ng ({approx}1.3{sup o} 10{sup 7} cells) in the presence background DNA. Strong linear relationships between signal intensity and target DNA and RNA concentration were observed (r{sup 2} = 0.95-0.99). Application of this microarray to naphthalene-amended enrichments and soil microcosms demonstrated that composition of the microflora varied depending on incubation conditions. While the naphthalene-degrading genes from Rhodococcus-type microorganisms were dominant in enrichments, the genes involved in naphthalene degradation from Gram-negative microorganisms such as Ralstonia, Comamonas, and Burkholderia were most abundant in the soil microcosms (as well as those for polyaromatic hydrocarbon and nitrotoluene degradation). Although naphthalene degradation is widely known and studied in Pseudomonas, Pseudomonas genes were not detected in either system. Real-time PCR analysis of 4 representative genes was consistent with microarray-based quantification (r{sup 2} = 0.95). Currently, we are also applying this microarray to the study of several different microbial communities and processes at the NABIR-FRC in Oak Ridge, TN. One project involves the monitoring of the development and dynamics of the microbial community of a fluidized bed reactor (FBR) used for reducing nitrate and the other project monitors microbial community responses to stimulation of uranium reducing populations via ethanol donor additions in situ and in a model system. Additionally, we are developing novel strategies for increasing microarray hybridization sensitivity. Finally, great improvements to our methods of probe design were made by the development of a new computer program, CommOligo. CommOligo designs unique and group-specific oligo probes for whole-genomes, metagenomes, and groups of environmental sequences and uses a new global alignment algorithm to design single or multiple probes for each gene or group. We are now using this program to design a more comprehensive functional gene array for environmental studies. Overall, our results indicate that the 50mer-based microarray technology has potential as a specific and quantitative tool to reveal the composition of microbial communities and their dynamics important to processes within contaminated environments.« less
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.
Spatial and temporal variation of fecal indicator organisms in two creeks in Beltsville, Maryland

USDA-ARS?s Scientific Manuscript database

Evaluation of microbial water quality is commonly achieved by monitoring populations of indicator bacteria such as E. coli and enterococci. Monitoring data are utilized by water managers to predict potential fecal contaminations as well as a decision tool to improve microbial water quality. Both te...
Statistical analysis of environmental monitoring data: does a worst case time for monitoring clean rooms exist?

PubMed

Cundell, A M; Bean, R; Massimore, L; Maier, C

1998-01-01

To determine the relationship between the sampling time of the environmental monitoring, i.e., viable counts, in aseptic filling areas and the microbial count and frequency of alerts for air, surface and personnel microbial monitoring, statistical analyses were conducted on 1) the frequency of alerts versus the time of day for routine environmental sampling conducted in calendar year 1994, and 2) environmental monitoring data collected at 30-minute intervals during routine aseptic filling operations over two separate days in four different clean rooms with multiple shifts and equipment set-ups at a parenteral manufacturing facility. Statistical analyses showed, except for one floor location that had significantly higher number of counts but no alert or action level samplings in the first two hours of operation, there was no relationship between the number of counts and the time of sampling. Further studies over a 30-day period at the floor location showed no relationship between time of sampling and microbial counts. The conclusion reached in the study was that there is no worst case time for environmental monitoring at that facility and that sampling any time during the aseptic filling operation will give a satisfactory measure of the microbial cleanliness in the clean room during the set-up and aseptic filling operation.
RAPID HEALTH-BASED METHOD FOR MEASURING MICROBIAL INDICATORS OF RECREATIONAL WATER QUALITY

EPA Science Inventory

Because the currently approved cultural methods for monitoring indicator bacteria in recreational water require 24 hours to produce results, the public may be exposed to potentially contaminated water before the water has been identified as hazardous. This project was initiated t...
Microbial community structure in a shallow hydrocarbon-contaminated aquifer associated with high electrical conductivity

NASA Astrophysics Data System (ADS)

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

2003-04-01

Little is known about the complex interactions between microbial communities and electrical properties in contaminated aquifers. In order to investigate possible connections between these parameters a study was undertaken to investigate the hypothesis that the degradation of hydrocarbons by resident microbial communities causes a local increase in organic acid concentrations, which in turn cause an increase in native mineral weathering and a concurrent increase in the bulk electrical conductivity of soil. Microbial community structure was analyzed using a 96-well most probable number (MPN) method and rDNA intergenic spacer region analysis (RISA). Microbial community structure was found to change in the presence of hydrocarbon contaminants and these changes were consistently observed in regions of high electrical conductivity. We infer from this relationship that geophysical methods for monitoring the subsurface are a promising new technology for monitoring changes in microbial community structure and simultaneous changes in geochemistry that are associated with hydrocarbon degradation.
GPU-Meta-Storms: computing the structure similarities among massive amount of microbial community samples using GPU.

PubMed

Su, Xiaoquan; Wang, Xuetao; Jing, Gongchao; Ning, Kang

2014-04-01

The number of microbial community samples is increasing with exponential speed. Data-mining among microbial community samples could facilitate the discovery of valuable biological information that is still hidden in the massive data. However, current methods for the comparison among microbial communities are limited by their ability to process large amount of samples each with complex community structure. We have developed an optimized GPU-based software, GPU-Meta-Storms, to efficiently measure the quantitative phylogenetic similarity among massive amount of microbial community samples. Our results have shown that GPU-Meta-Storms would be able to compute the pair-wise similarity scores for 10 240 samples within 20 min, which gained a speed-up of >17 000 times compared with single-core CPU, and >2600 times compared with 16-core CPU. Therefore, the high-performance of GPU-Meta-Storms could facilitate in-depth data mining among massive microbial community samples, and make the real-time analysis and monitoring of temporal or conditional changes for microbial communities possible. GPU-Meta-Storms is implemented by CUDA (Compute Unified Device Architecture) and C++. Source code is available at http://www.computationalbioenergy.org/meta-storms.html.
Monitoring of oil hydrocarbons pollution in the Sea of Japan, based on detection of marker genes in microbial communities

NASA Astrophysics Data System (ADS)

Kim, A. V.; Buzoleva, L. S.; Bogatyrenko, E. A.; Zemskaya, T. I.; Mamaeva, E. V.

2018-01-01

By means of molecular biology techniques, metabolic potential of microbial communities within the regions of inshore water areas in the Sea of Japan with various anthropogenic load was explored. Presence of functional genes, responsible for oil hydrocarbons destruction, for microbial communities within the regions of inshore water areas in the Sea of Japan was first researched. In total microbial DNA from water mass in the regions with chronic anthropogenic pollution, the genes, responsible for oxidation of broad range of n-alkanes and polycyclic aromatic hydrocarbons, were found. Detection of marker genes in the background water area (in the Vostok Bay) was ever indicating ecological deterioration within this territory. Thereby, it was demonstrated, that molecular genetic methods, aimed at marker gene detection in total bacterial DNA from environment objects, proved themselves to be more effective technique for identification of oil hydrocarbons water pollution, in comparison with trivial culturable methods.
Enhancement of the microbial community biomass and diversity during air sparging bioremediation of a soil highly contaminated with kerosene and BTEX.

PubMed

Kabelitz, Nadja; Machackova, Jirina; Imfeld, Gwenaël; Brennerova, Maria; Pieper, Dietmar H; Heipieper, Hermann J; Junca, Howard

2009-03-01

In order to obtain insights in complexity shifts taking place in natural microbial communities under strong selective pressure, soils from a former air force base in the Czech Republic, highly contaminated with jet fuel and at different stages of a bioremediation air sparging treatment, were analyzed. By tracking phospholipid fatty acids and 16S rRNA genes, a detailed monitoring of the changes in quantities and composition of the microbial communities developed at different stages of the bioventing treatment progress was performed. Depending on the length of the air sparging treatment that led to a significant reduction in the contamination level, we observed a clear shift in the soil microbial community being dominated by Pseudomonads under the harsh conditions of high aromatic contamination to a status of low aromatic concentrations, increased biomass content, and a complex composition with diverse bacterial taxonomical branches.
Microbiological test results using three urine pretreatment regimes with 316L stainless steel

NASA Technical Reports Server (NTRS)

Huff, Timothy L.

1993-01-01

Three urine pretreatments, (1) Oxone (Dupont) and sulfuric acid, (2) sodium hypochlorite and sulfuric acid, (3) and ozone, were studied for their ability to reduce microbial levels in urine and minimize surface attachment to 316L stainless steel coupons. Urine samples inoculated with Bacillus insolitus and a filamentous mold, organisms previously recovered from the vapor compression distillation subsystem of NASA Space Station Freedom water recovery test were tested in glass corrosion cells containing base or weld metal coupons. Microbial levels, changes in pH, color, turbidity, and odor of the fluid were monitored over the course of the 21-day test. Specimen surfaces were examined by scanning electron microscopy at completion of the test for microbial attachment. Ozonated urine samples were less turbid and had lower microbial levels than controls or samples receiving other pretreatments. Base metal coupons receiving pretreatment were relatively free of attached bacteria. However, well-developed biofilms were found in the heat-affected regions of welded coupons receiving Oxone and hypochlorite pretreatments. Few bacteria were observed in the same regions of the ozone pretreatment sample.
Study to determine the aquatic biological effects on the Solid Rocket Booster (SRB). [technique for monitoring marine microbial fouling

NASA Technical Reports Server (NTRS)

Colwell, R. R.; Zachary, A.

1979-01-01

The surface of the reusable solid rocket boosters (SRB), which are jettisoned from the Shuttle Orbiter to parachute in the sea, are studied for colonization by marine life. Techniques for monitoring the marine microbial fouling of SRB materials are presented. An assessment of the nature and degree of the biofouling expected on the SRB materials in the recovery zone is reported. A determination of the degree and the effects of seasonal variation occurring on microbial fouling in the retrieval zone waters is made. The susceptibility of the SRB parachute recovery system to microbial fouling and biodeterioration is investigated. The development of scanning electron microscopy and epifluorescence microscopic observation techniques for rapid assessment of microbial fouling is discussed.
Noninvasive methods for dynamic mapping of microbial populations across the landscape

NASA Astrophysics Data System (ADS)

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

2017-12-01

Soil microorganisms drive key ecosystem processes, and yet characterizing their distribution and activity in soil has been notoriously difficult. This is due, in part, to the heterogeneous nature of their response to changing environmental and nutrient conditions across time and space. These dynamics are challenging to constrain in both natural and experimental systems because of sampling difficulty and constraints. For example, soil microbial sampling at the Landscape Evolution Observatory (LEO) infrastructure in Biosphere 2 is limited in efforts to minimize soil disruption to the long term experiment that aims to characterize the interacting biological, hydrological, and geochemical processes driving soil evolution. In this and other systems, new methods are needed to monitor soil microbial communities and their genetic potential over time. In this study, we take advantage of the well-defined boundary conditions on hydrological flow at LEO to develop a new method to nondestructively characterize in situ microbial populations. In our approach, we sample microbes from the seepage flow at the base of each of three replicate LEO hillslopes and use hydrological models to `map back' in situ microbial populations. Over the course of a 3-month periodic rainfall experiment we collected samples from the LEO outflow for DNA and extraction and microbial community composition analysis. These data will be used to describe changes in microbial community composition over the course of the experiment. In addition, we will use hydrological flow models to identify the changing source region of discharge water over the course of periodic rainfall pulses, thereby mapping back microbial populations onto their geographic origin in the slope. These predictions of in situ microbial populations will be ground-truthed against those derived from destructive soil sampling at the beginning and end of the rainfall experiment. Our results will show the suitability of this method for long-term, non-destructive monitoring of the microbial communities that contribute to soil evolution in this large-scale model system. Furthermore, this method may be useful for other study systems with limitations to destructive sampling including other model infrastructures and natural landscapes.
A Pilot Study of Microbial Contamination of Subtropical Recreational Waters

PubMed Central

Fleming, Lora E; Solo, Gabriele H.; Elmir, Samir; Shibata, Tomoyuki; Squicciarini, Dominick; Quirino, Wendy; Arguello, Margia; Van de Bogart, Gayl

2009-01-01

Microbial water quality indicators are used to determine whether a water body is safe for recreational purposes. There have been concerns raised about the appropriate use of microbial indicators to regulate recreational uses of water bodies, in particular those located in tropical and sub-tropical environments. This prospective cohort pilot study evaluated the relationship between microbial water quality indicators and public health within two public beaches without known sewage discharge, but with historically high microbial levels for one beach, in subtropical Miami-Dade County (Florida). Monitoring was conducted in three phases: daily water monitoring, beach sand sampling, and spatially intense water sampling. An epidemiological questionnaire from a Los Angeles recreational beach-goer study was used to assess the self-reported swimming-related symptoms and exposures. There was no significant association between the number nor the type of reported symptoms and the different sampling months or beach sites, although persons who returned repeatedly to the beach were more likely to report symptoms. The number of indicator organisms correlated negatively with the frequency of symptoms reported by recreational beach goers. Results of the daily monitoring indicated that different indicators provided conflicting results concerning beach water quality. Larger epidemiologic studies with individual exposure monitoring are recommended to further evaluate these potentially important associations in subtropical recreational waters. PMID:20151031
Microbial Fuels Cell-Based Biosensor for Toxicity Detection: A Review

PubMed Central

Zhou, Tuoyu; Han, Huawen; Liu, Pu; Xiong, Jian; Tian, Fake; Li, Xiangkai

2017-01-01

With the unprecedented deterioration of environmental quality, rapid recognition of toxic compounds is paramount for performing in situ real-time monitoring. Although several analytical techniques based on electrochemistry or biosensors have been developed for the detection of toxic compounds, most of them are time-consuming, inaccurate, or cumbersome for practical applications. More recently, microbial fuel cell (MFC)-based biosensors have drawn increasing interest due to their sustainability and cost-effectiveness, with applications ranging from the monitoring of anaerobic digestion process parameters (VFA) to water quality detection (e.g., COD, BOD). When a MFC runs under correct conditions, the voltage generated is correlated with the amount of a given substrate. Based on this linear relationship, several studies have demonstrated that MFC-based biosensors could detect heavy metals such as copper, chromium, or zinc, as well as organic compounds, including p-nitrophenol (PNP), formaldehyde and levofloxacin. Both bacterial consortia and single strains can be used to develop MFC-based biosensors. Biosensors with single strains show several advantages over systems integrating bacterial consortia, such as selectivity and stability. One of the limitations of such sensors is that the detection range usually exceeds the actual pollution level. Therefore, improving their sensitivity is the most important for widespread application. Nonetheless, MFC-based biosensors represent a promising approach towards single pollutant detection. PMID:28956857
Microbial Fuels Cell-Based Biosensor for Toxicity Detection: A Review.

PubMed

Zhou, Tuoyu; Han, Huawen; Liu, Pu; Xiong, Jian; Tian, Fake; Li, Xiangkai

2017-09-28

With the unprecedented deterioration of environmental quality, rapid recognition of toxic compounds is paramount for performing in situ real-time monitoring. Although several analytical techniques based on electrochemistry or biosensors have been developed for the detection of toxic compounds, most of them are time-consuming, inaccurate, or cumbersome for practical applications. More recently, microbial fuel cell (MFC)-based biosensors have drawn increasing interest due to their sustainability and cost-effectiveness, with applications ranging from the monitoring of anaerobic digestion process parameters (VFA) to water quality detection (e.g., COD, BOD). When a MFC runs under correct conditions, the voltage generated is correlated with the amount of a given substrate. Based on this linear relationship, several studies have demonstrated that MFC-based biosensors could detect heavy metals such as copper, chromium, or zinc, as well as organic compounds, including p -nitrophenol (PNP), formaldehyde and levofloxacin. Both bacterial consortia and single strains can be used to develop MFC-based biosensors. Biosensors with single strains show several advantages over systems integrating bacterial consortia, such as selectivity and stability. One of the limitations of such sensors is that the detection range usually exceeds the actual pollution level. Therefore, improving their sensitivity is the most important for widespread application. Nonetheless, MFC-based biosensors represent a promising approach towards single pollutant detection.

Neural network processing of microbial fuel cell signals for the identification of chemicals present in water.

PubMed

Feng, Yinghua; Barr, William; Harper, W F

2013-05-15

Biosensing is emerging as an important element of water quality monitoring. This research demonstrated that microbial fuel cell (MFC)-based biosensing can be integrated with artificial neural networks (ANNs) to identify specific chemicals present in water samples. The non-fermentable substrates, acetate and butyrate, induced peak areas (PA) and peak heights (PH) that were generally larger than those caused by the injection of fermentable substrates, glucose and corn starch. The ANN successfully identified peaks associated with these four chemicals under a variety of experimental conditions and for two MFCs that had different levels of sensitivity. ANNs that employ the hyperbolic tangent sigmoid transfer function performed better than those using non-continuous transfer functions. ANNs should be integrated into water quality monitoring efforts for smart biosensing. Published by Elsevier Ltd.
Terbium-sensitized luminescence screening method for fluoroquinolones in beef serum

USDA-ARS?s Scientific Manuscript database

Enrofloxacin is one of only two fluoroquinolone antibiotics approved for use in cattle in the U.S. Microbial screening methods commonly used for monitoring veterinary drug residues are not sensitive or selective for fluoroquinolones. In this work, a luminescence-based screening assay was developed...
Can the black box be cracked? The augmentation of microbial ecology by high-resolution, automated sensing technologies.

PubMed

Shade, Ashley; Carey, Cayelan C; Kara, Emily; Bertilsson, Stefan; McMahon, Katherine D; Smith, Matthew C

2009-08-01

Automated sensing technologies, 'ASTs,' are tools that can monitor environmental or microbial-related variables at increasingly high temporal resolution. Microbial ecologists are poised to use AST data to couple microbial structure, function and associated environmental observations on temporal scales pertinent to microbial processes. In the context of aquatic microbiology, we discuss three applications of ASTs: windows on the microbial world, adaptive sampling and adaptive management. We challenge microbial ecologists to push AST potential in helping to reveal relationships between microbial structure and function.
Overview of Microbial Monitoring Technologies Considered for Use Inside Long Duration Spaceflights and Planetary Habitats

NASA Technical Reports Server (NTRS)

Roman, Monsi C.; Ott, C. Mark

2015-01-01

The purpose of this presentation is to start a conversation including the Crew Health, ECLSS, and Planetary Protection communities about the best approach for inflight microbial monitoring as part of a risk mitigation strategy to prevent forward and back contamination while protecting the crew and vehicle.
Identification of microbes from the surfaces of food-processing lines based on the flow cytometric evaluation of cellular metabolic activity combined with cell sorting.

PubMed

Juzwa, W; Duber, A; Myszka, K; Białas, W; Czaczyk, K

2016-09-01

In this study the design of a flow cytometry-based procedure to facilitate the detection of adherent bacteria from food-processing surfaces was evaluated. The measurement of the cellular redox potential (CRP) of microbial cells was combined with cell sorting for the identification of microorganisms. The procedure enhanced live/dead cell discrimination owing to the measurement of the cell physiology. The microbial contamination of the surface of a stainless steel conveyor used to process button mushrooms was evaluated in three independent experiments. The flow cytometry procedure provided a step towards monitoring of contamination and enabled the assessment of microbial food safety hazards by the discrimination of active, mid-active and non-active bacterial sub-populations based on determination of their cellular vitality and subsequently single cell sorting to isolate microbial strains from discriminated sub-populations. There was a significant correlation (r = 0.97; p < 0.05) between the bacterial cell count estimated by the pour plate method and flow cytometry, despite there being differences in the absolute number of cells detected. The combined approach of flow cytometric CRP measurement and cell sorting allowed an in situ analysis of microbial cell vitality and the identification of species from defined sub-populations, although the identified microbes were limited to culturable cells.
Exploring the Impacts of Anthropogenic Disturbance on Seawater and Sediment Microbial Communities in Korean Coastal Waters Using Metagenomics Analysis

PubMed Central

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

2017-01-01

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

PubMed

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

2017-01-27

The coastal ecosystems are considered as one of the most dynamic and vulnerable environments under various anthropogenic developments and the effects of climate change. Variations in the composition and diversity of microbial communities may be a good indicator for determining whether the marine ecosystems are affected by complex forcing stressors. DNA sequence-based metagenomics has recently emerged as a promising tool for analyzing the structure and diversity of microbial communities based on environmental DNA (eDNA). However, few studies have so far been performed using this approach to assess the impacts of human activities on the microbial communities in marine systems. In this study, using metagenomic DNA sequencing (16S ribosomal RNA gene), we analyzed and compared seawater and sediment communities between sand mining and control (natural) sites in southern coastal waters of Korea to assess whether anthropogenic activities have significantly affected the microbial communities. The sand mining sites harbored considerably lower levels of microbial diversities in the surface seawater community during spring compared with control sites. Moreover, the sand mining areas had distinct microbial taxonomic group compositions, particularly during spring season. The microbial groups detected solely in the sediment load/dredging areas (e.g., Marinobacter, Alcanivorax, Novosphingobium) are known to be involved in degradation of toxic chemicals such as hydrocarbon, oil, and aromatic compounds, and they also contain potential pathogens. This study highlights the versatility of metagenomics in monitoring and diagnosing the impacts of human disturbance on the environmental health of marine ecosystems from eDNA.
40 CFR Appendix 4 to Subpart A of... - Protocol for the Determination of Degradation of Non-Aqueous Base Fluids in a Marine Closed...

Code of Federal Regulations, 2014 CFR

2014-07-01

... test evaluates base fluid biodegradation rates by monitoring gas production due to microbial... ppm) evaluates the anaerobic (redox) condition of the bottles (dye is blue when oxygen is present... this publication is for descriptive use only, and does not constitute endorsement by EPA or the authors...
40 CFR Appendix 4 to Subpart A of... - Protocol for the Determination of Degradation of Non-Aqueous Base Fluids in a Marine Closed...

Code of Federal Regulations, 2012 CFR

2012-07-01

... test evaluates base fluid biodegradation rates by monitoring gas production due to microbial... ppm) evaluates the anaerobic (redox) condition of the bottles (dye is blue when oxygen is present... this publication is for descriptive use only, and does not constitute endorsement by EPA or the authors...
40 CFR Appendix 4 to Subpart A of... - Protocol for the Determination of Degradation of Non-Aqueous Base Fluids in a Marine Closed...

Code of Federal Regulations, 2013 CFR

2013-07-01

... test evaluates base fluid biodegradation rates by monitoring gas production due to microbial... ppm) evaluates the anaerobic (redox) condition of the bottles (dye is blue when oxygen is present... this publication is for descriptive use only, and does not constitute endorsement by EPA or the authors...
Microorganisms with a Taste for Vanilla: Microbial Ecology of Traditional Indonesian Vanilla Curing

PubMed Central

Röling, Wilfred F. M.; Kerler, Josef; Braster, Martin; Apriyantono, Anton; Stam, Hein; van Verseveld, Henk W.

2001-01-01

The microbial ecology of traditional postharvesting processing of vanilla beans (curing) was examined using a polyphasic approach consisting of conventional cultivation, substrate utilization-based and molecular identification of isolates, and cultivation-independent community profiling by 16S ribosomal DNA based PCR-denaturing gradient gel electrophoresis. At two different locations, a batch of curing beans was monitored. In both batches a major shift in microbial communities occurred after short-term scalding of the beans in hot water. Fungi and yeast disappeared, although regrowth of fungi occurred in one batch during a period in which process conditions were temporarily not optimal. Conventional plating showed that microbial communities consisting of thermophilic and thermotolerant bacilli (mainly closely related to Bacillus subtilis, B. licheniformis,, and B. smithii) developed under the high temperatures (up to 65°C) that were maintained for over a week after scalding. Only small changes in the communities of culturable bacteria occurred after this period. Molecular analysis revealed that a proportion of the microbial communities could not be cultured on conventional agar medium, especially during the high-temperature period. Large differences between both batches were observed in the numbers of microorganisms, in species composition, and in the enzymatic abilities of isolated bacteria. These large differences indicate that the effects of microbial activities on the development of vanilla flavor could be different for each batch of cured vanilla beans. PMID:11319073
Optical fiber-based sensors: application to chemical biology.

PubMed

Brogan, Kathryn L; Walt, David R

2005-10-01

Optical fibers have been used to develop sensors based on nucleic acids and cells. Sensors employing DNA probes have been developed for various genomics applications and microbial pathogen detection. Live cell-based sensors have enabled the monitoring of environmental toxins, and have been used for fundamental studies on populations of individual cells. Both single-core optical fiber sensors and optical fiber sensor arrays have been used for sensing based on nucleic acids and live cells.
Insights into environmental controls on microbial communities in a continental serpentinite aquifer using a microcosm-based approach

PubMed Central

Crespo-Medina, Melitza; Twing, Katrina I.; Kubo, Michael D. Y.; Hoehler, Tori M.; Cardace, Dawn; McCollom, Tom; Schrenk, Matthew O.

2014-01-01

Geochemical reactions associated with serpentinization alter the composition of dissolved organic compounds in circulating fluids and potentially liberate mantle-derived carbon and reducing power to support subsurface microbial communities. Previous studies have identified Betaproteobacteria from the order Burkholderiales and bacteria from the order Clostridiales as key components of the serpentinite–hosted microbiome, however there is limited knowledge of their metabolic capabilities or growth characteristics. In an effort to better characterize microbial communities, their metabolism, and factors limiting their activities, microcosm experiments were designed with fluids collected from several monitoring wells at the Coast Range Ophiolite Microbial Observatory (CROMO) in northern California during expeditions in March and August 2013. The incubations were initiated with a hydrogen atmosphere and a variety of carbon sources (carbon dioxide, methane, acetate, and formate), with and without the addition of nutrients and electron acceptors. Growth was monitored by direct microscopic counts; DNA yield and community composition was assessed at the end of the 3 month incubation. For the most part, results indicate that bacterial growth was favored by the addition of acetate and methane, and that the addition of nutrients and electron acceptors had no significant effect on microbial growth, suggesting no nutrient- or oxidant-limitation. However, the addition of sulfur amendments led to different community compositions. The dominant organisms at the end of the incubations were closely related to Dethiobacter sp. and to the family Comamonadaceae, which are also prominent in culture-independent gene sequencing surveys. These experiments provide one of first insights into the biogeochemical dynamics of the serpentinite subsurface environment and will facilitate experiments to trace microbial activities in serpentinizing ecosystems. PMID:25452748
Insights into environmental controls on microbial communities in a continental serpentinite aquifer using a microcosm-based approach.

PubMed

Crespo-Medina, Melitza; Twing, Katrina I; Kubo, Michael D Y; Hoehler, Tori M; Cardace, Dawn; McCollom, Tom; Schrenk, Matthew O

2014-01-01

Geochemical reactions associated with serpentinization alter the composition of dissolved organic compounds in circulating fluids and potentially liberate mantle-derived carbon and reducing power to support subsurface microbial communities. Previous studies have identified Betaproteobacteria from the order Burkholderiales and bacteria from the order Clostridiales as key components of the serpentinite-hosted microbiome, however there is limited knowledge of their metabolic capabilities or growth characteristics. In an effort to better characterize microbial communities, their metabolism, and factors limiting their activities, microcosm experiments were designed with fluids collected from several monitoring wells at the Coast Range Ophiolite Microbial Observatory (CROMO) in northern California during expeditions in March and August 2013. The incubations were initiated with a hydrogen atmosphere and a variety of carbon sources (carbon dioxide, methane, acetate, and formate), with and without the addition of nutrients and electron acceptors. Growth was monitored by direct microscopic counts; DNA yield and community composition was assessed at the end of the 3 month incubation. For the most part, results indicate that bacterial growth was favored by the addition of acetate and methane, and that the addition of nutrients and electron acceptors had no significant effect on microbial growth, suggesting no nutrient- or oxidant-limitation. However, the addition of sulfur amendments led to different community compositions. The dominant organisms at the end of the incubations were closely related to Dethiobacter sp. and to the family Comamonadaceae, which are also prominent in culture-independent gene sequencing surveys. These experiments provide one of first insights into the biogeochemical dynamics of the serpentinite subsurface environment and will facilitate experiments to trace microbial activities in serpentinizing ecosystems.
Final Report Real Time Monitoring of Rates of Subsurface Microbial Activity Associated with Natural Attenuation and Electron Donor Availability

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

Lovley, Derek R.

The project was successful in developing new sensing technologies for monitoring rates of microbial activity in soils and sediments and also developed a novel proof-of-concept for monitoring the presence of bioavailable concentrations of a diversity of metabolites and toxic components in sedimentary environments. These studies led not only to publications in the peer-reviewed literature, but also two patent applications and a start-up company.
RAPID HEALTH-BASED METHOD FOR MEASURING MICROBIAL INDICATORS OF RECREATIONAL WATER QUALITY - 2006 EPA SCIENCE FORUM

EPA Science Inventory

Because the current approved cultural methods for monitoring indicator bacteria in recreational water require 24 hours to produce results, the public may be exposed to potentially contaminated water before the water has been identified as hazardous. This project was initiated to...
Time-resolved luminescence screening method for enrofloxacin in beef serum

USDA-ARS?s Scientific Manuscript database

Enrofloxacin is one of only two fluoroquinolone antibiotics approved for use in cattle in the U.S. Microbial screening methods currently used in the U.S. for monitoring veterinary drug residues are not sensitive or selective for fluoroquinolones. In this work, a luminescence-based screening assay ...
Continuous monitoring of bacterial biofilm growth using uncoated Thickness-Shear Mode resonators

NASA Astrophysics Data System (ADS)

Castro, P.; Resa, P.; Durán, C.; Maestre, J. R.; Mateo, M.; Elvira, L.

2012-12-01

Quartz Crystal Microbalances (QCM) were used to nondestructively monitor in real time the microbial growth of the bacteria Staphylococcus epidermidis (S. epidermidis) in a liquid broth. QCM, sometimes referred to as Thickness-Shear Mode (TSM) resonators, are highly sensitive sensors not only able to measure very small mass, but also non-gravimetric contributions of viscoelastic media. These devices can be used as biosensors for bacterial detection and are employed in many applications including their use in the food industry, water and environment monitoring, pharmaceutical sciences and clinical diagnosis. In this work, three strains of S. epidermidis (which differ in the ability to produce biofilm) have been continuously monitored using an array of piezoelectric TSM resonators, at 37 °C in a selective culturing media. Microbial growth was followed by measuring the changes in the crystal resonant frequency and bandwidth at several harmonics. It was shown that microbial growth can be monitored in real time using multichannel and multiparametric QCM sensors.
A Terrestrial Single Chamber Microbial Fuel Cell-based Biosensor for Biochemical Oxygen Demand of Synthetic Rice Washed Wastewater

PubMed Central

Logroño, Washington; Guambo, Alex; Pérez, Mario; Kadier, Abudukeremu; Recalde, Celso

2016-01-01

Microbial fuel cells represent an innovative technology which allow simultaneous waste treatment, electricity production, and environmental monitoring. This study provides a preliminary investigation of the use of terrestrial Single chamber Microbial Fuel Cells (SMFCs) as biosensors. Three cells were created using Andean soil, each one for monitoring a BOD concentration of synthetic washed rice wastewater (SRWW) of 10, 100, and 200 mg/L for SMFC1, SMFC2 and SMFC3, respectively. The results showed transient, exponential, and steady stages in the SMFCs. The maximum open circuit voltage (OCV) peaks were reached during the elapsed time of the transient stages, according to the tested BOD concentrations. A good linearity between OCV and time was observed in the increasing stage. The average OCV in this stage increased independently of the tested concentrations. SMFC1 required less time than SMFC2 to reach the steady stage, suggesting the BOD concentration is an influencing factor in SMFCs, and SMFC3 did not reach it. The OCV ratios were between 40.6–58.8 mV and 18.2–32.9 mV for SMFC1 and SMFC2. The reproducibility of the SMFCs was observed in four and three cycles for SMFC1 and SMFC2, respectively. The presented SMFCs had a good response and reproducibility as biosensor devices, and could be an alternative for environmental monitoring. PMID:26784197
Use of PCR-DGGE Based Molecular Methods to Analyse Microbial Community Diversity and Stability during the Thermophilic Stages of an ATAD Wastewater Sludge Treatment Process as an Aid to Performance Monitoring

PubMed Central

Piterina, Anna V.; Pembroke, J. Tony

2013-01-01

PCR and PCR-DGGE techniques have been evaluated to monitor biodiversity indexes within an ATAD (autothermal thermophilic aerobic digestion) system treating domestic sludge for land spread, by examining microbial dynamics in response to elevated temperatures during treatment. The ATAD process utilises a thermophilic population to generate heat and operates at elevated pH due to degradation of sludge solids, thus allowing pasteurisation and stabilisation of the sludge. Genera-specific PCR revealed that Archaea, Eukarya and Fungi decline when the temperature reaches 59°C, while the bacterial lineage constitutes the dominant group at this stage. The bacterial community at the thermophilic stage, its similarity index to the feed material, and the species richness present were evaluated by PCR-DGGE. Parameters such as choice of molecular target (16S rDNA or rpoB genes), and electrophoresis condition, were optimised to maximise the resolution of the method for ATAD. Dynamic analysis of microbial communities was best observed utilising PCR-DGGE analysis of the V6-V8 region of 16S rDNA, while rpoB gene profiles were less informative. Unique thermophilic communities were shown to quickly adapt to process changes, and shown to be quite stable during the process. Such techniques may be used as a monitoring technique for process health and efficiency. PMID:25937969

A Terrestrial Single Chamber Microbial Fuel Cell-based Biosensor for Biochemical Oxygen Demand of Synthetic Rice Washed Wastewater.

PubMed

Logroño, Washington; Guambo, Alex; Pérez, Mario; Kadier, Abudukeremu; Recalde, Celso

2016-01-15

Microbial fuel cells represent an innovative technology which allow simultaneous waste treatment, electricity production, and environmental monitoring. This study provides a preliminary investigation of the use of terrestrial Single chamber Microbial Fuel Cells (SMFCs) as biosensors. Three cells were created using Andean soil, each one for monitoring a BOD concentration of synthetic washed rice wastewater (SRWW) of 10, 100, and 200 mg/L for SMFC1, SMFC2 and SMFC3, respectively. The results showed transient, exponential, and steady stages in the SMFCs. The maximum open circuit voltage (OCV) peaks were reached during the elapsed time of the transient stages, according to the tested BOD concentrations. A good linearity between OCV and time was observed in the increasing stage. The average OCV in this stage increased independently of the tested concentrations. SMFC1 required less time than SMFC2 to reach the steady stage, suggesting the BOD concentration is an influencing factor in SMFCs, and SMFC3 did not reach it. The OCV ratios were between 40.6-58.8 mV and 18.2-32.9 mV for SMFC1 and SMFC2. The reproducibility of the SMFCs was observed in four and three cycles for SMFC1 and SMFC2, respectively. The presented SMFCs had a good response and reproducibility as biosensor devices, and could be an alternative for environmental monitoring.
Recent advances in electronic nose techniques for monitoring of fermentation process.

PubMed

Jiang, Hui; Zhang, Hang; Chen, Quansheng; Mei, Congli; Liu, Guohai

2015-12-01

Microbial fermentation process is often sensitive to even slight changes of conditions that may result in unacceptable end-product quality. Thus, the monitoring of the process is critical for discovering unfavorable deviations as early as possible and taking the appropriate measures. However, the use of traditional analytical techniques is often time-consuming and labor-intensive. In this sense, the most effective way of developing rapid, accurate and relatively economical method for quality assurance in microbial fermentation process is the use of novel chemical sensor systems. Electronic nose techniques have particular advantages in non-invasive monitoring of microbial fermentation process. Therefore, in this review, we present an overview of the most important contributions dealing with the quality control in microbial fermentation process using the electronic nose techniques. After a brief description of the fundamentals of the sensor techniques, some examples of potential applications of electronic nose techniques monitoring are provided, including the implementation of control strategies and the combination with other monitoring tools (i.e. sensor fusion). Finally, on the basis of the review, the electronic nose techniques are critically commented, and its strengths and weaknesses being highlighted. In addition, on the basis of the observed trends, we also propose the technical challenges and future outlook for the electronic nose techniques.
To What Extent is Drinking Water Tested in Sub-Saharan Africa? A Comparative Analysis of Regulated Water Quality Monitoring.

PubMed

Peletz, Rachel; Kumpel, Emily; Bonham, Mateyo; Rahman, Zarah; Khush, Ranjiv

2016-03-02

Water quality information is important for guiding water safety management and preventing water-related diseases. To assess the current status of regulated water quality monitoring in sub-Saharan Africa, we evaluated testing programs for fecal contamination in 72 institutions (water suppliers and public health agencies) across 10 countries. Data were collected through written surveys, in-person interviews, and analysis of microbial water quality testing levels. Though most institutions did not achieve the testing levels specified by applicable standards or World Health Organization (WHO) Guidelines, 85% of institutions had conducted some microbial water testing in the previous year. Institutions were more likely to meet testing targets if they were suppliers (as compared to surveillance agencies), served larger populations, operated in urban settings, and had higher water quality budgets (all p < 0.05). Our results indicate that smaller water providers and rural public health offices will require greater attention and additional resources to achieve regulatory compliance for water quality monitoring in sub-Saharan Africa. The cost-effectiveness of water quality monitoring should be improved by the application of risk-based water management approaches. Efforts to strengthen monitoring capacity should pay greater attention to program sustainability and institutional commitment to water safety.
To What Extent is Drinking Water Tested in Sub-Saharan Africa? A Comparative Analysis of Regulated Water Quality Monitoring

PubMed Central

Peletz, Rachel; Kumpel, Emily; Bonham, Mateyo; Rahman, Zarah; Khush, Ranjiv

2016-01-01

Water quality information is important for guiding water safety management and preventing water-related diseases. To assess the current status of regulated water quality monitoring in sub-Saharan Africa, we evaluated testing programs for fecal contamination in 72 institutions (water suppliers and public health agencies) across 10 countries. Data were collected through written surveys, in-person interviews, and analysis of microbial water quality testing levels. Though most institutions did not achieve the testing levels specified by applicable standards or World Health Organization (WHO) Guidelines, 85% of institutions had conducted some microbial water testing in the previous year. Institutions were more likely to meet testing targets if they were suppliers (as compared to surveillance agencies), served larger populations, operated in urban settings, and had higher water quality budgets (all p < 0.05). Our results indicate that smaller water providers and rural public health offices will require greater attention and additional resources to achieve regulatory compliance for water quality monitoring in sub-Saharan Africa. The cost-effectiveness of water quality monitoring should be improved by the application of risk-based water management approaches. Efforts to strengthen monitoring capacity should pay greater attention to program sustainability and institutional commitment to water safety. PMID:26950135
Microbiology and Crew Medical Events on the International Space Station

NASA Technical Reports Server (NTRS)

Oubre, Cherie M.; Charvat, Jacqueline M.; Kadwa, Biniafer; Taiym, Wafa; Ott, C. Mark; Pierson, Duane; Baalen, Mary Van

2014-01-01

The closed environment of the International Space Station (ISS) creates an ideal environment for microbial growth. Previous studies have identified the ubiquitous nature of microorganisms throughout the space station environment. To ensure safety of the crew, microbial monitoring of air and surface within ISS began in December 2000 and continues to be monitored on a quarterly basis. Water monitoring began in 2009 when the potable water dispenser was installed on ISS. However, it is unknown if high microbial counts are associated with inflight medical events. The microbial counts are determined for the air, surface, and water samples collected during flight operations and samples are returned to the Microbiology laboratory at the Johnson Space Center for identification. Instances of microbial counts above the established microbial limit requirements were noted and compared inflight medical events (any non-injury event such as illness, rashes, etc.) that were reported during the same calendar-quarter. Data were analyzed using repeated measures logistic regression for the forty-one US astronauts flew on ISS between 2000 and 2012. In that time frame, instances of microbial counts being above established limits were found for 10 times for air samples, 22 times for surface samples and twice for water. Seventy-eight inflight medical events were reported among the astronauts. A three times greater risk of a medical event was found when microbial samples were found to be high (OR = 3.01; p =.007). Engineering controls, crew training, and strict microbial limits have been established to mitigate the crew medical events and environmental risks. Due to the timing issues of sampling and the samples return to earth, identification of particular microorganisms causing a particular inflight medical event is difficult. Further analyses are underway.
Development of bacteriophage-based bioluminescent bioreporters for monitoring of microbial pathogens

NASA Astrophysics Data System (ADS)

Ozen, Aysu; Montgomery, Kacey; Jegier, Pat; Patterson, Stacey; Daumer, Kathleen A.; Ripp, Steven A.; Garland, Jay L.; Sayler, Gary S.

2004-03-01

Microorganisms pose numerous problems when present in human occupied enclosed environments. Primary among these are health related hazards, manifested as infectious diseases related to contaminated drinking water, food, or air circulation systems or non-infectious allergy related complications associated with microbial metabolites (sick building syndrome). As a means towards rapid detection of microbial pathogens, we are attempting to harness the specificity of bacterial phage for their host with a modified quorum sensing amplification signal to produce quantifiable bioluminescent (lux) detection on a silicon microluminometer. The bacteriophage itself is metabolically inactive, only achieving replicative capabilities upon infection of its specific host bacterium. Bacteriophage bioluminescent bioreporters contain a genomically inserted luxI component. During an infection event, the phage genes and accompanying luxI construct are taken up by the host bacterium and transcribed, resulting in luxI expression and subsequent activation of a homoserine lactone inducible bioluminescent bioreporter. We constructed a vector carrying the luxI gene under the control of a strong E. coli promoter and cloned it into E. coli. We have shown that it can induce luminescence up to 14,000 counts per second when combined with the bioreporter strain. In their final embodiment, these sensors will be fully independent microelectronic monitors for microbial contamination, requiring only exposure of the biochip to the sample, with on-chip signal processing downloaded directly to the local area network of the environmental control system.
Terroir is a key driver of seed-associated microbial assemblages.

PubMed

Klaedtke, Stephanie; Jacques, Marie-Agnès; Raggi, Lorenzo; Préveaux, Anne; Bonneau, Sophie; Negri, Valeria; Chable, Véronique; Barret, Matthieu

2016-06-01

Seeds have evolved in association with diverse microbial assemblages that may influence plant growth and health. However, little is known about the composition of seed-associated microbial assemblages and the ecological processes shaping their structures. In this work, we monitored the relative influence of the host genotypes and terroir on the structure of the seed microbiota through metabarcoding analysis of different microbial assemblages associated to five different bean cultivars harvested in two distinct farms. Overall, few bacterial and fungal operational taxonomic units (OTUs) were conserved across all seed samples. The lack of shared OTUs between samples is explained by a significant effect of the farm site on the structure of microbial assemblage, which explained 12.2% and 39.7% of variance in bacterial and fungal diversity across samples. This site-specific effect is reflected by the significant enrichment of 70 OTUs in Brittany and 88 OTUs in Luxembourg that lead to differences in co-occurrence patterns. In contrast, variance in microbial assemblage structure was not explained by host genotype. Altogether, these results suggest that seed-associated microbial assemblage is determined by niche-based processes and that the terroir is a key driver of these selective forces. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.
Environmental microbial contamination in a stem cell bank.

PubMed

Cobo, F; Concha, A

2007-04-01

The aim of this study was to evaluate the main environmental microbial contaminants of the clean rooms in our stem cell bank. We have measured the microbial air contamination by both passive and active air sampling and the microbial monitoring of surfaces by means of Rodac plates. The environmental monitoring tests were carried out in accordance with the guidelines of European Pharmacopeia and US Pharmacopeia. The micro-organisms were identified by means of an automated system (VITEK 2). During the monitoring, the clean rooms are continually under good manufacturing practices specifications. The most frequent contaminants were Gram-positive cocci. The main contaminants in our stem cell bank were coagulase-negative staphylococci and other opportunistic human pathogens. In order to assure the levels of potential contamination in both embryonic and adult stem cell lines, a continuous sampling of air particles and testing for viable microbiological contamination is necessary. This study is the first evaluation of the environmental contaminants in stem cell banks and can serve as initial evaluation for these establishments. The introduction of environmental monitoring programmes in the processing of stem cell lines could diminish the risk of contamination in stem cell cultures.
Non-destructive mobile monitoring of microbial contaminations on meat surfaces using porphyrin fluorescence intensities.

PubMed

Durek, J; Fröhling, A; Bolling, J; Thomasius, R; Durek, P; Schlüter, O K

2016-05-01

A non-destructive mobile system for meat quality monitoring was developed and investigated for the possible application along the whole production chain of fresh meat. Pork and lamb meat was stored at 5 °C for up to 20 days post mortem and measured with a fluorescence spectrometer. Additionally, the bacterial influence on the fluorescence signals was evaluated by different experimental procedures. Fluorescence of NADH and different porphyrins could be correlated to the growth of diverse bacteria and hence used for contamination monitoring. The increase of porphyrin fluorescence started after 9 days p.m. for pork and after 2 days p.m. for lamb meat. Based on the results, a mobile fluorescence system was built and compared with the laboratory system. The corrected function of the meat slices showed a root mean square error of 1156.97 r.u. and a mean absolute percentage error of 12.59%; for lamb the values were 470.81 r.u. and 15.55%, respectively. A mobile and non-invasive measurement system would improve the microbial security of fresh meat. Copyright © 2016 Elsevier Ltd. All rights reserved.
Intelligent infrastructure for sustainable potable water: a roundtable for emerging transnational research and technology development needs.

PubMed

Adriaens, Peter; Goovaerts, Pierre; Skerlos, Steven; Edwards, Elizabeth; Egli, Thomas

2003-12-01

Recent commercial and residential development have substantially impacted the fluxes and quality of water that recharge the aquifers and discharges to streams, lakes and wetlands and, ultimately, is recycled for potable use. Whereas the contaminant sources may be varied in scope and composition, these issues of urban water sustainability are of public health concern at all levels of economic development worldwide, and require cheap and innovative environmental sensing capabilities and interactive monitoring networks, as well as tailored distributed water treatment technologies. To address this need, a roundtable was organized to explore the potential role of advances in biotechnology and bioengineering to aid in developing causative relationships between spatial and temporal changes in urbanization patterns and groundwater and surface water quality parameters, and to address aspects of socioeconomic constraints in implementing sustainable exploitation of water resources. An interactive framework for quantitative analysis of the coupling between human and natural systems requires integrating information derived from online and offline point measurements with Geographic Information Systems (GIS)-based remote sensing imagery analysis, groundwater-surface water hydrologic fluxes and water quality data to assess the vulnerability of potable water supplies. Spatially referenced data to inform uncertainty-based dynamic models can be used to rank watershed-specific stressors and receptors to guide researchers and policymakers in the development of targeted sensing and monitoring technologies, as well as tailored control measures for risk mitigation of potable water from microbial and chemical environmental contamination. The enabling technologies encompass: (i) distributed sensing approaches for microbial and chemical contamination (e.g. pathogens, endocrine disruptors); (ii) distributed application-specific, and infrastructure-adaptive water treatment systems; (iii) geostatistical integration of monitoring data and GIS layers; and (iv) systems analysis of microbial and chemical proliferation in distribution systems. This operational framework is aimed at technology implementation while maximizing economic and public health benefits. The outcomes of the roundtable will further research agendas in information technology-based monitoring infrastructure development, integration of processes and spatial analysis, as well as in new educational and training platforms for students, practitioners and regulators. The potential for technology diffusion to emerging economies with limited financial resources is substantial.
Monitoring microbial responses to ocean deoxygenation in a model oxygen minimum zone.

PubMed

Hallam, Steven J; Torres-Beltrán, Mónica; Hawley, Alyse K

2017-10-31

Today in Scientific Data, two compendia of geochemical and multi-omic sequence information (DNA, RNA, protein) generated over almost a decade of time series monitoring in a seasonally anoxic coastal marine setting are presented to the scientific community. These data descriptors introduce a model ecosystem for the study of microbial responses to ocean deoxygenation, a phenotype that is currently expanding due to climate change. Public access to this time series information is intended to promote scientific collaborations and the generation of new hypotheses relevant to microbial ecology, biogeochemistry and global change issues.
Microbial source tracking in shellfish harvesting waters in the Gulf of Nicoya, Costa Rica.

PubMed

Symonds, E M; Young, S; Verbyla, M E; McQuaig-Ulrich, S M; Ross, E; Jiménez, J A; Harwood, V J; Breitbart, M

2017-03-15

Current microbial water quality monitoring is generally limited to culture-based measurements of fecal indicator bacteria (FIB). Given the many possible sources of fecal pollution within a watershed and extra-intestinal FIB reservoirs, it is important to determine source(s) of fecal pollution as a means to improve water quality and protect public health. The principal objective of this investigation was to characterize the microbial water quality of shellfish harvesting areas in the Gulf of Nicoya, Costa Rica during 2015. In order to achieve this objective, the specificity and sensitivity of 11 existing microbial source tracking (MST) PCR assays, associated with cows (BacCow), dogs (BacCan, DogBac), domestic wastewater (PMMoV), general avian (GFD), gulls (Gull2), horses (HorseBac, HoF), humans (HF183, HPyV), and pigs (PF), were evaluated using domestic wastewater and animal fecal samples collected from the region. The sensitivity of animal-associated assays ranged from 13 to 100%, while assay specificity ranged from 38 to 100%. The specificity of pepper mild mottle virus (PMMoV) and human polyomavirus (HPyV) was 100% for domestic wastewater, as compared to 94% specificity of the HF183 Bacteroidales marker. PMMoV was identified as a useful domestic wastewater-associated marker, with concentrations as high as 1.1 × 10 5 copies/ml and 100% sensitivity and specificity. Monthly surface water samples collected from four shellfish harvesting areas were analyzed using culture-based methods for Escherichia coli as well as molecular methods for FIB and a suite of MST markers, which were selected for their specificity in the region. While culturable E. coli results suggested possible fecal pollution during the monitoring period, the absence of human/domestic wastewater-associated markers and low FIB concentrations determined using molecular methods indicated sufficient microbial water quality for shellfish harvesting. This is the first study to our knowledge to test the performance of MST markers in Costa Rica as well as in Central America. Given the lack of wastewater treatment and the presence of secondary sources of FIB, this study highlights the importance of an MST toolbox approach to characterize water quality in tropical regions. Furthermore, it confirms and extends the geographic range of PMMoV as an effective tool for monitoring domestic wastewater pollution. Copyright © 2017 Elsevier Ltd. All rights reserved.
Comparative analysis of microbial fuel cell based biosensors developed with a mixed culture and Shewanella loihica PV-4 and underlying biological mechanism.

PubMed

Yi, Yue; Xie, Beizhen; Zhao, Ting; Liu, Hong

2018-06-13

Microbial fuel cell based biosensors (MFC-biosensors) utilize anode biofilms as biological recognition elements to monitor biochemical oxygen demand (BOD) and biotoxicity. However, the relatively poor sensitivity constrains the application of MFC-biosensors. To address this limitation, this study provided a systematic comparison of sensitivity between the MFC-biosensors constructed with two inocula. Higher biomass density and viability were both observed in the anode biofilm of the mixed culture MFC, which resulted in better sensitivity for BOD assessment. Compared with using mixed culture as inoculum, the anode biofilm developed with Shewanella loihica PV-4 presented lower content of extracellular polymeric substances and poorer ability to secrete protein under toxic shocks. Moreover, the looser structure in the S. loihica PV-4 biofilm further facilitated its susceptibilities to toxic agents. Therefore, the MFC-biosensor with a pure culture of S. loihica PV-4 delivered higher sensitivity for biotoxicity monitoring. This study proposed a new perspective to enhance sensor performance. Copyright © 2018 Elsevier Ltd. All rights reserved.
Microbial Characterization and Comparison of Isolates During the Mir and ISS Missions

NASA Technical Reports Server (NTRS)

Fontenot, Sondra L.; Castro, Victoria; Bruce, Rebekah; Ott, C. Mark; Pierson, Duane L.

2004-01-01

Spacecraft represent a semi-closed ecosystem that provides a unique model of microbial interaction with other microbes, potential hosts, and their environment. Environmental samples from the Mir Space Station (1995-1998) and the International Space Station (ISS) (2000-Present) were collected and processed to provide insight into the characterization of microbial diversity aboard spacecraft over time and assess any potential health risks to the crew. All microbiota were isolated using standard media-based methodologies. Isolates from Mir and ISS were processed using various methods of analysis, including VITEK biochemical analysis, 16s ribosomal identification, and fingerprinting using rep-PCR analysis. Over the first 41 months of habitation, the diversity of the microbiota from air and surface samples aboard ISS increased from an initial six to 53 different bacterial species. During the same period, fungal diversity increased from 2 to 24 species. Based upon rep-PCR analysis, the majority of isolates were unique suggesting the need for increased sampling frequency and a more thorough analysis of samples to properly characterize the ISS microbiota. This limited fungal and bacterial data from environmental samples acquired during monitoring currently do not indicate a microbial hazard to ISS or any trends suggesting potential health risks.
Elucidation of Taste- and Odor-Producing Bacteria and Toxigenic Cyanobacteria in a Midwestern Drinking Water Supply Reservoir by Shotgun Metagenomic Analysis.

PubMed

Otten, Timothy G; Graham, Jennifer L; Harris, Theodore D; Dreher, Theo W

2016-09-01

While commonplace in clinical settings, DNA-based assays for identification or enumeration of drinking water pathogens and other biological contaminants remain widely unadopted by the monitoring community. In this study, shotgun metagenomics was used to identify taste-and-odor producers and toxin-producing cyanobacteria over a 2-year period in a drinking water reservoir. The sequencing data implicated several cyanobacteria, including Anabaena spp., Microcystis spp., and an unresolved member of the order Oscillatoriales as the likely principal producers of geosmin, microcystin, and 2-methylisoborneol (MIB), respectively. To further demonstrate this, quantitative PCR (qPCR) assays targeting geosmin-producing Anabaena and microcystin-producing Microcystis were utilized, and these data were fitted using generalized linear models and compared with routine monitoring data, including microscopic cell counts, sonde-based physicochemical analyses, and assays of all inorganic and organic nitrogen and phosphorus forms and fractions. The qPCR assays explained the greatest variation in observed geosmin (adjusted R(2) = 0.71) and microcystin (adjusted R(2) = 0.84) concentrations over the study period, highlighting their potential for routine monitoring applications. The origin of the monoterpene cyclase required for MIB biosynthesis was putatively linked to a periphytic cyanobacterial mat attached to the concrete drinking water inflow structure. We conclude that shotgun metagenomics can be used to identify microbial agents involved in water quality deterioration and to guide PCR assay selection or design for routine monitoring purposes. Finally, we offer estimates of microbial diversity and metagenomic coverage of our data sets for reference to others wishing to apply shotgun metagenomics to other lacustrine systems. Cyanobacterial toxins and microbial taste-and-odor compounds are a growing concern for drinking water utilities reliant upon surface water resources. Specific identification of the microorganism(s) responsible for water quality degradation is often complicated by the presence of co-occurring taxa capable of producing these undesirable metabolites. Here we present a framework for how shotgun metagenomics can be used to definitively identify problematic microorganisms and how these data can guide the development of rapid genetic assays for routine monitoring purposes. Copyright © 2016, American Society for Microbiology. All Rights Reserved.
Elucidation of Taste- and Odor-Producing Bacteria and Toxigenic Cyanobacteria in a Midwestern Drinking Water Supply Reservoir by Shotgun Metagenomic Analysis

PubMed Central

Graham, Jennifer L.; Harris, Theodore D.

2016-01-01

ABSTRACT While commonplace in clinical settings, DNA-based assays for identification or enumeration of drinking water pathogens and other biological contaminants remain widely unadopted by the monitoring community. In this study, shotgun metagenomics was used to identify taste-and-odor producers and toxin-producing cyanobacteria over a 2-year period in a drinking water reservoir. The sequencing data implicated several cyanobacteria, including Anabaena spp., Microcystis spp., and an unresolved member of the order Oscillatoriales as the likely principal producers of geosmin, microcystin, and 2-methylisoborneol (MIB), respectively. To further demonstrate this, quantitative PCR (qPCR) assays targeting geosmin-producing Anabaena and microcystin-producing Microcystis were utilized, and these data were fitted using generalized linear models and compared with routine monitoring data, including microscopic cell counts, sonde-based physicochemical analyses, and assays of all inorganic and organic nitrogen and phosphorus forms and fractions. The qPCR assays explained the greatest variation in observed geosmin (adjusted R2 = 0.71) and microcystin (adjusted R2 = 0.84) concentrations over the study period, highlighting their potential for routine monitoring applications. The origin of the monoterpene cyclase required for MIB biosynthesis was putatively linked to a periphytic cyanobacterial mat attached to the concrete drinking water inflow structure. We conclude that shotgun metagenomics can be used to identify microbial agents involved in water quality deterioration and to guide PCR assay selection or design for routine monitoring purposes. Finally, we offer estimates of microbial diversity and metagenomic coverage of our data sets for reference to others wishing to apply shotgun metagenomics to other lacustrine systems. IMPORTANCE Cyanobacterial toxins and microbial taste-and-odor compounds are a growing concern for drinking water utilities reliant upon surface water resources. Specific identification of the microorganism(s) responsible for water quality degradation is often complicated by the presence of co-occurring taxa capable of producing these undesirable metabolites. Here we present a framework for how shotgun metagenomics can be used to definitively identify problematic microorganisms and how these data can guide the development of rapid genetic assays for routine monitoring purposes. PMID:27342564
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
Resolution of habitat-associated ecogenomic signatures in bacteriophage genomes and application to microbial source tracking.

PubMed

Ogilvie, Lesley A; Nzakizwanayo, Jonathan; Guppy, Fergus M; Dedi, Cinzia; Diston, David; Taylor, Huw; Ebdon, James; Jones, Brian V

2018-04-01

Just as the expansion in genome sequencing has revealed and permitted the exploitation of phylogenetic signals embedded in bacterial genomes, the application of metagenomics has begun to provide similar insights at the ecosystem level for microbial communities. However, little is known regarding this aspect of bacteriophage associated with microbial ecosystems, and if phage encode discernible habitat-associated signals diagnostic of underlying microbiomes. Here we demonstrate that individual phage can encode clear habitat-related 'ecogenomic signatures', based on relative representation of phage-encoded gene homologues in metagenomic data sets. Furthermore, we show the ecogenomic signature encoded by the gut-associated ɸB124-14 can be used to segregate metagenomes according to environmental origin, and distinguish 'contaminated' environmental metagenomes (subject to simulated in silico human faecal pollution) from uncontaminated data sets. This indicates phage-encoded ecological signals likely possess sufficient discriminatory power for use in biotechnological applications, such as development of microbial source tracking tools for monitoring water quality.
An Autonomous System for Experimental Evolution of Microbial Cultures: Test Results Using Ultraviolet-C Radiation and Escherichia Coli.

NASA Technical Reports Server (NTRS)

Ouandji, Cynthia; Wang, Jonathan; Arismendi, Dillon; Lee, Alonzo; Blaich, Justin; Gentry, Diana

2017-01-01

At its core, the field of microbial experimental evolution seeks to elucidate the natural laws governing the history of microbial life by understanding its underlying driving mechanisms. However, observing evolution in nature is complex, as environmental conditions are difficult to control. Laboratory-based experiments for observing population evolution provide more control, but manually culturing and studying multiple generations of microorganisms can be time consuming, labor intensive, and prone to inconsistency. We have constructed a prototype, closed system device that automates the process of directed evolution experiments in microorganisms. It is compatible with any liquid microbial culture, including polycultures and field samples, provides flow control and adjustable agitation, continuously monitors optical density (OD), and can dynamically control environmental pressures such as ultraviolet-C (UV-C) radiation and temperature. Here, the results of the prototype are compared to iterative exposure and survival assays conducted using a traditional hood, UV-C lamp, and shutter system.
A novel microbial fuel cell sensor with a gas diffusion biocathode sensing element for water and air quality monitoring.

PubMed

Jiang, Yong; Liang, Peng; Huang, Xia; Ren, Zhiyong Jason

2018-07-01

Toxicity monitoring is essential for the protection of public health and ecological safety. Microbial fuel cell (MFC) sensors demonstrated good potential in toxicity monitoring, but current MFC sensors can only be used for anaerobic water monitoring. In this study, a novel gas diffusion (GD)-biocathode sensing element was fabricated using a simple method. The GD-biocathode MFC sensor can directly be used for formaldehyde detection (from 0.0005% to 0.005%) in both aerobic and anaerobic water bodies. Electrochemical analysis indicated that the response by the sensor was caused by the toxic inhibition to the microbial activity for the oxygen reduction reaction (ORR). This study for the first time demonstrated that the GD-biocathode MFC sensor has a detection limit of 20 ppm for formaldehyde and can be used to monitor air pollution. Selective sensitivity to formaldehyde was not achieved as the result of using a mixed-culture, which confirms that it can serve as a generic biosensor for monitoring gaseous pollutants. This study expands the realm of knowledge for MFC sensor applications. Copyright © 2018 Elsevier Ltd. All rights reserved.

Elucidating Microbial Adaptation Dynamics via Autonomous Exposure and Sampling

NASA Technical Reports Server (NTRS)

Grace, Joseph M.; Verseux, Cyprien; Gentry, Diana; Moffet, Amy; Thayabaran, Ramanen; Wong, Nathan; Rothschild, Lynn

2013-01-01

The adaptation of micro-organisms to their environments is a complex process of interaction between the pressures of the environment and of competition. Reducing this multifactorial process to environmental exposure in the laboratory is a common tool for elucidating individual mechanisms of evolution, such as mutation rates. Although such studies inform fundamental questions about the way adaptation and even speciation occur, they are often limited by labor-intensive manual techniques. Current methods for controlled study of microbial adaptation limit the length of time, the depth of collected data, and the breadth of applied environmental conditions. Small idiosyncrasies in manual techniques can have large effects on outcomes; for example, there are significant variations in induced radiation resistances following similar repeated exposure protocols. We describe here a project under development to allow rapid cycling of multiple types of microbial environmental exposure. The system allows continuous autonomous monitoring and data collection of both single species and sampled communities, independently and concurrently providing multiple types of controlled environmental pressure (temperature, radiation, chemical presence or absence, and so on) to a microbial community in dynamic response to the ecosystem's current status. When combined with DNA sequencing and extraction, such a controlled environment can cast light on microbial functional development, population dynamics, inter- and intra-species competition, and microbe-environment interaction. The project's goal is to allow rapid, repeatable iteration of studies of both natural and artificial microbial adaptation. As an example, the same system can be used both to increase the pH of a wet soil aliquot over time while periodically sampling it for genetic activity analysis, or to repeatedly expose a culture of bacteria to the presence of a toxic metal, automatically adjusting the level of toxicity based on the number or growth rate of surviving cells. We are on our second prototype iteration, with demonstrated functions of microbial growth monitoring and dynamic exposure to UV-C radiation and temperature. We plan to add functionality for general chemical presence or absence by Nov. 2013. By making the project low-cost and open-source, we hope to encourage others to use it as a basis for future development of a common microbial environmental adaptation testbed.
Batteryless, wireless sensor powered by a sediment microbial fuel cell.

PubMed

Donovan, Conrad; Dewan, Alim; Heo, Deukhyoun; Beyenal, Haluk

2008-11-15

Sediment microbial fuel cells (SMFCs) are considered to be an alternative renewable power source for remote monitoring. There are two main challenges to using SMFCs as power sources: 1) a SMFC produces a low potential at which most sensor electronics do not operate, and 2) a SMFC cannot provide continuous power, so energy from the SMFC must be stored and then used to repower sensor electronics intermittently. In this study, we developed a SMFC and a power management system (PMS) to power a batteryless, wireless sensor. A SMFC operating with a microbial anode and cathode, located in the Palouse River, Pullman, Washington, U.S.A., was used to demonstrate the utility of the developed system. The designed PMS stored microbial energy and then started powering the wireless sensor when the SMFC potential reached 320 mV. It continued powering until the SMFC potential dropped below 52 mV. The system was repowered when the SMFC potential increased to 320 mV, and this repowering continued as long as microbial reactions continued. We demonstrated that a microbial fuel cell with a microbial anode and cathode can be used as an effective renewable power source for remote monitoring using custom-designed electronics.
Chemical sensors for space applications

NASA Technical Reports Server (NTRS)

Bonting, Sjoerd L.

1992-01-01

The payload of the Space Station Freedom will include sensors for frequent monitoring of the water recycling process and for measuring the many biochemical parameters related to onboard experiments. This paper describes the sensor technologies and the types of transducers and selectors considered for these sensors. Particular attention is given to such aspects of monitoring of the water recycling process as the types of water use, the sources of water and their hazards, the sensor systems for monitoring, microbial monitoring, and monitoring toxic metals and organics. An approach for monitoring water recycling is suggested, which includes microbial testing with a potentiometric device (which should be in first line of tests), the use of an ion-selective electrode for inorganic ion determinations, and the use of optic fiber techniques for the determination of total organic carbon.
Monitoring Acidophilic Microbes with Real-Time Polymerase Chain Reaction (PCR) Assays

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

Frank F. Roberto

2008-08-01

Many techniques that are used to characterize and monitor microbial populations associated with sulfide mineral bioleaching require the cultivation of the organisms on solid or liquid media. Chemolithotrophic species, such as Acidithiobacillus ferrooxidans and Leptospirillum ferrooxidans, or thermophilic chemolithotrophs, such as Acidianus brierleyi and Sulfolobus solfataricus can grow quite slowly, requiring weeks to complete efforts to identify and quantify these microbes associated with bioleach samples. Real-time PCR (polymerase chain reaction) assays in which DNA targets are amplified in the presence of fluorescent oligonucleotide primers, allowing the monitoring and quantification of the amplification reactions as they progress, provide a means ofmore » rapidly detecting the presence of microbial species of interest, and their relative abundance in a sample. This presentation will describe the design and use of such assays to monitor acidophilic microbes in the environment and in bioleaching operations. These assays provide results within 2-3 hours, and can detect less than 100 individual microbial cells.« less
Single-chamber microbial fuel cells as on-line shock-sensors for volatile fatty acids in anaerobic digesters.

PubMed

Schievano, Andrea; Colombo, Alessandra; Cossettini, Alessandra; Goglio, Andrea; D'Ardes, Vincenzo; Trasatti, Stefano; Cristiani, Pierangela

2018-01-01

In anaerobic digesters (AD), volatile fatty acids (VFAs) concentration is a critical operative parameter, which is usually manually monitored to prevent inhibition of microbial consortia. An on-line VFAs monitoring system as early-warning for increasing concentrations would be of great help for operators. Here, air-cathode membraneless microbial fuel cells (MFCs) were investigated as potential biosensors, whose electrical signal instantaneously moves from its steady value with the accumulation of VFAs in the anodic solution. MFCs were operated equipping four lab-scale ADs with carbon-based electrodes. Reactors were filled with the digestate from a full-scale AD and fed in batch with four kinds of feedstock (cheese whey, kitchen waste, citrus pulp and fishery waste). The MFC signal initially increased in parallel to VFAs production, then tended to a steady value for VFAs concentrations above 1000mg Ac L -1 . Peak concentrations of tVFAs (2500-4500mg Ac L -1 ) and MFCs potentials were negatively correlated (r=0.916, p<0.05), regardless of the type of substrate. Inhibition of the MFC system occurred when VFAs increased fast above 4000mg Ac L -1 . Polarization curves of electrodes stressed that electroactive bacteria on bioanodes were strongly subjected to inhibition. The inhibition of electroactivity on bioanode trended like typical shock-sensors, opening to direct application as early-warning monitoring system in full-scale ADs. Copyright © 2017 Elsevier Ltd. All rights reserved.
Direct Application of Rep-PCR on Type I Sourdough Matrix to Monitor the Dominance and Persistence of a Lactobacillus plantarum Starter Throughout Back-Slopping.

