Reconstituted yogurt from yogurt cultured milk powder mix has better overall characteristics than reconstituted yogurt from commercial yogurt powder.

PubMed

Song, Lijie; Aryana, Kayanush J

2014-10-01

For manufacture of commercial yogurt powder, yogurt has to go through a drying process, which substantially lowers the yogurt culture counts, so the potential health benefits of the yogurt culture bacteria are reduced. Also, upon reconstitution, commercial yogurt powder does not taste like yogurt and has an off-flavor. The objective was to study the microbial, physicochemical, and sensory characteristics of reconstituted yogurt from yogurt cultured milk powder (YCMP) mix and reconstituted yogurt from commercial yogurt powder (CYP). The CYP reconstituted yogurt was the control and YCMP mix reconstituted yogurt was the treatment. Microbial and physicochemical characteristics of the CYP reconstituted yogurt and YCMP mix reconstituted yogurt were analyzed daily for the first week and then weekly for a period of 8 wk. Sensory consumer testing of CYP reconstituted yogurt and YCMP mix reconstituted yogurt was conducted with 100 consumers. At 56 d, YCMP mix reconstituted yogurt had 5 log cfu/mL higher counts of Streptococcus thermophilus than the control (CYP reconstituted yogurt). Also, Lactobacillus bulgaricus counts of YCMP mix reconstituted yogurt were 6.55 log cfu/mL at 28 d and were 5.35 log cfu/mL at 56 d, whereas the CYP reconstituted yogurt from 28 d onwards had a count of <10 cfu/mL. The YCMP mix reconstituted yogurt also had significantly higher apparent viscosity and sensory scores for appearance, color, aroma, taste, thickness, overall liking, consumer acceptability, and purchase intent than CYP reconstituted yogurt. Overall, YCMP mix reconstituted yogurt had more desirable characteristics than CYP reconstituted yogurt. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Microbial Biosynthesis of Silver Nanoparticles in Different Culture Media.

PubMed

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

2018-01-31

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

Culture-Independent Metagenomic Surveillance of Commercially Available Probiotics with High-Throughput Next-Generation Sequencing.

PubMed

Patro, Jennifer N; Ramachandran, Padmini; Barnaba, Tammy; Mammel, Mark K; Lewis, Jada L; Elkins, Christopher A

2016-01-01

Millions of people consume dietary supplements either following a doctor's recommendation or at their own discretion to improve their overall health and well-being. This is a rapidly growing trend, with an associated and expanding manufacturing industry to meet the demand for new health-related products. In this study, we examined the contents and microbial viability of several popular probiotic products on the United States market. Culture-independent methods are proving ideal for fast and efficient analysis of foodborne pathogens and their associated microbial communities but may also be relevant for analyzing probiotics containing mixed microbial constituents. These products were subjected to next-generation whole-genome sequencing and analyzed by a custom in-house-developed k-mer counting method to validate manufacturer label information. In addition, the batch variability of respective products was examined to determine if any changes in their formulations and/or the manufacturing process occurred. Overall, the products we tested adhered to the ingredient claims and lot-to-lot differences were minimal. However, there were a few discrepancies in the naming of closely related Lactobacillus and Bifidobacterium species, whereas one product contained an apparent Enterococcus contaminant in two of its three lots. With the microbial contents of the products identified, we used traditional PCR and colony counting methods to comparatively assess our results and verify the viability of the microbes in these products with regard to the labeling claims. Of all the supplements examined, only one was found to be inaccurate in viability. Our use of next-generation sequencing as an analytical tool clearly demonstrated its utility for quickly analyzing commercially available products containing multiple microbes to ensure consumer safety. IMPORTANCE The rapidly growing supplement industry operates without a formal premarket approval process. Consumers rely on product labels to

Culture-Independent Metagenomic Surveillance of Commercially Available Probiotics with High-Throughput Next-Generation Sequencing

PubMed Central

Patro, Jennifer N.; Ramachandran, Padmini; Barnaba, Tammy; Mammel, Mark K.; Lewis, Jada L.

2016-01-01

ABSTRACT Millions of people consume dietary supplements either following a doctor’s recommendation or at their own discretion to improve their overall health and well-being. This is a rapidly growing trend, with an associated and expanding manufacturing industry to meet the demand for new health-related products. In this study, we examined the contents and microbial viability of several popular probiotic products on the United States market. Culture-independent methods are proving ideal for fast and efficient analysis of foodborne pathogens and their associated microbial communities but may also be relevant for analyzing probiotics containing mixed microbial constituents. These products were subjected to next-generation whole-genome sequencing and analyzed by a custom in-house-developed k-mer counting method to validate manufacturer label information. In addition, the batch variability of respective products was examined to determine if any changes in their formulations and/or the manufacturing process occurred. Overall, the products we tested adhered to the ingredient claims and lot-to-lot differences were minimal. However, there were a few discrepancies in the naming of closely related Lactobacillus and Bifidobacterium species, whereas one product contained an apparent Enterococcus contaminant in two of its three lots. With the microbial contents of the products identified, we used traditional PCR and colony counting methods to comparatively assess our results and verify the viability of the microbes in these products with regard to the labeling claims. Of all the supplements examined, only one was found to be inaccurate in viability. Our use of next-generation sequencing as an analytical tool clearly demonstrated its utility for quickly analyzing commercially available products containing multiple microbes to ensure consumer safety. IMPORTANCE The rapidly growing supplement industry operates without a formal premarket approval process. Consumers rely on

Film forming microbial biopolymers for commercial applications--a review.

PubMed

Vijayendra, S V N; Shamala, T R

2014-12-01

Microorganisms synthesize intracellular, structural and extracellular polymers also referred to as biopolymers for their function and survival. These biopolymers play specific roles as energy reserve materials, protective agents, aid in cell functioning, the establishment of symbiosis, osmotic adaptation and support the microbial genera to function, adapt, multiply and survive efficiently under changing environmental conditions. Viscosifying, gelling and film forming properties of these have been exploited for specific significant applications in food and allied industries. Intensive research activities and recent achievements in relevant and important research fields of global interest regarding film forming microbial biopolymers is the subject of this review. Microbial polymers such as pullulan, kefiran, bacterial cellulose (BC), gellan and levan are placed under the category of exopolysaccharides (EPS) and have several other functional properties including film formation, which can be used for various applications in food and allied industries. In addition to EPS, innumerable bacterial genera are found to synthesis carbon energy reserves in their cells known as polyhydroxyalkanoates (PHAs), microbial polyesters, which can be extruded into films with excellent moisture and oxygen barrier properties. Blow moldable biopolymers like PHA along with polylactic acid (PLA) synthesized chemically in vitro using lactic acid (LA), which is produced by LA bacteria through fermentation, are projected as biodegradable polymers of the future for packaging applications. Designing and creating of new property based on requirements through controlled synthesis can lead to improvement in properties of existing polysaccharides and create novel biopolymers of great commercial interest and value for wider applications. Incorporation of antimicrobials such as bacteriocins or silver and copper nanoparticles can enhance the functionality of polymer films especially in food packaging

Microbial ecology and starter culture technology in coffee processing.

PubMed

Vinícius de Melo Pereira, Gilberto; Soccol, Vanete Thomaz; Brar, Satinder Kaur; Neto, Ensei; Soccol, Carlos Ricardo

2017-09-02

Coffee has been for decades the most commercialized food product and most widely consumed beverage in the world, with over 600 billion cups served per year. Before coffee cherries can be traded and processed into a final industrial product, they have to undergo postharvest processing on farms, which have a direct impact on the cost and quality of a coffee. Three different methods can be used for transforming the coffee cherries into beans, known as wet, dry, and semi-dry methods. In all these processing methods, a spontaneous fermentation is carried out in order to eliminate any mucilage still stuck to the beans and helps improve beverage flavor by microbial metabolites. The microorganisms responsible for the fermentation (e.g., yeasts and lactic acid bacteria) can play a number of roles, such as degradation of mucilage (pectinolytic activity), inhibition of mycotoxin-producing fungi growth, and production of flavor-active components. The use of starter cultures (mainly yeast strains) has emerged in recent years as a promising alternative to control the fermentation process and to promote quality development of coffee product. However, scarce information is still available about the effects of controlled starter cultures in coffee fermentation performance and bean quality, making it impossible to use this technology in actual field conditions. A broader knowledge about the ecology, biochemistry, and molecular biology could facilitate the understanding and application of starter cultures for coffee fermentation process. This review provides a comprehensive coverage of these issues, while pointing out new directions for exploiting starter cultures in coffee processing.

Microbial co-culturing systems: butanol production from organic wastes through consolidated bioprocessing.

PubMed

Jiang, Yujia; Zhang, Ting; Lu, Jiasheng; Dürre, Peter; Zhang, Wenming; Dong, Weiliang; Zhou, Jie; Jiang, Min; Xin, Fengxue

2018-05-07

Biobutanol can be indigenously synthesized by solventogenic Clostridium species; however, these microorganisms possess inferior capability of utilizing abundant and renewable organic wastes, such as starch, lignocellulose, and even syngas. The common strategy to achieve direct butanol production from these organic wastes is through genetic modification of wild-type strains. However, due to the complex of butanol synthetic and hydrolytic enzymes expression systems, the recombinants show unsatisfactory results. Recently, setting up microbial co-culturing systems became more attractive, as they could not only perform more complicated tasks, but also endure changeable environments. Hence, this mini-review comprehensively summarized the state-of-the-art biobutanol production from different substrates by using microbial co-culturing systems. Furthermore, strategies regarding establishment principles of microbial co-culturing systems were also analyzed and compared.

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

PubMed

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

2017-07-01

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

Microbial profiles of commercial, vacuum-packaged, fresh pork of normal or short storage life.

PubMed

Holley, Richard A; Peirson, Michael D; Lam, Jocelyn; Tan, Kit Bee

2004-12-01

The microbial ecology of fresh vacuum-packed pork cuts during storage at -1.5 degrees C for up to 45 days was examined to characterize rates of microbial growth and pH changes in commercially prepared products of normal storage quality. Pork loins in commercial distribution with odour defects were also studied to determine a possible cause of the defects and avoid future problems. In addition, microbial profiles of pork cuts from two plants were compared, after storage for 25 days at -1.5 degrees C, to identify possible reasons for differences in the storage life of product from the plants. The effects of a change in sanitation procedures on the microbial populations of products stored for 25 days were also studied. With normal product, microbial growth in different packages progressed at different rates, reflecting differences in initial levels of bacterial contamination. All samples in the study reached 8 weeks without apparent organoleptic change and samples carried 5.8+/-1.2 log bacteria cm(-2) (mean+/-S.D.). The flora of loins with the odour defect were predominately lactic acid bacteria (LAB) and carnobacteria, but they contained large fractions of Enterobacteriaceae <35 days after packaging. Aeromonas spp. and Shewanella spp. were likely responsible for the sulfide-putrid smell of these spoiled products, but species of Enterobacteriaceae and lactic acid bacteria could have contributed to spoilage. Comparison of microbial groups present in 16 other cuts, half from each of two commercial plants, which were stored for 25 days at -1.5 degrees C, showed that larger fractions of Enterobacteriaceae were present in samples from the plant having difficulty achieving the desired storage life. Additional bacterial samples from 12 cuts supplied by the latter plant obtained after adoption of an acid sanitizer step in the plant cleaning regimen, and also stored for 25 days at -1.5 degrees C, yielded few Enterobacteriaceae, Aeromonas or Shewanella. Use of an acid sanitizer

Linking microbial community structure and product spectrum of rice straw fermentation with undefined mixed culture

NASA Astrophysics Data System (ADS)

Ai, Binling; Chi, Xue; Meng, Jia; Sheng, Zhanwu; Zheng, Lili; Zheng, Xiaoyan; Li, Jianzheng

2017-12-01

Undefined mixed culture-based fermentation is an alternative strategy for biofuels and bioproducts production from lignocellulosic biomass without supplementary cellulolytic enzymes. Mixed culture produces mixed carboxylates. To estimate the relationship between microbial community structure and product spectrum, carboxylate production was initiated by mixed cultures with different microbial community structure. All the inoculum cultures were derived from the same enrichment culture from the combination of cattle manure, pig manure compost, corn field soil and rotten wood. Due to the differences in the preparation method and culture time, the inoculum cultures for batch fermentation had high similarity in microbial community structure, while the community structure of each inoculum culture for repeated batch fermentation differed from that of another. The inoculum cultures with similar community structure led to a similar product spectrum. In batch fermentation, the selectivity of main product butyric acid stabilized around 76%. The inoculum cultures with different community structures resulted in different product spectra. In repeated batch fermentation, the butyric acid content gradually decreased to 27%, and the by-product acetic acid content steadily increased to 56%. The other by-products including propionic, valeric and caproic acids were also increased. It is deduced that keeping the microbial community structure stable makes the basic and key precondition for steady production of specific carboxylic acid with undefined mixed culture.

Microbial composition during Chinese soy sauce koji-making based on culture dependent and independent methods.

PubMed

Yan, Yin-zhuo; Qian, Yu-lin; Ji, Feng-di; Chen, Jing-yu; Han, Bei-zhong

2013-05-01

Koji-making is a key process for production of high quality soy sauce. The microbial composition during koji-making was investigated by culture-dependent and culture-independent methods to determine predominant bacterial and fungal populations. The culture-dependent methods used were direct culture and colony morphology observation, and PCR amplification of 16S/26S rDNA fragments followed by sequencing analysis. The culture-independent method was based on the analysis of 16S/26S rDNA clone libraries. There were differences between the results obtained by different methods. However, sufficient overlap existed between the different methods to identify potentially significant microbial groups. 16 and 20 different bacterial species were identified using culture-dependent and culture-independent methods, respectively. 7 species could be identified by both methods. The most predominant bacterial genera were Weissella and Staphylococcus. Both 6 different fungal species were identified using culture-dependent and culture-independent methods, respectively. Only 3 species could be identified by both sets of methods. The most predominant fungi were Aspergillus and Candida species. This work illustrated the importance of a comprehensive polyphasic approach in the analysis of microbial composition during soy sauce koji-making, the knowledge of which will enable further optimization of microbial composition and quality control of koji to upgrade Chinese traditional soy sauce product. Copyright © 2013 Elsevier Ltd. All rights reserved.

Applications Research of Microbial Ecological Preparation in Sea Cucumber Culture

NASA Astrophysics Data System (ADS)

Jiang, Jiahui; Wang, Guangyu

2017-12-01

At present, micro ecological preparation is widely applied in aquaculture with good effect. The application of micro ecological preparation in sea cucumber culture can effectively improve the economic benefits. The micro ecological preparation can play the role of inhibiting harmful bacteria, purifying water quality and saving culture cost in the process of sea cucumber culture. We should select appropriate bacteria, guarantee stable environment and use with long-term in the applications of microbial ecological preparation in sea cucumber culture to obtain good effects.

TSCA Section 5(a)(3)(C) Determination for Microbial Commercial Activity Notice (MCAN) J-16-0036 -- 0041

EPA Pesticide Factsheets

This document describes EPA's Microbial Commercial Activity Notice (MCAN) review determination under amended TSCA for J-16-0036 -- J-16-0041, biofuel producing modified microorganisms, with chromosomally-borne modifications.

Culturability as an indicator of succession in microbial communities

NASA Technical Reports Server (NTRS)

Garland, J. L.; Cook, K. L.; Adams, J. L.; Kerkhof, L.

2001-01-01

Successional theory predicts that opportunistic species with high investment of energy in reproduction and wide niche width will be replaced by equilibrium species with relatively higher investment of energy in maintenance and narrower niche width as communities develop. Since the ability to rapidly grow into a detectable colony on nonselective agar medium could be considered as characteristic of opportunistic types of bacteria, the percentage of culturable cells may be an indicator of successional state in microbial communities. The ratios of culturable cells (colony forming units on R2A agar) to total cells (acridine orange direct microscopic counts) and culturable cells to active cells (reduction of 5-cyano-2,3-ditolyl tetrazolium chloride) were measured over time in two types of laboratory microcosms (the rhizosphere of hydroponically grown wheat and aerobic, continuously stirred tank reactors containing plant biomass) to determine the effectiveness of culturabilty as an index of successional state. The culturable cell:total cell ratio in the rhizosphere decreased from approximately 0.25 to less than 0.05 during the first 30-50 days of plant growth, and from 0.65 to 0.14 during the first 7 days of operation of the bioreactor. The culturable cell:active cell ratio followed similar trends, but the values were consistently greater than the culturable cell:total cell ratio, and even exceeded I in early samples. Follow-up studies used a cultivation-independent method, terminal restriction fragment length polymorphisms (TRFLP) from whole community DNA, to assess community structure. The number of TRFLP peaks increased with time, while the number of culturable types did not, indicating that the general decrease in culturability is associated with a shift in community structure. The ratio of respired to assimilated C-14-labeled amino acids increased with the age of rhizosphere communities, supporting the hypothesis that a shift in resource allocation from growth to

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.

[Correlation between microbial growth in conjunctival swabs of corneal donors and contamination of organ culture media].

PubMed

Li, S; Bischoff, M; Schirra, F; Langenbucher, A; Ong, M; Halfmann, A; Herrmann, M; Seitz, B

2014-06-01

The aim of the study was to determine the rate of contamination in conjunctival swabs from corneal donors by microbiological investigations and to correlate this with microbial contamination of the culture medium. Contamination of conjunctival swabs and culture media was analyzed retrospectively for the years 2009, 2010 and 2011 at the LIONS corneal bank of Saar-Lor-Lux Trier/Westpfalz at the Saarland University Medical Center. The total annual number of conjunctival swabs was 316 in 2009, 341 in 2010 and 381 in 2011. Conjunctival swabs were taken prior to 1.25% povidone-iodine application. After disinfection donor corneas were harvested by in situ corneoscleral disc excision in all cases. The correlation between positive conjunctival swabs and microbial contamination of the culture medium was analyzed. In every year examined the contamination rate of the culture medium was significantly higher in cases of contaminated conjunctival swabs (p < 0.05 in 2009, p < 0.001 in 2010 and p = 0.004 in 2011). Of the conjunctival swabs 38.3% (2009), 53.7% (2010) and 55.6% (2011), respectively exhibited microbial growth. The principal microorganisms detected in the conjunctival swabs were coagulase negative staphylococci, gram negative rods and Staphylococcus aureus. Extending the exposure time to povidone-iodine prior to removal of the corneoscleral disc from 3 min in the year 2009 to 5 min since the year 2010 resulted in a highly statistically significant (p < 0.001) reduction in contamination frequency of the medium from 10.8% (2009) to 7.0% (2010) and 4.5% (2011) was observed. In 2009, 2010 and 2011 the culture medium was contaminated in 16.5%, 11.5% and 7.6% of the donated corneas with positive conjunctival swabs and in 7.2%, 1.9% and 0.6% in donated corneas with negative conjunctival swabs, respectively. A positive correlation was found between contamination of the culture medium and microbial colonization of the conjunctival swabs, Nevertheless, microbial colonization of

Relative contributions of mercury bioavailability and microbial growth rate on net methylmercury production by anaerobic mixed cultures

DOE PAGES

Kucharzyk, Katarzyna H.; Deshusses, Marc A.; Porter, Kaitlyn A.; ...