PubMed

Dolci, Paola; Cocolin, Luca

2017-08-01

This study describes the optimization and application of repetitive element-PCR (rep-PCR) technique directly on microbial DNA extracted from type I sourdoughs for fast monitoring of a Lb. plantarum starter strain (P1FMC) throughout daily back-slopping. The challenge was to follow and study the performance of a starter culture directly in sourdoughs without cultivation on selective media. The extraction of good quality microbial DNA suitable for amplification from a complex matrix such as dough was the first target. In addition, the objective to obtain a clear rep-PCR profile referable to a specific starter strain among a microbial community was pursued. Co-inoculum trials, in flour matrix, with Lb. plantarum P1FMC and L. lactis LC71 strains and, subsequently, type I sourdough back-slopping trials were performed. The rep-PCR amplification profiles obtained were clearly referable to that of Lb. plantarum P1FMC starter in both co-inoculum trials (also when it was present with one order of magnitude less with respect to L. lactis LC71) and back-slopping trials where it dominated the fermentation process with loads of 10 8 cfu g -1 and prevailed on the autochthonous microbiota. Thus, the approach proposed in this paper could be considered a methodological advancement, based on a culture-independent one-step rep-PCR, suitable for fast monitoring of starter performance. © 2017 Institute of Food Technologists®.
Microbial Load Monitor

NASA Technical Reports Server (NTRS)

Gibson, S. F.; Royer, E. R.

1979-01-01

The Microbial Load Monitor (MLM) is an automated and computerized system for detection and identification of microorganisms. Additionally, the system is designed to enumerate and provide antimicrobic susceptibility profiles for medically significant bacteria. The system is designed to accomplish these tasks in a time of 13 hours or less versus the traditional time of 24 hours for negatives and 72 hours or more for positives usually required for standard microbiological analysis. The MLM concept differs from other methods of microbial detection in that the system is designed to accept raw untreated clinical samples and to selectively identify each group or species that may be present in a polymicrobic sample.
Outward electron transfer by Saccharomyces cerevisiae monitored with a bi-cathodic microbial fuel cell-type activity sensor.

PubMed

Ducommun, Raphaël; Favre, Marie-France; Carrard, Delphine; Fischer, Fabian

2010-03-01

A Janus head-like bi-cathodic microbial fuel cell was constructed to monitor the electron transfer from Saccharomyces cerevisiae to a woven carbon anode. The experiments were conducted during an ethanol cultivation of 170 g/l glucose in the presence and absence of yeast-peptone medium. First, using a basic fuel-cell type activity sensor, it was shown that yeast-peptone medium contains electroactive compounds. For this purpose, 1% solutions of soy peptone and yeast extract were subjected to oxidative conditions, using a microbial fuel cell set-up corresponding to a typical galvanic cell, consisting of culture medium in the anodic half-cell and 0.5 M K(3)Fe(CN)(6) in the cathodic half-cell. Second, using a bi-cathodic microbial fuel cell, it was shown that electrons were transferred from yeast cells to the carbon anode. The participation of electroactive compounds in the electron transport was separated as background current. This result was verified by applying medium-free conditions, where only glucose was fed, confirming that electrons are transferred from yeast cells to the woven carbon anode. Knowledge about the electron transfer through the cell membrane is of importance in amperometric online monitoring of yeast fermentations and for electricity production with microbial fuel cells. Copyright (c) 2009 John Wiley & Sons, Ltd.
Microbial community dynamics during assays of harbour oil spill bioremediation: a microscale simulation study.

PubMed

Cappello, S; Caruso, G; Zampino, D; Monticelli, L S; Maimone, G; Denaro, R; Tripodo, B; Troussellier, M; Yakimov, M; Giuliano, L

2007-01-01

Microcosm experiments simulating an oil spill event were performed to evaluate the response of the natural microbial community structure of Messina harbour seawater following the accidental load of petroleum. An experimental harbour seawater microcosm, supplemented with nutrients and crude oil, was monitored above 15 days in comparison with unpolluted ones (control microcosms). Bacterial cells were counted with a Live/Dead BacLight viability kit; leucine aminopeptidase, beta-glucosidase, alkaline phosphatase, lipase and esterase enzymes were measured using fluorogenic substrates. The microbial community dynamic was monitored by isolation of total RNA, RT-PCR amplification of 16S rRNA, cloning and sequencing. Oil addition stimulated an increase of the total bacterial abundance, leucine aminopeptidase and phosphatase activity rates, as well as a change in the community structure. This suggested a prompt response of micro-organisms to the load of petroleum hydrocarbons. The present study on the viability, specific composition and metabolic characteristics of the microbial community allows a more precise assessment of oil pollution. Both structural and functional parameters offer interesting perspectives as indicators to monitor changes caused by petroleum hydrocarbons. A better knowledge of microbial structural successions at oil-polluted sites is essential for environmental bioremediation. Data obtained in microcosm studies improve our understanding of natural processes occurring during oil spills.
Monitoring of Microbial Loads During Long Duration Missions as a Risk Reduction Tool

NASA Astrophysics Data System (ADS)

Roman, M. C.; Mena, K. D.

2012-01-01

Humans have been exploring space for more than 40 years. For all those years, microorganisms have accompanied both un-manned spacecraft/cargo and manned vessels. Microorganisms are everywhere on Earth, could easily adapt to new environments, and/or can rapidly mutate to survive in very harsh conditions. Their presence in spacecraft and cargo have caused a few inconveniences over the years of human spaceflight, ranging from crew health, life support systems challenges, and material degradation. The sterilization of spacecraft that will host humans in long duration mission would be a costly operation that will not provide a long-term solution to the microbial colonization of the vessels. As soon as a human is exposed to the spacecraft, microorganisms start populating the new environment during the mission. As the human presence in space increases in length, the risk from the microbial load to hardware and crew will also increase. Mitigation of this risk involves several different strategies that will include minimizing the microbial load (in numbers and diversity) and monitoring. This paper will provide a list of the risk mitigation strategies that should be implemented during ground processing, and during the mission. It will also discuss the areas that should be reviewed before an effective in-flight microbial monitoring regimen is implemented.
Field Confirmation and Monitoring Tools for Aerobic Bioremediation of TBA and MTBE

NASA Astrophysics Data System (ADS)

North, K.; Rasa, E.; Mackay, D. M.; Scow, K. M.; Hristova, K. R.

2009-12-01

We have been investigating in situ biotreatment of an existing tert-butyl alcohol (TBA) plume at Vandenberg AFB by recirculation/oxygenation and evaluating monitoring tools for microbial community composition and activity inside and outside of the treatment zone. Results indicate that recirculation/oxygenation by two pairs of recirculation wells is effective at adding oxygen and decreasing methyl tert-butyl ether (MTBE) and TBA concentrations to detection limits along the flowpaths predicted. Compound-specific isotope analyses (CSIA) of groundwater and microbial community analyses (extraction and analysis of DNA) of groundwater and sediments are underway for sampling locations along flowpaths inside and outside of the treatment zone to seek confirmation of in situ biodegradation. We are also evaluating a novel approach to compare the performance of microbial “traps” in characterizing microbial communities: groundwater from the aerobic treatment zone is extracted, separated and directed to multiple chambers located in an air-conditioned ex situ experimental setup. The “traps” under evaluation are in separate chambers; influent and effluent are monitored. The traps being evaluated include Bio-Trap® housings containing Bio-Sep® beads baited with MTBE or TBA labeled with 13C and various unbaited materials. Insights from the various monitoring approaches will be discussed and compared.
Low Frequencies of Interference to EPA Quantitative Polymerase Chain Reaction (qPCR) Methods for Microbial Water Quality Monitoring in U.S. Rivers and Streams and Coastal Waters

EPA Science Inventory

In collaboration with U.S States and Tribes, the United States Environmental Protection Agency (EPA) conducts periodic and rotating, statistically based surveys of U.S. rivers and streams (National Rivers and Streams Assessment, NRSA), estuarine and Great Lakes nearshore coastal ...
Chapter 11. Community analysis-based methods

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

Cao, Y.; Wu, C.H.; Andersen, G.L.

2010-05-01

Microbial communities are each a composite of populations whose presence and relative abundance in water or other environmental samples are a direct manifestation of environmental conditions, including the introduction of microbe-rich fecal material and factors promoting persistence of the microbes therein. As shown by culture-independent methods, different animal-host fecal microbial communities appear distinctive, suggesting that their community profiles can be used to differentiate fecal samples and to potentially reveal the presence of host fecal material in environmental waters. Cross-comparisons of microbial communities from different hosts also reveal relative abundances of genetic groups that can be used to distinguish sources. Inmore » increasing order of their information richness, several community analysis methods hold promise for MST applications: phospholipid fatty acid (PLFA) analysis, denaturing gradient gel electrophoresis (DGGE), terminal restriction fragment length polymorphism (TRFLP), cloning/sequencing, and PhyloChip. Specific case studies involving TRFLP and PhyloChip approaches demonstrate the ability of community-based analyses of contaminated waters to confirm a diagnosis of water quality based on host-specific marker(s). The success of community-based MST for comprehensively confirming fecal sources relies extensively upon using appropriate multivariate statistical approaches. While community-based MST is still under evaluation and development as a primary diagnostic tool, results presented herein demonstrate its promise. Coupled with its inherently comprehensive ability to capture an unprecedented amount of microbiological data that is relevant to water quality, the tools for microbial community analysis are increasingly accessible, and community-based approaches have unparalleled potential for translation into rapid, perhaps real-time, monitoring platforms.« less
Enterovirus and Norovirus Monitoring under UCMR3

EPA Science Inventory

This presentation describes the Unregulated Contaminant Monitoring Rule round 3 (UCMR3) monitoring program for enterovirus and norovirus in groundwater. It provides the data on microbial indicators and virus occurrence during the monitoring period. Enteric virus occurrence was ab...
The influence of in situ chemical oxidation on microbial community composition in groundwater contaminated with chlorinated solvents.

PubMed

Sercu, Bram; Jones, Antony D G; Wu, Cindy H; Escobar, Mauricio H; Serlin, Carol L; Knapp, Timothy A; Andersen, Gary L; Holden, Patricia A

2013-01-01

In situ chemical oxidation with permanganate has become an accepted remedial treatment for groundwater contaminated with chlorinated solvents. This study focuses on the immediate and short-term effects of sodium permanganate (NaMnO(4)) on the indigenous subsurface microbial community composition in groundwater impacted by trichloroethylene (TCE). Planktonic and biofilm microbial communities were studied using groundwater grab samples and reticulated vitreous carbon passive samplers, respectively. Microbial community composition was analyzed by terminal restriction fragment length polymorphism and a high-density phylogenetic microarray (PhyloChip). Significant reductions in microbial diversity and biomass were shown during NaMnO(4) exposure, followed by recovery within several weeks after the oxidant concentrations decreased to <1 mg/L. Bray-Curtis similarities and nonmetric multidimensional scaling showed that microbial community composition before and after NaMnO(4) was similar, when taking into account the natural variation of the microbial communities. Also, 16S rRNA genes of two reductive dechlorinators (Desulfuromonas spp. and Sulfurospirillum spp.) and diverse taxa capable of cometabolic TCE oxidation were detected in similar quantities by PhyloChip across all monitoring wells, irrespective of NaMnO(4) exposure and TCE concentrations. However, minimal biodegradation of TCE was observed in this study, based on oxidized conditions, concentration patterns of chlorinated and nonchlorinated hydrocarbons, geochemistry, and spatiotemporal distribution of TCE-degrading bacteria.
Soil microbial respiration and PICT responses to an industrial and historic lead pollution: a field study.

PubMed

Bérard, Annette; Capowiez, Line; Mombo, Stéphane; Schreck, Eva; Dumat, Camille; Deola, Frédéric; Capowiez, Yvan

2016-03-01

We performed a field investigation to study the long-term impacts of Pb soil contamination on soil microbial communities and their catabolic structure in the context of an industrial site consisting of a plot of land surrounding a secondary lead smelter. Microbial biomass, catabolic profiles, and ecotoxicological responses (PICT) were monitored on soils sampled at selected locations along 110-m transects established on the site. We confirmed the high toxicity of Pb on respirations and microbial and fungal biomasses by measuring positive correlations with distance from the wall factory and negative correlation with total Pb concentrations. Pb contamination also induced changes in microbial and fungal catabolic structure (from carbohydrates to amino acids through carboxylic malic acid). Moreover, PICT measurement allowed to establish causal linkages between lead and its effect on biological communities taking into account the contamination history of the ecosystem at community level. The positive correlation between qCO2 (based on respiration and substrate use) and PICT suggested that the Pb stress-induced acquisition of tolerance came at a greater energy cost for microbial communities in order to cope with the toxicity of the metal. In this industrial context of long-term polymetallic contamination dominated by Pb in a field experiment, we confirmed impacts of this metal on soil functioning through microbial communities, as previously observed for earthworm communities.
Functional gene array-based analysis of microbial community structure in groundwaters with a gradient of contaminant levels

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

Waldron, P.J.; Wu, L.; Van Nostrand, J.D.

2009-06-15

To understand how contaminants affect microbial community diversity, heterogeneity, and functional structure, six groundwater monitoring wells from the Field Research Center of the U.S. Department of Energy Environmental Remediation Science Program (ERSP; Oak Ridge, TN), with a wide range of pH, nitrate, and heavy metal contamination were investigated. DNA from the groundwater community was analyzed with a functional gene array containing 2006 probes to detect genes involved in metal resistance, sulfate reduction, organic contaminant degradation, and carbon and nitrogen cycling. Microbial diversity decreased in relation to the contamination levels of the wells. Highly contaminated wells had lower gene diversity butmore » greater signal intensity than the pristine well. The microbial composition was heterogeneous, with 17-70% overlap between different wells. Metal-resistant and metal-reducing microorganisms were detected in both contaminated and pristine wells, suggesting the potential for successful bioremediation of metal-contaminated groundwaters. In addition, results of Mantel tests and canonical correspondence analysis indicate that nitrate, sulfate, pH, uranium, and technetium have a significant (p < 0.05) effect on microbial community structure. This study provides an overall picture of microbial community structure in contaminated environments with functional gene arrays by showing that diversity and heterogeneity can vary greatly in relation to contamination.« less
Monitoring of Immune and Microbial Reconstitution in (HCT) and Novel Immunotherapies

ClinicalTrials.gov

2018-06-25

Immune and Microbial Reconstitution; Systemic Viral Infection; Acute-graft-versus-host Disease; Chronic Graft-versus-host-disease; Recurrent Malignancy; Cytokine Release Syndrome; Allogenic Related Donors; Cell Therapy/Immunotherapy Patients
An MFC-Based Online Monitoring and Alert System for Activated Sludge Process

PubMed Central

Xu, Gui-Hua; Wang, Yun-Kun; Sheng, Guo-Ping; Mu, Yang; Yu, Han-Qing

2014-01-01

In this study, based on a simple, compact and submersible microbial fuel cell (MFC), a novel online monitoring and alert system with self-diagnosis function was established for the activated sludge (AS) process. Such a submersible MFC utilized organic substrates and oxygen in the AS reactor as the electron donor and acceptor respectively, and could provide an evaluation on the status of the AS reactor and thus give a reliable early warning of potential risks. In order to evaluate the reliability and sensitivity of this online monitoring and alert system, a series of tests were conducted to examine the response of this system to various shocks imposed on the AS reactor. The results indicate that this online monitoring and alert system was highly sensitive to the performance variations of the AS reactor. The stability, sensitivity and repeatability of this online system provide feasibility of being incorporated into current control systems of wastewater treatment plants to real-time monitor, diagnose, alert and control the AS process. PMID:25345502
Critical moisture content for microbial growth in dried food-processing residues.

PubMed

Rezaei, Farzaneh; Vandergheynst, Jean S

2010-09-01

Food-processing residues are good feedstocks for biofuel and biochemical production because they have high energy content and are abundant. Year-round biofuel and biochemical production requires proper storage to prevent microbial decomposition and thermal runaway. In this study, microbial activity of tomato pomace (TP), grape pomace (GP), fermented grape pomace (FGP) and sugar beet pulp (SBP) was monitored at nine different moisture contents. Maximum and cumulative respirations for each feedstock with respect to moisture content followed a sigmoidal relationship. The critical moisture content below which no microbial activity was detected for SBP, TP, FGP and GP was 24-31, 16-21, 23-33 and 43-46% (dry basis) respectively. A logarithmic relationship was observed (R(2) = 0.94) between critical moisture content and initial water-soluble carbohydrate (WSC) content of the processing residues. The critical moisture content below which no microbial activity was detected and the relationship between critical moisture content and initial WSC content were determined in this study for four food-processing residues. Both parameters permit evaluation of the potential for deterioration of food-processing residues during storage based on moisture content and WSC content. Copyright 2010 Society of Chemical Industry.

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

Deng, Ye; Zhang, Ping; Qin, Yujia

When trying to discern network interactions among different species/populations in microbial communities interests have been evoked in recent years, but little information is available about temporal dynamics of microbial network interactions in response to environmental perturbations. We modified the random matrix theory-based network approach to discern network succession in groundwater microbial communities in response to emulsified vegetable oil (EVO) amendment for uranium bioremediation. Groundwater microbial communities from one control and seven monitor wells were analysed with a functional gene array (GeoChip 3.0), and functional molecular ecological networks (fMENs) at different time points were reconstructed. Our results showed that the networkmore » interactions were dramatically altered by EVO amendment. Dynamic and resilient succession was evident: fairly simple at the initial stage (Day 0), increasingly complex at the middle period (Days 4, 17, 31), most complex at Day 80, and then decreasingly complex at a later stage (140–269 days). Unlike previous studies in other habitats, negative interactions predominated in a time-series fMEN, suggesting strong competition among different microbial species in the groundwater systems after EVO injection. In particular, several keystone sulfate-reducing bacteria showed strong negative interactions with their network neighbours. These results provide mechanistic understanding of the decreased phylogenetic diversity during environmental perturbations.« less
Next Generation Microbiology Requirements

NASA Technical Reports Server (NTRS)

Ott, C. M.; Oubre, C. M.; Elliott, T. F.; Castro, V. A.; Pierson, D. L.

2012-01-01

As humans continue to explore deep into space, microorganisms will travel with them. The primary means to mitigate the risk of infectious disease are a combination of prudent spacecraft design and rigorous operational controls. The effectiveness of these methods are evaluated by microbiological monitoring of spacecraft, food, water, and the crew that is performed preflight, in-flight, and post-flight. Current NASA requirements associated with microbiological monitoring are based on culture-based methodology where microorganisms are grown on a semi-solid growth medium and enumerated. Subsequent identification of the organisms requires specialized labor and large equipment, which historically has been performed on Earth. Requirements that rely strictly on culture-based units limit the use of non-culture based monitoring technology. Specifically, the culture-based "measurement criteria" are Colony Forming Units (CFU, representing the growth of one microorganism at a single location on the agar medium) per a given volume, area, or sample size. As the CFU unit by definition is culture-based, these requirements limit alternative technologies for spaceflight applications. As spaceflight missions such as those to Mars extend further into space, culture-based technology will become difficult to implement due to the (a) limited shelf life of the culture media, (b) mass/volume necessary to carry these consumables, and (c) problems associated with the production of biohazardous material in the habitable volume of the spacecraft. In addition, an extensive amount of new knowledge has been obtained during the Space Shuttle, NASA-Mir, and International Space Station Programs, which gave direction for new or modified microbial control requirements for vehicle design and mission operations. The goal of this task is to develop and recommend a new set of requirements for vehicle design and mission operations, including microbiological monitoring, based upon "lessons learned" and new technology. During 2011, this study focused on evaluating potable water requirements by assembling a forum of internal and external experts from NASA, other federal agencies, and academia. Key findings from this forum included: (1) Preventive design and operational strategies should be stringent and the primary focus of NASA's mitigation efforts, as they are cost effective and can be attained with conventional technology. (2) Microbial monitoring hardware should be simple and must be able to measure the viability of microorganisms in a sample. Multiple monitoring technologies can be utilized as long as at the microorganisms being identified can also be confirmed as viable. (3) Evidence showing alterations in the crew immune function and microbial virulence complicates risk assessments and creates the need for very conservative requirements. (4) One key source of infectious agents will always be the crew, and appropriate preventative measures should be taken preflight. (5) Water systems should be thoroughly disinfected (sterilized if possible) preflight and retain a residual biocide throughout the mission. Future forums will cover requirements for other types of samples, specifically spaceflight food and environmental samples, such as vehicle air and vehicle and cargo surfaces. An interim report on the potable water forum has been delivered to the Human Research Program with a final report on the recommendations for all sample types being delivered in September 2013.
Biosensoric potential of microbial fuel cells.

PubMed

Schneider, György; Kovács, Tamás; Rákhely, Gábor; Czeller, Miklós

2016-08-01

Recent progress in microbial fuel cell (MFC) technology has highlighted the potential of these devices to be used as biosensors. The advantages of MFC-based biosensors are that they are phenotypic and can function in either assay- or flow-through formats. These features make them appropriate for contiguous on-line monitoring in laboratories and for in-field applications. The selectivity of an MFC biosensor depends on the applied microorganisms in the anodic compartment where electron transfer (ET) between the artificial surface (anode) and bacterium occurs. This process strongly determines the internal resistance of the sensoric system and thus influences signal outcome and response time. Despite their beneficial characteristics, the number of MFC-based biosensoric applications has been limited until now. The aim of this mini-review is to turn attention to the biosensoric potential of MFCs by summarizing ET mechanisms on which recently established and future sensoric devices are based.
The Influence of Microbiology on Spacecraft Design and Controls: A Historical Perspective of the Shuttle and International Space Station Programs

NASA Technical Reports Server (NTRS)

Castro, Victoria A.; Bruce, Rebekah J.; Ott, C. Mark; Pierson, D. L.

2006-01-01

For over 40 years, NASA has been putting humans safely into space in part by minimizing microbial risks to crew members. Success of the program to minimize such risks has resulted from a combination of engineering and design controls as well as active monitoring of the crew, food, water, hardware, and spacecraft interior. The evolution of engineering and design controls is exemplified by the implementation of HEPA filters for air treatment, antimicrobial surface materials, and the disinfection regimen currently used on board the International Space Station. Data from spaceflight missions confirm the effectiveness of current measures; however, fluctuations in microbial concentrations and trends in contamination events suggest the need for continued diligence in monitoring and evaluation as well as further improvements in engineering systems. The knowledge of microbial controls and monitoring from assessments of past missions will be critical in driving the design of future spacecraft.
Anaerobic digestion of slaughterhouse waste: main process limitations and microbial community interactions.

PubMed

Palatsi, J; Viñas, M; Guivernau, M; Fernandez, B; Flotats, X

2011-02-01

Fresh pig/cattle slaughterhouse waste mixtures, with different lipid-protein ratios, were characterized and their anaerobic biodegradability assessed in batch tests. The resultant methane potentials were high (270-300 L(CH4) kg(-1)(COD)) making them interesting substrates for the anaerobic digestion process. However, when increasing substrate concentrations in consecutive batch tests, up to 15 g(COD) kg(-1), a clear inhibitory process was monitored. Despite the reported severe inhibition, related to lipid content, the system was able to recover activity and successfully degrade the substrate. Furthermore, 16SrRNA gene-based DGGE results showed an enrichment of specialized microbial populations, such as β-oxidizing/proteolitic bacteria (Syntrophomonas sp., Coprothermobacter sp. and Anaerobaculum sp.), and syntrophic methanogens (Methanosarcina sp.). Consequently, the lipid concentration of substrate and the structure of the microbial community are the main limiting factors for a successful anaerobic treatment of fresh slaughterhouse waste. Copyright © 2010 Elsevier Ltd. All rights reserved.
Rapid Monitoring of Bacteria and Fungi aboard the International Space Station (ISS)

NASA Technical Reports Server (NTRS)

Gunter, D.; Flores, G.; Effinger, M.; Maule, J.; Wainwright, N.; Steele, A.; Damon, M.; Wells, M.; Williams, S.; Morris, H.;

2009-01-01

Microorganisms within spacecraft have traditionally been monitored with culture-based techniques. These techniques involve growth of environmental samples (cabin water, air or surfaces) on agar-type media for several days, followed by visualization of resulting colonies or return of samples to Earth for ground-based analysis. Data obtained over the past 4 decades have enhanced our understanding of the microbial ecology within space stations. However, the approach has been limited by the following factors: i) Many microorganisms (estimated > 95%) in the environment cannot grow on conventional growth media; ii) Significant time lags (3-5 days for incubation and up to several months to return samples to ground); iii) Condensation in contact slides hinders colony counting by crew; and iv) Growth of potentially harmful microorganisms, which must then be disposed of safely. This report describes the operation of a new culture-independent technique onboard the ISS for rapid analysis (within minutes) of endotoxin and beta-1, 3-glucan, found in the cell walls of gramnegative bacteria and fungi, respectively. The technique involves analysis of environmental samples with the Limulus Amebocyte Lysate (LAL) assay in a handheld device, known as the Lab-On-a-Chip Application Development Portable Test System (LOCAD-PTS). LOCADPTS was launched to the ISS in December 2006, and here we present data obtained from Mach 2007 until the present day. These data include a comparative study between LOCADPTS analysis and existing culture-based methods; and an exploratory survey of surface endotoxin and beta-1, 3-glucan throughout the ISS. While a general correlation between LOCAD-PTS and traditional culture-based methods should not be expected, we will suggest new requirements for microbial monitoring based upon culture-independent parameters measured by LOCAD-PTS.

Colonization of the Cecal Mucosa by Helicobacter hepaticus Impacts the Diversity of the Indigenous Microbiota

PubMed Central

Kuehl, Carole J.; Wood, Heather D.; Marsh, Terence L.; Schmidt, Thomas M.; Young, Vincent B.

2005-01-01

Establishment of mucosal and/or luminal colonization is the first step in the pathogenesis of many gastrointestinal bacterial pathogens. The pathogen must be able to establish itself in the face of competition from the complex microbial community that is already in place. We used culture-independent methods to monitor the colonization of the cecal mucosa of Helicobacter-free mice following experimental infection with the pathogen Helicobacter hepaticus. Two days after infection, H. hepaticus comprised a minor component of the mucosa-associated microbiota, but within 14 days, it became the dominant member of the community. Colonization of the mucosa by H. hepaticus was associated with a decrease in the overall diversity of the microbial community, in large part due to changes in evenness resulting from the relative dominance of H. hepaticus as a member of the community. Our results demonstrate that invasion of the complex gastrointestinal microbial community by a pathogenic microorganism causes reproducible and significant disturbances in the community structure. The use of non-culture-based methods to monitor these changes should lead to a greater understanding of the ecological principles that govern pathogen invasion and may lead to novel methods for the prevention and control of gastrointestinal pathogens. PMID:16177375
In-Flight Microbial Monitor

NASA Technical Reports Server (NTRS)

Zeitlin, Nancy; Mullenix, Pamela; Wheeler, Raymond M.; Ruby, Anna Maria

2015-01-01

Previous research has shown that potential human pathogens have been detected on the International Space Station (ISS). New microorganisms are introduced with every exchange of crew and cargo. Microorganisms introduced to the ISS are readily transferred between crew and subsystems (i.e., ECLSS, environmental control and life support systems). Current microbial characterization methods require a culture-based enrichment of microorganisms and at least a 48-hour incubation time. This increases the microbial load while detecting only a limited number of microorganisms. The culture-based method detects approximately 1-10% of the total organisms present and provides no identification. To identify and enumerate ISS samples requires that the microbes be returned to Earth for complete analysis. Therefore, a more expedient, low-cost, inflight method of microbial detection, identification, and enumeration is needed. The RAZOR EX, a ruggedized, commercial off the shelf, real-time PCR field instrument was tested for its ability to detect microorganisms at low concentrations within one hour. Escherichia coli, Salmonella enterica Typhimurium, and Pseudomonas aeruginosa were detected at low levels using real-time DNA amplification. Total heterotrophic counts could also be detected using a 16S gene marker that can identify up to 98% of all bacteria. To reflect viable cells found in the samples, RNA was also detectable using a modified, single-step reverse transcription reaction.
Monitoring of biofilm formation on different material surfaces of medical devices using hyperspectral imaging method

NASA Astrophysics Data System (ADS)

Kim, Do-Hyun; Kim, Moon S.; Hwang, Jeeseong

2012-03-01

Contamination of the inner surface of indwelling (implanted) medical devices by microbial biofilm is a serious problem. Some microbial bacteria such as Escherichia coli form biofilms that lead to potentially lifethreatening infections. Other types of medical devices such as bronchoscopes and duodenoscopes account for the highest number of reported endoscopic infections where microbial biofilm is one of the major causes for these infections. We applied a hyperspectral imaging method to detect biofilm contamination on the surface of several common materials used for medical devices. Such materials include stainless steel, titanium, and stainless-steeltitanium alloy. Potential uses of hyperspectral imaging technique to monitor biofilm attachment to different material surfaces are discussed.
"STOP: Can You Drink That Water?" Microbiology, Chemistry, & Advocacy in an Inquiry-Based Water Quality Curriculum for 8th Graders

ERIC Educational Resources Information Center

Valauri-Orton, Alexis; Bernd, Karen K.

2015-01-01

For many middle school students, connections between their lives and concepts like chemical reactivity, microbial contamination, and experimental sampling are not obvious. They may also feel that, even if there were connections, understanding the monitoring and quality of natural resources is something for grown-ups and beyond their…
A Novel Early Warning System Based on a Sediment Microbial Fuel Cell for In Situ and Real Time Hexavalent Chromium Detection in Industrial Wastewater.

PubMed

Zhao, Shuai; Liu, Pu; Niu, Yongyan; Chen, Zhengjun; Khan, Aman; Zhang, Pengyun; Li, Xiangkai

2018-02-22

Hexavalent chromium (Cr(VI)) is a well-known toxic heavy metal in industrial wastewater, but in situ and real time monitoring cannot be achieved by current methods used during industrial wastewater treatment processes. In this study, a Sediment Microbial Fuel Cell (SMFC) was used as a biosensor for in situ real-time monitoring of Cr(VI), which was the organic substrate is oxidized in the anode and Cr(VI) is reduced at the cathode simultaneously. The pH 6.4 and temperature 25 °C were optimal conditions for the operation. Under the optimal conditions, linearity (R² = 0.9935) of the generated voltage was observed in the Cr(VI) concentration range from 0.2 to 0.7 mg/L. The system showed high specificity for Cr(VI), as other co-existing ions such as Cu 2+ , Zn 2+ , and Pb 2+ did not interfere with Cr(VI) detection. In addition, when the sediment MFC-based biosensor was applied for measuring Cr(VI) in actual wastewater samples, a low deviation (<8%) was obtained, which indicated its potential as a reliable biosensor device. MiSeq sequencing results showed that electrochemically active bacteria ( Geobacter and Pseudomonas ) were enriched at least two-fold on the biofilm of the anode in the biosensor as compared to the SMFC without Cr(VI). Cyclic voltammetry curves indicated that a pair of oxidation/reduction peaks appeared at -111 mV and 581 mV, respectively. These results demonstrated that the proposed sediment microbial fuel cell-based biosensor can be applied as an early warning device for real time in situ detection of Cr(VI) in industrial wastewaters.
A Novel Early Warning System Based on a Sediment Microbial Fuel Cell for In Situ and Real Time Hexavalent Chromium Detection in Industrial Wastewater

PubMed Central

Zhao, Shuai; Liu, Pu; Niu, Yongyan; Chen, Zhengjun; Khan, Aman; Zhang, Pengyun; Li, Xiangkai

2018-01-01

Hexavalent chromium (Cr(VI)) is a well-known toxic heavy metal in industrial wastewater, but in situ and real time monitoring cannot be achieved by current methods used during industrial wastewater treatment processes. In this study, a Sediment Microbial Fuel Cell (SMFC) was used as a biosensor for in situ real-time monitoring of Cr(VI), which was the organic substrate is oxidized in the anode and Cr(VI) is reduced at the cathode simultaneously. The pH 6.4 and temperature 25 °C were optimal conditions for the operation. Under the optimal conditions, linearity (R2 = 0.9935) of the generated voltage was observed in the Cr(VI) concentration range from 0.2 to 0.7 mg/L. The system showed high specificity for Cr(VI), as other co-existing ions such as Cu2+, Zn2+, and Pb2+ did not interfere with Cr(VI) detection. In addition, when the sediment MFC-based biosensor was applied for measuring Cr(VI) in actual wastewater samples, a low deviation (<8%) was obtained, which indicated its potential as a reliable biosensor device. MiSeq sequencing results showed that electrochemically active bacteria (Geobacter and Pseudomonas) were enriched at least two-fold on the biofilm of the anode in the biosensor as compared to the SMFC without Cr(VI). Cyclic voltammetry curves indicated that a pair of oxidation/reduction peaks appeared at −111 mV and 581 mV, respectively. These results demonstrated that the proposed sediment microbial fuel cell-based biosensor can be applied as an early warning device for real time in situ detection of Cr(VI) in industrial wastewaters. PMID:29470394
Fluorescent labeling of NASBA amplified tmRNA molecules for microarray applications

PubMed Central

Scheler, Ott; Glynn, Barry; Parkel, Sven; Palta, Priit; Toome, Kadri; Kaplinski, Lauris; Remm, Maido; Maher, Majella; Kurg, Ants

2009-01-01

Background Here we present a novel promising microbial diagnostic method that combines the sensitivity of Nucleic Acid Sequence Based Amplification (NASBA) with the high information content of microarray technology for the detection of bacterial tmRNA molecules. The NASBA protocol was modified to include aminoallyl-UTP (aaUTP) molecules that were incorporated into nascent RNA during the NASBA reaction. Post-amplification labeling with fluorescent dye was carried out subsequently and tmRNA hybridization signal intensities were measured using microarray technology. Significant optimization of the labeled NASBA protocol was required to maintain the required sensitivity of the reactions. Results Two different aaUTP salts were evaluated and optimum final concentrations were identified for both. The final 2 mM concentration of aaUTP Li-salt in NASBA reaction resulted in highest microarray signals overall, being twice as high as the strongest signals with 1 mM aaUTP Na-salt. Conclusion We have successfully demonstrated efficient combination of NASBA amplification technology with microarray based hybridization detection. The method is applicative for many different areas of microbial diagnostics including environmental monitoring, bio threat detection, industrial process monitoring and clinical microbiology. PMID:19445684
Application of next-generation sequencing methods for microbial monitoring of anaerobic digestion of lignocellulosic biomass.

PubMed

Bozan, Mahir; Akyol, Çağrı; Ince, Orhan; Aydin, Sevcan; Ince, Bahar

2017-09-01

The anaerobic digestion of lignocellulosic wastes is considered an efficient method for managing the world's energy shortages and resolving contemporary environmental problems. However, the recalcitrance of lignocellulosic biomass represents a barrier to maximizing biogas production. The purpose of this review is to examine the extent to which sequencing methods can be employed to monitor such biofuel conversion processes. From a microbial perspective, we present a detailed insight into anaerobic digesters that utilize lignocellulosic biomass and discuss some benefits and disadvantages associated with the microbial sequencing techniques that are typically applied. We further evaluate the extent to which a hybrid approach incorporating a variation of existing methods can be utilized to develop a more in-depth understanding of microbial communities. It is hoped that this deeper knowledge will enhance the reliability and extent of research findings with the end objective of improving the stability of anaerobic digesters that manage lignocellulosic biomass.
A PCR Based Microbial Monitoring Alternative Method of Detection and Identification of Microbes Aboard ISS

NASA Technical Reports Server (NTRS)

Khodadad, Christina; Oubre, Cherie; Castro, Victoria; Flint, Stephanie; Ott, Mark; Roman, Monserrate; Wheeler, Ray; Melendez, Orlando

2017-01-01

Previous research has shown that microorganisms and potential human pathogens have been detected on the International Space Station (ISS) with additional introduction of new microflora occurring with every exchange of crew or addition of equipment and supplies. These microbes are readily transferred between crew and subsystems (i.e. ECLSS, environmental control and life support systems). As this can be detrimental to astronaut health and optimal performance of ISS systems, monitoring of systems such as ECLSS to include identification of microbial contaminants could prevent adverse effects on human health and life support systems. Current monitoring on ISS is laborious and utilizes culture based methods followed by sample return to Earth for complete analysis. Future, long-distance spaceflight missions will require real-time monitoring capabilities that enable efficient and rapid assessments of the microbial environment allowing for expedited decisions and more targeted response to cope with anomalies. Polymerase chain reaction (PCR), a molecular microbial monitoring method was chosen and numerous PCR instruments investigated for their potential to perform in microgravity conditions. Using ISS as a test bed for PCR verification in microgravity will enable NASA to assess whether molecular based microbiological sensors may be components of reliable, closed-loop life support and habitation systems in spacecraft, enhancing infrastructure capabilities through increased efficiency, reliability, and time savings by enabling sample analysis on orbit. NASA selected the Water Monitoring Suite as one of the rapid spaceflight hardware demonstration activities utilizing a streamlined process to minimize the time required to fly experimental flight hardware. The RAZOR EX (BioFire Defense, Salt Lake City, UT) system was part of the water monitoring suite and is a commercial off-the-shelf (COTS) real-time PCR instrument designed for field work. The RAZOR EX was originally designed for Department of Defense (DoD) under a small business innovative research (SBIR) grant and is ruggedized, compact and provides a rapid, sample to answer in less than an hour. PCR assays using a fluorescent probe were optimized and spiked with known concentrations of DNA (Pseudomonas aeruginosa) ranging from 0.002 to 20 ng. PCR reagents were lyophilized and configured in customized pouches and tested for flight readiness. Three types of water were used to rehydrate the reagents and demonstrate the fidelity of the PCR reaction in microgravity. Molecular grade deionized water served as a control while filtered and unfiltered ISS potable water served to test for chemical or biological inhibitors. All three types were compared to parallel ground test results. Nine tests were run on ISS (3 of each water type) and the critical threshold cycle (Ct) was compared to parallel ground tests completed at Kennedy Space Center, FL and Johnson Space Center, TX. All concentrations of Pseudomonas aeruginosa DNA were detected. A comparison of the Ct produced in real time PCR indicated similarity between flight and ground samples. There appeared to be no significant difference between flight or ground PCR reactions or between any of the three water types. This testing demonstrated the ability to perform molecular testing during spaceflight operations with similar sensitivity. It will allow for future ground development of molecular protocols and minimize the need for spaceflight testing. Future testing will include development of additional targets including environmental and health related organisms.
Sustainable microbial water quality monitoring programme design using phage-lysis and multivariate techniques.

PubMed

Nnane, Daniel Ekane

2011-11-15

Contamination of surface waters is a pervasive threat to human health, hence, the need to better understand the sources and spatio-temporal variations of contaminants within river catchments. River catchment managers are required to sustainably monitor and manage the quality of surface waters. Catchment managers therefore need cost-effective low-cost long-term sustainable water quality monitoring and management designs to proactively protect public health and aquatic ecosystems. Multivariate and phage-lysis techniques were used to investigate spatio-temporal variations of water quality, main polluting chemophysical and microbial parameters, faecal micro-organisms sources, and to establish 'sentry' sampling sites in the Ouse River catchment, southeast England, UK. 350 river water samples were analysed for fourteen chemophysical and microbial water quality parameters in conjunction with the novel human-specific phages of Bacteroides GB-124 (Bacteroides GB-124). Annual, autumn, spring, summer, and winter principal components (PCs) explained approximately 54%, 75%, 62%, 48%, and 60%, respectively, of the total variance present in the datasets. Significant loadings of Escherichia coli, intestinal enterococci, turbidity, and human-specific Bacteroides GB-124 were observed in all datasets. Cluster analysis successfully grouped sampling sites into five clusters. Importantly, multivariate and phage-lysis techniques were useful in determining the sources and spatial extent of water contamination in the catchment. Though human faecal contamination was significant during dry periods, the main source of contamination was non-human. Bacteroides GB-124 could potentially be used for catchment routine microbial water quality monitoring. For a cost-effective low-cost long-term sustainable water quality monitoring design, E. coli or intestinal enterococci, turbidity, and Bacteroides GB-124 should be monitored all-year round in this river catchment. Copyright © 2011 Elsevier B.V. All rights reserved.
Monitoring and managing microbes in aquaculture - Towards a sustainable industry.

PubMed

Bentzon-Tilia, Mikkel; Sonnenschein, Eva C; Gram, Lone

2016-09-01

Microorganisms are of great importance to aquaculture where they occur naturally, and can be added artificially, fulfilling different roles. They recycle nutrients, degrade organic matter and, occasionally, they infect and kill the fish, their larvae or the live feed. Also, some microorganisms may protect fish and larvae against disease. Hence, monitoring and manipulating the microbial communities in aquaculture environments hold great potential; both in terms of assessing and improving water quality, but also in terms of controlling the development of microbial infections. Using microbial communities to monitor water quality and to efficiently carry out ecosystem services within the aquaculture systems may only be a few years away. Initially, however, we need to thoroughly understand the microbiomes of both healthy and diseased aquaculture systems, and we need to determine how to successfully manipulate and engineer these microbiomes. Similarly, we can reduce the need to apply antibiotics in aquaculture through manipulation of the microbiome, i.e. by the use of probiotic bacteria. Recent studies have demonstrated that fish pathogenic bacteria in live feed can be controlled by probiotics and that mortality of infected fish larvae can be reduced significantly by probiotic bacteria. However, the successful management of the aquaculture microbiota is currently hampered by our lack of knowledge of relevant microbial interactions and the overall ecology of these systems. © 2016 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.
Real-time monitoring of subsurface microbial metabolism with graphite electrodes

DOE PAGES

Wardman, Colin; Nevin, Kelly P.; Lovley, Derek R.

2014-11-21

Monitoring in situ microbial activity in anoxic submerged soils and aquatic sediments can be labor intensive and technically difficult, especially in dynamic environments in which a record of changes in microbial activity over time is desired. Microbial fuel cell concepts have previously been adapted to detect changes in the availability of relatively high concentrations of organic compounds in waste water but, in most soils and sediments, rates of microbial activity are not linked to the concentrations of labile substrates, but rather to the turnover rates of the substrate pools with steady state concentrations in the nM-μ M range. In ordermore » to determine whether levels of current produced at a graphite anode would correspond to the rates of microbial metabolism in anoxic sediments, small graphite anodes were inserted in sediment cores and connected to graphite brush cathodes in the overlying water. Currents produced were compared with the rates of [2- 14C]-acetate metabolism. There was a direct correlation between current production and the rate that [2- 14C]-acetate was metabolized to 14CO 2 and 14CH 4 in sediments in which Fe(III) reduction, sulfate reduction, or methane production was the predominant terminal electron-accepting process. At comparable acetate turnover rates, currents were higher in the sediments in which sulfate-reduction or Fe(III) reduction predominated than in methanogenic sediments. This was attributed to reduced products (Fe(II), sulfide) produced at distance from the anode contributing to current production in addition to the current that was produced from microbial oxidation of organic substrates with electron transfer to the anode surface in all three sediment types. In conclusion, the results demonstrate that inexpensive graphite electrodes may provide a simple strategy for real-time monitoring of microbial activity in a diversity of anoxic soils and sediments.« less
Microbial Monitoring from the Frontlines to Space: A Successful Validation of a Department of Defense (DoD) Funded Small Business Innovation Research (SBIR) Technology on Board the International Space Station (ISS)

NASA Technical Reports Server (NTRS)

Oubre, Cherie; Khodadad, Christina; Castro, Victoria; Ott, Mark; Pollack, Lawrence; Roman, Monsi

2017-01-01

The RAZOR EX (Registered Trademark) PCR unit was initially developed by the DoD as part of an SBIR project to detect and identify biothreats during field deployment. The system was evaluated by NASA as a commercial technology for future microbial monitoring requirements and has been successfully demonstrated in microgravity on-board the International Space Station.
Utilization of subsurface microbial electrochemical systems to elucidate the mechanisms of competition between methanogenesis and microbial iron(III)/humic acid reduction in Arctic peat soils

NASA Astrophysics Data System (ADS)

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

2012-12-01

High-latitude peat soils are a major carbon reservoir, and there is growing concern that previously dormant carbon from this reservoir could be released to the atmosphere as a result of continued climate change. Microbial processes, such as methanogenesis and carbon dioxide production via iron(III) or humic acid reduction, are at the heart of the carbon cycle in Arctic peat soils [1]. A deeper understanding of the factors governing microbial dominance in these soils is crucial for predicting the effects of continued climate change. In previous years, we have demonstrated the viability of a potentiostatically-controlled subsurface microbial electrochemical system-based biosensor that measures microbial respiration via exocellular electron transfer [2]. This system utilizes a graphite working electrode poised at 0.1 V NHE to mimic ferric iron and humic acid compounds. Microbes that would normally utilize these compounds as electron acceptors donate electrons to the electrode instead. The resulting current is a measure of microbial respiration with the electrode and is recorded with respect to time. Here, we examine the mechanistic relationship between methanogenesis and iron(III)- or humic acid-reduction by using these same microbial-three electrode systems to provide an inexhaustible source of alternate electron acceptor to microbes in these soils. Chamber-based carbon dioxide and methane fluxes were measured from soil collars with and without microbial three-electrode systems over a period of four weeks. In addition, in some collars we simulated increased fermentation by applying acetate treatments to understand possible effects of continued climate change on microbial processes in these carbon-rich soils. The results from this work aim to increase our fundamental understanding of competition between electron acceptors, and will provide valuable data for climate modeling scenarios. 1. Lipson, D.A., et al., Reduction of iron (III) and humic substances plays a major role in anaerobic respiration in an Arctic peat soil. Journal of Geophysical Research-Biogeosciences, 2010. 115. 2. Friedman, E.S., et al., A cost-effective and field-ready potentiostat that poises subsurface electrodes to monitor bacterial respiration. Biosensors and Bioelectronics, 2012. 32(1): p. 309-313.

Harnessing Insect-Microbe Chemical Communications To Control Insect Pests of Agricultural Systems.

PubMed

Beck, John J; Vannette, Rachel L

2017-01-11

Insect pests cause serious economic, yield, and food safety problems to managed crops worldwide. Compounding these problems, insect pests often vector pathogenic or toxigenic microbes to plants. Previous work has considered plant-insect and plant-microbe interactions separately. Although insects are well-understood to use plant volatiles to locate hosts, microorganisms can produce distinct and abundant volatile compounds that in some cases strongly attract insects. In this paper, we focus on the microbial contribution to plant volatile blends, highlighting the compounds emitted and the potential for variation in microbial emission. We suggest that these aspects of microbial volatile emission may make these compounds ideal for use in agricultural applications, as they may be more specific or enhance methods currently used in insect control or monitoring. Our survey of microbial volatiles in insect-plant interactions suggests that these emissions not only signal host suitability but may indicate a distinctive time frame for optimal conditions for both insect and microbe. Exploitation of these host-specific microbe semiochemicals may provide important microbe- and host-based attractants and a basis for future plant-insect-microbe chemical ecology investigations.
Hard surface biocontrol in hospitals using microbial-based cleaning products.

PubMed

Vandini, Alberta; Temmerman, Robin; Frabetti, Alessia; Caselli, Elisabetta; Antonioli, Paola; Balboni, Pier Giorgio; Platano, Daniela; Branchini, Alessio; Mazzacane, Sante

2014-01-01

Healthcare-Associated Infections (HAIs) are one of the most frequent complications occurring in healthcare facilities. Contaminated environmental surfaces provide an important potential source for transmission of many healthcare-associated pathogens, thus indicating the need for new and sustainable strategies. This study aims to evaluate the effect of a novel cleaning procedure based on the mechanism of biocontrol, on the presence and survival of several microorganisms responsible for HAIs (i.e. coliforms, Staphyloccus aureus, Clostridium difficile, and Candida albicans) on hard surfaces in a hospital setting. The effect of microbial cleaning, containing spores of food grade Bacillus subtilis, Bacillus pumilus and Bacillus megaterium, in comparison with conventional cleaning protocols, was evaluated for 24 weeks in three independent hospitals (one in Belgium and two in Italy) and approximately 20000 microbial surface samples were collected. Microbial cleaning, as part of the daily cleaning protocol, resulted in a reduction of HAI-related pathogens by 50 to 89%. This effect was achieved after 3-4 weeks and the reduction in the pathogen load was stable over time. Moreover, by using microbial or conventional cleaning alternatively, we found that this effect was directly related to the new procedure, as indicated by the raise in CFU/m2 when microbial cleaning was replaced by the conventional procedure. Although many questions remain regarding the actual mechanisms involved, this study demonstrates that microbial cleaning is a more effective and sustainable alternative to chemical cleaning and non-specific disinfection in healthcare facilities. This study indicates microbial cleaning as an effective strategy in continuously lowering the number of HAI-related microorganisms on surfaces. The first indications on the actual level of HAIs in the trial hospitals monitored on a continuous basis are very promising, and may pave the way for a novel and cost-effective strategy to counteract or (bio)control healthcare-associated pathogens.
Hard Surface Biocontrol in Hospitals Using Microbial-Based Cleaning Products

PubMed Central

Vandini, Alberta; Temmerman, Robin; Frabetti, Alessia; Caselli, Elisabetta; Antonioli, Paola; Balboni, Pier Giorgio; Platano, Daniela; Branchini, Alessio; Mazzacane, Sante

2014-01-01

Background Healthcare-Associated Infections (HAIs) are one of the most frequent complications occurring in healthcare facilities. Contaminated environmental surfaces provide an important potential source for transmission of many healthcare-associated pathogens, thus indicating the need for new and sustainable strategies. Aim This study aims to evaluate the effect of a novel cleaning procedure based on the mechanism of biocontrol, on the presence and survival of several microorganisms responsible for HAIs (i.e. coliforms, Staphyloccus aureus, Clostridium difficile, and Candida albicans) on hard surfaces in a hospital setting. Methods The effect of microbial cleaning, containing spores of food grade Bacillus subtilis, Bacillus pumilus and Bacillus megaterium, in comparison with conventional cleaning protocols, was evaluated for 24 weeks in three independent hospitals (one in Belgium and two in Italy) and approximately 20000 microbial surface samples were collected. Results Microbial cleaning, as part of the daily cleaning protocol, resulted in a reduction of HAI-related pathogens by 50 to 89%. This effect was achieved after 3–4 weeks and the reduction in the pathogen load was stable over time. Moreover, by using microbial or conventional cleaning alternatively, we found that this effect was directly related to the new procedure, as indicated by the raise in CFU/m2 when microbial cleaning was replaced by the conventional procedure. Although many questions remain regarding the actual mechanisms involved, this study demonstrates that microbial cleaning is a more effective and sustainable alternative to chemical cleaning and non-specific disinfection in healthcare facilities. Conclusions This study indicates microbial cleaning as an effective strategy in continuously lowering the number of HAI-related microorganisms on surfaces. The first indications on the actual level of HAIs in the trial hospitals monitored on a continuous basis are very promising, and may pave the way for a novel and cost-effective strategy to counteract or (bio)control healthcare-associated pathogens. PMID:25259528
Comparison of different incubation conditions for microbiological environmental monitoring.

PubMed

Gordon, Oliver; Berchtold, Manfred; Staerk, Alexandra; Roesti, David

2014-01-01

Environmental monitoring represents an integral part of the microbiological quality control system of a pharmaceutical manufacturing operation. However, guidance documents differ regarding recommendation of a procedure, particularly regarding incubation time, incubation temperature, or nutrient media. Because of these discrepancies, many manufacturers decide for a particular environmental monitoring sample incubation strategy and support this decision with validation data. Such validations are typically laboratory-based in vitro studies, meaning that these are based on comparing incubation conditions and nutrient media through use of cultured microorganisms. An informal survey of the results of these in vitro studies performed at Novartis or European manufacturing sites of different pharmaceutical companies highlighted that no consensus regarding the optimal incubation conditions for microbial recovery existed. To address this question differently, we collected a significant amount of samples directly from air, inanimate surfaces, and personnel in pharmaceutical production and packaging rooms during manufacturing operation (in situ study). Samples were incubated under different conditions suggested in regulatory guidelines, and recovery of total aerobic microorganisms as well as moulds was assessed. We found the highest recovery of total aerobic count from areas with personnel flow using a general microbiological growth medium incubated at 30-35 °C. The highest recovery of moulds was obtained with mycological medium incubated at 20-25 °C. Single-plate strategies (two-temperature incubation or an intermediate incubation temperature of 25-30 °C) also yielded reasonable recovery of total aerobic count and moulds. However, recovery of moulds was found to be highly inefficient at 30-35 °C compared to lower incubation temperatures. This deficiency could not be rectified by subsequent incubation at 20-25 °C. A laboratory-based in vitro study performed in parallel was inconclusive. We consider our results potentially conferrable to other pharmaceutical manufacturing sites in moderate climate zones and believe that these should represent a valuable reference for definition of the incubation strategy of microbiological environmental monitoring samples. Microbiological environmental monitoring confirms that pharmaceutical cleanrooms are in an appropriate hygienic condition for manufacturing of drug products. Guidance documents from different health authorities or expert groups differ regarding recommendation of the applied incubation time, incubation temperature, or nutrient media. Therefore, many pharmaceutical manufacturers perform studies that aim to identify the optimal incubation setup for environmental monitoring samples. An informal survey of the results of such studies, which had been performed at Novartis or European manufacturing sites of different pharmaceutical companies, highlighted no consensus regarding the optimal incubation conditions for microbial recovery. All these studies had been conducted in the laboratory using selections of cultured microbial strains. We tried to solve this disagreement by collecting a significant amount of real environmental monitoring samples directly from the environment in pharmaceutical production and packaging rooms during manufacturing operation. These samples were then incubated under different conditions suggested in the regulatory guidelines. We believe that the results of our study are more meaningful than laboratory-based experiments because we used environmental samples with microorganisms directly isolated from the manufacturing area. Therefore, we believe that our results should represent a valuable reference for definition of the incubation strategy of microbiological environmental monitoring samples. © PDA, Inc. 2014.
LOCAD-PTS: Operation of a New System for Microbial Monitoring Aboard the International Space Station (ISS)

NASA Technical Reports Server (NTRS)

Maule, J.; Wainwright, N.; Steele, A.; Gunter, D.; Flores, G.; Effinger, M.; Danibm N,; Wells, M.; Williams, S.; Morris, H.;

2008-01-01

Microorganisms within the space stations Salyut, Mir and the International Space Station (ISS), have traditionally been monitored with culture-based techniques. These techniques involve growing environmental samples (cabin water, air or surfaces) on agar-type media for several days, followed by visualization of resulting colonies; and return of samples to Earth for ground-based analysis. This approach has provided a wealth of useful data and enhanced our understanding of the microbial ecology within space stations. However, the approach is also limited by the following: i) More than 95% microorganisms in the environment cannot grow on conventional growth media; ii) Significant time lags occur between onboard sampling and colony visualization (3-5 days) and ground-based analysis (as long as several months); iii) Colonies are often difficult to visualize due to condensation within contact slide media plates; and iv) Techniques involve growth of potentially harmful microorganisms, which must then be disposed of safely. This report describes the operation of a new culture-independent technique onboard the ISS for rapid analysis (within minutes) of endotoxin and -1, 3-glucan, found in the cell walls of gram-negative bacteria and fungi, respectively. This technique involves analysis of environmental samples with the Limulus Amebocyte Lysate (LAL) assay in a handheld device. This handheld device and sampling system is known as the Lab-On-a-Chip Application Development Portable Test System (LOCAD-PTS). A poster will be presented that describes a comparative study between LOCAD-PTS analysis and existing culture-based methods onboard the ISS; together with an exploratory survey of surface endotoxin throughout the ISS. It is concluded that while a general correlation between LOCAD-PTS and traditional culture-based methods should not necessarily be expected, a combinatorial approach can be adopted where both sets of data are used together to generate a more complete story of the microbial ecology on the ISS.

SPECIES-SPECIFIC DETECTION OF HYDROCARBON UTILIZING BACTERIA. (R825810)

EPA Science Inventory

Rapid detection and quantitative assessment of specific microbial species in environmental samples is desirable for monitoring changes in ecosystems and for tracking natural or introduced microbial species during bioremediation of contaminated sites. In the interests of develo...
Indirect microbial detection

NASA Technical Reports Server (NTRS)

Wilkins, J. R. (Inventor)

1981-01-01

The growth of microorganisms in a sample is detected and monitored by culturing microorganisms in a growth medium and detecting a change in potential between two electrodes, separated from the microbial growth by a barrier which is permeable to charged paticles but microorganism impermeable.
Quantitative Monitoring of Microbial Species during Bioleaching of a Copper Concentrate.

PubMed

Hedrich, Sabrina; Guézennec, Anne-Gwenaëlle; Charron, Mickaël; Schippers, Axel; Joulian, Catherine

2016-01-01

Monitoring of the microbial community in bioleaching processes is essential in order to control process parameters and enhance the leaching efficiency. Suitable methods are, however, limited as they are usually not adapted to bioleaching samples and often no taxon-specific assays are available in the literature for these types of consortia. Therefore, our study focused on the development of novel quantitative real-time PCR (qPCR) assays for the quantification of Acidithiobacillus caldus, Leptospirillum ferriphilum, Sulfobacillus thermosulfidooxidans , and Sulfobacillus benefaciens and comparison of the results with data from other common molecular monitoring methods in order to evaluate their accuracy and specificity. Stirred tank bioreactors for the leaching of copper concentrate, housing a consortium of acidophilic, moderately thermophilic bacteria, relevant in several bioleaching operations, served as a model system. The microbial community analysis via qPCR allowed a precise monitoring of the evolution of total biomass as well as abundance of specific species. Data achieved by the standard fingerprinting methods, terminal restriction fragment length polymorphism (T-RFLP) and capillary electrophoresis single strand conformation polymorphism (CE-SSCP) on the same samples followed the same trend as qPCR data. The main added value of qPCR was, however, to provide quantitative data for each species whereas only relative abundance could be deduced from T-RFLP and CE-SSCP profiles. Additional value was obtained by applying two further quantitative methods which do not require nucleic acid extraction, total cell counting after SYBR Green staining and metal sulfide oxidation activity measurements via microcalorimetry. Overall, these complementary methods allow for an efficient quantitative microbial community monitoring in various bioleaching operations.
Quantitative Monitoring of Microbial Species during Bioleaching of a Copper Concentrate

PubMed Central

Hedrich, Sabrina; Guézennec, Anne-Gwenaëlle; Charron, Mickaël; Schippers, Axel; Joulian, Catherine

2016-01-01

Monitoring of the microbial community in bioleaching processes is essential in order to control process parameters and enhance the leaching efficiency. Suitable methods are, however, limited as they are usually not adapted to bioleaching samples and often no taxon-specific assays are available in the literature for these types of consortia. Therefore, our study focused on the development of novel quantitative real-time PCR (qPCR) assays for the quantification of Acidithiobacillus caldus, Leptospirillum ferriphilum, Sulfobacillus thermosulfidooxidans, and Sulfobacillus benefaciens and comparison of the results with data from other common molecular monitoring methods in order to evaluate their accuracy and specificity. Stirred tank bioreactors for the leaching of copper concentrate, housing a consortium of acidophilic, moderately thermophilic bacteria, relevant in several bioleaching operations, served as a model system. The microbial community analysis via qPCR allowed a precise monitoring of the evolution of total biomass as well as abundance of specific species. Data achieved by the standard fingerprinting methods, terminal restriction fragment length polymorphism (T-RFLP) and capillary electrophoresis single strand conformation polymorphism (CE-SSCP) on the same samples followed the same trend as qPCR data. The main added value of qPCR was, however, to provide quantitative data for each species whereas only relative abundance could be deduced from T-RFLP and CE-SSCP profiles. Additional value was obtained by applying two further quantitative methods which do not require nucleic acid extraction, total cell counting after SYBR Green staining and metal sulfide oxidation activity measurements via microcalorimetry. Overall, these complementary methods allow for an efficient quantitative microbial community monitoring in various bioleaching operations. PMID:28066365
Assessment of the impact of textile effluents on microbial diversity in Tirupur district, Tamil Nadu

NASA Astrophysics Data System (ADS)

Prabha, Shashi; Gogoi, Anindita; Mazumder, Payal; Ramanathan, AL.; Kumar, Manish

2017-09-01

The expedited advent of urbanization and industrialization for economic growth has adversely affected the biological diversity, which is one of the major concerns of the developing countries. Microbes play a crucial role in decontaminating polluted sites and degrades pollution load of textile effluent. The present study was based on identification of microbial diversity along the Noyaal river of Tirupur area. River water samples from industrial and non-industrial sites and effluent samples of before and after treatment were tested and it was found that microbial diversity was higher in the river water at the industrial site (Kasipalayam) as compared to the non-industrial site (Perur). Similarly, the microbial populations were found to be high in the untreated effluent as compared to the treated one by conventional treatment systems. Similar trends were observed for MBR treatment systems as well. Pseudomonas sp ., Achromobacter sp. (bacterial species) and Aspergillus fumigates (fungal species), found exclusively at the industrial site have been reported to possess decolorization potential of dye effluent, thus can be used for treatment of dye effluent. The comparison of different microbial communities from different dye wastewater sources and textile effluents was done, which showed that the microbes degrade dyestuffs, reduce toxicity of wastewaters, etc. From the study, it can be concluded that the microbial community helps to check on the pollutants and minimize their affect. Therefore, there is a need to understand the systematic variation in microbial diversity with the accumulation of pollution load through monitoring.
A microbiology-based multi-parametric approach towards assessing biological stability in drinking water distribution networks.

PubMed

Lautenschlager, Karin; Hwang, Chiachi; Liu, Wen-Tso; Boon, Nico; Köster, Oliver; Vrouwenvelder, Hans; Egli, Thomas; Hammes, Frederik

2013-06-01

Biological stability of drinking water implies that the concentration of bacterial cells and composition of the microbial community should not change during distribution. In this study, we used a multi-parametric approach that encompasses different aspects of microbial water quality including microbial growth potential, microbial abundance, and microbial community composition, to monitor biological stability in drinking water of the non-chlorinated distribution system of Zürich. Drinking water was collected directly after treatment from the reservoir and in the network at several locations with varied average hydraulic retention times (6-52 h) over a period of four months, with a single repetition two years later. Total cell concentrations (TCC) measured with flow cytometry remained remarkably stable at 9.5 (± 0.6) × 10(4) cells/ml from water in the reservoir throughout most of the distribution network, and during the whole time period. Conventional microbial methods like heterotrophic plate counts, the concentration of adenosine tri-phosphate, total organic carbon and assimilable organic carbon remained also constant. Samples taken two years apart showed more than 80% similarity for the microbial communities analysed with denaturing gradient gel electrophoresis and 454 pyrosequencing. Only the two sampling locations with the longest water retention times were the exceptions and, so far for unknown reasons, recorded a slight but significantly higher TCC (1.3 (± 0.1) × 10(5) cells/ml) compared to the other locations. This small change in microbial abundance detected by flow cytometry was also clearly observed in a shift in the microbial community profiles to a higher abundance of members from the Comamonadaceae (60% vs. 2% at other locations). Conventional microbial detection methods were not able to detect changes as observed with flow cytometric cell counts and microbial community analysis. Our findings demonstrate that the multi-parametric approach used provides a powerful and sensitive tool to assess and evaluate biological stability and microbial processes in drinking water distribution systems. Copyright © 2013 Elsevier Ltd. All rights reserved.
Microbial Contamination Detection in Water Resources: Interest of Current Optical Methods, Trends and Needs in the Context of Climate Change

PubMed Central

Jung, Aude-Valérie; Le Cann, Pierre; Roig, Benoit; Thomas, Olivier; Baurès, Estelle; Thomas, Marie-Florence

2014-01-01

Microbial pollution in aquatic environments is one of the crucial issues with regard to the sanitary state of water bodies used for drinking water supply, recreational activities and harvesting seafood due to a potential contamination by pathogenic bacteria, protozoa or viruses. To address this risk, microbial contamination monitoring is usually assessed by turbidity measurements performed at drinking water plants. Some recent studies have shown significant correlations of microbial contamination with the risk of endemic gastroenteresis. However the relevance of turbidimetry may be limited since the presence of colloids in water creates interferences with the nephelometric response. Thus there is a need for a more relevant, simple and fast indicator for microbial contamination detection in water, especially in the perspective of climate change with the increase of heavy rainfall events. This review focuses on the one hand on sources, fate and behavior of microorganisms in water and factors influencing pathogens’ presence, transportation and mobilization, and on the second hand, on the existing optical methods used for monitoring microbiological risks. Finally, this paper proposes new ways of research. PMID:24747537
Oligo-DNA Custom Macroarray for Monitoring Major Pathogenic and Non-Pathogenic Fungi and Bacteria in the Phyllosphere of Apple Trees

PubMed Central

He, Ying-Hong; Isono, Sayaka; Shibuya, Makoto; Tsuji, Masaharu; Adkar Purushothama, Charith-Raj; Tanaka, Kazuaki; Sano, Teruo

2012-01-01

Background To monitor the richness in microbial inhabitants in the phyllosphere of apple trees cultivated under various cultural and environmental conditions, we developed an oligo-DNA macroarray for major pathogenic and non-pathogenic fungi and bacteria inhabiting the phyllosphere of apple trees. Methods and Findings First, we isolated culturable fungi and bacteria from apple orchards by an agar-plate culture method, and detected 32 fungal and 34 bacterial species. Alternaria, Aureobasidium, Cladosporium, Rhodotorula, Cystofilobasidium, and Epicoccum genera were predominant among the fungi, and Bacillus, Pseudomonas, Sphingomonas, Methylobacterium, and Pantoea genera were predominant among the bacteria. Based on the data, we selected 29 major non-pathogenic and 12 phytopathogenic fungi and bacteria as the targets of macroarray. Forty-one species-specific 40-base pair long oligo-DNA sequences were selected from the nucleotide sequences of rDNA-internal transcribed spacer region for fungi and 16S rDNA for bacteria. The oligo-DNAs were fixed on nylon membrane and hybridized with digoxigenin-labeled cRNA probes prepared for each species. All arrays except those for Alternaria, Bacillus, and their related species, were specifically hybridized. The array was sensitive enough to detect 103 CFU for Aureobasidium pullulans and Bacillus cereus. Nucleotide sequencing of 100 each of independent fungal rDNA-ITS and bacterial 16S-rDNA sequences from apple tree was in agreement with the macroarray data obtained using the same sample. Finally, we analyzed the richness in the microbial inhabitants in the samples collected from apple trees in four orchards. Major apple pathogens that cause scab, Alternaria blotch, and Marssonina blotch were detected along with several non-phytopathogenic fungal and bacterial inhabitants. Conclusions The macroarray technique presented here is a strong tool to monitor the major microbial species and the community structures in the phyllosphere of apple trees and identify key species antagonistic, supportive or co-operative to specific pathogens in the orchard managed under different environmental conditions. PMID:22479577
Oligo-DNA custom macroarray for monitoring major pathogenic and non-pathogenic fungi and bacteria in the phyllosphere of apple trees.

PubMed

He, Ying-Hong; Isono, Sayaka; Shibuya, Makoto; Tsuji, Masaharu; Adkar Purushothama, Charith-Raj; Tanaka, Kazuaki; Sano, Teruo

2012-01-01

To monitor the richness in microbial inhabitants in the phyllosphere of apple trees cultivated under various cultural and environmental conditions, we developed an oligo-DNA macroarray for major pathogenic and non-pathogenic fungi and bacteria inhabiting the phyllosphere of apple trees. First, we isolated culturable fungi and bacteria from apple orchards by an agar-plate culture method, and detected 32 fungal and 34 bacterial species. Alternaria, Aureobasidium, Cladosporium, Rhodotorula, Cystofilobasidium, and Epicoccum genera were predominant among the fungi, and Bacillus, Pseudomonas, Sphingomonas, Methylobacterium, and Pantoea genera were predominant among the bacteria. Based on the data, we selected 29 major non-pathogenic and 12 phytopathogenic fungi and bacteria as the targets of macroarray. Forty-one species-specific 40-base pair long oligo-DNA sequences were selected from the nucleotide sequences of rDNA-internal transcribed spacer region for fungi and 16S rDNA for bacteria. The oligo-DNAs were fixed on nylon membrane and hybridized with digoxigenin-labeled cRNA probes prepared for each species. All arrays except those for Alternaria, Bacillus, and their related species, were specifically hybridized. The array was sensitive enough to detect 10(3) CFU for Aureobasidium pullulans and Bacillus cereus. Nucleotide sequencing of 100 each of independent fungal rDNA-ITS and bacterial 16S-rDNA sequences from apple tree was in agreement with the macroarray data obtained using the same sample. Finally, we analyzed the richness in the microbial inhabitants in the samples collected from apple trees in four orchards. Major apple pathogens that cause scab, Alternaria blotch, and Marssonina blotch were detected along with several non-phytopathogenic fungal and bacterial inhabitants. The macroarray technique presented here is a strong tool to monitor the major microbial species and the community structures in the phyllosphere of apple trees and identify key species antagonistic, supportive or co-operative to specific pathogens in the orchard managed under different environmental conditions.
Changes in microbial communities associated with the sea anemone Anemonia viridis in a natural pH gradient.

PubMed

Meron, Dalit; Buia, Maria-Cristina; Fine, Maoz; Banin, Ehud

2013-02-01

Ocean acidification, resulting from rising atmospheric carbon dioxide concentrations, is a pervasive stressor that can affect many marine organisms and their symbionts. Studies which examine the host physiology and microbial communities have shown a variety of responses to the ocean acidification process. Recently, several studies were conducted based on field experiments, which take place in natural CO(2) vents, exposing the host to natural environmental conditions of varying pH. This study examines the sea anemone Anemonia viridis which is found naturally along the pH gradient in Ischia, Italy, with an aim to characterize whether exposure to pH impacts the holobiont. The physiological parameters of A. viridis (Symbiodinium density, protein, and chlorophyll a+c concentration) and its microbial community were monitored. Although reduction in pH was seen to have had an impact on composition and diversity of associated microbial communities, no significant changes were observed in A. viridis physiology, and no microbial stress indicators (i.e., pathogens, antibacterial activity, etc.) were detected. In light of these results, it appears that elevated CO(2) does not have a negative influence on A. viridis that live naturally in the site. This suggests that natural long-term exposure and dynamic diverse microbial communities may contribute to the acclimation process of the host in a changing pH environment.
Subsurface Environment Sampler for Improved In Situ Characterization of Subsurface Microbial Communities

NASA Astrophysics Data System (ADS)

Barnhart, E. P.; Ruppert, L. F.; Orem, W. H.; McIntosh, J. C.; Cunningham, A. B.; Fields, M. W.; Hiebert, R.; Hyatt, R.

2016-12-01

There is an increasing threat that deep aquifers, an important drinking water resource, may be contaminated by the extraction and transport of fossil fuels. This threat increases the need for improved groundwater monitoring and the ability to predict the extent to which microbial activity may remediate such contamination. The characterization of subsurface microbial communities could provide an ideal biomonitoring tool for the assessment of subsurface contamination due to prokaryotes environmental ubiquity, rapidity of response to environmental perturbation and the important role they play in hydrocarbon degradation and bioremediation. New DNA sequencing technologies provide the opportunity to cost-effectively identify the vast subsurface microbial ecosystem, but use of this new technology is restricted due to issues with sampling. Prior subsurface microbiology studies have relied on core samples that are expensive to obtain hard to collect aseptically and/or ground water samples that do not reflect in situ microbial densities or activities. The development of down-well incubation of sterile sediment with a Diffusive Microbial Sampler (DMS) has emerged as an alternative method to sample subsurface microbial communities that minimizes cost and contamination issues associated with traditional methods. We have designed a Subsurface Environment Sampler with a DMS module that could enable the anaerobic transport of the in situ microbial community from the field for laboratory bioremediation studies. This sampler could provide an inexpensive and standard method for subsurface microbial sampling which would make this tool useful for Federal, State, private and local agencies interested in monitoring contamination or the effectiveness of bioremediation activities in subsurface aquifers.
A Universally Applicable and Rapid Method for Measuring the Growth of Streptomyces and Other Filamentous Microorganisms by Methylene Blue Adsorption-Desorption

PubMed Central

Fischer, Marco

2013-01-01

Quantitative assessment of growth of filamentous microorganisms, such as streptomycetes, is generally restricted to determination of dry weight. Here, we describe a straightforward methylene blue-based sorption assay to monitor microbial growth quantitatively, simply, and rapidly. The assay is equally applicable to unicellular and filamentous bacterial and eukaryotic microorganisms. PMID:23666340
Opening the black box of spring water microbiology from alpine karst aquifers to support proactive drinking water resource management.

PubMed

Savio, Domenico; Stadler, Philipp; Reischer, Georg H; Kirschner, Alexander K T; Demeter, Katalin; Linke, Rita; Blaschke, Alfred P; Sommer, Regina; Szewzyk, Ulrich; Wilhartitz, Inés C; Mach, Robert L; Stadler, Hermann; Farnleitner, Andreas H

2018-01-01

Over the past 15 years, pioneering interdisciplinary research has been performed on the microbiology of hydrogeologically well-defined alpine karst springs located in the Northern Calcareous Alps (NCA) of Austria. This article gives an overview on these activities and links them to other relevant research. Results from the NCA springs and comparable sites revealed that spring water harbors abundant natural microbial communities even in aquifers with high water residence times and the absence of immediate surface influence. Apparently, hydrogeology has a strong impact on the concentration and size of the observed microbes, and total cell counts (TCC) were suggested as a useful means for spring type classification. Measurement of microbial activities at the NCA springs revealed extremely low microbial growth rates in the base flow component of the studied spring waters and indicated the importance of biofilm-associated microbial activities in sediments and on rock surfaces. Based on genetic analysis, the autochthonous microbial endokarst community (AMEC) versus transient microbial endokarst community (TMEC) concept was proposed for the NCA springs, and further details within this overview article are given to prompt its future evaluation. In this regard, it is well known that during high-discharge situations, surface-associated microbes and nutrients such as from soil habitats or human settlements-potentially containing fecal-associated pathogens as the most critical water-quality hazard-may be rapidly flushed into vulnerable karst aquifers. In this context, a framework for the comprehensive analysis of microbial pollution has been proposed for the NCA springs to support the sustainable management of drinking water safety in accordance with recent World Health Organization guidelines. Near-real-time online water quality monitoring, microbial source tracking (MST) and MST-guided quantitative microbial-risk assessment (QMRA) are examples of the proposed analytical tools. In this context, this overview article also provides a short introduction to recently emerging methodologies in microbiological diagnostics to support reading for the practitioner. Finally, the article highlights future research and development needs. This article is categorized under: 1Engineering Water > Water, Health, and Sanitation2Science of Water > Water Extremes3Water and Life > Nature of Freshwater Ecosystems.
Spatial & Temporal Geophysical Monitoring of Microbial Growth and Biofilm Formation

EPA Science Inventory

Previous studies have examined the effect of biogenic gases and biomineralization on the acoustic properties of porous media. In this study, we investigated the spatiotemporal effect of microbial growth and biofilm formation on compressional waves and complex conductivity in sand...
THE NEAR-EQUILIBRIUM OF MICROBIALLY MEDIATED REDOX COUPLES IN REDUCING GROUNDWATER ENVIRONMENTS

EPA Science Inventory

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

Design and analysis of surface plasmon resonance (SPR) sensor to check the quality of food from adulteration

NASA Astrophysics Data System (ADS)

Kumar, Manish; Raghuwanshi, Sanjeev Kumar

2018-02-01

In recent years, food safety issues caused by contamination of chemical substances or microbial species have raised a major area of concern to mankind. The conventional chromatography-based methods for detection of chemical are based on human-observation and slow for real-time monitoring. The surface plasmon resonance (SPR) sensors offers the capability of detection of very low concentrations of adulterated chemical and biological agents for real-time by monitoring. Thus, adulterant agent in food gives change in refractive index of pure food result in corresponding phase change. These changes can be detected at the output and can be related to the concentration of the chemical species present at the point.
16S rRNA beacons for bacterial monitoring during human space missions.

PubMed

Larios-Sanz, Maia; Kourentzi, Katerina D; Warmflash, David; Jones, Jeffrey; Pierson, Duane L; Willson, Richard C; Fox, George E

2007-04-01

Microorganisms are unavoidable in space environments and their presence has, at times, been a source of problems. Concerns about disease during human space missions are particularly important considering the significant changes the immune system incurs during spaceflight and the history of microbial contamination aboard the Mir space station. Additionally, these contaminants may have adverse effects on instrumentation and life-support systems. A sensitive, highly specific system to detect, characterize, and monitor these microbial populations is essential. Herein we describe a monitoring approach that uses 16S rRNA targeted molecular beacons to successfully detect several specific bacterial groupings. This methodology will greatly simplify in-flight monitoring by minimizing sample handling and processing. We also address and provide solutions to target accessibility problems encountered in hybridizations that target 16S rRNA.
Microbial competition between Bacillus subtilis and Staphylococcus aureus monitored by imaging mass spectrometry

PubMed Central

Gonzalez, David J.; Haste, Nina M.; Hollands, Andrew; Fleming, Tinya C.; Hamby, Matthew; Pogliano, Kit; Nizet, Victor

2011-01-01

Microbial competition exists in the general environment, such as soil or aquatic habitats, upon or within unicellular or multicellular eukaryotic life forms. The molecular actions that govern microbial competition, leading to niche establishment and microbial monopolization, remain undetermined. The emerging technology of imaging mass spectrometry (IMS) enabled the observation that there is directionality in the metabolic output of the organism Bacillus subtilis when co-cultured with Staphylococcus aureus. The directionally released antibiotic alters S. aureus virulence factor production and colonization. Therefore, IMS provides insight into the largely hidden nature of competitive microbial encounters and niche establishment, and provides a paradigm for future antibiotic discovery. PMID:21719540
Isotopic insights into microbial sulfur cycling in oil reservoirs

PubMed Central

Hubbard, Christopher G.; Cheng, Yiwei; Engelbrekston, Anna; Druhan, Jennifer L.; Li, Li; Ajo-Franklin, Jonathan B.; Coates, John D.; Conrad, Mark E.

2014-01-01

Microbial sulfate reduction in oil reservoirs (biosouring) is often associated with secondary oil production where seawater containing high sulfate concentrations (~28 mM) is injected into a reservoir to maintain pressure and displace oil. The sulfide generated from biosouring can cause corrosion of infrastructure, health exposure risks, and higher production costs. Isotope monitoring is a promising approach for understanding microbial sulfur cycling in reservoirs, enabling early detection of biosouring, and understanding the impact of souring. Microbial sulfate reduction is known to result in large shifts in the sulfur and oxygen isotope compositions of the residual sulfate, which can be distinguished from other processes that may be occurring in oil reservoirs, such as precipitation of sulfate and sulfide minerals. Key to the success of this method is using the appropriate isotopic fractionation factors for the conditions and processes being monitored. For a set of batch incubation experiments using a mixed microbial culture with crude oil as the electron donor, we measured a sulfur fractionation factor for sulfate reduction of −30‰. We have incorporated this result into a simplified 1D reservoir reactive transport model to highlight how isotopes can help discriminate between biotic and abiotic processes affecting sulfate and sulfide concentrations. Modeling results suggest that monitoring sulfate isotopes can provide an early indication of souring for reservoirs with reactive iron minerals that can remove the produced sulfide, especially when sulfate reduction occurs in the mixing zone between formation waters (FW) containing elevated concentrations of volatile fatty acids (VFAs) and injection water (IW) containing elevated sulfate. In addition, we examine the role of reservoir thermal, geochemical, hydrological, operational and microbiological conditions in determining microbial souring dynamics and hence the anticipated isotopic signatures. PMID:25285094
Inflight Microbial Monitoring- An Alternative Method to Culture Based Detection Currently Used on the International Space Station

NASA Technical Reports Server (NTRS)

Khodadad, Christina L.; Birmele, Michele N.; Roman, Monsi; Hummerick, Mary E.; Smith, David J.; Wheeler, Raymond M.

2015-01-01

Previous research has shown that potentially destructive microorganisms and human pathogens have been detected on the International Space Station (ISS). The likelihood of introducing new microorganisms occurs with every exchange of crew or addition of equipment or supplies. Microorganisms introduced to the ISS are readily transferred between crew and subsystems (i.e. ECLSS, environmental control and life support systems). Current microbial characterization methods require enrichment of microorganisms and at least a 48-hour incubation time. This increases the microbial load while detecting only a limited number of the total microorganisms. The culture based method detects approximately 1-10% of the total organisms present and provides no identification. To identify and enumerate ISS microbes requires that samples be returned to Earth for complete analysis. Therefore, a more expedient, low-cost, in-flight method of microbial detection, identification, and enumeration is warranted. The RAZOR EX, a ruggedized, commercial off the shelf, real-time PCR field instrument was tested for its ability to detect microorganisms at low concentrations within one hour. Escherichia coli, Salmonella enterica Typhimurium, and Pseudomonas aeruginosa were detected at low levels using real-time DNA amplification. Total heterotrophic counts could also be detected using a 16S gene marker that can identify up to 98% of all bacteria. To reflect viable cells found in the samples, RNA was also detectable using a modified, single-step reverse transcription reaction.
Inflight Microbial Monitoring-An Alternative Method to Culture Based Detection Currently Used on International Space Station

NASA Technical Reports Server (NTRS)

Khodadad, Christina L.; Birmele, Michele N.; Roman, Monsi; Hummerick, Mary E.; Smith, David J.; Wheeler, Raymond M.

2015-01-01

Previous research has shown that microorganisms and potential human pathogens have been detected on the International Space Station (ISS). The potential to introduce new microorganisms occurs with every exchange of crew or addition of equipment or supplies. Previous research has shown that microorganisms introduced to the ISS are readily transferred between crew and subsystems and back (i.e. ECLSS, environmental control and life support systems). Current microbial characterization methods require enrichment of microorganisms and a 48-hour incubation time. This increases the microbial load while detecting a limited number of microorganisms. The culture based method detects approximately 1-10% of the total organisms present and provides no identification, To identify and enumerate ISS samples requires that samples to be returned to Earth for complete analysis. Therefore, a more expedient, low-cost, in-flight method of microbial detection, identification, and enumeration is warranted. The RAZOR EX, a ruggedized, commercial off the shelf, real-time PCR field instrument was tested for its ability to detect microorganism at low concentrations within one hour. Escherichia coli, Salmonella enterica Typhimurium, and Pseudomonas aeruginosa were detected at low levels using real-time DNA amplification. Total heterotrophic counts could also be detected using a 16S gene marker that can identify up to 98% of all bacteria. To reflect viable cells found in the samples, RNA was also detectable using a modified, single-step reverse transcription reaction.
Evolution of microbiological analytical methods for dairy industry needs

PubMed Central

Sohier, Danièle; Pavan, Sonia; Riou, Armelle; Combrisson, Jérôme; Postollec, Florence

2014-01-01

Traditionally, culture-based methods have been used to enumerate microbial populations in dairy products. Recent developments in molecular methods now enable faster and more sensitive analyses than classical microbiology procedures. These molecular tools allow a detailed characterization of cell physiological states and bacterial fitness and thus, offer new perspectives to integration of microbial physiology monitoring to improve industrial processes. This review summarizes the methods described to enumerate and characterize physiological states of technological microbiota in dairy products, and discusses the current deficiencies in relation to the industry’s needs. Recent studies show that Polymerase chain reaction-based methods can successfully be applied to quantify fermenting microbes and probiotics in dairy products. Flow cytometry and omics technologies also show interesting analytical potentialities. However, they still suffer from a lack of validation and standardization for quality control analyses, as reflected by the absence of performance studies and official international standards. PMID:24570675
Evolution of microbiological analytical methods for dairy industry needs.

PubMed

Sohier, Danièle; Pavan, Sonia; Riou, Armelle; Combrisson, Jérôme; Postollec, Florence

2014-01-01

Traditionally, culture-based methods have been used to enumerate microbial populations in dairy products. Recent developments in molecular methods now enable faster and more sensitive analyses than classical microbiology procedures. These molecular tools allow a detailed characterization of cell physiological states and bacterial fitness and thus, offer new perspectives to integration of microbial physiology monitoring to improve industrial processes. This review summarizes the methods described to enumerate and characterize physiological states of technological microbiota in dairy products, and discusses the current deficiencies in relation to the industry's needs. Recent studies show that Polymerase chain reaction-based methods can successfully be applied to quantify fermenting microbes and probiotics in dairy products. Flow cytometry and omics technologies also show interesting analytical potentialities. However, they still suffer from a lack of validation and standardization for quality control analyses, as reflected by the absence of performance studies and official international standards.
Elucidation of taste- and odor-producing bacteria and toxigenic cyanobacteria in a Midwestern drinking water supply reservoir by shotgun metagenomics analysis

USGS Publications Warehouse

Otten, Timothy; Graham, Jennifer L.; Harris, Theodore D.; Dreher, Theo

2016-01-01

While commonplace in clinical settings, DNA-based assays for identification or enumeration of drinking water pathogens and other biological contaminants remain widely unadopted by the monitoring community. In this study, shotgun metagenomics was used to identify taste-and-odor producers and toxin-producing cyanobacteria over a 2-year period in a drinking water reservoir. The sequencing data implicated several cyanobacteria, including Anabaena spp.,Microcystis spp., and an unresolved member of the order Oscillatoriales as the likely principal producers of geosmin, microcystin, and 2-methylisoborneol (MIB), respectively. To further demonstrate this, quantitative PCR (qPCR) assays targeting geosmin-producing Anabaena and microcystin-producing Microcystis were utilized, and these data were fitted using generalized linear models and compared with routine monitoring data, including microscopic cell counts, sonde-based physicochemical analyses, and assays of all inorganic and organic nitrogen and phosphorus forms and fractions. The qPCR assays explained the greatest variation in observed geosmin (adjusted R2 = 0.71) and microcystin (adjusted R2 = 0.84) concentrations over the study period, highlighting their potential for routine monitoring applications. The origin of the monoterpene cyclase required for MIB biosynthesis was putatively linked to a periphytic cyanobacterial mat attached to the concrete drinking water inflow structure. We conclude that shotgun metagenomics can be used to identify microbial agents involved in water quality deterioration and to guide PCR assay selection or design for routine monitoring purposes. Finally, we offer estimates of microbial diversity and metagenomic coverage of our data sets for reference to others wishing to apply shotgun metagenomics to other lacustrine systems.
Evaluation of an Environmental Monitoring Program for the Microbial Safety of Air and Surfaces in a Dairy Plant Environment.

PubMed

Zacharski, Krzysztof A; Southern, Mark; Ryan, Alan; Adley, Catherine C

2018-07-01

Microbiological hazards can occur when foodstuffs come into contact with contaminated surfaces or infectious agents dispersed by air currents in the manufacturing environment. An environmental monitoring program (EMP) is a critical aspect of sustainable and safe food manufacturing used to evaluate the effectiveness of the microbial controls in place. An effective EMP should be based on risk analysis, taking into account previous sampling history to determine the selection of the sampling points, the scope of the test, and the frequency of analysis. This study involved evaluation of the environmental monitoring regime and microbiological status of a medium-sized dairy plant manufacturing food ingredients, e.g., proteins, milk powders, and dairy fats. The data specific to microbial tests ( n = 3,468), recorded across 124 fixed sampling locations over a 2-year period (2014 to 2015) from air ( n = 1,787) and surfaces ( n = 1,681) were analyzed. The aim of this study was to highlight the strengths and weaknesses of the EMP in a select dairy processing plant. The results of this study outline the selection of sampling locations, the scope of the test, and the frequency of analysis. An analysis of variance revealed subsections of the manufacturing areas with high risk factors, especially the packaging subsection specified for bulk packaging, the atomizer, and the fluidized bed. The temporal and spatial analysis showed the potential to reduce or relocate the monitoring effort, most notably related to total coliforms and Staphylococcus aureus, across the dairy plant due to homogeneity across the sampling subsections with little or no deviations. The results suggest a need to reevaluate the current EMP and the corrective action plan, especially with regard to detection of pathogens. Recommendations for optimization of the EMP are presented to assist the dairy industry with reviewing and revising the control measures and hazard assessment with regard to existing contamination issues.
Microbiological Monitoring in Geothermal Plants

NASA Astrophysics Data System (ADS)

Alawi, M.; Lerm, S.; Linder, R.; Vetter, A.; Vieth-Hillebrand, A.; Miethling-Graff, R.; Seibt, A.; Wolfgramm, M.; Wuerdemann, H.

2010-12-01

In the scope of the research projects “AquiScreen” and “MiProTherm” we investigated geothermally used groundwater systems under microbial, geochemical, mineralogical and petrological aspects. On one side an enhanced process understanding of engineered geothermal systems is mandatory to optimize plant reliability and economy, on the other side this study provides insights into the microbiology of terrestrial thermal systems. Geothermal systems located in the North German Basin and the Molasse Basin were analyzed by sampling of fluids and solid phases. The investigated sites were characterized by different temperatures, salinities and potential microbial substrates. The microbial population was monitored by the use of genetic fingerprinting techniques and PCR-cloning based on PCR-amplified 16S rRNA and dissimilatory sulfite reductase (DSR) genes. DNA-sequences of fingerprints and cloned PCR-products were compared to public databases and correlated with metabolic classes to provide information about the biogeochemical processes. In all investigated geothermal plants, covering a temperature range from 5° to 120°C, microorganisms were found. Phylogenetic gene analyses indicate a broad diversity of microorganisms adapted to the specific conditions in the engineered system. Beside characterized bacteria like Thermus scotoductus, Siderooxidans lithoautotrophicus and the archaeon Methanothermobacter thermoautotrophicus a high number of so far uncultivated microorganisms was detected. As it is known that - in addition to abiotic factors - microbes like sulfate-reducing bacteria (SRB) are involved in the processes of corrosion and scaling in plant components, we identified SRB by specific analyses of DSR genes. The SRB detected are closely related to thermotolerant and thermophilic species of Desulfotomaculum, Thermodesulfovibrio, Desulfohalobium and Thermodesulfobacterium, respectively. Overall, the detection of microbes known to be involved in biocorrosion and the examined precipitation products like iron sulfides are indicating that microorganisms play an important role for the understanding of processes in engineered geothermal systems. The further identification of crucial process parameters influencing microbial activities will help to develop appropriate counter measures against microbial induced clogging and corrosion.
Hyporheic Microbial Biofilms as Indicators of Heavy and Rare Earth Metals in the Clark Fork Basin, Montana

NASA Astrophysics Data System (ADS)

Barnhart, E. P.; Hornberger, M.; Hwang, C.; Dror, I.; Bouskill, N.; Short, T.; Cain, D.; Fields, M. W.

2016-12-01

The ability to effectively monitor the impact of hard rock mining activities on rivers and streams is a growing concern given the large number of active and abandoned mines in the western United States. One such example, the Clark Fork Basin (CFB), western Montana, was extensively mined for copper in the early 20th century: it is now one of largest U.S. EPA superfund sites. Microbial biofilms are at the base of the lotic food chain and may provide a useful biomonitoring tool for the assessment of metal toxicity due to their environmental ubiquity, rapidity of response to environmental perturbation, and importance in determining metal mobility. Hyporheic microbial biofilms from the CFB were sampled in 2014, concurrent with the USGS National Research Programs (NRP) long-term site monitoring of metals in bed sediment and aquatic benthic insects. Integration of the DNA sequencing results from the hyporheic biofilms with the sediment and insect metal concentrations correlated several bacterial phyla with metal contamination. For example, the genus Lysobacter was strongly associated with copper (Cu) bioaccumulation in the aquatic insect Hydropsyche. These results support previous studies identifying Lysobacter as a bacterial genus that is resistant to Cu ions. Our analysis is the first to indicate that specific microorganisms can act as biomarkers of Cu contamination in rivers. Moreover, our work demonstrates that changes at the microbial community level in the hyporheic zone can be coupled to observed perturbations across higher trophic levels. In 2015, extensive remediation occurred at several of the sites sampled in 2014, providing an excellent opportunity to revisit the sites and examine the temporal variability of identified biomarkers and the short-term effectiveness of remediation. In addition, samples were analyzed for rare earth metals, of which little is known, and could provide additional insight into other metals that change the microbial community structure.
Rapid Electrochemical Detection and Identification of Microbiological and Chemical Contaminants for Manned Spaceflight Project

NASA Technical Reports Server (NTRS)

Pierson, Duane; Botkin, Douglas; Gazda, Daniel

2014-01-01

Microbial control in the spacecraft environment is a daunting task, especially in the presence of human crew members. Currently, assessing the potential crew health risk associated with a microbial contamination event requires return of representative environmental samples that are analyzed in a ground-based laboratory. It is therefore not currently possible to quickly identify microbes during spaceflight. This project addresses the unmet need for spaceflight-compatible microbial identification technology. The electrochemical detection and identification platform is expected to provide a sensitive, specific, and rapid sample-to-answer capability for in-flight microbial monitoring that can distinguish between related microorganisms (pathogens and non-pathogens) as well as chemical contaminants. This will dramatically enhance our ability to monitor the spacecraft environment and the health risk to the crew. Further, the project is expected to eliminate the need for sample return while significantly reducing crew time required for detection of multiple targets. Initial work will focus on the optimization of bacterial detection and identification. The platform is designed to release nucleic acids (DNA and RNA) from microorganisms without the use of harmful chemicals. Bacterial DNA or RNA is captured by bacteria-specific probe molecules that are bound to a microelectrode, and that capture event can generate a small change in the electrical current (Lam, et al. 2012. Anal. Chem. 84(1): 21-5.). This current is measured, and a determination is made whether a given microbe is present in the sample analyzed. Chemical detection can be accomplished by directly applying a sample to the microelectrode and measuring the resulting current change. This rapid microbial and chemical detection device is designed to be a low-cost, low-power platform anticipated to be operated independently of an external power source, characteristics optimal for manned spaceflight and areas where power and computing resources are scarce.
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.
Predictive Modeling for the Growth of Salmonella Enteritidis in Chicken Juice by Real-Time Polymerase Chain Reaction.

PubMed

Noviyanti, Fia; Hosotani, Yukie; Koseki, Shigenobu; Inatsu, Yasuhiro; Kawasaki, Susumu

2018-04-02

The goals of this study were to monitor the growth kinetics of Salmonella Enteritidis in chicken juice using real-time polymerase chain reaction (PCR) and to evaluate its efficacy by comparing the results with an experimental database. Salmonella Enteritidis was inoculated in chicken juice samples at an initial inoculum of 10 4 CFU/mL with inoculated samples incubated at six different temperatures (10, 15, 20, 25, 30, and 35°C). Sampling was carried out for 36 h to observe the growth of Salmonella Enteritidis. The total DNA was extracted from the samples, and the copy number of the Salmonella invasion gene (invA) was quantified by real-time PCR and converted to Salmonella Enteritidis cell concentration. Growth kinetics data were analyzed by the Baranyi and Roberts model to obtain growth parameters, whereas the Ratkowsky's square-root model was used to describe the effect of the interactions between growth parameters and temperature on the growth of Salmonella Enteritidis. The growth parameters of Salmonella Enteritidis obtained from an experiment conducted at a constant temperature were validated with growth data from chicken juice samples that were incubated under fluctuating temperature conditions between 5°C and 30°C for 30-min periods. A high correlation was observed between maximum growth rate (μ max ) and storage temperature, indicating that the real-time PCR-monitoring method provides a precise estimation of Salmonella Enteritidis growth in food material with a microbial flora. Moreover, the μ max data reflected data from microbial responses viewer database and ComBase. The results of this study suggested that real-time PCR monitoring provides a precise estimation of Salmonella Enteritidis growth in food materials with a background microbial flora.
Microbiology on Space Station Freedom

NASA Technical Reports Server (NTRS)

Pierson, Duane L. (Editor); Mcginnis, Michael R. (Editor); Mishra, S. K. (Editor); Wogan, Christine F. (Editor)

1991-01-01

This panel discussion convened in Houston, Texas, at the Lunar and Planetary Institute, on November 6 to 8, 1989, to review NASA's plans for microbiology on Space Station Freedom. A panel of distinguished scientists reviewed, validated, and recommended revisions to NASA's proposed acceptability standards for air, water, and internal surfaces on board Freedom. Also reviewed were the proposed microbiology capabilities and monitoring plan, disinfection procedures, waste management, and clinical issues. In the opinion of this advisory panel, ensuring the health of the Freedom's crews requires a strong goal-oriented research effort to determine the potential effects of microorganisms on the crewmembers and on the physical environment of the station. Because there are very few data addressing the fundamental question of how microgravity influences microbial function, the panel recommended establishing a ground-based microbial model of Freedom, with subsequent evaluation using in-flight shuttle data. Sampling techniques and standards will be affected by both technological advances in microgravity-compatible instrumentation, and by changes in the microbial population over the life of the station.
Impact of Roadway Stormwater Runoff on Microbial Contamination in the Receiving Stream.

PubMed

Wyckoff, Kristen N; Chen, Si; Steinman, Andrew J; He, Qiang

2017-09-01

Stormwater runoff from roadways has increasingly become a regulatory concern for water pollution control. Recent work has suggested roadway stormwater runoff as a potential source of microbial pollutants. The objective of this study was to determine the impact of roadway runoff on the microbiological quality of receiving streams. Microbiological quality of roadway stormwater runoff and the receiving stream was monitored during storm events with both cultivation-dependent fecal bacteria enumeration and cultivation-independent high-throughput sequencing techniques. Enumeration of total coliforms as a measure of fecal microbial pollution found consistently lower total coliform counts in roadway runoff than those in the stream water, suggesting that roadway runoff was not a major contributor of microbial pollutants to the receiving stream. Further characterization of the microbial community in the stormwater samples by 16S ribosomal RNA gene-based high-throughput amplicon sequencing revealed significant differences in the microbial composition of stormwater runoff from the roadways and the receiving stream. The differences in microbial composition between the roadway runoff and stream water demonstrate that roadway runoff did not appear to have a major influence on the stream in terms of microbiological quality. Thus, results from both fecal bacteria enumeration and high-throughput amplicon sequencing techniques were consistent that roadway stormwater runoff was not the primary contributor of microbial loading to the stream. Further studies of additional watersheds with distinct characteristics are needed to validate these findings. Understanding gained in this study could support the development of more effective strategies for stormwater management in sensitive watersheds. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.
Modeling the interannual variability of microbial quality metrics of irrigation water in a Pennsylvania stream.

PubMed

Hong, Eun-Mi; Shelton, Daniel; Pachepsky, Yakov A; Nam, Won-Ho; Coppock, Cary; Muirhead, Richard

2017-02-01

Knowledge of the microbial quality of irrigation waters is extremely limited. For this reason, the US FDA has promulgated the Produce Rule, mandating the testing of irrigation water sources for many farms. The rule requires the collection and analysis of at least 20 water samples over two to four years to adequately evaluate the quality of water intended for produce irrigation. The objective of this work was to evaluate the effect of interannual weather variability on surface water microbial quality. We used the Soil and Water Assessment Tool model to simulate E. coli concentrations in the Little Cove Creek; this is a perennial creek located in an agricultural watershed in south-eastern Pennsylvania. The model performance was evaluated using the US FDA regulatory microbial water quality metrics of geometric mean (GM) and the statistical threshold value (STV). Using the 90-year time series of weather observations, we simulated and randomly sampled the time series of E. coli concentrations. We found that weather conditions of a specific year may strongly affect the evaluation of microbial quality and that the long-term assessment of microbial water quality may be quite different from the evaluation based on short-term observations. The variations in microbial concentrations and water quality metrics were affected by location, wetness of the hydrological years, and seasonality, with 15.7-70.1% of samples exceeding the regulatory threshold. The results of this work demonstrate the value of using modeling to design and evaluate monitoring protocols to assess the microbial quality of water used for produce irrigation. Copyright © 2016 Elsevier Ltd. All rights reserved.
Recovery of microbial community structure and functioning after wildfire in semi-arid environments: optimising methods for monitoring and assessment

NASA Astrophysics Data System (ADS)

Muñoz-Rojas, Miriam; Martini, Dylan; Erickson, Todd; Merritt, David; Dixon, Kingsley

2015-04-01

Introduction In semi-arid areas such as northern Western Australia, wildfires are a natural part of the environment and many ecosystems in these landscapes have evolved and developed a strong relationship with fire. Soil microbial communities play a crucial role in ecosystem processes by regulating the cycling of nutrients via decomposition, mineralization, and immobilization processes. Thus, the structure (e.g. soil microbial biomass) and functioning (e.g. soil microbial activity) of microbial communities, as well as their changes after ecosystem disturbance, can be useful indicators of soil quality and health recovery. In this research, we assess the impacts of fire on soil microbial communities and their recovery in a biodiverse semi-arid environment of Western Australia (Pilbara region). New methods for determining soil microbial respiration as an indicator of microbial activity and soil health are also tested. Methodology Soil samples were collected from 10 similar ecosystems in the Pilbara with analogous native vegetation, but differing levels of post-fire disturbance (i.e. 3 months, 1 year, 5, 7 and 14 years after wildfire). Soil microbial activity was measured with the Solvita test which determines soil microbial respiration rate based on the measurement of the CO2 burst of a dry soil after it is moistened. Soils were dried and re-wetted and a CO2 probe was inserted before incubation at constant conditions of 25°C during 24 h. Measurements were taken with a digital mini spectrometer. Microbial (bacteria and fungi) biomass and community composition were measured by phospholipid fatty acid analysis (PLFA). Results Immediately after the fire (i.e. 3 months), soil microbial activity and microbial biomass are similar to 14 years 'undisturbed' levels (53.18±3.68 ppm CO2-CO and 14.07±0.65 mg kg-1, respectively). However, after the first year post-fire, with larger plant productivity, microbial biomass and microbial activity increase rapidly, peaking after 5-7 years post fire (70.70±8.94 ppm CO2-CO and 21.67±2.62 mg kg-1, respectively). Microbial activity measured with the Solvita test was significantly correlated (R Pearson > 0.7; P < 0.001) with microbial parameters analysed with PLFA such as microbial biomass, bacteria biomass or mycorrhizhal fungi. This method has proven to be reliable, fast and easy to interpret for assessment of soil microbial activity in the recovery of soil quality during the recovery after fire. Keywords Pilbara region, biodiverse ecosystems, microbial biomass, microbial respiration, Solvita test, CO2 burst.
Long-Term Field Study of Microbial Community and Dechlorinating Activity Following Carboxymethyl Cellulose-Stabilized Nanoscale Zero-Valent Iron Injection.

PubMed

Kocur, Chris M D; Lomheim, Line; Molenda, Olivia; Weber, Kela P; Austrins, Leanne M; Sleep, Brent E; Boparai, Hardiljeet K; Edwards, Elizabeth A; O'Carroll, Denis M

2016-07-19

Nanoscale zerovalent iron (nZVI) is an emerging technology for the remediation of contaminated sites. However, there are concerns related to the impact of nZVI on in situ microbial communities. In this study, the microbial community composition at a contaminated site was monitored over two years following the injection of nZVI stabilized with carboxymethyl cellulose (nZVI-CMC). Enhanced dechlorination of chlorinated ethenes to nontoxic ethene was observed long after the expected nZVI oxidation. The abundance of Dehalococcoides (Dhc) and vinyl chloride reductase (vcrA) genes, monitored using qPCR, increased by over an order of magnitude in nZVI-CMC-impacted wells. The entire microbial community was tracked using 16S rRNA gene amplicon pyrosequencing. Following nZVI-CMC injection, a clear shift in microbial community was observed, with most notable increases in the dechlorinating genera Dehalococcoides and Dehalogenimonas. This study suggests that coupled abiotic degradation (i.e., from reaction with nZVI) and biotic degradation fueled by CMC led to the long-term degradation of chlorinated ethenes at this field site. Furthermore, nZVI-CMC addition stimulated dehalogenator growth (e.g., Dehalococcoides) and biotic degradation of chlorinated ethenes.

Small Microbial Three-Electrode Cell Based Biosensor for Online Detection of Acute Water Toxicity.

PubMed

Yu, Dengbin; Zhai, Junfeng; Liu, Changyu; Zhang, Xueping; Bai, Lu; Wang, Yizhe; Dong, Shaojun

2017-11-22

The monitoring of toxicity of water is very important to estimate the safety of drinking water and the level of water pollution. Herein, a small microbial three-electrode cell (M3C) biosensor filled with polystyrene particles was proposed for online monitoring of the acute water toxicity. The peak current of the biosensor related with the performance of the bioanode was regarded as the toxicity indicator, and thus the acute water toxicity could be determined in terms of inhibition ratio by comparing the peak current obtained with water sample to that obtained with nontoxic standard water. The incorporation of polystyrene particles in the electrochemical cell not only reduced the volume of the samples used, but also improved the sensitivity of the biosensor. Experimental conditions including washing time with PBS and the concentration of sodium acetate solution were optimized. The stability of the M3C biosensor under optimal conditions was also investigated. The M3C biosensor was further examined by formaldehyde at the concentration of 0.01%, 0.03%, and 0.05% (v/v), and the corresponding inhibition ratios were 14.6%, 21.6%, and 36.4%, respectively. This work provides a new insight into the development of an online toxicity detector based on M3C biosensor.
Use of Quantitative Microbial Risk Assessment to Improve Interpretation of a Recreational Water Epidemiological Study

EPA Science Inventory

We conducted a supplemental water quality monitoring study and quantitative microbial risk assessment (QMRA) to complement the United States Environmental Protection Agency’s (U.S. EPA) National Epidemiological and Environmental Assessment of Recreational Water study at Boquerón ...
Microbial Degradation of Octamethylcyclotetrasiloxane

PubMed Central

Grümping, R.; Michalke, K.; Hirner, A. V.; Hensel, R.

1999-01-01

The microbial degradation of low-molecular-weight polydimethylsiloxanes was investigated through laboratory experiments. Octamethylcyclotetrasiloxane was found to be biodegraded under anaerobic conditions in composted sewage sludge, as monitored by the occurrence of the main polydimethylsiloxane degradation product, dimethylsilanediol, compared to that found in experiments with sterilized control samples. PMID:10224038
Drilling Automation Demonstrations in Subsurface Exploration for Astrobiology

NASA Technical Reports Server (NTRS)

Glass, Brian; Cannon, H.; Lee, P.; Hanagud, S.; Davis, K.

2006-01-01

This project proposes to study subsurface permafrost microbial habitats at a relevant Arctic Mars-analog site (Haughton Crater, Devon Island, Canada) while developing and maturing the subsurface drilling and drilling automation technologies that will be required by post-2010 missions. It builds on earlier drilling technology projects to add permafrost and ice-drilling capabilities to 5m with a lightweight drill that will be automatically monitored and controlled in-situ. Frozen cores obtained with this drill under sterilized protocols will be used in testing three hypotheses pertaining to near-surface physical geology and ground H2O ice distribution, viewed as a habitat for microbial life in subsurface ice and ice-consolidated sediments. Automation technologies employed will demonstrate hands-off diagnostics and drill control, using novel vibrational dynamical analysis methods and model-based reasoning to monitor and identify drilling fault states before and during faults. Three field deployments, to a Mars-analog site with frozen impact crater fallback breccia, will support science goals, provide a rigorous test of drilling automation and lightweight permafrost drilling, and leverage past experience with the field site s particular logistics.
Monitoring microbial growth and activity using spectral induced polarization and low-field nuclear magnetic resonance

NASA Astrophysics Data System (ADS)

Zhang, Chi; Keating, Kristina; Revil, Andre

2015-04-01

Microbes and microbial activities in the Earth's subsurface play a significant role in shaping subsurface environments and are involved in environmental applications such as remediation of contaminants in groundwater and oil fields biodegradation. Stimulated microbial growth in such applications could cause wide variety of changes of physical/chemical properties in the subsurface. It is critical to monitor and determine the fate and transportation of microorganisms in the subsurface during such applications. Recent geophysical studies demonstrate the potential of two innovative techniques, spectral induced polarization (SIP) and low-field nuclear magnetic resonance (NMR), for monitoring microbial growth and activities in porous media. The SIP measures complex dielectric properties of porous media at low frequencies of exciting electric field, and NMR studies the porous structure of geologic media and characterizes fluids subsurface. In this laboratory study, we examined both SIP and NMR responses from bacterial growth suspension as well as suspension mixed with silica sands. We focus on the direct contribution of microbes to the SIP and NMR signals in the absence of biofilm formation or biomineralization. We used Zymomonas mobilis and Shewanella oneidensis (MR-1) for SIP and NMR measurements, respectively. The SIP measurements were collected over the frequency range of 0.1 - 1 kHz on Z. mobilis growth suspension and suspension saturated sands at different cell densities. SIP data show two distinct peaks in imaginary conductivity spectra, and both imaginary and real conductivities increased as microbial density increased. NMR data were collected using both CPMG pulse sequence and D-T2 mapping to determine the T2-distribution and diffusion properties on S. oneidensis suspension, pellets (live and dead), and suspension mixed with silica sands. NMR data show a decrease in the T2-distribution in S. oneidensis suspension saturated sands as microbial density increase. A clear distinction in the T2-distribution and D-T2 plots between live and dead cell pellets was also observed. These results will provide a basis for understanding the effect of microbes within geologic media on SIP and low-field NMR measurements. This research suggests that both SIP and NMR have the potential to monitor microbial growth and activities in the subsurface and could provide spatiotemporal variations in bacterial abundance in porous media.
Enriching acid rock drainage related microbial communities from surface-deposited oil sands tailings.

PubMed

Dean, Courtney; Xiao, Yeyuan; Roberts, Deborah J

2016-10-01

Little is known about the microbial communities native to surface-deposited pyritic oil sands tailings, an environment where acid rock drainage (ARD) could occur. The goal of this study was to enrich sulfur-oxidizing organisms from these tailings and determine whether different populations exist at pH levels 7, 4.5, and 2.5. Using growth-based methods provides model organisms for use in the future to predict potential activities and limitations of these organisms and to develop possible control methods. Thiosulfate-fed enrichment cultures were monitored for approximately 1 year. The results showed that the enrichments at pH 4.5 and 7 were established quicker than at pH 2.5. Different microbial community structures were found among the 3 pH environments. The sulfur-oxidizing microorganisms identified were most closely related to Halothiobacillus neapolitanus, Achromobacter spp., and Curtobacterium spp. While microorganisms related to Chitinophagaceae and Acidocella spp. were identified as the only possible iron-oxidizing and -reducing microbes. These results contribute to the general knowledge of the relatively understudied microbial communities that exist in pyritic oil sands tailings and indicate these communities may have a potential role in ARD generation, which may have implications for future tailings management.
Applicability of a microbial Time Temperature Indicator (TTI) for monitoring spoilage of modified atmosphere packed minced meat.

PubMed

Vaikousi, Hariklia; Biliaderis, Costas G; Koutsoumanis, Konstantinos P

2009-08-15

The applicability of a microbial Time Temperature Indicator (TTI) prototype, based on the growth and metabolic activity of a Lactobacillus sakei strain developed in a previous study, in monitoring quality of modified atmosphere packed (MAP) minced beef was evaluated at conditions simulating the chill chain. At all storage temperatures examined (0, 5, 10, 15 degrees C), the results showed that lactic acid bacteria (LAB) were the dominant bacteria and can be used as a good spoilage index of MAP minced beef. The end of product's shelf life as revealed by the sensory evaluation coincided with a LAB population level of 7 log(10) CFU/g. For all temperatures tested, the growth of L. sakei in the TTI resembled closely the growth of LAB in the meat product, with similar temperature dependence of the micro(max) and thus similar activation energy values calculated as 111.90 and 106.90 kJ/mol, for the two systems, respectively. In addition, the end point of TTI colour change coincided with the time of sensory rejection point of the beef product during its storage under isothermal chilled temperature conditions. The estimated activation energy, E(alpha), values obtained for parameters related to the response of DeltaE (total colour change of the TTI) describing the kinetics of colour change of the TTI during isothermal storage (i.e. the maximum specific rate of DeltaEpsilon evolution curve, micro(DeltaEpsilon), and also the reciprocal of t(i), time at which half of the maximum DeltaEpsilon is reached), were 112.77 and 127.28 kJ/mol, respectively. Finally, the application of the microbial TTI in monitoring the quality deterioration of MAP minced beef due to spoilage was further evaluated under dynamic conditions of storage, using two separate low temperature periodic changing scenarios, resembling the actual conditions occurring in the distribution chill chain. The results showed that the end point of TTI, after storage at those fluctuating temperature conditions, was noted very close to the end of product's sensorial shelf life. This finding points to the applicability of the developed microbial TTI as a valuable tool for monitoring the quality status during distribution and storage of chilled meat products, which are spoiled by lactic acid bacteria or other bacteria exhibiting similar kinetic responses and spoilage potential.
Water quality program elements for Space Station Freedom

NASA Technical Reports Server (NTRS)

Sauer, Richard L.; Ramanathan, Raghupathy; Straub, John E.; Schultz, John R.

1991-01-01

A strategy is outlined for the development of water-quality criteria and standards relevant to recycling and monitoring the in-flight water for the Space Station Freedom (SSF). The water-reclamation subsystem of the SSF's ECLSS is described, and the objectives of the water-quality are set forth with attention to contaminants. Quality parameters are listed for potable and hygiene-related water including physical and organic parameters, inorganic constituents, bactericides, and microbial content. Comparisons are made to the quality parameters established for the Shuttle's potable water and to the EPA's current standards. Specific research is required to develop in-flight monitoring techniques for unique SSF contaminants, ECLSS microbial control, and on- and off-line monitoring. After discussing some of the in-flight water-monitoring hardware it is concluded that water reclamation and recycling are necessary and feasible for the SSF.
Physicochemical and biological quality of soil in hexavalent chromium-contaminated soils as affected by chemical and microbial remediation.

PubMed

Liao, Yingping; Min, Xiaobo; Yang, Zhihui; Chai, Liyuan; Zhang, Shujuan; Wang, Yangyang

2014-01-01

Chemical and microbial methods are the main remediation technologies for chromium-contaminated soil. These technologies have progressed rapidly in recent years; however, there is still a lack of methods for evaluating the chemical and biological quality of soil after different remediation technologies have been applied. In this paper, microbial remediation with indigenous bacteria and chemical remediation with ferrous sulphate were used for the remediation of soils contaminated with Cr(VI) at two levels (80 and 1,276 mg kg(-1)) through a column leaching experiment. After microbial remediation with indigenous bacteria, the average concentration of water-soluble Cr(VI) in the soils was reduced to less than 5.0 mg kg(-1). Soil quality was evaluated based on 11 soil properties and the fuzzy comprehensive assessment method, including fuzzy mathematics and correlative analysis. The chemical fertility quality index was improved by one grade using microbial remediation with indigenous bacteria, and the biological fertility quality index increased by at least a factor of 6. Chemical remediation with ferrous sulphate, however, resulted in lower levels of available phosphorus, dehydrogenase, catalase and polyphenol oxidase. The result showed that microbial remediation with indigenous bacteria was more effective for remedying Cr(VI)-contaminated soils with high pH value than chemical remediation with ferrous sulphate. In addition, the fuzzy comprehensive evaluation method was proven to be a useful tool for monitoring the quality change in chromium-contaminated soils.
Field Evidence for Magnetite Formation by a Methanogenic Microbial Community

NASA Astrophysics Data System (ADS)

Rossbach, S.; Beaver, C. L.; Williams, A.; Atekwana, E. A.; Slater, L. D.; Ntarlagiannis, D.; Lund, A.

2015-12-01

The aged, subsurface petroleum spill in Bemidji, Minnesota, has been surveyed with magnetic susceptibility (MS) measurements. High MS values were found in the free-product phase around the fluctuating water table. Although we had hypothesized that high MS values are related to the occurrence of the mineral magnetite resulting from the activity of iron-reducing bacteria, our microbial analysis pointed to the presence of a methanogenic microbial community at the locations and depths of the highest MS values. Here, we report on a more detailed microbial analysis based on high-throughput sequencing of the 16S rRNA gene of sediment samples from four consecutive years. In addition, we provide geochemical data (FeII/FeIII concentrations) to refine our conceptual model of methanogenic hydrocarbon degradation at aged petroleum spills and demonstrate that the microbial induced changes of sediment properties can be monitored with MS. The methanogenic microbial community at the Bemidji site consisted mainly of the syntrophic, hydrocarbon-degrading Smithella and the hydrogenotrophic, methane-generating Methanoregula. There is growing evidence in the literature that not only Bacteria, but also some methanogenic Archaea are able to reduce iron. In fact, a recent study reported that the methanogen Methanosarcina thermophila produced magnetite during the reduction of ferrihydrite in a laboratory experiment when hydrogen was present. Therefore, our finding of high MS values and the presence of magnetite in the methanogenic zone of an aged, subsurface petroleum spill could very well be the first field evidence for magnetite formation during methanogenic hydrocarbon degradation.
Controlling Microbial Byproducts using Model-Based Substrate Monitoring and Control Strategies

NASA Technical Reports Server (NTRS)

Smernoff, David T.; Blackwell, Charles; Mancinelli, Rocco L.; DeVincenzi, Donald (Technical Monitor)

2000-01-01

We have developed a computer-controlled bioreactor system to study various aspects of microbially-mediated nitrogen cycling. The system has been used to investigate methods for controlling microbial denitrification (the dissimilatory reduction of nitrate to N2O and N2) in hydroponic plant growth chambers. Such chambers are key elements of advanced life support systems being designed for use on long duration space missions, but nitrogen use efficiency in them is reduced by denitrification. Control software architecture was designed which permits the heterogeneous control of system hardware using traditional feedback control, and quantitative and qualitative models of various system features. Model-based feed forward control entails prediction of future systems in states and automated regulation of system parameters to achieve desired and avoid undesirable system states. A bacterial growth rate model based on the classic Monod model of saturation kinetics was used to evaluate the response of several individual denitrifying species to varying environmental conditions. The system and models are now being applied to mixed microbial communities harvested from the root zone of a hydroponic growth chamber. The use of a modified Monod organism interaction model was evaluated as a means of achieving more accurate description of the dynamic behavior of the communities. A minimum variance parameter estimation routine was also' used to calibrate the constant parameters in the model by iterative evaluation of substrate (nitrate) uptake and growth kinetics. This representation of processes and interactions aids in the formulation of control laws. The feed forward control strategy being developed will increase system autonomy, reduce crew intervention and limit the accumulation of undesirable waste products (NOx).
76 FR 58266 - Agency Information Collection Activities; Proposed Collection; Comment Request; Reporting...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-09-20

... contents of the docket, and access those documents in the public docket that are available electronically... monitor recreational water quality; assess, manage, and communicate health risks from waterborne microbial... public exposure to microbial pathogens. To qualify for a BEACH Act Grant, a state must submit information...
Soil microbial diversity and activity as terroir elements of Sangiovese vineyards in the Chianti Classico region (Italy)

NASA Astrophysics Data System (ADS)

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

2016-04-01

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

PubMed Central

Savio, Domenico; Stadler, Philipp; Reischer, Georg H.; Kirschner, Alexander K.T.; Demeter, Katalin; Linke, Rita; Blaschke, Alfred P.; Sommer, Regina; Szewzyk, Ulrich; Wilhartitz, Inés C.; Mach, Robert L.; Stadler, Hermann

2018-01-01

Over the past 15 years, pioneering interdisciplinary research has been performed on the microbiology of hydrogeologically well‐defined alpine karst springs located in the Northern Calcareous Alps (NCA) of Austria. This article gives an overview on these activities and links them to other relevant research. Results from the NCA springs and comparable sites revealed that spring water harbors abundant natural microbial communities even in aquifers with high water residence times and the absence of immediate surface influence. Apparently, hydrogeology has a strong impact on the concentration and size of the observed microbes, and total cell counts (TCC) were suggested as a useful means for spring type classification. Measurement of microbial activities at the NCA springs revealed extremely low microbial growth rates in the base flow component of the studied spring waters and indicated the importance of biofilm‐associated microbial activities in sediments and on rock surfaces. Based on genetic analysis, the autochthonous microbial endokarst community (AMEC) versus transient microbial endokarst community (TMEC) concept was proposed for the NCA springs, and further details within this overview article are given to prompt its future evaluation. In this regard, it is well known that during high‐discharge situations, surface‐associated microbes and nutrients such as from soil habitats or human settlements—potentially containing fecal‐associated pathogens as the most critical water‐quality hazard—may be rapidly flushed into vulnerable karst aquifers. In this context, a framework for the comprehensive analysis of microbial pollution has been proposed for the NCA springs to support the sustainable management of drinking water safety in accordance with recent World Health Organization guidelines. Near‐real‐time online water quality monitoring, microbial source tracking (MST) and MST‐guided quantitative microbial‐risk assessment (QMRA) are examples of the proposed analytical tools. In this context, this overview article also provides a short introduction to recently emerging methodologies in microbiological diagnostics to support reading for the practitioner. Finally, the article highlights future research and development needs. This article is categorized under: 1Engineering Water > Water, Health, and Sanitation2Science of Water > Water Extremes3Water and Life > Nature of Freshwater Ecosystems PMID:29780584
A novel biosensor for p-nitrophenol based on an aerobic anode microbial fuel cell.

PubMed

Chen, Zhengjun; Niu, Yongyan; Zhao, Shuai; Khan, Aman; Ling, Zhenmin; Chen, Yong; Liu, Pu; Li, Xiangkai

2016-11-15

P-nitrophenol is one of the most common contaminants in chemical industrial wastewater, and in situ real-time monitoring of PNP cannot be achieved by conventional analytical techniques. Here, a two-chamber microbial fuel cell with an aerobic anode chamber was tested as a biosensor for in situ real-time monitoring of PNP. Pseudomonas monteilii LZU-3, which was used as the biological recognition element, can form a biofilm on the anode electrode using PNP as a sole substrate. The optimal operation parameters of the biosensor were as follows: external resistance 1000Ω, pH 7.8, temperature 30°C, and maximum PNP concentration 50mgL(-1). Under these conditions, the maximum voltages showed a linear relationship with PNP concentrations ranging from 15±5 to 44±4.5mgL(-1). Furthermore, we developed a novel portable device for in situ real-time monitoring of PNP. When the device was applied to measure PNP in wastewater containing various additional aromatic compounds and metal ions, the performance of the biosensor was not affected and the correlation between the maximum voltages and the PNP concentrations ranging from 9±4mgL(-1) to 36 ± 5mgL(-1) was conserved. The results demonstrated that the MFC biosensor provides a rapid and cost-efficient analytical method for real-time monitoring of toxic and recalcitrant pollutants in environmental samples. Copyright © 2016 Elsevier B.V. All rights reserved.
Spaceflight Microbiology: Benefits for Long Duration Spaceflight and Our Understanding of Microorganisms on Earth

NASA Technical Reports Server (NTRS)

Ott, C. Mark

2014-01-01

Spaceflight microbiology is composed of both operational and experimental components that complement each other in our understanding of microbial interactions and their responses in the microgravity of spaceflight. Operationally, efforts to mitigate microbiological risk to the crew and the spacecraft have historically focused on minimizing the number of detectable organisms, relying heavily on preventative measures, including appropriate vehicle design, crew quarantine prior to flight, and stringent microbial monitoring. Preflight monitoring targets have included the astronauts, spaceflight foods, potable water systems, the vehicle air and surfaces, and the cargo carried aboard the spacecraft. This approach has been very successful for earlier missions; however, the construction and long-term habitation of the International Space Station (ISS) has created the need for additional inflight monitoring of the environment and potable water systems using hardware designed for both in-flight microbial enumeration and sample collection and return to Earth. In addition to operational activities, the ISS is providing a research platform to advance our understanding of microbiomes in the built environment. Adding to the research possibilities of this system are multiple reports of unique changes in microbial gene expression and phenotypic responses, including virulence and biofilm formation, in response to spaceflight culture. The tremendous potential of the ISS research platform led the National Research Council to recommend that NASA utilize the ISS as a microbial observatory. Collectively, the findings from operational and research activities on the ISS are expected to both enable future space exploration and translate to basic and applied research on Earth.
Microorganisms in Confined Habitats: Microbial Monitoring and Control of Intensive Care Units, Operating Rooms, Cleanrooms and the International Space Station

PubMed Central

Mora, Maximilian; Mahnert, Alexander; Koskinen, Kaisa; Pausan, Manuela R.; Oberauner-Wappis, Lisa; Krause, Robert; Perras, Alexandra K.; Gorkiewicz, Gregor; Berg, Gabriele; Moissl-Eichinger, Christine

2016-01-01

Indoor environments, where people spend most of their time, are characterized by a specific microbial community, the indoor microbiome. Most indoor environments are connected to the natural environment by high ventilation, but some habitats are more confined: intensive care units, operating rooms, cleanrooms and the international space station (ISS) are extraordinary living and working areas for humans, with a limited exchange with the environment. The purposes for confinement are different: a patient has to be protected from infections (intensive care unit, operating room), product quality has to be assured (cleanrooms), or confinement is necessary due to extreme, health-threatening outer conditions, as on the ISS. The ISS represents the most secluded man-made habitat, constantly inhabited by humans since November 2000 – and, inevitably, also by microorganisms. All of these man-made confined habitats need to be microbiologically monitored and controlled, by e.g., microbial cleaning and disinfection. However, these measures apply constant selective pressures, which support microbes with resistance capacities against antibiotics or chemical and physical stresses and thus facilitate the rise of survival specialists and multi-resistant strains. In this article, we summarize the available data on the microbiome of aforementioned confined habitats. By comparing the different operating, maintenance and monitoring procedures as well as microbial communities therein, we emphasize the importance to properly understand the effects of confinement on the microbial diversity, the possible risks represented by some of these microorganisms and by the evolution of (antibiotic) resistances in such environments – and the need to reassess the current hygiene standards. PMID:27790191
Microorganisms in Confined Habitats: Microbial Monitoring and Control of Intensive Care Units, Operating Rooms, Cleanrooms and the International Space Station.

PubMed

Mora, Maximilian; Mahnert, Alexander; Koskinen, Kaisa; Pausan, Manuela R; Oberauner-Wappis, Lisa; Krause, Robert; Perras, Alexandra K; Gorkiewicz, Gregor; Berg, Gabriele; Moissl-Eichinger, Christine

2016-01-01

Indoor environments, where people spend most of their time, are characterized by a specific microbial community, the indoor microbiome. Most indoor environments are connected to the natural environment by high ventilation, but some habitats are more confined: intensive care units, operating rooms, cleanrooms and the international space station (ISS) are extraordinary living and working areas for humans, with a limited exchange with the environment. The purposes for confinement are different: a patient has to be protected from infections (intensive care unit, operating room), product quality has to be assured (cleanrooms), or confinement is necessary due to extreme, health-threatening outer conditions, as on the ISS. The ISS represents the most secluded man-made habitat, constantly inhabited by humans since November 2000 - and, inevitably, also by microorganisms. All of these man-made confined habitats need to be microbiologically monitored and controlled, by e.g., microbial cleaning and disinfection. However, these measures apply constant selective pressures, which support microbes with resistance capacities against antibiotics or chemical and physical stresses and thus facilitate the rise of survival specialists and multi-resistant strains. In this article, we summarize the available data on the microbiome of aforementioned confined habitats. By comparing the different operating, maintenance and monitoring procedures as well as microbial communities therein, we emphasize the importance to properly understand the effects of confinement on the microbial diversity, the possible risks represented by some of these microorganisms and by the evolution of (antibiotic) resistances in such environments - and the need to reassess the current hygiene standards.
Microbial Growth and Metabolism in Soil - Refining the Interpretation of Carbon Use Efficiency

NASA Astrophysics Data System (ADS)

Geyer, K.; Frey, S. D.

2016-12-01

Carbon use efficiency (CUE) describes a critical step in the terrestrial carbon cycle where microorganisms partition organic carbon (C) between stabilized organic forms and CO2. Application of this concept, however, begins with accurate measurements of CUE. Both traditional and developing approaches still depend on numerous assumptions that render them difficult to interpret and potentially incompatible with one another. Here we explore the soil processes inherent to traditional (e.g., substrate-based, biomass-based) and emerging (e.g., growth rate-based, calorimetry) CUE techniques in order to better understand the information they provide. Soil from the Harvard Forest Long Term Ecological Research (LTER) site in Massachusetts, USA, was amended with both 13C-glucose and 18O-water and monitored over 72 h for changes in dissolved organic carbon (DOC), respiration (R), microbial biomass (MB), DNA synthesis, and heat flux (Q). Four different CUE estimates were calculated: 1) (ΔDOC - R)/ΔDOC (substrate-based), 2) Δ13C-MB/(Δ13C-MB + R) (biomass-based), 3) Δ18O-DNA/(Δ18O-DNA + R) (growth rate-based), 4) Q/R (energy-based). Our results indicate that microbial growth (estimated by both 13C and 18O techniques) was delayed for 40 h after amendment even though DOC had declined to pre-amendment levels within 48 h. Respiration and heat flux also peaked after 40 h. Although these soils have a relatively high organic C content (5% C), respired CO2 was greater than 88% glucose-derived throughout the experiment. All estimates of microbial growth (Spearman's ρ >0.83, p<0.01) and efficiency (Spearman's ρ >0.65, p<0.05) were positively correlated, but strong differences in the magnitude of CUE suggest incomplete C accounting. This work increases the transparency of CUE techniques for researchers looking to choose the most appropriate measure for their scale of inquiry or to use CUE estimates in modeling applications.
Nitrifying biomass characterization and monitoring during bioaugmentation in a membrane bioreactor.

PubMed

D'Anteo, Sibilla; Mannucci, Alberto; Meliani, Matteo; Verni, Franco; Petroni, Giulio; Munz, Giulio; Lubello, Claudio; Mori, Gualtiero; Vannini, Claudia

2015-01-01

A membrane bioreactor (MBR), fed with domestic wastewater, was bioaugmented with nitrifying biomass selected in a side-stream MBR fed with a synthetic high nitrogen-loaded influent. Microbial communities evolution was monitored and comparatively analysed through an extensive bio-molecular investigation (16S rRNA gene library construction and terminal-restriction fragment length polymorphism techniques) followed by statistical analyses. As expected, a highly specialized nitrifying biomass was selected in the side-stream reactor fed with high-strength ammonia synthetic wastewater. The bioaugmentation process caused an increase of nitrifying bacteria of the genera Nitrosomonas (up to more than 30%) and Nitrobacter in the inoculated MBR reactor. The overall structure of the microbial community changed in the mainstream MBR as a result of bioaugmentation. The effect of bioaugmentation in the shift of the microbial community was also verified through statistical analysis.

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.
Identifying microbial carbon sources during ethanol and toluene biodegradation in a pilot-scale experimental aquifer system using isotopic analysis

NASA Astrophysics Data System (ADS)

Clay, S.; McLeod, H.; Smith, J. E.; Roy, J. W.; Slater, G. F.

2013-12-01

Combining ethanol with gasoline has become increasingly common in order to create more environmentally conscience transportation fuels. These blended fuels are favourable alternatives since ethanol is a non-toxic and highly labile renewable biomass-based resource which is an effective fuel oxygenate that reduces air pollution. Recent research however, has indicated that upon accidental release into groundwater systems, the preferential microbial metabolism of ethanol can cause progressively reducing conditions leading to slower biodegradation of petroleum hydrocarbons. Therefore, the presence of ethanol can result in greater persistence of BTEX compounds and longer hydrocarbon plumes in groundwater systems. Microbial biodegradation and community carbon sources coupled to aqueous geochemistry were monitored in a pilot-scale laboratory tank (80cm x 525cm x 175cm) simulating an unconfined sand aquifer. Dissolved ethanol and toluene were continuously injected into the aquifer at a controlled rate over 330 days. Carbon isotope analyses were performed on phospholipid fatty acid (PLFA) samples collected from 4 different locations along the aquifer. Initial stable carbon isotope values measured over days 160-185 in the bacterial PLFA ranged from δ13C = -10 to -21‰, which is indicative of dominant ethanol incorporation by the micro-organisms based on the isotopic signature of ethanol derived from corn, a C4 plant. A negative shift to δ13C = -10 to -30‰ observed over days 185-200, suggests a change in microbial metabolisms associated with less ethanol incorporation. This generally corresponds to a decrease in ethanol concentrations from day 40 to full attenuation at approximately day 160, and the onset of toluene depletion observed on day 120 and continuing thereafter. In addition, aqueous methane concentrations first detected on day 115 continued to rise to 0.38-0.70 mmol/L at all monitoring locations, demonstrating a significant redox shift to low energy methanogenic metabolisms. On-going archaeal lipid analyses are expected to capture the establishment of methanogenic communities and provide insight into carbon use by these communities. Furthermore, radiocarbon analysis will aid in tracking the biodegradation of ethanol and toluene. Ultimately this research aims to illustrate the preferential biodegradation of ethanol in a gasoline mixture, and identify the carbon sources utilized by an evolving microbial community using isotopic analyses to improve assessments and remediation strategies at sites contaminated with ethanol-blended fuels.
Planned Environmental Microbiology Aspects of Future Lunar and Mars Missions

NASA Technical Reports Server (NTRS)

Ott, C. Mark; Castro, Victoria A.; Pierson, Duane L.