2015-07-17

Monomethylmercury (MeHg) is produced in many aquatic environments by anaerobic microorganisms that take up and methylate inorganic forms of Hg(II). Net methylation of Hg(II) appears to be correlated with factors that affect the activity of the anaerobic microbial community and factors that increase the bioavailability of Hg(II) to these organisms. However, the relative importance of one versus the other is difficult to elucidate even though this information can greatly assist remediation efforts and risk assessments. Here in this study, we investigated the effects of Hg speciation (dissolved Hg and nanoparticulate HgS) and microbial activity on the net production of MeHgmore » using two mixed microbial cultures that were enriched from marine sediments under sulfate reducing conditions. The cultures were amended with dissolved Hg (added as a dissolved nitrate salt) and nanoparticulate HgS, and grown under different carbon substrate concentrations. The results indicated that net mercury methylation was the highest for cultures incubated in the greatest carbon substrate concentration (60 mM) compared to incubations with less carbon (0.6 and 6 mM), regardless of the form of mercury amended. Net MeHg production in cultures exposed to HgS nanoparticles was significantly slower than in cultures exposed to dissolved Hg; however, the difference diminished with slower growing cultures with low carbon addition (0.6 mM). The net Hg methylation rate was found to correlate with sulfate reduction rate in cultures exposed to dissolved Hg, while methylation rate was roughly constant for cultures exposed to nanoparticulate HgS. These results indicated a potential threshold of microbial productivity: below this point net MeHg production was limited by microbial activity, regardless of Hg bioavailability. Lastly, above this threshold of productivity, Hg speciation became a contributing factor towards net MeHg production.« less

Commercial materials as cathode for hydrogen production in microbial electrolysis cell.

PubMed

Farhangi, Sara; Ebrahimi, Sirous; Niasar, Mojtaba Shariati

2014-10-01

The use of commercial electrodes as cathodes in a single-chamber microbial electrolysis cell has been investigated. The cell was operated in sequencing batch mode and the performance of the electrodes was compared with carbon cloth containing 0.5 mg Pt cm(-2). Overall H2 recovery [Formula: see text] was 66.7 ± 1.4, 58.7 ± 1.1 and 55.5 ± 1.5 % for Pt/CC, Ni and Ti mesh electrodes, respectively. Columbic efficiencies of the three cathodes were in the same range (74.8 ± 1.5, 77.6 ± 1.7 and 75.7 ± 1.2 % for Pt/CC, Ni and Ti mesh electrodes, respectively). A similar performance for the three cathodes under near-neutral pH and ambient temperature was obtained. The commercial electrodes are much cheaper than carbon cloth containing Pt. Low cost and good performance of these electrodes suggest they are suitable cathode materials for large scale application.

Microbial lipid production by oleaginous Rhodococci cultured in lignocellulosic autohydrolysates

DOE PAGES

Wei, Zhen; Zeng, Guangming; Huang, Fang; ...

2015-07-04

Metabolic synthesis of single cell oils (SCOs) for biodiesel application by heterotrophic oleaginous microorganisms is being hampered by the high cost of culture media. This study investigated the possibility of using loblolly pine and sweetgum autohydrolysates as economic feedstocks for microbial lipid production by oleaginous Rhodococcus opacus ( R. opacus) PD630 and DSM 1069. Results revealed that when the substrates were detoxified by the removal of inhibitors (such as HMF—hydroxymethyl-furfural), the two strains exhibited viable growth patterns after a short adaptation/lag phase. R. opacus PD630 accumulated as much as 28.6 % of its cell dry weight (CDW) in lipids whilemore » growing on detoxified sweetgum autohydrolysate (DSAH) that translates to 0.25 g/l lipid yield. The accumulation of SCOs reached the level of oleagenicity in DSM 1069 cells (28.3 % of CDW) as well, while being cultured on detoxified pine autohydrolysate (DPAH), with the maximum lipid yield of 0.31 g/l. The composition of the obtained microbial oils varied depending on the substrates provided. These results indicate that lignocellulosic autohydrolysates can be used as low-cost fermentation substrates for microbial lipid production by wild-type R. opacus species. Furthermore, the variety of applications for aqueous liquors from lignocellulosic pretreatment has been expanded, allowing for the further optimization of the integrated biorefinery.« less

Application of polydimethylsiloxane-based optical system for measuring optical density of microbial culture.

PubMed

Takahashi, Yurika

2016-12-01

The performance of recently developed polydimethylsiloxane (PDMS)-based optical system was tested for measuring optical density of microbial culture. The data showed that PDMS-based spectrometer is superior to "one drop" spectrometers in the accuracy, and has an advantage over conventional spectrometers in measuring dense culture without dilution.

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.

Microbial Standards of Commercially Available Produce

NASA Technical Reports Server (NTRS)

Scotten, Jessica

2017-01-01

Limits and guidelines are set on microbial counts in produce to protect the consumer. Different agencies make specifications, which constitute when a product becomes unsafe for human consumption. Producers design their procedures to comply with the limits, but they are responsible creating their own internal standards. The limits and guidelines are summarized here to be applied to assess the microbial safety of the NASA Veggie Program.

Characterisation of culture-independent and -dependent microbial communities in a high-temperature offshore chalk petroleum reservoir.

PubMed

Kaster, Krista M; Bonaunet, Kristin; Berland, Harald; Kjeilen-Eilertsen, Grethe; Brakstad, Odd Gunnar

2009-11-01

Recent studies have indicated that oil reservoirs harbour diverse microbial communities. Culture-dependent and culture-independent methods were used to evaluate the microbial diversity in produced water samples of the Ekofisk oil field, a high temperature, and fractured chalk reservoir in the North Sea. DGGE analyses of 16S rRNA gene fragments were used to assess the microbial diversity of both archaeal and bacterial communities in produced water samples and enrichment cultures from 4 different wells (B-08, X-08, X-18 and X-25). Low diversity communities were found when 16S rDNA libraries of bacterial and archaeal assemblages were generated from total community DNA obtained from produced water samples and enrichment cultures. Sequence analysis of the clones indicated close matches to microbes associated with high-temperature oil reservoirs or other similar environments. Sequences were found to be similar to members of the genera Thermotoga, Caminicella, Thermoanaerobacter, Archaeoglobus, Thermococcus, and Methanobulbus. Enrichment cultures obtained from the produced water samples were dominated by sheathed rods. Sequence analyses of the cultures indicated predominance of the genera Petrotoga, Arcobacter, Archaeoglobus and Thermococcus. The communities of both produced water and enrichment cultures appeared to be dominated by thermophilic fermenters capable of reducing sulphur compounds. These results suggest that the biochemical processes in the Ekofisk chalk reservoir are similar to those observed in high-temperature sandstone reservoirs.

Rapid culture-independent microbial analysis aboard the international space station (ISS) stage two: quantifying three microbial biomarkers.

PubMed

Morris, Heather C; Damon, Michael; Maule, Jake; Monaco, Lisa A; Wainwright, Norm

2012-09-01

Abstract A portable, rapid, microbial detection unit, the Lab-On-a-Chip Application Development Portable Test System (LOCAD-PTS), was launched to the International Space Station (ISS) as a technology demonstration unit in December 2006. Results from the first series of experiments designed to detect Gram-negative bacteria on ISS surfaces by quantifying a single microbial biomarker lipopolysaccharide (LPS) were reported in a previous article. Herein, we report additional technology demonstration experiments expanding the on-orbit capabilities of the LOCAD-PTS to detecting three different microbial biomarkers on ISS surfaces. Six different astronauts on more than 20 occasions participated in these experiments, which were designed to test the new beta-glucan (fungal cell wall molecule) and lipoteichoic acid (LTA; Gram-positive bacterial cell wall component) cartridges individually and in tandem with the existing Limulus Amebocyte Lysate (LAL; Gram-negative bacterial LPS detection) cartridges. Additionally, we conducted the sampling side by side with the standard culture-based detection method currently used on the ISS. Therefore, we present data on the distribution of three microbial biomarkers collected from various surfaces in every module present on the ISS at the time of sampling. In accordance with our previous experiments, we determined that spacecraft surfaces known to be frequently in contact with crew members demonstrated higher values of all three microbial molecules. Key Words: Planetary protection-Spaceflight-Microbiology-Biosensor. Astrobiology 12, 830-840.

Metagenomics analysis of microbial communities associated with a traditional rice wine starter culture (Xaj-pitha) of Assam, India.

PubMed

Bora, Sudipta Sankar; Keot, Jyotshna; Das, Saurav; Sarma, Kishore; Barooah, Madhumita

2016-12-01

This is the first report on the microbial diversity of xaj-pitha, a rice wine fermentation starter culture through a metagenomics approach involving Illumine-based whole genome shotgun (WGS) sequencing method. Metagenomic DNA was extracted from rice wine starter culture concocted by Ahom community of Assam and analyzed using a MiSeq ® System. A total of 2,78,231 contigs, with an average read length of 640.13 bp, were obtained. Data obtained from the use of several taxonomic profiling tools were compared with previously reported microbial diversity studies through the culture-dependent and culture-independent method. The microbial community revealed the existence of amylase producers, such as Rhizopus delemar, Mucor circinelloides, and Aspergillus sp. Ethanol producers viz., Meyerozyma guilliermondii, Wickerhamomyces ciferrii, Saccharomyces cerevisiae, Candida glabrata, Debaryomyces hansenii, Ogataea parapolymorpha, and Dekkera bruxellensis, were found associated with the starter culture along with a diverse range of opportunistic contaminants. The bacterial microflora was dominated by lactic acid bacteria (LAB). The most frequent occurring LAB was Lactobacillus plantarum, Lactobacillus brevis, Leuconostoc lactis, Weissella cibaria, Lactococcus lactis, Weissella para mesenteroides, Leuconostoc pseudomesenteroides, etc. Our study provided a comprehensive picture of microbial diversity associated with rice wine fermentation starter and indicated the superiority of metagenomic sequencing over previously used techniques.

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.

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

NASA Astrophysics Data System (ADS)

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

2016-11-01

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

Biodeterioration of epoxy resin: a microbial survey through culture-independent and culture-dependent approaches.

PubMed

Pangallo, Domenico; Bučková, Maria; Kraková, Lucia; Puškárová, Andrea; Šaková, Nikoleta; Grivalský, Tomaš; Chovanová, Katarina; Zemánková, Milina

2015-02-01

During the 20th century, synthetic polymers were greatly used in the field of art. In particular, the epoxy resins were used for both conservation and for creating sculptures. The biodeterioration of these polymers has not been adequately studied. The aim of this investigation was to examine the microflora responsible for the deterioration of an epoxy statue exposed to outdoor conditions. Fungal and bacterial microflora were isolated from the art object, clustered by fluorescence-ITS (internal transcribed spacer), identified by ITS and 16S rRNA sequencing and tested for their lipolytic abilities by three agar assays. Different algal, bacterial, cyanobacterial and fungal clone libraries were constructed. The surrounding airborne microflora was analyzed using culture-dependent and culture-independent approaches. The results indicated the presence, on the statue surface, of an interesting and differentiate microbial community composed of rock-inhabiting members, algal photobionts (Trebouxia spp., Chloroidium ellipsoideum and Chlorella angustoellipsoidea), Cyanobacteria (Leptolyngbya sp., Phormidium sp., Cylindrospermum stagnale, Hassallia byssoidea and Geitlerinema sp.), black yeasts related to the species Friedmanniomyces endolithicus, Pseudotaeniolina globosa, Phaeococcomyces catenatus and Catenulostroma germanicum and several plant-associated fungi. This investigation provides new information on the potential microfloral inhabitants of epoxy resin discovering a new ecological niche, occupied mainly by several members of rock-colonizing microbial species. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

TSCA Section 5(a)(3)(C) Determination for Microbial Commercial Activity Notice (MCAN) J-17-0001, 0002, 0003, 0004, and 0005

EPA Pesticide Factsheets

This document describes EPA's Microbial Commercial Activity Notice (MCAN) review determination under amended TSCA for J-17-0001, 0002, 0003, 0004, and 0005, modified versions of saccharomyches cerevisiae.

Studying Microbial Mat Functioning Amidst "Unexpected Diversity": Methodological Approaches and Initial Results from Metatranscriptomes of Mats Over Diel cycles, iTags from Long Term Manipulations, and Biogeochemical Cycling in Simplified Microbial Mats Constructed from Cultures

NASA Astrophysics Data System (ADS)

Bebout, B.; Bebout, L. E.; Detweiler, A. M.; Everroad, R. C.; Lee, J.; Pett-Ridge, J.; Weber, P. K.

2014-12-01

Microbial mats are famously amongst the most diverse microbial ecosystems on Earth, inhabiting some of the most inclement environments known, including hypersaline, dry, hot, cold, nutrient poor, and high UV environments. The high microbial diversity of microbial mats makes studies of microbial ecology notably difficult. To address this challenge, we have been using a combination of metagenomics, metatranscriptomics, iTags and culture-based simplified microbial mats to study biogeochemical cycling (H2 production, N2 fixation, and fermentation) in microbial mats collected from Elkhorn Slough, Monterey Bay, California. Metatranscriptomes of microbial mats incubated over a diel cycle have revealed that a number of gene systems activate only during the day in Cyanobacteria, while the remaining appear to be constitutive. The dominant cyanobacterium in the mat (Microcoleus chthonoplastes) expresses several pathways for nitrogen scavenging undocumented in cultured strains, as well as the expression of two starch storage and utilization cycles. Community composition shifts in response to long term manipulations of mats were assessed using iTags. Changes in community diversity were observed as hydrogen fluxes increased in response to a lowering of sulfate concentrations. To produce simplified microbial mats, we have isolated members of 13 of the 15 top taxa from our iTag libraries into culture. Simplified microbial mats and simple co-cultures and consortia constructed from these isolates reproduce many of the natural patterns of biogeochemical cycling in the parent natural microbial mats, but against a background of far lower overall diversity, simplifying studies of changes in gene expression (over the short term), interactions between community members, and community composition changes (over the longer term), in response to environmental forcing.

Commercial production of microbials by Reuter Laboratories, inc., for control of the gypsy moth and the spruce budworm

Treesearch

F. D. Obenchain

1985-01-01

Reuter Laboratories announces additions to its line of microbial insecticides with the 1984-85 introduction of a Bacillus thuringiensis, Berliner, variety Kurstaki (HD-1, H-3A3B) wettable powder formulation. Gypsy moth nucleopolyhedrosis virus, in experimental production since 1982, is scheduled for commercial introduction as a...

Characterization of microbial compositions in a thermophilic chemostat of mixed culture fermentation.

PubMed

Zhang, Fang; Yang, Jing-Hua; Dai, Kun; Chen, Yun; Li, Qiu-Rong; Gao, Fa-Ming; Zeng, Raymond J

2016-02-01

The microbial community compositions of a chemostat enriched in a thermophilic (55 °C) mixed culture fermentation (MCF) for hydrogen production under different operational conditions were revealed in this work by integrating denaturing gradient gel electrophoresis (DGGE), Illumina Miseq high-throughput sequencing, and 16S rRNA clone library sequencing. The results showed that the community structure of the enriched cultures was relatively simple. Clones close to the genera of Thermoanaerobacter and/or Bacillus mainly dominated the bacteria. And homoacetogens and archaea were washed out and not detected even by Illumina Miseq high-throughput sequencing which supported the benefit for hydrogen production. On the other hand, the results revealed that the metabolic shift was clearly associated with the change of dominated bacterial groups. The effects of hydrogen partial pressure (PH2) and pH from 4.0 to 5.5 on the microbial compositions were not notable and Thermoanaerobacter was dominant, thus, the metabolites were also not changed. While Bacillus, Thermoanaerobacter and Propionispora hippei dominated the bacteria communities at neutral pH, or Bacillus and Thermoanaerobacter dominated at high influent glucose concentrations, consequently the main metabolites shifted to acetate, ethanol, propionate, or lactate. Thereby, the effect of microbial composition on the metabolite distribution and shift shall be considered when modeling thermophilic MCF in the future.

In vitro inhibition of commercial douche products against vaginal microflora.

PubMed Central

Pavlova, S I; Tao, L

2000-01-01

Recently, vaginal douching has been associated with many health risks in women. The aim of this study was to analyze the effect of commercial douche products against various vaginal microorganisms, including lactobacilli. Seven commercial douches were tested against eight Lactobacillus clinical isolates and three type strains from the American Type Culture Collection. BV-associated bacteria included six strains of five genera: Gardnerella, Mobiluncus, Mycoplasma, Peptostreptococcus, and Ureaplasma. Two isolates of group B Streptococcus, and three species of Candida were also tested. The minimal inhibition concentrations and minimal contact times for these products against vaginal microorganisms were determined in broth cultures. Four antiseptic-containing douche products showed a strong inhibitory effect against all vaginal microorganisms tested with a short contact time (less than 1 min). Three vinegar-containing douche products selectively inhibited vaginal pathogens associated with bacterial vaginosis, group B streptococcal vaginitis, and candidiasis, but not lactobacilli. The antimicrobial effects of the commercial douche products varied among different brands and microbial species tested. PMID:10805365

On the way to commercializing plant cell culture platform for biopharmaceuticals: present status and prospect.

PubMed

Xu, Jianfeng; Zhang, Ningning

2014-12-01

Plant cell culture is emerging as an alternative bioproduction system for recombinant pharmaceuticals. Growing plant cells in vitro under controlled environmental conditions allows for precise control over cell growth and protein production, batch-to-batch product consistency and a production process aligned with current good manufacturing practices. With the recent US FDA approval and commercialization of the world's first plant cell-based recombinant pharmaceutical for human use, β-glucocerebrosidase for treatment of Gaucher's disease, a new era has come in which plant cell culture shows high potential to displace some established platform technologies in niche markets. This review updates the progress in plant cell culture processing technology, highlights recent commercial successes and discusses the challenges that must be overcome to make this platform commercially viable.

Comparative analysis of microbial community of novel lactic acid fermentation inoculated with different undefined mixed cultures.