2006-01-01

With the establishment of the Constellation Program, NASA has initiated efforts designed similar to the Apollo Program to return to the moon and subsequently travel to Mars. Early lunar sorties will take 4 crewmembers to the moon for 4 to 7 days. Later missions will increase in duration up to 6 months as a lunar habitat is constructed. These missions and vehicle designs are the forerunners of further missions destined for human exploration of Mars. Throughout the planning and design process, lessons learned from the International Space Station (ISS) and past programs will be implemented toward future exploration goals. The standards and requirements for these missions will vary depending on life support systems, mission duration, crew activities, and payloads. From a microbiological perspective, preventative measures will remain the primary techniques to mitigate microbial risk. Thus, most of the effort will focus on stringent preflight monitoring requirements and engineering controls designed into the vehicle, such as HEPA air filters. Due to volume constraints in the CEV, in-flight monitoring will be limited for short-duration missions to the measurement of biocide concentration for water potability. Once long-duration habitation begins on the lunar surface, a more extensive environmental monitoring plan will be initiated. However, limited in-flight volume constraints and the inability to return samples to Earth will increase the need for crew capabilities in determining the nature of contamination problems and method of remediation. In addition, limited shelf life of current monitoring hardware consumables and limited capabilities to dispose of biohazardous trash will drive flight hardware toward non-culture based methodologies, such as hardware that rapidly distinguishes biotic versus abiotic surface contamination. As missions progress to Mars, environmental systems will depend heavily on regeneration of air and water and biological waste remediation and regeneration systems, increasing the need for environmental monitoring. Almost complete crew autonomy will be needed for assessment and remediation of contamination problems. Cabin capacity will be limited; thus, current methods of microbial monitoring will be inadequate. Future methodology must limit consumables, and these consumables must have a shelf life of over three years. In summary, missions to the moon and Mars will require a practical design that prudently uses available resources to mitigate microbial risk to the crew.
Network succession reveals the importance of competition in response to emulsified vegetable oil amendment for uranium bioremediation.

PubMed

Deng, Ye; Zhang, Ping; Qin, Yujia; Tu, Qichao; Yang, Yunfeng; He, Zhili; Schadt, Christopher Warren; Zhou, Jizhong

2016-01-01

Discerning network interactions among different species/populations in microbial communities has evoked substantial interests in recent years, but little information is available about temporal dynamics of microbial network interactions in response to environmental perturbations. Here, we modified the random matrix theory-based network approach to discern network succession in groundwater microbial communities in response to emulsified vegetable oil (EVO) amendment for uranium bioremediation. Groundwater microbial communities from one control and seven monitor wells were analysed with a functional gene array (GeoChip 3.0), and functional molecular ecological networks (fMENs) at different time points were reconstructed. Our results showed that the network interactions were dramatically altered by EVO amendment. Dynamic and resilient succession was evident: fairly simple at the initial stage (Day 0), increasingly complex at the middle period (Days 4, 17, 31), most complex at Day 80, and then decreasingly complex at a later stage (140-269 days). Unlike previous studies in other habitats, negative interactions predominated in a time-series fMEN, suggesting strong competition among different microbial species in the groundwater systems after EVO injection. Particularly, several keystone sulfate-reducing bacteria showed strong negative interactions with their network neighbours. These results provide mechanistic understanding of the decreased phylogenetic diversity during environmental perturbations. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.
Network succession reveals the importance of competition in response to emulsified vegetable oil amendment for uranium bioremediation: Competition in bioremediation system

DOE PAGES

Deng, Ye; Zhang, Ping; Qin, Yujia; ...

2015-08-11

When trying to discern network interactions among different species/populations in microbial communities interests have been evoked in recent years, but little information is available about temporal dynamics of microbial network interactions in response to environmental perturbations. We modified the random matrix theory-based network approach to discern network succession in groundwater microbial communities in response to emulsified vegetable oil (EVO) amendment for uranium bioremediation. Groundwater microbial communities from one control and seven monitor wells were analysed with a functional gene array (GeoChip 3.0), and functional molecular ecological networks (fMENs) at different time points were reconstructed. Our results showed that the networkmore » interactions were dramatically altered by EVO amendment. Dynamic and resilient succession was evident: fairly simple at the initial stage (Day 0), increasingly complex at the middle period (Days 4, 17, 31), most complex at Day 80, and then decreasingly complex at a later stage (140–269 days). Unlike previous studies in other habitats, negative interactions predominated in a time-series fMEN, suggesting strong competition among different microbial species in the groundwater systems after EVO injection. In particular, several keystone sulfate-reducing bacteria showed strong negative interactions with their network neighbours. These results provide mechanistic understanding of the decreased phylogenetic diversity during environmental perturbations.« less
The cryptoendolithic microbial environment in the Ross Desert of Antarctica: satellite-transmitted continuous nanoclimate data, 1984 to 1986.

PubMed

Friedmann, E I; McKay, C P; Nienow, J A

1987-01-01

A satellite mediated station for monitoring nanoclimate (climate in the millimeter range) data, suitable for use in polar regions is described. The station, located in the Ross desert of Antarctica, has been in operation for more than 3 years, measuring rock temperatures, air temperature, light, snow, wind, and moisture. The data indicate that biological activity in the cryptoendolithic microbial ecosystem is limited to the period from mid November to mid February. The total number of hours of biological activity, based on assumptions of the minimum light, temperature and moisture requirements of the community, is less than 1000 h/year. The time above 0 degrees C, representing more nearly optimal conditions, is between 50 and 550 h/year, depending on the orientation of the surface.
The cryptoendolithic microbial environment in the Ross Desert of Antarctica: satellite-transmitted continuous nanoclimate data, 1984 to 1986

NASA Technical Reports Server (NTRS)

Friedmann, E. I.; McKay, C. P.; Nienow, J. A.

1987-01-01

A satellite mediated station for monitoring nanoclimate (climate in the millimeter range) data, suitable for use in polar regions is described. The station, located in the Ross desert of Antarctica, has been in operation for more than 3 years, measuring rock temperatures, air temperature, light, snow, wind, and moisture. The data indicate that biological activity in the cryptoendolithic microbial ecosystem is limited to the period from mid November to mid February. The total number of hours of biological activity, based on assumptions of the minimum light, temperature and moisture requirements of the community, is less than 1000 h/year. The time above 0 degrees C, representing more nearly optimal conditions, is between 50 and 550 h/year, depending on the orientation of the surface.
Evaluation of ATP measurements to detect microbial ingress by wastewater and surface water in drinking water.

PubMed

Vang, Óluva K; Corfitzen, Charlotte B; Smith, Christian; Albrechtsen, Hans-Jørgen

2014-11-01

Fast and reliable methods are required for monitoring of microbial drinking water quality in order to protect public health. Adenosine triphosphate (ATP) was investigated as a potential real-time parameter for detecting microbial ingress in drinking water contaminated with wastewater or surface water. To investigate the ability of the ATP assay in detecting different contamination types, the contaminant was diluted with non-chlorinated drinking water. Wastewater, diluted at 10(4) in drinking water, was detected with the ATP assay, as well as 10(2) to 10(3) times diluted surface water. To improve the performance of the ATP assay in detecting microbial ingress in drinking water, different approaches were investigated, i.e. quantifying microbial ATP or applying reagents of different sensitivities to reduce measurement variations; however, none of these approaches contributed significantly in this respect. Compared to traditional microbiological methods, the ATP assay could detect wastewater and surface water in drinking water to a higher degree than total direct counts (TDCs), while both heterotrophic plate counts (HPC 22 °C and HPC 37 °C) and Colilert-18 (Escherichia coli and coliforms) were more sensitive than the ATP measurements, though with much longer response times. Continuous sampling combined with ATP measurements displays definite monitoring potential for microbial drinking water quality, since microbial ingress in drinking water can be detected in real-time with ATP measurements. The ability of the ATP assay to detect microbial ingress is influenced by both the ATP load from the contaminant itself and the ATP concentration in the specific drinking water. Consequently, a low ATP concentration of the specific drinking water facilitates a better detection of a potential contamination of the water supply with the ATP assay. Copyright © 2014 Elsevier Ltd. All rights reserved.
Monitoring of antibiotic-induced alterations in the human intestinal microflora and detection of probiotic strains by use of terminal restriction fragment length polymorphism.

PubMed

Jernberg, Cecilia; Sullivan, Asa; Edlund, Charlotta; Jansson, Janet K

2005-01-01

Terminal restriction fragment length polymorphism (T-RFLP) was investigated as a tool for monitoring the human intestinal microflora during antibiotic treatment and during ingestion of a probiotic product. Fecal samples from eight healthy volunteers were taken before, during, and after administration of clindamycin. During treatment, four subjects were given a probiotic, and four subjects were given a placebo. Changes in the microbial intestinal community composition and relative abundance of specific microbial populations in each subject were monitored by using viable counts and T-RFLP fingerprints. T-RFLP was also used to monitor specific bacterial populations that were either positively or negatively affected by clindamycin. Some dominant bacterial groups, such as Eubacterium spp., were easily monitored by T-RFLP, while they were hard to recover by cultivation. Furthermore, the two probiotic Lactobacillus strains were easily tracked by T-RFLP and were shown to be the dominant Lactobacillus community members in the intestinal microflora of subjects who received the probiotic.
Monitoring of Antibiotic-Induced Alterations in the Human Intestinal Microflora and Detection of Probiotic Strains by Use of Terminal Restriction Fragment Length Polymorphism

PubMed Central

Jernberg, Cecilia; Sullivan, Åsa; Edlund, Charlotta; Jansson, Janet K.

2005-01-01

Terminal restriction fragment length polymorphism (T-RFLP) was investigated as a tool for monitoring the human intestinal microflora during antibiotic treatment and during ingestion of a probiotic product. Fecal samples from eight healthy volunteers were taken before, during, and after administration of clindamycin. During treatment, four subjects were given a probiotic, and four subjects were given a placebo. Changes in the microbial intestinal community composition and relative abundance of specific microbial populations in each subject were monitored by using viable counts and T-RFLP fingerprints. T-RFLP was also used to monitor specific bacterial populations that were either positively or negatively affected by clindamycin. Some dominant bacterial groups, such as Eubacterium spp., were easily monitored by T-RFLP, while they were hard to recover by cultivation. Furthermore, the two probiotic Lactobacillus strains were easily tracked by T-RFLP and were shown to be the dominant Lactobacillus community members in the intestinal microflora of subjects who received the probiotic. PMID:15640226
Comparison of characterization and microbial communities in rice straw- and wheat straw-based compost for Agaricus bisporus production.

PubMed

Wang, Lin; Mao, Jiugeng; Zhao, Hejuan; Li, Min; Wei, Qishun; Zhou, Ying; Shao, Heping

2016-09-01

Rice straw (RS) is an important raw material for the preparation of Agaricus bisporus compost in China. In this study, the characterization of composting process from RS and wheat straw (WS) was compared for mushroom production. The results showed that the temperature in RS compost increased rapidly compared with WS compost, and the carbon (C)/nitrogen (N) ratio decreased quickly. The microbial changes during the Phase I and Phase II composting process were monitored using denaturing gradient gel electrophoresis (DGGE) and phospholipid fatty acid (PLFA) analysis. Bacteria were the dominant species during the process of composting and the bacterial community structure dramatically changed during heap composting according to the DGGE results. The bacterial community diversity of RS compost was abundant compared with WS compost at stages 4-5, but no distinct difference was observed after the controlled tunnel Phase II process. The total amount of PLFAs of RS compost, as an indicator of microbial biomass, was higher than that of WS. Clustering by DGGE and principal component analysis of the PLFA compositions revealed that there were differences in both the microbial population and community structure between RS- and WS-based composts. Our data indicated that composting of RS resulted in improved degradation and assimilation of breakdown products by A. bisporus, and suggested that the RS compost was effective for sustaining A. bisporus mushroom growth as well as conventional WS compost.
A Comparison of Microbial Community Structures by Depth and Season Under Switchgrass

NASA Astrophysics Data System (ADS)

Fansler, S. J.; Smith, J. L.; Bolton, H.; Bailey, V. L.

2008-12-01

As part of a multidisciplinary study of C sequestration in switchgrass production systems, the soil microbial community structure was monitored at 6 different depths (reaching 90 cm) in both spring and autumn. Microbial community structure was assessed using ribosomal intergenic spacer analysis (RISA), and primers were used specific to either bacteria or fungi, generating microbial community fingerprints for each taxonomic group. Diverse microbial communities for both groups were detected throughout the soil profile. It is notable that while community structure clearly changed with depth, there was the deepest soil samples still retained relatively diverse communities. Seasonally, differences are clearly evident within plots at the surface. As the plots were replicated, significant differences in the community fingerprints with depth and season are reported.
Microbial diversity and structure are drivers of the biological barrier effect against Listeria monocytogenes in soil.

PubMed

Vivant, Anne-Laure; Garmyn, Dominique; Maron, Pierre-Alain; Nowak, Virginie; Piveteau, Pascal

2013-01-01

Understanding the ecology of pathogenic organisms is important in order to monitor their transmission in the environment and the related health hazards. We investigated the relationship between soil microbial diversity and the barrier effect against Listeria monocytogenes invasion. By using a dilution-to-extinction approach, we analysed the consequence of eroding microbial diversity on L. monocytogenes population dynamics under standardised conditions of abiotic parameters and microbial abundance in soil microcosms. We demonstrated that highly diverse soil microbial communities act as a biological barrier against L. monocytogenes invasion and that phylogenetic composition of the community also has to be considered. This suggests that erosion of diversity may have damaging effects regarding circulation of pathogenic microorganisms in the environment.
Using blue mussels (Mytilus spp.) as biosentinels of Cryptosporidium spp. and Toxoplasma gondii contamination in marine aquatic environments

USDA-ARS?s Scientific Manuscript database

Methods to monitor microbial contamination typically involve collecting discrete samples at specific time-points and analyzing for a single contaminant. While informative, many of these methods suffer from poor recovery rates and only provide a snapshot of the microbial load at the time of collectio...
IN SITU BIOREMEDIATION OF TRICHLOROETHYLENE USING BURKHOLDERIA CEPACIA G4 PR1: ANALYSIS OF MICROBIAL ECOLOGY PARAMETERS FOR RISK ASSESSMENT (RESEARCH BRIEF)

EPA Science Inventory

The introduction of bacteria into aquifers for bioremediation purposes requires monitoring of the persistence and activity of microbial populations for efficacy and risk assessment purposes. Burkholderia cepacia G4 PR1 constitutively expresses a toluene ortho-monooxygenase (tom) ...
Monitoring pathogens from irradiated agriculture products

NASA Astrophysics Data System (ADS)

Butterweck, Joseph S.

The final food and environmental safety assessment of agriculture product irradiation can only be determined by product history. Product history will be used for future research and development, regulations, commercial practices and implementation of agriculture and food irradiation on a regional basis. The commercial irradiator treats large varieties and amounts of products that are used in various environments. It, in time, will generate a large data base of product history. Field product monitoring begins when food irradiation progresses from the pilot/demonstration phase to the commercial phase. At that time, it is important that there be in place a monitoring system to collect and analyze field data. The systems managers, public health authorities and exotic disease specialists will use this information to assess the reduction of food pathogens on the populace and the environment. The common sources of monitoring data are as follows: 1) Host Monitoring a) Medical Diagnosis b) Autopsy c) Serology Surveys 2) Environmental Monitoring a) Sentinel b) Pest Surveys/Microbial Counts c) Sanitary Inspections 3) Food Industries Quality Assurance Monitoring a) End Product Inspection b) Complaints c) Continual Use of the Product
Exploitation of microbial forensics and nanotechnology for the monitoring of emerging pathogens.

PubMed

Bokhari, Habib

2018-03-07

Emerging infectious diseases remain among the leading causes of global mortality. Traditional laboratory diagnostic approaches designed to detect and track infectious disease agents provide a framework for surveillance of bio threats. However, surveillance and outbreak investigations using such time-consuming approaches for early detection of pathogens remain the major pitfall. Hence, reasonable real-time surveillance systems to anticipate threats to public health and environment are critical for identifying specific aetiologies and preventing the global spread of infectious disease. The current review discusses the growing need for monitoring and surveillance of pathogens with the same zeal and approach as adopted by microbial forensics laboratories, and further strengthening it by integrating with the innovative nanotechnology for rapid detection of microbial pathogens. Such innovative diagnostics platforms will help to track pathogens from high risk areas and environment by pre-emptive approach that will minimize damages. The various scenarios with the examples are discussed where the high risk associated human pathogens in particular were successfully detected using various nanotechnology approaches with potential future prospects in the field of microbial forensics.
Dynamics of oral microbial community profiling during severe early childhood caries development monitored by PCR-DGGE.

PubMed

Tao, Ye; Zhou, Yan; Ouyang, Yong; Lin, HuanCai

2013-09-01

To monitor the longitudinal changes in oral microbial diversity of children with severe early childhood caries (S-ECC) compared to caries free (CF) controls. Dental plaque samples of 12 children in each group at 8, 14, 20, 26 and 32 months of age were analysed. Total microbial genomic DNA was isolated from each sample, and PCR-denaturing gradient gel electrophoresis (DGGE) analyses were carried out. The number of bands was significantly higher in the CF group (18.17±4.91 bands) than in the S-ECC group (14.54±5.56 bands) at 32 months of age (P<0.05). A total of 21 genera were identified in all subjects, and there were no significant differences between the two groups at genus level. DGGE profiles showed that most of the clusters were constructed from one individual over time in the both groups. The onset of S-ECC is accompanied by a decrease in microbial diversity. The overall composition of the microbiota is highly similar within an individual over time. Copyright © 2013 Elsevier Ltd. All rights reserved.
Microbial sequencing methods for monitoring of anaerobic treatment of antibiotics to optimize performance and prevent system failure.

PubMed

Aydin, Sevcan

2016-06-01

As a result of developments in molecular technologies and the use of sequencing technologies, the analyses of the anaerobic microbial community in biological treatment process has become increasingly prevalent. This review examines the ways in which microbial sequencing methods can be applied to achieve an extensive understanding of the phylogenetic and functional characteristics of microbial assemblages in anaerobic reactor if the substrate is contaminated by antibiotics which is one of the most important toxic compounds. It will discuss some of the advantages and disadvantages associated with microbial sequencing techniques that are more commonly employed and will assess how a combination of the existing methods may be applied to develop a more comprehensive understanding of microbial communities and improve the validity and depth of the results for the enhancement of the stability of anaerobic reactors.
Microbial growth associated with granular activated carbon in a pilot water treatment facility.

PubMed Central

Wilcox, D P; Chang, E; Dickson, K L; Johansson, K R

1983-01-01

The microbial dynamics associated with granular activated carbon (GAC) in a pilot water treatment plant were investigated over a period of 16 months. Microbial populations were monitored in the influent and effluent waters and on the GAC particles by means of total plate counts and ATP assays. Microbial populations between the influent and effluent waters of the GAC columns generally increased, indicating microbial growth. The dominant genera of microorganisms isolated from interstitial waters and GAC particles were Achromobacter, Acinetobacter, Aeromonas, Alcaligenes, Bacillus, Chromobacterium, Corynebacterium, Micrococcus, Microcyclus, Paracoccus, and Pseudomonas. Coliform bacteria were found in small numbers in the effluents from some of the GAC columns in the later months of the study. Oxidation of influent waters with ozone and maintenance of aerobic conditions on the GAC columns failed to appreciably enhance the microbial growth on GAC. PMID:6625567

Microbial Diversity Aboard Spacecraft: Evaluation of the International Space Station

NASA Technical Reports Server (NTRS)

Castro, Victoria A.; Thrasher, Adrianna N.; Healy, Mimi; Ott, C. Mark; Pierson, Duane L.

2003-01-01

An evaluation of the microbial flora from air, water, and surface samples provided a baseline of microbial diversity onboard the International Space Station (ISS) to gain insight into bacterial and fungal contamination during the initial stages of construction and habitation. Using 16S genetic sequencing and rep-PeR, 63 bacterial strains were isolated for identification and fingerprinted for microbial tracking. The use of these molecular tools allowed for the identification of bacteria not previously identified using automated biochemical analysis and provided a clear indication of the source of several ISS contaminants. Fungal and bacterial data acquired during monitoring do not suggest there is a current microbial hazard to the spacecraft, nor does any trend indicate a potential health risk. Previous spacecraft environmental analysis indicated that microbial contamination will increase with time and require continued surveillance.
Spectral induced polarization and electrodic potential monitoring of microbially mediated iron sulfide transformations

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

Hubbard, Susan; Personna, Y.R.; Ntarlagiannis, D.

2008-02-15

Stimulated sulfate-reduction is a bioremediation technique utilized for the sequestration of heavy metals in the subsurface.We performed laboratory column experiments to investigate the geoelectrical response of iron sulfide transformations by Desulfo vibriovulgaris. Two geoelectrical methods, (1) spectral induced polarization (SIP), and (2) electrodic potential measurements, were investigated. Aqueous geochemistry (sulfate, lactate, sulfide, and acetate), observations of precipitates (identified from electron microscopy as iron sulfide), and electrodic potentials on bisulfide ion (HS) sensitive silver-silver chloride (Ag-AgCl) electrodes (630 mV) were diagnostic of induced transitions between an aerobic iron sulfide forming conditions and aerobic conditions promoting iron sulfide dissolution. The SIP datamore » showed 10m rad anomalies during iron sulfide mineralization accompanying microbial activity under an anaerobic transition. These anomalies disappeared during iron sulfide dissolution under the subsequent aerobic transition. SIP model parameters based on a Cole-Cole relaxation model of the polarization at the mineral-fluid interface were converted to (1) estimated biomineral surface area to pore volume (Sp), and (2) an equivalent polarizable sphere diameter (d) controlling the relaxation time. The temporal variation in these model parameters is consistent with filling and emptying of pores by iron sulfide biofilms, as the system transitions between anaerobic (pore filling) and aerobic (pore emptying) conditions. The results suggest that combined SIP and electrodic potential measurements might be used to monitor spatiotemporal variability in microbial iron sulfide transformations in the field.« less
Nutrient gradients in a granular activated carbon biofilter drives bacterial community organization and dynamics.

PubMed

Boon, Nico; Pycke, Benny F G; Marzorati, Massimo; Hammes, Frederik

2011-12-01

The quality of drinking water is ensured by hygienic barriers and filtration steps, such as ozonation and granular activated carbon (GAC) filtration. Apart from adsorption, GAC filtration involves microbial processes that remove biodegradable organic carbon from the ozonated ground or surface water and ensures biological stability of the treated water. In this study, microbial community dynamics in were monitored during the start-up and maturation of an undisturbed pilot-scale GAC filter at 4 depths (10, 45, 80 and 115 cm) over a period of 6 months. New ecological tools, based on 16S rRNA gene-DGGE, were correlated to filter performance and microbial activity and showed that the microbial gradients developing in the filter was of importance. At 10 cm from the top, receiving the freshly ozonated water with the highest concentration of nutrients, the microbial community dynamics were minimal and the species richness remained low. However, the GAC samples at 80-115 cm showed a 2-3 times higher species richness than the 10-45 cm samples. The highest biomass densities were observed at 45-80 cm, which corresponded with maximum removal of dissolved and assimilable organic carbon. Furthermore, the start-up period was clearly distinguishable using the Lorenz analysis, as after 80 days, the microbial community shifted to an apparent steady-state condition with increased evenness. This study showed that GAC biofilter performance is not necessarily correlated to biomass concentration, but rather that an elevated functionality can be the result of increased microbial community richness, evenness and dynamics. Copyright Â© 2011 Elsevier Ltd. All rights reserved.
Complex electrical monitoring of biopolymer and iron mineral precipitation for microbial enhanced hydrocarbon recovery

NASA Astrophysics Data System (ADS)

Wu, Y.; Hubbard, C. G.; Dong, W.; Hubbard, S. S.

2011-12-01

Microbially enhanced hydrocarbon recovery (MEHR) mechanisms are expected to be impacted by processes and properties that occur over a wide range of scales, ranging from surface interactions and microbial metabolism at the submicron scale to changes in wettability and pore geometry at the pore scale to geological heterogeneities at the petroleum reservoir scale. To eventually ensure successful, production-scale implementation of laboratory-developed MEHR procedures under field conditions, it is necessary to develop approaches that can remotely monitor and accurately predict the complex microbially-facilitated transformations that are expected to occur during MEHR treatments in reservoirs (such as the evolution of redox profiles, oil viscosity or matrix porosity/permeability modifications). Our initial studies are focused on laboratory experiments to assess the geophysical signatures of MEHR-induced biogeochemical transformations, with an ultimate goal of using these approaches to monitor field treatments. Here, we explore the electrical signatures of two MEHR processes that are designed to produce end-products that will plug high permeability zones in reservoirs and thus enhance sweep efficiency. The MEHR experiments to induce biopolymers (in this case dextran) and iron mineral precipitates were conducted using flow-through columns. Leuconostoc mesenteroides, a facultative anaerobe, known to produce dextran from sucrose was used in the biopolymer experiments. Paused injection of sucrose, following inoculation and initial microbial attachment, was carried out on daily basis, allowing enough time for dextran production to occur based on batch experiment observations. Electrical data were collected on daily basis and fluid samples were extracted from the column for characterization. Changes in electrical signal were not observed during initial microbial inoculation. Increase of electrical resistivity and decrease of electrical phase response were observed during the experiment and is correlated with the accumulation of dextran in the column. The changes of the electrical signals are interpreted to be due to surface masking of sand grains by dextran that reduces polarizable surface area of the sand grains. A second experiment was conducted to evaluate the sensitivity of electrical geophysical methods to iron mineral precipitation as an alternative plugging mechanism. Although anaerobic iron oxidation coupled with nitrate reduction is the targeted process, aerobic experiments were first conducted as a simplified case without biologically related effects. In this experiment, iron minerals were precipitated through oxidation of ferrous iron by oxygen. Changes in geophysical signals as well as hydraulic permeability across the column were measured. Quantification of iron mineral precipitation was carried out through mass balance and the precipitate morphology and mineralogy were analyzed with optical and electron microscopy and XRD at the end of the experiments. Correlation between geophysical signature and iron mineral precipitation was established and will be used to guide the next experiment, which will focus on microbial facilitated iron oxidation coupled with nitrate reduction under anaerobic conditions.
Microbial and nutritional aspects on the production of live feeds in a fish farming industry.

PubMed

De Donno, A; Lugoli, F; Bagordo, F; Vilella, S; Campa, A; Grassi, T; Guido, M

2010-03-01

Aquaculture is an enterprise in constant development, in particular relating to its effect on the environment and also the quality of its products. It represents a valid alternative to traditional fishing, facing the increasing demand for fish products. To guarantee to the consumer a product of high nutritional, organoleptic and hygienic quality, it is fundamental to monitor every phase of the fish farming industry, isolating the potential risk points. For this reason there has been a rapid evolution of productive technique, particularly in the technology, artificial reproduction and feed sectors. The aim of this research has been the monitoring of the evolution of certain microbial and nutritional quality indexes (total microbial counts and lipid analysis on suspensions of Rotifers and Artemia, used as live feed) in the larval phase of the productive cycle of the farm raised fish, in an intensive system. The study has shown an increment in the total microbial counts in the fish farming industry within the production of Rotifers and Artemia, more evident in the suspensions of Rotifers. In addition the study has demonstrated that the maintenance phase, in the enrichment protocol, can reduce the EPA and DHA content. The results confirm the importance of microbial and nutritional control of the live feeds before they get supplied to fish larvae.
Impact of the reusing of food manufacturing wastewater for irrigation in a closed system on the microbiological quality of the food crops.

PubMed

Beneduce, Luciano; Gatta, Giuseppe; Bevilacqua, Antonio; Libutti, Angela; Tarantino, Emanuele; Bellucci, Micol; Troiano, Eleonora; Spano, Giuseppe

2017-11-02

In order to evaluate if the reuse of food industry treated wastewater is compatible for irrigation of food crops, without increased health risk, in the present study a cropping system, in which ground water and treated wastewater were used for irrigation of tomato and broccoli, during consecutive crop seasons was monitored. Water, crop environment and final products were monitored for microbial indicators and pathogenic bacteria, by conventional and molecular methods. The microbial quality of the irrigation waters influenced sporadically the presence of microbial indicators in soil. No water sample was found positive for pathogenic bacteria, independently from the source. Salmonella spp. and Listeria monocytogenes were detected in soil samples, independently from the irrigation water source. No pathogen was found to contaminate tomato plants, while Listeria monocytogenes and E. coli O157:H7 were detected on broccoli plant, but when final produce were harvested, no pathogen was detected on edible part. The level of microbial indicators and detection of pathogenic bacteria in field and plant was not dependent upon wastewater used. Our results, suggest that reuse of food industry wastewater for irrigation of agricultural crop can be applied without significant increase of potential health risk related to microbial quality. Copyright © 2017 Elsevier B.V. All rights reserved.
[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, Paenibacillus, Bacillales, Clostridiales were vital species for microbial consortia F1 and F2 decomposing rice straw.
Yeast Based 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 yeast based sensors have been developed as analytical tools. Yeasts are known as facultative anaerobes. Facultative anaerobes can survive in both aerobic and anaerobic conditions. The yeast based sensor consisted of a DO electrode and an immobilized omnivorous yeast. In yeast based sensor development, many kinds of yeast have been employed by applying their characteristics to adapt to the analyte. For example, Trichosporon cutaneum was used to estimate organic pollution in industrial wastewater. Yeast based sensors are suitable for online control of biochemical processes and for environmental monitoring. In this review, principles and applications of yeast based sensors are summarized.
Water Quality Monitoring in Developing Countries; Can Microbial Fuel Cells be the Answer?

PubMed Central

Chouler, Jon; Di Lorenzo, Mirella

2015-01-01

The provision of safe water and adequate sanitation in developing countries is a must. A range of chemical and biological methods are currently used to ensure the safety of water for consumption. These methods however suffer from high costs, complexity of use and inability to function onsite and in real time. The microbial fuel cell (MFC) technology has great potential for the rapid and simple testing of the quality of water sources. MFCs have the advantages of high simplicity and possibility for onsite and real time monitoring. Depending on the choice of manufacturing materials, this technology can also be highly cost effective. This review covers the state-of-the-art research on MFC sensors for water quality monitoring, and explores enabling factors for their use in developing countries. PMID:26193327
Water Quality Monitoring in Developing Countries; Can Microbial Fuel Cells be the Answer?

PubMed

Chouler, Jon; Di Lorenzo, Mirella

2015-07-16

The provision of safe water and adequate sanitation in developing countries is a must. A range of chemical and biological methods are currently used to ensure the safety of water for consumption. These methods however suffer from high costs, complexity of use and inability to function onsite and in real time. The microbial fuel cell (MFC) technology has great potential for the rapid and simple testing of the quality of water sources. MFCs have the advantages of high simplicity and possibility for onsite and real time monitoring. Depending on the choice of manufacturing materials, this technology can also be highly cost effective. This review covers the state-of-the-art research on MFC sensors for water quality monitoring, and explores enabling factors for their use in developing countries.
Microbial Burden Approach : New Monitoring Approach for Measuring Microbial Burden

NASA Technical Reports Server (NTRS)

Venkateswaran, Kasthuri; Vaishampayan, Parag; Barmatz, Martin

2013-01-01

Advantages of new approach for differentiating live cells/ spores from dead cells/spores. Four examples of Salmonella outbreaks leading to costly destruction of dairy products. List of possible collaboration activities between JPL and other industries (for future discussion). Limitations of traditional microbial monitoring approaches. Introduction to new approach for rapid measurement of viable (live) bacterial cells/spores and its areas of application. Detailed example for determining live spores using new approach (similar procedure for determining live cells). JPL has developed a patented approach for measuring amount of live and dead cells/spores. This novel "molecular" method takes less than 5 to 7 hrs. compared to the seven days required using conventional techniques. Conventional "molecular" techniques can not discriminate live cells/spores among dead cells/spores. The JPL-developed novel method eliminates false positive results obtained from conventional "molecular" techniques that lead to unnecessary delay in the processing and to unnecessary destruction of food products.
Monitoring biodiversity in libraries: a pilot study and perspectives for indoor air quality.

PubMed

Valeriani, F; Cianfanelli, C; Gianfranceschi, G; Santucci, S; Romano Spica, V; Mucci, N

2017-09-01

Indoor Air Quality (IAQ) in libraries is influenced by the presence of specific factors which can impact on both paper storage as well as people health. Microclimatic conditions induce and support a biodiversity pattern involving environmental and anthropic microorganisms. We used a multidisciplinary monitoring model to characterize microflora biodiversity by Next Generation Sequencing (NGS). Biodiversity indexes were adapted to evaluate anthropic vs environmental pollution by combining Shannon mean index (H), species representativeness (E H ), human/environmental pollution ratio (SA) to better characterize the NGS output and acquire synthetic information on Indoor Air Microbial Biodiversity (IAMB). Results indicate a frequently low microbial load (IGCM/m 3 < 1000) characterized by different species (n = 102), including several cellulose metabolizing bacteria. Workers and visitors appeared a relevant source of microbial contamination. Air biodiversity assayed by NGS seems a promising marker for studying IAQ.
Biofilm formation and control in a simulated spacecraft water system - Two-year results

NASA Technical Reports Server (NTRS)

Schultz, John R.; Taylor, Robert D.; Flanagan, David T.; Carr, Sandra E.; Bruce, Rebekah J.; Svoboda, Judy V.; Huls, M. H.; Sauer, Richard L.; Pierson, Duane L.

1991-01-01

The ability of iodine to maintain microbial water quality in a simulated spacecraft water system is being studied. An iodine level of about 2.0 mg/L is maintained by passing ultrapure influent water through an iodinated ion exchange resin. Six liters are withdrawn daily and the chemical and microbial quality of the water is monitored regularly. Stainless steel coupons used to monitor biofilm formation are being analyzed by culture methods, epifluorescence microscopy, and scanning electron microscopy. Results from the first two years of operation show a single episode of high bacterial colony counts in the iodinated system. This growth was apparently controlled by replacing the iodinated ion exchange resin. Scanning electron microscopy indicates that the iodine has limited but not completely eliminated the formation of biofilm during the first two years of operation. Significant microbial contamination has been present continuously in a parallel noniodinated system since the third week of operation.
Development of transparent microwell arrays for optical monitoring and dissection of microbial communities

DOE PAGES

Halsted, Michelle; Wilmoth, Jared L.; Briggs, Paige A.; ...

2016-09-29

Microbial communities are incredibly complex systems that dramatically and ubiquitously influence our lives. They help to shape our climate and environment, impact agriculture, drive business, and have a tremendous bearing on healthcare and physical security. Spatial confinement, as well as local variations in physical and chemical properties, affects development and interactions within microbial communities that occupy critical niches in the environment. Recent work has demonstrated the use of silicon based microwell arrays, combined with parylene lift-off techniques, to perform both deterministic and stochastic assembly of microbial communities en masse, enabling the high-throughput screening of microbial communities for their response tomore » growth in confined environments under different conditions. The implementation of a transparent microwell array platform can expand and improve the imaging modalities that can be used to characterize these assembled communities. In this paper, the fabrication and characterization of a next generation transparent microwell array is described. The transparent arrays, comprised of SU-8 patterned on a glass coverslip, retain the ability to use parylene lift-off by integrating a low temperature atomic layer deposition of silicon dioxide into the fabrication process. This silicon dioxide layer prevents adhesion of the parylene material to the patterned SU-8, facilitating dry lift-off, and maintaining the ability to easily assemble microbial communities within the microwells. These transparent microwell arrays can screen numerous community compositions using continuous, high resolution, imaging. Finally, the utility of the design was successfully demonstrated through the stochastic seeding and imaging of green fluorescent protein expressing Escherichia coli using both fluorescence and brightfield microscopies.« less
Microbial Sulfate Reduction Enhances Arsenic Mobility Downstream of Zerovalent-Iron-Based Permeable Reactive Barrier.

PubMed

Kumar, Naresh; Couture, Raoul-Marie; Millot, Romain; Battaglia-Brunet, Fabienne; Rose, Jérôme

2016-07-19

We assessed the potential of zerovalent-iron- (Fe(0)) based permeable reactive barrier (PRB) systems for arsenic (As) remediation in the presence or absence of microbial sulfate reduction. We conducted long-term (200 day) flow-through column experiments to investigate the mechanisms of As transformation and mobility in aquifer sediment (in particular, the PRB downstream linkage). Changes in As speciation in the aqueous phase were monitored continuously. Speciation in the solid phase was determined at the end of the experiment using X-ray absorption near-edge structure (XANES) spectroscopy analysis. We identified thio-As species in solution and AsS in solid phase, which suggests that the As(V) was reduced to As(III) and precipitated as AsS under sulfate-reducing conditions and remained as As(V) under abiotic conditions, even with low redox potential and high Fe(II) content (4.5 mM). Our results suggest that the microbial sulfate reduction plays a key role in the mobilization of As from Fe-rich aquifer sediment under anoxic conditions. Furthermore, they illustrate that the upstream-downstream linkage of PRB affects the speciation and mobility of As in downstream aquifer sediment, where up to 47% of total As initially present in the sediment was leached out in the form of mobile thio-As species.
Gene-Based Detection of Microorganisms in Environmental Samples Using PCR

NASA Technical Reports Server (NTRS)

Glass, John I.; Lefkowitz, Elliot J.; Cassell, Gail H.; Wechser, Mark; Taylor, Theresa B.; Albin, Michael; Paszko-Kolva, Christine; Roman, Monsi C.

1997-01-01

Contaminating microorganisms pose a serious potential risk to the crew's well being and water system integrity aboard the International Space Station (ISS). We are developing a gene-based microbial monitor that functions by replicating specific segments of DNA as much as 10(exp 12) x. Thus a single molecule of DNA can be replicated to detectable levels, and the kinetics of that molecule's accumulation can be used to determine the original concentration of specific microorganisms in a sample. Referred to as the polymerase chain reaction (PCR), this enzymatic amplification of specific segments of the DNA or RNA from contaminating microbes offers the promise of rapid, sensitive, quantitative detection and identification of bacteria, fungi, viruses, and parasites. We envision a small instrument capable of assaying an ISS water sample for 48 different microbes in a 24 hour period. We will report on both the developments in the chemistry necessary for the PCR assays to detect microbial contaminants in ISS water, and on progress towards the miniaturization and automation of the instrumentation.
Micro CSI: A Microbial Citizen Science Initiative in Urban Watersheds

EPA Science Inventory

Across the Nation, a number of citizen science efforts have been conducted to monitor water quality. Efforts have included monitoring of bacteriological parameters (E. coli, enterococci, and fecal coliforms) and/or physicochemical parameters (temperature, turbidity, pH, conducti...
Respiration and enzymatic activities as indicators of stabilization of sewage sludge composting.

PubMed

Nikaeen, Mahnaz; Nafez, Amir Hossein; Bina, Bijan; Nabavi, BiBi Fatemeh; Hassanzadeh, Akbar

2015-05-01

The objective of this work was to study the evolution of physico-chemical and microbial parameters in the composting process of sewage sludge (SS) with pruning wastes (PW) in order to compare these parameters with respect to their applicability in the evaluation of organic matter (OM) stabilization. To evaluate the composting process and organic matter stability, different microbial activities were compared during composting of anaerobically digested SS with two volumetric ratios, 1:1 and 3:1 of PW:SS and two aeration techniques including aerated static piles (ASP) and turned windrows (TW). Dehydrogenase activity, fluorescein diacetate hydrolysis, and specific oxygen uptake rate (SOUR) were used as microbial activity indices. These indices were compared with traditional parameters, including temperature, pH, moisture content, organic matter, and C/N ratio. The results showed that the TW method and 3:1 (PW:SS) proportion was superior to the ASP method and 1:1 proportion, since the former accelerate the composting process by catalyzing the OM stabilization. Enzymatic activities and SOUR, which reflect microbial activity, correlated well with temperature fluctuations. Based on these results it appears that SOUR and the enzymatic activities are useful parameters to monitor the stabilization of SS compost. Copyright © 2015 Elsevier Ltd. All rights reserved.
Environmental proteomics reveals early microbial community responses to biostimulation at a uranium- and nitrate-contaminated site.

PubMed

Chourey, Karuna; Nissen, Silke; Vishnivetskaya, Tatiana; Shah, Manesh; Pfiffner, Susan; Hettich, Robert L; Löffler, Frank E

2013-10-01

High-performance MS instrumentation coupled with improved protein extraction techniques enables metaproteomics to identify active members of soil and groundwater microbial communities. Metaproteomics workflows were applied to study the initial responses (i.e. 4 days post treatment) of the indigenous aquifer microbiota to biostimulation with emulsified vegetable oil (EVO) at a uranium-contaminated site. Members of the Betaproteobacteria (i.e. Dechloromonas, Ralstonia, Rhodoferax, Polaromonas, Delftia, Chromobacterium) and the Firmicutes dominated the biostimulated aquifer community. Proteome characterization revealed distinct differences between the microbial biomass collected from groundwater influenced by biostimulation and groundwater collected upgradient of the EVO injection points. In particular, proteins involved in ammonium assimilation, EVO degradation, and polyhydroxybutyrate granule formation were prominent following biostimulation. Interestingly, the atypical NosZ of Dechloromonas spp. was highly abundant, suggesting active nitrous oxide (N2 O) respiration. c-Type cytochromes were barely detected, as was citrate synthase, a biomarker for hexavalent uranium reduction activity, suggesting that uranium reduction has not commenced 4 days post EVO amendment. Environmental metaproteomics identified microbial community responses to biostimulation and elucidated active pathways demonstrating the value of this technique as a monitoring tool and for complementing nucleic acid-based approaches. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Medusa Sea Floor Monitoring System

NASA Technical Reports Server (NTRS)

Flynn, Michael

2004-01-01

The objective of the research described in this poster presentation is to develop technologies to enable fundamental research into understanding the potential for and limits to chemolithoautotrophic life. The Medusa Isosampler (isobaric sampler), for sampling fluids eminating from deep sea hydrothermal vents and cold seep sites analogous to extraterrestrial environments, is described by the presentation. The following instruments are integrated with the isosampler, and also described: in situ flow-through chemical sensor, intrinsic fluorescent-based microbial detector, isotope ratio spectral detector.

Dynamics of Viral Abundance and Diversity in a Sphagnum-Dominated Peatland: Temporal Fluctuations Prevail Over Habitat.

PubMed

Ballaud, Flore; Dufresne, Alexis; Francez, André-Jean; Colombet, Jonathan; Sime-Ngando, Télesphore; Quaiser, Achim

2015-01-01

Viruses impact microbial activity and carbon cycling in various environments, but their diversity and ecological importance in Sphagnum-peatlands are unknown. Abundances of viral particles and prokaryotes were monitored bi-monthly at a fen and a bog at two different layers of the peat surface. Viral particle abundance ranged from 1.7 x 10(6) to 5.6 x 10(8) particles mL(-1), and did not differ between fen and bog but showed seasonal fluctuations. These fluctuations were positively correlated with prokaryote abundance and dissolved organic carbon, and negatively correlated with water-table height and dissolved oxygen. Using shotgun metagenomics we observed a shift in viral diversity between winter/spring and summer/autumn, indicating a seasonal succession of viral communities, mainly driven by weather-related environmental changes. Based on the seasonal asynchrony between viral and microbial diversity, we hypothesize a seasonal shift in the active microbial communities associated with a shift from lysogenic to lytic lifestyles. Our results suggest that temporal variations of environmental conditions rather than current habitat differences control the dynamics of virus-host interactions in Sphagnum-dominated peatlands.
Rapid classification of hairtail fish and pork freshness using an electronic nose based on the PCA method.

PubMed

Tian, Xiu-Ying; Cai, Qiang; Zhang, Yong-Ming

2012-01-01

We report a method for building a simple and reproducible electronic nose based on commercially available metal oxide sensors (MOS) to monitor the freshness of hairtail fish and pork stored at 15, 10, and 5 °C. After assembly in the laboratory, the proposed product was tested by a manufacturer. Sample delivery was based on the dynamic headspace method, and two features were extracted from the transient response of each sensor using an unsupervised principal component analysis (PCA) method. The compensation method and pattern recognition based on PCA are discussed in the current paper. PCA compensation can be used for all storage temperatures, however, pattern recognition differs according to storage conditions. Total volatile basic nitrogen (TVBN) and aerobic bacterial counts of the samples were measured simultaneously with the standard indicators of hairtail fish and pork freshness. The PCA models based on TVBN and aerobic bacterial counts were used to classify hairtail fish samples as "fresh" (TVBN ≤ 25 g and microbial counts ≤ 10(6) cfu/g) or "spoiled" (TVBN ≥ 25 g and microbial counts ≥ 10(6) cfu/g) and pork samples also as "fresh" (TVBN ≤ 15 g and microbial counts ≤ 10(6) cfu/g) or "spoiled" (TVBN ≥ 15 g and microbial counts ≥ 10(6) cfu/g). Good correlation coefficients between the responses of the electronic nose and the TVBN and aerobic bacterial counts of the samples were obtained. For hairtail fish, correlation coefficients were 0.97 and 0.91, and for pork, correlation coefficients were 0.81 and 0.88, respectively. Through laboratory simulation and field application, we were able to determine that the electronic nose could help ensure the shelf life of hairtail fish and pork, especially when an instrument is needed to take measurements rapidly. The results also showed that the electronic nose could analyze the process and level of spoilage for hairtail fish and pork.
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.
Innovative biological approaches for monitoring and improving water quality

PubMed Central

Aracic, Sanja; Manna, Sam; Petrovski, Steve; Wiltshire, Jennifer L.; Mann, Gülay; Franks, Ashley E.

2015-01-01

Water quality is largely influenced by the abundance and diversity of indigenous microbes present within an aquatic environment. Physical, chemical and biological contaminants from anthropogenic activities can accumulate in aquatic systems causing detrimental ecological consequences. Approaches exploiting microbial processes are now being utilized for the detection, and removal or reduction of contaminants. Contaminants can be identified and quantified in situ using microbial whole-cell biosensors, negating the need for water samples to be tested off-site. Similarly, the innate biodegradative processes can be enhanced through manipulation of the composition and/or function of the indigenous microbial communities present within the contaminated environments. Biological contaminants, such as detrimental/pathogenic bacteria, can be specifically targeted and reduced in number using bacteriophages. This mini-review discusses the potential application of whole-cell microbial biosensors for the detection of contaminants, the exploitation of microbial biodegradative processes for environmental restoration and the manipulation of microbial communities using phages. PMID:26322034
Microbial Diversity and Structure Are Drivers of the Biological Barrier Effect against Listeria monocytogenes in Soil

PubMed Central

Vivant, Anne-Laure; Garmyn, Dominique; Maron, Pierre-Alain; Nowak, Virginie; Piveteau, Pascal

2013-01-01

Understanding the ecology of pathogenic organisms is important in order to monitor their transmission in the environment and the related health hazards. We investigated the relationship between soil microbial diversity and the barrier effect against Listeria monocytogenes invasion. By using a dilution-to-extinction approach, we analysed the consequence of eroding microbial diversity on L. monocytogenes population dynamics under standardised conditions of abiotic parameters and microbial abundance in soil microcosms. We demonstrated that highly diverse soil microbial communities act as a biological barrier against L. monocytogenes invasion and that phylogenetic composition of the community also has to be considered. This suggests that erosion of diversity may have damaging effects regarding circulation of pathogenic microorganisms in the environment. PMID:24116193
Field-Integrated Studies of Long-Term Sustainability of Chromium Bioreduction at Hanford 100H Site

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

Long, Philip E.

2006-06-01

The objectives of the project are to investigate coupled hydraulic, geochemical, and microbial conditions, and to determine the critical biogeochemical parameters necessary to maximize the extent of Cr(VI) bioreduction and minimize Cr(III) reoxidation in groundwater. Specific goals of the project are as follows: (1) Field testing and monitoring of Cr(VI) bioreduction in ground water and its transformation into insoluble species of Cr(III) at the Hanford 100H site, to develop the optimal strategy of water sampling for chemical, microbial, stable isotope analyses, and noninvasive geophysical monitoring; (2) Bench-scale flow and transport investigations using columns of undisturbed sediments to obtain diffusion andmore » kinetic parameters needed for the development of a numerical model, predictions of Cr(VI) bioreduction, and potential of Cr(III) reoxidation; and (3) Development of a multiphase, multi-component 3D reactive transport model and a code, TOUGHREACT-BIO, to predict coupled biogeochemical-hydrological processes associated with bioremediation, and to calibrate and validate the developed code based on the results of bench-scale and field-scale Cr(VI) biostimulation experiments in ground water at the Hanford Site.« less
Personalizing Protein Nourishment

PubMed Central

DALLAS, DAVID C.; SANCTUARY, MEGAN R.; QU, YUNYAO; KHAJAVI, SHABNAM HAGHIGHAT; VAN ZANDT, ALEXANDRIA E.; DYANDRA, MELISSA; FRESE, STEVEN A.; BARILE, DANIELA; GERMAN, J. BRUCE

2016-01-01

Proteins are not equally digestible—their proteolytic susceptibility varies by their source and processing method. Incomplete digestion increases colonic microbial protein fermentation (putrefaction), which produces toxic metabolites that can induce inflammation in vitro and have been associated with inflammation in vivo. Individual humans differ in protein digestive capacity based on phenotypes, particularly disease states. To avoid putrefaction-induced intestinal inflammation, protein sources and processing methods must be tailored to the consumer’s digestive capacity. This review explores how food processing techniques alter protein digestibility and examines how physiological conditions alter digestive capacity. Possible solutions to improving digestive function or matching low digestive capacity with more digestible protein sources are explored. Beyond the ileal digestibility measurements of protein digestibility, less invasive, quicker and cheaper techniques for monitoring the extent of protein digestion and fermentation are needed to personalize protein nourishment. Biomarkers of protein digestive capacity and efficiency can be identified with the toolsets of peptidomics, metabolomics, microbial sequencing and multiplexed protein analysis of fecal and urine samples. By monitoring individual protein digestive function, the protein component of diets can be tailored via protein source and processing selection to match individual needs to minimize colonic putrefaction and, thus, optimize gut health. PMID:26713355
Geophysical Monitoring of Coupled Microbial and Geochemical Processes During Stimulated Subsurface Bioremediation

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

Williams, Kenneth H.; Kemna, Andreas; Wilkins, Michael J.

2009-08-05

Understanding how microorganisms alter their physical and chemical environment during bioremediation is hindered by our inability to resolve subsurface microbial activity with high spatial resolution. Here we demonstrate the use of a minimally invasive geophysical technique to monitor stimulated microbial activity during acetate amendment in an aquifer near Rifle, Colorado. During electrical induced polarization (IP) measurements, spatiotemporal variations in the phase response between imposed electric current and the resultant electric field correlated with changes in groundwater geochemistry accompanying stimulated iron and sulfate reduction and sulfide mineral precipitation. The magnitude of the phase response varied with measurement frequency (0.125 and 1more » Hz) andwasdependent upon the dominant metabolic process. The spectral effect was corroborated using a biostimulated column experiment containing Rifle sediments and groundwater. Fluids and sediments recovered from regions exhibiting an anomalous phase response were enriched in Fe(II), dissolved sulfide, and cell-associated FeS nanoparticles. The accumulation of mineral precipitates and electroactive ions altered the ability of pore fluids to conduct electrical charge, accounting for the anomalous IP response and revealing the usefulness of multifrequency IP measurements for monitoring mineralogical and geochemical changes accompanying stimulated subsurface bioremediation.« less
Water quality and microbial diversity in cisterns from semiarid areas in Brazil.

PubMed

Alves, Fellipe; Köchling, Thorsten; Luz, Julio; Santos, Sylvana Melo; Gavazza, Savia

2014-09-01

Harvesting rainwater is a common practice worldwide, particularly in areas with no access to a public water supply or insufficient groundwater reserves. More than two million people living in semiarid regions of Brazil consume rainwater stored in cisterns, and little information is available regarding the water quality. Despite the initial good quality of the rainwater, its harvest and storage can introduce contaminants that must be eliminated before consumption. To evaluate the influence of handling, cistern age and precipitation on the quality of harvested rainwater, we monitored seven cisterns in the semiarid Brazilian Northeast over 4 years. Microbial and physicochemical parameters were monitored once a month, and denaturant gradient gel electrophoresis (DGGE) was performed at the end of the monitoring period. Coliform bacteria were detected in 100% of samples, while Escherichia coli were observed in 73.8%. The alkalinity and conductivity were the highest for the recently built cisterns due to the dissolution of construction materials. The DGGE of the 16S r DNA did not reveal the presence of E. coli. Instead, DGGE bands sequencing indicated that species primarily affiliated with Alphaproteobacteria were present in all cisterns, indicating the presence of microbial ecosystems capable of purifying and stabilizing the stored rainwater.
Microbial trophic interactions and mcrA gene expression in monitoring of anaerobic digesters.

PubMed

Alvarado, Alejandra; Montañez-Hernández, Lilia E; Palacio-Molina, Sandra L; Oropeza-Navarro, Ricardo; Luévanos-Escareño, Miriam P; Balagurusamy, Nagamani

2014-01-01

Anaerobic digestion (AD) is a biological process where different trophic groups of microorganisms break down biodegradable organic materials in the absence of oxygen. A wide range of AD technologies is being used to convert livestock manure, municipal and industrial wastewaters, and solid organic wastes into biogas. AD gains importance not only because of its relevance in waste treatment but also because of the recovery of carbon in the form of methane, which is a renewable energy and is used to generate electricity and heat. Despite the advances on the engineering and design of new bioreactors for AD, the microbiology component always poses challenges. Microbiology of AD processes is complicated as the efficiency of the process depends on the interactions of various trophic groups involved. Due to the complex interdependence of microbial activities for the functionality of the anaerobic bioreactors, the genetic expression of mcrA, which encodes a key enzyme in methane formation, is proposed as a parameter to monitor the process performance in real time. This review evaluates the current knowledge on microbial groups, their interactions, and their relationship to the performance of anaerobic biodigesters with a focus on using mcrA gene expression as a tool to monitor the process.
Bioremediation of diesel oil in a co-contaminated soil by bioaugmentation with a microbial formula tailored with native strains selected for heavy metals resistance.

PubMed

Alisi, Chiara; Musella, Rosario; Tasso, Flavia; Ubaldi, Carla; Manzo, Sonia; Cremisini, Carlo; Sprocati, Anna Rosa

2009-04-01

The aim of the work is to assess the feasibility of bioremediation of a soil, containing heavy metals and spiked with diesel oil (DO), through a bioaugmentation strategy based on the use of a microbial formula tailored with selected native strains. The soil originated from the metallurgic area of Bagnoli (Naples, Italy). The formula, named ENEA-LAM, combines ten bacterial strains selected for multiple resistance to heavy metals among the native microbial community. The biodegradation process of diesel oil was assessed in biometer flasks by monitoring the following parameters: DO composition by GC-MS, CO2 evolution rate, microbial load and composition of the community by T-RFLP, physiological profile in Biolog ECOplates and ecotoxicity of the system. The application of this microbial formula allowed to obtain, in the presence of heavy metals, the complete degradation of n-C(12-20), the total disappearance of phenantrene, a 60% reduction of isoprenoids and an overall reduction of about 75% of the total diesel hydrocarbons in 42 days. Concurrently with the increase of metabolic activity at community level and the microbial load, the gradual abatement of the ecotoxicity was observed. The T-RFLP analysis highlighted that most of the ENEA-LAM strains survived and some minor native strains, undetectable in the soil at the beginning of the experiment, developed. Such a bioaugmentation approach allows the newly established microbial community to strike a balance between the introduced and the naturally present microorganisms. The results indicate that the use of a tailored microbial formula may efficiently facilitate and speed up the bioremediation of matrices co-contaminated with hydrocarbons and heavy metals. The study represents the first step for the scale up of the system and should be verified at a larger scale. In this view, this bioaugmentation strategy may contribute to overcome a critical bottleneck of the bioremediation technology.
Geophysical methods for monitoring soil stabilization processes

NASA Astrophysics Data System (ADS)

Saneiyan, Sina; Ntarlagiannis, Dimitrios; Werkema, D. Dale; Ustra, Andréa

2018-01-01

Soil stabilization involves methods used to turn unconsolidated and unstable soil into a stiffer, consolidated medium that could support engineered structures, alter permeability, change subsurface flow, or immobilize contamination through mineral precipitation. Among the variety of available methods carbonate precipitation is a very promising one, especially when it is being induced through common soil borne microbes (MICP - microbial induced carbonate precipitation). Such microbial mediated precipitation has the added benefit of not harming the environment as other methods can be environmentally detrimental. Carbonate precipitation, typically in the form of calcite, is a naturally occurring process that can be manipulated to deliver the expected soil strengthening results or permeability changes. This study investigates the ability of spectral induced polarization and shear-wave velocity for monitoring calcite driven soil strengthening processes. The results support the use of these geophysical methods as soil strengthening characterization and long term monitoring tools, which is a requirement for viable soil stabilization projects. Both tested methods are sensitive to calcite precipitation, with SIP offering additional information related to long term stability of precipitated carbonate. Carbonate precipitation has been confirmed with direct methods, such as direct sampling and scanning electron microscopy (SEM). This study advances our understanding of soil strengthening processes and permeability alterations, and is a crucial step for the use of geophysical methods as monitoring tools in microbial induced soil alterations through carbonate precipitation.
Dynamics of microbial community composition and function during in-situ bioremediation of a uranium-contaminated aquifer

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

Nostrand, J.D. Van; Wu, L.; Wu, W.M.

2010-08-15

A pilot-scale system was established to examine the feasibility of in situ U(VI) immobilization at a highly contaminated aquifer (U.S. DOE Integrated Field Research Challenge site, Oak Ridge, TN). Ethanol was injected intermittently as an electron donor to stimulate microbial U(VI) reduction, and U(VI) concentrations fell to below the Environmental Protection Agency drinking water standard (0.03 mg liter{sup -1}). Microbial communities from three monitoring wells were examined during active U(VI) reduction and maintenance phases with GeoChip, a high-density, comprehensive functional gene array. The overall microbial community structure exhibited a considerable shift over the remediation phases examined. GeoChip-based analysis revealed thatmore » Fe(III)-reducing bacterial (FeRB), nitrate-reducing bacterial (NRB), and sulfate-reducing bacterial (SRB) functional populations reached their highest levels during the active U(VI) reduction phase (days 137 to 370), in which denitrification and Fe(III) and sulfate reduction occurred sequentially. A gradual decrease in these functional populations occurred when reduction reactions stabilized, suggesting that these functional populations could play an important role in both active U(VI) reduction and maintenance of the stability of reduced U(IV). These results suggest that addition of electron donors stimulated the microbial community to create biogeochemical conditions favorable to U(VI) reduction and prevent the reduced U(IV) from reoxidation and that functional FeRB, SRB, and NRB populations within this system played key roles in this process.« less
The microbial community at laguna Figueroa, Baja California Mexico: From miles to microns

NASA Astrophysics Data System (ADS)

Stolz, John F.

1985-12-01

Laguna Figueroa is a lagoonal complex on the Pacific coast of the Baja California penisula 200 km south of the Mexican-United States border. The hypersaline lagoon is 16 km long and 2 3 km wide with a salt marsh and evaporite flat and is separated from the ocean by a barrier dune and beach. At the salt marsh-evaporite flat interface a stratified microbial community dominated byMicrocoleus chthonoplastes is depositing laminated sediments. Similar stratiform deposits with associated microbial mat communities have been found in cherts of the Fig Tree Group, South Africa which are 3.4 GE in age. Heavy rains in the winters of 1978 1979 and 1979 1980 flooded the evaporite flat with 1 3 meters of meteoric water and buried the laminated sediment under 5 10 cm of siliciclastic and clay sediment. These flooding events had a dramatic effect on the composition of the mat community. TheMicrocoleus dominated community, with species ofChloroflexus sp. and anEctothiorhodospira-like filamentous purple phototroph, disappeared leaving a community dominated by the purple phototrophsChromatium sp. andThiocapsa sp. Recolonization of the surface by species of the cyanobacteriaOscillatoria sp. andSpirulina sp. preceded the return of theMicrocoleus community. Field conditions were monitored by ground based observations and supplemented with LandSat and Skylab imagery. The microbial community was studied with light microscopy and transmission electron microscopy. The change in dominating microbial species was correlated with the episodes of flooding.
Dynamics of Microbial Community Composition and Function during In Situ Bioremediation of a Uranium-Contaminated Aquifer▿‡

PubMed Central

Van Nostrand, Joy D.; Wu, Liyou; Wu, Wei-Min; Huang, Zhijian; Gentry, Terry J.; Deng, Ye; Carley, Jack; Carroll, Sue; He, Zhili; Gu, Baohua; Luo, Jian; Criddle, Craig S.; Watson, David B.; Jardine, Philip M.; Marsh, Terence L.; Tiedje, James M.; Hazen, Terry C.; Zhou, Jizhong

2011-01-01

A pilot-scale system was established to examine the feasibility of in situ U(VI) immobilization at a highly contaminated aquifer (U.S. DOE Integrated Field Research Challenge site, Oak Ridge, TN). Ethanol was injected intermittently as an electron donor to stimulate microbial U(VI) reduction, and U(VI) concentrations fell to below the Environmental Protection Agency drinking water standard (0.03 mg liter−1). Microbial communities from three monitoring wells were examined during active U(VI) reduction and maintenance phases with GeoChip, a high-density, comprehensive functional gene array. The overall microbial community structure exhibited a considerable shift over the remediation phases examined. GeoChip-based analysis revealed that Fe(III)-reducing bacterial (FeRB), nitrate-reducing bacterial (NRB), and sulfate-reducing bacterial (SRB) functional populations reached their highest levels during the active U(VI) reduction phase (days 137 to 370), in which denitrification and Fe(III) and sulfate reduction occurred sequentially. A gradual decrease in these functional populations occurred when reduction reactions stabilized, suggesting that these functional populations could play an important role in both active U(VI) reduction and maintenance of the stability of reduced U(IV). These results suggest that addition of electron donors stimulated the microbial community to create biogeochemical conditions favorable to U(VI) reduction and prevent the reduced U(IV) from reoxidation and that functional FeRB, SRB, and NRB populations within this system played key roles in this process. PMID:21498771
Cellulose digestion in primitive hexapods: Effect of ingested antibiotics on gut microbial populations and gut cellulase levels in the firebrat,Thermobia domestica (Zygentoma, Lepismatidae).

PubMed

Treves, D S; Martin, M M

1994-08-01

Antibiotic feeding studies were conducted on the firebrat,Thermobia domestica (Zygentoma, Lepismatidae) to determine if the insect's gut cellulases were of insect or microbial origin. Firebrats were fed diets containing either nystatin, metronidazole, streptomycin, tetracycline, or an antibiotic cocktail consisting of all four antibiotics, and then their gut microbial populations and gut cellulase levels were monitored and compared with the gut microbial populations and gut cellulase levels in firebrats feeding on antibiotic-free diets. Each antibiotic significantly reduced the firebrat's gut micro-flora. Nystatin reduced the firebrat's viable gut fungi by 89%. Tetracycline and the antibiotic cocktail reduced the firebrat's viable gut bacteria by 81% and 67%, respectively, and metronidazole, streptomycin, tetracycline, and the antibiotic cocktail reduced the firebrat's total gut flora by 35%, 32%, 55%, and 64%, respectively. Although antibiotics significantly reduced the firebrat's viable and total gut flora, gut cellulase levels in firebrats fed antibiotics were not significantly different from those in firebrats on an antibiotic-free diet. Furthermore, microbial populations in the firebrat's gut decreased significantly over time, even in firebrats feeding on the antibiotic-free diet, without corresponding decreases in gut cellulase levels. Based on this evidence, we conclude that the gut cellulases of firebrats are of insect origin. This conclusion implies that symbiont-independent cellulose digestion is a primitive trait in insects and that symbiont-mediated cellulose digestion is a derived condition.
A QRM Discussion of Microbial Contamination of Non-sterile Drug Products, Using FDA and EMA Warning Letters Recorded between 2008 and 2016.

PubMed

Santos, Ana M C; Doria, Mara S; Meirinhos-Soares, Luís; Almeida, António J; Menezes, José C

2018-01-01

Microbial quality control of non-sterile drug products has been a concern to regulatory agencies and the pharmaceutical industry since the 1960s. Despite being an old challenge to companies, microbial contamination still affects a high number of manufacturers of non-sterile products. Consequences go well beyond the obvious direct costs related to batch rejections or product recalls, as human lives and a company's reputation are significantly impacted if such events occur. To better manage risk and establish effective mitigation strategies, it is necessary to understand the microbial hazards involved in non-sterile drug products manufacturing, be able to evaluate their potential impact on final product quality, and apply mitigation actions. Herein we discuss the most likely root causes involved in microbial contaminations referenced in warning letters issued by US health authorities and non-compliance reports issued by European health authorities over a period of several years. The quality risk management tools proposed were applied to the data gathered from those databases, and a generic risk ranking was provided based on a panel of non-sterile drug product manufacturers that was assembled and given the opportunity to perform the risk assessments. That panel identified gaps and defined potential mitigation actions, based on their own experience of potential risks expected for their processes. Major findings clearly indicate that the manufacturers affected by the warning letters should focus their attention on process improvements and microbial control strategies, especially those related to microbial analysis and raw material quality control. Additionally, the WLs considered frequently referred to failures in quality-related issues, which indicates that the quality commitment should be reinforced at most companies to avoid microbiological contaminations. LAY ABSTRACT: Microbial contamination of drug products affects the quality of non-sterile drug products produced by numerous manufacturers, representing a major risk to patients. It is necessary to understand the microbial hazards involved in the manufacturing process and evaluate their impact on final product quality so that effective prevention strategies can be implemented. A risk-based classification of most likely root causes for microbial contamination found in the warning letters issued by the US Food and Drug Administration and the European Medicines Agency is proposed. To validate the likely root causes extracted from the warning letters, a subject matter expert panel made of several manufacturers was formed and consulted. A quality risk management approach to assess microbiological contamination of non-sterile drug products is proposed for the identification of microbial hazards involved in the manufacturing process. To enable ranking of microbial contamination risks, quality risk management metrics related to criticality and overall risk were applied. The results showed that manufacturers of non-sterile drug products should improve their microbial control strategy, with special attention to quality controls of raw materials, primary containers, and closures. Besides that, they should invest in a more robust quality system and culture. As a start, manufacturers may consider investigating their specific microbiological risks, adressing their sites' own microbial ecology, type of manufacturing processes, and dosage form characteristics, as these may lead to increased contamination risks. Authorities should allow and enforce innovative, more comprehensive, and more effective approaches to in-process contamination monitoring and controls. © PDA, Inc. 2018.
Metaproteomics Reveals Functional Shifts in Microbial and Human Proteins During Infant Gut Colonization Case

DOE PAGES

Young, Jacque C.; Pan, Chongle; Adams, Rachel M.; ...

2015-01-01

The microbial colonization of the human gastrointestinal tract plays an important role in establishing health and homeostasis. However, the time-dependent functional signatures of microbial and human proteins during early colonization of the gut have yet to be determined. Thus, we employed shotgun proteomics to simultaneously monitor microbial and human proteins in fecal samples from a preterm infant during the first month of life. Microbial community complexity and functions increased over time, with compositional changes that were consistent with previous metagenomic and rRNA gene data indicating three distinct colonization phases. Overall microbial community functions were established relatively early in development andmore » remained stable. Human proteins detected included those responsible for epithelial barrier function and antimicrobial activity. Some neutrophil-derived proteins increased in abundance early in the study period, suggesting activation of the innate immune system. Moreover, abundances of cytoskeletal and mucin proteins increased later in the time course, suggestive of subsequent adjustment to the increased microbial load. Our study provides the first snapshot of coordinated human and microbial protein expression in the infant gut during early development.« less
Mapping and determinism of soil microbial community distribution across an agricultural landscape

PubMed Central

Constancias, Florentin; Terrat, Sébastien; Saby, Nicolas P A; Horrigue, Walid; Villerd, Jean; Guillemin, Jean-Philippe; Biju-Duval, Luc; Nowak, Virginie; Dequiedt, Samuel; Ranjard, Lionel; Chemidlin Prévost-Bouré, Nicolas

2015-01-01

Despite the relevance of landscape, regarding the spatial patterning of microbial communities and the relative influence of environmental parameters versus human activities, few investigations have been conducted at this scale. Here, we used a systematic grid to characterize the distribution of soil microbial communities at 278 sites across a monitored agricultural landscape of 13 km². Molecular microbial biomass was estimated by soil DNA recovery and bacterial diversity by 16S rRNA gene pyrosequencing. Geostatistics provided the first maps of microbial community at this scale and revealed a heterogeneous but spatially structured distribution of microbial biomass and diversity with patches of several hundreds of meters. Variance partitioning revealed that both microbial abundance and bacterial diversity distribution were highly dependent of soil properties and land use (total variance explained ranged between 55% and 78%). Microbial biomass and bacterial richness distributions were mainly explained by soil pH and texture whereas bacterial evenness distribution was mainly related to land management. Bacterial diversity (richness, evenness, and Shannon index) was positively influenced by cropping intensity and especially by soil tillage, resulting in spots of low microbial diversity in soils under forest management. Spatial descriptors also explained a small but significant portion of the microbial distribution suggesting that landscape configuration also shapes microbial biomass and bacterial diversity. PMID:25833770
Inferring Microbial Interactions in the Gut of the Hong Kong Whipping Frog (Polypedates megacephalus) and a Validation Using Probiotics

PubMed Central

Weng, Francis Cheng-Hsuan; Shaw, Grace Tzun-Wen; Weng, Chieh-Yin; Yang, Yi-Ju; Wang, Daryi

2017-01-01

The concerted activity of intestinal microbes is crucial to the health and development of their host organisms. Investigation of microbial interactions in the gut should deepen our understanding of how these micro-ecosystems function. Due to advances in Next Generation Sequencing (NGS) technologies, various bioinformatic strategies have been proposed to investigate these microbial interactions. However, due to the complexity of the intestinal microbial community and difficulties in monitoring their interactions, at present there is a gap between the theory and biological application. In order to construct and validate microbial relationships, we first induce a community shift from simple to complex by manipulating artificial hibernation (AH) in the treefrog Polypedates megacephalus. To monitor community growth and microbial interactions, we further performed a time-course screen using a 16S rRNA amplicon approach and a Lotka-Volterra model. Lotka-Volterra models, also known as predator–prey equations, predict the dynamics of microbial communities and how communities are structured and sustained. An interaction network of gut microbiota at the genus level in the treefrog was constructed using Metagenomic Microbial Interaction Simulator (MetaMIS) package. The interaction network obtained had 1,568 commensal, 1,737 amensal, 3,777 mutual, and 3,232 competitive relationships, e.g., Lactococcus garvieae has a commensal relationship with Corynebacterium variabile. To validate the interacting relationships, the gut microbe composition was analyzed after probiotic trials using single strain (L. garvieae, C. variabile, and Bacillus coagulans, respectively) and a combination of L. garvieae, C. variabile, and B. coagulans, because of the cooperative relationship among their respective genera identified in the interaction network. After a 2 week trial, we found via 16S rRNA amplicon analysis that the combination of cooperative microbes yielded significantly higher probiotic concentrations than single strains, and the immune response (interleukin-10 expression) also significantly changed in a manner consistent with improved probiotic effects. By taking advantage of microbial community shift from simple to complex, we thus constructed a reliable microbial interaction network, and validated it using probiotic strains as a test system. PMID:28424669

Metagenomes of Microbial Communities in Arsenic- and Pathogen-Contaminated Well and Surface Water from Bangladesh

PubMed Central

Layton, Alice C.; Chauhan, Archana; Williams, Daniel E.; Mailloux, Brian; Knappett, Peter S. K.; Ferguson, Andrew S.; McKay, Larry D.; Alam, M. Jahangir; Matin Ahmed, Kazi; van Geen, Alexander

2014-01-01

The contamination of drinking water from both arsenic and microbial pathogens occurs in Bangladesh. A general metagenomic survey of well water and surface water provided information on the types of pathogens present and may help elucidate arsenic metabolic pathways and potential assay targets for monitoring surface-to-ground water pathogen transport. PMID:25414497
Profiling In Situ Microbial Community Structure with an Amplification Microarray

PubMed Central

Knickerbocker, Christopher; Bryant, Lexi; Golova, Julia; Wiles, Cory; Williams, Kenneth H.; Peacock, Aaron D.; Long, Philip E.

2013-01-01

The objectives of this study were to unify amplification, labeling, and microarray hybridization chemistries within a single, closed microfluidic chamber (an amplification microarray) and verify technology performance on a series of groundwater samples from an in situ field experiment designed to compare U(VI) mobility under conditions of various alkalinities (as HCO3−) during stimulated microbial activity accompanying acetate amendment. Analytical limits of detection were between 2 and 200 cell equivalents of purified DNA. Amplification microarray signatures were well correlated with 16S rRNA-targeted quantitative PCR results and hybridization microarray signatures. The succession of the microbial community was evident with and consistent between the two microarray platforms. Amplification microarray analysis of acetate-treated groundwater showed elevated levels of iron-reducing bacteria (Flexibacter, Geobacter, Rhodoferax, and Shewanella) relative to the average background profile, as expected. Identical molecular signatures were evident in the transect treated with acetate plus NaHCO3, but at much lower signal intensities and with a much more rapid decline (to nondetection). Azoarcus, Thaurea, and Methylobacterium were responsive in the acetate-only transect but not in the presence of bicarbonate. Observed differences in microbial community composition or response to bicarbonate amendment likely had an effect on measured rates of U reduction, with higher rates probable in the part of the field experiment that was amended with bicarbonate. The simplification in microarray-based work flow is a significant technological advance toward entirely closed-amplicon microarray-based tests and is generally extensible to any number of environmental monitoring applications. PMID:23160129
Uncertainty in monitoring E. coli concentrations in streams and stormwater runoff

USDA-ARS?s Scientific Manuscript database

Microbial contamination in surface waters is a substantial public health concern throughout the world. Contamination is typically identified by, and restoration plans predicated upon, fecal indicator bacteria such as E. coli. Thus, monitoring of E. coli concentrations is critical to evaluate curre...
Seasonal dynamics of microbial community composition and function in oak canopy and open grassland soils

USGS Publications Warehouse

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

2006-01-01

Soil microbial communities are closely associated with aboveground plant communities, with multiple potential drivers of this relationship. Plants can affect available soil carbon, temperature, and water content, which each have the potential to affect microbial community composition and function. These same variables change seasonally, and thus plant control on microbial community composition may be modulated or overshadowed by annual climatic patterns. We examined microbial community composition, C cycling processes, and environmental data in California annual grassland soils from beneath oak canopies and in open grassland areas to distinguish factors controlling microbial community composition and function seasonally and in association with the two plant overstory communities. Every 3 months for up to 2 years, we monitored microbial community composition using phospholipid fatty acid (PLFA) analysis, microbial biomass, respiration rates, microbial enzyme activities, and the activity of microbial groups using isotope labeling of PLFA biomarkers (13C-PLFA) . Distinct microbial communities were associated with oak canopy soils and open grassland soils and microbial communities displayed seasonal patterns from year to year. The effects of plant species and seasonal climate on microbial community composition were similar in magnitude. In this Mediterranean ecosystem, plant control of microbial community composition was primarily due to effects on soil water content, whereas the changes in microbial community composition seasonally appeared to be due, in large part, to soil temperature. Available soil carbon was not a significant control on microbial community composition. Microbial community composition (PLFA) and 13C-PLFA ordination values were strongly related to intra-annual variability in soil enzyme activities and soil respiration, but microbial biomass was not. In this Mediterranean climate, soil microclimate appeared to be the master variable controlling microbial community composition and function. ?? 2006 Springer Science+Business Media, Inc.
On-line detection of Escherichia coli intrusion in a pilot-scale drinking water distribution system.

PubMed

Ikonen, Jenni; Pitkänen, Tarja; Kosse, Pascal; Ciszek, Robert; Kolehmainen, Mikko; Miettinen, Ilkka T

2017-08-01

Improvements in microbial drinking water quality monitoring are needed for the better control of drinking water distribution systems and for public health protection. Conventional water quality monitoring programmes are not always able to detect a microbial contamination of drinking water. In the drinking water production chain, in addition to the vulnerability of source waters, the distribution networks are prone to contamination. In this study, a pilot-scale drinking-water distribution network with an on-line monitoring system was utilized for detecting bacterial intrusion. During the experimental Escherichia coli intrusions, the contaminant was measured by applying a set of on-line sensors for electric conductivity (EC), pH, temperature (T), turbidity, UV-absorbance at 254 nm (UVAS SC) and with a device for particle counting. Monitored parameters were compared with the measured E. coli counts using the integral calculations of the detected peaks. EC measurement gave the strongest signal compared with the measured baseline during the E. coli intrusion. Integral calculations showed that the peaks in the EC, pH, T, turbidity and UVAS SC data were detected corresponding to the time predicted. However, the pH and temperature peaks detected were barely above the measured baseline and could easily be mixed with the background noise. The results indicate that on-line monitoring can be utilized for the rapid detection of microbial contaminants in the drinking water distribution system although the peak interpretation has to be performed carefully to avoid being mixed up with normal variations in the measurement data. Copyright © 2017 Elsevier Ltd. All rights reserved.
Seasonality in ocean microbial communities.

PubMed

Giovannoni, Stephen J; Vergin, Kevin L

2012-02-10

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

PubMed

Bárcenas-Moreno, Gema; García-Orenes, Fuensanta; Mataix-Solera, Jorge; Mataix-Beneyto, Jorge

2016-12-15

Plant community influence on microbial response after fire has been studied in a Sierra Nevada National Park area affected by a wildfire in 2005. Two different plant communities adapted to different altitudes were selected to analyse possible differences on soil microbial recolonisation process after fire, in oak forest and high mountain shrub communities. Microbial abundance, activity and community composition were monitored to evaluate medium-term changes. Microbial abundance was studied by mean of microbial biomass carbon and plate count methods; microbial activity was analysed by microbial respiration and bacterial growth while microbial community composition was determined by analysing phospholipid fatty acid pattern. Under unburnt conditions oak forest showed higher nutrient content, pH and microbial abundance and activity values than the high mountain shrubs community. Different parameters studied showed different trends with time, highlighting important changes in microbial community composition in high mountain shrubs from first sampling to the second one. Post-fire recolonisation process was different depending on plant community studied. Highlighting fungal response and microbial activity were stimulated in burnt high mountain shrubs community whilst it was negatively affected in oak forest. Fire induced changes in oak forest were almost neutralized 20months after the fire, while high mountain shrubs community still showed fire-induced changes at the end of the study. Copyright Â© 2016 Elsevier B.V. All rights reserved.
Microbial Community Structure of an Alluvial Aquifer Treated to Encourage Microbial Induced Calcite Precipitation

NASA Astrophysics Data System (ADS)

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

2017-12-01

An oligotrophic aquifer in the Colorado River floodplain (Rifle, CO) was treated with molasses and urea to encourage microbial induced calcite precipitation (MICP). This would stabilize the soil mass by reducing porosity and strengthening the mineral fabric. Over the course of a 15-day treatment period, microbial biomass was collected from monitoring well groundwater for DNA extraction and sequencing. Bromide, a conservative tracer, was co-injected and subsequently detected in downgradient wells, confirming effective nutrient delivery. Conductivity increased during the injection regime and an overall decrease in pH was observed. Groundwater chemistry showed a marked increase in ammonia, suggesting urea hydrolysis - a process catalyzed by the enzyme urease - the primary enzyme implicated in MICP. Additionally, soluble iron was detected, suggesting a general increase in microbial activity; possibly as iron-reducing bacteria changed insoluble ferric oxide to soluble ferrous hydroxide in the anoxic aquifer. DNA sequencing of the 16S rRNA gene confirmed the presence of iron reducing bacteria, including Shewanella and Desulfuromonadales. Generally, a decrease in microbial community diversity was observed when pre-injection community taxa were compared with post-injection community taxa. Phyla indicative of anoxic aquifers were represented in accordance with previous literature at the Rifle site. Linear discriminant analysis showed significant differences in representative phyla over the course of the injection series. Geophysical monitoring of the site further suggested changes that could be due to MICP. Induced polarization increased the phase shift in the primary treated area, in agreement with laboratory experiments. Cross-hole seismic testing confirmed that the shear wave velocities increased in the treated soil mass, implying the soil matrix became more stable. Future investigations will help elucidate the viability and efficacy of MICP treatment in changing microbial community structure, and the functional attributes associated with community change, so that physical strengthening of soils by microbial action can be accomplished.
Environmental Monitoring as Part of Life Support for the Crew Habitat for Lunar and Mars Missions

NASA Technical Reports Server (NTRS)

Jan, Darrell L.

2010-01-01

Like other crewed space missions, future missions to the moon and Mars will have requirements for monitoring the chemical and microbial status of the crew habitat. Monitoring the crew habitat becomes more critical in such long term missions. This paper will describe the state of technology development for environmental monitoring of lunar lander and lunar outpost missions, and the state of plans for future missions.
Investigating the relationship between peat biogeochemistry and above-ground plant phenology with remote sensing along a gradient of permafrost thaw.

NASA Astrophysics Data System (ADS)

Garnello, A.; Dye, D. G.; Bogle, R.; Hough, M.; Raab, N.; Dominguez, S.; Rich, V. I.; Crill, P. M.; Saleska, S. R.

2016-12-01

Global climate models predict a 50% - 85% decrease in permafrost area in northern regions by 2100 due to increased temperature and precipitation variability, potentially releasing large stores of carbon as greenhouse gases (GHG) due to microbial activity. Linking belowground biogeochemical processes with observable above ground plant dynamics would greatly increase the ability to track and model GHG emissions from permafrost thaw, but current research has yet to satisfactorily develop this link. We hypothesized that seasonal patterns in peatland biogeochemistry manifests itself as observable plant phenology due to the tight coupling resulting from plant-microbial interactions. We tested this by using an automated, tower-based camera to acquire daily composite (red, green, blue) and near infrared (NIR) images of a thawing permafrost peatland site near Abisko, Sweden. The images encompassed a range of exposures which were merged into high-dynamic-range images, a novel application to remote sensing of plant phenology. The 2016 growing season camera images are accompanied by mid-to-late season CH4 and CO2 fluxes measured from soil collars, and by early-mid-late season peat core samples of the composition of microbial communities and key metabolic genes, and of the organic matter and trace gas composition of peat porewater. Additionally, nearby automated gas flux chambers measured sub-hourly fluxes of CO2 and CH4 from the peat, which will also be incorporated into analysis of relationships between seasonal camera-derived vegetation indices and gas fluxes from habitats with different vegetation types. While remote sensing is a proven method in observing plant phenology, this technology has yet to be combined with soil biogeochemical and microbial community data in regions of permafrost thaw. Establishing a high resolution phenology monitoring system linked to soil biogeochemical processes in subarctic peatlands will advance the understanding of how observable patterns in plant phenology can be used to monitor permafrost thaw and ecosystem carbon cycling.
Effect Of Spaceflight On Microbial Gene Expression And Virulence: Preliminary Results From Microbe Payload Flown On-Board STS-115

NASA Technical Reports Server (NTRS)

Wilson, J. W.; HonerzuBentrup, K,; Schurr, M. J.; Buchanan, K.; Morici, L.; Hammond, T.; Allen, P.; Baker, C.; Ott, C. M.; Nelman-Gonzalez M.;

2007-01-01

Human presence in space, whether permanent or temporary, is accompanied by the presence of microbes. However, the extent of microbial changes in response to spaceflight conditions and the corresponding changes to infectious disease risk is unclear. Previous studies have indicated that spaceflight weakens the immune system in humans and animals. In addition, preflight and in-flight monitoring of the International Space Station (ISS) and other spacecraft indicates the presence of opportunistic pathogens and the potential of obligate pathogens. Altered antibiotic resistance of microbes in flight has also been shown. As astronauts and cosmonauts live for longer periods in a closed environment, especially one using recycled water and air, there is an increased risk to crewmembers of infectious disease events occurring in-flight. Therefore, understanding how the space environment affects microorganisms and their disease potential is critically important for spaceflight missions and requires further study. The goal of this flight experiment, operationally called MICROBE, is to utilize three model microbial pathogens, Salmonella typhimurium, Pseudomonas aeruginosa, and Candida albicans to examine the global effects of spaceflight on microbial gene expression and virulence attributes. Specifically, the aims are (1) to perform microarray-mediated gene expression profiling of S. typhimurium, P. aeruginosa, and C. albicans, in response to spaceflight in comparison to ground controls and (2) to determine the effect of spaceflight on the virulence potential of these microorganisms immediately following their return from spaceflight using murine models. The model microorganisms were selected as they have been isolated from preflight or in-flight monitoring, represent different degrees of pathogenic behavior, are well characterized, and have sequenced genomes with available microarrays. In particular, extensive studies of S. typhimurium by the Principal Investigator, Dr. Nickerson, using ground-based analog systems demonstrate important changes in the genotypic, phenotypic, and virulence characteristics of this pathogen resulting from exposure to a flight-like environment (i.e. modeled microgravity).

Influence of red mud on soil microbial communities: Application and comprehensive evaluation of the Biolog EcoPlate approach as a tool in soil microbiological studies.

PubMed

Feigl, Viktória; Ujaczki, Éva; Vaszita, Emese; Molnár, Mónika

2017-10-01

Red mud can be applied as soil ameliorant to acidic, sandy and micronutrient deficient soils. There are still knowledge gaps regarding the effects of red mud on the soil microbial community. The Biolog EcoPlate technique is a promising tool for community level physiological profiling. This study presents a detailed evaluation of Biolog EcoPlate data from two case studies. In experiment "A" red mud from Ajka (Hungary) was mixed into acidic sandy soil in soil microcosms at 5-50 w/w%. In experiement "B" red mud soil mixture was mixed into low quality subsoil in a field experiment at 5-50 w/w%. According to average well color development, substrate average well color development and substrate richness 5-20% red mud increased the microbial activity of the acidic sandy soil over the short term, but the effect did not last for 10months. Shannon diversity index showed that red mud at up to 20% did not change microbial diversity over the short term, but the diversity decreased by the 10th month. 30-50% red mud had deteriorating effect on the soil microflora. 5-20% red mud soil mixture in the low quality subsoil had a long lasting enhancing effect on the microbial community based on all Biolog EcoPlate parameters. However, 50% red mud soil mixture caused a decrease in diversity and substrate richness. With the Biolog EcoPlate we were able to monitor the changes of the microbial community in red mud affected soils and to assess the amount of red mud and red mud soil mixture applicable for soil treatment in these cases. Copyright © 2017 Elsevier B.V. All rights reserved.
Microbial sensor for drug susceptibility testing of Mycobacterium tuberculosis.

PubMed

Zhang, Z-T; Wang, D-B; Li, C-Y; Deng, J-Y; Zhang, J-B; Bi, L-J; Zhang, X-E

2018-01-01

Drug susceptibility testing (DST) of clinical isolates of Mycobacterium tuberculosis is critical in treating tuberculosis. We demonstrate the possibility of using a microbial sensor to perform DST of M. tuberculosis and shorten the time required for DST. The sensor is made of an oxygen electrode with M. tuberculosis cells attached to its surface. This sensor monitors the residual oxygen consumption of M. tuberculosis cells after treatment with anti-TB drugs with glycerine as a carbon source. In principle, after drug pretreatment for 4-5 days, the response differences between the sensors made of drug-sensitive isolates are distinguishable from the sensors made of drug-resistant isolates. The susceptibility of the M. tuberculosis H37Ra strain, its mutants and 35 clinical isolates to six common anti-TB drugs: rifampicin, isoniazid, streptomycin, ethambutol, levofloxacin and para-aminosalicylic acid were tested using the proposed method. The results agreed well with the gold standard method (LJ) and were determined in significantly less time. The whole procedure takes approximately 11 days and therefore has the potential to inform clinical decisions. To our knowledge, this is the first study that demonstrates the possible application of a dissolved oxygen electrode-based microbial sensor in M. tuberculosis drug resistance testing. This study used the microbial sensor to perform DST of M. tuberculosis and shorten the time required for DST. The overall detection result of the microbial sensor agreed well with that of the conventional LJ proportion method and takes less time than the existing phenotypic methods. In future studies, we will build an O 2 electrode array microbial sensor reactor to enable a high-throughput drug resistance analysis. © 2017 The Authors. Journal of Applied Microbiology published by John Wiley & Sons Ltd on behalf of The Society for Applied Microbiology.
Time-lapse electrical geophysical monitoring of amendment-based biostimulation

USGS Publications Warehouse

Johnson, Timothy C.; Versteeg, Roelof J.; Day-Lewis, Frederick D.; Major, William; Lane, John W.

2015-01-01

Biostimulation is increasingly used to accelerate microbial remediation of recalcitrant groundwater contaminants. Effective application of biostimulation requires successful emplacement of amendment in the contaminant target zone. Verification of remediation performance requires postemplacement assessment and contaminant monitoring. Sampling-based approaches are expensive and provide low-density spatial and temporal information. Time-lapse electrical resistivity tomography (ERT) is an effective geophysical method for determining temporal changes in subsurface electrical conductivity. Because remedial amendments and biostimulation-related biogeochemical processes often change subsurface electrical conductivity, ERT can complement and enhance sampling-based approaches for assessing emplacement and monitoring biostimulation-based remediation.Field studies demonstrating the ability of time-lapse ERT to monitor amendment emplacement and behavior were performed during a biostimulation remediation effort conducted at the Department of Defense Reutilization and Marketing Office (DRMO) Yard, in Brandywine, Maryland, United States. Geochemical fluid sampling was used to calibrate a petrophysical relation in order to predict groundwater indicators of amendment distribution. The petrophysical relations were field validated by comparing predictions to sequestered fluid sample results, thus demonstrating the potential of electrical geophysics for quantitative assessment of amendment-related geochemical properties. Crosshole radar zero-offset profile and borehole geophysical logging were also performed to augment the data set and validate interpretation.In addition to delineating amendment transport in the first 10 months after emplacement, the time-lapse ERT results show later changes in bulk electrical properties interpreted as mineral precipitation. Results support the use of more cost-effective surface-based ERT in conjunction with limited field sampling to improve spatial and temporal monitoring of amendment emplacement and remediation performance.
Preparing for the crewed Mars journey: microbiota dynamics in the confined Mars500 habitat during simulated Mars flight and landing.

PubMed

Schwendner, Petra; Mahnert, Alexander; Koskinen, Kaisa; Moissl-Eichinger, Christine; Barczyk, Simon; Wirth, Reinhard; Berg, Gabriele; Rettberg, Petra

2017-10-04

The Mars500 project was conceived as the first full duration simulation of a crewed return flight to Mars. For 520 days, six crew members lived confined in a specifically designed spacecraft mock-up. The herein described "MIcrobial ecology of Confined Habitats and humAn health" (MICHA) experiment was implemented to acquire comprehensive microbiota data from this unique, confined manned habitat, to retrieve important information on the occurring microbiota dynamics, the microbial load and diversity in the air and on various surfaces. In total, 360 samples from 20 (9 air, 11 surface) locations were taken at 18 time-points and processed by extensive cultivation, PhyloChip and next generation sequencing (NGS) of 16S rRNA gene amplicons. Cultivation assays revealed a Staphylococcus and Bacillus-dominated microbial community on various surfaces, with an average microbial load that did not exceed the allowed limits for ISS in-flight requirements indicating adequate maintenance of the facility. Areas with high human activity were identified as hotspots for microbial accumulation. Despite substantial fluctuation with respect to microbial diversity and abundance throughout the experiment, the location within the facility and the confinement duration were identified as factors significantly shaping the microbial diversity and composition, with the crew representing the main source for microbial dispersal. Opportunistic pathogens, stress-tolerant or potentially mobile element-bearing microorganisms were predicted to be prevalent throughout the confinement, while the overall microbial diversity dropped significantly over time. Our findings clearly indicate that under confined conditions, the community structure remains a highly dynamic system which adapts to the prevailing habitat and micro-conditions. Since a sterile environment is not achievable, these dynamics need to be monitored to avoid spreading of highly resistant or potentially pathogenic microorganisms and a potentially harmful decrease of microbial diversity. If necessary, countermeasures are required, to maintain a healthy, diverse balance of beneficial, neutral and opportunistic pathogenic microorganisms. Our results serve as an important data collection for (i) future risk estimations of crewed space flight, (ii) an optimized design and planning of a spacecraft mission and (iii) for the selection of appropriate microbial monitoring approaches and potential countermeasures, to ensure a microbiologically safe space-flight environment.
Amoeba-related health risk in drinking water systems: could monitoring of amoebae be a complementary approach to current quality control strategies?

PubMed

Codony, Francesc; Pérez, Leonardo Martín; Adrados, Bárbara; Agustí, Gemma; Fittipaldi, Mariana; Morató, Jordi

2012-01-01

Culture-based methods for fecal indicator microorganisms are the standard protocol to assess potential health risk from drinking water systems. However, these traditional fecal indicators are inappropriate surrogates for disinfection-resistant fecal pathogens and the indigenous pathogens that grow in drinking water systems. There is now a range of molecular-based methods, such as quantitative PCR, which allow detection of a variety of pathogens and alternative indicators. Hence, in addition to targeting total Escherichia coli (i.e., dead and alive) for the detection of fecal pollution, various amoebae may be suitable to indicate the potential presence of pathogenic amoeba-resisting microorganisms, such as Legionellae. Therefore, monitoring amoeba levels by quantitative PCR could be a useful tool for directly and indirectly evaluating health risk and could also be a complementary approach to current microbial quality control strategies for drinking water systems.
A novel, optical, on-line bacteria sensor for monitoring drinking water quality

PubMed Central

Højris, Bo; Christensen, Sarah Christine Boesgaard; Albrechtsen, Hans-Jørgen; Smith, Christian; Dahlqvist, Mathis

2016-01-01

Today, microbial drinking water quality is monitored through either time-consuming laboratory methods or indirect on-line measurements. Results are thus either delayed or insufficient to support proactive action. A novel, optical, on-line bacteria sensor with a 10-minute time resolution has been developed. The sensor is based on 3D image recognition, and the obtained pictures are analyzed with algorithms considering 59 quantified image parameters. The sensor counts individual suspended particles and classifies them as either bacteria or abiotic particles. The technology is capable of distinguishing and quantifying bacteria and particles in pure and mixed suspensions, and the quantification correlates with total bacterial counts. Several field applications have demonstrated that the technology can monitor changes in the concentration of bacteria, and is thus well suited for rapid detection of critical conditions such as pollution events in drinking water. PMID:27040142
A novel, optical, on-line bacteria sensor for monitoring drinking water quality.

PubMed

Højris, Bo; Christensen, Sarah Christine Boesgaard; Albrechtsen, Hans-Jørgen; Smith, Christian; Dahlqvist, Mathis

2016-04-04

Today, microbial drinking water quality is monitored through either time-consuming laboratory methods or indirect on-line measurements. Results are thus either delayed or insufficient to support proactive action. A novel, optical, on-line bacteria sensor with a 10-minute time resolution has been developed. The sensor is based on 3D image recognition, and the obtained pictures are analyzed with algorithms considering 59 quantified image parameters. The sensor counts individual suspended particles and classifies them as either bacteria or abiotic particles. The technology is capable of distinguishing and quantifying bacteria and particles in pure and mixed suspensions, and the quantification correlates with total bacterial counts. Several field applications have demonstrated that the technology can monitor changes in the concentration of bacteria, and is thus well suited for rapid detection of critical conditions such as pollution events in drinking water.
Microbial Biogeography on the Legacies of Historical Events in the Arctic Subsurface Sediments

NASA Astrophysics Data System (ADS)

Han, Dukki; Nam, Seung-Il; Hur, Hor-Gil

2017-04-01

The Arctic marine environment consists of various microbial habitats. The niche preference of microbial assemblages in the Arctic Ocean has been surveyed with the modern environmental change by oceanographic traits such as sea-ice dynamics, current circulation, and sedimentation. The North Pacific inflow from the shallow and narrow Bering Strait is highly susceptible to sea-level fluctuations, and thus the water mass exchange mediated by the history of sea-ice between the North Pacific and the Chukchi Sea in the Arctic Ocean. Over geological timescale, the climate change may provide putative evidences for ecological niche for the Arctic microbial assemblages as well as geological records in response to the paleoclimate change. In the present study, the multidisciplinary approach, based on microbiology, geology, and geochemistry, was applied to survey the microbial assemblages in the Arctic subsurface sediments and help further integrate the microbial biogeography and biogeochemical patterns in the Arctic subsurface biosphere. Our results describe microbial assemblages with high-resolution paleoceanographic records in the Chukchi Sea sediment core (ARA02B/01A-GC; 5.4 mbsf) to show the processes that drive microbial biogeographic patterns in the Arctic subsurface sediments. We found microbial habitat preferences closely linked to Holocene paleoclimate records as well as geological, geochemical, and microbiological evidence for the inference of the sulphate-methane transition zone (SMTZ) in the Chukchi Sea. Especially, the vertically distributed predominant populations of Gammaproteobacteria and Marine Group II Euryarchaeota in the ARA02B/01A-GC consistent with the patterns of the known global SMTZs and Holocene sedimentary records, suggesting that in-depth microbiological profiles integrated with geological records may be indirectly useful for reconstructing Arctic paleoclimate changes. In the earliest phase of Mid Holocene in the ARA02B/01A-GC with concentrated crenarchaeol (a unique biomarker for Marine Group I Thaumarchaea), the most abundant archaeal population was Marine Group II Euryarchaeota rather than Marine Group I Thaumarchaea, suggesting that the interpretation of archaeal tetraether lipids in subsurface sediments needs careful consideration for paleoceanography. In conclusion, our findings have important implications for the availability of microbial biogeography in the sedimentary record. The present study offers a deeper understanding of the legacies of historical events during the Holocene and implies that the survey of microbial biogeography may be an appropriate tool to monitor potential effects from the climate change in the Arctic Ocean.
GeoChip-based Analysis of Groundwater Microbial Diversity in Norman Landfill

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

Lu, Zhenmei; He, Zhili; Parisi, Victoria

The Norman Landfill is a closed municipal solid waste landfill located on an alluvium associated with the Canadian River in Norman, Oklahoma. It has operated as a research site since 1994 because it is typical of many closed landfill sites across the U.S. Leachate from the unlined landfill forms a groundwater plume that extends downgradient approximately 250 m from the landfill toward the Canadian River. To investigate the impact of the landfill leachate on the diversity and functional structure of microbial communities, groundwater samples were taken from eight monitoring wells at a depth of 5m, and analyzed using a comprehensivemore » functional gene array covering about 50,000 genes involved in key microbial processes, such as biogeochemical cycling of C, N, P, and S, and bioremediation of organic contaminants and metals. Wells are located within a transect along a presumed flow path with different distances to the center of the leachate plume. Our analyses showed that microbial communities were obviously impacted by the leachate-component from the landfill. The number of genes detected and microbial diversity indices in the center (LF2B) and its closest (MLS35) wells were significantly less than those detected in other more downgradient wells, while no significant changes were observed in the relative abundance (i.e., percentage of each gene category) for most gene categories. However, the microbial community composition or structure of the landfill groundwater did not clearly show a significant correlation with the distance from well LF2B. Burkholderia sp. and Pseudomonas sp. were found to be the dominant microbial populations detected in all wells, while Bradyrhizobium sp. and Ralstonia sp. were dominant populations for seven wells except LF2B. In addition, Mantel test and canonical correspondence analysis (CCA) indicate that pH, sulfate, ammonia nitrogen and dissolved organic carbon (DOC) have significant effects on the microbial community structure. The results suggest that the leachate from unlined landfills significantly impact the structures of groundwater microbial communities, and that more distal wells recover by natural attenuation.« less

Zero-power autonomous buoyancy system controlled by microbial gas production

NASA Astrophysics Data System (ADS)

Wu, Peter K.; Fitzgerald, Lisa A.; Biffinger, Justin C.; Spargo, Barry J.; Houston, Brian H.; Bucaro, Joseph A.; Ringeisen, Bradley R.

2011-05-01

A zero-power ballast control system that could be used to float and submerge a device solely using a gas source was built and tested. This system could be used to convey sensors, data loggers, and communication devices necessary for water quality monitoring and other applications by periodically maneuvering up and down a water column. Operational parameters for the system such as duration of the submerged and buoyant states can be varied according to its design. The gas source can be of any origin, e.g., compressed air, underwater gas vent, gas produced by microbes, etc. The zero-power ballast system was initially tested using a gas pump and further tested using gas produced by Clostridium acetobutylicum. Using microbial gas production as the only source of gas and no electrical power during operation, the system successfully floated and submerged periodically with a period of 30 min for at least 24 h. Together with microbial fuel cells, this system opens up possibilities for underwater monitoring systems that could function indefinitely.
Remote Sensing of Subsurface Microbial Transformations

NASA Astrophysics Data System (ADS)

Williams, K. H.; Ntarlagiannis, D.; Slater, L.; Long, P.; Dohnalkova, A.; Hubbard, S. S.; Banfield, J. F.

2004-12-01

Understanding how microorganisms influence the physical and chemical properties of the subsurface is hindered by our inability to detect microbial dynamics in real time with high spatial resolution. Here we have used non-invasive geophysical methods to monitor biomineralization and related processes during biostimulation at both laboratory and field scales. Alterations in saturated sediment characteristics resulting from microbe-mediated transformations were concomitant with changes in complex resistivity, spontaneous potential, and acoustic wave signatures. Variability in complex resistivity and acoustic wave amplitudes appears tied to the nucleation, growth, and development of nanoparticulate precipitates along grain surfaces and within the pore space. In contrast, time-varying spontaneous potentials appear primarily sensitive to the electrochemical gradients resulting from metabolic pathways, such as iron- and sulfate-reduction. Furthermore, they enable us to track mobile fronts of active respiration that arise due to microbial chemotaxis. In this way, geophysical data may be used to image the distribution of mineral precipitates, biomass, and biogeochemical fronts evolving over time and suggest the ability to remotely monitor contaminated aquifers undergoing bioremediation.
Microbial fuel cells for biosensor applications.

PubMed

Yang, Huijia; Zhou, Minghua; Liu, Mengmeng; Yang, Weilu; Gu, Tingyue

2015-12-01

Microbial fuel cells (MFCs) face major hurdles for real-world applications as power generators with the exception of powering small sensor devices. Despite tremendous improvements made in the last two decades, MFCs are still too expensive to build and operate and their power output is still too small. In view of this, in recently years, intensive researches have been carried out to expand the applications into other areas such as acid and alkali production, bioremediation of aquatic sediments, desalination and biosensors. Unlike power applications, MFC sensors have the immediate prospect to be practical. This review covers the latest developments in various proposed biosensor applications using MFCs including monitoring microbial activity, testing biochemical oxygen demand, detection of toxicants and detection of microbial biofilms that cause biocorrosion.
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.
A Spike Cocktail Approach to Improve Microbial Performance Monitoring for Water Reuse.

PubMed

Zimmerman, Brian D; Korajkic, Asja; Brinkman, Nichole E; Grimm, Ann C; Ashbolt, Nicholas J; Garland, Jay L

Water reuse, via either centralized treatment of traditional wastewater or decentralized treatment and on-site reuse, is becoming an increasingly important element of sustainable water management. Despite advances in waterborne pathogen detection methods, low and highly variable pathogen levels limit their utility for routine evaluation of health risks in water reuse systems. Therefore, there is a need to improve our understanding of the linkage between pathogens and more readily measured process indicators during treatment. This paper describes an approach for constructing spiking experiments to relate the behavior of viral, bacterial, and protozoan pathogens with relevant process indicators. General issues are reviewed, and the spiking protocol is applied as a case study example to improve microbial performance monitoring and health risk evaluation in a water reuse system. This approach provides a foundation for the development of novel approaches to improve real or near-real time performance monitoring of water recycling systems.
Metagenomic applications in environmental monitoring and bioremediation.

PubMed

Techtmann, Stephen M; Hazen, Terry C

2016-10-01

With the rapid advances in sequencing technology, the cost of sequencing has dramatically dropped and the scale of sequencing projects has increased accordingly. This has provided the opportunity for the routine use of sequencing techniques in the monitoring of environmental microbes. While metagenomic applications have been routinely applied to better understand the ecology and diversity of microbes, their use in environmental monitoring and bioremediation is increasingly common. In this review we seek to provide an overview of some of the metagenomic techniques used in environmental systems biology, addressing their application and limitation. We will also provide several recent examples of the application of metagenomics to bioremediation. We discuss examples where microbial communities have been used to predict the presence and extent of contamination, examples of how metagenomics can be used to characterize the process of natural attenuation by unculturable microbes, as well as examples detailing the use of metagenomics to understand the impact of biostimulation on microbial communities.
Mapping and determinism of soil microbial community distribution across an agricultural landscape.

PubMed

Constancias, Florentin; Terrat, Sébastien; Saby, Nicolas P A; Horrigue, Walid; Villerd, Jean; Guillemin, Jean-Philippe; Biju-Duval, Luc; Nowak, Virginie; Dequiedt, Samuel; Ranjard, Lionel; Chemidlin Prévost-Bouré, Nicolas

2015-06-01

Despite the relevance of landscape, regarding the spatial patterning of microbial communities and the relative influence of environmental parameters versus human activities, few investigations have been conducted at this scale. Here, we used a systematic grid to characterize the distribution of soil microbial communities at 278 sites across a monitored agricultural landscape of 13 km². Molecular microbial biomass was estimated by soil DNA recovery and bacterial diversity by 16S rRNA gene pyrosequencing. Geostatistics provided the first maps of microbial community at this scale and revealed a heterogeneous but spatially structured distribution of microbial biomass and diversity with patches of several hundreds of meters. Variance partitioning revealed that both microbial abundance and bacterial diversity distribution were highly dependent of soil properties and land use (total variance explained ranged between 55% and 78%). Microbial biomass and bacterial richness distributions were mainly explained by soil pH and texture whereas bacterial evenness distribution was mainly related to land management. Bacterial diversity (richness, evenness, and Shannon index) was positively influenced by cropping intensity and especially by soil tillage, resulting in spots of low microbial diversity in soils under forest management. Spatial descriptors also explained a small but significant portion of the microbial distribution suggesting that landscape configuration also shapes microbial biomass and bacterial diversity. © 2015 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.
Cost-Effective Live Cell Density Determination of Liquid Cultured Microorganisms.

PubMed

Kutschera, Alexander; Lamb, Jacob J

2018-02-01

Live monitoring of microorganisms growth in liquid medium is a desired parameter for many research fields. A wildly used approach for determining microbial liquid growth quantification is based on light scattering as the result of the physical interaction of light with microbial cells. These measurements are generally achieved using costly table-top instruments; however, a live, reliable, and straight forward instrument constructed using parts that are inexpensive may provide opportunities for many researchers. Here, such an instrument has been constructed and tested. It consists of modular test tube holding chambers, each with a low power monochromatic light-emitting diode, and a monolithic photodiode. A microcontroller connects to all modular chambers to control the diodes, and send the live data to either an LCD screen, or a computer. This work demonstrate that this modular instrument can determine precise cell concentrations for the bacteria Escherichia coli and Pseudomonas syringae pv. tomato DC3000, as well as Saccharomyces cerevisiae yeast.
Linking the development and functioning of a carnivorous pitcher plant's microbial digestive community.

PubMed

Armitage, David W

2017-11-01

Ecosystem development theory predicts that successional turnover in community composition can influence ecosystem functioning. However, tests of this theory in natural systems are made difficult by a lack of replicable and tractable model systems. Using the microbial digestive associates of a carnivorous pitcher plant, I tested hypotheses linking host age-driven microbial community development to host functioning. Monitoring the yearlong development of independent microbial digestive communities in two pitcher plant populations revealed a number of trends in community succession matching theoretical predictions. These included mid-successional peaks in bacterial diversity and metabolic substrate use, predictable and parallel successional trajectories among microbial communities, and convergence giving way to divergence in community composition and carbon substrate use. Bacterial composition, biomass, and diversity positively influenced the rate of prey decomposition, which was in turn positively associated with a host leaf's nitrogen uptake efficiency. Overall digestive performance was greatest during late summer. These results highlight links between community succession and ecosystem functioning and extend succession theory to host-associated microbial communities.
Influence of microbial growth in the redox potential of fermented cucumbers

USDA-ARS?s Scientific Manuscript database

Commonly, pH measurements are used during the production of fermented cucumbers to indirectly monitor growth of lactic acid bacteria (LAB) and acid production. Redox potential (Eh) measurements, which are determined by the flux of electrons in a system, could serve as a more accurate tool to monitor...
INFLUENCE OF EQUINE FECAL CONTAMINATION ON MICROBIAL COMMUNITY STRUCTURE IN A SUB-WATERSHED

EPA Science Inventory

As monitoring of watershed water quality is directly related to proposed uses, it is important for our Naton's water systems that the d4etemrination of and distinction between fecal contamination source is made. The most common water quality monitoring approach is to screen for f...
Water level changes affect carbon turnover and microbial community composition in lake sediments.

PubMed

Weise, Lukas; Ulrich, Andreas; Moreano, Matilde; Gessler, Arthur; Kayler, Zachary E; Steger, Kristin; Zeller, Bernd; Rudolph, Kristin; Knezevic-Jaric, Jelena; Premke, Katrin

2016-05-01

Due to climate change, many lakes in Europe will be subject to higher variability of hydrological characteristics in their littoral zones. These different hydrological regimes might affect the use of allochthonous and autochthonous carbon sources. We used sandy sediment microcosms to examine the effects of different hydrological regimes (wet, desiccating, and wet-desiccation cycles) on carbon turnover. (13)C-labelled particulate organic carbon was used to trace and estimate carbon uptake into bacterial biomass (via phospholipid fatty acids) and respiration. Microbial community changes were monitored by combining DNA- and RNA-based real-time PCR quantification and terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA. The shifting hydrological regimes in the sediment primarily caused two linked microbial effects: changes in the use of available organic carbon and community composition changes. Drying sediments yielded the highest CO2 emission rates, whereas hydrological shifts increased the uptake of allochthonous organic carbon for respiration. T-RFLP patterns demonstrated that only the most extreme hydrological changes induced a significant shift in the active and total bacterial communities. As current scenarios of climate change predict an increase of drought events, frequent variations of the hydrological regimes of many lake littoral zones in central Europe are anticipated. Based on the results of our study, this phenomenon may increase the intensity and amplitude in rates of allochthonous organic carbon uptake and CO2 emissions. © FEMS 2016.
Molecular-based approaches to characterize coastal microbial community and their potential relation to the trophic state of Red Sea

PubMed Central

Ansari, Mohd Ikram; Harb, Moustapha; Jones, Burton; Hong, Pei-Ying

2015-01-01

Molecular-based approaches were used to characterize the coastal microbiota and to elucidate the trophic state of Red Sea. Nutrient content and enterococci numbers were monitored, and used to correlate with the abundance of microbial markers. Microbial source tracking revealed the presence of >1 human-associated Bacteroides spp. at some of the near-shore sampling sites and at a heavily frequented beach. Water samples collected from the beaches had occasional exceedances in enterococci numbers, higher total organic carbon (TOC, 1.48–2.18 mg/L) and nitrogen (TN, 0.15–0.27 mg/L) than that detected in the near-shore waters. Enterococci abundances obtained from next-generation sequencing did not correlate well with the cultured enterococci numbers. The abundance of certain genera, for example Arcobacter, Pseudomonas and unclassified Campylobacterales, was observed to exhibit slight correlation with TOC and TN. Low abundance of functional genes accounting for up to 41 copies/L of each Pseudomonas aeruginosa and Campylobacter coli were detected. Arcobacter butzleri was also detected in abundance ranging from 111 to 238 copies/L. Operational taxonomic units (OTUs) associated with cyanobacteria, Prochlorococcus, Ostreococcus spp. and Gramella were more prevalent in waters that were likely impacted by urban runoffs and recreational activities. These OTUs could potentially serve as quantifiable markers indicative of the water quality. PMID:25758166
Water level changes affect carbon turnover and microbial community composition in lake sediments

PubMed Central

Weise, Lukas; Ulrich, Andreas; Moreano, Matilde; Gessler, Arthur; E. Kayler, Zachary; Steger, Kristin; Zeller, Bernd; Rudolph, Kristin; Knezevic-Jaric, Jelena; Premke, Katrin

2016-01-01

Due to climate change, many lakes in Europe will be subject to higher variability of hydrological characteristics in their littoral zones. These different hydrological regimes might affect the use of allochthonous and autochthonous carbon sources. We used sandy sediment microcosms to examine the effects of different hydrological regimes (wet, desiccating, and wet-desiccation cycles) on carbon turnover. 13C-labelled particulate organic carbon was used to trace and estimate carbon uptake into bacterial biomass (via phospholipid fatty acids) and respiration. Microbial community changes were monitored by combining DNA- and RNA-based real-time PCR quantification and terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA. The shifting hydrological regimes in the sediment primarily caused two linked microbial effects: changes in the use of available organic carbon and community composition changes. Drying sediments yielded the highest CO2 emission rates, whereas hydrological shifts increased the uptake of allochthonous organic carbon for respiration. T-RFLP patterns demonstrated that only the most extreme hydrological changes induced a significant shift in the active and total bacterial communities. As current scenarios of climate change predict an increase of drought events, frequent variations of the hydrological regimes of many lake littoral zones in central Europe are anticipated. Based on the results of our study, this phenomenon may increase the intensity and amplitude in rates of allochthonous organic carbon uptake and CO2 emissions. PMID:26902802
Meeting report: knowledge and gaps in developing microbial criteria for inland recreational waters

USGS Publications Warehouse

Dorevitch, Samuel; Ashbolt, Nicholas J.; Ferguson, Christobel M.; Fujioka, Roger; McGee, Charles D.; Soller, Jeffrey A.; Whitman, Richard L.

2010-01-01

The U.S. Environmental Protection Agency (EPA) has committed to issuing in 2012 new or revised criteria designed to protect the health of those who use surface waters for recreation. For this purpose, the U.S. EPA has been conducting epidemiologic studies to establish relationships between microbial measures of water quality and adverse health outcomes among swimmers. New methods for testing water quality that would provide same-day results will likely be elements of the new criteria. Although the epidemiologic studies upon which the criteria will be based were conducted at Great Lakes and marine beaches, the new water quality criteria may be extended to inland waters (IWs). Similarities and important differences between coastal waters (CWs) and IWs that should be considered when developing criteria for IWs were the focus of an expert workshop. Here, we summarize the state of knowledge and research needed to base IWs microbial criteria on sound science. Two key differences between CWs and IWs are the sources of indicator bacteria, which may modify the relationship between indicator microbes and health risk, and the relationship between indicators and pathogens, which also may vary within IWs. Monitoring using rapid molecular methods will require the standardization and simplification of analytical methods, as well as greater clarity about their interpretation. Research needs for the short term and longer term are described.
Aging of biomixtures: Effects on carbofuran removal and microbial community structure.

PubMed

Castro-Gutiérrez, Víctor; Masís-Mora, Mario; Diez, María Cristina; Tortella, Gonzalo R; Rodríguez-Rodríguez, Carlos E

2017-02-01

The aim of this work was to determine the efficiency of a straw/compost/soil biomixture for pesticide depuration during its aging and continuous use, for a period of over a year, based on its capacity to remove carbofuran (CFN), while simultaneously monitoring the variations in microbial community structure. Successive CFN spikings were applied in the biomixture at 6-week intervals, and the removal efficiency was determined 48 h post-application. Initially, only a discrete degradation performance was observed (9.9%), but one CFN application was sufficient to induce efficient elimination (>88.5%) of the pesticide at subsequent influxes for a period of over 6 months. A statistically significant reduction on CFN removal efficiency after this time was detected, reaching levels similar to the fresh-prepared biomixture (14.8%) at the end of the experiment. Simultaneous DGGE analyses showed only modest changes on microbial community patterns through time for both, bacteria and fungi. The clustering of genetic fingerprints in chronological groups corresponding to significantly different CFN degradation efficiencies indicates that biomixture aging changes not only the composition of microbial communities, but also their suitability to engage in pesticide degradation. Periodic substitution of straw/compost/soil biomixture in biopurification systems or regular provision of easily-degradable organic substrates should be considered to maintain an adequate depuration capacity on this system. Copyright © 2016 Elsevier Ltd. All rights reserved.
Biogeography and organic matter removal shape long-term effects of timber harvesting on forest soil microbial communities.

PubMed

Wilhelm, Roland C; Cardenas, Erick; Maas, Kendra R; Leung, Hilary; McNeil, Larisa; Berch, Shannon; Chapman, William; Hope, Graeme; Kranabetter, J M; Dubé, Stephane; Busse, Matt; Fleming, Robert; Hazlett, Paul; Webster, Kara L; Morris, David; Scott, D Andrew; Mohn, William W

2017-11-01

The growing demand for renewable, carbon-neutral materials and energy is leading to intensified forest land-use. The long-term ecological challenges associated with maintaining soil fertility in managed forests are not yet known, in part due to the complexity of soil microbial communities and the heterogeneity of forest soils. This study determined the long-term effects of timber harvesting, accompanied by varied organic matter (OM) removal, on bacterial and fungal soil populations in 11- to 17-year-old reforested coniferous plantations at 18 sites across North America. Analysis of highly replicated 16 S rRNA gene and ITS region pyrotag libraries and shotgun metagenomes demonstrated consistent changes in microbial communities in harvested plots that included the expansion of desiccation- and heat-tolerant organisms and decline in diversity of ectomycorrhizal fungi. However, the majority of taxa, including the most abundant and cosmopolitan groups, were unaffected by harvesting. Shifts in microbial populations that corresponded to increased temperature and soil dryness were moderated by OM retention, which also selected for sub-populations of fungal decomposers. Biogeographical differences in the distribution of taxa as well as local edaphic and environmental conditions produced substantial variation in the effects of harvesting. This extensive molecular-based investigation of forest soil advances our understanding of forest disturbance and lays the foundation for monitoring long-term impacts of timber harvesting.
Application of atomic force microscopy to microbial surfaces: from reconstituted cell surface layers to living cells.

PubMed

Dufrêne, Y F

2001-02-01

The application of atomic force microscopy (AFM) to probe the ultrastructure and physical properties of microbial cell surfaces is reviewed. The unique capabilities of AFM can be summarized as follows: imaging surface topography with (sub)nanometer lateral resolution; examining biological specimens under physiological conditions; measuring local properties and interaction forces. AFM is being used increasingly for: (i) visualizing the surface ultrastructure of microbial cell surface layers, including bacterial S-layers, purple membranes, porin OmpF crystals and fungal rodlet layers; (ii) monitoring conformational changes of individual membrane proteins; (iii) examining the morphology of bacterial biofilms, (iv) revealing the nanoscale structure of living microbial cells, including fungi, yeasts and bacteria, (v) mapping interaction forces at microbial surfaces, such as van der Waals and electrostatic forces, solvation forces, and steric/bridging forces; and (vi) probing the local mechanical properties of cell surface layers and of single cells.
Monitoring Microbial Mineralization Using Reverse Stable Isotope Labeling Analysis by Mid-Infrared Laser Spectroscopy

PubMed Central

2017-01-01

Assessing the biodegradation of organic compounds is a frequent question in environmental science. Here, we present a sensitive, inexpensive, and simple approach to monitor microbial mineralization using reverse stable isotope labeling analysis (RIL) of dissolved inorganic carbon (DIC). The medium for the biodegradation assay contains regular organic compounds and 13C-labeled DIC with 13C atom fractions (x(13C)DIC) higher than natural abundance (typically 2–50%). The produced CO2 (x(13C) ≈ 1.11%) gradually dilutes the initial x(13C)DIC allowing to quantify microbial mineralization using mass-balance calculations. For 13C-enriched CO2 samples, a newly developed isotope ratio mid-infrared spectrometer was introduced with a precision of x(13C) < 0.006%. As an example for extremely difficult and slowly degradable compounds, CO2 production was close to the theoretical stoichiometry for anaerobic naphthalene degradation by a sulfate-reducing enrichment culture. Furthermore, we could measure the aerobic degradation of dissolved organic carbon (DOC) adsorbed to granular activated carbon in a drinking water production plant, which cannot be labeled with 13C. Thus, the RIL approach can be applied to sensitively monitor biodegradation of various organic compounds under anoxic or oxic conditions. PMID:28903553
Microbial trophic interactions and mcrA gene expression in monitoring of anaerobic digesters

PubMed Central

Alvarado, Alejandra; Montañez-Hernández, Lilia E.; Palacio-Molina, Sandra L.; Oropeza-Navarro, Ricardo; Luévanos-Escareño, Miriam P.; Balagurusamy, Nagamani

2014-01-01

Anaerobic digestion (AD) is a biological process where different trophic groups of microorganisms break down biodegradable organic materials in the absence of oxygen. A wide range of AD technologies is being used to convert livestock manure, municipal and industrial wastewaters, and solid organic wastes into biogas. AD gains importance not only because of its relevance in waste treatment but also because of the recovery of carbon in the form of methane, which is a renewable energy and is used to generate electricity and heat. Despite the advances on the engineering and design of new bioreactors for AD, the microbiology component always poses challenges. Microbiology of AD processes is complicated as the efficiency of the process depends on the interactions of various trophic groups involved. Due to the complex interdependence of microbial activities for the functionality of the anaerobic bioreactors, the genetic expression of mcrA, which encodes a key enzyme in methane formation, is proposed as a parameter to monitor the process performance in real time. This review evaluates the current knowledge on microbial groups, their interactions, and their relationship to the performance of anaerobic biodigesters with a focus on using mcrA gene expression as a tool to monitor the process. PMID:25429286

Implications of altered rainfall and exotic plants on soil microbial communities and carbon biomass

NASA Astrophysics Data System (ADS)

Castro, S.; Lipson, D.; Cleland, E. E.

2016-12-01

Climate and exotic plant disturbances are among the most significant threats to Mediterranean-type ecosystems, compromising their renowned biodiversity and role in the global carbon cycle. Predicted shifts in rainfall patterns have become a particular concern, especially when interactions with other stressors and effects on biogeochemical processes remain poorly understood. To understand the impacts of altered rainfall on belowground dynamics as well as the role of inter- and intra-annual variation and plant community composition, we monitored soil microbial communities under native and exotic plant dominated plots with rainfall manipulation treatments in a semi-arid Mediterranean-type ecosystem. We measured microbial biomass, respiration rates, and community structure across treatments and vegetation types. Soil moisture and dissolved organic carbon were also measured to characterize abiotic soil properties. The soil moisture gradient established by the rainfall treatments had a positive correlation with microbial biomass carbon under native- and exotic-dominated plots but had no effect on respiration rates. A significant reduction in microbial biomass under exotic plants was found in 2013 but not in 2014 and 2015. Substrate-induced respiration values were higher in the exotic-dominated plots during the spring seasons, resulting in a significant interaction between plant community type and season. Bacterial communities showed little variation except in the Proteobacteria phyla, which was lower in exotic plants-dominated plots. Dissolved organic carbon was significantly reduced in exotic-dominated plots by approximately 26% based on average values of all plots throughout. Our results illustrate that rainfall quantity and exotic plants can cause changes in microbial biomass, community composition and respiration rates jeopardizing soil carbon storage. They also reinforce the importance of temporal variability and the need for repeated sampling to correctly interpret environmental changes in semi-arid ecosystems. We conclude that to improve predictions of the implications of global stressors on biogeochemical cycles in semi-arid ecosystems, there is a need to incorporate microbial data with the understanding that it is highly dependent on temporal dynamics and plant community.
A bioenergetics-kinetics coupled modeling study on subsurface microbial metabolism in a field biostimulation experiment

NASA Astrophysics Data System (ADS)

Jin, Q.; Zheng, Z.; Zhu, C.

2006-12-01

Microorganisms in nature conserve energy by catalyzing various geochemical reactions. To build a quantitative relationship between geochemical conditions and metabolic rates, we propose a bioenergetics-kinetics coupled modeling approach. This approach describes microbial community as a metabolic network, i.e., fermenting microbes degrade organic substrates while aerobic respirer, nitrate reducer, metal reducer, sulfate reducer, and methanogen consume the fermentation products. It quantifies the control of substrate availability and biological energy conservation on the metabolic rates using thermodynamically consistent rate laws. We applied this simulation approach to study the progress of microbial metabolism during a field biostimulation experiment conducted in Oak Ridge, Tennessee. In the experiment, ethanol was injected into a monitoring well and groundwater was sampled to monitor changes in the chemistry. With time, concentrations of ethanol and SO42- decreased while those of NH4+, Fe2+, and Mn2+ increased. The simulation results fitted well to the observation, indicating simultaneous ethanol degradation and terminal electron accepting processes. The rates of aerobic respiration and denitrification were mainly controlled by substrate concentrations while those of ethanol degradation, sulfate reduction, and methanogenesis were controlled dominantly by the energy availability. The simulation results suggested two different microbial growth statuses in the subsurface. For the functional groups with significant growth, variations with time in substrate concentrations demonstrated a typical S curve. For the groups without significant growth, initial decreases in substrate concentrations were linear with time. Injecting substrates followed by monitoring environmental chemistry therefore provides a convenient approach to characterize microbial growth in the subsurface where methods for direct observation are currently unavailable. This research was funded by the NABIR program, DOE, under grant No. DE-FG02-04ER63740 to CZ. We thank J. Istok, David Watson, and Philip Jardine for their help. The views and opinions of authors expressed herein do not necessarily state or reflect those of the DOE.
Rapid spectrofluorometric screening of poly-hydroxyalkanoate-producing bacteria from microbial mats.

PubMed

Berlanga, Mercedes; Montero, M T; Fernández-Borrell, Jordi; Guerrero, Ricardo

2006-06-01

Microbial mat ecosystems are characterized by both seasonal and diel fluctuations in several physicochemical variables, so that resident microorganisms must frequently adapt to the changing conditions of their environment. It has been pointed out that, under stress conditions, bacterial cells with higher contents of poly-hydroxyalkanoates (PHA) survive longer than those with lower PHA content. In the present study, PHA-producing strains from Ebro Delta microbial mats were selected using the Nile red dying technique and the relative accumulation of PHA was monitored during further laboratory cultivation. The number of heterotrophic isolates in trypticase soy agar (TSA) was ca. 107 colony-forming units/g microbial mat. Of these, 100 randomly chosen colonies were replicated on mineral salt agar limited in nitrogen, and Nile red was added to the medium to detect PHA. Orange fluorescence, produced upon binding of the dye to polymer granules in the cell, was detected in approximately 10% of the replicated heterotrophic isolates. The kinetics of PHA accumulation in Pseudomonas putida, and P. oleovorans were compared with those of several of the environmental isolates spectrofluorometry. PHA accumulation, measured as relative fluorescence intensity, resulted in a steady-state concentration after 48 h of incubation in all strains assayed. At 72 h, the maximum fluorescence intensity of each strain incubated with glucose and fructose was usually similar. MAT-28 strain accumulated more PHA than the other isolates. The results show that data obtained from environmental isolates can highly improve studies based on modeling-simulation programs, and that microbial mats constitute an excellent source for the isolation of PHA-producing strains with industrial applications.
Ferrous iron- and ammonium-rich diffuse vents support habitat-specific communities in a shallow hydrothermal field off the Basiluzzo Islet (Aeolian Volcanic Archipelago).

PubMed

Bortoluzzi, G; Romeo, T; La Cono, V; La Spada, G; Smedile, F; Esposito, V; Sabatino, G; Di Bella, M; Canese, S; Scotti, G; Bo, M; Giuliano, L; Jones, D; Golyshin, P N; Yakimov, M M; Andaloro, F

2017-09-01

Ammonium- and Fe(II)-rich fluid flows, known from deep-sea hydrothermal systems, have been extensively studied in the last decades and are considered as sites with high microbial diversity and activity. Their shallow-submarine counterparts, despite their easier accessibility, have so far been under-investigated, and as a consequence, much less is known about microbial communities inhabiting these ecosystems. A field of shallow expulsion of hydrothermal fluids has been discovered at depths of 170-400 meters off the base of the Basiluzzo Islet (Aeolian Volcanic Archipelago, Southern Tyrrhenian Sea). This area consists predominantly of both actively diffusing and inactive 1-3 meters-high structures in the form of vertical pinnacles, steeples and mounds covered by a thick orange to brown crust deposits hosting rich benthic fauna. Integrated morphological, mineralogical, and geochemical analyses revealed that, above all, these crusts are formed by ferrihydrite-type Fe 3+ oxyhydroxides. Two cruises in 2013 allowed us to monitor and sampled this novel ecosystem, certainly interesting in terms of shallow-water iron-rich site. The main objective of this work was to characterize the composition of extant communities of iron microbial mats in relation to the environmental setting and the observed patterns of macrofaunal colonization. We demonstrated that iron-rich deposits contain complex and stratified microbial communities with a high proportion of prokaryotes akin to ammonium- and iron-oxidizing chemoautotrophs, belonging to Thaumarchaeota, Nitrospira, and Zetaproteobacteria. Colonizers of iron-rich mounds, while composed of the common macrobenthic grazers, predators, filter-feeders, and tube-dwellers with no representatives of vent endemic fauna, differed from the surrounding populations. Thus, it is very likely that reduced electron donors (Fe 2+ and NH 4 + ) are important energy sources in supporting primary production in microbial mats, which form a habitat-specific trophic base of the whole Basiluzzo hydrothermal ecosystem, including macrobenthic fauna. © 2017 John Wiley & Sons Ltd.
New perspective on functional capabilities of microbiome associated with spacecraft assembly facilities

NASA Astrophysics Data System (ADS)

Vaishampayan, Parag

2016-07-01

In compliance with Planetary Protection policy, NASA monitors the total microbial burden of spacecraft and associated environments as a means for minimizing forward contamination. Despite numerous characterizations of microbial populations in spacecraft assembly cleanrooms, understanding the metabolic traits responsible for their persistence and survival remains a significant challenge. The principal objective of this study is to establish functional traits by exploring the entire gene content (metagenome) of the cleanroom microbial community. DNA-based techniques are incapable of distinguishing viable microorganisms from dead microbial cells in samples. Consequently, metagenomic analyses based on total environmental DNA extracts do not render a meaningful understanding of the metabolic and/or functional characteristics of living microorganisms in cleanrooms. A molecular viability marker was applied to samples collected from a cleanroom facility, and subsequent metagenomic sequencing experiments showed considerable differences between the resulting viable-only and total microbiomes. Nevertheless, analyses of sequence abundance suggested that the viable microbiome was influenced by both the human microbiome and the ambient ecosystem external to the facility, which resulted in a complex community profile. Also detected were the first viral signatures ever retrieved from a cleanroom facility: the genomes of human cyclovirus 7078A and Propionibacterium phage P14.4. We also wanted to evaluate if the strict cleaning and decontamination procedures selectively favor survival and growth of hardy microrganisms, such as pathogens. Three geographically distinct cleanrooms were sampled during the assembly of three NASA spacecraft: Dawn, Phoenix, and Mars Science Laboratory. Potential pathogens and their corresponding virulence factors were present in all the samples. Decreased microbial and pathogenic diversity during spacecraft assembly, compared to before and after, indicates that decontamination and preventative measures were effective and well implemented. The findings presented here, as well as the innovative methods that enabled their discovery, promise to have profound implications for the design and interpretation of ongoing and future studies in cleanrooms, indoor environments, and potential future human missions to Mars.
Evaluation and control of microbial and chemical contamination in dialysis water plants of Italian nephrology wards.

PubMed

Totaro, M; Casini, B; Valentini, P; Miccoli, M; Giorgi, S; Porretta, A; Privitera, G; Lopalco, P L; Baggiani, A

2017-10-01

Patients receiving haemodialysis are exposed to a large volume of dialysis fluid. The Italian Society of Nephrology (ISN) has published guidelines and microbial quality standards on dialysis water (DW) and solutions to ensure patient safety. To identify microbial and chemical hazards, and evaluate the quality of disinfection treatment in DW plants. In 2015 and 2016, water networks and DW plants (closed loop and online monitors) of nine dialysis wards of Italian hospitals, hosting 162 dialysis beds overall, were sampled on a monthly basis to determine the parameters provided by ISN guidelines. Chlorinated drinking water was desalinated by reverse osmosis and distributed to the closed loop which feeds all online monitors. Disinfection with peracetic acid was performed in all DW plants on a monthly basis. Over the 24-month study period, seven out of nine DW plants (78%) recorded negative results for all investigated parameters. Closed loop contamination with Burkholderia cepacia was detected in a DW plant from January 2015 to March 2015. Pseudomonas aeruginosa was isolated from March 2016 to May 2016 in the closed loop of another DW plant. These microbial contaminations were eradicated by shock disinfection with sodium hypochlorite and peracetic acid, followed by water flushing. These results highlight the importance of chemical and physical methods of DW disinfection. The maintenance of control measures in water plants hosted in dialysis wards ensures a microbial risk reduction for all dialysis patients. Copyright © 2017 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.
Bacterial community changes during bioremediation of aliphatic hydrocarbon-contaminated soil.

PubMed

Militon, Cécile; Boucher, Delphine; Vachelard, Cédric; Perchet, Geoffrey; Barra, Vincent; Troquet, Julien; Peyretaillade, Eric; Peyret, Pierre

2010-12-01

The microbial community response during the oxygen biostimulation process of aged oil-polluted soils is poorly documented and there is no reference for the long-term monitoring of the unsaturated zone. To assess the potential effect of air supply on hydrocarbon fate and microbial community structure, two treatments (0 and 0.056 mol h⁻¹ molar flow rate of oxygen) were performed in fixed bed reactors containing oil-polluted soil. Microbial activity was monitored continuously over 2 years throughout the oxygen biostimulation process. Microbial community structure before and after treatment for 12 and 24 months was determined using a dual rRNA/rRNA gene approach, allowing us to characterize bacteria that were presumably metabolically active and therefore responsible for the functionality of the community in this polluted soil. Clone library analysis revealed that the microbial community contained many rare phylotypes. These have never been observed in other studied ecosystems. The bacterial community shifted from Gammaproteobacteria to Actinobacteria during the treatment. Without aeration, the samples were dominated by a phylotype linked to the Streptomyces. Members belonging to eight dominant phylotypes were well adapted to the aeration process. Aeration stimulated an Actinobacteria phylotype that might be involved in restoring the ecosystem studied. Phylogenetic analyses suggested that this phylotype is a novel, deep-branching member of the Actinobacteria related to the well-studied genus Acidimicrobium. FEMS Microbiology Ecology © 2010 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. No claim to original French government works.
Impact of seasonal variation on Escherichia coli concentrations in the riverbed sediments in the Apies River, South Africa.