PubMed

Liang, Shaobo; Gliniewicz, Karol; Mendes-Soares, Helena; Settles, Matthew L; Forney, Larry J; Coats, Erik R; McDonald, Armando G

2015-03-01

Three undefined mixed cultures (activated sludge) from different municipal wastewater treatment plants were used as seeds in a novel lactic acid fermentation process fed with potato peel waste (PPW). Anaerobic sequencing batch fermenters were run under identical conditions to produce predominantly lactic acid. Illumina sequencing was used to examine the 16S rRNA genes of bacteria in the three seeds and fermenters. Results showed that the structure of microbial communities of three seeds were different. All three fermentation products had unique community structures that were dominated (>96%) by species of the genus Lactobacillus, while members of this genus constituted <0.1% in seeds. The species of Lactobacillus sp. differed among the three fermentations. Results of this study suggest the structure of microbial communities in lactic acid fermentation of PPW with undefined mixed cultures were robust and resilient, which provided engineering prospects for the microbial utilization of carbohydrate wastes to produce lactic acid. Copyright © 2014 Elsevier Ltd. All rights reserved.

The maturing of microbial ecology.

PubMed

Schmidt, Thomas M

2006-09-01

A.J. Kluyver and C.B. van Niel introduced many scientists to the exceptional metabolic capacity of microbes and their remarkable ability to adapt to changing environments in The Microbe's Contribution to Biology. Beyond providing an overview of the physiology and adaptability of microbes, the book outlined many of the basic principles for the emerging discipline of microbial ecology. While the study of pure cultures was highlighted, provided a unifying framework for understanding the vast metabolic potential of microbes and their roles in the global cycling of elements, extrapolation from pure cultures to natural environments has often been overshadowed by microbiologists inability to culture many of the microbes seen in natural environments. A combination of genomic approaches is now providing a culture-independent view of the microbial world, revealing a more diverse and dynamic community of microbes than originally anticipated. As methods for determining the diversity of microbial communities become increasingly accessible, a major challenge to microbial ecologists is to link the structure of natural microbial communities with their functions. This article presents several examples from studies of aquatic and terrestrial microbial communities in which culture and culture-independent methods are providing an enhanced appreciation for the microbe's contribution to the evolution and maintenance of life on Earth, and offers some thoughts about the graduate-level educational programs needed to enhance the maturing field of microbial ecology.

On the way to commercializing plant cell culture platform for biopharmaceuticals: present status and prospect

PubMed Central

Xu, Jianfeng; Zhang, Ningning

2014-01-01

Plant cell culture is emerging as an alternative bioproduction system for recombinant pharmaceuticals. Growing plant cells in vitro under controlled environmental conditions allows for precise control over cell growth and protein production, batch-to-batch product consistency and a production process aligned with current good manufacturing practices. With the recent US FDA approval and commercialization of the world’s first plant cell-based recombinant pharmaceutical for human use, β-glucocerebrosidase for treatment of Gaucher’s disease, a new era has come in which plant cell culture shows high potential to displace some established platform technologies in niche markets. This review updates the progress in plant cell culture processing technology, highlights recent commercial successes and discusses the challenges that must be overcome to make this platform commercially viable. PMID:25621170

Microbial consortia: a critical look at microalgae co-cultures for enhanced biomanufacturing.

PubMed

Padmaperuma, Gloria; Kapoore, Rahul Vijay; Gilmour, Daniel James; Vaidyanathan, Seetharaman

2018-08-01

Monocultures have been the preferred production route in the bio-industry, where contamination has been a major bottleneck. In nature, microorganisms usually exist as part of organized communities and consortia, gaining benefits from co-habitation, keeping invaders at bay. There is increasing interest in the use of co-cultures to tackle contamination issues, and simultaneously increase productivity and product diversity. The feasibility of extending the natural phenomenon of co-habitation to the biomanufacturing industry in the form of co-cultures requires careful and systematic consideration of several aspects. This article will critically examine and review current work on microbial co-cultures, with the intent of examining the concept and proposing a design pipeline that can be developed in a biomanufacturing context.

Electrochemically Driven Fermentation of Organic Substrates with Undefined Mixed Microbial Cultures.

PubMed

Villano, Marianna; Paiano, Paola; Palma, Enza; Miccheli, Alfredo; Majone, Mauro

2017-08-10

Growing scientific interest in mixed microbial culture-based anaerobic biotechnologies for the production of value-added chemicals and fuels from organic waste residues requires a parallel focus on the development and implementation of strategies to control the distribution of products. This study examined the feasibility of an electrofermentation approach, based on the introduction of a polarized (-700 mV vs. the standard hydrogen electrode) graphite electrode in the fermentation medium, to steer the product distribution during the conversion of organic substrates (glucose, ethanol, and acetate supplied as single compounds or in mixtures) by undefined mixed microbial cultures. In batch experiments, the polarized electrode triggered a nearly 20-fold increase (relative to open circuit controls) in the yield of isobutyrate production (0.43±0.01 vs. 0.02±0.02 mol mol -1 glucose) during the anaerobic fermentation of the ternary mixture of substrates, without adversely affecting the rate of substrate bioconversion. The observed change in the fermentative metabolism was most likely triggered by the (potentiostatic) regulation of the oxidation-reduction potential of the reaction medium rather than by the electrode serving as an electron donor. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Evaluation of microbial diversity in the pilot-scale beer brewing process by culture-dependent and culture-independent method.

PubMed

Takahashi, M; Kita, Y; Kusaka, K; Mizuno, A; Goto-Yamamoto, N

2015-02-01

In the brewing industry, microbial management is very important for stabilizing the quality of the product. We investigated the detailed microbial community of beer during fermentation and maturation, to manage beer microbiology in more detail. We brewed a beer (all-malt) and two beerlike beverages (half- and low-malt) in pilot-scale fermentation and investigated the microbial community of them using a next-generation sequencer (454 GS FLX titanium), quantitative PCR, flow cytometry and a culture-dependent method. From 28 to 88 genera of bacteria and from 9 to 38 genera of eukaryotic micro-organisms were detected in each sample. Almost all micro-organisms died out during the boiling process. However, bacteria belonging to the genera Acidovorax, Bacillus, Brevundimonas, Caulobacter, Chryseobacterium, Methylobacterium, Paenibacillus, Polaromonas, Pseudomonas, Ralstonia, Sphingomonas, Stenotrophomonas, Tepidimonas and Tissierella were detected at the early and middle stage of fermentation, even though their cell densities were low (below approx. 10(3) cells ml(-1) ) and they were not almost detected at the end of fermentation. We revealed that the microbial community of beer during fermentation and maturation is very diverse and several bacteria possibly survive during fermentation. In this study, we revealed the detailed microbial communities of beer using next-generation sequencing. Some of the micro-organisms detected in this study were found in beer brewing process for the first time. Additionally, the possibility of growth of several bacteria at the early and middle stage of fermentation was suggested. © 2014 The Society for Applied Microbiology.

A defined co-culture of Geobacter sulfurreducens and Escherichia coli in a membrane-less microbial fuel cell.

PubMed

Bourdakos, Nicholas; Marsili, Enrico; Mahadevan, Radhakrishnan

2014-04-01

Wastewater-fed microbial fuel cells (MFCs) are a promising technology to treat low-organic carbon wastewater and recover part of the chemical energy in wastewater as electrical power. However, the interactions between electrochemically active and fermentative microorganisms cannot be easily studied in wastewater-fed MFCs because of their complex microbial communities. Defined co-culture MFCs provide a detailed understanding of such interactions. In this study, we characterize the extracellular metabolites in laboratory-scale membrane-less MFCs inoculated with Geobacter sulfurreducens and Escherichia coli co-culture and compare them with pure culture MFCs. G. sulfurreducens MFCs are sparged to maintain anaerobic conditions, while co-culture MFCs rely on E. coli for oxygen removal. G. sulfurreducens MFCs have a power output of 128 mW m(-2) , compared to 63 mW m(-2) from the co-culture MFCs. Analysis of metabolites shows that succinate production in co-culture MFCs decreases current production by G. sulfurreducens and that the removal of succinate is responsible for the increased current density in the late co-culture MFCs. Interestingly, pH adjustment is not required for co-culture MFCs but a base addition is necessary for E. coli MFCs and cultures in vials. Our results show that defined co-culture MFCs provide clear insights into metabolic interactions among bacteria while maintaining a low operational complexity. © 2013 Wiley Periodicals, Inc.

Diabetic glucose meter for the determination of glucose in microbial cultures.

PubMed

Flavigny, Raphael

2014-05-01

In wastewater, biological phosphate removal can fail because of the presence of glycogen accumulating organism (GAO), therefore measuring glycogen stored in microbial cultures provides information on the bacterial population type. Once glycogen is hydrolysed to glucose it was accurately measured using a human glucose meter. The standard curves demonstrate linearity regardless of the pre-treatment of the glucose solution at neutral pH. Copyright © 2014 Elsevier B.V. All rights reserved.

Microbial pollution indicators and culturable heterotrophic bacteria in a Mediterranean area (Southern Adriatic Sea Italian coasts)

NASA Astrophysics Data System (ADS)

Stabili, L.; Cavallo, R. A.

2011-05-01

In the present study we evaluated the degree of microbial water pollution along the coast line between Brindisi and Santa Maria di Leuca (Southern Adriatic Sea) as well as the culturable heterotrophic bacteria abundances and biodiversity in relation to the microbiological quality of the water. A total of 3773 colonies were isolated, subcultured and identified by several morphological, cultural and biochemical methods including the standardized API 20 E and API 20 NE tests. Along the examined coastal tract the microbial pollution indicators were always below the tolerance limits for bathing waters defined by the CEE directive, suggesting a good sanitary quality. Concerning culturable heterotrophic bacteria, different temporal density trends were observed in the four sites in relation to their geographical position. A positive relationship between the bacterial abundances and the temperature was observed in S. Cataldo and Otranto. The culturable bacterial community was mainly composed of the genera Aeromonas, Pseudomonas, Photobacterium and Flavobacterium. The Enterobacteriaceae family represented a conspicuous component of the bacterial community too. Bacilli were predominant among the Gram-positive bacteria. Of interest is the isolation of yeasts (2% at the surface and 1% at the bottom) taking into account their capability of biodegradation of various materials. Because of the low level of microbial pollution recorded, our results are indicative of the natural variation and diversity of the culturable bacterial community in such an oligotrophic ecosystem and could represent a good point of comparison with other ecosystems as well as a baseline for long term studies aimed to evaluate the effects of environmental fluctuations and human impacts on this aspect of biodiversity in coastal areas.

From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems.

PubMed

Garza, Daniel R; Dutilh, Bas E

2015-11-01

Microorganisms and the viruses that infect them are the most numerous biological entities on Earth and enclose its greatest biodiversity and genetic reservoir. With strength in their numbers, these microscopic organisms are major players in the cycles of energy and matter that sustain all life. Scientists have only scratched the surface of this vast microbial world through culture-dependent methods. Recent developments in generating metagenomes, large random samples of nucleic acid sequences isolated directly from the environment, are providing comprehensive portraits of the composition, structure, and functioning of microbial communities. Moreover, advances in metagenomic analysis have created the possibility of obtaining complete or nearly complete genome sequences from uncultured microorganisms, providing important means to study their biology, ecology, and evolution. Here we review some of the recent developments in the field of metagenomics, focusing on the discovery of genetic novelty and on methods for obtaining uncultured genome sequences, including through the recycling of previously published datasets. Moreover we discuss how metagenomics has become a core scientific tool to characterize eco-evolutionary patterns of microbial ecosystems, thus allowing us to simultaneously discover new microbes and study their natural communities. We conclude by discussing general guidelines and challenges for modeling the interactions between uncultured microorganisms and viruses based on the information contained in their genome sequences. These models will significantly advance our understanding of the functioning of microbial ecosystems and the roles of microbes in the environment.

Microbial oxidation of elemental selenium in soil slurries and bacterial cultures

USGS Publications Warehouse

Dowdle, P.R.; Oremland, R.S.

1998-01-01

The microbial oxidation of elemental selenium [Se(O)] was studied by employing 75Se(O) as a tracer. Live, oxic soil slurries demonstrated a linear production of mostly Se(IV), with the formation of smaller quantities of Se(VI). Production of both Se(IV) and Se(VI) was inhibited by autoclaving, formalin, antibiotics, azide, and 2,4-dinitrophenol, thereby indicating the involvement of microbes. Oxidation of Se(O) in slurries was enhanced by addition of acetate, glucose, or sulfide, which implied involvement of chemoheterotrophs as well as chemoautotrophic thiobacilli. Cultures of Thiobacillus ASN-1, Leptothrix MnB1, and a heterotrophic soil enrichment all oxidized Se(O) with Se(VI) observed as the major product rather than Se(IV). This indicated that microbial oxidation in soils is partly constrained by the adsorption of Se(IV) onto soil surfaces. Rate constants for unamended soil slurry Se(O) oxidation ranged from 0.0009 to 0.0117 day-1 which were 3-4 orders of magnitude lower than those reported for dissimilatory Se(VI) reduction in organic-rich, anoxic sediments.The microbial oxidation of elemental selenium [Se(0)] was studied by employing 75Se(0) as a tracer. Live, oxic soil slurries demonstrated a linear production of mostly Se(IV), with the formation of smaller quantities of Se(VI). Production of both Se(IV) and Se(VI) was inhibited by autoclaving, formalin, antibiotics, azide, and 2,4-dinitrophenol, thereby indicating the involvement of microbes. Oxidation of Se(O) in slurries was enhanced by addition of acetate, glucose, or sulfide, which implied involvement of chemoheterotrophs as well as chemoautotrophic thiobacilli. Cultures of Thiobacillus ASN-1, Leptothrix MnB1, and a heterotrophic soil enrichment all oxidized Se(O) with Se(VI) observed as the major product rather than Se(IV). This indicated that microbial oxidation in soils is partly constrained by the adsorption of Se(IV) onto soil surfaces. Rate constants for unamended soil slurry Se(O) oxidation

Commercially Available Gas-Permeable Cell Culture Bags May Not Prevent Anoxia in Cultured or Shipped Islets

PubMed Central

Avgoustiniatos, E.S.; Hering, B.J.; Rozak, P.R.; Wilson, J.R.; Tempelman, L.A.; Balamurugan, A.N.; Welch, D.P.; Weegman, B.P.; Suszynski, T.M.; Papas, K.K.

2009-01-01

Prolonged anoxia has deleterious effects on islets. Gas-permeable cell culture devices can be used to minimize anoxia during islet culture and especially during shipment when elimination of gas-liquid interfaces is required to prevent the formation of damaging gas bubbles. Gas-permeable bags may have several drawbacks, such as propensity for puncture and contamination, difficult islet retrieval, and significantly lower oxygen permeability than silicone rubber membranes (SRM). We hypothesized that oxygen permeability of bags may be insufficient for islet oxygenation. We measured oxygen transmission rates through the membrane walls of three different types of commercially available bags and through SRM currently used for islet shipment. We found that the bag membranes have oxygen transmission rates per unit area about 100-fold lower than SRM. We solved the oxygen diffusion-reaction equation for 150-μm diameter islets seeded at 3000 islet equivalents per cm2, a density adequate to culture and ship an entire human or porcine islet preparation in a single gas-permeable device, predicting that about 40% of the islet volume would be anoxic at 22°C and about 70% would be anoxic at 37°C. Islets of larger size or islets accumulated during shipment would be even more anoxic. The model predicted no anoxia in islets similarly seeded in devices with SRM bottoms. We concluded that commercially available bags may not prevent anoxia during islet culture or shipment; devices with SRM bottoms are more suitable alternatives. PMID:18374080

Effect of temperature on microbial composition of starter culture for Chinese light aroma style liquor fermentation.

PubMed

Wang, H Y; Xu, Y

2015-01-01

Light aroma style liquor is one of the basic types of Chinese liquor and is produced with a special technique of using a combination of three types of Daqu as starter culture. The succession of incubation temperature, a main operating parameter, and microbial composition in Daqu were investigated during the manufacturing process. The most significant difference in temperature occurred during the middle stage at which the highest and the lowest temperatures were detected in Houhuo (HH) and Qingcha (QC), respectively. It was shown that for the counting data, the population of fungi was identical and that of bacteria was different between three types of Daqu. According to analysis results of microbial community structure using PCR-denaturing gradient gel electrophoresis (PCR-DGGE), lactic acid bacteria were one of the dominant bacterial groups in all of Daqu and fungal diversity in QC was higher than that in HH and Hongxin (HX). The difference in incubation temperature led to the accumulation of different heat-tolerant and heat-sensitive fungi in the completed Daqu. PCA of DGGE profiles revealed that microbial community structure was distinct between three types of Daqu. It was presumed that temperature might play a decisive role in the formation of micro-organism composition in starter cultures. The usage of a combination of three types of Daqu including Qingcha, Hongxin and Houhuo as starter culture is an important characteristic of production technology of Chinese light aroma style liquor. Micro-organisms from the environment naturally inoculated in Daqu are propagated to form the special microbial community under the control of several operating parameters, especially temperature, and finally play various roles in the fermentation process of liquor. An in-depth study of the relationship between incubation temperature and microbiota in Daqu during the manufacturing is fundamental to understand this complicated process and to prepare high-quality starter culture for

Microbial diversity associated with odor modification for production of fertilizers from chicken litter.

PubMed

Enticknap, Julie J; Nonogaki, Hirofumi; Place, Allen R; Hill, Russell T

2006-06-01

Litter from the chicken industry can present several environmental challenges, including offensive odors and runoff into waterways leading to eutrophication. An economically viable solution to the disposal of waste from chicken houses is treatment to produce a natural, granulated fertilizer that can be commercially marketed for garden and commercial use. Odor of the final product is important in consumer acceptance, and an earthy odor is desirable. By understanding and manipulating the microbial processes occurring during this process, it may be possible to modify the odors produced. Geosmin and related volatiles produced by soil actinomycetes are responsible for earthy odors, and actinomycetes are likely to be present in the composting manure. Bacterial communities at each stage of the process were analyzed by culturing studies and denaturing gradient gel electrophoresis (DGGE). The processing steps changed the culturable bacterial community, but the total community was shown by DGGE to be stable throughout the process. A local agricultural soil was analyzed in parallel as a potential source of geosmin-producing actinomycetes. This agricultural soil had higher microbial diversity than the compost at both the culturable and the molecular levels. Actinomycete bacteria were isolated and analyzed by AromaTrax, a gas chromatography-olfactometry system. This system enables the odor production of individual isolates to be monitored, allowing for rational selection of strains for augmentation experiments to improve the odor of the final fertilizer product.

Microbial Diversity Associated with Odor Modification for Production of Fertilizers from Chicken Litter†

PubMed Central

Enticknap, Julie J.; Nonogaki, Hirofumi; Place, Allen R.; Hill, Russell T.