PubMed

Abia, Akebe Luther King; Ubomba-Jaswa, Eunice; Momba, Maggy Ndombo Benteke

2015-12-15

Many South Africans living in resource-poor settings with little or no access to pipe-borne water still rely on rivers as alternative water sources for drinking and other purposes. The poor microbial quality of such water bodies calls for appropriate monitoring. However, routine monitoring only takes into consideration the microbial quality of the water column, and does not include monitoring of the riverbed sediments for microbial pollution. This study sought to investigate the microbial quality of riverbed sediments in the Apies River, Gauteng Province, South Africa, using Escherichia coli as a faecal indicator organism and to investigate the impact of seasonal variation on its abundance. Weekly samples were collected at 10 sampling sites on the Apies River between May and August 2013 (dry season) and between January and February 2014 (wet season). E. coli was enumerated using the Colilert®-18 Quanti-Tray® 2000 system. All sites tested positive for E. coli. Wastewater treatment work effluents had the highest negative impact on the river water quality. Seasonal variations had an impact on the concentration of E. coli both in water and sediments with concentrations increasing during the wet season. A strong positive correlation was observed between temperature and the E. coli concentrations. We therefore conclude that the sediments of the Apies River are heavily polluted with faecal indicator bacteria and could also harbour other microorganisms including pathogens. The release of such pathogens into the water column as a result of the resuspension of sediments due to extreme events like floods or human activities could increase the health risk of the populations using the untreated river water for recreation and other household purposes. There is therefore an urgent need to reconsider and review the current South African guidelines for water quality monitoring to include sediments, so as to protect human health and other aquatic lives. Copyright © 2015 Elsevier B.V. All rights reserved.
Automated Sampling Procedures Supported by High Persistence of Bacterial Fecal Indicators and Bacteroidetes Genetic Microbial Source Tracking Markers in Municipal Wastewater during Short-Term Storage at 5°C

PubMed Central

Mayer, R. E.; Vierheilig, J.; Egle, L.; Reischer, G. H.; Saracevic, E.; Mach, R. L.; Kirschner, A. K. T.; Zessner, M.; Farnleitner, A. H.

2015-01-01

Because of high diurnal water quality fluctuations in raw municipal wastewater, the use of proportional autosampling over a period of 24 h at municipal wastewater treatment plants (WWTPs) to evaluate carbon, nitrogen, and phosphorus removal has become a standard in many countries. Microbial removal or load estimation at municipal WWTPs, however, is still based on manually recovered grab samples. The goal of this study was to establish basic knowledge regarding the persistence of standard bacterial fecal indicators and Bacteroidetes genetic microbial source tracking markers in municipal wastewater in order to evaluate their suitability for automated sampling, as the potential lack of persistence is the main argument against such procedures. Raw and secondary treated wastewater of municipal origin from representative and well-characterized biological WWTPs without disinfection (organic carbon and nutrient removal) was investigated in microcosm experiments at 5 and 21°C with a total storage time of 32 h (including a 24-h autosampling component and an 8-h postsampling phase). Vegetative Escherichia coli and enterococci, as well as Clostridium perfringens spores, were selected as indicators for cultivation-based standard enumeration. Molecular analysis focused on total (AllBac) and human-associated genetic Bacteroidetes (BacHum-UCD, HF183 TaqMan) markers by using quantitative PCR, as well as 16S rRNA gene-based next-generation sequencing. The microbial parameters showed high persistence in both raw and treated wastewater at 5°C under the storage conditions used. Surprisingly, and in contrast to results obtained with treated wastewater, persistence of the microbial markers in raw wastewater was also high at 21°C. On the basis of our results, 24-h autosampling procedures with 5°C storage conditions can be recommended for the investigation of fecal indicators or Bacteroidetes genetic markers at municipal WWTPs. Such autosampling procedures will contribute to better understanding and monitoring of municipal WWTPs as sources of fecal pollution in water resources. PMID:26002900
16S rRNA Gene-Based Metagenomic Analysis of Ozark Cave Bacteria.

PubMed

Oliveira, Cássia; Gunderman, Lauren; Coles, Cathryn A; Lochmann, Jason; Parks, Megan; Ballard, Ethan; Glazko, Galina; Rahmatallah, Yasir; Tackett, Alan J; Thomas, David J

2017-09-01

The microbial diversity within cave ecosystems is largely unknown. Ozark caves maintain a year-round stable temperature (12-14 °C), but most parts of the caves experience complete darkness. The lack of sunlight and geological isolation from surface-energy inputs generate nutrient-poor conditions that may limit species diversity in such environments. Although microorganisms play a crucial role in sustaining life on Earth and impacting human health, little is known about their diversity, ecology, and evolution in community structures. We used five Ozark region caves as test sites for exploring bacterial diversity and monitoring long-term biodiversity. Illumina MiSeq sequencing of five cave soil samples and a control sample revealed a total of 49 bacterial phyla, with seven major phyla: Proteobacteria, Acidobacteria, Actinobacteria, Firmicutes, Chloroflexi, Bacteroidetes, and Nitrospirae. Variation in bacterial composition was observed among the five caves studied. Sandtown Cave had the lowest richness and most divergent community composition. 16S rRNA gene-based metagenomic analysis of cave-dwelling microbial communities in the Ozark caves revealed that species abundance and diversity are vast and included ecologically, agriculturally, and economically relevant taxa.
Trait-based approaches for understanding microbial biodiversity and ecosystem functioning

PubMed Central

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

2014-01-01

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

PubMed

Holcomb, David A; Messier, Kyle P; Serre, Marc L; Rowny, Jakob G; Stewart, Jill R

2018-06-25

Predictive modeling is promising as an inexpensive tool to assess water quality. We developed geostatistical predictive models of microbial water quality that empirically modeled spatiotemporal autocorrelation in measured fecal coliform (FC) bacteria concentrations to improve prediction. We compared five geostatistical models featuring different autocorrelation structures, fit to 676 observations from 19 locations in North Carolina's Jordan Lake watershed using meteorological and land cover predictor variables. Though stream distance metrics (with and without flow-weighting) failed to improve prediction over the Euclidean distance metric, incorporating temporal autocorrelation substantially improved prediction over the space-only models. We predicted FC throughout the stream network daily for one year, designating locations "impaired", "unimpaired", or "unassessed" if the probability of exceeding the state standard was ≥90%, ≤10%, or >10% but <90%, respectively. We could assign impairment status to more of the stream network on days any FC were measured, suggesting frequent sample-based monitoring remains necessary, though implementing spatiotemporal predictive models may reduce the number of concurrent sampling locations required to adequately assess water quality. Together, these results suggest that prioritizing sampling at different times and conditions using geographically sparse monitoring networks is adequate to build robust and informative geostatistical models of water quality impairment.
Integration of 3 Consecutive Years of Aqueous Geochemistry Monitoring Serpentinization at the Coast Range Ophiolite Microbial Observatory (CROMO), Northern California, USA

NASA Astrophysics Data System (ADS)

Cardace, D.; Hoehler, T. M.; McCollom, T. M.; Schrenk, M. O.; Kubo, M. D.

2014-12-01

In August 2011, a set of 8 groundwater monitoring wells were established in actively serpentinizing ultramafic rocks of the Coast Range Ophiolite near Lower Lake, CA, as a NASA Astrobiology Institute project (Cardace et al., 2013). These wells have enabled repeated sampling and analysis of aqueous geochemistry, which we now present in an integrated model of the progress of serpentinization at this locality. The Coast Range Ophiolite Microbial Observatory (CROMO) plumbs groundwaters percolating through a tectonic mélange of Jurassic-aged oceanic crust, with blocks of metabasalt and metagabbro, variably serpentinized ultramafics, Great Valley Sequence sedimentary rocks including the Jurassic Knoxville formation and the Cretaceous Crack Canyon formation, as well as rocks resulting from silica-carbonate alteration of serpentinites (marginal listvenites). All of these rock units are accessible in the McLaughlin Natural Reserve (administered by the University of California-Davis). In this work, we report on persistent geochemical trends in CROMO waters, which are gas-rich, high pH (11+), Ca2+-OH- type waters, contrast their characteristics with other continental sites of serpentinization and deep sea serpentinizing vent systems, and place the evolution of these waters in a water-rock reaction context based on geochemical modeling.
Time-Lapse Electrical Geophysical Monitoring of Amendment-Based Biostimulation

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

Johnson, Timothy C.; Versteeg, Roelof; Day-Lewis, Frederick D.

Biostimulation is increasingly used to accelerate microbial remediation of recalcitrant groundwater contaminants. Effective application of biostimulation requires successful emplacement of amendment in the contaminant target zone. Verification of remediation performance requires postemplacement assessment and contaminant monitoring. Sampling based approaches are expensive and provide low-density spatial and temporal information. Time-lapse electrical resistivity tomography (ERT) is an effective geophysical method for determining temporal changes in subsurface electrical conductivity. Because remedial amendments and biostimulation-related biogeochemical processes often change subsurface electrical conductivity, ERT can complement and enhance sampling-based approaches for assessing emplacement and monitoring biostimulation-based remediation. Field studies demonstrating the ability of time-lapse ERTmore » to monitor amendment emplacement and behavior were performed during a biostimulation remediation effort conducted at the Department of Defense Reutilization and Marketing Office (DRMO) Yard, in Brandywine, Maryland, United States. Geochemical fluid sampling was used to calibrate a petrophysical relation in order to predict groundwater indicators of amendment distribution. The petrophysical relations were field validated by comparing predictions to sequestered fluid sample results, thus demonstrating the potential of electrical geophysics for quantitative assessment of amendment-related geochemical properties. Crosshole radar zero-offset profile and borehole geophysical logging were also performed to augment the data set and validate interpretation. In addition to delineating amendment transport in the first 10 months after emplacement, the time-lapse ERT results show later changes in bulk electrical properties interpreted as mineral precipitation. Results support the use of more cost-effective surfacebased ERT in conjunction with limited field sampling to improve spatial and temporal monitoring of amendment emplacement and remediation performance.« less
Response of microbial community composition and function to soil climate change

USGS Publications Warehouse

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

2006-01-01

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

PubMed

Nijenhuis, Ivonne; Kuntze, Kevin

2016-04-01

Contamination and remediation of groundwater with halogenated organics and understanding of involved microbial reactions still poses a challenge. Over the last years, research in anaerobic microbial dehalogenation has advanced in many aspects providing information about the reaction, physiology of microorganisms as well as approaches to investigate the activity of microorganisms in situ. Recently published crystal structures of reductive dehalogenases (Rdh), heterologous expression systems and advanced analytical, proteomic and stable isotope approaches allow addressing the overall reaction and specific enzymes as well as co-factors involved during anaerobic microbial dehalogenation. In addition to Dehalococcoides spp., Dehalobacter and Dehalogenimonas strains have been recognized as important and versatile organohalide respirers. Together, these provide perspectives for integrated concepts allowing to improve and monitor in situ biodegradation. Copyright © 2015 Elsevier Ltd. All rights reserved.
Pilot scale application of nanosized iron oxides as electron acceptors for bioremediation

NASA Astrophysics Data System (ADS)

Bosch, Julian; Fritzsche, Andreas; Frank-Fahle, Beatrice; Lüders, Tilmann; Höss, Sebastian; Eisenmann, Heinrich; Held, Thomas; Totsche, Kai U.; Meckenstock, Rainer U.

2014-05-01

Microbial reduction of ferric iron is a major biogeochemical process in groundwater aquifer ecosystems and often associated with the degradation of organic contaminants, as bacteria couple iron reduction to the oxidation reduced carbon like e.g. BTEX. Yet in general the low bioavailability of natural iron oxides limits microbial reduction rates. However, nanosized iron oxides have an unequally enhanced bioavailability and reactivity compared to their respective bulk, macro-sized, and more crystalline materials. At the same time, nanosized iron oxides can be produced in stable colloidal suspensions, permitting efficient injections into contaminated aquifers. We examined the reactivity of nanosized synthetic colloidal iron oxides in microbial iron reduction. Application of colloidal nanoparticles led to a strong and sustainable enhancement of microbial reaction rates in batch experiments and sediment columns. Toluene oxidation was increased five-fold as compared to bulk, non-colloidal ferrihydrite as electron acceptor. Furthermore, we developed a unique approach for custom-tailoring the subsurface mobility of these particles after being injected into a contaminant plume. In a field pilot application, we injected 18 m3 of an iron oxide nanoparticle solution into a BTEX contaminated aquifer with a maximum excess pressure as low as 0.2 bar. The applied suspension showed a superior subsurface mobility, creating a reactive zone of 4 m height (corresponding to the height of the confined aquifer) and 6 m in diameter. Subsequent monitoring of BTEX, microbial BTEX degradation metabolites, ferrous iron generation, stable isotopes fractionation, microbial populations, and methanogenesis demonstrated the strong impact of our approach. Mathematic processed X-ray diffractograms and FTIR spectra provided a semi-quantitatively estimate of the long-term fate of the iron oxide colloids in the aquifer. Potential environmental risks of the injection itself were monitored with ecotoxicological investigations. Our data suggest that the injection of ferric iron nanoparticles as electron acceptors into contaminated aquifers for the enhancement of microbial contaminant degradation might develop into a novel bioremediation strategy.
DEVELOPMENT AND APPLICATION OF MICROBIAL ECOGENOMIC INDICATORS FOR MONITORING WATER QUALITY: REPORT OF A WORKSHOP ASSESSING THE STATE OF THE SCIENCE, RESEARCH.....

EPA Science Inventory

This article brings forth recommendations from a workshop sponsored by the U.S. Environmental Protection Agency's Science to Achieve Results (STAR) and Environmental Monitoring and Assessment (EMAP) Programs and by the Council of State Governments, held during May 2002 in Kansas ...
Hollow-fiber ultrafiltration for simultaneous recovery of viruses, bacteria and parasites from reclaimed water.

PubMed

Liu, Pengbo; Hill, Vincent R; Hahn, Donghyun; Johnson, Trisha B; Pan, Yi; Jothikumar, Narayanan; Moe, Christine L

2012-01-01

Hollow-fiber ultrafiltration (UF) is a technique that has been reported to be effective for recovering a diverse array of microbes from water, and may also be potentially useful for microbial monitoring of effluent from water reclamation facilities. However, few data are available to indicate the potential limitations and efficacy of the UF technique for treated wastewater. In this study, recovery efficiencies were determined for various options available for performing the tangential-flow UF technique, including hollow-fiber ultrafilter (i.e., dialyzer) type, ultrafilter pre-treatment (i.e., blocking), and elution. MS2 and ΦX174 bacteriophages, Clostridium perfringens spores, Escherichia coli, and Cryptosporidium parvum oocysts were seeded into 10-L reclaimed water samples to evaluate UF options. Then a single UF protocol was established and studied using seeded and non-seeded 100-L samples from two water reclamation facilities in Georgia, USA. Baxter Exeltra Plus 210 and Fresenius F200NR dialyzers were found to provide significantly higher microbial recovery than Minntech HPH 1400 hemoconcentrators. The selected final UF method incorporated use of a non-blocked ultrafilter for UF followed by elution using a surfactant-based solution. For 10-L samples, this method achieved recovery efficiencies of greater than 50% recovery of seeded viruses, bacteria, and parasites. There was no significant difference in overall microbial recovery efficiency when the method was applied to 10- and 100-L samples. In addition, detection levels for pathogens in seeded 100-L reclaimed water samples were 1000 PFU HAV, 10,000 GI norovirus particles, <500 Salmonella and <200 Cryptosporidium oocysts. These data demonstrate that UF can be an effective technique for recovering diverse microbes in reclaimed water to monitor and improve effluent water quality in wastewater treatment plants. Published by Elsevier B.V.
Time-Lapse Electrical Geophysical Monitoring of Amendment-Based Biostimulation.

PubMed

Johnson, Timothy C; Versteeg, Roelof J; Day-Lewis, Frederick D; Major, William; Lane, John W

2015-01-01

Biostimulation is increasingly used to accelerate microbial remediation of recalcitrant groundwater contaminants. Effective application of biostimulation requires successful emplacement of amendment in the contaminant target zone. Verification of remediation performance requires postemplacement assessment and contaminant monitoring. Sampling-based approaches are expensive and provide low-density spatial and temporal information. Time-lapse electrical resistivity tomography (ERT) is an effective geophysical method for determining temporal changes in subsurface electrical conductivity. Because remedial amendments and biostimulation-related biogeochemical processes often change subsurface electrical conductivity, ERT can complement and enhance sampling-based approaches for assessing emplacement and monitoring biostimulation-based remediation. Field studies demonstrating the ability of time-lapse ERT to monitor amendment emplacement and behavior were performed during a biostimulation remediation effort conducted at the Department of Defense Reutilization and Marketing Office (DRMO) Yard, in Brandywine, Maryland, United States. Geochemical fluid sampling was used to calibrate a petrophysical relation in order to predict groundwater indicators of amendment distribution. The petrophysical relations were field validated by comparing predictions to sequestered fluid sample results, thus demonstrating the potential of electrical geophysics for quantitative assessment of amendment-related geochemical properties. Crosshole radar zero-offset profile and borehole geophysical logging were also performed to augment the data set and validate interpretation. In addition to delineating amendment transport in the first 10 months after emplacement, the time-lapse ERT results show later changes in bulk electrical properties interpreted as mineral precipitation. Results support the use of more cost-effective surface-based ERT in conjunction with limited field sampling to improve spatial and temporal monitoring of amendment emplacement and remediation performance. Published 2014. This article is a U.S. Government work and is in the public domain in the USA.

Post-Genomics Approaches towards Monitoring Changes within the Microbial Ecology of the Gut

NASA Astrophysics Data System (ADS)

Tuohy, Kieran M.; Abecia, Leticia; Deaville, Eddie R.; Fava, Francesca; Klinder, Annett; Shen, Qing

The human gut microbiota, comprising many hundreds of different microbial species, has closely co-evolved with its human host over the millennia. Diet has been a major driver of this co-evolution, in particular dietary non-digestible carbohydrates. This dietary fraction reaches the colon and becomes available for microbial fermentation, and it is in the colon that the great diversity of gut microorganisms resides. For the vast majority of our evolutionary history humans followed hunter-gatherer life-styles and consumed diets with many times more non-digestible carbohydrates, fiber and whole plant polyphenol rich foods than typical Western style diets today.
Elucidating Microbial Adaptation Dynamics via Autonomous Exposure and Sampling

NASA Astrophysics Data System (ADS)

Grace, J. M.; Verseux, C.; Gentry, D.; Moffet, A.; Thayabaran, R.; Wong, N.; Rothschild, L.

2013-12-01

The adaptation of micro-organisms to their environments is a complex process of interaction between the pressures of the environment and of competition. Reducing this multifactorial process to environmental exposure in the laboratory is a common tool for elucidating individual mechanisms of evolution, such as mutation rates[Wielgoss et al., 2013]. Although such studies inform fundamental questions about the way adaptation and even speciation occur, they are often limited by labor-intensive manual techniques[Wassmann et al., 2010]. Current methods for controlled study of microbial adaptation limit the length of time, the depth of collected data, and the breadth of applied environmental conditions. Small idiosyncrasies in manual techniques can have large effects on outcomes; for example, there are significant variations in induced radiation resistances following similar repeated exposure protocols[Alcántara-Díaz et al., 2004; Goldman and Travisano, 2011]. We describe here a project under development to allow rapid cycling of multiple types of microbial environmental exposure. The system allows continuous autonomous monitoring and data collection of both single species and sampled communities, independently and concurrently providing multiple types of controlled environmental pressure (temperature, radiation, chemical presence or absence, and so on) to a microbial community in dynamic response to the ecosystem's current status. When combined with DNA sequencing and extraction, such a controlled environment can cast light on microbial functional development, population dynamics, inter- and intra-species competition, and microbe-environment interaction. The project's goal is to allow rapid, repeatable iteration of studies of both natural and artificial microbial adaptation. As an example, the same system can be used both to increase the pH of a wet soil aliquot over time while periodically sampling it for genetic activity analysis, or to repeatedly expose a culture of bacteria to the presence of a toxic metal, automatically adjusting the level of toxicity based on the number or growth rate of surviving cells. We are on our second prototype iteration, with demonstrated functions of microbial growth monitoring and dynamic exposure to UV-C radiation and temperature. We plan to add functionality for general chemical presence or absence by Nov. 2013. By making the project low-cost and open-source, we hope to encourage others to use it as a basis for future development of a common microbial environmental adaptation testbed. References: Alcantara-Diaz, D. et al. (2004), Divergent adaptation of Escherichia coli to cyclic ultraviolet light exposures, Mutagenesis, 19(5), 349-354, doi:10.1093/mutage/geh039. Goldman, R. P., and Travisano, M. (2011), Experimental evolution of ultraviolet radiation resistance in Escherichia coli, Evolution, 65(12), 3486-3498, doi:10.1111/j.1558-5646.2011.01438.x. Wassmann, M. et al. (2010), Adaptation of Bacillus subtilis cells to Archean-like UV climate: relevant hints of microbial evolution to remarkably increased radiation resistance, Astrobiology, 10(6), 605-615, doi:10.1089/ast.2009.0455. Wielgoss, S. et al. (2013), Mutation rate dynamics in a bacterial population reflect tension between adaptation and genetic load, Proc Natl Acad Sci USA, 110(1), 222-227, doi:10.1073/pnas.1219574110.
Development and validation of an open source O2-sensitive gel for physiological profiling of soil microbial communities.

PubMed

McLamore, E S; Garland, J L; Mackowiak, C; Desaunay, A; Garland, N; Chaturvedi, P; Taguchi, M; Dreaden, K; Catechis, John; Ullman, J L

2014-01-01

Community level physiological profiling is a simple, high-throughput technique for assessing microbial community physiology. Initial methods relying on redox-dye based detection of respiration were subject to strong enrichment bias, but subsequent development of a microtiter assay using an oxygen-quenched dye reduced this bias and improved the versatility of the approach. Commercial production of the oxygen microplates recently stopped, which led to the present effort to develop and validate a system using a luminophore dye (platinum tetrakis pentafluorophenyl) immobilized at the bottom of wells within a 96 well microtiter plate. The technique was used to analyze three well-characterized Florida soils: oak saw palmetto scrub, coastal mixed hardwood, and soil from an agricultural field used to grow corn silage. Substrate induced respiration was monitored by measuring respiration rates in soils under basal conditions and comparing to soils supplemented with nitrogen and various carbon sources (mannose, casein, asparagine, coumaric acid). All data was compared to a previously available commercial assay. There were no significant differences in the maximum peak intensity or the time to peak response for all soils tested (p<0.001, α=0.05). The experimental assay plates can be reused on soils up to four times (based on a deviation of less than 5%), where the commercial assay should not be reused. The results indicate that the new oxygen-based bioassay is a cost effective, open source tool for functional profiling of microbial communities. Copyright © 2013 Elsevier B.V. All rights reserved.
Fourier transform infrared spectroscopy as a metabolite fingerprinting tool for monitoring the phenotypic changes in complex bacterial communities capable of degrading phenol.

PubMed

Wharfe, Emma S; Jarvis, Roger M; Winder, Catherine L; Whiteley, Andrew S; Goodacre, Royston

2010-12-01

The coking process produces great volumes of wastewater contaminated with pollutants such as cyanides, sulfides and phenolics. Chemical and physical remediation of this wastewater removes the majority of these pollutants; however, these processes do not remove phenol and thiocyanate. The removal of these compounds has been effected during bioremediation with activated sludge containing a complex microbial community. In this investigation we acquired activated sludge from an industrial bioreactor capable of degrading phenol. The sludge was incubated in our laboratory and monitored for its ability to degrade phenol over a 48 h period. Multiple samples were taken across the time-course and analysed by Fourier transform infrared (FT-IR) spectroscopy. FT-IR was used as a whole-organism fingerprinting approach to monitor biochemical changes in the bacterial cells during the degradation of phenol. We also investigated the ability of the activated sludge to degrade phenol following extended periods (2-131 days) of storage in the absence of phenol. A reduction was observed in the ability of the microbial community to degrade phenol and this was accompanied by a detectable biochemical change in the FT-IR fingerprint related to cellular phenotype of the microbial community. In the absence of phenol a decrease in thiocyanate vibrations was observed, reflecting the ability of these communities to degrade this substrate. Actively degrading communities showed an additional new band in their FT-IR spectra that could be attributed to phenol degradation products from the ortho- and meta-cleavage of the aromatic ring. This study demonstrates that FT-IR spectroscopy when combined with chemometric analysis is a very powerful high throughput screening approach for assessing the metabolic capability of complex microbial communities. © 2010 Society for Applied Microbiology and Blackwell Publishing Ltd.
Development of a multiple-step process for the microbial decontamination of beef trim.

PubMed

Kang, D H; Koohmaraie, M; Dorsa, W J; Siragusa, G R

2001-01-01

A multiple-hurdle antimicrobial process for beef trim was developed. The microbial profiles of inoculated lean beef trim tissue (BTL) and fat-covered lean beef trim (BTF) were monitored during prolonged refrigerated storage following the application of successive multiple antimicrobial treatments applied to inoculated beef trim on a processing conveyor belt set at a belt speed of 1 cm/s. Beef trim (meat size approximately 15 by 15 cm) was preinoculated with bovine feces before all treatments that included the following: control, no treatment; water wash at 65 psi for five passes; water plus lactic acid (2% [vol/vol] room temperature lactic acid wash at 30 psi for three passes); combination treatment 1 (water plus 65 degrees C hot water at 30 psi for one pass plus hot air at 510 degrees C for four passes plus lactic acid), combination treatment 2 (water plus hot water at 82 degrees C for one pass plus hot air at 510 degrees C for five passes plus lactic acid), and combination treatment 3 (water plus hot water at 82 degrees C for three passes plus hot air at 510 degrees C for six passes plus lactic acid). The effects of treatments on bacterial populations were monitored by enumerating mesophilic aerobic bacteria (APC), presumptive lactic acid bacteria (PLAB), psychrotrophic bacteria (PCT), coliforms, and Escherichia coli biotype 1 on product stored for up to 7 days at 4 degrees C. In the case of BTL, the numbers of APC, PCT, and PLAB increased during storage at 5 degrees C, whereas the numbers of coliform and E. coli decreased on average by 1.8 log CFU/cm2, then remained constant following the initial reduction. Negligible effects on color quality were observed from multihurdle treatment combination 1. In the case of the BTF, the microbial reductions by treatments were much greater than the reduction on BTL. The pH of treated BTF increased more slowly than the pH of treated BTL, resulting in further reduction of the microflora on BTF. Except for control and water treatments, all sample treatments involving lactic acid resulted in continuously decreasing microbial populations. Based on microbial reduction and quality aspects, it was concluded that successively applied combination antimicrobial treatments for meat trim could offer potential food safety benefits.
An investigation of the sensitivity of low-field nuclear magnetic resonance to microbial growth and activity

NASA Astrophysics Data System (ADS)

Zhang, C.; Keating, K.

2014-12-01

Microbes and microbial processes play a significant role in shaping subsurface environments and are involved in applications ranging from microbially enhanced oil recovery to soil and groundwater contaminant remediation. Stimulated microbial growth in such applications could cause wide variety of changes of physical/chemical properties in the subsurface; however, due to the complexity of subsurface systems,it is difficult to monitor the growth of microbes and microbial activity in porous media. The focus of this research is to determine if low-field nuclear magnetic resonance (NMR), a method used in well logging to characterize fluids in hydrocarbon reservoirs or water in aquifers, can be used to directly detect the presence and the growth of microbes in geologic media. In this laboratory study, low-field NMR (2 MHz) relaxation measurements were collected on microbial suspensions with measured densities (i.e. biomasses), microbial pellets (live and dead), and inoculated silica. We focus on the direct contribution of microbes to the NMR signals in the absence of biomineralization. Shewanella oneidensis (MR-1), a facultative metal reducer known to play an important role in subsurface environments, were used as a model organism and were inoculated under aerobic condition. Data were collected using a CPMG pulse sequence, which was to determine the T2-distribution, and using a gradient spin-echo (PGSE) plus CPMG pulse sequence, which was used to encode diffusion properties and determine the effective diffusion-spin-spin relaxation correlation (D-T2) plot. Our data show no obvious change in the T2-distribution as S. oneidensis density varied in suspension, but show a clear distinction in the T2-distribution and D-T2 plots between live and dead cell pellets. A decrease in the T2-distribution is observed in the inoculated sand column. These results will provide a basis for understanding the effect of microbes within geologic media on low-field NMR measurements. This research is necessary to determine if NMR measurements can ultimately to be used to monitor microbial growth and activity in oil reservoirs or contaminated aquifers.
Modular spectral imaging system for discrimination of pigments in cells and microbial communities.

PubMed

Polerecky, Lubos; Bissett, Andrew; Al-Najjar, Mohammad; Faerber, Paul; Osmers, Harald; Suci, Peter A; Stoodley, Paul; de Beer, Dirk

2009-02-01

Here we describe a spectral imaging system for minimally invasive identification, localization, and relative quantification of pigments in cells and microbial communities. The modularity of the system allows pigment detection on spatial scales ranging from the single-cell level to regions whose areas are several tens of square centimeters. For pigment identification in vivo absorption and/or autofluorescence spectra are used as the analytical signals. Along with the hardware, which is easy to transport and simple to assemble and allows rapid measurement, we describe newly developed software that allows highly sensitive and pigment-specific analyses of the hyperspectral data. We also propose and describe a number of applications of the system for microbial ecology, including identification of pigments in living cells and high-spatial-resolution imaging of pigments and the associated phototrophic groups in complex microbial communities, such as photosynthetic endolithic biofilms, microbial mats, and intertidal sediments. This system provides new possibilities for studying the role of spatial organization of microorganisms in the ecological functioning of complex benthic microbial communities or for noninvasively monitoring changes in the spatial organization and/or composition of a microbial community in response to changing environmental factors.
Modular Spectral Imaging System for Discrimination of Pigments in Cells and Microbial Communities▿ †

PubMed Central

Polerecky, Lubos; Bissett, Andrew; Al-Najjar, Mohammad; Faerber, Paul; Osmers, Harald; Suci, Peter A.; Stoodley, Paul; de Beer, Dirk

2009-01-01

Here we describe a spectral imaging system for minimally invasive identification, localization, and relative quantification of pigments in cells and microbial communities. The modularity of the system allows pigment detection on spatial scales ranging from the single-cell level to regions whose areas are several tens of square centimeters. For pigment identification in vivo absorption and/or autofluorescence spectra are used as the analytical signals. Along with the hardware, which is easy to transport and simple to assemble and allows rapid measurement, we describe newly developed software that allows highly sensitive and pigment-specific analyses of the hyperspectral data. We also propose and describe a number of applications of the system for microbial ecology, including identification of pigments in living cells and high-spatial-resolution imaging of pigments and the associated phototrophic groups in complex microbial communities, such as photosynthetic endolithic biofilms, microbial mats, and intertidal sediments. This system provides new possibilities for studying the role of spatial organization of microorganisms in the ecological functioning of complex benthic microbial communities or for noninvasively monitoring changes in the spatial organization and/or composition of a microbial community in response to changing environmental factors. PMID:19074609
Microbial diversity in restored wetlands of San Francisco Bay

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

Theroux, Susanna; Hartman, Wyatt; He, Shaomei

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

NASA Astrophysics Data System (ADS)

Kim, J.; Lee, J.; Kang, H.

2017-12-01

Phragmites australis is one of the representative vegetation of coastal wetlands which is distributed in North America, East Asia and European Countries. In North America, P. australis has invaded large areas of coastal wetlands, which causes various ecological problems such as increases in methane emission and reduction in biodiversity. In South Korea, P. australis is rapidly expanded in tidal marshes in Suncheon Bay. The expansion of P. australis enhanced methane emission by increasing dissolved organic carbon and soil moisture, and changing in relative abundances of methanogen, methanotroph, and sulfate reducing bacteria. Microbial community structure might be also shifted and affect methane cycle, but accurate observation on microbial community structure has not been fully illustrated yet. Therefore, we tried to monitor the changing microbial community structure due to P. australis expansion by using Next Generation Sequencing (NGS). NGS results showed that microbial community was substantially changed with the expansion. We also observed seasonal variations and chronosequence of microbial community structures along the expansion of P. australis, which showed distinctive changing patterns. P. australis expansion substantially affected microbial community structure in tidal marsh which may play an important role in methane cycle in tidal marshes.
[Oxidation of sulfur-containing substrates by aboriginal and experimentally designed microbial communities].

PubMed

Pivovarova, T A; Bulaev, A G; Roshchupko, P V; Belyĭ, A V; Kondrat'eva, T F

2012-01-01

Aboriginal and experimental (constructed of pure microbial cultures) communities of acidophilic chemolithotrophs have been studied. The oxidation of elemental sulfur, sodium thiosulfate, and potassium tetrathionate as sole sources of energy has been monitored. The oxidation rate of the experimental community is higher as compared to the aboriginal community isolated from a flotation concentrate of pyrrhotine-containing pyrite-arsenopyrite gold-arsenic sulfide ore. The degree of oxidation of the mentioned S substrates amounts to 17.91, 68.30, and 93.94% for the experimental microbial community and to 10.71, 56.03, and 79.50% for the aboriginal community, respectively. The degree of oxidation of sulfur sulfide forms in the ore flotation concentrate is 59.15% by the aboriginal microbial community and 49.40% by the experimental microbial community. Despite a higher rate of oxidation of S substrates as a sole source of energy by the experimental microbial community, the aboriginal community oxidizes S substrates at a higher rate in the flotation concentrate of pyrrhotine-containing pyrite-arsenopyrite gold-arsenic sulfide ore, from which it was isolated. Bacterial-chemical oxidation of the flotation concentrate by the aboriginal microbial community allows for the extraction of an additional 32.3% of gold from sulfide minerals, which is by 5.7% larger compared to the yield obtained by the experimental microbial community.
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.
Environmental Regulation of Microbial Community Structure

NASA Technical Reports Server (NTRS)

Bebout, Leslie; DesMarais, D.; Heyenga, G.; Nelson, F.; DeVincenzi, D. (Technical Monitor)

2002-01-01

Most naturally occurring microbes live in complex microbial communities consisting of thousands of phylotypes of microorganisms living in close proximity. Each of these draws nutrients from the environment and releases metabolic waste products, which may in turn serve as substrates for other microbial groups. Gross environmental changes, such as irradiance level, hydrodynamic flow regime, temperature or water chemistry can directly affect the productivity of some community members, which in turn will affect other dependent microbial populations and rate processes. As a first step towards the development of "standard" natural communities of microorganisms for a variety of potential NASA applications, we are measuring biogeochemical cycling in artificially structured communities of microorganisms, created using natural microbial mat communities as inoculum. The responses of these artificially assembled communities of microorganisms to controlled shifts in ecosystem incubation conditions is being determined. This research requires close linking of environmental monitoring, with community composition in a closed and controlled incubation setting. We are developing new incubation chamber designs to allow for this integrated approach to examine the interplay between environmental conditions, microbial community composition and biogeochemical processes.
How do microlocal environmental variations affect microbial activities of a Pinus halepensis litter in a Mediterranean coastal area?

PubMed

Qasemian, Leila; Guiral, Daniel; Farnet, Anne-Marie

2014-10-15

Mediterranean coastal ecosystems suffer many different types of natural and anthropogenic environmental pressure. Microbial communities, major conductors of organic matter decomposition are also subject to these environmental constraints. In this study, our aim was to understand how microbial activities vary at a small spatio-temporal scale in a Mediterranean coastal environment. Microbial activities were monitored in a Pinus halepensis litter collected from two areas, one close to (10 m) and one far from (300 m) the French Mediterranean coast. Litters were transferred from one area to the other using litterbags and studied via different microbial indicators after 2, 5 and 13 months. Microbial Basal Respiration, qCO₂, certain enzyme activities (laccase, cellulase, β-glucosidase and acid phosphatase) and functional diversity via Biolog microplates were assayed in litterbags left in the area of origin as well as in litterbags transferred from one area to the other. Results highlight that microbial activities differ significantly in this short spatial scale over time. The influence of microlocal conditions more intensified for litters situated close to the sea, especially during summer seems to have a stressful effect on microbial communities, leading to less efficient functional activities. However, microbial activities were more strongly influenced by temporal variations linked to seasonality than by location. Copyright © 2014 Elsevier B.V. All rights reserved.
Microbial Surveillance of Potable Water Sources of the International Space Station

NASA Technical Reports Server (NTRS)

Bruce, Rebekah J.; Ott, C. Mark; Skuratov, Vladimir M.; Pierson, Duane L.

2005-01-01

To mitigate risk to the crew, the microbial surveillance of the quality of potable water sources of the International Space Station (ISS) has been ongoing since before the arrival of the first permanent crew. These water sources have included stored ground-supplied water, water produced by the shuttle fuel cells during flight, and ISS humidity condensate that is reclaimed and processed. Monitoring was accomplished using a self-contained filter designed to allow bacterial growth and enumeration during flight. Upon return to earth, microbial isolates were identified using 16S ribosomal gene sequencing. While the predominant isolates were common Gramnegative bacteria including Ralstonia eutropha, Methylobacterium fujisawaense, and Spingomonas paucimobilis, opportunistic pathogens such as Stenotrophomonas maltophilia and Pseudomonas aeruginosa were also isolated. Results of in-flight enumeration have indicated a fluctuation of bacterial counts above system design specifications. Additional in-flight monitoring capability for the specific detection of coliforms was added in 2004; no coliforms have been detected from any potable water source. Neither the bacterial concentrations nor the identification of the isolates recovered from these samples has suggested a threat to crew health.
Application of a genetically encoded biosensor for live cell imaging of L-valine production in pyruvate dehydrogenase complex-deficient Corynebacterium glutamicum strains.

PubMed

Mustafi, Nurije; Grünberger, Alexander; Mahr, Regina; Helfrich, Stefan; Nöh, Katharina; Blombach, Bastian; Kohlheyer, Dietrich; Frunzke, Julia

2014-01-01

The majority of biotechnologically relevant metabolites do not impart a conspicuous phenotype to the producing cell. Consequently, the analysis of microbial metabolite production is still dominated by bulk techniques, which may obscure significant variation at the single-cell level. In this study, we have applied the recently developed Lrp-biosensor for monitoring of amino acid production in single cells of gradually engineered L-valine producing Corynebacterium glutamicum strains based on the pyruvate dehydrogenase complex-deficient (PDHC) strain C. glutamicum ΔaceE. Online monitoring of the sensor output (eYFP fluorescence) during batch cultivation proved the sensor's suitability for visualizing different production levels. In the following, we conducted live cell imaging studies on C. glutamicum sensor strains using microfluidic chip devices. As expected, the sensor output was higher in microcolonies of high-yield producers in comparison to the basic strain C. glutamicum ΔaceE. Microfluidic cultivation in minimal medium revealed a typical Gaussian distribution of single cell fluorescence during the production phase. Remarkably, low amounts of complex nutrients completely changed the observed phenotypic pattern of all strains, resulting in a phenotypic split of the population. Whereas some cells stopped growing and initiated L-valine production, others continued to grow or showed a delayed transition to production. Depending on the cultivation conditions, a considerable fraction of non-fluorescent cells was observed, suggesting a loss of metabolic activity. These studies demonstrate that genetically encoded biosensors are a valuable tool for monitoring single cell productivity and to study the phenotypic pattern of microbial production strains.
Development of a novel colorimetric sensor based on alginate beads for monitoring rainbow trout spoilage.

PubMed

Majdinasab, Marjan; Hosseini, Seyed Mohammad Hashem; Sepidname, Marziyeh; Negahdarifar, Manizheh; Li, Peiwu

2018-05-01

Alginate is a non-toxic, renewable, and linear copolymer obtained from the brown algae Laminaria digitata that can be easily shaped into beads. Its good gel forming properties have made it useful for entrapping food and pharmaceutical ingredients. In this study, alginate beads were used in a novel application as a colorimetric sensor in food intelligent packaging. Colorimetric sensor was developed through entrapping red cabbage extract as a pH indicator in alginate beads. The pH indicator beads were used in rainbow trout packaging for monitoring fillets spoilage. Color change of beads during fish storage was measured using the CIELab method. The alginate bead colorimetric sensor is validated by measuring total volatile basic nitrogen (TVB-N) levels and microbial populations in fish samples. Moreover, peroxide value (PV) and thiobarbituric acid reactive substances (TBARS) were evaluated during storage. Results indicated that increasing the bacterial population during storage and production of proteolytic enzymes resulted in protein degradation, accumulation of volatile amine compounds, increase in the pH and finally color change of alginate beads. The values of TVB-N, pH, PV and TBARS increased with time of storage. The results of TVB-N and microbial growth were in accordance with color change of beads and CIELab data. Therefore, the proposed system enjoys a high sensitivity to pH variations and is capable of monitoring the spoilage of fish or other protein-rich products through its wide range of color changes. The alginate beads containing the red cabbage extract can, thus, be used as a low-cost colorimetric sensor for intelligent packaging applications.
Application of a Genetically Encoded Biosensor for Live Cell Imaging of L-Valine Production in Pyruvate Dehydrogenase Complex-Deficient Corynebacterium glutamicum Strains

PubMed Central

Mahr, Regina; Helfrich, Stefan; Nöh, Katharina; Blombach, Bastian; Kohlheyer, Dietrich; Frunzke, Julia

2014-01-01

The majority of biotechnologically relevant metabolites do not impart a conspicuous phenotype to the producing cell. Consequently, the analysis of microbial metabolite production is still dominated by bulk techniques, which may obscure significant variation at the single-cell level. In this study, we have applied the recently developed Lrp-biosensor for monitoring of amino acid production in single cells of gradually engineered L-valine producing Corynebacterium glutamicum strains based on the pyruvate dehydrogenase complex-deficient (PDHC) strain C. glutamicum ΔaceE. Online monitoring of the sensor output (eYFP fluorescence) during batch cultivation proved the sensor's suitability for visualizing different production levels. In the following, we conducted live cell imaging studies on C. glutamicum sensor strains using microfluidic chip devices. As expected, the sensor output was higher in microcolonies of high-yield producers in comparison to the basic strain C. glutamicum ΔaceE. Microfluidic cultivation in minimal medium revealed a typical Gaussian distribution of single cell fluorescence during the production phase. Remarkably, low amounts of complex nutrients completely changed the observed phenotypic pattern of all strains, resulting in a phenotypic split of the population. Whereas some cells stopped growing and initiated L-valine production, others continued to grow or showed a delayed transition to production. Depending on the cultivation conditions, a considerable fraction of non-fluorescent cells was observed, suggesting a loss of metabolic activity. These studies demonstrate that genetically encoded biosensors are a valuable tool for monitoring single cell productivity and to study the phenotypic pattern of microbial production strains. PMID:24465669
Pathophysiological evaluation of subacute ruminal acidosis (SARA) by continuous ruminal pH monitoring

PubMed Central

2016-01-01

Abstract Evaluation of the radio‐transmission pH‐measurement system for monitoring the ruminal pH and subacute ruminal acidosis (SARA) in cattle is described. This is done in order to reveal the possible application of this system for detection and pathophysiological research of SARA by continuous ruminal pH measurement. The possibility of using this system for assessment of the ruminal pH in SARA cattle, and the presence of negative correlation between the ruminal pH and ruminal temperature in heathy and SARA cattle were determined. In addition, the 16S rRNA gene pyrosequencing analysis showed that the ruminal microbial community was simpler in SARA cattle, and the bacterial numbers in SARA cattle were lower than those in healthy hay‐fed cattle. Concentrate feeding might have reduced the diversity of the ruminal microbial community. Changes in the ruminal microbial community of SARA cattle might be related to the changes in ruminal pH followed by the decrease in the number of some bacteria. Continuous monitoring of the ruminal pH using the radio‐transmission pH‐measurement system would be applied for detection and prevention of SARA in the field and pathophysiological research of SARA, including ruminal zymology and bacteriology, which have been determined previously by sampling of the ruminal fluid and measuring of ruminal pH. PMID:26279060
Four-year bacterial monitoring in the International Space Station-Japanese Experiment Module "Kibo" with culture-independent approach.

PubMed

Ichijo, Tomoaki; Yamaguchi, Nobuyasu; Tanigaki, Fumiaki; Shirakawa, Masaki; Nasu, Masao

2016-01-01

Studies on the relationships between humans and microbes in space habitation environments are critical for success in long-duration space missions, to reduce potential hazards to the crew and the spacecraft infrastructure. We performed microbial monitoring in the Japanese Experiment Module "Kibo", a part of the International Space Station, for 4 years after its completion, and analyzed samples with modern molecular microbiological techniques. Sampling was performed in September 2009, February 2011, and October 2012. The surface of the incubator, inside the door of the incubator, an air intake, air diffuser, and handrail were selected as sampling sites. Sampling was performed using the optimized swabbing method. Abundance and phylogenetic affiliation of bacteria on the interior surfaces of Kibo were determined by quantitative PCR and pyrosequencing, respectively. Bacteria in the phyla Proteobacteria (γ-subclass) and Firmicutes were frequently detected on the interior surfaces in Kibo. Families Staphylococcaceae and Enterobacteriaceae were dominant. Most bacteria detected belonged to the human microbiota; thus, we suggest that bacterial cells are transferred to the surfaces in Kibo from the astronauts. Environmental bacteria such as Legionella spp. were also detected. From the data on bacterial abundance and phylogenetic affiliation, Kibo has been microbiologically well maintained; however, the microbial community structure in Kibo may change with prolonged stay of astronauts. Continuous monitoring is required to obtain information on changes in the microbial community structure in Kibo.

40 CFR 141.402 - Ground water source microbial monitoring and analytical methods.

Code of Federal Regulations, 2011 CFR

2011-07-01

... approves the use of E. coli as a fecal indicator for source water monitoring under this paragraph (a). If the repeat sample collected from the ground water source is E.coli positive, the system must comply... listed in the in paragraph (c)(2) of this section for the presence of E. coli, enterococci, or coliphage...
40 CFR 141.402 - Ground water source microbial monitoring and analytical methods.

Code of Federal Regulations, 2013 CFR

2013-07-01

... for the presence of E. coli, enterococci, or coliphage: Analytical Methods for Source Water Monitoring... Microbiology, 62:3881-3884. 10 EPA Method 1601: Male-specific (F+) and Somatic Coliphage in Water by Two-step... 20460. 11 EPA Method 1602: Male-specific (F+) and Somatic Coliphage in Water by Single Agar Layer (SAL...
40 CFR 141.402 - Ground water source microbial monitoring and analytical methods.

Code of Federal Regulations, 2014 CFR

2014-07-01

... for the presence of E. coli, enterococci, or coliphage: Analytical Methods for Source Water Monitoring... Microbiology, 62:3881-3884. 10 EPA Method 1601: Male-specific (F+) and Somatic Coliphage in Water by Two-step... 20460. 11 EPA Method 1602: Male-specific (F+) and Somatic Coliphage in Water by Single Agar Layer (SAL...
On-line biofilm monitoring by "BIOX" electrochemical probe.

PubMed

Mollica, A; Cristiani, P

2003-01-01

The innovative electrochemical monitoring probe (BIOX) recently developed to improve the antifouling treatments of cooling systems in industrial plants is presented. On the basis of the good results obtained from applications on marine sites, some research has been stated to validate this technique in biofilm growth and prevention of microbial corrosion in fresh and drinking waters.
The relationship between blood and muscle samples to monitor for residues of the antibiotic enrofloxacin in chickens

USDA-ARS?s Scientific Manuscript database

Use of antibiotics in food animals has generated concern as the presence of these residues in food may contribute to increased microbial resistance in humans. Fluoroquinolone antibiotics are thus now no longer allowed by the U.S. Food and Drug Administration for use in poultry and monitoring of the...
Biochar modulates heavy metal toxicity and improves microbial carbon use efficiency in soil.

PubMed

Xu, Yilu; Seshadri, Balaji; Sarkar, Binoy; Wang, Hailong; Rumpel, Cornelia; Sparks, Donald; Farrell, Mark; Hall, Tony; Yang, Xiaodong; Bolan, Nanthi

2018-04-15

Soil organic carbon is essential to improve soil fertility and ecosystem functioning. Soil microorganisms contribute significantly to the carbon transformation and immobilisation processes. However, microorganisms are sensitive to environmental stresses such as heavy metals. Applying amendments, such as biochar, to contaminated soils can alleviate the metal toxicity and add carbon inputs. In this study, Cd and Pb spiked soils treated with macadamia nutshell biochar (5% w/w) were monitored during a 49days incubation period. Microbial phospholipid fatty acids (PLFAs) were extracted and analysed as biomarkers in order to identify the microbial community composition. Soil properties, metal bioavailability, microbial respiration, and microbial biomass carbon were measured after the incubation period. Microbial carbon use efficiency (CUE) was calculated from the ratio of carbon incorporated into microbial biomass to the carbon mineralised. Total PLFA concentration decreased to a greater extent in metal contaminated soils than uncontaminated soils. Microbial CUE also decreased due to metal toxicity. However, biochar addition alleviated the metal toxicity, and increased total PLFA concentration. Both microbial respiration and biomass carbon increased due to biochar application, and CUE was significantly (p<0.01) higher in biochar treated soils than untreated soils. Heavy metals reduced the microbial carbon sequestration in contaminated soils by negatively influencing the CUE. The improvement of CUE through biochar addition in the contaminated soils could be attributed to the decrease in metal bioavailability, thereby mitigating the biotoxicity to soil microorganisms. Copyright © 2017 Elsevier B.V. All rights reserved.
ATP as a biomarker of viable microorganisms in clean-room facilities

NASA Technical Reports Server (NTRS)

Venkateswaran, Kasthuri; Hattori, Noriaki; La Duc, Myron T.; Kern, Roger

2003-01-01

A new firefly luciferase bioluminescence assay method that differentiates free extracellular ATP (dead cells, etc.) from intracellular ATP (viable microbes) was used to determine the viable microbial cleanliness of various clean-room facilities. For comparison, samples were taken from both clean-rooms, where the air was filtered to remove particles >0.5 microm, and ordinary rooms with unfiltered air. The intracellular ATP was determined after enzymatically degrading the sample's free ATP. Also for comparison, cultivable microbial populations were counted on nutrient-rich trypticase soy agar (TSA) plates. Both the cultivable and ATP-based determinations indicate that the microbial burden was lower in clean-room facilities than in ordinary rooms. However, there was no direct correlation between the two sets of measurements because the two assays measured very different populations. A large fraction of the samples yielded no colony formers on TSA, but were positive for intracellular ATP. Subsequently, genomic DNA was isolated directly from selected samples and 16S rDNA fragments were cloned and sequenced, identifying nearest neighbors, many of which are known to be noncultivable in the media employed. It was concluded that viable microbial contamination can be reliably monitored by measurement of intracellular ATP, and that this method may be considered superior to cultivable colony counts due to its speed and its ability to report the presence of viable but noncultivable organisms. When the detection of nonviable microbes is of interest, the ATP assay can be supplemented with DNA analysis.
Characterization of the fecal microbiota using high-throughput sequencing reveals a stable microbial community during storage.

PubMed

Carroll, Ian M; Ringel-Kulka, Tamar; Siddle, Jennica P; Klaenhammer, Todd R; Ringel, Yehuda

2012-01-01

The handling and treatment of biological samples is critical when characterizing the composition of the intestinal microbiota between different ecological niches or diseases. Specifically, exposure of fecal samples to room temperature or long term storage in deep freezing conditions may alter the composition of the microbiota. Thus, we stored fecal samples at room temperature and monitored the stability of the microbiota over twenty four hours. We also investigated the stability of the microbiota in fecal samples during a six month storage period at -80°C. As the stability of the fecal microbiota may be affected by intestinal disease, we analyzed two healthy controls and two patients with irritable bowel syndrome (IBS). We used high-throughput pyrosequencing of the 16S rRNA gene to characterize the microbiota in fecal samples stored at room temperature or -80°C at six and seven time points, respectively. The composition of microbial communities in IBS patients and healthy controls were determined and compared using the Quantitative Insights Into Microbial Ecology (QIIME) pipeline. The composition of the microbiota in fecal samples stored for different lengths of time at room temperature or -80°C clustered strongly based on the host each sample originated from. Our data demonstrates that fecal samples exposed to room or deep freezing temperatures for up to twenty four hours and six months, respectively, exhibit a microbial composition and diversity that shares more identity with its host of origin than any other sample.
Evaluation of food storage racks available on the Polish market in the hygienic context

PubMed

Grzesińska, Wiesława; Tomaszewska, Marzena; Bilska, Beata; Trafiałek, Joanna; Dziadek, Michał

Providing safe food products to the consumer depends on the material and technology used and adherence to hygienic practices, throughout the production process. The degree of microbial contamination of a surface is an important indicator of equipment cleanliness and effectiveness of cleaning and disinfection. Used material, construction solutions and quality of the applied devices also have an effect on hygienic status. The objective of the present study was to evaluate the influence of the design and construction material of selected food storage racks, available on the Polish market, on their hygienic status. The study was based on determination of the capability of microbial growth on the surface of the racks and the effectiveness of their cleaning. Microbiological cleanliness on the surface of the racks was monitored by the contact plates which are able to estimate the total number of icroorganisms. Examination of effectiveness of cleaning was conducted by the use of ATP bioluminescence method. This experiment has proven a significant influence of adopted construction solutions on the hygienic status of the examined racks. Presence of antibacterial layer and a choice of the appropriate construction material characterized by a low surface roughness impedes the microbial growth and increases the effectiveness of cleaning. Design solutions have significant impact on the hygienic status of shelves. Selection of a suitable material for the construction of racks can greatly reduce the possibility of the development of microorganism, despite the low efficiency of the cleaning. The application of antimicrobial coatings inhibits microbial growth.
ATP as a biomarker of viable microorganisms in clean-room facilities.

PubMed

Venkateswaran, Kasthuri; Hattori, Noriaki; La Duc, Myron T; Kern, Roger

2003-03-01

A new firefly luciferase bioluminescence assay method that differentiates free extracellular ATP (dead cells, etc.) from intracellular ATP (viable microbes) was used to determine the viable microbial cleanliness of various clean-room facilities. For comparison, samples were taken from both clean-rooms, where the air was filtered to remove particles >0.5 microm, and ordinary rooms with unfiltered air. The intracellular ATP was determined after enzymatically degrading the sample's free ATP. Also for comparison, cultivable microbial populations were counted on nutrient-rich trypticase soy agar (TSA) plates. Both the cultivable and ATP-based determinations indicate that the microbial burden was lower in clean-room facilities than in ordinary rooms. However, there was no direct correlation between the two sets of measurements because the two assays measured very different populations. A large fraction of the samples yielded no colony formers on TSA, but were positive for intracellular ATP. Subsequently, genomic DNA was isolated directly from selected samples and 16S rDNA fragments were cloned and sequenced, identifying nearest neighbors, many of which are known to be noncultivable in the media employed. It was concluded that viable microbial contamination can be reliably monitored by measurement of intracellular ATP, and that this method may be considered superior to cultivable colony counts due to its speed and its ability to report the presence of viable but noncultivable organisms. When the detection of nonviable microbes is of interest, the ATP assay can be supplemented with DNA analysis.
Remediation of antimony-rich mine waters: Assessment of antimony removal and shifts in the microbial community of an onsite field-scale bioreactor.

PubMed

Sun, Weimin; Xiao, Enzong; Kalin, Margarete; Krumins, Valdis; Dong, Yiran; Ning, Zengping; Liu, Tong; Sun, Min; Zhao, Yanlong; Wu, Shiliang; Mao, Jianzhong; Xiao, Tangfu

2016-08-01

An on-site field-scale bioreactor for passive treatment of antimony (Sb) contamination was installed downstream of an active Sb mine in Southwest China, and operated for one year (including a six month monitoring period). This bioreactor consisted of five treatment units, including one pre-aerobic cell, two aerobic cells, and two microaerobic cells. With the aerobic cells inoculated with indigenous mine water microflora, the bioreactor removed more than 90% of total soluble Sb and 80% of soluble antimonite (Sb(III)). An increase in pH and decrease of oxidation-reduction potential (Eh) was also observed along the flow direction. High-throughput sequencing of the small subunit ribosomal RNA (SSU rRNA) gene variable (V4) region revealed that taxonomically diverse microbial communities developed in the bioreactor. Metal (loid)-oxidizing bacteria including Ferrovum, Thiomonas, Gallionella, and Leptospirillum, were highly enriched in the bioreactor cells where the highest total Sb and Sb(III) removal occurred. Canonical correspondence analysis (CCA) indicated that a suite of in situ physicochemical parameters including pH and Eh were substantially correlated with the overall microbial communities. Based on an UPGMA (Unweighted Pair Group Method with Arithmetic Mean) tree and PCoA (Principal Coordinates Analysis), the microbial composition of each cell was distinct, indicating these in situ physicochemical parameters had an effect in shaping the indigenous microbial communities. Overall, this study was the first to employ a field-scale bioreactor to treat Sb-rich mine water onsite and, moreover, the findings suggest the feasibility of the bioreactor in removing elevated Sb from mine waters. Copyright © 2016 Elsevier Ltd. All rights reserved.
Distinct respiratory responses of soils to complex organic substrate are governed predominantly by soil architecture and its microbial community.

PubMed

Fraser, F C; Todman, L C; Corstanje, R; Deeks, L K; Harris, J A; Pawlett, M; Whitmore, A P; Ritz, K

2016-12-01

Factors governing the turnover of organic matter (OM) added to soils, including substrate quality, climate, environment and biology, are well known, but their relative importance has been difficult to ascertain due to the interconnected nature of the soil system. This has made their inclusion in mechanistic models of OM turnover or nutrient cycling difficult despite the potential power of these models to unravel complex interactions. Using high temporal-resolution respirometery (6 min measurement intervals), we monitored the respiratory response of 67 soils sampled from across England and Wales over a 5 day period following the addition of a complex organic substrate (green barley powder). Four respiratory response archetypes were observed, characterised by different rates of respiration as well as different time-dependent patterns. We also found that it was possible to predict, with 95% accuracy, which type of respiratory behaviour a soil would exhibit based on certain physical and chemical soil properties combined with the size and phenotypic structure of the microbial community. Bulk density, microbial biomass carbon, water holding capacity and microbial community phenotype were identified as the four most important factors in predicting the soils' respiratory responses using a Bayesian belief network. These results show that the size and constitution of the microbial community are as important as physico-chemical properties of a soil in governing the respiratory response to OM addition. Such a combination suggests that the 'architecture' of the soil, i.e. the integration of the spatial organisation of the environment and the interactions between the communities living and functioning within the pore networks, is fundamentally important in regulating such processes.
Monitoring of activated sludge settling ability through image analysis: validation on full-scale wastewater treatment plants.

PubMed

Mesquita, D P; Dias, O; Amaral, A L; Ferreira, E C

2009-04-01

In recent years, a great deal of attention has been focused on the research of activated sludge processes, where the solid-liquid separation phase is frequently considered of critical importance, due to the different problems that severely affect the compaction and the settling of the sludge. Bearing that in mind, in this work, image analysis routines were developed in Matlab environment, allowing the identification and characterization of microbial aggregates and protruding filaments in eight different wastewater treatment plants, for a combined period of 2 years. The monitoring of the activated sludge contents allowed for the detection of bulking events proving that the developed image analysis methodology is adequate for a continuous examination of the morphological changes in microbial aggregates and subsequent estimation of the sludge volume index. In fact, the obtained results proved that the developed image analysis methodology is a feasible method for the continuous monitoring of activated sludge systems and identification of disturbances.
Metagenomic applications in environmental monitoring and bioremediation

DOE PAGES

Techtmann, Stephen M.; Hazen, Terry C.

2016-01-01

With the rapid advances in sequencing technology, the cost of sequencing has dramatically dropped and the scale of sequencing projects has increased accordingly. This has provided the opportunity for the routine use of sequencing techniques in the monitoring of environmental microbes. While metagenomic applications have been routinely applied to better understand the ecology and diversity of microbes, their use in environmental monitoring and bioremediation is increasingly common. In this review we seek to provide an overview of some of the metagenomic techniques used in environmental systems biology, addressing their application and limitation. We will also provide several recent examples ofmore » the application of metagenomics to bioremediation. We discuss examples where microbial communities have been used to predict the presence and extent of contamination, examples of how metagenomics can be used to characterize the process of natural attenuation by unculturable microbes, as well as examples detailing the use of metagenomics to understand the impact of biostimulation on microbial communities.« less
Carbonate mineralisation in sabkha microbial mats; a comparative study of field and laboratory systems

NASA Astrophysics Data System (ADS)

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

2017-04-01

Microbial mats and their lithified counterparts are some of the earliest evidence of life on Earth. The coastal sabkha in Abu Dhabi, United Arab Emirates, is a modern setting where microbial mats flourish in a hypersaline and arid environment. These microbial communities are composed of microbes such as cyanobacteria, thermoplasmata and sulphate-reducing bacteria. The mats thrive as they are protected from predators, which are excluded by the extreme environmental conditions. Microbial mats are highly reactive to change, with their microbial communities and geochemistry varying on a millimetre scale, likely controlling mineralisation processes. Exact carbonate mineralisation rates within coastal sabkha microbial mats have not to date been quantified. Defining the mineralisation pathways and knowledge of precise mineralisation rates will help to explain how these organosedimentary structures are retained in the rock record. A fundamental understanding of the role of microbial mats in the formation of different carbonate phases is important, yet there are also other practical implications. For example, structures observed in core from the oil-bearing Arab Formation have been likened to modern microbial mats in terms of structure and mineralogy. The depositional configuration and primary mineralogy generated by microbial mats may control syndepositional lithification and later diagenesis thereby influencing reservoir porosity and permeability. In order to constrain factors effecting mineralisation and early lithification, experimentation in a controlled laboratory environment is required. Parameters for experimentation have been established during fieldwork and were applied to a tank-based laboratory simulation of sabkha microbial mats. These parameters include light, salinity and cation and anion water chemistry, gas production chemistry and vertical mat growth. Parameters were measured weekly with sampling for mineralogical and microbial community analysis on a biweekly basis. In addition to these parameter measurements already in place in current experiments, temperature and tidal cycle were monitored in the field. Over the course of the first three months, the microbial mat, which was submerged in an artificial seawater medium, grew vertically and developed a green surface at the top and sides. Thermogravimetric analysis has established that the top 1 mm surface mat biomass contains carbonate minerals, leading to an initial inferred carbonate mineralisation rate of approximately 0.5 g per 1 cm2 per year (approx. per 10 g surface mat material). This rate of mineralisation will become more accurate as more analysis is completed particularly comparing samples of mat, initially before they went in to the tank experiment and after incremental time periods, 3 months, 6 months etc. Further analysis of mat growth will establish the extent to which the precipitated carbonate minerals result from microbial activity and the types of minerals precipitated. The rate of mineralisation can be scaled-up to the km scale with the potential to isolate mineralisation rates promoted by different communities and in different types of microbial mat.
A review on the applications of microbial electrolysis cells in anaerobic digestion.

PubMed

Yu, Zhengsheng; Leng, Xiaoyun; Zhao, Shuai; Ji, Jing; Zhou, Tuoyu; Khan, Aman; Kakde, Apurva; Liu, Pu; Li, Xiangkai

2018-05-01

Anaerobic digestion (AD) has been widely used for biogas or biofuel generation from waste treatment. Because a low production rate and instability of AD occur frequently, various technologies have been applied to improvement of AD. Microbial electrolysis cells (MECs), an emerging technology, can convert organic matter into hydrogen, methane, and other value-added products. Recent studies showed that application of MEC to AD (MEC-AD) can accelerate degradation of a substrate (including recalcitrant compounds) and alter AD microbial community by enriching exoelectrogens and methanogens thus increasing biogas production. With stable microbial communities established, improvement of MEC-AD for methane production was achieved. MEC-AD process can be monitored in real-time by detecting electric signals, which linearly correlate with substrate concentrations. This review attempts to evaluate interactions among the decomposition of substrates, MEC-AD system, and the microbial community. This analysis should provide useful insights into the improvement of methane production and the performance of MEC-AD. Copyright © 2018 Elsevier Ltd. All rights reserved.
Temporal dynamics of the gut microbiota in people sharing a confined environment, a 520-day ground-based space simulation, MARS500.

PubMed

Turroni, Silvia; Rampelli, Simone; Biagi, Elena; Consolandi, Clarissa; Severgnini, Marco; Peano, Clelia; Quercia, Sara; Soverini, Matteo; Carbonero, Franck G; Bianconi, Giovanna; Rettberg, Petra; Canganella, Francesco; Brigidi, Patrizia; Candela, Marco

2017-03-24

The intestinal microbial communities and their temporal dynamics are gaining increasing interest due to the significant implications for human health. Recent studies have shown the dynamic behavior of the gut microbiota in free-living, healthy persons. To date, it is not known whether these dynamics are applicable during prolonged life sharing in a confined and controlled environment. The MARS500 project, the longest ground-based space simulation ever, provided us with a unique opportunity to trace the crew microbiota over 520 days of isolated confinement, such as that faced by astronauts in real long-term interplanetary space flights, and after returning to regular life, for a total of 2 years. According to our data, even under the strictly controlled conditions of an enclosed environment, the human gut microbiota is inherently dynamic, capable of shifting between different steady states, typically with rearrangements of autochthonous members. Notwithstanding a strong individuality in the overall gut microbiota trajectory, some key microbial components showed conserved temporal dynamics, with potential implications for the maintenance of a health-promoting, mutualistic microbiota configuration. Sharing life in a confined habitat does not affect the resilience of the individual gut microbial ecosystem, even in the long term. However, the temporal dynamics of certain microbiota components should be monitored when programming future mission simulations and real space flights, to prevent breakdowns in the metabolic and immunological homeostasis of the crewmembers.
Advanced Environmental Monitoring and Control Program: Technology Development Requirements

NASA Technical Reports Server (NTRS)

Jan, Darrell (Editor); Seshan, Panchalam (Editor); Ganapathi, Gani (Editor); Schmidt, Gregory (Editor); Doarn, Charles (Editor)

1996-01-01

Human missions in space, from the International Space Station on towards potential human exploration of the moon, Mars and beyond into the solar system, will require advanced systems to maintain an environment that supports human life. These systems will have to recycle air and water for many months or years at a time, and avoid harmful chemical or microbial contamination. NASA's Advanced Environmental Monitoring and Control program has the mission of providing future spacecraft with advanced, integrated networks of microminiaturized sensors to accurately determine and control the physical, chemical and biological environment of the crew living areas. This document sets out the current state of knowledge for requirements for monitoring the crew environment, based on (1) crew health, and (2) life support monitoring systems. Both areas are updated continuously through research and space mission experience. The technologies developed must meet the needs of future life support systems and of crew health monitoring. These technologies must be inexpensive and lightweight, and use few resources. Using these requirements to continue to push the state of the art in miniaturized sensor and control systems will produce revolutionary technologies to enable detailed knowledge of the crew environment.
Microbial Monitoring of the International Space Station

NASA Technical Reports Server (NTRS)

Pierson, Duane L.; Botkin, Douglas J.; Bruce, Rebekah J.; Castro, Victoria A.; Smith, Melanie J.; Oubre, Cherie M.; Ott, C. Mark

2013-01-01

Humans living and working in the harsh environment of space present many challenges for habitability engineers and microbiologists. Spacecraft must provide an internal environment in which physical (gas composition, pressure, temperature, and humidity), chemical, and biological environmental parameters are maintained at safe levels. Microorganisms are ubiquitous and will accompany all human-occupied spacecraft, but if biological contamination were to reach unacceptable levels, long-term human space flight would be impossible. Prevention of microbiological problems, therefore, must have a high priority. Historically, prevention of infectious disease in the crew has been the highest priority, but experience gained from the NASA-Mir program showed that microbial contamination of vehicle and life-support systems, such as biofouling of water and food, are of equal importance. The major sources of microbiological risk factors for astronauts include food, drinking water, air, surfaces, payloads, research animals, crew members, and personnel in close contact with the astronauts. In our efforts to eliminate or mitigate the negative effects of microorganisms in spacecraft, the National Aeronautics and Space Administration (NASA) implemented comprehensive microbial analyses of the major risk factors. This included the establishment of acceptability requirements for food, water, air, surfaces, and crew members. A robust monitoring program was then implemented to verify that the risks were within acceptable limits. Prevention of microbiological problems is preferred over mitigation of problems during flight, and preventive steps must begin very early in the design phase. Spacecraft development must include requirements to control free water from humidity, condensate, hygiene activities, and other releases. If water is available, microbes are likely to grow because sufficient nutrients are potentially available. Materials selected for the spacecraft must not promote or support microbial growth. Air filtration can dramatically reduce the number of airborne bacteria, fungi, and particulates in spacecraft breathing air. Waterborne bacteria can be reduced to acceptable levels by thermal inactivation of bacteria during water processing, along with a residual biocide, and filtration at the point of use can ensure safety. System design must include onboard capability to achieve recovery of the system from contamination. Robust housekeeping procedures that include periodic cleaning and disinfection will prevent high levels of microbial growth on surfaces. Food for consumption in space must be thoroughly tested for excessive microbial content and pathogens before launch. Thorough preflight examination of flight crews, consumables, payloads, and the environment can greatly reduce pathogens in spacecraft. Many of the lessons learned from the Space Shuttle and previous programs were applied in the early design phase of the International Space Station, resulting in the safest space habitat to date. This presentation describes the monitoring program for the International Space Station and will summarize results from preflight and on-orbit monitoring.
Understanding, Monitoring, and Controlling Biofilm Growth in Drinking Water Distribution Systems.