2006-01-01

Litter from the chicken industry can present several environmental challenges, including offensive odors and runoff into waterways leading to eutrophication. An economically viable solution to the disposal of waste from chicken houses is treatment to produce a natural, granulated fertilizer that can be commercially marketed for garden and commercial use. Odor of the final product is important in consumer acceptance, and an earthy odor is desirable. By understanding and manipulating the microbial processes occurring during this process, it may be possible to modify the odors produced. Geosmin and related volatiles produced by soil actinomycetes are responsible for earthy odors, and actinomycetes are likely to be present in the composting manure. Bacterial communities at each stage of the process were analyzed by culturing studies and denaturing gradient gel electrophoresis (DGGE). The processing steps changed the culturable bacterial community, but the total community was shown by DGGE to be stable throughout the process. A local agricultural soil was analyzed in parallel as a potential source of geosmin-producing actinomycetes. This agricultural soil had higher microbial diversity than the compost at both the culturable and the molecular levels. Actinomycete bacteria were isolated and analyzed by AromaTrax, a gas chromatography-olfactometry system. This system enables the odor production of individual isolates to be monitored, allowing for rational selection of strains for augmentation experiments to improve the odor of the final fertilizer product. PMID:16751521

Composition of commercial media used for human embryo culture.

PubMed

Morbeck, Dean E; Krisher, Rebecca L; Herrick, Jason R; Baumann, Nikola A; Matern, Dietrich; Moyer, Thomas

2014-09-01

To determine the composition of commercially available culture media and test whether differences in composition are biologically relevant in a murine model. Experimental laboratory study. University-based laboratory. Cryopreserved hybrid mouse one-cell embryos were used in experiments. Amino acid, organic acid, ions, and metal content were determined for two different lots of media from Cook, In Vitro Care, Origio, Sage, Vitrolife, Irvine CSC, and Global. To determine whether differences in the composition of these media are biologically relevant, mouse one-cell embryos were thawed and cultured for 120 hours in each culture media at 5% and 20% oxygen in the presence or absence of protein in an EmbryoScope time-lapse incubator. The compositions of seven culture media were analyzed for concentrations of 39 individual amino acids, organic acids, ions, and elements. Blastocyst rates and cell cycle timings were calculated at 96 hours of culture, and the experiments were repeated in triplicate. Of the 39 analytes, concentrations of glucose, lactate, pyruvate, amino acids, phosphate, calcium, and magnesium were present in variable concentrations, likely reflecting differences in the interpretation of animal studies. Essential trace elements, such as copper and zinc, were not detected. Mouse embryos failed to develop in one culture medium and were differentially affected by oxygen in two other media. Culture media composition varies widely, with differences in pyruvate, lactate, and amino acids especially notable. Blastocyst development was culture media dependent and showed an interaction with oxygen concentration and presence of protein. Copyright © 2014 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

Difference of microbial community stressed in artificial pit muds for Luzhou-flavour liquor brewing revealed by multiphase culture-independent technology.

PubMed

Zhang, L; Zhou, R; Niu, M; Zheng, J; Wu, C

2015-11-01

Artificial pit muds (APMs) is produced by peats, aged pit muds, yellow and black clays etc. and is one of essential factors for Luzhou-flavour liquor production. The microbial community of APMs significantly influence the quality of Luzhou-flavour liquor. The aim of this study was to investigate the differences in bacterial, archaeal and fungal community of APMs, starters and materials. Multiphase culture-independent technology were employed in this study, including nested PCR-denaturing gradient gel electrophoresis (nested PCR-DGGE), phospholipid fatty acid (PLFA), phospholipid ether lipids (PLEL) and fluorescence in situ hybridization (FISH) analysis. Results suggested that the microbial diversity significantly changed under environmental stress and different culture patterns during APMs cultivation. The dominant bacteria in APMs mainly fell into Clostridiales, Lactobacillales, Bacteroidales and Rhizobiales, Archaea affiliated with Methanomicrobiales and Methanosarcinales, and fungi belonged to Saccharomycetales and Eurotiales. Furthermore, the microbial community structures of APMs cultured by ground pile pattern were more similar with that of aged pit muds, meanwhile, the relative bands intensities of microbes, which are the main contributors for liquor brewing, increased with the culture times. Not only the niche selection and biogeochemical properties of APMs, but also the mutual collaboration and constraint between different microbes may result in enriching different liquor-brewing microbes into APMs. APM cultivation technology was necessary to promote enriching functional liquor-brewing microbes into APMs. These results may facilitate understanding the microbial succession during APMs manufacture. © 2015 The Society for Applied Microbiology.

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.

Xanthan gum: an economical substitute for agar in plant tissue culture media.

PubMed

Jain, R; Babbar, S B

2006-03-01

Xanthan gum, a microbial desiccation-resistant polysaccharide prepared commercially by aerobic submerged fermentation from Xanthomonas campestris, has been successfully used as a solidifying agent for plant tissue culture media. Its suitability as a substitute to agar was demonstrated for in vitro seed germination, caulogenesis and rhizogenesis of Albizzia lebbeck, androgenesis in anther cultures of Datura innoxia, and somatic embryogenesis in callus cultures of Calliandra tweedii. Culture media used for eliciting these morphogenic responses were gelled with either 1% xanthan gum or 0.9% agar. Xanthan gum, like agar, supported all these responses.

Biodegradation Of Thiocyanate Using Microbial Consortia Cultured From Gold Mine Tailings

NASA Astrophysics Data System (ADS)

Moreau, J. W.; Watts, M. P.; Spurr, L. P.; Vu, H. P.

2015-12-01

Some bacteria possess the capability to degrade SCN-; therefore, harnessing this metabolic trait offers a biotechnological remediation strategy for SCN- produced in gold ore processing. A tailings storage facility (TSF) at a gold mine in Victoria, Australia holds large quantities of thiocyanate (SCN-) contaminated mine waste. The surface water in the TSF typically contains SCN- concentrations of >800 mg L-1, and seepage from the facility has contaminated the groundwater at the site. This study aimed to culture SCN-degrading microbes from the TSF, characterize the microbial consortia and test its operational parameters for use in a thiocyanate-degrading bioreactor. Surface samples were obtained from several locations around the TSF facility and used to inoculate medium reflective of the moderately saline and alkaline tailings water at the TSF, in the absence of organic carbon but subject to additions of phosphate and trace metals. Four microbial consortia capable of rapid SCN- degradation were successfully cultured. Sequencing of 16S rRNA genes found that the consortia were dominated by Thiobacillus species, a genus of known SCN- degraders. Lower abundances of other SCN- degraders; Sphingopyxis and Rhodobacter, were also identified. The impact of a number of geochemical conditions, including pH, temperature and SCN- concentration, upon the growth and SCN- degrading capacity of these consortia was determined. These results informed the optimization of a lab-scale thiocyanate degrading bioreactor. In summary, the cultured bacterial consortia proved effective towards SCN- degradation at the prevailing geochemical conditions of the TSF, requiring minimal nutrient additions. These consortia were dominated by genera of known autotrophic SCN- degraders. The comprehensive characterisation of these SCN- degrading consortia will provide the fundamental operational parameters required for deployment of this technique at the field scale.

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.

Unraveling microbial ecology of industrial-scale Kombucha fermentations by metabarcoding and culture-based methods.

PubMed

Coton, Monika; Pawtowski, Audrey; Taminiau, Bernard; Burgaud, Gaëtan; Deniel, Franck; Coulloumme-Labarthe, Laurent; Fall, Abdoulaye; Daube, Georges; Coton, Emmanuel

2017-05-01

Kombucha, historically an Asian tea-based fermented drink, has recently become trendy in Western countries. Producers claim it bears health-enhancing properties that may come from the tea or metabolites produced by its microbiome. Despite its long history of production, microbial richness and dynamics have not been fully unraveled, especially at an industrial scale. Moreover, the impact of tea type (green or black) on microbial ecology was not studied. Here, we compared microbial communities from industrial-scale black and green tea fermentations, still traditionally carried out by a microbial biofilm, using culture-dependent and metabarcoding approaches. Dominant bacterial species belonged to Acetobacteraceae and to a lesser extent Lactobacteriaceae, while the main identified yeasts corresponded to Dekkera, Hanseniaspora and Zygosaccharomyces during all fermentations. Species richness decreased over the 8-day fermentation. Among acetic acid bacteria, Gluconacetobacter europaeus, Gluconobacter oxydans, G. saccharivorans and Acetobacter peroxydans emerged as dominant species. The main lactic acid bacteria, Oenococcus oeni, was strongly associated with green tea fermentations. Tea type did not influence yeast community, with Dekkera bruxellensis, D. anomala, Zygosaccharomyces bailii and Hanseniaspora valbyensis as most dominant. This study unraveled a distinctive core microbial community which is essential for fermentation control and could lead to Kombucha quality standardization. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Microbial culture collections as pillars for promoting fungal diversity, conservation and exploitation.

PubMed

Sette, Lara Durães; Pagnocca, Fernando Carlos; Rodrigues, André

2013-11-01

Fungi are a diverse group of organisms with an overall global number of 1.5M up to 3.3M species on Earth. Besides their ecological roles as decomposers, fungi are important in several aspects of applied research. Here, we review how culture collections may promote the knowledge on diversity, conservation and biotechnological exploitation of fungi. The impact of fungi diversity on biotechnological studies is discussed. We point out the major roles of microbial repositories, including fungal preservation, prospecting, identification, authentication and supply. A survey on the World Data Center for Microorganisms (WDCM) powered by the World Federation for Culture Collections and on the Genetic Heritage Management Council (CGEN) database revealed that 46 Brazilian culture collections registered in these databases are dedicate to preserving fungi. Most of these culture collections are located in the Southeast of Brazil. This scenario also demonstrates that Brazil has many collections focused on fungal strains, but the lack of up-to-date information in WDCM as well as of a solid national platform for culture collections registration do not allow accurate assessment of fungal preservation. Copyright © 2013 Elsevier Inc. All rights reserved.

The role of lactic acid bacteria (Lactobacillus sp yel133) from beef in inhibiting of microbial contaminants on various fillers of starter culture

NASA Astrophysics Data System (ADS)

Yunilas; Mirwandhono, E.

2018-02-01

The role of Lactic Acid Bacteria (LAB) on the starter culture can be seen from the ability to grow and suppress the growth of microbial contaminants (fungi). The research aimed to investigate the role of LAB (Lactobacillus sp YEL133) in inhibiting microbial contaminants (fungi) on starter cultures of various fillers. The materials used in this research was Lactobacillus sp YEL133 from beef and various fillers (rice flour, corn starch and wheat flour). The research methods used completely randomized design (CRD) with 3 treatments and 4 replications. The treatments of this research was P1(rice flour), P2 (corn starch) and P3 (wheat flour) that inoculated with Lactobacillus sp YEL133. Parameters which is observed such as: growth of lactic acid bacteria, total microbes and total fungi as microbial contaminants. The results showed that the starter culture with a filler material of rice flour produce lactic acid bacteria and microbes were highly significant (P <0.01) for corn starch and wheat flour, as well as able to suppress the growth of microbial contaminants (fungi). The conclusion of the research is the use Lactobacillus sp YEL133 can suppress the growth of fungi on the starter culture using rice flour.

A Comprehensive Assessment of Biologicals Contained Within Commercial Airliner Cabin Air

NASA Technical Reports Server (NTRS)

LaDuc, Myron T.; Osman, Shariff; Dekas, Anne; Stuecker, Tara; Newcombe, Dave; Piceno, Yvette; Fuhrman, J.; Andersen, Gary; Venkateswaran, Kasthuri; Bearman, Greg

2006-01-01

Both culture-based and culture-independent, biomarker-targeted microbial enumeration and identification technologies were employed to estimate total microbial and viral burden and diversity within the cabin air of commercial airliners. Samples from each of twenty flights spanning three commercial carriers were collected via air-impingement. When the total viable microbial population was estimated by assaying relative concentrations of the universal energy carrier ATP, values ranged from below detection limits (BDL) to 4.1 x 106 cells/cubic m of air. The total viable microbial population was extremely low in both of Airline A (approximately 10% samples) and C (approximately 18% samples) compared to the samples collected aboard flights on Airline A and B (approximately 70% samples). When samples were collected as a function of time over the course of flights, a gradual accumulation of microbes was observed from the time of passenger boarding through mid-flight, followed by a sharp decline in microbial abundance and viability from the initiation of descent through landing. It is concluded in this study that only 10% of the viable microbes of the cabin air were cultivable and suggested a need to employ state-of-the art molecular assay that measures both cultivable and viable-but-non-cultivable microbes. Among the cultivable bacteria, colonies of Acinetobacter sp. were by far the most profuse in Phase I, and Gram-positive bacteria of the genera Staphylococcus and Bacillus were the most abundant during Phase II. The isolation of the human pathogens Acinetobacter johnsonii, A. calcoaceticus, Janibacter melonis, Microbacterium trichotecenolyticum, Massilia timonae, Staphylococcus saprophyticus, Corynebacterium lipophiloflavum is concerning, as these bacteria can cause meningitis, septicemia, and a handful of sometimes fatal diseases and infections. Molecular microbial community analyses exhibited presence of the alpha-, beta-, gamma-, and delta- proteobacteria, as well as

Application of multiple antimicrobial interventions for microbial decontamination of commercial beef trim.

PubMed

Kang, D H; Koohmaraie, M; Siragusa, G R

2001-02-01

Commercially produced, irregularly sized (range, 100 to 400 cm2), uninoculated beef trim was treated by a previously optimized multihurdle antimicrobial process under spray system or hot air gun with set-up speed (1 cm/s): W (water wash at 65 psi for five passes) + HW (82 degrees C water at 30 psi for three passes) + HA (510 degrees C air for five passes) + L (2% [vol/vol] room temperature lactic acid wash at 30 psi for three passes). After treatment, the trim was finely ground, vacuum packaged, and stored at 4 degrees C for up to 20 days. At regular intervals (0, 5, 10, 15, and 20 days of storage at 4 degrees C), the ground beef was analyzed to measure mesophilic aerobic bacteria (APC), coliforms, psychrotrophic bacteria (PCT), and presumptive lactic acid bacteria (PLAB) and compared with the untreated control. The numbers of APC, coliforms, PCT, and PLAB were reduced to nearly nondetectable levels immediately after treatment, with significant differences compared with the control (P < 0.05), then started to increase after 5 to 10 days of storage at 4 degrees C. After 20 days, microbial populations of treated ground beef were significantly lower than those of nontreated ground beef for the numbers of APC, coliforms, PCT, and PLAB (P < 0.05), with differences of 1.2, 2.4, 1.6, and 1.6 log CFU/g, respectively. Based on microbial reduction and quality aspects, the multihurdle antimicrobial process was identified as an effective intervention to reduce coliforms on beef trim.

Production of microbial medium from defatted brebra (Milletia ferruginea) seed flour to substitute commercial peptone agar

PubMed Central

Andualem, Berhanu; Gessesse, Amare

2013-01-01

Objective To investigate and optimize microbial media that substitute peptone agar using brebra seed defatted flour. Methods 'Defatted process, inoculums preparation, evaluation of bacterial growth, preparation of cooked and hydrolyzed media and growth turbidity of tested bacteria were determined. Results Two percent defatted flour was found to be suitable concentration for the growth of pathogenic bacteria: Escherichia coli (ATCC 25922) (E. coli), Pseudomonas aeruginosa (ATCC 27853), Salmonella (NCTC 8385) and Shigella flexneri (ATCC 12022) (S. flexneri), while 3% defatted flour was suitable for Staphylococcus aureus (ATCC 25923) (S. aureus). E. coli (93±1) and S. flexneri (524±1) colony count were significantly (P≤0.05) greater in defatted flour without supplement than in supplemented medium. E. coli [(3.72×109±2) CFU/mL], S. aureus [(7.4×109±2) CFU/mL], S. flexneri [(4.03×109±2) CFU/mL] and Salmonella [(2.37×109±1) CFU/mL] in non-hydrolyzed sample were statistically (P≤0.05) greater than hydrolyzed one and commercial peptone agar. Colony count of Salmonella [(4.55×109±3) CFU/mL], S. flexneri [(5.40×109±3) CFU/mL] and Lyesria moncytogenes (ATCC 19116) [(5.4×109±3) CFU/mL] on raw defatted flour agar was significantly (P≤0.05) greater than cooked defatted flour and commercial peptone agar. Biomass of E. coli, S. aureus, Salmonella and Enterococcus faecalis in non-hydrolyzed defatted flour is highly increased over hydrolyzed defatted flour and commercial peptone broth. Conclusions The defatted flour agar was found to be better microbial media or comparable with peptone agar. The substances in it can serve as sources of carbon, nitrogen, vitamins and minerals that are essential to support the growth of microorganisms without any supplements. Currently, all supplements of peptone agar are very expensive in the market. PMID:24075344

Production of microbial medium from defatted brebra (Milletia ferruginea) seed flour to substitute commercial peptone agar.

PubMed

Andualem, Berhanu; Gessesse, Amare

2013-10-01

To investigate and optimize microbial media that substitute peptone agar using brebra seed defatted flour. Defatted process, inoculums preparation, evaluation of bacterial growth, preparation of cooked and hydrolyzed media and growth turbidity of tested bacteria were determined. Two percent defatted flour was found to be suitable concentration for the growth of pathogenic bacteria: Escherichia coli (ATCC 25922) (E. coli), Pseudomonas aeruginosa (ATCC 27853), Salmonella (NCTC 8385) and Shigella flexneri (ATCC 12022) (S. flexneri), while 3% defatted flour was suitable for Staphylococcus aureus (ATCC 25923) (S. aureus). E. coli (93±1) and S. flexneri (524±1) colony count were significantly (P≤0.05) greater in defatted flour without supplement than in supplemented medium. E. coli [(3.72×10(9)±2) CFU/mL], S. aureus [(7.4×10(9)±2) CFU/mL], S. flexneri [(4.03×10(9)±2) CFU/mL] and Salmonella [(2.37×10(9)±1) CFU/mL] in non-hydrolyzed sample were statistically (P≤0.05) greater than hydrolyzed one and commercial peptone agar. Colony count of Salmonella [(4.55×10(9)±3) CFU/mL], S. flexneri [(5.40×10(9)±3) CFU/mL] and Lyesria moncytogenes (ATCC 19116) [(5.4×10(9)±3) CFU/mL] on raw defatted flour agar was significantly (P≤0.05) greater than cooked defatted flour and commercial peptone agar. Biomass of E. coli, S. aureus, Salmonella and Enterococcus faecalis in non-hydrolyzed defatted flour is highly increased over hydrolyzed defatted flour and commercial peptone broth. The defatted flour agar was found to be better microbial media or comparable with peptone agar. The substances in it can serve as sources of carbon, nitrogen, vitamins and minerals that are essential to support the growth of microorganisms without any supplements. Currently, all supplements of peptone agar are very expensive in the market. Copyright © 2013 Asian Pacific Tropical Biomedical Magazine. Published by Elsevier B.V. All rights reserved.