PubMed

Liu, Sanly; Gunawan, Cindy; Barraud, Nicolas; Rice, Scott A; Harry, Elizabeth J; Amal, Rose

2016-09-06

In drinking water distribution systems (DWDS), biofilms are the predominant mode of microbial growth, with the presence of extracellular polymeric substance (EPS) protecting the biomass from environmental and shear stresses. Biofilm formation poses a significant problem to the drinking water industry as a potential source of bacterial contamination, including pathogens, and, in many cases, also affecting the taste and odor of drinking water and promoting the corrosion of pipes. This article critically reviews important research findings on biofilm growth in DWDS, examining the factors affecting their formation and characteristics as well as the various technologies to characterize and monitor and, ultimately, to control their growth. Research indicates that temperature fluctuations potentially affect not only the initial bacteria-to-surface attachment but also the growth rates of biofilms. For the latter, the effect is unique for each type of biofilm-forming bacteria; ammonia-oxidizing bacteria, for example, grow more-developed biofilms at a typical summer temperature of 22 °C compared to 12 °C in fall, and the opposite occurs for the pathogenic Vibrio cholerae. Recent investigations have found the formation of thinner yet denser biofilms under high and turbulent flow regimes of drinking water, in comparison to the more porous and loosely attached biofilms at low flow rates. Furthermore, in addition to the rather well-known tendency of significant biofilm growth on corrosion-prone metal pipes, research efforts also found leaching of growth-promoting organic compounds from the increasingly popular use of polymer-based pipes. Knowledge of the unique microbial members of drinking water biofilms and, importantly, the influence of water characteristics and operational conditions on their growth can be applied to optimize various operational parameters to minimize biofilm accumulation. More-detailed characterizations of the biofilm population size and structure are now feasible with fluorescence microscopy (epifluorescence and CLSM imaging with DNA, RNA, EPS, and protein and lipid stains) and electron microscopy imaging (ESEM). Importantly, thorough identification of microbial fingerprints in drinking water biofilms is achievable with DNA sequencing techniques (the 16S rRNA gene-based identification), which have revealed a prevalence of previously undetected bacterial members. Technologies are now moving toward in situ monitoring of biomass growth in distribution networks, including the development of optical fibers capable of differentiating biomass from chemical deposits. Taken together, management of biofilm growth in water distribution systems requires an integrated approach, starting from the treatment of water prior to entering the networks to the potential implementation of "biofilm-limiting" operational conditions and, finally, ending with the careful selection of available technologies for biofilm monitoring and control. For the latter, conventional practices, including chlorine-chloramine disinfection, flushing of DWDS, nutrient removal, and emerging technologies are discussed with their associated challenges.

Anaerobic digestion of food waste: A review focusing on process stability.

PubMed

Li, Lei; Peng, Xuya; Wang, Xiaoming; Wu, Di

2018-01-01

Food waste (FW) is rich in biomass energy, and increasing numbers of national programs are being established to recover energy from FW using anaerobic digestion (AD). However process instability is a common operational issue for AD of FW. Process monitoring and control as well as microbial management can be used to control instability and increase the energy conversion efficiency of anaerobic digesters. Here, we review research progress related to these methods and identify existing limitations to efficient AD; recommendations for future research are also discussed. Process monitoring and control are suitable for evaluating the current operational status of digesters, whereas microbial management can facilitate early diagnosis and process optimization. Optimizing and combining these two methods are necessary to improve AD efficiency. Copyright © 2017 Elsevier Ltd. All rights reserved.
Hospital microbial surface colonization revealed during monitoring of Klebsiella spp., Pseudomonas aeruginosa, and non-tuberculous mycobacteria.

PubMed

Geadas Farias, Pedro; Gama, Fernando; Reis, Diogo; Alarico, Susana; Empadinhas, Nuno; Martins, José Carlos; de Almeida, Ana Figueiredo; Morais, Paula Vasconcelos

2017-07-01

Hospital environmental conditions, human occupancy, and the characteristics of the equipment influence the survival of microbial communities and raise a concern with regard to nosocomial infections. The objective of the present work was to use the monitoring of Pseudomonas aeruginosa, Klebsiella spp. and non-tuberculous mycobacteria as a strategy to improve knowledge on microbial colonization of non-critical equipment and surfaces, in a tertiary hospital from Central Portugal. A 3-month microbiological survey was performed in a district teaching hospital. A total of 173 samples were obtained from the wards Hematology, Urology, Medicine, and Renal Transplants, and 102 presumptive strains recovered. Per sampling, Pseudomonas Isolation agar showed 42.8 to 73.3% of presumptive P. aeruginosa colonies and MacConkey agar recovered mostly Staphylococcus. Most of the colonies recovered in Middlebrook 7H10-PANTA belonged to the genus Methylobacterium. Taps and WC shower curtains carry high bacterial species diversity. The Redundancy Analysis grouped the samples in those mostly handled by patients, and those mostly handled by healthcare staff or of mixed use. This study shows that the preferential users of the space and equipment seem to be important contributors to the microbial community. The most recovered genus was Methylobacterium, known as colonizer of the water distribution system therefore, it is possible that the water points and biofilms in taps also contribute as dispersion hotspots.
Fast and sensitive optical toxicity bioassay based on dual wavelength analysis of bacterial ferricyanide reduction kinetics.

PubMed

Pujol-Vila, F; Vigués, N; Díaz-González, M; Muñoz-Berbel, X; Mas, J

2015-05-15

Global urban and industrial growth, with the associated environmental contamination, is promoting the development of rapid and inexpensive general toxicity methods. Current microbial methodologies for general toxicity determination rely on either bioluminescent bacteria and specific medium solution (i.e. Microtox(®)) or low sensitivity and diffusion limited protocols (i.e. amperometric microbial respirometry). In this work, fast and sensitive optical toxicity bioassay based on dual wavelength analysis of bacterial ferricyanide reduction kinetics is presented, using Escherichia coli as a bacterial model. Ferricyanide reduction kinetic analysis (variation of ferricyanide absorption with time), much more sensitive than single absorbance measurements, allowed for direct and fast toxicity determination without pre-incubation steps (assay time=10 min) and minimizing biomass interference. Dual wavelength analysis at 405 (ferricyanide and biomass) and 550 nm (biomass), allowed for ferricyanide monitoring without interference of biomass scattering. On the other hand, refractive index (RI) matching with saccharose reduced bacterial light scattering around 50%, expanding the analytical linear range in the determination of absorbent molecules. With this method, different toxicants such as metals and organic compounds were analyzed with good sensitivities. Half maximal effective concentrations (EC50) obtained after 10 min bioassay, 2.9, 1.0, 0.7 and 18.3 mg L(-1) for copper, zinc, acetic acid and 2-phenylethanol respectively, were in agreement with previously reported values for longer bioassays (around 60 min). This method represents a promising alternative for fast and sensitive water toxicity monitoring, opening the possibility of quick in situ analysis. Copyright © 2014 Elsevier B.V. All rights reserved.
High Resolution Measurement of Rhizosphere Priming Effects and Temporal Variability of CO2 Fluxes under Zea Mays

NASA Astrophysics Data System (ADS)

Splettstößer, T.; Pausch, J.

2016-12-01

Plant induced increase of soil organic matter turnover rates contribute to carbon emissions in agricultural land use systems. In order to better understand these rhizosphere priming effects, we conducted an experiment, which enabled us to monitor CO2 fluxes under zea mays plants with high resolution. The experiment was conducted in a climate chamber where the plants were grown in thin, tightly sealed boxes for 40 days and CO2 efflux from soil was measured twice a day. 13C-CO2 was introduced to allow differentiation between plant and soil derived CO2.This enabled us to monitor root respiration and soil organic matter turnover in the early stages of plant growth and to highlight changes in soil CO2 emissions and priming effects between day and night. The measurements were conducted with a PICARRO G2131-I δ13C high-precision isotopic CO2 Analyzer (PICARRO INC.) utilizing an automated valve system governed by a CR1000 data logger (Campbell Scientific). After harvest roots and shoots were analyzed for 13C content. Microbial biomass, root length density and enzymatic activities in soil were measured and linked to soil organic matter turnover rates. In order to visualize the spatial distribution of carbon allocation to the root system a few plants were additionally labeled with 14C and 14C distribution was monitored by 14C imaging of the root systems over 4 days. Based on the 14C distribution a grid was chosen and the soil was sampled from each square of the grid to investigate the impact of carbon allocation hotspots on enzymatic activities and microbial biomass. First initial results show an increase of soil CO2 efflux in the night periods, whereby the contribution of priming is not fully analyzed yet. Additionally, root tips were identified as hotspots of short term carbon allocation via 14C imaging and an in increase in microbial biomass could be measured in this regions. The full results will be shown at AGU 2016.
Impact of electrochemical treatment of soil washing solution on PAH degradation efficiency and soil respirometry.

PubMed

Mousset, Emmanuel; Huguenot, David; van Hullebusch, Eric D; Oturan, Nihal; Guibaud, Gilles; Esposito, Giovanni; Oturan, Mehmet A

2016-04-01

The remediation of a genuinely PAH-contaminated soil was performed, for the first time, through a new and complete investigation, including PAH extraction followed by advanced oxidation treatment of the washing solution and its recirculation, and an analysis of the impact of the PAH extraction on soil respirometry. The study has been performed on the remediation of genuine PAH-contaminated soil, in the following three steps: (i) PAH extraction with soil washing (SW) techniques, (ii) PAH degradation with an electro-Fenton (EF) process, and (iii) recirculation of the partially oxidized effluent for another SW cycle. The following criteria were monitored during the successive washing cycles: PAH extraction efficiency, PAH oxidation rates and yields, extracting agent recovery, soil microbial activity, and pH of soil. Two representative extracting agents were compared: hydroxypropyl-beta-cyclodextrin (HPCD) and a non-ionic surfactant, Tween(®) 80. Six PAH with different numbers of rings were monitored: acenaphthene (ACE), phenanthrene (PHE), fluoranthene (FLA), pyrene (PYR), benzo(a)pyrene (BaP), and benzo(g,h,i)perylene (BghiP). Tween(®) 80 showed much better PAH extraction efficiency (after several SW cycles) than HPCD, regardless of the number of washing cycles. Based on successive SW experiments, a new mathematical relation taking into account the soil/water partition coefficient (Kd*) was established, and could predict the amount of each PAH extracted by the surfactant with a good correlation with experimental results (R(2) > 0.975). More HPCD was recovered (89%) than Tween(®) 80 (79%), while the monitored pollutants were completely degraded (>99%) after 4 h and 8 h, respectively. Even after being washed with partially oxidized solutions, the Tween(®) 80 solutions extracted significantly more PAH than HPCD and promoted better soil microbial activity, with higher oxygen consumption rates. Moreover, neither the oxidation by-products nor the acidic media (pH approximately 3) of the partially oxidized solution inhibited the general soil microbial activity during the washing cycle. Copyright © 2016 Elsevier Ltd. All rights reserved.
Plant Growth Module (PGM) conceptual design

NASA Technical Reports Server (NTRS)

Schwartzkopf, Steven H.; Rasmussen, Daryl

1987-01-01

The Plant Growth Module for the Controlled Ecological Life Support System (CELSS), designed to answer basic science questions related to growing plants in closed systems, is described functionally with artist's conception drawings. Subsystems are also described, including enclosure and access; data acquisition and control; gas monitor and control; heating, ventilation, and air conditioning; air delivery; nutrient monitor and control; microbial monitoring and control; plant support and nutrient delivery; illumination; and internal operations. The hardware development plan is outlined.
Innovative Methods for Integrating Knowledge for Long-Term Monitoring of Contaminated Groundwater Sites: Understanding Microorganism Communities and their Associated Hydrochemical Environment

NASA Astrophysics Data System (ADS)

Mouser, P. J.; Rizzo, D. M.; Druschel, G.; O'Grady, P.; Stevens, L.

2005-12-01

This interdisciplinary study integrates hydrochemical and genome-based data to estimate the redox processes occurring at long-term monitoring sites. Groundwater samples have been collected from a well-characterized landfill-leachate contaminated aquifer in northeastern New York. Primers from the 16S rDNA gene were used to amplify Bacteria and Archaea in groundwater taken from monitoring wells located in clean, fringe, and contaminated locations within the aquifer. PCR-amplified rDNA were digested with restriction enzymes to evaluate terminal restriction fragment length polymorphism (T-RFLP) community profiles. The rDNA was cloned, sequenced, and partial sequences were matched against known organisms using the NCBI Blast database. Phylogenetic trees and bootstrapping were used to identify classifications of organisms and compare the communities from clean, fringe, and contaminated locations. We used Artificial Neural Network (ANN) models to incorporate microbial data with hydrochemical information for improving our understanding of subsurface processes.
Exploring the Association between Alzheimer's Disease, Oral Health, Microbial Endocrinology and Nutrition.

PubMed

Harding, Alice; Gonder, Ulrike; Robinson, Sarita J; Crean, StJohn; Singhrao, Sim K

2017-01-01

Longitudinal monitoring of patients suggests a causal link between chronic periodontitis and the development of Alzheimer's disease (AD). However, the explanation of how periodontitis can lead to dementia remains unclear. A working hypothesis links extrinsic inflammation as a secondary cause of AD. This hypothesis suggests a compromised oral hygiene leads to a dysbiotic oral microbiome whereby Porphyromonas gingivalis , a keystone periodontal pathogen, with its companion species, orchestrates immune subversion in the host. Brushing and chewing on teeth supported by already injured soft tissues leads to bacteremias. As a result, a persistent systemic inflammatory response develops to periodontal pathogens. The pathogens, and the host's inflammatory response, subsequently lead to the initiation and progression of multiple metabolic and inflammatory co-morbidities, including AD. Insufficient levels of essential micronutrients can lead to microbial dysbiosis through the growth of periodontal pathogens such as demonstrated for P. gingivalis under low hemin bioavailability. An individual's diet also defines the consortium of microbial communities that take up residency in the oral and gastrointestinal (GI) tract microbiomes. Their imbalance can lead to behavioral changes. For example, probiotics enriched in Lactobacillus genus of bacteria, when ingested, exert some anti-inflammatory influence through common host/bacterial neurochemicals, both locally, and through sensory signaling back to the brain. Early life dietary behaviors may cause an imbalance in the host/microbial endocrinology through a dietary intake incompatible with a healthy GI tract microbiome later in life. This imbalance in host/microbial endocrinology may have a lasting impact on mental health. This observation opens up an opportunity to explore the mechanisms, which may underlie the previously detected relationship between diet, oral/GI microbial communities, to anxiety, cognition and sleep patterns. This review suggests healthy diet based interventions that together with improved life style/behavioral changes may reduce and/or delay the incidence of AD.
The effect of in-stream activities on the Njoro River, Kenya. Part II: Microbial water quality

NASA Astrophysics Data System (ADS)

Yillia, Paul T.; Kreuzinger, Norbert; Mathooko, Jude M.

The influence of periodic in-stream activities of people and livestock on the microbial water quality of the Njoro River in Kenya was monitored at two disturbed pools (Turkana Flats and Njoro Bridge) at the middle reaches. A total of 96 sets of samples were obtained from the two pools in six weeks during dry weather (January-April) in 2006. On each sampling day, two trips were made before and during in-stream activities and on each trip, two sets of samples were collected upstream and downstream of activities. This schedule was repeated four times each for Wednesday, Saturday and Sunday. Samples were processed for heterotrophic plate count bacteria (HPC), total coliform (TC), presumptive Escherichia coli and presumptive Enterococci. Additional samples were analysed for total suspended solids (TSS), turbidity, BOD 5 and ammonium-N. The microbial water quality deteriorated significant ( p < 0.05) downstream during activities at both pools. A similar trend was observed with the chemical indicators (TSS, turbidity, BOD 5 and ammonium-N). The two groups of indicators demonstrated high capacity for site segregation based on pollution levels. Pollution levels for specific days were not significantly different ( p > 0.05). This was incompatible with the variability of in-stream activities with specific days. The pooled data was explained largely by three significant principal components - recent pollution (PC1), metabolic activity (PC2) and residual pollution (PC3). It was concluded that the empirical site parity/disparity in the levels of microbial and non-microbial indicators reflected the diurnal periodicity of in-stream activities and the concomitant pollution they caused. However, microbial source tracking studies are required to distinguish faecal sources. In the meantime, measures should be undertaken to regulate in-stream activities along the stream and minimize the movement of livestock in the catchment.
Exploring the Association between Alzheimer’s Disease, Oral Health, Microbial Endocrinology and Nutrition

PubMed Central

Harding, Alice; Gonder, Ulrike; Robinson, Sarita J.; Crean, StJohn; Singhrao, Sim K.

2017-01-01

Longitudinal monitoring of patients suggests a causal link between chronic periodontitis and the development of Alzheimer’s disease (AD). However, the explanation of how periodontitis can lead to dementia remains unclear. A working hypothesis links extrinsic inflammation as a secondary cause of AD. This hypothesis suggests a compromised oral hygiene leads to a dysbiotic oral microbiome whereby Porphyromonas gingivalis, a keystone periodontal pathogen, with its companion species, orchestrates immune subversion in the host. Brushing and chewing on teeth supported by already injured soft tissues leads to bacteremias. As a result, a persistent systemic inflammatory response develops to periodontal pathogens. The pathogens, and the host’s inflammatory response, subsequently lead to the initiation and progression of multiple metabolic and inflammatory co-morbidities, including AD. Insufficient levels of essential micronutrients can lead to microbial dysbiosis through the growth of periodontal pathogens such as demonstrated for P. gingivalis under low hemin bioavailability. An individual’s diet also defines the consortium of microbial communities that take up residency in the oral and gastrointestinal (GI) tract microbiomes. Their imbalance can lead to behavioral changes. For example, probiotics enriched in Lactobacillus genus of bacteria, when ingested, exert some anti-inflammatory influence through common host/bacterial neurochemicals, both locally, and through sensory signaling back to the brain. Early life dietary behaviors may cause an imbalance in the host/microbial endocrinology through a dietary intake incompatible with a healthy GI tract microbiome later in life. This imbalance in host/microbial endocrinology may have a lasting impact on mental health. This observation opens up an opportunity to explore the mechanisms, which may underlie the previously detected relationship between diet, oral/GI microbial communities, to anxiety, cognition and sleep patterns. This review suggests healthy diet based interventions that together with improved life style/behavioral changes may reduce and/or delay the incidence of AD. PMID:29249963
New insight into microbial diversity and functions in traditional Vietnamese alcoholic fermentation.

PubMed

Thanh, Vu Nguyen; Thuy, Nguyen Thanh; Chi, Nguyen Thuy; Hien, Dinh Duc; Ha, Bui Thi Viet; Luong, Dao Thi; Ngoc, Pham Duc; Ty, Pham Van

2016-09-02

The roles of microorganisms in traditional alcoholic fermentation are often assumed based on abundance in the starter and activity in pure culture. There is a serious lack of hard evidence on the behavior and activity of individual microbial species during the actual fermentation process. In this study, microbial succession and metabolite changes during 7days of traditional Vietnamese alcoholic fermentation were monitored. Special attention was devoted to starch degradation. In total, 22 microbial species, including 6 species of filamentous fungi (Rhizopus microsporus, Rhizopus arrhizus, Mucor indicus, Mucor circinelloides, Cunninghamella elegans, Aspergillus niger), 1 yeast-like fungus (Saccharomycopsis fibuligera), 7 yeasts (Saccharomyces cerevisiae, Clavispora lusitaniae, Wickerhamomyces anomalus, Lindnera fabianii, Pichia kudriavzevii, Candida rugosa, Candida tropicalis), and 8 bacteria (Stenotrophomonas maltophilia, Lactobacillus brevis, Lactobacillus helveticus, Acinetobacter baumannii, Staphylococcus hominis, Bacillus megaterium, Enterobacter asburiae, Pediococcus pentosaceus) were identified. Despite the presence of a complex microbiota in the starter, the fermentation process is consistent and involves a limited number of functional species. Rapid change in microbial composition of fermentation mash was observed and it was correlated with ethanol content. Microbial biomass reached maximum during first 2days of solid state fermentation. Acidification of the medium took place in day 1, starch degradation in days 2, 3, 4, and alcohol accumulation from day 3. Although Sm. fibuligera dominated by cell count amongst potential starch degraders, zymography indicated that it did not produce amylase in the fermentation mash. In mixed culture with Rhizopus, amylase production by Sm. fibuligera is regulated by the moisture content of the substrate. Rhizopus was identified as the main starch degrader and S. cerevisiae as the main ethanol producer. Bacterial load was high but unstable in species composition and dominated by acid producers. M. indicus, Sm. fibuligera, W. anomalus and bacteria were regarded as satellite microorganisms. Their possible influence on organoleptic quality of fermentation product was discussed. Copyright © 2016 Elsevier B.V. All rights reserved.
Microbial Monitoring from the Frontlines to Space: Department of Defense Small Business Innovation Research Technology Aboard the International Space Station

NASA Technical Reports Server (NTRS)

Oubre, Cherie M.; Khodadad, Christina L.; Castro, Victoria A.; Ott, C. Mark; Flint, Stephanie; Pollack, Lawrence P.; Roman, Monserrate C.

2017-01-01

The RAZOR (trademark) EX, a quantitative Polymerase Chain Reaction (qPCR) instrument, is a portable, ruggedized unit that was designed for the Department of Defense (DoD) with its reagent chemistries traceable to a Small Business Innovation Research (SBIR) contract beginning in 2002. The PCR instrument's primary function post 9/11 was to enable frontline soldiers and first responders to detect biological threat agents and bioterrorism activities in remote locations to include field environments. With its success for DoD, the instrument has also been employed by other governmental agencies including Department of Homeland Security (DHS). The RAZOR (Trademark) EX underwent stringent testing by the vendor, as well as through the DoD, and was certified in 2005. In addition, the RAZOR (trademark) EX passed DHS security sponsored Stakeholder Panel on Agent Detection Assays (SPADA) rigorous evaluation in 2011. The identification and quantitation of microbial pathogens is necessary both on the ground as well as during spaceflight to maintain the health of astronauts and to prevent biofouling of equipment. Currently, culture-based monitoring technology has been adequate for short-term spaceflight missions but may not be robust enough to meet the requirements for long-duration missions. During a NASA-sponsored workshop in 2011, it was determined that the more traditional culture-based method should be replaced or supplemented with more robust technologies. NASA scientists began investigating innovative molecular technologies for future space exploration and as a result, PCR was recommended. Shortly after, NASA sponsored market research in 2012 to identify and review current, commercial, cutting edge PCR technologies for potential applicability to spaceflight operations. Scientists identified and extensively evaluated three candidate technologies with the potential to function in microgravity. After a thorough voice-of-the-customer trade study and extensive functional and safety evaluations, the RAZOR (trademark) EX PCR instrument(Bio-Fire Defense, Salt Lake City, UT) was selected as the most promising current technology for spaceflight monitoring applications.
Development of a microbial time/temperature indicator prototype for monitoring the microbiological quality of chilled foods.

PubMed

Vaikousi, Hariklia; Biliaderis, Costas G; Koutsoumanis, Konstantinos P

2008-05-01

A time/temperature indicator (TTI) system based on the growth and metabolic activity of a Lactobacillus sakei strain was developed for monitoring food quality throughout the chilled-food chain. In the designed system, an irreversible color change of a chemical chromatic indicator (from red to yellow) progressively occurs due to the pH decline that results from microbial growth and metabolism in a selected medium. The relation of the TTI response (color change) to the growth and metabolic activity (glucose consumption, lactic acid production, pH decrease) of L. sakei was studied. In addition, the temperature dependence of the TTI kinetics was investigated isothermally in the range of 0 to 16 degrees C and modeled with a system of differential equations. At all temperatures tested, the pH and color changes of the TTI system followed closely the growth of L. sakei, with the endpoint (the time at which a distinct visual color change to the final yellow was observed) of the TTI coinciding with a population level of 10(7) to 10(8) CFU/ml. The endpoint decreased from 27 days at 0 degrees C to 2.5 days at 16 degrees C, yielding an activation energy of 97.7 kJ/mol, which was very close to the activation energy of the L. sakei growth rate in the TTI substrate (103.2 kJ/mol). Furthermore, experiments conducted on the effect of the inoculum level showed a negative linear relationship between the level of L. sakei inoculated in the system medium and the endpoint of the TTI. For example, the endpoint at 8 degrees C ranged from 6 to 2 days for inoculum levels of 10(1) and 10(6) CFU/ml, respectively. This relationship allows the easy adjustment of the TTI endpoint at a certain temperature according to the shelf life of the food product of concern by using an appropriate inoculum level of L. sakei. The microbial TTI prototype developed in the present study could be used as an effective tool for monitoring shelf life during the distribution and storage of food products that are spoiled primarily by lactic acid bacteria or other bacteria exhibiting similar kinetic responses and spoilage potentials. Apart from the low cost, the main advantage of the proposed TTI is that its response closely matches the loss of the quality of a food product by simulating the microbial spoilage process in particular environments.
Development of a Microbial Time/Temperature Indicator Prototype for Monitoring the Microbiological Quality of Chilled Foods▿

PubMed Central

Vaikousi, Hariklia; Biliaderis, Costas G.; Koutsoumanis, Konstantinos P.

2008-01-01

A time/temperature indicator (TTI) system based on the growth and metabolic activity of a Lactobacillus sakei strain was developed for monitoring food quality throughout the chilled-food chain. In the designed system, an irreversible color change of a chemical chromatic indicator (from red to yellow) progressively occurs due to the pH decline that results from microbial growth and metabolism in a selected medium. The relation of the TTI response (color change) to the growth and metabolic activity (glucose consumption, lactic acid production, pH decrease) of L. sakei was studied. In addition, the temperature dependence of the TTI kinetics was investigated isothermally in the range of 0 to 16°C and modeled with a system of differential equations. At all temperatures tested, the pH and color changes of the TTI system followed closely the growth of L. sakei, with the endpoint (the time at which a distinct visual color change to the final yellow was observed) of the TTI coinciding with a population level of 107 to 108 CFU/ml. The endpoint decreased from 27 days at 0°C to 2.5 days at 16°C, yielding an activation energy of 97.7 kJ/mol, which was very close to the activation energy of the L. sakei growth rate in the TTI substrate (103.2 kJ/mol). Furthermore, experiments conducted on the effect of the inoculum level showed a negative linear relationship between the level of L. sakei inoculated in the system medium and the endpoint of the TTI. For example, the endpoint at 8°C ranged from 6 to 2 days for inoculum levels of 101 and 106 CFU/ml, respectively. This relationship allows the easy adjustment of the TTI endpoint at a certain temperature according to the shelf life of the food product of concern by using an appropriate inoculum level of L. sakei. The microbial TTI prototype developed in the present study could be used as an effective tool for monitoring shelf life during the distribution and storage of food products that are spoiled primarily by lactic acid bacteria or other bacteria exhibiting similar kinetic responses and spoilage potentials. Apart from the low cost, the main advantage of the proposed TTI is that its response closely matches the loss of the quality of a food product by simulating the microbial spoilage process in particular environments. PMID:18326676
Effects of carbon amendment on in situ atrazine degradation and total microbial biomass.

PubMed

Ngigi, Anastasiah N; Getenga, Zachary M; Dörfler, Ulrike; Boga, Hamadi I; Kuria, Benson; Ndalut, Paul; Schroll, Reiner

2013-01-01

This study elucidates the effects of carbon amendment on metabolic degradation of atrazine (6-chloro-N(2)-ethyl-N(4)-isopropyl-1,3,5-triazine-2,4-diamine) and total microbial biomass in soil. Degradation of (14)C-ring-labelled atrazine was monitored in laboratory incubations of soils supplemented with 0, 10, 100 and 1000 μg g(-1) sucrose concentrations. An experiment to determine the effect of carbon amendment on total microbial biomass and soil respiration was carried out with different concentrations of sucrose and non-labelled atrazine. The soils were incubated at a constant temperature and constant soil moisture at water potential of -15 kPa and a soil density of 1.3 g cm(-3). Mineralization of (14)C-ring-labelled atrazine was monitored continuously over a period of 59 d in the first experiment. The CO(2) production was monitored for 62 d in the second experiment and microbial biomass determined at the end of the incubation period. The addition of 1000 μg g(-1) sucrose reduced atrazine mineralization to 43.5% compared to 51.7% of the applied amount for the treatment without sucrose. The addition of 1000 μg g(-1) sucrose modified the transformation products to 1.08 μg g(-1) deisopropylatrazine (DIA), 0.32 μg g(-1) desethylatrazine (DEA) and 0.18 μg g(-1) deisopropyl-2-hydroxyatrazine (OH-DIA). Treatment without sucrose resulted in formation of 0.64 μg g(-1) hydroxyatrazine (HA), 0.28 μg g(-1) DIA and 0.20 μg g(-1) OH-DIA. Atrazine dealkylation was enhanced in treatments with 100 and 1000 μg g(-1) of sucrose added. HA metabolite was formed in the control (no sucrose) and in the presence of 10 μg g(-1) of sucrose, whereas DEA was only detected in treatment with 1000 μg g(-1) sucrose. Results indicate that total microbial biomass increased significantly (P < 0.001) with the addition of 1000 μg g(-1) sucrose.
Fluctuations in Species-Level Protein Expression Occur during Element and Nutrient Cycling in the Subsurface

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

Wilkins, Michael J.; Wrighton, Kelly C.; Nicora, Carrie D.

2013-03-05

While microbial activities in environmental systems play a key role in the utilization and cycling of essential elements and compounds, microbial activity and growth frequently fluctuates in response to environmental stimuli and perturbations. To investigate these fluctuations within a saturated aquifer system, we monitored a carbon-stimulated in situ Geobacter population while iron reduction was occurring, using 16S rRNA abundances and high-resolution tandem mass spectrometry proteome measurements. Following carbon amendment, 16S rRNA analysis of temporally separated samples revealed the rapid enrichment of Geobacter-like environmental strains with strong similarity to G. bemidjiensis. Tandem mass spectrometry proteomics measurements suggest high carbon flux throughmore » Geobacter respiratory pathways, and the synthesis of anapleurotic four carbon compounds from acetyl-CoA via pyruvate ferredoxin oxidoreductase activity. Across a 40-day period where Fe(III) reduction was occurring, fluctuations in protein expression reflected changes in anabolic versus catabolic reactions, with increased levels of biosynthesis occurring soon after acetate arrival in the aquifer. In addition, localized shifts in nutrient limitation were inferred based on expression of nitrogenase enzymes and phosphate uptake proteins. These temporal data offer the first example of differing microbial protein expression associated with changing geochemical conditions in a subsurface environment.« less
Comparison of Different Strategies for Selection/Adaptation of Mixed Microbial Cultures Able to Ferment Crude Glycerol Derived from Second-Generation Biodiesel.

PubMed

Varrone, C; Heggeset, T M B; Le, S B; Haugen, T; Markussen, S; Skiadas, I V; Gavala, H N

2015-01-01

Objective of this study was the selection and adaptation of mixed microbial cultures (MMCs), able to ferment crude glycerol generated from animal fat-based biodiesel and produce building-blocks and green chemicals. Various adaptation strategies have been investigated for the enrichment of suitable and stable MMC, trying to overcome inhibition problems and enhance substrate degradation efficiency, as well as generation of soluble fermentation products. Repeated transfers in small batches and fed-batch conditions have been applied, comparing the use of different inoculum, growth media, and Kinetic Control. The adaptation of activated sludge inoculum was performed successfully and continued unhindered for several months. The best results showed a substrate degradation efficiency of almost 100% (about 10 g/L glycerol in 21 h) and different dominant metabolic products were obtained, depending on the selection strategy (mainly 1,3-propanediol, ethanol, or butyrate). On the other hand, anaerobic sludge exhibited inactivation after a few transfers. To circumvent this problem, fed-batch mode was used as an alternative adaptation strategy, which led to effective substrate degradation and high 1,3-propanediol and butyrate production. Changes in microbial composition were monitored by means of Next Generation Sequencing, revealing a dominance of glycerol consuming species, such as Clostridium, Klebsiella, and Escherichia.
Oxygen exposure promotes fuel diversity for Shewanella oneidensis microbial fuel cells.

PubMed

Biffinger, Justin C; Byrd, Jacqueline N; Dudley, Breanna L; Ringeisen, Bradley R

2008-01-18

Miniature microbial fuel cells (mini-MFCs) were used to monitor the current generated by Shewanella oneidensis DSP10 under both anaerobic and aerobic conditions when exposed to glucose as a potential electron donor. In addition to glucose, other carbon fuels including fructose, sucrose, acetate, and ascorbic acid were also tested. When the anolyte containing S. oneidensis was grown in the presence of oxygen, power densities of 270+/-10, 350+/-20, and 120+/-10 W/m(3) were recorded from the mini-MFC for glucose, fructose, and ascorbic acid electron donors, respectively, while sucrose and acetate produced no response. The power produced from glucose decreased considerably (
Alginate-Encapsulated Bacteria for the Treatment of Hypersaline Solutions in Microbial Fuel Cells.

PubMed

Alkotaini, Bassam; Tinucci, Samantha L; Robertson, Stuart J; Hasan, Kamrul; Minteer, Shelley D; Grattieri, Matteo

2018-04-27

A microbial fuel cell (MFC) based on a new wild-type strain of Salinivibrio sp. allowed the self-sustained treatment of hypersaline solutions (100 g L -1 , 1.71 m NaCl), reaching a removal of (87±11) % of the initial chemical oxygen demand after five days of operation, being the highest value achieved for hypersaline MFC. The degradation process and the evolution of the open circuit potential of the MFCs were correlated, opening the possibility for online monitoring of the treatment. The use of alginate capsules to trap bacterial cells, increasing cell density and stability, resulted in an eightfold higher power output, together with a more stable system, allowing operation up to five months with no maintenance required. The reported results are of critical importance to efforts to develop a sustainable and cost-effective system that treats hypersaline waste streams and reduces the quantity of polluting compounds released. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
Lineage Tracking for Probing Heritable Phenotypes at Single-Cell Resolution

PubMed Central

Cottinet, Denis; Condamine, Florence; Bremond, Nicolas; Griffiths, Andrew D.; Rainey, Paul B.; de Visser, J. Arjan G. M.; Baudry, Jean; Bibette, Jérôme

2016-01-01

Determining the phenotype and genotype of single cells is central to understand microbial evolution. DNA sequencing technologies allow the detection of mutants at high resolution, but similar approaches for phenotypic analyses are still lacking. We show that a drop-based millifluidic system enables the detection of heritable phenotypic changes in evolving bacterial populations. At time intervals, cells were sampled and individually compartmentalized in 100 nL drops. Growth through 15 generations was monitored using a fluorescent protein reporter. Amplification of heritable changes–via growth–over multiple generations yields phenotypically distinct clusters reflecting variation relevant for evolution. To demonstrate the utility of this approach, we follow the evolution of Escherichia coli populations during 30 days of starvation. Phenotypic diversity was observed to rapidly increase upon starvation with the emergence of heritable phenotypes. Mutations corresponding to each phenotypic class were identified by DNA sequencing. This scalable lineage-tracking technology opens the door to large-scale phenotyping methods with special utility for microbiology and microbial population biology. PMID:27077662

Lineage Tracking for Probing Heritable Phenotypes at Single-Cell Resolution.

PubMed

Cottinet, Denis; Condamine, Florence; Bremond, Nicolas; Griffiths, Andrew D; Rainey, Paul B; de Visser, J Arjan G M; Baudry, Jean; Bibette, Jérôme

2016-01-01

Determining the phenotype and genotype of single cells is central to understand microbial evolution. DNA sequencing technologies allow the detection of mutants at high resolution, but similar approaches for phenotypic analyses are still lacking. We show that a drop-based millifluidic system enables the detection of heritable phenotypic changes in evolving bacterial populations. At time intervals, cells were sampled and individually compartmentalized in 100 nL drops. Growth through 15 generations was monitored using a fluorescent protein reporter. Amplification of heritable changes-via growth-over multiple generations yields phenotypically distinct clusters reflecting variation relevant for evolution. To demonstrate the utility of this approach, we follow the evolution of Escherichia coli populations during 30 days of starvation. Phenotypic diversity was observed to rapidly increase upon starvation with the emergence of heritable phenotypes. Mutations corresponding to each phenotypic class were identified by DNA sequencing. This scalable lineage-tracking technology opens the door to large-scale phenotyping methods with special utility for microbiology and microbial population biology.
Applications of chemiluminescence to bacterial analysis

NASA Technical Reports Server (NTRS)

Searle, N. D.

1975-01-01

Luminol chemiluminescence method for detecting bacteria was based on microbial activation of the oxidation of the luminol monoanion by hydrogen peroxide. Elimination of the prior lysing step, previously used in the chemiluminescence technique, was shown to improve considerably the reproducibility and accuracy of the method in addition to simplifying it. An inexpensive, portable photomultiplier detector was used to measure the maximum light intensity produced when the sample is added to the reagent. Studies of cooling tower water show that the luminol chemiluminescence technique can be used to monitor changes in viable cell population both under normal conditions and during chlorine treatment. Good correlation between chemiluminescence and plate counts was also obtained in the analysis of process water used in paper mills. This method showed good potential for monitoring the viable bacteria populations in activated sludge used in waste treatment plants to digest organic matter.
Color identification and fuzzy reasoning based monitoring and controlling of fermentation process of branched chain amino acid

NASA Astrophysics Data System (ADS)

Ma, Lei; Wang, Yizhong; Xu, Qingyang; Huang, Huafang; Zhang, Rui; Chen, Ning

2009-11-01

The main production method of branched chain amino acid (BCAA) is microbial fermentation. In this paper, to monitor and to control the fermentation process of BCAA, especially its logarithmic phase, parameters such as the color of fermentation broth, culture temperature, pH, revolution, dissolved oxygen, airflow rate, pressure, optical density, and residual glucose, are measured and/or controlled and/or adjusted. The color of fermentation broth is measured using the HIS color model and a BP neural network. The network's input is the histograms of hue H and saturation S, and output is the color description. Fermentation process parameters are adjusted using fuzzy reasoning, which is performed by inference rules. According to the practical situation of BCAA fermentation process, all parameters are divided into four grades, and different fuzzy rules are established.
21 CFR 866.2560 - Microbial growth monitor.

Code of Federal Regulations, 2010 CFR

2010-04-01

... measures the concentration of bacteria suspended in a liquid medium by measuring changes in light.... With the exception of automated blood culturing system devices that are used in testing for bacteria...
21 CFR 866.2560 - Microbial growth monitor.

Code of Federal Regulations, 2011 CFR

2011-04-01

... measures the concentration of bacteria suspended in a liquid medium by measuring changes in light.... With the exception of automated blood culturing system devices that are used in testing for bacteria...
Good Manufacturing Practices and Microbial Contamination Sources in Orange Fleshed Sweet Potato Puree Processing Plant in Kenya

PubMed Central

Abong', George Ooko

2018-01-01

Limited information exists on the status of hygiene and probable sources of microbial contamination in Orange Fleshed Sweet Potato (OFSP) puree processing. The current study is aimed at determining the level of compliance to Good Manufacturing Practices (GMPs), hygiene, and microbial quality in OFSP puree processing plant in Kenya. Intensive observation and interviews using a structured GMPs checklist, environmental sampling, and microbial analysis by standard microbiological methods were used in data collection. The results indicated low level of compliance to GMPs with an overall compliance score of 58%. Microbial counts on food equipment surfaces, installations, and personnel hands and in packaged OFSP puree were above the recommended microbial safety and quality legal limits. Steaming significantly (P < 0.05) reduced microbial load in OFSP cooked roots but the counts significantly (P < 0.05) increased in the puree due to postprocessing contamination. Total counts, yeasts and molds, Enterobacteriaceae, total coliforms, and E. coli and S. aureus counts in OFSP puree were 8.0, 4.0, 6.6, 5.8, 4.8, and 5.9 log10 cfu/g, respectively. In conclusion, equipment surfaces, personnel hands, and processing water were major sources of contamination in OFSP puree processing and handling. Plant hygiene inspection, environmental monitoring, and food safety trainings are recommended to improve hygiene, microbial quality, and safety of OFSP puree. PMID:29808161
Good Manufacturing Practices and Microbial Contamination Sources in Orange Fleshed Sweet Potato Puree Processing Plant in Kenya.

PubMed

Malavi, Derick Nyabera; Muzhingi, Tawanda; Abong', George Ooko

2018-01-01

Limited information exists on the status of hygiene and probable sources of microbial contamination in Orange Fleshed Sweet Potato (OFSP) puree processing. The current study is aimed at determining the level of compliance to Good Manufacturing Practices (GMPs), hygiene, and microbial quality in OFSP puree processing plant in Kenya. Intensive observation and interviews using a structured GMPs checklist, environmental sampling, and microbial analysis by standard microbiological methods were used in data collection. The results indicated low level of compliance to GMPs with an overall compliance score of 58%. Microbial counts on food equipment surfaces, installations, and personnel hands and in packaged OFSP puree were above the recommended microbial safety and quality legal limits. Steaming significantly ( P < 0.05) reduced microbial load in OFSP cooked roots but the counts significantly ( P < 0.05) increased in the puree due to postprocessing contamination. Total counts, yeasts and molds, Enterobacteriaceae, total coliforms, and E. coli and S. aureus counts in OFSP puree were 8.0, 4.0, 6.6, 5.8, 4.8, and 5.9 log 10 cfu/g, respectively. In conclusion, equipment surfaces, personnel hands, and processing water were major sources of contamination in OFSP puree processing and handling. Plant hygiene inspection, environmental monitoring, and food safety trainings are recommended to improve hygiene, microbial quality, and safety of OFSP puree.
Development of a QuEChERS-Based Stable-Isotope Dilution LC-MS/MS Method To Quantitate Ferulic Acid and Its Main Microbial and Hepatic Metabolites in Milk.

PubMed

Waterstraat, Martin; Hildebrand, Andreas; Rosler, Margit; Bunzel, Mirko

2016-11-16

Forage plants of the Poaceae family are grown as pasturage or used for the production of hay, straw, corn stover, etc. Although ferulic acid contents of grasses are generally high, the amount of ingested ferulic acid differs depending on the type of forage, resulting in varying contents of ferulic acid and its microbial and hepatic metabolites in milk. Concentrations and patterns of these metabolites may be used as markers to track different forages in livestock feeding. Therefore, we developed a stable isotope dilution assay to quantitate ferulic acid, 12 ferulic acid-based metabolites, p-coumaric acid, and cinnamic acid in milk. Because most analytes were not commercially available as stable isotope labeled standard compounds, they were synthesized as 13 C- or deuterium-labeled standard compounds. A modification of the QuEChERS method, a Quick, Easy, Cheap, Effective, Rugged, and Safe approach usually applied to analyze pesticides in plant-based products, was used to extract the phenolic acids from milk. Determination was carried out by LC-ESI-MS/MS in scheduled multiple reaction monitoring modus. By using three different milk samples, the applicability of the validated approach was demonstrated.
Microbial Metabolism in Serpentinite Fluids

NASA Astrophysics Data System (ADS)

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

2013-12-01

Serpentinization is the process in which ultramafic rocks, characteristic of the upper mantle, react with water liberating mantle carbon and reducing power to potenially support chemosynthetic microbial communities. These communities may be important mediators of carbon and energy exchange between the deep Earth and the surface biosphere. Our work focuses on the Coast Range Ophiolite Microbial Observatory (CROMO) in Northern California where subsurface fluids are accessible through a series of wells. Preliminary analyses indicate that the highly basic fluids (pH 9-12) have low microbial diversity, but there is limited knowledge about the metabolic capabilities of these communties. Metagenomic data from similar serpentine environments [1] have identified Betaproteobacteria belonging to the order Burkholderiales and Gram-positive bacteria from the order Clostridiales as key components of the serpentine microbiome. In an effort to better characterize the microbial community, metabolism, and geochemistry at CROMO, fluids from two representative wells (N08B and CSWold) were sampled during recent field campaigns. Geochemical characterization of the fluids includes measurements of dissolved gases (H2, CO, CH4), dissolved inorganic and organic carbon, volatile fatty acids, and nutrients. The wells selected can be differentiated in that N08B had higher pH (10-11), lower dissolved oxygen, and cell counts ranging from 105-106 cells mL-1 of fluid, with an abundance of the betaproteobacterium Hydrogenophaga. In contrast, fluids from CSWold have slightly lower pH (9-9.5), DO, and conductivity, as well as higher TDN and TDP. CSWold fluid is also characterized for having lower cell counts (~103 cells mL-1) and an abundance of Dethiobacter, a taxon within the phylum Clostridiales. Microcosm experiments were conducted with the purpose of monitoring carbon fixation, methanotrophy and metabolism of small organic compounds, such as acetate and formate, while tracing changes in fluid chemistry and microbial community composition. These experiments are expected to provide insight into the biogeochemical dynamics of the serpentinite subsurface at CROMO and represent a first step for developing metatranscriptomic and RNA-based Stable Isotope Probing (RNA-SIP) experiments to trace microbial activity at this site. [1] Brazelton et al. (2012) Frontiers in Microbiology 2:268
Time-dependent effect of composted tannery sludge on the chemical and microbial properties of soil.

PubMed

de Sousa, Ricardo Silva; Santos, Vilma Maria; de Melo, Wanderley Jose; Nunes, Luis Alfredo Pinheiro Leal; van den Brink, Paul J; Araújo, Ademir Sérgio Ferreira

2017-12-01

Composting has been suggested as an efficient method for tannery sludge recycling before its application to the soil. However, the application of composted tannery sludge (CTS) should be monitored to evaluate its effect on the chemical and microbial properties of soil. This study evaluated the time-dependent effect of CTS on the chemical and microbial properties of soil. CTS was applied at 0, 2.5, 5, 10, and 20 Mg ha -1 and the soil chemical and microbial properties were evaluated at 0, 45, 75, 150, and 180 days. Increased CTS rates increased the levels of Ca, Cr, and Mg. While Soil pH, organic C, and P increased with the CTS rates initially, this effect decreased over time. Soil microbial biomass, respiration, metabolic quotient, and dehydrogenase increased with the application of CTS, but decreased over time. Analysis of the Principal Response Curve showed a significant effect of CTS rate on the chemical and microbial properties of the soil over time. The weight of each variable indicated that all soil properties, except β-glucosidase, dehydrogenase and microbial quotient, increased due to the CTS application. However, the highest weights were found for Cr, pH, Ca, P, phosphatase and total organic C. The application of CTS in the soil changed the chemical and microbial properties over time, indicating Cr, pH, Ca, phosphatase, and soil respiration as the more responsive chemical and microbial variables by CTS application.
Limited recovery of soil microbial activity after transient exposure to gasoline vapors.

PubMed

Modrzyński, Jakub J; Christensen, Jan H; Mayer, Philipp; Brandt, Kristian K

2016-09-01

During gasoline spills complex mixtures of toxic volatile organic compounds (VOCs) are released to terrestrial environments. Gasoline VOCs exert baseline toxicity (narcosis) and may thus broadly affect soil biota. We assessed the functional resilience (i.e. resistance and recovery of microbial functions) in soil microbial communities transiently exposed to gasoline vapors by passive dosing via headspace for 40 days followed by a recovery phase of 84 days. Chemical exposure was characterized with GC-MS, whereas microbial activity was monitored as soil respiration (CO2 release) and soil bacterial growth ([(3)H]leucine incorporation). Microbial activity was strongly stimulated and inhibited at low and high exposure levels, respectively. Microbial growth efficiency decreased with increasing exposure, but rebounded during the recovery phase for low-dose treatments. Although benzene, toluene, ethylbenzene and xylene (BTEX) concentrations decreased by 83-97% during the recovery phase, microbial activity in high-dose treatments did not recover and numbers of viable bacteria were 3-4 orders of magnitude lower than in control soil. Re-inoculation with active soil microorganisms failed to restore microbial activity indicating residual soil toxicity, which could not be attributed to BTEX, but rather to mixture toxicity of more persistent gasoline constituents or degradation products. Our results indicate a limited potential for functional recovery of soil microbial communities after transient exposure to high, but environmentally relevant, levels of gasoline VOCs which therefore may compromise ecosystem services provided by microorganisms even after extensive soil VOC dissipation. Copyright © 2016 Elsevier Ltd. All rights reserved.
Quantitative analysis of microbial biomass yield in aerobic bioreactor.

PubMed

Watanabe, Osamu; Isoda, Satoru

2013-12-01

We have studied the integrated model of reaction rate equations with thermal energy balance in aerobic bioreactor for food waste decomposition and showed that the integrated model has the capability both of monitoring microbial activity in real time and of analyzing biodegradation kinetics and thermal-hydrodynamic properties. On the other hand, concerning microbial metabolism, it was known that balancing catabolic reactions with anabolic reactions in terms of energy and electron flow provides stoichiometric metabolic reactions and enables the estimation of microbial biomass yield (stoichiometric reaction model). We have studied a method for estimating real-time microbial biomass yield in the bioreactor during food waste decomposition by combining the integrated model with the stoichiometric reaction model. As a result, it was found that the time course of microbial biomass yield in the bioreactor during decomposition can be evaluated using the operational data of the bioreactor (weight of input food waste and bed temperature) by the combined model. The combined model can be applied to manage a food waste decomposition not only for controlling system operation to keep microbial activity stable, but also for producing value-added products such as compost on optimum condition. Copyright © 2013 The Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences. Published by Elsevier B.V. All rights reserved.
Rapid Response of Eastern Mediterranean Deep Sea Microbial Communities to Oil

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

Liu, Jiang; Techtmann, Stephen M.; Woo, Hannah L.

Deep marine oil spills like the Deepwater Horizon (DWH) in the Gulf of Mexico have the potential to drastically impact marine systems. Crude oil contamination in marine systems remains a concern, especially for countries around the Mediterranean Sea with off shore oil production. The goal of this study was to investigate the response of indigenous microbial communities to crude oil in the deep Eastern Mediterranean Sea (E. Med.) water column and to minimize potential bias associated with storage and shifts in microbial community structure from sample storage. 16S rRNA amplicon sequencing was combined with GeoChip metagenomic analysis to monitor themore » microbial community changes to the crude oil and dispersant in on-ship microcosms set up immediately after water collection. After 3 days of incubation at 14 °C, the microbial communities from two different water depths: 824 m and 1210 m became dominated by well-known oil degrading bacteria. The archaeal population and the overall microbial community diversity drastically decreased. Similarly, GeoChip metagenomic analysis revealed a tremendous enrichment of genes related to oil biodegradation, which was consistent with the results from the DWH oil spill. These results highlight a rapid microbial adaption to oil contamination in the deep E. Med., and indicate strong oil biodegradation potentia« less
Risk of Adverse Health Effects Due to Host-Microorganism Interactions

NASA Technical Reports Server (NTRS)

Ott, C. Mark; Oubre, Cherie; Wallace, Sarah; Mehta, Satish; Pierson, Duane

2016-01-01

Numerous spaceflight experiments have been conducted to investigate alterations in microbial responses resulting from culture during spaceflight and spaceflight-analogs. However, recent studies investigating spaceflight-associated alterations in microbial virulence have initiated the review and production of evidence to better understand the impact these alterations would have on the incidence of infectious disease during a spaceflight exploration mission. The preponderance of evidence indicates that alterations in microbial gene expression and phenotype (including virulence) are occurring; however, the clinical implications of such changes are still unclear. Greater knowledge is required including a better understanding of the mechanism behind unique spaceflight-associated microbial responses to determine how this environmental stimulus impacts various microorganisms, their diversity and concentration in the spacecraft and crew microbiome, their impact on the vehicle and crew, and their resistance to current mitigation and antibiotic regimens. This knowledge will enable us to determine requirements, guidelines, and processes for design and monitoring of the next generation vehicles.
Microbial monitoring by molecular tools of an upflow anaerobic filter treating abattoir wastewaters.

PubMed

Gannoun, Hana; Khelifi, Eltaief; Omri, Ilhem; Jabari, Linda; Fardeau, Marie-Laure; Bouallagui, Hassib; Godon, Jean-Jacques; Hamdi, Moktar

2013-08-01

The performance of anaerobic digestion of abattoir wastewaters (AW) in an upflow anaerobic filter (UAF) was investigated under mesophilic (37°C) and thermophilic (55°C) conditions. The effects of increasing temperature on the performance of the UAF and on the dynamics of the microbial community of the anaerobic sludge were studied. The results showed that chemical oxygen demand (COD) removal efficiency of 90% was achieved for organic loading rates (OLRs) up to 4.5g CODL(-1)d(-1) in mesophilic conditions, while in thermophilic conditions, the highest OLRs of 9 g CODL(-1)d(-1) led to the efficiency of 72%. The use of molecular and microbiological methods to recover microbial populations involved in this process showed that fermentative bacteria were the prominent members of the sludge microbial community. Three novel strains were identified as Macellibacteroides fermentans, Desulfotomaculum peckii and Defluviitalea saccharophila. Copyright © 2013 Elsevier Ltd. All rights reserved.
Microbial succession and the functional potential during the fermentation of Chinese soy sauce brine

PubMed Central

Sulaiman, Joanita; Gan, Han Ming; Yin, Wai-Fong; Chan, Kok-Gan

2014-01-01

The quality of traditional Chinese soy sauce is determined by microbial communities and their inter-related metabolic roles in the fermentation tank. In this study, traditional Chinese soy sauce brine samples were obtained periodically to monitor the transitions of the microbial population and functional properties during the 6 months of fermentation process. Whole genome shotgun method revealed that the fermentation brine was dominated by the bacterial genus Weissella and later dominated by the fungal genus Candida. Metabolic reconstruction of the metagenome sequences demonstrated a characteristic profile of heterotrophic fermentation of proteins and carbohydrates. This was supported by the detection of ethanol with stable decrease of pH values. To the best of our knowledge, this is the first study that explores the temporal changes in microbial successions over a period of 6 months, through metagenome shotgun sequencing in traditional Chinese soy sauce fermentation and the biological processes therein. PMID:25400624
Microbial succession and the functional potential during the fermentation of Chinese soy sauce brine.

PubMed

Sulaiman, Joanita; Gan, Han Ming; Yin, Wai-Fong; Chan, Kok-Gan

2014-01-01

The quality of traditional Chinese soy sauce is determined by microbial communities and their inter-related metabolic roles in the fermentation tank. In this study, traditional Chinese soy sauce brine samples were obtained periodically to monitor the transitions of the microbial population and functional properties during the 6 months of fermentation process. Whole genome shotgun method revealed that the fermentation brine was dominated by the bacterial genus Weissella and later dominated by the fungal genus Candida. Metabolic reconstruction of the metagenome sequences demonstrated a characteristic profile of heterotrophic fermentation of proteins and carbohydrates. This was supported by the detection of ethanol with stable decrease of pH values. To the best of our knowledge, this is the first study that explores the temporal changes in microbial successions over a period of 6 months, through metagenome shotgun sequencing in traditional Chinese soy sauce fermentation and the biological processes therein.
Investigation of the microbial community structure and activity as indicators of compost stability and composting process evolution.

PubMed

Chroni, Christina; Kyriacou, Adamadini; Manios, Thrassyvoulos; Lasaridi, Konstantia-Ekaterini

2009-08-01

In a bid to identify suitable microbial indicators of compost stability, the process evolution during windrow composting of poultry manure (PM), green waste (GW) and biowaste was studied. Treatments were monitored with regard to abiotic factors, respiration activity (determined using the SOUR test) and functional microflora. The composting process went through typical changes in temperature, moisture content and microbial properties, despite the inherent feedstock differences. Nitrobacter and pathogen indicators varied as a monotonous function of processing time. Some microbial groups have shown a potential to serve as fingerprints of the different process stages, but still they should be examined in context with respirometric tests and abiotic parameters. Respiration activity reflected well the process stage, verifying the value of respirometric tests to access compost stability. SOUR values below 1 mg O(2)/g VS/h were achieved for the PM and the GW compost.
Electron beam inactivation of selected microbial pathogens and indicator organisms in aerobically and anaerobically digested sewage sludge.

PubMed

Praveen, Chandni; Jesudhasan, Palmy R; Reimers, Robert S; Pillai, Suresh D

2013-09-01

Microbial pathogens in municipal sewage sludges need to be inactivated prior to environmental disposal. The efficacy of high energy (10 MeV) e-beam irradiation to inactivate a variety of selected microbial pathogens and indicator organisms in aerobically and anaerobically digested sewage sludge was evaluated. Both bacterial and viral pathogens and indicator organisms are susceptible to e-beam irradiation. However, as expected there was a significant difference in their respective e-beam irradiation sensitivity. Somatic coliphages, bacterial endospores and enteric viruses were more resistant compared to bacterial pathogens. The current US EPA mandated 10 kGy minimum dose was capable of achieving significant reduction of both bacterial and viral pathogens. Somatic coliphages can be used as a microbial indicator for monitoring e-beam processes in terms of pathogen inactivation in sewage sludges. Copyright © 2013 Elsevier Ltd. All rights reserved.
Microbial ecology laboratory procedures manual NASA/MSFC

NASA Technical Reports Server (NTRS)

Huff, Timothy L.

1990-01-01

An essential part of the efficient operation of any microbiology laboratory involved in sample analysis is a standard procedures manual. The purpose of this manual is to provide concise and well defined instructions on routine technical procedures involving sample analysis and methods for monitoring and maintaining quality control within the laboratory. Of equal importance is the safe operation of the laboratory. This manual outlines detailed procedures to be followed in the microbial ecology laboratory to assure safety, analytical control, and validity of results.

Long term impacts of CMC/nZVI amendment injection on organohalide-respiring microbial communities at a chlorinated solvent field site

NASA Astrophysics Data System (ADS)

Kocur, C. M.; Lomheim, L.; Boparai, H. K.; Chowdhury, A. I.; Weber, K.; Austrins, L. M.; Sleep, B.; O'Carroll, D. M.; Edwards, E.

2014-12-01

Injection of carboxymethyl-cellulose stabilized nanoscale Zero Valent Iron (CMC/nZVI) has received significant attention in the last decade as an emerging alternative for in-situ remediation of chlorinated solvents and other recalcitrant compounds. There has also been some indication that injection of nZVI will create conditions that will stimulate in-situ microbial populations, leading to further contaminant degradation. Carboxy-methyl cellulose (CMC) is commonly used for nZVI synthesis as it provides steric stabilization for the nanoparticles, however, the CMC is equally important as a subsurface amendment as it may act as a fermentable substrate for microorganisms in-situ. In this study, microbial communities were monitored over a 2.5 year period following the injection of CMC/nZVI at a chlorinated solvent remediation site. Dehalococcoides spp. genetic markers and vinyl chloride reductase genes (vcrA) were targeted in the 16s RNA using quantitative polymerase chain reaction (qPCR). This analysis was complimented with a suite of aqueous chlorinated ethene, ethane, and methane compounds to monitor degradation. Following the injection of CMC/nZVI a decline of parent chlorinated compound concentrations was observed as well as the emergence of daughter products. A period of abiotic nZVI oxidation is believed to be responsible for a portion of the degradation at the site, however, a prolonged period of contaminant degradation followed and is believed to be the result of organohalide-respiring microorganisms native to the site. Further analysis was performed on the microbial samples using 454 pyrotag sequencing of amplified 16S rRNA genes to obtain the genetic profile of the microbial community. Of particular interest within this large genomic profile is the characterization of the stable population of important organohalide-respiring microorganisms on site. Results suggest that there is a distinctly different response in the organohalide-respiring microbial community in areas of the site where CMC/nZVI amendments were injected compared to a background response.
Microbial toxicity of methyl tert-butyl ether (MTBE) determined with fluorescent and luminescent bioassays.

PubMed

Roslev, Peter; Lentz, Trine; Hesselsoe, Martin

2015-02-01

The inhibitory effects of the fuel additive methyl tert-butyl ether (MTBE) and potential degradation products tert-butanol (TBA) and formaldehyde was examined using mixed microbial biomass, and six strains of bioluminescent bacteria and yeast. The purpose was to assess microbial toxicity with quantitative bioluminescent and fluorescent endpoints, and to identify sensitive proxies suitable for monitoring MTBE contamination. Bioluminescent Aliivibrio fischeri DSM 7151 (formerly Vibrio fischeri) appeared highly sensitive to MTBE exposure, and was a superior test organisms compared to lux-tagged Escherichia coli DH5α, Pseudomonas fluorescens DF57-40E7 and Saccharomyces cerevisiae BLYR. EC10 and EC50 for acute MTBE toxicity in A. fischeri were 1.1 and 10.9 mg L(-1), respectively. Long term (24h) MTBE exposure resulted in EC10 values of 0.01 mg L(-1). TBA was significantly less toxic with EC10 and EC50 for acute and chronic toxicity >1000 mg L(-1). Inhibition of bioluminescence was generally a more sensitive endpoint for MTBE toxicity than measuring intracellular ATP levels and heterotrophic CO2 assimilation. A weak estrogenic response was detected for MTBE at concentrations ⩾ 3.7 g L(-1) using an estrogen inducible bioluminescent yeast strain (S. cerevisiae BLYES). Microbial hydrolytic enzyme activity in groundwater was affected by MTBE with EC10 values of 0.5-787 mg L(-1), and EC50 values of 59-3073 for alkaline phosphatase, arylsulfatase, beta-1,4-glucanase, N-acetyl-beta-d-glucosaminidase, and leucine-aminopeptidase. Microbial alkaline phosphatase and beta-1,4-glucanase activity were most sensitive to MTBE exposure with EC50 ⩽ 64.8 mg L(-1). The study suggests that bioassays with luminescent A. fischeri, and fluorescent assays targeting hydrolytic enzyme activity are good candidates for monitoring microbial MTBE toxicity in contaminated water. Copyright © 2014 Elsevier Ltd. All rights reserved.
Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass-Spectrometry (MALDI-TOF MS) Based Microbial Identifications: Challenges and Scopes for Microbial Ecologists

PubMed Central

Rahi, Praveen; Prakash, Om; Shouche, Yogesh S.

2016-01-01

Matrix-assisted laser desorption/ionization time-of-flight mass-spectrometry (MALDI-TOF MS) based biotyping is an emerging technique for high-throughput and rapid microbial identification. Due to its relatively higher accuracy, comprehensive database of clinically important microorganisms and low-cost compared to other microbial identification methods, MALDI-TOF MS has started replacing existing practices prevalent in clinical diagnosis. However, applicability of MALDI-TOF MS in the area of microbial ecology research is still limited mainly due to the lack of data on non-clinical microorganisms. Intense research activities on cultivation of microbial diversity by conventional as well as by innovative and high-throughput methods has substantially increased the number of microbial species known today. This important area of research is in urgent need of rapid and reliable method(s) for characterization and de-replication of microorganisms from various ecosystems. MALDI-TOF MS based characterization, in our opinion, appears to be the most suitable technique for such studies. Reliability of MALDI-TOF MS based identification method depends mainly on accuracy and width of reference databases, which need continuous expansion and improvement. In this review, we propose a common strategy to generate MALDI-TOF MS spectral database and advocated its sharing, and also discuss the role of MALDI-TOF MS based high-throughput microbial identification in microbial ecology studies. PMID:27625644
The Dry Aerosol Deposition Device (DADD): An Instrument for Depositing Microbial Aerosols onto Surfaces

DTIC Science & Technology

2008-12-01

5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 5d. PROJECT NUMBER 5e. TASK NUMBER 5f. WORK UNIT NUMBER 6. AUTHOR( S ) 7...PERFORMING ORGANIZATION NAME( S ) AND ADDRESS(ES) 8. PERFORMING ORGANIZATION REPORT NUMBER 9. SPONSORING/MONITORING AGENCY NAME( S ) AND ADDRESS(ES) 10. SPONSOR...MONITOR’S ACRONYM( S ) 11. SPONSOR/MONITOR’S REPORT NUMBER( S ) 12. DISTRIBUTION/AVAILABILITY STATEMENT 13. SUPPLEMENTARY NOTES 14. ABSTRACT 15
The Primary Results of Analyses on The Archaeal and Bacterial Diversity of Active Cave Environments Settled in Limestones at Southern Turkey

NASA Astrophysics Data System (ADS)

Tok, Ezgi; Kurt, Halil; Tunga Akarsubasi, A.

2016-04-01

The microbial diversity of cave sediments which are obtained from three different caves named Insuyu, Balatini and Altınbeşik located at Southern Turkey has been investigated using molecular methods for biomineralization . The total number of 22 samples were taken in duplicates from the critical zones of the caves at where the water activity is observed all year round. Microbial communities were monitored by 16S rRNA gene based PCR-DGGE (Polymerase Chain Reaction - Denaturating Gradient Gel Electrophoresis) methodology. DNA were extracted from the samples by The PowerSoil® DNA Isolation Kit (MO BIO Laboratories inc., CA) with the modifications on the producer's protocol. The synthetic DNA molecule poly-dIdC was used to increase the yield of PCR amplification via blocking the reaction between CaCO3 and DNA molecules. Thereafter samples were amplified by using both Archaeal and Bacterial universal primers (ref). Subsequently, archaeal and bacterial diversities in cave sediments, were investigated to be able to compare with respect to their similarities by using DGGE. DGGE patterns were analysed with BioNumerics software 5.1. Similarity matrix and dendograms of the DGGE profiles were generated based on the Dice correlation coefficient (band-based) and unweighted pair-group method with arithmetic mean (UPGMA). The structural diversity of the microbial community was examined by the Shannon index of general diversity (H). Similtaneously, geochemical analyses of the sediment samples were performed within the scope of this study. Total organic carbon (TOC), x-ray diffraction spectroscopy (XRD) and x-ray fluorescence spectroscopy (XRF) analysis of sediments were also implemented. The extensive results will be obtained at the next stages of the study currently carried on.
16S rRNA Gene-Based Metagenomic Analysis of Ozark Cave Bacteria

PubMed Central

Oliveira, Cássia; Gunderman, Lauren; Coles, Cathryn A.; Lochmann, Jason; Parks, Megan; Ballard, Ethan; Glazko, Galina; Rahmatallah, Yasir; Tackett, Alan J.; Thomas, David J.