DIFFERENCES IN CULTURAL YIELD OF MYCOBACTERIUM TUBERCULOSIS ON MEDIA PREPARED USING COMMERCIAL AND HOUSEHOLD EGGS.

PubMed

Noori, Muhammad Yahya; AJi, Zaheer; Khan, Ghazala; Sharafat, Shaheen; Masroor, Muhammad

2015-01-01

Mycobacterial culture is considered as the gold standard for TB diagnosis. It is performed on egg-based media using commercially available eggs to grow Mycobacteria from clinical samples. These eggs are known to contain high concentration of antibiotics, including fluoroquinolones, given to chicken to prevent early mortality. This study was performed to compare Mycobacterial growth on media prepared from commercial and antibiotic free household eggs. Sputum samples from negative (No bacilli in 100 oil immersion field), scanty (1-9 AFB in 100 fields), 1+ (10-99 bacilli per field), 2+ (1-10 bacilli per field) and 3+ (>10 bacilli per field) were inoculated dually on Ogawa medium prepared from commercial and household eggs. Tubes were inspected every fourth day for the appearance of colonies till 60 days. Data tabulations and statistical analysis (F test for variation and unpaired Student's t test) were performed on Microsoft Excel. One microscopically negative sample showed growth on media prepared from household eggs, while all were negative on that prepared from commercial eggs. There were significant differences in time to culture positivity for samples graded 1+ (p = 0.02), 2+ (p = 0.002) and 3+ (p = 0.0003). Commercial eggs containing antibiotics can be a source of false negativity in cultures especially in microscopically negative samples. This can be of special concern in HIV patients who have high smear negativity. It is therefore important to either develop provision of antibiotic free eggs for media preparation or to develop and validate other laboratory investigations for smear negative TB patients.

A novel process-based model of microbial growth: self-inhibition in Saccharomyces cerevisiae aerobic fed-batch cultures.

PubMed

Mazzoleni, Stefano; Landi, Carmine; Cartenì, Fabrizio; de Alteriis, Elisabetta; Giannino, Francesco; Paciello, Lucia; Parascandola, Palma

2015-07-30

Microbial population dynamics in bioreactors depend on both nutrients availability and changes in the growth environment. Research is still ongoing on the optimization of bioreactor yields focusing on the increase of the maximum achievable cell density. A new process-based model is proposed to describe the aerobic growth of Saccharomyces cerevisiae cultured on glucose as carbon and energy source. The model considers the main metabolic routes of glucose assimilation (fermentation to ethanol and respiration) and the occurrence of inhibition due to the accumulation of both ethanol and other self-produced toxic compounds in the medium. Model simulations reproduced data from classic and new experiments of yeast growth in batch and fed-batch cultures. Model and experimental results showed that the growth decline observed in prolonged fed-batch cultures had to be ascribed to self-produced inhibitory compounds other than ethanol. The presented results clarify the dynamics of microbial growth under different feeding conditions and highlight the relevance of the negative feedback by self-produced inhibitory compounds on the maximum cell densities achieved in a bioreactor.

Microbial dynamics and biodiversity in table olive fermentation: culture-dependent and -independent approaches

PubMed Central

Botta, Cristian; Cocolin, Luca

2012-01-01

The microbial ecology of the table olive fermentation process is a complex set of dynamics in which the roles of the lactic acid bacteria (LAB) and yeast populations are closely related, and this synergism is of fundamental importance to obtain high quality products. Several studies on the ecology of table olives, both in spontaneous fermentations and in inoculated ones, have focused on the identification and characterization of yeasts, as they play a key role in the definition of the final organoleptic profiles through the production of volatile compounds. Moreover, these are able to promote the growth of LAB, which is responsible for the stabilization of the final product through the acidification activity and the inhibition of the growth of pathogenic bacteria. The current empirical production process of table olives could be improved through the development of mixed starter cultures. These can only be developed after a deep study of the population dynamics of yeasts and LAB by means of molecular methods. Until now, most studies have exploited culture-dependent approaches to define the natural microbiota of brine and olives. These approaches have identified two main species of LAB, namely Lactobacillus plantarum and L. pentosus, while, as far as yeasts are concerned, the most frequently isolated genera are Candida, Pichia, and Saccharomyces. However, there are a few studies in literature in which a culture-independent approach has been employed. This review summarizes the state of the art of the microbial ecology of table olive fermentations and it focuses on the different approaches and molecular methods that have been applied. PMID:22783248

Water velocity in commercial RAS culture tanks for Atlantic salmon smolt production

USDA-ARS?s Scientific Manuscript database

An optimal flow domain in culture tanks is vital for fish growth and welfare. This paper presents empirical data on rotational velocity and water quality in circular and octagonal tanks at two large commercial smolt production sites, with an approximate production rate of 1000 and 1300 ton smolt ann...

Incubation of Aquilaria subintegra with Microbial Culture Supernatants Enhances Production of Volatile Compounds and Improves Quality of Agarwood Oil.

PubMed

Monggoot, Sakon; Kulsing, Chadin; Wong, Yong Foo; Pripdeevech, Patcharee

2018-06-01

Incubation with microbial culture supernatants improved essential oil yield from Aquilaria subintegra woodchips. The harvested woodchips were incubated with de man, rogosa and sharpe (MRS) agar, yeast mold (YM) agar medium and six different microbial culture supernatants obtained from Lactobacillus bulgaricus , L. acidophilus , Streptococcus thermophilus , Lactococcus lactis , Saccharomyces carlsbergensis and S. cerevisiae prior to hydrodistillation. Incubation with lactic acid bacteria supernatants provided higher yield of agarwood oil (0.45% w/w) than that obtained from yeast (0.25% w/w), agar media (0.23% w/w) and water (0.22% w/w). The composition of agarwood oil from all media and microbial supernatant incubations was investigated by using gas chromatography-mass spectrometry. Overall, three major volatile profiles were obtained, which corresponded to water soaking (control), as well as, both YM and MRS media, lactic acid bacteria, and yeast supernatant incubations. Sesquiterpenes and their oxygenated derivatives were key components of agarwood oil. Fifty-two volatile components were tentatively identified in all samples. Beta-agarofuran, α-eudesmol, karanone, α-agarofuran and agarospirol were major components present in most of the incubated samples, while S. cerevisiae -incubated A. subintegra provided higher amount of phenyl acetaldehyde. Microbial culture supernatant incubation numerically provided the highest yield of agarwood oil compared to water soaking traditional method, possibly resulting from activity of extracellular enzymes produced by the microbes. Incubation of agarwood with lactic acid bacteria supernatant significantly enhanced oil yields without changing volatile profile/composition of agarwood essential oil, thus this is a promising method for future use.

Starter Culture Selection for Making Chinese Sesame-Flavored Liquor Based on Microbial Metabolic Activity in Mixed-Culture Fermentation

PubMed Central

Wu, Qun; Ling, Jie

2014-01-01

Selection of a starter culture with excellent viability and metabolic activity is important for inoculated fermentation of traditional food. To obtain a suitable starter culture for making Chinese sesame-flavored liquor, the yeast and bacterium community structures were investigated during spontaneous and solid-state fermentations of this type of liquor. Five dominant species in spontaneous fermentation were identified: Saccharomyces cerevisiae, Pichia membranaefaciens, Issatchenkia orientalis, Bacillus licheniformis, and Bacillus amyloliquefaciens. The metabolic activity of each species in mixed and inoculated fermentations of liquor was investigated in 14 different cocultures that used different combinations of these species. The relationships between the microbial species and volatile metabolites were analyzed by partial least-squares (PLS) regression analysis. We found that S. cerevisiae was positively correlated to nonanal, and B. licheniformis was positively associated with 2,3-butanediol, isobutyric acid, guaiacol, and 4-vinyl guaiacol, while I. orientalis was positively correlated to butyric acid, isovaleric acid, hexanoic acid, and 2,3-butanediol. These three species are excellent flavor producers for Chinese liquor. Although P. membranaefaciens and B. amyloliquefaciens were not efficient flavor producers, the addition of them alleviated competition among the other three species and altered their growth rates and flavor production. As a result, the coculture of all five dominant species produced the largest amount of flavor compounds. The result indicates that flavor producers and microbial interaction regulators are important for inoculated fermentation of Chinese sesame-flavored liquor. PMID:24814798

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

PubMed

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

2014-03-01

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

Feasibility of biohydrogen production from industrial wastes using defined microbial co-culture.

PubMed

Chen, Peng; Wang, Yuxia; Yan, Lei; Wang, Yiqing; Li, Suyue; Yan, Xiaojuan; Wang, Ningbo; Liang, Ning; Li, Hongyu

2015-05-06

The development of clean or novel alternative energy has become a global trend that will shape the future of energy. In the present study, 3 microbial strains with different oxygen requirements, including Clostridium acetobutylicum ATCC 824, Enterobacter cloacae ATCC 13047 and Kluyveromyces marxianus 15D, were used to construct a hydrogen production system that was composed of a mixed aerobic-facultative anaerobic-anaerobic consortium. The effects of metal ions, organic acids and carbohydrate substrates on this system were analyzed and compared using electrochemical and kinetic assays. It was then tested using small-scale experiments to evaluate its ability to convert starch in 5 L of organic wastewater into hydrogen. For the one-step biohydrogen production experiment, H1 medium (nutrient broth and potato dextrose broth) was mixed directly with GAM broth to generate H2 medium (H1 medium and GAM broth). Finally, Clostridium acetobutylicum ATCC 824, Enterobacter cloacae ATCC 13047 and Kluyveromyces marxianus 15D of three species microbial co-culture to produce hydrogen under anaerobic conditions. For the two-step biohydrogen production experiment, the H1 medium, after cultured the microbial strains Enterobacter cloacae ATCC 13047 and Kluyveromyces marxianus 15D, was centrifuged to remove the microbial cells and then mixed with GAM broth (H2 medium). Afterward, the bacterial strain Clostridium acetobutylicum ATCC 824 was inoculated into the H2 medium to produce hydrogen by anaerobic fermentation. The experimental results demonstrated that the optimum conditions for the small-scale fermentative hydrogen production system were at pH 7.0, 35°C, a mixed medium, including H1 medium and H2 medium with 0.50 mol/L ferrous chloride, 0.50 mol/L magnesium sulfate, 0.50 mol/L potassium chloride, 1% w/v citric acid, 5% w/v fructose and 5% w/v glucose. The overall hydrogen production efficiency in the shake flask fermentation group was 33.7 mL/h(-1).L(-1), and those the two

The effect of microbial starter composition on cassava chips fermentation for the production of fermented cassava flour

NASA Astrophysics Data System (ADS)

Kresnowati, M. T. A. P.; Listianingrum, Zaenudin, Ahmad; Trihatmoko, Kharisrama

2015-12-01

The processing of cassava into fermented cassava flour (fercaf) or the widely known as modified cassava flour (mocaf) presents an alternative solution to improve the competitiveness of local foods and to support national food security. However, the mass production of fercaf is being limited by several problems, among which is the availability of starter cultures. This paper presents the mapping of the effect of microbial starter compositions on the nutritional content of fercaf in order to obtain the suitable nutritional composition. Based on their enzymatic activities, the combination of Lactobacillus plantarum, Bacillus subtilis, and Aspergillus oryzae were tested during the study. In addition, commercial starter was also tested. During the fermentation, the dynamics in microbial population were measured as well as changes in cyanogenic glucoside content. The microbial starter composition was observed to affect the dynamics in microbial populationcynaogenic glucoside content of the produced fercaf. In general, steady state microbial population was reached within 12 hours of fermentation. Cyanogenic glucoside was observed to decrease along the fermentation.

Analysis of the Gull Fecal Microbial Community Reveals the Dominance of Catellicoccus marimammalium in Relation to Culturable Enterococci

PubMed Central

Koskey, Amber M.; Fisher, Jenny C.; Traudt, Mary F.; Newton, Ryan J.

2014-01-01

Gulls are prevalent in beach environments and can be a major source of fecal contamination. Gulls have been shown to harbor a high abundance of fecal indicator bacteria (FIB), such as Escherichia coli and enterococci, which can be readily detected as part of routine beach monitoring. Despite the ubiquitous presence of gull fecal material in beach environments, the associated microbial community is relatively poorly characterized. We generated comprehensive microbial community profiles of gull fecal samples using Roche 454 and Illumina MiSeq platforms to investigate the composition and variability of the gull fecal microbial community and to measure the proportion of FIB. Enterococcaceae and Enterobacteriaceae were the two most abundant families in our gull samples. Sequence comparisons between short-read data and nearly full-length 16S rRNA gene clones generated from the same samples revealed Catellicoccus marimammalium as the most numerous taxon among all samples. The identification of bacteria from gull fecal pellets cultured on membrane-Enterococcus indoxyl-β-d-glucoside (mEI) plates showed that the dominant sequences recovered in our sequence libraries did not represent organisms culturable on mEI. Based on 16S rRNA gene sequencing of gull fecal isolates cultured on mEI plates, 98.8% were identified as Enterococcus spp., 1.2% were identified as Streptococcus spp., and none were identified as C. marimammalium. Illumina deep sequencing indicated that gull fecal samples harbor significantly higher proportions of C. marimammalium 16S rRNA gene sequences (>50-fold) relative to typical mEI culturable Enterococcus spp. C. marimammalium therefore can be confidently utilized as a genetic marker to identify gull fecal pollution in the beach environment. PMID:24242244

Microbial electrosynthetic cells

DOEpatents

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

2018-01-30

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

Short communication: Microbial quality of raw milk following commercial long-distance hauling.

PubMed

Darchuk, Emily M; Meunier-Goddik, Lisbeth; Waite-Cusic, Joy

2015-12-01

Hauling is a critical part of the commercial milk supply chain, yet very few studies have aimed to understand its effect on raw milk quality. This study focused on the effect of extended-duration tanker use during hauling on raw milk quality at a commercial facility. Standard tanker use [cleaned-in-place (CIP) once per 24h] served as a control and an incremental between-load water rinse with sanitizer treatment (RS) was evaluated to mitigate any effect from extended duration hauling. During this study, 1 commercial truck with 2 trailers was monitored for 10d. The truck collected milk at a large dairy farm, transported the milk to a manufacturing facility, and then returned to the same farm for a second load. Each round-trip journey took between 10 and 12h, allowing for 2 loads per 24-h use period. Following the second delivery, the truck was cleaned by CIP treatment starting a new treatment day. Producer samples were collected from the raw milk bulk tank on the farm before loading milk into the tanker. The same milk was sampled directly out of the tanker truck before unloading at the manufacturer. Effect on individual bacteria count, thermophilic spore count, and preliminary incubation count was quantified through common industry tests. Surface sponge swabs were also used to monitor tanker sanitation and the efficacy of cleaning treatments. Results did not identify a negative effect on raw milk quality due to extended duration hauling. Whereas the addition of RS did not provide any measurable quality benefits for the microbial milk quality, swab results demonstrated that the RS treatment was able to reduce surface bacteria in the tanker, although not to the same level as the full CIP treatment. Based on this study, current CIP practices for long distance milk hauling appear to be effective in mitigating any measurable effect on raw milk quality. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Microbial Succession and Nitrogen Cycling in Cultured Biofilms as Affected by the Inorganic Nitrogen Availability.

PubMed

Li, Shuangshuang; Peng, Chengrong; Wang, Chun; Zheng, Jiaoli; Hu, Yao; Li, Dunhai

2017-01-01

Biofilms play important roles in nutrients and energy cycling in aquatic ecosystems. We hypothesized that as eutrophication could change phytoplankton community and decrease phytoplankton diversity, ambient inorganic nitrogen level will affect the microbial community and diversity of biofilms and the roles of biofilms in nutrient cycling. Biofilms were cultured using a flow incubator either with replete inorganic nitrogen (N-rep) or without exogenous inorganic nitrogen supply (N-def). The results showed that the biomass and nitrogen and phosphorous accumulation of biofilms were limited by N deficiency; however, as expected, the N-def biofilms had significantly higher microbial diversity than that of N-rep biofilms. The microbial community of biofilms shifted in composition and abundance in response to ambient inorganic nitrogen level. For example, as compared between the N-def and the N-rep biofilms, the former consisted of more diazotrophs, while the latter consisted of more denitrifying bacteria. As a result of the shift of the functional microbial community, the N concentration of N-rep medium kept decreasing, while that of N-def medium showed an increasing trend in the late stage. This indicates that biofilms can serve as the source or the sink of nitrogen in aquatic ecosystems, and it depends on the inorganic nitrogen availability.

Influence of Culture Media on Microbial Fingerprints Using Raman Spectroscopy.

PubMed

Mlynáriková, Katarína; Samek, Ota; Bernatová, Silvie; Růžička, Filip; Ježek, Jan; Hároniková, Andrea; Šiler, Martin; Zemánek, Pavel; Holá, Veronika

2015-11-24

Raman spectroscopy has a broad range of applications across numerous scientific fields, including microbiology. Our work here monitors the influence of culture media on the Raman spectra of clinically important microorganisms (Escherichia coli, Staphylococcus aureus, Staphylococcus epidermidis and Candida albicans). Choosing an adequate medium may enhance the reproducibility of the method as well as simplifying the data processing and the evaluation. We tested four different media per organism depending on the nutritional requirements and clinical usage directly on a Petri dish. Some of the media have a significant influence on the microbial fingerprint (Roosvelt-Park Institute Medium, CHROMagar) and should not be used for the acquisition of Raman spectra. It was found that the most suitable medium for microbiological experiments regarding these organisms was Mueller-Hinton agar.

Design of serum-free medium for suspension culture of CHO cells on the basis of general commercial media.

PubMed

Miki, Hideo; Takagi, Mutsumi

2015-08-01

The design of serum-free media for suspension culture of genetically engineered Chinese hamster ovary (CHO) cells using general commercial media as a basis was investigated. Subcultivation using a commercial serum-free medium containing insulin-like growth factor (IGF)-1 with or without FCS necessitated additives other than IGF-1 to compensate for the lack of FCS and improve cell growth. Suspension culture with media containing several combinations of growth factors suggested the effectiveness of addition of both IGF-1 and the lipid signaling molecule lysophosphatidic acid (LPA) for promoting cell growth. Subcultivation of CHO cells in suspension culture using the commercial serum-free medium EX-CELL™302, which contained an IGF-1 analog, supplemented with LPA resulted in gradually increasing specific growth rate comparable to the serum-containing medium and in almost the same high antibody production regardless of the number of generations. The culture with EX-CELL™302 supplemented with LPA in a jar fermentor with pH control at 6.9 showed an apparently higher cell growth rate than the cultures without pH control and with pH control at 6.8. The cell growth in the medium supplemented with aurintricarboxylic acid (ATA), which was much cheaper than IGF-1, in combination with LPA was synergistically promoted similarly to that in the medium supplemented with IGF-1 and LPA. In conclusion, the serum-free medium designed on the basis of general commercial media could support the growth of CHO cells and antibody production comparable to serum-containing medium in suspension culture. Moreover, the possibility of cost reduction by the substitution of IGF-1 with ATA was also shown.