2018-01-01

The microbial diversity within cave ecosystems is largely unknown. Ozark caves maintain a year-round stable temperature (12–14 °C), but most parts of the caves experience complete darkness. The lack of sunlight and geological isolation from surface-energy inputs generate nutrient-poor conditions that may limit species diversity in such environments. Although microorganisms play a crucial role in sustaining life on Earth and impacting human health, little is known about their diversity, ecology, and evolution in community structures. We used five Ozark region caves as test sites for exploring bacterial diversity and monitoring long-term biodiversity. Illumina MiSeq sequencing of five cave soil samples and a control sample revealed a total of 49 bacterial phyla, with seven major phyla: Proteobacteria, Acidobacteria, Actinobacteria, Firmicutes, Chloroflexi, Bacteroidetes, and Nitrospirae. Variation in bacterial composition was observed among the five caves studied. Sandtown Cave had the lowest richness and most divergent community composition. 16S rRNA gene-based metagenomic analysis of cave-dwelling microbial communities in the Ozark caves revealed that species abundance and diversity are vast and included ecologically, agriculturally, and economically relevant taxa. PMID:29551950
Microbial community analysis in the autotrophic denitrification process using spent sulfidic caustic by denaturing gradient gel electrophoresis of PCR-amplified genes.

PubMed

Lee, J-H; Lee, S-M; Choi, G-C; Park, H-S; Kang, D-H; Park, J-J

2011-01-01

Spent sulfidic caustic (SSC) produced from petrochemical plants contains a high concentration of hydrogen sulfide and alkalinity, and some almost non-biodegradable organic compounds such as benzene, toluene, ethylbenzene and xylenes (BTEX). SSC is mainly incinerated with auxiliary fuel, leading to secondary pollution problems. The reuse of this waste is becoming increasingly important from economic and environmental viewpoints. To denitrify wastewater with low COD/N ratio, additional carbon sources are required. Thus, autotrophic denitrification has attracted increasing attention. In this study, SSC was injected as an electron donor for sulfur-based autotrophic denitrification in the modified Ludzack-Ettinger (MLE) process. The efficiencies of nitrification, COD, and total nitrogen (TN) removal were evaluated with varying SSC dosage. Adequate SSC injection exhibited stable autotrophic denitrification. No BTEX were detected in the monitored BTEX concentrations of the effluent. To analyse the microbial community of the MLE process, PCR-DGGE based on 16 S rDNA with EUB primers, TD primers and nirK gene with nirK primers was performed in order to elucidate the application of the MLE process to SSC.
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.
Effect of an essential oil-containing dentifrice on dental plaque microbial composition.

PubMed

Charles, C H; Vincent, J W; Borycheski, L; Amatnieks, Y; Sarina, M; Qaqish, J; Proskin, H M

2000-09-01

To determine the effect of 6 months use of an essential oil-containing (EO) antiplaque/antigingivitis fluoride dentifrice on the balance of the oral microbial flora and on the emergence of resistant microbial forms by analysis of dental plaque and saliva. The dentifrice essential oils consisted of a fixed combination of thymol, menthol, methyl salicylate, and eucalyptol. An identical fluoride-containing dentifrice without the essential oils served as the control. A subgroup of 66 subjects from a clinical trial population of 321 was randomly selected for characterization of their dental plaque microflora. Saliva was also cultured to monitor for the emergence of opportunistic pathogens. Supragingival plaque and saliva were harvested at baseline, after which subjects received a dental prophylaxis. Subjects were sampled again after 3 and 6 months of product use prior to clinical examination. Plaque was characterized for microbial content by phase contrast microscopy for recognizable cellular morphotypes and by cultivation on nonselective and selective culture media. Determination of the minimum inhibitory concentrations of the test agent against selected Actinomyces and Veillonella isolated bacterial species was conducted at all time points to monitor for the potential development of bacterial resistance. There were no statistically significant differences between the microbial flora obtained from subjects using the essential oil-containing dentifrice and the vehicle control for all parameters and time periods except for the percentage of spirochetes at 6 months and for percentage of "other" microorganisms at 3 months. The EO group exhibited a lower adjusted mean for both parameters. Additionally, there was no evidence of the development of bacterial resistance to the antimicrobial activity of the essential oils or the emergence of opportunistic pathogens.
Microbial Enrichment from Six Hydraulic Fracturing Fluids and Biogeochemical Characteristics of Flowback Waters in Oklahoma Shale Formations

NASA Astrophysics Data System (ADS)

Krzmarzick, M. J.; McCutchan, A.; Carroll, J.; Lozano, T.

2017-12-01

Hydraulic fracturing of oil and gas formations has revolutionized the industry, but little is known regarding the interactions of the microbiology in formations and the hydraulic fracturing chemicals used. In the first part of this study, six representative hydraulic fracturing fluids were incubated in bench scale microcosms with surface soils over six months at 1× concentrations used in the field. These fluids differed greatly in terms of biocide, surfactants, corrosion inhibitors and crosslinking agents (if any). The changes in microbial communities were measured by Illumina 16S rRNA gene analysis and quantitative-PCR. As a whole, the microbial communities enriched were significantly varied between fluids, with the magnitude of the difference tightly linked to the total organic carbon of each fluid. Most enriched bacteria heavily grew within just the first couple of weeks, and belonged to genera well-linked to xenobiotic degradation, such as Azospirillum, Ralstonia, and Comamonas. This, combined with bulk parameters such as chemical oxygen demand of the water, indicates that a significant fraction of these fluids are readily degradable, though individual chemicals were not monitored for recalcitrance. In the second component of this work, the flowback waters from sixteen newly completed wells in south-central Oklahoma were monitored over two months for compositions of boron, dissolved solids, BTEX, chloride, and their microbial communities. As expected, dissolved solids increased over time as the flowback waters became more characteristic of the formation waters. In these wells, boron, a carefully measured component of the fracturing fluid for cross-linking applications, was either stable or increased over time. The microbial community characteristics are pending but will be compared between formations, to the chemical data, and to the results in the bench-top degradation study.
A protocol for assessing the biotreatability of hydrocarbon contaminated exploration and production site soils

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

Tezak, J.; Miller, J.A.; Lawrence, A.W.

1995-12-01

It is estimated that there are over 260,000 natural gas production wells in the continental United States. Production or reserve pits exist which ma require remediation depending on several conditions such as: the manner in which they were initially closed; whether or not they were lined; and the local climate, soil type, and depth to groundwater. As part of the Gas Research Institute (GRI) research program on exploration and production (E&P) site remediation, a treatability Protocol is being developed to facilitate the rapid assessment of the amenability of the contaminated soils to remediation by biological processes. This paper describes themore » treatability protocol and the results of a series of treatability tests on a spectrum of hydrocarbon contaminated E&P soils collected from various operating locations throughout the United States. The soils are subjected to physical and chemical characterization prior to treatability testing. Potential biotoxic characteristics of the soils are determined by a respirometry screening technique. Presuming that the soils are not toxic to aerobic soil microorganisms, 20 percent by weight aqueous slurries of the soils are prepared and subjected to continuous batch aeration for a six week period. Conditions favorable to microbial growth are maintained in the reactors by monitoring and augmentation is needed of pH, microbial nutrients and oxygen for microbial respiration. The extent of microbial degradation of the contaminant hydrocarbons is monitored by periodic measurement of total petroleum hydrocarbons (TPH), oil and grease, and individual hydrocarbon compounds as determined by gas chromatography. Microbial plate counts are prepared to document the biological viability of the treatment process. The factors influencing the amenability of these soils to bioremediation as determined from the test results are discussed.« less
Evolution of microbial dynamics during the maturation phase of the composting of different types of waste.

PubMed

Villar, Iria; Alves, David; Garrido, Josefina; Mato, Salustiano

2016-08-01

During composting, facilities usually exert greater control over the bio-oxidative phase of the process, which uses a specific technology and generally has a fixed duration. After this phase, the material is deposited to mature, with less monitoring during the maturation phase. While there has been considerable study of biological parameters during the thermophilic phase, there is less research on the stabilization and maturation phase. This study evaluates the effects of the type of starting material on the evolution of microbial dynamics during the maturation phase of composting. Three waste types were used: sludge from the fish processing industry, municipal sewage sludge and pig manure, each independently mixed with shredded pine wood as bulking agent. The composting system for each waste type comprised a static reactor with capacity of 600L for the bio-oxidative phase followed by stabilization and maturation phase in triplicate 200L boxes for 112days. Phospholipid fatty acids, enzyme activities and physico-chemical parameters were measured throughout the maturation phase. The evolution of the total microbial biomass, Gram + bacteria, Gram - bacteria, fungi and enzymatic activities (β-glucosidase, cellulase, protease, acid and alkaline phosphatase) depended significantly on the waste type (p<0.001). The predominant microbial community for each waste type remained present throughout the maturation process, indicating that the waste type determines the microorganisms that are able to develop at this stage. While fungi predominated during fish sludge maturation, manure and municipal sludge were characterized by a greater proportion of bacteria. Both the structure of the microbial community and enzymatic activities provided important information for monitoring the composting process. More attention should be paid to the maturation phase in order to optimize composting. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.
Short-term microbial dynamics in a drinking water plant treating groundwater with occasional high microbial loads.

PubMed

Besmer, Michael D; Hammes, Frederik

2016-12-15

Short-term fluctuations in bacterial concentrations in drinking water systems, occurring on time scales of hours-to-weeks, are essentially unexplored due to a lack of microbial monitoring tools that allow high frequency measurements. Here, we applied fully automated online flow cytometry to measure the total cell concentrations (TCC) in both raw water (karstic groundwater) and treated water (flocculation - ultrafiltration (UF) - ozonation - granular active carbon (GAC) filtration) during a period of 70 days at high temporal resolution (n > 4000 for both water types). We detected and characterized in considerable detail aperiodic fluctuations in the raw water following regional precipitation, with TCC increasing up to 50-fold from a dry weather baseline of approximately 120 cells μl -1 to an event peak of > 5000 cells μl -1 . Moreover, we observed the buffering of the treatment plant against these fluctuations, but in addition we recorded a completely unexpected periodic fluctuation of TCC in the treated water after GAC filtration. We concluded that the latter was the result of fluctuating water abstraction from the treatment plant reservoir by two connected water utilities, which resulted in variations in water throughput in the plant. This in turn influenced bacterial detachment and dilution in the GAC filter. This study provides strong evidence of multiple different microbial dynamics occurring in a drinking water treatment system. Given numerous possible sources of natural and operational fluctuations in raw water and drinking water treatment plants, such microbial fluctuations should be expected in many systems. The high-frequency monitoring approach presented herein can improve the understanding and eventual mitigation of such fluctuations. Copyright © 2016 Elsevier Ltd. All rights reserved.
Understanding aquatic microbial processes using EEM's and in-situ fluorescence sensors

NASA Astrophysics Data System (ADS)

Fox, Bethany; Attridge, John; Rushworth, Cathy; Cox, Tim; Anesio, Alexandre; Reynolds, Darren

2015-04-01

The diverse origin of dissolved organic matter (DOM) in aquatic systems is well documented within the literature. Previous literature indicates that coloured dissolved organic matter (CDOM) is, in part, transformed by aquatic microbial processes, and that dissolved organic material derived from a microbial origin exhibits tryptophan-like fluorescence. However, this phenomenon is not fully understood and very little data is available within the current literature. The overall aim of our work is to reveal the microbial-CDOM interactions that give rise to the observed tryptophan-like fluorescence. The work reported here investigates the microbial processes that occur within freshwater aquatic samples, as defined by the biochemical oxygen demand (BOD) test, as a function of the T1 peak (λex/em 280/330-370 nm). A series of standard water samples were prepared using glucose, glutamic acid, BOD dilution water and a bacterial seed (Cole-Parmer BOD microbe capsules). Samples were spiked with CDOM (derived from an environmental water body) and subjected to time resolved BOD analysis and as excitation-emission fluorescence spectroscopy. All EEM spectral data was interrogated using parallel factor analysis (PARAFAC) in an attempt to determine the presence and dominance (relative intensities) of the CDOM-related and T1-related fluorophores within the samples. In-situ fluorescence sensors (Chelsea Technologies Group Ltd.) were also used to monitor the T1 fluorescence peak (UviLux Tryptophan) and the CDOM fluorescence peak (UviLux CDOM) during experiments. Tryptophan-like fluorescence was observed (albeit transient) in both spiked and un-spiked standard water samples. By furthering our understanding of aquatic organic matter fluorescence, its origin, transformation, fate and interaction with aquatic microbiological processes, we aim to inform the design of a new generation in-situ fluorescence sensor for the monitoring of aquatic ecosystem health.
Application of Sequence-based Methods in Human MicrobialEcology

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

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

2005-08-29

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

NASA Astrophysics Data System (ADS)

Xu, X.; Song, C.; Wang, Y.; Ricciuto, D. M.; Lipson, D.; Shi, X.; Zona, D.; Song, X.; Yuan, F.; Oechel, W. C.; Thornton, P. E.

2017-12-01

A microbial model is introduced for simulating microbial mechanisms controlling soil carbon and nitrogen biogeochemical cycling and methane fluxes. The model is built within the CN (carbon-nitrogen) framework of Community Land Model 4.5, named as CLM-Microbe to emphasize its explicit representation of microbial mechanisms to biogeochemistry. Based on the CLM4.5, three new pools were added: bacteria, fungi, and dissolved organic matter. It has 11 pools and 34 transitional processes, compared with 8 pools and 9 transitional flow in the CLM4.5. The dissolve organic carbon was linked with a new microbial functional group based methane module to explicitly simulate methane production, oxidation, transport and their microbial controls. Comparing with CLM4.5-CN, the CLM-Microbe model has a number of new features, (1) microbial control on carbon and nitrogen flows between soil carbon/nitrogen pools; (2) an implicit representation of microbial community structure as bacteria and fungi; (3) a microbial functional-group based methane module. The model sensitivity analysis suggests the importance of microbial carbon allocation parameters on soil biogeochemistry and microbial controls on methane dynamics. Preliminary simulations validate the model's capability for simulating carbon and nitrogen dynamics and methane at a number of sites across the globe. The regional application to Asia has verified the model in simulating microbial mechanisms in controlling methane dynamics at multiple scales.
In vitro characteristics of an Atlantic salmon (Salmo salar L.) hind gut microbial community in relation to different dietary treatments.

PubMed

Zarkasi, Kamarul Zaman; Taylor, Richard S; Glencross, Brett D; Abell, Guy C J; Tamplin, Mark L; Bowman, John P

2017-10-01

In this study, microbial community dynamics were assessed within a simple in vitro model system in order to understand those changes influenced by diet. The abundance and diversity of bacteria were monitored within different treatment slurries inoculated with salmon faecal samples in order to mimic the effects of dietary variables. A total of five complete diets and two ingredients (plant meal) were tested. The total viable counts (TVCs) and sequencing data revealed that there was very clear separation between the complete diets and the plant meal treatments, suggesting a dynamic response by the allochthonous bacteria to the treatments. Automated ribosomal intergenic spacer analysis (ARISA) results showed that different diet formulations produced different patterns of fragments, with no separation between the complete diets. However, plant-based protein ingredients were clearly separated from the other treatments. 16S rRNA Illumina-based sequencing analysis showed that members of the genera Aliivibrio, Vibrio and Photobacterium became predominant for all complete diets treatments. The plant-based protein ingredient treatments only sustained weak growth of the genus Sphingomonas. In vitro based testing of diets could be a useful strategy to determine the potential impact of either complete feeds or ingredients on major fish gastrointestinal tract microbiome members. Copyright © 2017 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.
Sensor systems for bacterial reactors: A new flavin-phenol composite film for the in situ voltammetric measurement of pH.

PubMed

Casimero, Charnete; McConville, Aaron; Fearon, John-Joe; Lawrence, Clare L; Taylor, Charlotte M; Smith, Robert B; Davis, James

2018-10-16

Monitoring pH within microbial reactors has become an important requirement across a host of applications ranging from the production of functional foods (probiotics) to biofuel cell systems. An inexpensive and scalable composite sensor capable of monitoring the pH within the demanding environments posed by microbial reactors has been developed. A custom designed flavin derivative bearing an electropolymerisable phenol monomer was used to create a redox film sensitive to pH but free from the interferences that can impede conventional pH systems. The film was integrated within a composite carbon-fibre-polymer laminate and was shown to exhibit Nernstian behaviour (55 mV/pH) with minimal drift and robust enough to operate within batch reactors. Copyright © 2018 Elsevier B.V. All rights reserved.
Four-year bacterial monitoring in the International Space Station—Japanese Experiment Module “Kibo” with culture-independent approach

PubMed Central

Ichijo, Tomoaki; Yamaguchi, Nobuyasu; Tanigaki, Fumiaki; Shirakawa, Masaki; Nasu, Masao

2016-01-01

Studies on the relationships between humans and microbes in space habitation environments are critical for success in long-duration space missions, to reduce potential hazards to the crew and the spacecraft infrastructure. We performed microbial monitoring in the Japanese Experiment Module “Kibo”, a part of the International Space Station, for 4 years after its completion, and analyzed samples with modern molecular microbiological techniques. Sampling was performed in September 2009, February 2011, and October 2012. The surface of the incubator, inside the door of the incubator, an air intake, air diffuser, and handrail were selected as sampling sites. Sampling was performed using the optimized swabbing method. Abundance and phylogenetic affiliation of bacteria on the interior surfaces of Kibo were determined by quantitative PCR and pyrosequencing, respectively. Bacteria in the phyla Proteobacteria (γ-subclass) and Firmicutes were frequently detected on the interior surfaces in Kibo. Families Staphylococcaceae and Enterobacteriaceae were dominant. Most bacteria detected belonged to the human microbiota; thus, we suggest that bacterial cells are transferred to the surfaces in Kibo from the astronauts. Environmental bacteria such as Legionella spp. were also detected. From the data on bacterial abundance and phylogenetic affiliation, Kibo has been microbiologically well maintained; however, the microbial community structure in Kibo may change with prolonged stay of astronauts. Continuous monitoring is required to obtain information on changes in the microbial community structure in Kibo. PMID:28725725
Pathophysiological evaluation of subacute ruminal acidosis (SARA) by continuous ruminal pH monitoring.

PubMed

Sato, Shigeru

2016-02-01

Evaluation of the radio-transmission pH-measurement system for monitoring the ruminal pH and subacute ruminal acidosis (SARA) in cattle is described. This is done in order to reveal the possible application of this system for detection and pathophysiological research of SARA by continuous ruminal pH measurement. The possibility of using this system for assessment of the ruminal pH in SARA cattle, and the presence of negative correlation between the ruminal pH and ruminal temperature in heathy and SARA cattle were determined. In addition, the 16S rRNA gene pyrosequencing analysis showed that the ruminal microbial community was simpler in SARA cattle, and the bacterial numbers in SARA cattle were lower than those in healthy hay-fed cattle. Concentrate feeding might have reduced the diversity of the ruminal microbial community. Changes in the ruminal microbial community of SARA cattle might be related to the changes in ruminal pH followed by the decrease in the number of some bacteria. Continuous monitoring of the ruminal pH using the radio-transmission pH-measurement system would be applied for detection and prevention of SARA in the field and pathophysiological research of SARA, including ruminal zymology and bacteriology, which have been determined previously by sampling of the ruminal fluid and measuring of ruminal pH. © 2015 The Authors. Animal Science Journal published by Wiley Publishing Asia Pty Ltd on behalf of Japanese Society of Animal Science.

What heat is telling us about microbial conversions in nature and technology: from chip‐ to megacalorimetry

PubMed Central

Maskow, Thomas; Kemp, Richard; Buchholz, Friederike; Schubert, Torsten; Kiesel, Baerbel; Harms, Hauke

2010-01-01

Summary The exploitation of microorganisms in natural or technological systems calls for monitoring tools that reflect their metabolic activity in real time and, if necessary, are flexible enough for field application. The Gibbs energy dissipation of assimilated substrates or photons often in the form of heat is a general feature of life processes and thus, in principle, available to monitor and control microbial dynamics. Furthermore, the combination of measured heat fluxes with material fluxes allows the application of Hess' law to either prove expected growth stoichiometries and kinetics or identify and estimate unexpected side reactions. The combination of calorimetry with respirometry is theoretically suited for the quantification of the degree of coupling between catabolic and anabolic reactions. New calorimeter developments overcome the weaknesses of conventional devices, which hitherto limited the full exploitation of this powerful analytical tool. Calorimetric systems can be integrated easily into natural and technological systems of interest. They are potentially suited for high‐throughput measurements and are robust enough for field deployment. This review explains what information calorimetric analyses provide; it introduces newly emerging calorimetric techniques and it exemplifies the application of calorimetry in different fields of microbial research. PMID:21255327
Enzyme and microbial sensors for environmental monitoring

NASA Astrophysics Data System (ADS)

Wollenberger, U.; Neumann, B.; Scheller, Frieder W.

1993-03-01

Biosensors employing the biocatalyst on a different level of integration have been developed for monitoring environmental pollution. These probes range from laboratory specimen to commercial detectors applied to analyzers. This paper presents a selection of recent developments on amperometric enzyme and microbial biosensors. A monoenzymatic bulk type carbon electrode is described for biosensing organic hydroperoxides in aqueous solutions. Here, peroxidase is immobilized within the electrode body and the direct electron transfer between electrode and enzyme is measured. Both, reversible and irreversible inhibitors of acetylcholinesterase have been quantified by using a kinetically controlled acetylcholine enzyme sequence electrode. The inhibitory effect of pesticides such as butoxycarboxime, dimethoate, and trichlorfon could be quantified within 6 min in micrometers olar concentrations. Different multi-enzyme electrodes have been developed for the determination of inorganic phosphate. These sensors represent examples of sequentially acting enzymes in combination with enzymatic analyte recycling. Using this type of amplification nanomolar concentrations could be measured. A very fast responding microbial sensor for biological oxygen demand has been developed by immobilizing Trichosporon cutaneum onto an oxygen electrode. With this whole cell sensor waste water can be assayed with a sample frequency of 20 per hour and a working stability of more than 30 days.
Evaluation of the fate and transport of chlorinated ethenes in a complex groundwater system discharging to a stream in Wonju, Korea

NASA Astrophysics Data System (ADS)

Lee, Seong-Sun; Kaown, Dugin; Lee, Kang-Kun

2015-11-01

Chlorinated ethenes such as trichloroethylene (TCE) are common and persistent groundwater contaminants. If contaminated groundwater discharges to a stream, then stream water pollution near the contamination site also becomes a problem. In this respect, the fate and transport of chlorinated ethenes around a stream in an industrial complex were evaluated using the concentration of each component, and hydrogeochemical, microbial, and compound-specific carbon isotope data. Temporal and spatial monitoring reveal that a TCE plume originating from main and local source zones continues to be discharged to a stream. Groundwater geochemical data indicate that aerobic conditions prevail in the upgradient area of the studied aquifer, whereas conditions become anaerobic in the downgradient. The TCE molar fraction is high at the main and local source zones, ranging from 87.4 to 99.2% of the total volatile organic compounds (VOCs). An increasing trend in the molar fraction of cis-1, 2-Dichloroethene (cis-DCE) and vinyl chloride (VC) was observed in the downgradient zone of the study area. The enriched δ13C values of TCE and depleted values of cis-DCE in the stream zone, compared to those of the source zone, also suggest biodegradation of VOCs. Microbial community structures in monitoring wells adjacent to the stream zone in the downgradient area were analyzed using 16S rRNA gene-based pyrosequencing to identify the microorganisms responsible for biodegradation. This was attributed to the high relative abundance of dechlorinating bacteria in monitoring wells under anaerobic conditions farthest from the stream in the downgradient area. The multilateral approaches adopted in this study, combining hydrogeochemical and biomolecular methods with compound-specific analyses, indicate that contaminants around the stream were naturally attenuated by active anaerobic biotransformation processes.
A potential approach for monitoring drinking water quality from groundwater systems using organic matter fluorescence as an early warning for contamination events.

PubMed

Stedmon, Colin A; Seredyńska-Sobecka, Bożena; Boe-Hansen, Rasmus; Le Tallec, Nicolas; Waul, Christopher K; Arvin, Erik

2011-11-15

The fluorescence characteristics of natural organic matter in a groundwater based drinking water supply plant were studied with the aim of applying it as a technique to identify contamination of the water supply. Excitation-emission matrices were measured and modeled using parallel factor analysis (PARAFAC) and used to identify which wavelengths provide the optimal signal for monitoring contamination events. The fluorescence was characterized by four components: three humic-like and one amino acid-like. The results revealed that the relative amounts of two of the humic-like components were very stable within the supply plant and distribution net and changed in a predictable fashion depending on which wells were supplying the water. A third humic-like component and an amino acid-like component did not differ between wells. Laboratory contamination experiments with wastewater revealed that combined they could be used as an indicator of microbial contamination. Their fluorescence spectra did not overlap with the other components and therefore the raw broadband fluorescence at the wavelengths specific to their fluorescence could be used to detect contamination. Contamination could be detected at levels equivalent to the addition of 60 μg C/L in drinking water with a TOC concentration of 3.3 mg C/L. The results of this study suggest that these types of drinking water systems, which are vulnerable to microbial contamination due to the lack of disinfectant treatment, can be easily monitored using online organic matter fluorescence as an early warning system to prompt further intensive sampling and appropriate corrective measures. Copyright © 2011 Elsevier Ltd. All rights reserved.
The high energy multicharged particle exposure of the microbial ecology evaluation device on board the Apollo 16 spacecraft

NASA Technical Reports Server (NTRS)

Benton, E. V.; Henke, R. P.

1973-01-01

The high energy multicharged cosmic-ray-particle exposure of the Microbial Ecology Evaluation Device package on board the Apollo 16 spacecraft was monitored using cellulose nitrate, Lexan polycarbonate, nuclear emulsion, and silver chloride crystal nuclear-track detectors. The results of the analysis of these detectors include the measured particle fluences, the linear energy transfer spectra, and the integral atomic number spectrum of stopping particle density. The linear energy transfer spectrum is used to compute the fractional cell loss in human kidney (T1) cells caused by heavy particles. Because the Microbial Ecology Evaluation Device was better shielded, the high-energy multicharged particle exposure was less than that measured on the crew passive dosimeters.
Consistency of Use and Effectiveness of Household Water Treatment among Indian Households Claiming to Treat Their Water.

PubMed

Rosa, Ghislaine; Clasen, Thomas

2017-07-01

Household water treatment (HWT) can improve drinking water quality and prevent disease if used correctly and consistently by populations at risk. Current international monitoring estimates by the Joint Monitoring Programme for water and sanitation suggest that at least 1.1 billion people practice HWT. These estimates, however, are based on surveys that may overstate the level of consistent use and do not address microbial effectiveness. We sought to assess how HWT is practiced among households identified as HWT users according to these monitoring standards. After a baseline survey (urban: 189 households, rural: 210 households) to identify HWT users, 83 urban and 90 rural households were followed up for 6 weeks. Consistency of reported HWT practices was high in both urban (100%) and rural (93.3%) settings, as was availability of treated water (based on self-report) in all three sampling points (urban: 98.8%, rural: 76.0%). Nevertheless, only 13.7% of urban and 25.8% of rural households identified at baseline as users of adequate HWT had water free of thermotolerant coliforms at all three water sampling points. Our findings raise questions about the value of the data gathered through the international monitoring of HWT as predictors of water quality in the home, as well as questioning the ability of HWT, as actually practiced by vulnerable populations, to reduce exposure to waterborne diseases.
Proteogenemic Approaches for the Molecular Characterization of Natural Microbial Communities

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

Banfield, Jillian F.

2014-04-25

Microbial biofilms involved in acid mine drainage formation have served as a model systems for the study of microbial communities. Over the grant period we developed community metagenomic methods for recovery of genomes of uncultivated bacteria, archaea, viruses/phage, and plasmids from natural systems. We leveraged highly curated metagenomic datasets to develop methods to monitor microbial function in situ. Beyond new insight into extremophilic microbial ecosystems, we have shown that our strain-resolved proteogenomic methods can be applied to other systems. Our studies have uncovered new patters of inter-species recombination that likely lead to fine-scale environmental adaptation, defined the importance of inter-speciesmore » vs. intra-species recombination in archaea, and evaluated the processes shaping fine-scale sequence variation. The project was the subject of study for six Ph.D. students, two of whom are now Associate Professors, the others are post docs; for M.S. or undergraduate researchers, and thirteen post docs, ten of which are now Assistant or Associate professors. The research generated 53 publications, five of which appeard in Science or Nature.« less
Microbial Transformation of Esters of Chlorinated Carboxylic Acids

PubMed Central

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

1984-01-01

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

PubMed

Wang, Taojun; Zhao, Liang; Sun, Yanan; Ren, Fazheng; Chen, Shanbin; Zhang, Hao; Guo, Huiyuan

2016-11-01

Changes in the microbiota of lamb were investigated under vacuum packaging (VP) and under 20% CO2/80% N2 (LC), 60% CO2/40% N2 (MC), and 100% CO2 (HC) modified atmosphere packaging (MAP) during chilled storage. Viable counts were monitored, and the total microbial communities were assessed by high-throughput sequencing. The starting community had the highest microbial diversity, after which Lactococcus and Carnobacterium spp. outcompeted during the 28-day storage. The relative abundances of Brochothrix spp. in the LC atmosphere were much higher than those of the other groups on days 7 and 28. The bacterial inhibiting effect of the MAP environments on microbial growth was positively correlated with the CO2 concentration. The HC atmosphere inhibited microbial growth and delayed changes in the microbial community composition, extending the lamb's shelf life by approximately 7days compared with the VP atmosphere. Lamb packaged in the VP atmosphere had a more desirable colour but a higher weight loss than lamb packaged in the MAP atmospheres. Copyright © 2016 Elsevier Ltd. All rights reserved.
Temporal and spatial constraints on community assembly during microbial colonization of wood in seawater.

PubMed

Kalenitchenko, Dimitri; Fagervold, Sonja K; Pruski, Audrey M; Vétion, Gilles; Yücel, Mustafa; Le Bris, Nadine; Galand, Pierre E

2015-12-01

Wood falls on the ocean floor form chemosynthetic ecosystems that remain poorly studied compared with features such as hydrothermal vents or whale falls. In particular, the microbes forming the base of this unique ecosystem are not well characterized and the ecology of communities is not known. Here we use wood as a model to study microorganisms that establish and maintain a chemosynthetic ecosystem. We conducted both aquaria and in situ deep-sea experiments to test how different environmental constraints structure the assembly of bacterial, archaeal and fungal communities. We also measured changes in wood lipid concentrations and monitored sulfide production as a way to detect potential microbial activity. We show that wood falls are dynamic ecosystems with high spatial and temporal community turnover, and that the patterns of microbial colonization change depending on the scale of observation. The most illustrative example was the difference observed between pine and oak wood community dynamics. In pine, communities changed spatially, with strong differences in community composition between wood microhabitats, whereas in oak, communities changed more significantly with time of incubation. Changes in community assembly were reflected by changes in phylogenetic diversity that could be interpreted as shifts between assemblies ruled by species sorting to assemblies structured by competitive exclusion. These ecological interactions followed the dynamics of the potential microbial metabolisms accompanying wood degradation in the sea. Our work showed that wood is a good model for creating and manipulating chemosynthetic ecosystems in the laboratory, and attracting not only typical chemosynthetic microbes but also emblematic macrofaunal species.
Hardwood biochar and manure co-application to a calcareous soil.

PubMed

Ippolito, J A; Stromberger, M E; Lentz, R D; Dungan, R S

2016-01-01

Biochar may affect the mineralization rate of labile organic C sources such as manures via microbial community shifts, and subsequently affect nutrient release. In order to ascertain the positive or negative priming effect of biochar on manure, dairy manure (2% by wt.) and a hardwood-based, fast pyrolysis biochar were applied (0%, 1%, 2%, and 10% by wt.) to a calcareous soil. Destructive sampling occurred at 1, 2, 3, 4, 6 and 12 months to monitor for changes in soil chemistry, water content, microbial respiration, bacterial populations, and microbial community structure. Overall results showed that increasing biochar application rate improved the soil water content, which may be beneficial in limited irrigation or rainfall areas. Biochar application increased soil organic C content and plant-available Fe and Mn, while a synergistic biochar-manure effect increased plant-available Zn. Compared to the other rates, the 10% biochar application lowered concentrations of NO3-N; effects appeared masked at lower biochar rates due to manure application. Over time, soil NO3-N increased likely due to manure N mineralization, yet soil NO3-N in the 10% biochar rate remained lower as compared to other treatments. In the presence of manure, only the 10% biochar application caused subtle microbial community structure shifts by increasing the relative amounts of two fatty acids associated with Gram-negative bacteria and decreasing Gram-positive bacterial fatty acids, each by ∼1%. Our previous findings with biochar alone suggested an overall negative priming effect with increasing biochar application rates, yet when co-applied with manure the negative priming effect was eliminated. Published by Elsevier Ltd.
Monitoring bacterial indicators of water quality in a tidally influenced delta: A Sisyphean pursuit.

PubMed

Partyka, Melissa L; Bond, Ronald F; Chase, Jennifer A; Atwill, Edward R

2017-02-01

The Sacramento-San Joaquin Delta Estuary (Delta) is the confluence of two major watersheds draining the Western Sierra Nevada mountains into the Central Valley of California, ultimately terminating into San Francisco Bay. We sampled 88 sites once a month for two years (2006-2008) over 87 separate sampling events for a total of 1740 samples. Water samples were analyzed for fecal indicator bacteria (Escherichia coli, enterococci and fecal coliforms), and 53 other physiochemical, land use, and environmental characteristics. The purpose of the study was to create a baseline of microbial water quality in the Delta and to identify various factors (climatic, land use, tidal, etc.) that were associated with elevated concentrations of indicator bacteria. Fecal indicator bacteria generally had weak to modest relationships to environmental conditions; the strength and direction of which varied for each microbial indicator, drainage region, and across seasons. Measured and unmeasured, site-specific effects accounted for large portions of variance in model predictions (ρ=0.086 to 0.255), indicating that spatial autocorrelation was a major component of water quality outcomes. The effects of tidal cycling and lack of connectivity between waterways and surrounding landscapes likely contributed to the lack of association between local land uses and microbial outcomes, though weak associations may also be indicative of mismatched spatiotemporal scales. The complex nature of this system necessitates continued monitoring and regular updates to statistical models designed to predict microbial water quality. Copyright © 2016 Elsevier B.V. All rights reserved.
Effect of microbial-based inoculants on nutrient concentrations and early root morphology of corn (Zea mays)

USDA-ARS?s Scientific Manuscript database

Microbial-based inoculants have been reported to stimulate plant growth and nutrient uptake. However, their effect may vary depending on the growth stage when evaluated and on the chemical fertilizer applied. Thus, the objective of this study was to test the hypothesis that microbial-based inoculant...
Functional responses and adaptation of mesophilic microbial communities to psychrophilic anaerobic digestion.

PubMed

Gunnigle, Eoin; Nielsen, Jeppe L; Fuszard, Matthew; Botting, Catherine H; Sheahan, Jerome; O'Flaherty, Vincent; Abram, Florence

2015-12-01

Psychrophilic (<20°C) anaerobic digestion (AD) represents an attractive alternative to mesophilic wastewater treatment. In order to investigate the AD microbiome response to temperature change, with particular emphasis on methanogenic archaea, duplicate laboratory-scale AD bioreactors were operated at 37°C followed by a temperature drop to 15°C. A volatile fatty acid-based wastewater (composed of propionic acid, butyric acid, acetic acid and ethanol) was used to provide substrates representing the later stages of AD. Community structure was monitored using 16S rRNA gene clone libraries, as well as DNA and cDNA-based DGGE analysis, while the abundance of relevant methanogens was followed using qPCR. In addition, metaproteomics, microautoradiography-fluorescence in situ hybridization, and methanogenic activity measurements were employed to investigate microbial activities and functions. Methanomicrobiales abundance increased at low temperature, which correlated with an increased contribution of CH4 production from hydrogenotrophic methanogenesis at 15°C. Methanosarcinales utilized acetate and H2/CO2 as CH4 precursors at both temperatures and a partial shift from acetoclastic to hydrogenotrophic methanogenesis was observed for this archaeal population at 15°C. An upregulation of protein expression was reported at low temperature as well as the detection of chaperones indicating that mesophilic communities experienced stress during long-term exposure to 15°C. Overall, changes in microbial community structure and function were found to underpin the adaptation of mesophilic sludge to psychrophilic AD. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
Microbial biosurfactants with their high-value functional properties

USDA-ARS?s Scientific Manuscript database

Microbial world is a rich source for finding valuable industrial chemicals and ingredients. Specifically, many microbial metabolites are surface-active compounds that can be developed into bio-based surfactants, detergents, and emulsifiers. Techno-economic analyses for the production of bio-based ...
Microbial Communities as Environmental Indicators of Ecological Disturbance in Restored Carbonate Fen-Results of 10 Years of Studies.

PubMed

Mieczan, Tomasz; Tarkowska-Kukuryk, Monika

2017-08-01

Interactions between bacteria and protists are essential to the ecosystem ecology of fens. Until now, however, there has been almost no information on how restoration procedures in carbonate fens affect the functioning of microbial food webs. Changes in vegetation patterns resulting from restoration may take years to be observed, whereas microbial processes display effects even after short-term exposure to changes in environmental conditions caused by restoration. Therefore, microbial processes and patterns can be used as sensitive indicators of changes in environmental conditions. The present study attempts to verify the hypothesis that the species richness and abundance of microbial loop components would differ substantially before and after restoration. The effect of restoration processes on the functioning of the food web was investigated for a 10 years in a carbonate-rich fen, before and after restoration. The restoration procedure (particularly the improvement in hydrological conditions) distinctly modified the taxonomic composition and functioning of microbial food webs. This is reflected in the increased abundance and diversity of testate amoeba, i.e. top predators, within the microbial food web and in the pronounced increase in the abundance of bacteria. This study suggests potential use of microbial loop components as bio-indicators and bio-monitoring tools for hydrological status of fens and concentrations of nutrients. Better understanding of what regulates microbial populations and activity in fens and unravelling of these fundamental mechanisms are particularly critical in order to more accurately predict how fens will respond to global change or anthropogenic disturbances.
Regime Shift and Microbial Dynamics in a Sequencing Batch Reactor for Nitrification and Anammox Treatment of Urine ▿†

PubMed Central

Bürgmann, Helmut; Jenni, Sarina; Vazquez, Francisco; Udert, Kai M.

2011-01-01

The microbial population and physicochemical process parameters of a sequencing batch reactor for nitrogen removal from urine were monitored over a 1.5-year period. Microbial community fingerprinting (automated ribosomal intergenic spacer analysis), 16S rRNA gene sequencing, and quantitative PCR on nitrogen cycle functional groups were used to characterize the microbial population. The reactor combined nitrification (ammonium oxidation)/anammox with organoheterotrophic denitrification. The nitrogen elimination rate initially increased by 400%, followed by an extended period of performance degradation. This phase was characterized by accumulation of nitrite and nitrous oxide, reduced anammox activity, and a different but stable microbial community. Outwashing of anammox bacteria or their inhibition by oxygen or nitrite was insufficient to explain reactor behavior. Multiple lines of evidence, e.g., regime-shift analysis of chemical and physical parameters and cluster and ordination analysis of the microbial community, indicated that the system had experienced a rapid transition to a new stable state that led to the observed inferior process rates. The events in the reactor can thus be interpreted to be an ecological regime shift. Constrained ordination indicated that the pH set point controlling cycle duration, temperature, airflow rate, and the release of nitric and nitrous oxides controlled the primarily heterotrophic microbial community. We show that by combining chemical and physical measurements, microbial community analysis and ecological theory allowed extraction of useful information about the causes and dynamics of the observed process instability. PMID:21724875
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.
Series quartz crystal sensor for remote bacteria population monitoring in raw milk via the Internet.

PubMed

Chang, Ku-Shang; Jang, Hung-Der; Lee, Ching-Fu; Lee, Yuan-Guey; Yuan, Chiun-Jye; Lee, Sheng-Hsien

2006-02-15

A remote monitoring system based on a piezoelectric quartz crystal (SPQC) sensor was developed for the determination of the bacteria population in raw milk. The system employs the Windows XP server operating system, and its programs for data acquisition, display and transmission were developed using the LabVIEW 7.1 programming language. The circuit design consists of a circuit with a piezoelectric quartz crystal (SPQC) and a pair of electrodes. This system can provide dynamic data monitoring on a web-page via the Internet. Immersion of the electrodes in a cell culture with bacteria inoculums resulted in a change of frequency caused by the impedance change due to microbial metabolism and the adherence of bacteria on the surface of the electrodes. The calibration curve of detection times against density of bacteria showed a linear correlation coefficient (R(2) = 0.9165) over the range of 70-10(6) CFU ml(-1). The sensor could acquire sufficient data rapidly (within 4 h) and thus enabled real-time monitoring of bacteria growth via the Internet. This system has potential application in the detection of bacteria concentration of milk at dairy farms.
mRNA-Based Parallel Detection of Active Methanotroph Populations by Use of a Diagnostic Microarray

PubMed Central

Bodrossy, Levente; Stralis-Pavese, Nancy; Konrad-Köszler, Marianne; Weilharter, Alexandra; Reichenauer, Thomas G.; Schöfer, David; Sessitsch, Angela

2006-01-01

A method was developed for the mRNA-based application of microbial diagnostic microarrays to detect active microbial populations. DNA- and mRNA-based analyses of environmental samples were compared and confirmed via quantitative PCR. Results indicated that mRNA-based microarray analyses may provide additional information on the composition and functioning of microbial communities. PMID:16461725

An Overview on Recent Progress in Electrochemical Biosensors for Antimicrobial Drug Residues in Animal-Derived Food

PubMed Central

Majdinasab, Marjan; Yaqub, Mustansara; Rahim, Abdur; Catanante, Gaelle; Hayat, Akhtar; Marty, Jean Louis

2017-01-01

Anti-microbial drugs are widely employed for the treatment and cure of diseases in animals, promotion of animal growth, and feed efficiency. However, the scientific literature has indicated the possible presence of antimicrobial drug residues in animal-derived food, making it one of the key public concerns for food safety. Therefore, it is highly desirable to design fast and accurate methodologies to monitor antimicrobial drug residues in animal-derived food. Legislation is in place in many countries to ensure antimicrobial drug residue quantities are less than the maximum residue limits (MRL) defined on the basis of food safety. In this context, the recent years have witnessed a special interest in the field of electrochemical biosensors for food safety, based on their unique analytical features. This review article is focused on the recent progress in the domain of electrochemical biosensors to monitor antimicrobial drug residues in animal-derived food. PMID:28837093
Ecogenomics of microbial communities in bioremediation of chlorinated contaminated sites

PubMed Central

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

2012-01-01

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

PubMed

Bouhajja, Emna; Agathos, Spiros N; George, Isabelle F

2016-12-01

Polluted environments are a reservoir of microbial species able to degrade or to convert pollutants to harmless compounds. The proper management of microbial resources requires a comprehensive characterization of their genetic pool to assess the fate of contaminants and increase the efficiency of bioremediation processes. Metagenomics offers appropriate tools to describe microbial communities in their whole complexity without lab-based cultivation of individual strains. After a decade of use of metagenomics to study microbiomes, the scientific community has made significant progress in this field. In this review, we survey the main steps of metagenomics applied to environments contaminated with organic compounds or heavy metals. We emphasize technical solutions proposed to overcome encountered obstacles. We then compare two metagenomic approaches, i.e. library-based targeted metagenomics and direct sequencing of metagenomes. In the former, environmental DNA is cloned inside a host, and then clones of interest are selected based on (i) their expression of biodegradative functions or (ii) sequence homology with probes and primers designed from relevant, already known sequences. The highest score for the discovery of novel genes and degradation pathways has been achieved so far by functional screening of large clone libraries. On the other hand, direct sequencing of metagenomes without a cloning step has been more often applied to polluted environments for characterization of the taxonomic and functional composition of microbial communities and their dynamics. In this case, the analysis has focused on 16S rRNA genes and marker genes of biodegradation. Advances in next generation sequencing and in bioinformatic analysis of sequencing data have opened up new opportunities for assessing the potential of biodegradation by microbes, but annotation of collected genes is still hampered by a limited number of available reference sequences in databases. Although metagenomics is still facing technical and computational challenges, our review of the recent literature highlights its value as an aid to efficiently monitor the clean-up of contaminated environments and develop successful strategies to mitigate the impact of pollutants on ecosystems. Copyright © 2016 Elsevier Inc. All rights reserved.
Connecting Water Quality With Air Quality Through Microbial Aerosols

NASA Astrophysics Data System (ADS)

Dueker, M. Elias

Aerosol production from surface waters results in the transfer of aquatic materials (including nutrients and bacteria) to air. These materials can then be transported by onshore winds to land, representing a biogeochemical connection between aquatic and terrestrial systems not normally considered. In urban waterfront environments, this transfer could result in emissions of pathogenic bacteria from contaminated waters. Despite the potential importance of this link, sources, near-shore deposition, identity and viability of microbial aerosols are largely uncharacterized. This dissertation focuses on the environmental and biological mechanisms that define this water-air connection, as a means to build our understanding of the biogeochemical, biogeographical, and public health implications of the transfer of surface water materials to the near-shore environment in both urban and non-urban environments. The effects of tidal height, wind speed and fog on coastal aerosols and microbial content were first quantified on a non-urban coast of Maine, USA. Culture-based, culture-independent, and molecular methods were used to simultaneously sample microbial aerosols while monitoring meteorological parameters. Aerosols at this site displayed clear marine influence and high concentrations of ecologically-relevant nutrients. Coarse aerosol concentrations significantly increased with tidal height, onshore wind speed, and fog presence. Tidal height and fog presence did not significantly influence total microbial aerosol concentrations, but did have a significant effect on culturable microbial aerosol fallout. Molecular analyses of the microbes settling out of near-shore aerosols provided further evidence of local ocean to terrestrial transport of microbes. Aerosol and surface ocean bacterial communities shared species and in general were dominated by organisms previously sampled in marine environments. Fog presence strengthened the microbial connection between water and land through air by increasing microbial aerosol settling rates and enhancing viability of aerosolized marine microbes. Using methods developed for the non-urban site, the role of local environment and winds in mediating water-air connections was further investigated in the urban environment. The local environment, including water surfaces, was an important source of microbial aerosols at urban sites. Large portions of the urban waterfront microbial aerosol communities were aquatic and, at a highly polluted Superfund waterfront, were closely related to bacteria previously described in environments contaminated with hydrocarbons, heavy metals, sewage and other industrial waste. Culturable urban aerosols and surface waters contained bacterial genera known to include human pathogens and asthma agents. High onshore winds strengthened this water-air connection by playing both a transport and production role. The microbial connection between water and air quality outlined by this dissertation highlights the need for information on the mechanisms that deliver surface water materials to terrestrial systems on a much larger scale. Moving from point measurements to landscape-level analyses will allow for the quantitative assessment of implications for this microbial water-air-land transfer in both urban and non-urban arenas.
Important considerations in the use of carbon and hydrogen stable isotopes to determine the origin of hydrocarbons in groundwater – A case study from pre-shale gas Tioga County

EPA Pesticide Factsheets

stable carbon and hydrogen isotopic compositional ranges of methanes (δ13C and δ2H (D)) enable us to distinguish between microbial and thermogenic origin of natural gases. To identify stray gas origins, identify possible gas sources, create baseline, carry out site-specific monitoring, and monitor long-term changes
HydroGrid: Technologies for Global Water Quality and Sustainability

NASA Astrophysics Data System (ADS)

Yeghiazarian, L.

2017-12-01

Humans have been transforming planet Earth for millennia. We have recently come to understand that the collective impact of our decisions and actions has brought about severe water quality problems, which are likely to worsen in the light of rapid population growth to the projected nine billion by 2050. To sustainably manage our global water resources and possibly reverse these effects requires efforts in real-time monitoring of water contamination, analysis of monitoring data, and control of the state of water contamination. We develop technologies to address all three areas: monitoring, analysis and control. These efforts are carried out in the conceptual framework of the HydroGrid, an interconnected water system, which is (1) firmly rooted in the fundamental understanding of processes that govern microbial dynamics on multiple scales; and (2) used to develop watershed-specific management strategies. In the area of monitoring we are developing mobile autonomous sensors to detect surface water contamination, an effort supported by extensive materials research to provide multifunctional materials. We analyze environmental data within a stochastic modeling paradigm that bridges microscopic particle interactions to macroscopic manifestation of microbial population behavior in time and space in entire watersheds. These models are supported with laboratory and field experiments. Finally, we combine control and graph theories to derive controllability metrics of natural watersheds.
The Dry Aerosol Deposition Device (DADD): An Instrument for Depositing Microbial Aerosols onto Surfaces (PREPRINT)

DTIC Science & Technology

2008-12-01

TASK NUMBER 5f. WORK UNIT NUMBER 6. AUTHOR( S ) 7. PERFORMING ORGANIZATION NAME( S ) AND ADDRESS(ES) 8. PERFORMING ORGANIZATION REPORT NUMBER 9...SPONSORING/MONITORING AGENCY NAME( S ) AND ADDRESS(ES) 10. SPONSOR/MONITOR’S ACRONYM( S ) 11. SPONSOR/MONITOR’S REPORT NUMBER( S ) 12. DISTRIBUTION...exceeding 1X104 CFU/cm2. The coefficient of variation (CV) 38 for sample-to-sample loading within an experiment was 13.6% for spores and 6.1% for 39 S
Microbial quantification in activated sludge: the hits and misses.

PubMed

Hall, S J; Keller, J; Blackall, L L

2003-01-01

Since the implementation of the activated sludge process for treating wastewater, there has been a reliance on chemical and physical parameters to monitor the system. However, in biological nutrient removal (BNR) processes, the microorganisms responsible for some of the transformations should be used to monitor the processes with the overall goal to achieve better treatment performance. The development of in situ identification and rapid quantification techniques for key microorganisms involved in BNR are required to achieve this goal. This study explored the quantification of Nitrospira, a key organism in the oxidation of nitrite to nitrate in BNR. Two molecular genetic microbial quantification techniques were evaluated: real-time polymerase chain reaction (PCR) and fluorescence in situ hybridisation (FISH) followed by digital image analysis. A correlation between the Nitrospira quantitative data and the nitrate production rate, determined in batch tests, was attempted. The disadvantages and advantages of both methods will be discussed.
Tracking Silent Hypersensitivity Reactions to Asparaginase during Leukemia Therapy Using Single-Chip Indirect Plasmonic and Fluorescence Immunosensing.

PubMed

Charbonneau, David M; Breault-Turcot, Julien; Sinnett, Daniel; Krajinovic, Maja; Leclerc, Jean-Marie; Masson, Jean-François; Pelletier, Joelle N

2017-12-22

Microbial asparaginase is an essential component of chemotherapy for the treatment of childhood acute lymphoblastic leukemia (cALL). Silent hypersensitivity reactions to this microbial enzyme need to be monitored accurately during treatment to avoid adverse effects of the drug and its silent inactivation. Here, we present a dual-response anti-asparaginase sensor that combines indirect SPR and fluorescence on a single chip to perform ELISA-type immunosensing, and correlate measurements with classical ELISA. Analysis of serum samples from children undergoing cALL therapy revealed a clear correlation between single-chip indirect SPR/fluorescence immunosensing and ELISA used in clinical settings (R 2 > 0.9). We also report that the portable SPR/fluorescence system had a better sensitivity than classical ELISA to detect antibodies in clinical samples with low antigenicity. This work demonstrates the reliability of dual sensing for monitoring clinically relevant antibody titers in clinical serum samples.
Online analysis of protein inclusion bodies produced in E. coli by monitoring alterations in scattered and reflected light.

PubMed

Ude, Christian; Ben-Dov, Nadav; Jochums, André; Li, Zhaopeng; Segal, Ester; Scheper, Thomas; Beutel, Sascha

2016-05-01

The online monitoring of recombinant protein aggregate inclusion bodies during microbial cultivation is an immense challenge. Measurement of scattered and reflected light offers a versatile and non-invasive measurement technique. Therefore, we investigated two methods to detect the formation of inclusion bodies and monitor their production: (1) online 180° scattered light measurement (λ = 625 nm) using a sensor platform during cultivation in shake flask and (2) online measurement of the light reflective interference using a porous Si-based optical biosensor (SiPA). It could be shown that 180° scattered light measurement allows monitoring of alterations in the optical properties of Escherichia coli BL21 cells, associated with the formation of inclusion bodies during cultivation. A reproducible linear correlation between the inclusion body concentration of the non-fluorescent protein human leukemia inhibitory factor (hLIF) carrying a thioredoxin tag and the shift ("Δamp") in scattered light signal intensity was observed. This was also observed for the glutathione-S-transferase-tagged green fluorescent protein (GFP-GST). Continuous online monitoring of reflective interference spectra reveals a significant increase in the bacterium refractive index during hLIF production in comparison to a non-induced reference that coincide with the formation of inclusion bodies. These online monitoring techniques could be applied for fast and cost-effective screening of different protein expression systems.
Coral transplantation triggers shift in microbiome and promotion of coral disease associated potential pathogens

PubMed Central

Casey, Jordan M.; Connolly, Sean R.; Ainsworth, Tracy D.

2015-01-01

By cultivating turf algae and aggressively defending their territories, territorial damselfishes in the genus Stegastes play a major role in shaping coral-algal dynamics on coral reefs. The epilithic algal matrix (EAM) inside Stegastes’ territories is known to harbor high abundances of potential coral disease pathogens. To determine the impact of territorial grazers on coral microbial assemblages, we established a coral transplant inside and outside of Stegastes’ territories. Over the course of one year, the percent mortality of transplanted corals was monitored and coral samples were collected for microbial analysis. As compared to outside damselfish territories, Stegastes were associated with a higher rate of mortality of transplanted corals. However, 16S rDNA sequencing revealed that territorial grazers do not differentially impact the microbial assemblage of corals exposed to the EAM. Regardless of Stegastes presence or absence, coral transplantation resulted in a shift in the coral-associated microbial community and an increase in coral disease associated potential pathogens. Further, transplanted corals that suffer low to high mortality undergo a microbial transition from a microbiome similar to that of healthy corals to that resembling the EAM. These findings demonstrate that coral transplantation significantly impacts coral microbial communities, and transplantation may increase susceptibility to coral disease. PMID:26144865
Cellulolytic potential under environmental changes in microbial communities from grassland litter

DOE PAGES

Berlemont, Renaud; Allison, Steven D.; Weihe, Claudia; ...

2014-11-25

We report that in many ecosystems, global changes are likely to profoundly affect microorganisms. In Southern California, changes in precipitation and nitrogen deposition may influence the composition and functional potential of microbial communities and their resulting ability to degrade plant material. To test whether such environmental changes impact the distribution of functional groups involved in leaf litter degradation, we determined how the genomic diversity of microbial communities in a semi-arid grassland ecosystem changed under reduced precipitation or increased N deposition. We monitored communities seasonally over a period of 2 years to place environmental change responses into the context of naturalmore » variation. Fungal and bacterial communities displayed strong seasonal patterns, Fungi being mostly detected during the dry season whereas Bacteria were common during wet periods. Most putative cellulose degraders were associated with 33 bacterial genera and predicted to constitute 18% of the microbial community. Precipitation reduction reduced bacterial abundance and cellulolytic potential whereas nitrogen addition did not affect the cellulolytic potential of the microbial community. Finally, we detected a strong correlation between the frequencies of genera of putative cellulose degraders and cellulase genes. Thus, microbial taxonomic composition was predictive of cellulolytic potential. This work provides a framework for how environmental changes affect microorganisms responsible for plant litter deconstruction.« less
Microbial Existence in Controlled Habitats and Their Resistance to Space Conditions

PubMed Central

Venkateswaran, Kasthuri; La Duc, Myron T.; Horneck, Gerda

2014-01-01

The National Research Council (NRC) has recently recognized the International Space Station (ISS) as uniquely suitable for furthering the study of microbial species in closed habitats. Answering the NRC’s call for the study, in particular, of uncommon microbial species in the ISS, and/or of those that have significantly increased or decreased in number, space microbiologists have begun capitalizing on the maturity, speed, and cost-effectiveness of molecular/genomic microbiological technologies to elucidate changes in microbial populations in the ISS and other closed habitats. Since investigators can only collect samples infrequently from the ISS itself due to logistical reasons, Earth analogs, such as spacecraft-assembly clean rooms, are used and extensively characterized for the presence of microbes. Microbiologists identify the predominant, problematic, and extremophilic microbial species in these closed habitats and use the ISS as a testbed to study their resistance to extreme extraterrestrial environmental conditions. Investigators monitor the microbes exposed to the real space conditions in order to track their genomic changes in response to the selective pressures present in outer space (external to the ISS) and the spaceflight (in the interior of the ISS). In this review, we discussed the presence of microbes in space research-related closed habitats and the resistance of some microbial species to the extreme environmental conditions of space. PMID:25130881
Microbial existence in controlled habitats and their resistance to space conditions.

PubMed

Venkateswaran, Kasthuri; La Duc, Myron T; Horneck, Gerda

2014-09-17

The National Research Council (NRC) has recently recognized the International Space Station (ISS) as uniquely suitable for furthering the study of microbial species in closed habitats. Answering the NRC's call for the study, in particular, of uncommon microbial species in the ISS, and/or of those that have significantly increased or decreased in number, space microbiologists have begun capitalizing on the maturity, speed, and cost-effectiveness of molecular/genomic microbiological technologies to elucidate changes in microbial populations in the ISS and other closed habitats. Since investigators can only collect samples infrequently from the ISS itself due to logistical reasons, Earth analogs, such as spacecraft-assembly clean rooms, are used and extensively characterized for the presence of microbes. Microbiologists identify the predominant, problematic, and extremophilic microbial species in these closed habitats and use the ISS as a testbed to study their resistance to extreme extraterrestrial environmental conditions. Investigators monitor the microbes exposed to the real space conditions in order to track their genomic changes in response to the selective pressures present in outer space (external to the ISS) and the spaceflight (in the interior of the ISS). In this review, we discussed the presence of microbes in space research-related closed habitats and the resistance of some microbial species to the extreme environmental conditions of space.
Microbial Community Profiles in Wastewaters from Onsite Wastewater Treatment Systems Technology

PubMed Central

Jałowiecki, Łukasz; Chojniak, Joanna Małgorzata; Dorgeloh, Elmar; Hegedusova, Berta; Ejhed, Helene; Magnér, Jörgen; Płaza, Grażyna Anna

2016-01-01

The aim of the study was to determine the potential of community-level physiological profiles (CLPPs) methodology as an assay for characterization of the metabolic diversity of wastewater samples and to link the metabolic diversity patterns to efficiency of select onsite biological wastewater facilities. Metabolic fingerprints obtained from the selected samples were used to understand functional diversity implied by the carbon substrate shifts. Three different biological facilities of onsite wastewater treatment were evaluated: fixed bed reactor (technology A), trickling filter/biofilter system (technology B), and aerated filter system (the fluidized bed reactor, technology C). High similarities of the microbial community functional structures were found among the samples from the three onsite wastewater treatment plants (WWTPs), as shown by the diversity indices. Principal components analysis (PCA) showed that the diversity and CLPPs of microbial communities depended on the working efficiency of the wastewater treatment technologies. This study provided an overall picture of microbial community functional structures of investigated samples in WWTPs and discerned the linkages between microbial communities and technologies of onsite WWTPs used. The results obtained confirmed that metabolic profiles could be used to monitor treatment processes as valuable biological indicators of onsite wastewater treatment technologies efficiency. This is the first step toward understanding relations of technology types with microbial community patterns in raw and treated wastewaters. PMID:26807728
Monitoring the microbial community during solid-state acetic acid fermentation of Zhenjiang aromatic vinegar.

PubMed

Xu, Wei; Huang, Zhiyong; Zhang, Xiaojun; Li, Qi; Lu, Zhenming; Shi, Jinsong; Xu, Zhenghong; Ma, Yanhe

2011-09-01

Zhenjiang aromatic vinegar is one of the most famous Chinese traditional vinegars. In this study, change of the microbial community during its fermentation process was investigated. DGGE results showed that microbial community was comparatively stable, and the diversity has a disciplinary series of changes during the fermentation process. It was suggested that domestication of microbes and unique cycle-inoculation style used in the fermentation of Zhenjiang aromatic vinegar were responsible for comparatively stable of the microbial community. Furthermore, two clone libraries were constructed. The results showed that bacteria presented in the fermentation belonged to genus Lactobacillus, Acetobacter, Gluconacetobacter, Staphylococcus, Enterobacter, Pseudomonas, Flavobacterium and Sinorhizobium, while the fungi were genus Saccharomyces. DGGE combined with clone library analysis was an effective and credible technique for analyzing the microbial community during the fermentation process of Zhenjiang aromatic vinegar. Real-time PCR results suggested that the biomass showed a "system microbes self-domestication" process in the first 5 days, then reached a higher level at the 7th day before gradually decreasing until the fermentation ended at the 20th day. This is the first report to study the changes of microbial community during fermentation process of Chinese traditional solid-state fermentation of vinegar. Copyright © 2011 Elsevier Ltd. All rights reserved.
Analysis of microbial community variation during the mixed culture fermentation of agricultural peel wastes to produce lactic acid.

PubMed

Liang, Shaobo; Gliniewicz, Karol; Gerritsen, Alida T; McDonald, Armando G

2016-05-01

Mixed cultures fermentation can be used to convert organic wastes into various chemicals and fuels. This study examined the fermentation performance of four batch reactors fed with different agricultural (orange, banana, and potato (mechanical and steam)) peel wastes using mixed cultures, and monitored the interval variation of reactor microbial communities with 16S rRNA genes using Illumina sequencing. All four reactors produced similar chemical profile with lactic acid (LA) as dominant compound. Acetic acid and ethanol were also observed with small fractions. The Illumina sequencing results revealed the diversity of microbial community decreased during fermentation and a community of largely lactic acid producing bacteria dominated by species of Lactobacillus developed. Copyright © 2016 Elsevier Ltd. All rights reserved.
PubMed Central

Valeriani, F.; Cianfanelli, C.; Gianfranceschi, G.; Santucci, S.; Romano Spica, V.

2017-01-01

Summary Indoor Air Quality (IAQ) in libraries is influenced by the presence of specific factors which can impact on both paper storage as well as people health. Microclimatic conditions induce and support a biodiversity pattern involving environmental and anthropic microorganisms. We used a multidisciplinary monitoring model to characterize microflora biodiversity by Next Generation Sequencing (NGS). Biodiversity indexes were adapted to evaluate anthropic vs environmental pollution by combining Shannon mean index (H), species representativeness (EH), human/environmental pollution ratio (SA) to better characterize the NGS output and acquire synthetic information on Indoor Air Microbial Biodiversity (IAMB). Results indicate a frequently low microbial load (IGCM/m3 < 1000) characterized by different species (n = 102), including several cellulose metabolizing bacteria. Workers and visitors appeared a relevant source of microbial contamination. Air biodiversity assayed by NGS seems a promising marker for studying IAQ. PMID:29123371
Carbon use efficiency (CUE) and biomass turnover of soil microbial communities as affected by bedrock, land management and soil temperature and moisture

NASA Astrophysics Data System (ADS)

Zheng, Qing; Hu, Yuntao; Richter, Andreas; Wanek, Wolfgang

2017-04-01

Soil microbial carbon use efficiency (CUE), defined as the proportion of organic C taken up that is allocated to microbial growth, represents an important synthetic representation of microbial community C metabolism that describes the flux partitioning between microbial respiration and growth. Therefore, studying microbial CUE is critical for the understanding of soil C cycling. Microbial CUE is thought to vary with environmental conditions (e.g. temperature and soil moisture). Microbial CUE is thought to decrease with increasing temperature and declining soil moisture, as the latter may trigger stress responses (e.g. the synthesis of stress metabolites), which may consequently lower microbial community CUE. However, these effects on microbial CUE have not been adequately measured so far due to methodological restrictions. The most widely used methods for microbial CUE estimation are based on tracing 13C-labeled substrates into microbial biomass and respiratory CO2, approaches that are known to overestimate microbial CUE of native organic matter in soil. Recently, a novel substrate-independent approach based on the measurement of (i) respiration rates and (ii) the incorporation rates of 18O from labelled water into newly formed microbial DNA has been developed in our laboratory for measuring microbial CUE. This approach overcomes the shortcomings of previously used methods and has already been shown to yield realistic estimations of soil microbial CUE. This approach can also be applied to concurrently measure microbial biomass turnover rates, which also influence the sequestration of soil organic C. Microbial turnover rates are also thought to be impacted by environmental factors, but rarely have been directly measured so far. Here, we aimed at determining the short-term effects of environmental factors (soil temperature and soil moisture) on microbial CUE and microbial biomass turnover rates based on the novel 18O approach. Soils from three land-use types (arable fields, pasture and forest) sampled from two geologies (silicate versus limestone) in the same region in Austria were incubated at three temperatures (5, 15 and 25 ˚ C) for 1 day and at three moisture levels (30, 60, 90% water-holding capacity) for 7 days in the laboratory, respectively. We will present the results and discuss major effects of environmental factors as well as of land management and geology on microbial growth, respiration, microbial CUE and microbial biomass turnover, and set those in relation to microbial community composition.
GIS-based analysis of drinking-water supply structures: a module for microbial risk assessment.

PubMed

Kistemann, T; Herbst, S; Dangendorf, F; Exner, M

2001-05-01

Water-related infections constitute an important health impact world-wide. A set of tools serving for Microbial Risk Assessment (MRA) of waterborne diseases should comprise the entire drinking-water management system and take into account the Hazard Analysis and Critical Control Point (HACCP) concept which provides specific Critical Control Points (CCPs) reflecting each step of drinking-water provision. A Geographical Information System (GIS) study concerning water-supply structure (WSS) was conducted in the Rhein-Berg District (North Rhine-Westphalia, Germany). As a result, suitability of the existing water databases HYGRIS (hydrological basis geo-information system) and TEIS (drinking-water recording and information system) for the development of a WSS-GIS module could be demonstrated. Spatial patterns within the integrated raw and drinking-water data can easily be uncovered by GIS-specific options. The application of WSS-GIS allows a rapid visualization and analysis of drinking-water supply structure and offers huge advantages concerning microbial monitoring of raw and drinking water as well as recognition and investigation of incidents and outbreaks. Increasing requests regarding health protection and health reporting, demands for a better outbreak management and water-related health impacts of global climate change are major challenges of future water management to be tackled with methods including spatial analysis. GIS is assumed to be a very useful tool to meet these requirements.

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