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

NASA Astrophysics Data System (ADS)

Ren, Jingli; Yuan, Qigang

2017-08-01

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

A Continuous Culture System for Assessing Microbial Activities in the Piezosphere

PubMed Central

Pérez-Rodríguez, Ileana

2015-01-01

Continuous culture under elevated pressures is an important technique for expanding the exploration of microbial growth and survival in extreme environments associated with the deep biosphere. Here we present a benchtop stirred continuous culture bioreactor capable of withstanding temperatures ranging from 25 to 120°C and pressures as high as 69 MPa. The system is configured to allow the employment of media enriched in dissolved gases, under oxic or anoxic conditions, while permitting periodic sampling of the incubated organisms with minimal physical/chemical disturbance inside the reactor. In a pilot experiment, the fermentative growth of the thermopiezophilic bacterium Marinitoga piezophila was investigated continuously for 382 h at 65°C and at pressures ranging from 0.1 to 40 MPa while the medium flow rate was varied from 2 to 0.025 ml/min. The enhanced growth observed at 30 and 40 MPa and 0.025 ml/min supports the pressure preferences of M. piezophila when grown fermentatively. This assay successfully demonstrates the capabilities of the bioreactor for continuous culturing at a variety of dilution rates, pressures, and temperatures. We anticipate that this technology will accelerate our understanding of the physiological and metabolic status of microorganisms under temperature, pressure, and energy regimes resembling those of the Earth's piezosphere. PMID:26209666

Method Analysis of Microbial Resistant Gypsum Products

EPA Science Inventory

Abstract: Several commercially available gypsum products are marketed as microbial-resistant. During previous test method research on a microbial resistant gypsum wallboard study, a common theme from both stakeholders and product vendors was the need for a unified and accepted m...

Direct cloning from enrichment cultures, a reliable strategy for isolation of complete operons and genes from microbial consortia.

PubMed

Entcheva, P; Liebl, W; Johann, A; Hartsch, T; Streit, W R

2001-01-01

Enrichment cultures of microbial consortia enable the diverse metabolic and catabolic activities of these populations to be studied on a molecular level and to be explored as potential sources for biotechnology processes. We have used a combined approach of enrichment culture and direct cloning to construct cosmid libraries with large (>30-kb) inserts from microbial consortia. Enrichment cultures were inoculated with samples from five environments, and high amounts of avidin were added to the cultures to favor growth of biotin-producing microbes. DNA was extracted from three of these enrichment cultures and used to construct cosmid libraries; each library consisted of between 6,000 and 35,000 clones, with an average insert size of 30 to 40 kb. The inserts contained a diverse population of genomic DNA fragments isolated from the consortia organisms. These three libraries were used to complement the Escherichia coli biotin auxotrophic strain ATCC 33767 Delta(bio-uvrB). Initial screens resulted in the isolation of seven different complementing cosmid clones, carrying biotin biosynthesis operons. Biotin biosynthesis capabilities and growth under defined conditions of four of these clones were studied. Biotin measured in the different culture supernatants ranged from 42 to 3,800 pg/ml/optical density unit. Sequencing the identified biotin synthesis genes revealed high similarities to bio operons from gram-negative bacteria. In addition, random sequencing identified other interesting open reading frames, as well as two operons, the histidine utilization operon (hut), and the cluster of genes involved in biosynthesis of molybdopterin cofactors in bacteria (moaABCDE).

Microbial Diversity of Commercial Makgeolli and Its Influence on the Organoleptic Characteristics of Korean Rice Sourdough, Jeung-Pyun.

PubMed

Park, Jaehyung; Seo, Ji Sun; Kim, Seul-Ah; Shin, So-Yeon; Park, Jong-Hyun; Han, Nam Soo

2017-10-28

Sourdough is made by fermentation of dough by lactic acid bacteria (LAB) and yeast to improve bread properties like volume, flavor, and texture. A Korean traditional sourdough was made by fermenting rice flour with rice wine (makgeolli) and used to make sponge-like bread (jeung-pyun). The aim of this study was to investigate the microbial diversity of makgeolli products and their influence on the organoleptic quality of jeung-pyun. Three commercial makgeolli were tested for jeung-pyun production, with each product exhibiting varied dough swelling rates and organoleptic qualities, and among them, J-product was ranked highest in texture and taste. Microbial analysis of the three makgeolli also showed a big difference in their population and diversity. J-product had the highest LAB and yeast counts, and the predominant species were Lactobacillus casei, Lactobacillus brevis, Leuconostoc pseudomenteroides, and Saccharomyces cerevisiae . Using J-product, sourdough was fermented at 25°C, 30°C, and 35°C, and the microbial growth in and textural properties of jeung-pyun were examined by instrumental and sensory tests. At high temperature (35°C), the rates of dough swelling and acidification were fast due to rapid microbial growth mainly caused by LAB, resulting in a short leavening time and soft and sour jeung-pyun. Sensory tests showed consumer preference for the soft and mild-sour jeung-pyun. This study shows that LAB in makgeolli play key roles in production of jeung-pyun, influencing the textural and sensory properties. For the production of high-quality jeung-pyun, development of LAB starters with high gas productivity and low acidity and establishment of an optimal fermentation procedure for rice dough are necessary.

Microbial Life Under Extreme Energy Limitation

NASA Technical Reports Server (NTRS)

Hoehler, Tori M.; Jorgensen, Bo Barker

2013-01-01

A great number of the bacteria and archaea on Earth are found in subsurface environments in a physiological state that is poorly represented or explained by laboratory cultures. Microbial cells in these very stable and oligotrophic settings catabolize 104- to 106-fold more slowly than model organisms in nutrient-rich cultures, turn over biomass on timescales of centuries to millennia rather than hours to days, and subsist with energy fluxes that are 1,000-fold lower than the typical culture-based estimates of maintenance requirements. To reconcile this disparate state of being with our knowledge of microbial physiology will require a revised understanding of microbial energy requirements, including identifying the factors that comprise true basal maintenance and the adaptations that might serve to minimize these factors.

Influence of Culture Media on Microbial Fingerprints Using Raman Spectroscopy

PubMed Central

Mlynáriková, Katarína; Samek, Ota; Bernatová, Silvie; Růžička, Filip; Ježek, Jan; Hároniková, Andrea; Šiler, Martin; Zemánek, Pavel; Holá, Veronika

2015-01-01

Raman spectroscopy has a broad range of applications across numerous scientific fields, including microbiology. Our work here monitors the influence of culture media on the Raman spectra of clinically important microorganisms (Escherichia coli, Staphylococcus aureus, Staphylococcus epidermidis and Candida albicans). Choosing an adequate medium may enhance the reproducibility of the method as well as simplifying the data processing and the evaluation. We tested four different media per organism depending on the nutritional requirements and clinical usage directly on a Petri dish. Some of the media have a significant influence on the microbial fingerprint (Roosvelt-Park Institute Medium, CHROMagar) and should not be used for the acquisition of Raman spectra. It was found that the most suitable medium for microbiological experiments regarding these organisms was Mueller-Hinton agar. PMID:26610516

Microbial community composition of the ileum and cecum of broiler chickens as revealed by molecular and culture-based techniques.

PubMed

Bjerrum, L; Engberg, R M; Leser, T D; Jensen, B B; Finster, K; Pedersen, K

2006-07-01

The microbial communities of the ileum and cecum of broiler chickens from a conventional and an organic farm were investigated using conventional culture techniques as well as cloning and sequencing of 16S rRNA genes. Eighty-five percent of the 557 cloned sequences were <97% related to known cultured species. The chicken ileum was dominated by lactobacilli, whereas the cecum harbored a more diverse microbial community. The cecum was dominated by a large group of bacteria with hitherto no close cultured relatives but most closely related to Faecalibacterium prausnitzii. Approximately 49 and 20% of the cecal clones belonged to this cluster in conventional and organic broiler chickens, respectively. We were, however, able to recover a number of these phylotypes by cultivation, and the isolates were shown to be butyric acid producers. The investigation was a descriptive rather than a comparative study of 2 different rearing systems; however, several differences were observed. For instance, Clostridium perfringens was found in significantly higher numbers in the birds from the organic farm compared with the conventional broilers, probably due to the addition of salinomycin to the conventional feed. In the ileum, the abundance of the different Lactobacillus species differed between the 2 broiler types. The culture-based and culture-independent techniques complemented each other well. Strengths and limitations of the different methods are discussed.

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

Rumen degradable protein supply affects microbial efficiency in continuous culture and growth in steers.

PubMed

Brooks, M A; Harvey, R M; Johnson, N F; Kerley, M S

2012-12-01

We hypothesized that microbial efficiency and output from fermentation in the rumen would be optimized when peptide supply was balanced with peptide requirement of ruminal microflora. This study was conducted to measure response of varying rumen degradable peptide (RDPep) supply on ruminal fermentation characteristics and steer growth. A continuous culture experiment was conducted with diets formulated to achieve a predicted RDPep balance (RDPep supplied above RDPep required) of -0.30 to 1.45% CP with rumen degradable N (RDN) balance (RDN supplied above RDN required) above dietary ammonia-N requirement of microbes. Two additional treatments had RDPep balances of -0.30 and 0.78% CP with insufficient ammonia-N supply to meet microbial requirements. Single-flow fermenters (N = 24; n = 6) were inoculated with rumen fluid and maintained anaerobically at 39°C with a 0.06 h(-1) dilution rate. Inadequate RDN decreased OM digestion and microbial N flow, and increased rumen undegradable N (P < 0.01). Microbial efficiency decreased in RDN-deficient diets and was greatest when RDPep balance did not excessively exceed microbial requirement of RDPep predicted (P < 0.01). A growth study was conducted with 49 yearling, crossbred, Angus steers (initial BW 370 ± 34 kg). Animals were assigned to 1 of 4 treatment groups by BW and further divided into 3 pens with 4 steers per pen to achieve similar initial pen weights. Treatments consisted of 4 isonitrogenous diets balanced for RDN but varying in predicted RDPep balance (0.55%, -0.02%, -0.25%, and -0.65% CP). Animals were maintained on treatment for 70 d with individual BW taken on d 0, 1, 21, 42, 70, and 71. Final BW decreased linearly with decreasing RDPep (P = 0.05). Average daily gain and G:F displayed a quadratic effect with greater ADG and G:F at greater and lesser RDPep levels (P = 0.02). We concluded that balancing RDPep supply to predicted requirement improved fermentation efficiency and microbial output, which in turn

Microbial Diversity Analysis of Fermented Mung Beans (Lu-Doh-Huang) by Using Pyrosequencing and Culture Methods

PubMed Central

Chao, Shiou-Huei; Huang, Hui-Yu; Chang, Chuan-Hsiung; Yang, Chih-Hsien; Cheng, Wei-Shen; Kang, Ya-Huei; Watanabe, Koichi; Tsai, Ying-Chieh

2013-01-01

In Taiwanese alternative medicine Lu-doh-huang (also called Pracparatum mungo), mung beans are mixed with various herbal medicines and undergo a 4-stage process of anaerobic fermentation. Here we used high-throughput sequencing of the 16S rRNA gene to profile the bacterial community structure of Lu-doh-huang samples. Pyrosequencing of samples obtained at 7 points during fermentation revealed 9 phyla, 264 genera, and 586 species of bacteria. While mung beans were inside bamboo sections (stages 1 and 2 of the fermentation process), family Lactobacillaceae and genus Lactobacillus emerged in highest abundance; Lactobacillus plantarum was broadly distributed among these samples. During stage 3, the bacterial distribution shifted to family Porphyromonadaceae, and Butyricimonas virosa became the predominant microbial component. Thereafter, bacterial counts decreased dramatically, and organisms were too few to be detected during stage 4. In addition, the microbial compositions of the liquids used for soaking bamboo sections were dramatically different: Exiguobacterium mexicanum predominated in the fermented soybean solution whereas B. virosa was predominant in running spring water. Furthermore, our results from pyrosequencing paralleled those we obtained by using the traditional culture method, which targets lactic acid bacteria. In conclusion, the microbial communities during Lu-doh-huang fermentation were markedly diverse, and pyrosequencing revealed a complete picture of the microbial consortium. PMID:23700436

Phenotypic responses to interspecies competition and commensalism in a naturally-derived microbial co-culture.

PubMed

Khan, Nymul; Maezato, Yukari; McClure, Ryan S; Brislawn, Colin J; Mobberley, Jennifer M; Isern, Nancy; Chrisler, William B; Markillie, Lye Meng; Barney, Brett M; Song, Hyun-Seob; Nelson, William C; Bernstein, Hans C

2018-01-10

The fundamental question of whether different microbial species will co-exist or compete in a given environment depends on context, composition and environmental constraints. Model microbial systems can yield some general principles related to this question. In this study we employed a naturally occurring co-culture composed of heterotrophic bacteria, Halomonas sp. HL-48 and Marinobacter sp. HL-58, to ask two fundamental scientific questions: 1) how do the phenotypes of two naturally co-existing species respond to partnership as compared to axenic growth? and 2) how do growth and molecular phenotypes of these species change with respect to competitive and commensal interactions? We hypothesized - and confirmed - that co-cultivation under glucose as the sole carbon source would result in competitive interactions. Similarly, when glucose was swapped with xylose, the interactions became commensal because Marinobacter HL-58 was supported by metabolites derived from Halomonas HL-48. Each species responded to partnership by changing both its growth and molecular phenotype as assayed via batch growth kinetics and global transcriptomics. These phenotypic responses depended on nutrient availability and so the environment ultimately controlled how they responded to each other. This simplified model community revealed that microbial interactions are context-specific and different environmental conditions dictate how interspecies partnerships will unfold.

Phenotypic responses to interspecies competition and commensalism in a naturally-derived microbial co-culture

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

Khan, Nymul; Maezato, Yukari; McClure, Ryan S.

The fundamental question of whether different microbial species will co-exist or compete in a given environment depends on context, composition and environmental constraints. Model microbial systems can yield some general principles related to this question. In this study we employed a naturally occurring co-culture composed of heterotrophic bacteria, Halomonas sp. HL-48 and Marinobacter sp. HL-58, to ask two fundamental scientific questions: 1) how do the phenotypes of two naturally co-existing species respond to partnership as compared to axenic growth? and 2) how do growth and molecular phenotypes of these species change with respect to competitive and commensal interactions? We hypothesizedmore » – and confirmed – that co-cultivation under glucose as the sole carbon source would result in a competitive interactions. Similarly, when glucose was swapped with xylose, the interactions became commensal because Marinobacter HL-58 was supported by metabolites derived from Halomonas HL-48. Each species responded to partnership by changing both its growth and molecular phenotype as assayed via batch growth kinetics and global transcriptomics. These phenotypic responses depended nutrient availability and so the environment ultimately controlled how they responded to each other. This simplified model community revealed that microbial interactions are context-specific and different environmental conditions dictate how interspecies partnerships will unfold.« less

Utilizing a Robotic Sprayer for High Lateral and Mass Resolution MALDI FT-ICR MSI of Microbial Cultures

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

Anderton, Christopher R.; Chu, Rosalie K.; Tolic, Nikola

The ability to visualize biochemical interactions between microbial communities using MALDI MSI has provided tremendous insights into a variety of biological fields. Matrix application using a sieve proved to be incredibly useful, but it had many limitations that include uneven matrix coverage and limitation in the types of matrices one could employ in their studies. Recently, there has been a concerted effort to improve matrix application for studying agar plated microbial cultures, many of which utilized automated matrix sprayers. Here, we describe the usefulness of using a robotic sprayer for matrix application. The robotic sprayer has two-dimensional control over wheremore » matrix is applied and a heated capillary that allows for rapid drying of the applied matrix. This method provided a significant increase in MALDI sensitivity over the sieve method, as demonstrated by FT-ICR MS analysis, facilitating the ability to gain higher lateral resolution MS images of Bacillus Subtilis than previously reported. This method also allowed for the use of different matrices to be applied to the culture surfaces.« less

Towards a Microbial Thermoelectric Cell

PubMed Central

Rodríguez-Barreiro, Raúl; Abendroth, Christian; Vilanova, Cristina; Moya, Andrés; Porcar, Manuel

2013-01-01

Microbial growth is an exothermic process. Biotechnological industries produce large amounts of heat, usually considered an undesirable by-product. In this work, we report the construction and characterization of the first microbial thermoelectric cell (MTC), in which the metabolic heat produced by a thermally insulated microbial culture is partially converted into electricity through a thermoelectric device optimized for low ΔT values. A temperature of 41°C and net electric voltage of around 250–600 mV was achieved with 1.7 L baker’s yeast culture. This is the first time microbial metabolic energy has been converted into electricity with an ad hoc thermoelectric device. These results might contribute towards developing a novel strategy to harvest excess heat in the biotechnology industry, in processes such as ethanol fermentation, auto thermal aerobic digestion (ATAD) or bioremediation, which could be coupled with MTCs in a single unit to produce electricity as a valuable by-product of the primary biotechnological product. Additionally, we propose that small portable MTCs could be conceived and inoculated with suitable thermophilic of hyperthermophilic starter cultures and used for powering small electric devices. PMID:23468862

Functional Stability Of A Mixed Microbial Consortia Producing PHA From Waste Carbon Sources

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

David N. Thompson; Erik R. Coats; William A. Smith

2006-04-01

Polyhydroxyalkanoates (PHAs), naturally-occurring biological polyesters that are microbially synthesized from a myriad of carbon sources, can be utilized as biodegradable substitutes for petroleum-derived thermoplastics. However, current PHA commercialization schemes are limited by high feedstock costs, the requirement for aseptic reactors, and high separation and purification costs. Bacteria indigenous to municipal waste streams can accumulate large quantities of PHA under environmentally controlled conditions; hence, a potentially more environmentally-effective method of production would utilize these consortia to produce PHAs from inexpensive waste carbon sources. In this study, PHA production was accomplished in sequencing batch bioreactors utilizing mixed microbial consortia from municipal activatedmore » sludge as inoculum, in cultures grown on real wastewaters. PHA production averaged 85%, 53%, and 10% of the cell dry weight from methanol-enriched pulp-and-paper mill foul condensate, fermented municipal primary solids, and biodiesel wastewater, respectively. The PHA-producing microbial consortia were examined to explore the microbial community changes that occurred during reactor operations, employing denaturing gradient gel electrophoresis (DGGE) of 16S-rDNA from PCR-amplified DNA extracts. Distinctly different communities were observed both between and within wastewaters following enrichment. More importantly, stable functions were maintained despite the differing and contrasting microbial populations.« less

Culture-independent diagnostic testing: have we opened Pandora's box for good?

PubMed

Janda, J Michael; Abbott, Sharon A

2014-11-01

The ability to accurately and quickly identify microbial agents associated with infectious diseases has been a longstanding and continuous goal of diagnostic microbiology laboratories. Over the course of several decades, technology and testing methodologies in this field have gradually evolved from traditional- or classic-based culture and identification approaches to antigen capture systems and more molecular-oriented applications. Recently, these molecular-based applications have signaled a new era in clinical diagnostic microbiology with the commercial introduction of culture-independent diagnostic testing (CIDT) systems. The first major commercial venture into the CIDT arena involves the detection of acute bacterial gastroenteritis. Several commercial products are now on the market globally with at least 4 Food and Drug Administration approved since January of 2013. These new systems offer the direct detection of a variety of enteropathogens quickly without the need for traditional culture. In Greek mythology, Pandora opened a "jar" or "box" out of curiosity thereby releasing all of humanity's evils most notably diseases and plagues according to Hesiod's Theogony. While not ill-intentioned the only thing left in the box was Hope. Copyright © 2014 Elsevier Inc. All rights reserved.

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.

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

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.;

Polyphasic Microbial Analysis of Traditional Korean Jeung-Pyun Sourdough Fermented with Makgeolli.

PubMed

Lim, Sae Bom; Tingirikari, Jagan Mohan Rao; Kwon, Ye Won; Li, Ling; Kim, Grace E; Han, Nam Soo

2017-02-28

Jeung-pyun, a fermented rice cake, is prepared by fermenting rice sourdough using makgeolli, a traditional Korean rice wine, in the presence of yeast and lactic acid bacteria (LAB). The goal of this study was to conduct biochemical and microbial analyses of five different rice sourdoughs, each fermented with a different commercial makgeolli, using culture-dependent and culture-independent approaches. All sourdough samples fermented with different makgeolli for 6.5 h showed different profiles in pH, total titratable acidity, organic acid concentration, and microbial growth. LAB belonging to different genera were identified based on colony morphology on modified MRS and sourdough bacteria agar medium. PCR-denaturinggradient gel electrophoresis analyses of the five sourdoughs showed different bands corresponding to LAB and yeast. 16S/26S rRNA gene sequence analyses of the samples confirmed that the predominant LAB in the five fermented rice doughs was Lactobacillus plantarum , Lb. pentosus , and Lb. brevis . Various other Lactobacillus spp. and Saccharomyces cerevisiae were common in all five fermented samples. This study provides comprehensive and comparative information on the microflora involved in fermentation of rice sourdough and signifies the need to develop effective starters to enrich the quality of jeung-pyun.

The diagnosis of chronic endometritis in infertile asymptomatic women: a comparative study of histology, microbial cultures, hysteroscopy, and molecular microbiology.

PubMed

Moreno, Inmaculada; Cicinelli, Ettore; Garcia-Grau, Iolanda; Gonzalez-Monfort, Marta; Bau, Davide; Vilella, Felipe; De Ziegler, Dominique; Resta, Leonardo; Valbuena, Diana; Simon, Carlos

2018-06-01

Chronic endometritis is a persistent inflammation of the endometrial mucosa caused by bacterial pathogens such as Enterobacteriaceae, Enterococcus, Streptococcus, Staphylococcus, Mycoplasma, and Ureaplasma. Although chronic endometritis can be asymptomatic, it is found in up to 40% of infertile patients and is responsible for repeated implantation failure and recurrent miscarriage. Diagnosis of chronic endometritis is based on hysteroscopy of the uterine cavity, endometrial biopsy with plasma cells being identified histologically, while specific treatment is determined based on microbial culture. However, not all microorganisms implicated are easily or readily culturable needing a turnaround time of up to 1 week. We sought to develop a molecular diagnostic tool for chronic endometritis based on real-time polymerase chain reaction equivalent to using the 3 classic methods together, overcoming the bias of using any of them alone. Endometrial samples from patients assessed for chronic endometritis (n = 113) using at least 1 or several conventional diagnostic methods namely histology, hysteroscopy, and/or microbial culture, were blindly evaluated by real-time polymerase chain reaction for the presence of 9 chronic endometritis pathogens: Chlamydia trachomatis, Enterococcus, Escherichia coli, Gardnerella vaginalis, Klebsiella pneumoniae, Mycoplasma hominis, Neisseria gonorrhoeae, Staphylococcus, and Streptococcus. The sensitivity and specificity of the molecular analysis vs the classic diagnostic techniques were compared in the 65 patients assessed by all 3 recognized classic methods. The molecular method showed concordant results with histological diagnosis in 30 samples (14 double positive and 16 double negative) with a matching accuracy of 46.15%. Concordance of molecular and hysteroscopic diagnosis was observed in 38 samples (37 double positive and 1 double negative), with an accuracy of 58.46%. When the molecular method was compared to microbial culture

Microbial diversity in sugarcane ethanol production in a Brazilian distillery using a culture-independent method.

PubMed

Costa, Ohana Yonara Assis; Souto, Betulia Morais; Tupinambá, Daiva Domenech; Bergmann, Jessica Carvalho; Kyaw, Cynthia Maria; Kruger, Ricardo Henrique; Barreto, Cristine Chaves; Quirino, Betania Ferraz

2015-01-01

Sugarcane ethanol production occurs in non-sterile conditions, and microbial contamination can decrease productivity. In this study, we assessed the microbial diversity of contaminants of ethanol production in an industrial facility in Brazil. Samples obtained at different stages were analyzed by pyrosequencing-based profiling of bacterial and archaeal 16S rRNA genes and the fungal internal transcribed spacer region. A total of 355 bacterial groups, 22 archaeal groups, and 203 fungal groups were identified, and community changes were related to temperature changes at certain stages. After fermentation, Lactobacillus and unclassified Lactobacillaceae accounted for nearly 100 % of the bacterial sequences. Predominant Fungi groups were "unclassified Fungi," Meyerozyma, and Candida. The predominant Archaea group was unclassified Thaumarchaeota. This is the first work to assess the diversity of Bacteria, and Archaea and Fungi associated with the industrial process of sugarcane-ethanol production using culture-independent techniques.

Deep-Subterranean Microbial Habitats in the Hishikari Epithermal Gold Mine: Active Thermophilic Microbial Communities and Endolithic Ancient Microbial Relicts.

NASA Astrophysics Data System (ADS)

Hirayama, H.; Takai, K.; Inagaki, F.; Horikoshi, K.

2001-12-01

Deep subterranean microbial community structures in an epithermal gold-silver deposit, Hishikari gold mine, southern part of Kyusyu Japan, were evaluated through the combined use of enrichment culture methods and culture-independent molecular surveys. The geologic setting of the Hishikari deposit is composed of three lithologies; basement oceanic sediments of the Cretaceous Shimanto Supergroup, Quaternary andesites, and auriferous quartz vein. We studied the drilled core rock of these, and the geothermal hot waters from the basement aquifers collected by means of the dewatering system located at the deepest level in the mining sites. Culture-independent molecular phylogenetic analyses of PCR-amplified ribosomal DNA (rDNA) recovered from drilled cores suggested that the deep-sea oceanic microbial communities were present as ancient indigenous relicts confined in the Shimanto basement. On the other hand, genetic signals of active thermophilic microbial communities, mainly consisting of thermophilic hydrogen-oxidizer within Aquificales, thermophilic methanotroph within g-Proteobacteria and yet-uncultivated bacterium OPB37 within b-Proteobacteria, were detected with these of oceanic relicts from the subterranean geothermal hot aquifers (temp. 70-100ºC). Successful cultivation and FISH analyses strongly supported that these thermophilic lithotrophic microorganisms could be exactly active and they grew using geochemically produced hydrogen and methane gasses as nutrients. Based on these results, the deep-subsurface biosphere occurring in the Hishikari epithermal gold mine was delineated as endolithic ancient microbial relicts and modern habitats raising active lithotrophic thermophiles associated with the geological and geochemical features of the epithermal gold deposit.

Microbial reductive dehalogenation of trihalomethanes by a Dehalobacter-containing co-culture.

PubMed

Zhao, Siyan; Rogers, Matthew J; He, Jianzhong

2017-07-01

Trihalomethanes such as chloroform and bromoform, although well-known as a prominent class of disinfection by-products, are ubiquitously distributed in the environment due to widespread industrial usage in the past decades. Chloroform and bromoform are particularly concerning, of high concentrations detected and with long half-lives up to several hundred days in soils and groundwater. In this study, we report a Dehalobacter- and Desulfovibrio-containing co-culture that exhibits dehalogenation of chloroform (~0.61 mM) to dichloromethane and bromoform (~0.67 mM) to dibromomethane within 10-15 days. This co-culture was further found to dechlorinate 1,1,1-trichloroethane (1,1,1-TCA) (~0.65 mM) to 1,1-dichloroethane within 12 days. The Dehalobacter species present in this co-culture, designated Dehalobacter sp. THM1, was found to couple growth with dehalogenation of chloroform, bromoform, and 1,1,1-TCA. Strain THM1 harbors a newly identified reductive dehalogenase (RDase), ThmA, which catalyzes chloroform, bromoform, and 1,1,1-TCA dehalogenation. Additionally, based on the sequences of thmA and other identified chloroform RDase genes, ctrA, cfrA, and tmrA, a pair of chloroform RDase gene-specific primers were designed and successfully applied to investigate the chloroform dechlorinating potential of microbial communities. The comparative analysis of chloroform RDases with tetrachloroethene RDases suggests a possible approach in predicting the substrate specificity of uncharacterized RDases in the future.

Harnessing the landscape of microbial culture media to predict new organism–media pairings

PubMed Central

Oberhardt, Matthew A.; Zarecki, Raphy; Gronow, Sabine; Lang, Elke; Klenk, Hans-Peter; Gophna, Uri; Ruppin, Eytan

2015-01-01

Culturing microorganisms is a critical step in understanding and utilizing microbial life. Here we map the landscape of existing culture media by extracting natural-language media recipes into a Known Media Database (KOMODO), which includes >18,000 strain–media combinations, >3300 media variants and compound concentrations (the entire collection of the Leibniz Institute DSMZ repository). Using KOMODO, we show that although media are usually tuned for individual strains using biologically common salts, trace metals and vitamins/cofactors are the most differentiating components between defined media of strains within a genus. We leverage KOMODO to predict new organism–media pairings using a transitivity property (74% growth in new in vitro experiments) and a phylogeny-based collaborative filtering tool (83% growth in new in vitro experiments and stronger growth on predicted well-scored versus poorly scored media). These resources are integrated into a web-based platform that predicts media given an organism's 16S rDNA sequence, facilitating future cultivation efforts. PMID:26460590

Automated analysis of food-borne pathogens using a novel microbial cell culture, sensing and classification system.

PubMed

Xiang, Kun; Li, Yinglei; Ford, William; Land, Walker; Schaffer, J David; Congdon, Robert; Zhang, Jing; Sadik, Omowunmi

2016-02-21

We hereby report the design and implementation of an Autonomous Microbial Cell Culture and Classification (AMC(3)) system for rapid detection of food pathogens. Traditional food testing methods require multistep procedures and long incubation period, and are thus prone to human error. AMC(3) introduces a "one click approach" to the detection and classification of pathogenic bacteria. Once the cultured materials are prepared, all operations are automatic. AMC(3) is an integrated sensor array platform in a microbial fuel cell system composed of a multi-potentiostat, an automated data collection system (Python program, Yocto Maxi-coupler electromechanical relay module) and a powerful classification program. The classification scheme consists of Probabilistic Neural Network (PNN), Support Vector Machines (SVM) and General Regression Neural Network (GRNN) oracle-based system. Differential Pulse Voltammetry (DPV) is performed on standard samples or unknown samples. Then, using preset feature extractions and quality control, accepted data are analyzed by the intelligent classification system. In a typical use, thirty-two extracted features were analyzed to correctly classify the following pathogens: Escherichia coli ATCC#25922, Escherichia coli ATCC#11775, and Staphylococcus epidermidis ATCC#12228. 85.4% accuracy range was recorded for unknown samples, and within a shorter time period than the industry standard of 24 hours.

Comparative analysis of four commercial on-farm culture methods to identify bacteria associated with clinical mastitis in dairy cattle.

PubMed

Ferreira, Jair C; Gomes, Marilia S; Bonsaglia, Erika C R; Canisso, Igor F; Garrett, Edgar F; Stewart, Jamie L; Zhou, Ziyao; Lima, Fabio S

2018-01-01

Several multiple-media culture systems have become commercially available for on-farm identification of mastitis-associated pathogens. However, the accuracy of these systems has not been thoroughly and independently validated against microbiological evaluations performed by referral laboratories. Therefore, the purpose of the present study was to evaluate the performance of commercially available culture plates (Accumast, Minnesota Easy System, SSGN and SSGNC Quad plates) to identify pathogens associated with clinical mastitis in dairy cows. Milk samples from the affected quarter with clinical mastitis were aerobically cultured with the on-farm culture systems and by two additional reference laboratories. Agreeing results from both standard laboratories were denoted as the reference standard (RS). Accuracy (Ac), sensitivity (Se), specificity (Sp), positive and negative predictive values (PPV and NPV, respectively) and Cohen's kappa coefficient (k) of on-farm plates were determined based on the RS culture of 211 milk samples. All four plate-systems correctly identified ≥ 84.9% of milk samples with no bacterial growth. Accumast had greater values for all overall predictive factors (Ac, Se, Sp, PPV and NPV) and a substantial agreement (k = 0.79) with RS. The inter-rater agreements of Minnesota, SSGN, and SSGNC with RS were moderate (0.45 ≤ k ≤ 0.55). The effectiveness to categorize bacterial colonies at the genus and species was numerically different amongst the commercial plates. Our findings suggest that Accumast was the most accurate on-farm culture system for identification of mastitis-associated pathogens of the four systems included in the analysis.

Comparative analysis of four commercial on-farm culture methods to identify bacteria associated with clinical mastitis in dairy cattle

PubMed Central

Ferreira, Jair C.; Gomes, Marilia S.; Bonsaglia, Erika C. R.; Canisso, Igor F.; Garrett, Edgar F.; Stewart, Jamie L.; Zhou, Ziyao

2018-01-01

Several multiple-media culture systems have become commercially available for on-farm identification of mastitis-associated pathogens. However, the accuracy of these systems has not been thoroughly and independently validated against microbiological evaluations performed by referral laboratories. Therefore, the purpose of the present study was to evaluate the performance of commercially available culture plates (Accumast, Minnesota Easy System, SSGN and SSGNC Quad plates) to identify pathogens associated with clinical mastitis in dairy cows. Milk samples from the affected quarter with clinical mastitis were aerobically cultured with the on-farm culture systems and by two additional reference laboratories. Agreeing results from both standard laboratories were denoted as the reference standard (RS). Accuracy (Ac), sensitivity (Se), specificity (Sp), positive and negative predictive values (PPV and NPV, respectively) and Cohen’s kappa coefficient (k) of on-farm plates were determined based on the RS culture of 211 milk samples. All four plate-systems correctly identified ≥ 84.9% of milk samples with no bacterial growth. Accumast had greater values for all overall predictive factors (Ac, Se, Sp, PPV and NPV) and a substantial agreement (k = 0.79) with RS. The inter-rater agreements of Minnesota, SSGN, and SSGNC with RS were moderate (0.45 ≤ k ≤ 0.55). The effectiveness to categorize bacterial colonies at the genus and species was numerically different amongst the commercial plates. Our findings suggest that Accumast was the most accurate on-farm culture system for identification of mastitis-associated pathogens of the four systems included in the analysis. PMID:29543852

Self-sustaining, solar-driven bioelectricity generation in micro-sized microbial fuel cell using co-culture of heterotrophic and photosynthetic bacteria

NASA Astrophysics Data System (ADS)

Liu, Lin; Choi, Seokheun

2017-04-01

Among many energy harvesting techniques with great potential, microbial fuel cell (MFC) technology is arguably the most underdeveloped. Even so, excitement is building, as microorganisms can harvest electrical power from any biodegradable organic source (e.g. wastewater) that is readily available in resource-limited settings. Nevertheless, the requirement for endless introduction of organic matter imposes a limiting factor to this technology, demanding an active feeding system and additional power. Here, we demonstrated self-sustaining bioelectricity generation from a microliter-scale microbial fuel cell (MFC) by using the syntrophic interaction between heterotrophic exoelectrogenic bacteria and phototrophs. The MFC continuously generated light-responsive electricity from the heterotrophic bacterial metabolic respiration with the organic substrates produced by photosynthetic bacteria. Without additional organic fuel, the mixed culture in a 90-μL-chamber MFC generated self-sustained current for more than 13 days, while the heterotrophic culture produced current that decreased dramatically within a few hours. The current from the mixed culture was about 70 times greater than that of the device with only photosynthetic bacteria. The miniaturization provided a short start-up time, a well-controlled environment, and small internal resistance. Those advantages will become the general design platform for micropower generation.

Retention and transport of an anaerobic trichloroethene dechlorinating microbial culture in anaerobic porous media.

PubMed

Zhang, Huixin; Ulrich, Ania C; Liu, Yang

2015-06-01

The influence of solution chemistry on microbial transport was examined using the strictly anaerobic trichloroethene (TCE) bioaugmentation culture KB-1(®). A column was employed to determine transport behaviors and deposition kinetics of three distinct functional species in KB-1(®), Dehalococcoides, Geobacter, and Methanomethylovorans, over a range of ionic strengths under a well-controlled anaerobic condition. A quantitative polymerase chain reaction (qPCR) was utilized to enumerate cell concentration and complementary techniques were implemented to evaluate cell surface electrokinetic potentials. Solution chemistry was found to positively affect the deposition rates, which was consistent with calculated Derjaguin-Landau-Verwey-Overbeek (DLVO) interaction energies. Retained microbial profiles showed spatially constant colloid deposition rate coefficients, in agreement with classical colloid filtration theory (CFT). It was interesting to note that the three KB-1(®) species displayed similar transport and retention behaviors under the defined experimental conditions despite their different cell electrokinetic properties. A deeper analysis of cell characteristics showed that factors, such as cell size and shape, concentration, and motility were involved in determining adhesion behavior. Copyright © 2015 Elsevier B.V. All rights reserved.

Synthetic microbial ecosystems for biotechnology.

PubMed

Pandhal, Jagroop; Noirel, Josselin

2014-06-01

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

Microbial enhanced oil recovery research. [Peptides

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

Sharma, M.M.; Georgiou, G.

1992-01-01

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

Microbial diversity and dynamics throughout manufacturing and ripening of surface ripened semi-hard Danish Danbo cheeses investigated by culture-independent techniques.

PubMed

Ryssel, Mia; Johansen, Pernille; Al-Soud, Waleed Abu; Sørensen, Søren; Arneborg, Nils; Jespersen, Lene

2015-12-23

Microbial successions on the surface and in the interior of surface ripened semi-hard Danish Danbo cheeses were investigated by culture-dependent and -independent techniques. Culture-independent detection of microorganisms was obtained by denaturing gradient gel electrophoresis (DGGE) and pyrosequencing, using amplicons of 16S and 26S rRNA genes for prokaryotes and eukaryotes, respectively. With minor exceptions, the results from the culture-independent analyses correlated to the culture-dependent plating results. Even though the predominant microorganisms detected with the two culture-independent techniques correlated, a higher number of genera were detected by pyrosequencing compared to DGGE. Additionally, minor parts of the microbiota, i.e. comprising <10.0% of the operational taxonomic units (OTUs), were detected by pyrosequencing, resulting in more detailed information on the microbial succession. As expected, microbial profiles of the surface and the interior of the cheeses diverged. During cheese production pyrosequencing determined Lactococcus as the dominating genus on cheese surfaces, representing on average 94.7%±2.1% of the OTUs. At day 6 Lactococcus spp. declined to 10.0% of the OTUs, whereas Staphylococcus spp. went from 0.0% during cheese production to 75.5% of the OTUs at smearing. During ripening, i.e. from 4 to 18 weeks, Corynebacterium was the dominant genus on the cheese surface (55.1%±9.8% of the OTUs), with Staphylococcus (17.9%±11.2% of the OTUs) and Brevibacterium (10.4%±8.3% of the OTUs) being the second and third most abundant genera. Other detected bacterial genera included Clostridiisalibacter (5.0%±4.0% of the OTUs), as well as Pseudoclavibacter, Alkalibacterium and Marinilactibacillus, which represented <2% of the OTUs. At smearing, yeast counts were low with Debaryomyces being the dominant genus accounting for 46.5% of the OTUs. During ripening the yeast counts increased significantly with Debaryomyces being the predominant genus

Effects of commercial marinade seasoning and a natural blend of cultured sugar and vinegar on Campylobacter jejuni and Salmonella Typhimurium and the texture of chicken breasts.

PubMed

Park, Na Yoon; Hong, Soo Hyeon; Yoon, Ki Sun

2014-03-01

Marination using various ingredients has been widely used to improve microbial safety and quality of chicken products at retail markets. The objective of this study was to investigate the effects of commercial marinade seasoning and cultured sugar/vinegar blend on Campylobacter jejuni and Salmonella Typhimurium populations during refrigerated storage. In addition, their effects on the texture of precooked chicken breasts during frozen and refrigerated storage was investigated. Chicken breasts inoculated with 4.5 to 5.0 log cfu/g of C. jejuni and Salmonella Typhimurium were treated with 3% cultured sugar/vinegar blend with and without 0.6% polish rub seasoning containing 32% herb content. Breasts were then vacuum-packaged and stored at 4 and 10°C. Survival and growth curves were fitted to the Baranyi equation to determine survival and growth kinetics of C. jejuni and Salmonella Typhimurium. In addition, the vacuum-packaged precooked chicken breasts with different marination treatments were subjected to 3 freeze-thaw cycles and shear force was measured. At 4°C, the populations of C. jejuni and Salmonella Typhimurium decreased, regardless of treatment group during storage. The greatest survival for C. jejuni was observed in untreated chicken breasts. At 10°C, the growth of Salmonella Typhimurium was completely prevented in precooked chicken breasts treated with 3% cultured sugar/vinegar blend, regardless of the presence of 0.6% seasoning. The 3% cultured sugar/vinegar blend also improved the tenderness of frozen chicken breasts and refrigerated, ready-to-eat chicken breast. Therefore, a natural blend of cultured sugar and vinegar can be used as antimicrobial and texture-modifying agents for poultry meat and poultry products.

Microbial succession in response to pollutants in batch-enrichment culture

PubMed Central

Jiao, Shuo; Chen, Weimin; Wang, Entao; Wang, Junman; Liu, Zhenshan; Li, Yining; Wei, Gehong

2016-01-01

As a global problem, environmental pollution is an important factor to shape the microbial communities. The elucidation of the succession of microbial communities in response to pollutants is essential for developing bioremediation procedures. In the present study, ten batches of soil-enrichment subcultures were subjected to four treatments: phenanthrene, n-octadecane, phenanthrene + n-octadecane, or phenanthrene + n-octadecane + CdCl2. Forty pollutant-degrading consortia, corresponding to each batch of the four treatments were obtained. High-throughput sequencing of the 16S rRNA gene revealed that the diversity, richness and evenness of the consortia decreased throughout the subculturing procedure. The well-known hydrocarbon degraders Acinetobacter, Gordonia, Sphingobium, Sphingopyxis, and Castellaniella and several other genera, including Niabella and Naxibacter, were detected in the enriched consortia. The predominant microbes varied and the microbial community in the consortia gradually changed during the successive subculturing depending on the treatment, indicating that the pollutants influenced the microbial successions. Comparison of the networks in the treatments indicated that organic pollutants and CdCl2 affected the co-occurrence patterns in enriched consortia. In conclusion, single environmental factors, such as the addition of nutrients or selection pressure, can shape microbial communities and partially explain the extensive differences in microbial community structures among diverse environments. PMID:26905741

Microbial Communities in Pre-Columbian Coprolites

PubMed Central

Santiago-Rodriguez, Tasha M.; Narganes-Storde, Yvonne M.; Chanlatte, Luis; Crespo-Torres, Edwin; Toranzos, Gary A.; Jimenez-Flores, Rafael; Hamrick, Alice; Cano, Raul J.

2013-01-01

The study of coprolites from earlier cultures represents a great opportunity to study an “unaltered” composition of the intestinal microbiota. To test this, pre-Columbian coprolites from two cultures, the Huecoid and Saladoid, were evaluated for the presence of DNA, proteins and lipids by cytochemical staining, human and/or dog-specific Bacteroides spp. by PCR, as well as bacteria, fungi and archaea using Terminal Restriction Fragment analyses. DNA, proteins and lipids, and human-specific Bacteroides DNA were detected in all coprolites. Multidimensional scaling analyses resulted in spatial arrangements of microbial profiles by culture, further supported by cluster analysis and ANOSIM. Differences between the microbial communities were positively correlated with culture, and SIMPER analysis indicated 68.8% dissimilarity between the Huecoid and Saladoid. Proteobacteria, Bacteroidetes and methanogens were found in all coprolite samples. Propionebacteria, Shewanella and lactic acid bacteria dominated in the Huecoid samples, while Acidobacteria, and peptococci were dominant in Saladoid samples. Yeasts, including Candida albicans and Crypotococcus spp. were found in all samples. Basidiomycetes were the most notable fungi in Huecoid samples while Ascomycetes predominated in Saladoid samples, suggesting differences in dietary habits. Our study provides an approach for the study of the microbial communities of coprolite samples from various cultures. PMID:23755194

Degradation of paracetamol by pure bacterial cultures and their microbial consortium.

PubMed

Zhang, Lili; Hu, Jun; Zhu, Runye; Zhou, Qingwei; Chen, Jianmeng

2013-04-01

Three bacterial strains utilizing paracetamol as the sole carbon, nitrogen, and energy source were isolated from a paracetamol-degrading aerobic aggregate, and assigned to species of the genera Stenotrophomonas and Pseudomonas. The Stenotrophomonas species have not included any known paracetamol degraders until now. In batch cultures, the organisms f1, f2, and fg-2 could perform complete degradation of paracetamol at concentrations of 400, 2,500, and 2,000 mg/L or below, respectively. A combination of three microbial strains resulted in significantly improved degradation and mineralization of paracetamol. The co-culture was able to use paracetamol up to concentrations of 4,000 mg/L, and mineralized 87.1 % of the added paracetamol at the initial of 2,000 mg/L. Two key metabolites of the biodegradation pathway of paracetamol, 4-aminophenol, and hydroquinone were detected. Paracetamol was degraded predominantly via 4-aminophenol to hydroquinone with subsequent ring fission, suggesting new pathways for paracetamol-degrading bacteria. The degradation of paracetamol could thus be performed by the single isolates, but is stimulated by a synergistic interaction of the three-member consortium, suggesting a possible complementary interaction among the various isolates. The exact roles of each of the strains in the consortium need to be further elucidated.

Microbial network of the carbonate precipitation process induced by microbial consortia and the potential application to crack healing in concrete.

PubMed

Zhang, Jiaguang; Zhou, Aijuan; Liu, Yuanzhen; Zhao, Bowei; Luan, Yunbo; Wang, Sufang; Yue, Xiuping; Li, Zhu

2017-11-06

Current studies have employed various pure-cultures for improving concrete durability based on microbially induced carbonate precipitation (MICP). However, there have been very few reports concerned with microbial consortia, which could perform more complex tasks and be more robust in their resistance to environmental fluctuations. In this study, we constructed three microbial consortia that are capable of MICP under aerobic (AE), anaerobic (AN) and facultative anaerobic (FA) conditions. The results showed that AE consortia showed more positive effects on inorganic carbon conversion than AN and FA consortia. Pyrosequencing analysis showed that clear distinctions appeared in the community structure between different microbial consortia systems. Further investigation on microbial community networks revealed that the species in the three microbial consortia built thorough energetic and metabolic interaction networks regarding MICP, nitrate-reduction, bacterial endospores and fermentation communities. Crack-healing experiments showed that the selected cracks of the three consortia-based concrete specimens were almost completely healed in 28 days, which was consistent with the studies using pure cultures. Although the economic advantage might not be clear yet, this study highlights the potential implementation of microbial consortia on crack healing in concrete.

The dominant microbial community associated with fermentation of Obushera (sorghum and millet beverages) determined by culture-dependent and culture-independent methods.

PubMed

Mukisa, Ivan M; Porcellato, Davide; Byaruhanga, Yusuf B; Muyanja, Charles M B K; Rudi, Knut; Langsrud, Thor; Narvhus, Judith A

2012-11-01

Obushera includes four fermented cereal beverages from Uganda namely: Obutoko, Enturire, Ekitiribita and Obuteire, whose microbial diversity has not hitherto been fully investigated. Knowledge of the microbial diversity and dynamics in these products is crucial for understanding their safety and development of appropriate starter cultures for controlled industrial processing. Culture-dependent and culture-independent techniques including denaturating gradient gel electrophoresis (DGGE) and mixed DNA sequencing of polymerase chain reaction (PCR) amplified ribosomal RNA genes were used to study the bacteria and yeast diversity of Obushera. The pH dropped from 6.0-4.6 to 3.5-4.0 within 1-2 days for Obutoko, Enturire and Obuteire whereas that of Ekitiribita decreased to 4.4 after 4 days. Counts of lactic acid bacteria (LAB) increased from 5.0 to 11.0 log cfug(-1) and yeasts increased from 3.4 to 7.1 log cfug(-1) while coliform counts decreased from 2.0 to <1 log cfug(-1) during four days of fermentation. LAB and yeast isolates were identified by rRNA gene sequence analysis. LAB isolates included: Enterococcus spp., Lactobacillus (Lb.) plantarum, Lb. fermentum, Lb. delbrueckii, Lactococcus lactis, Leuconostoc lactis, Streptococcus (S.) infantarius subsp. infantarius, Pediococcus pentosaceus and Weisella (W.) confusa. DGGE indicated predominance of S. gallolyticus, S. infantarius subsp. infantarius, Lb. fermentum, Lb. delbrueckii, W. confusa, Lb. reuteri, Fructobacillus spp., L. lactis and L. lactis. Yeast isolates included Clavispora lusitaniae, Cyberlindnera fabianii, Issatchenkia orientalis and Saccharomyces cerevisiae. DGGE indicated predominance of S. cerevisiae in Obutoko, Enturire and Obuteire and also detected Pichia spp. and I. orientalis in Obutoko. Obushera produced in the laboratory was initially dominated by Enterobacteriaceae and later by Lactococcus spp. Enterobacteriaceae and Bacillus spp. were also detected in Ekitiribita. Development of starters for

Integrated ‘omics analysis for studying the microbial community response to a pH perturbation of a cellulose-degrading bioreactor culture

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

Boaro, Amy A.; Kim, Young-Mo; Konopka, Allan

2014-12-01

Integrated ‘omics have been used on pure cultures and co-cultures, yet they have not been applied to complex microbial communities to examine questions of perturbation response. In this study, we used integrated ‘omics to measure the perturbation response of a cellulose-degrading bioreactor community fed with microcrystalline cellulose (Avicel). We predicted that a pH decrease by addition of a pulse of acid would reduce microbial community diversity and temporarily reduce reactor function such as cellulose degradation. However, 16S rDNA pyrosequencing results revealed increased alpha diversity in the microbial community after the perturbation, and a persistence of the dominant community members overmore » the duration of the experiment. Proteomics results showed a decrease in activity of proteins associated with Fibrobacter succinogenes two days after the perturbation followed by increased protein abundances six days after the perturbation. The decrease in cellulolytic activity suggested by the proteomics was confirmed by the accumulation of Avicel in the reactor. Metabolomics showed a pattern similar to that of the proteome, with amino acid production decreasing two days after the perturbation and increasing after six days. This study demonstrated that community ‘omics data provides valuable information about the interactions and function of anaerobic cellulolytic community members after a perturbation.« less

Evaluating standard operating procedures to mitigate off-flavor from Atlantic salmon Salmo salar cultured in a semi-commercial scale recirculating aquaculture system

USDA-ARS?s Scientific Manuscript database

Fish cultured within water recirculating aquaculture systems (RAS) can acquire “earthy” or “musty” off-flavors due to bioaccumulation of the compounds geosmin and 2-methylisoborneol (MIB), respectively, which are produced by certain bacterial species present in RAS biosolids and microbial biofilms. ...

Genome Sequence of Lactobacillus sakei subsp. sakei LS25, a Commercial Starter Culture Strain for Fermented Sausage.

PubMed

McLeod, Anette; Brede, Dag Anders; Rud, Ida; Axelsson, Lars

2013-07-11

Lactobacillus sakei is a lactic acid bacterium associated primarily with fermented meat and fish. Here, we present the draft genome sequence of L. sakei subsp. sakei strain LS25, a commercial starter culture strain for fermented sausage.

Characterizing The Microbial Lability And Isotopic (14C, 13C) Signatures Of Marine Organic Matter With A Novel Culture Vessel System

NASA Astrophysics Data System (ADS)

Beaupre, S. R.; Mahmoudi, N.; Pearson, A.

2016-02-01

The rate at which non-living organic matter is respired in the ocean is an unconstrained and important property of the marine carbon cycle. Studies of inherent mineralization rates are complicated by the fact that marine organic matter is a mixture of compounds that vary in reactivity and concentration. While natural radiocarbon ages (14C, half-life = 5730 yr) have served as proxies for lability, they have not been used extensively to characterize that fraction of marine organic matter that is biologically accessible. To address this problem, we developed a novel batch culture system to monitor the time-dependent production rates and isotopic signatures of CO2 released during microbial degradation of natural organic matter. The system simulated a nepheloid layer by maintaining a slurry of decarbonated sediment and minimal media (M9) in a custom 2-liter culture vessel. The natural microbial community was allowed to develop within the sediment, and respired CO2 was continuously sparged from the medium with helium and oxygen, quantified in real time with an infrared gas analyzer, and isolated as a series of contiguous fractions for subsequent isotopic (∆14C, d13C) characterization. Control experiments indicated the accumulation of just 4.5 mg of background carbon per hour of continuous gas flow, which constituted ≤ 10 % of the respired carbon mass in each fraction. Since ∆14C values are conserved during molecular transformations, this low-blank system enables the detection of subtle shifts in the "age" of organic matter respired during the course of a culture experiment. Analyses of sediments from Falmouth, MA revealed both a variable CO2 production rate and an increase in post-bomb ∆14C values during a 10-day incubation. This suggests that the microbial lability of organic matter at this site decreased non-linearly with apparent 14C age, and that the least labile fraction observed was not more than 50 years old. These results underscore the complex

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

PubMed

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

2015-05-01

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

Comparison of two commercially available rapid detection methods and a conventional culture method to detect naturally occurring salmonellae on broiler carcasses

USDA-ARS?s Scientific Manuscript database

Many different screening devices and sampling methods have been used to detect the presence of naturally occurring Salmonella on commercially processed broiler carcasses. The objective of this study was to compare two commercial screening systems (BAX® and Roka®) to a standard cultural procedure use...

Biodegradation of the sulfonamide antibiotic sulfamethoxazole by sulfamethoxazole acclimatized cultures in microbial fuel cells.

PubMed

Miran, Waheed; Jang, Jiseon; Nawaz, Mohsin; Shahzad, Asif; Lee, Dae Sung

2018-06-15

Microbial fuel cells (MFCs) are known for their ability to enhance the removal rate of toxins while generating power. This research presents a performance assessment of MFCs for power generation and sulfamethoxazole (SMX) degradation using SMX acclimatized cultures. Experiments were performed in MFC batch mode using different SMX concentrations in synthetic wastewater. The experimental results showed that voltage generation was >400mV up to the SMX concentration of 0.20mM (at 400Ω external resistance). Control experiments supported the inference that biodegradation was the main process for SMX removal compared to sorption by SMX acclimatized cultures and that the process results in efficient removal of SMX in MFC mode. The specific removal rates of SMX in MFC with SMX acclimatized sludge were 0.67, 1.37, 3.43, 7.32, and 13.36μm/h at initial SMX concentrations of 0.04, 0.08, 0.20, 0.39, and 0.79mM, respectively. Moreover, the MFC was able to remove >90% of the TOC from the wastewater up to SMX concentrations of 0.08mM. However, this TOC removal produces negative effects at higher SMX concentrations due to toxic intermediates. Microbial community analysis revealed large changes in bacterial communities at the phylum, class, and genus levels after SMX acclimatization and MFC operation. Thauera, a well-known aromatic-degrading bacteria, was the most dominant genus present in post-acclimatized conditions. In summary, this study showed that acclimatized sludge can play an important role in the biodegradation of SMX in MFCs. Copyright © 2018 Elsevier B.V. All rights reserved.

Systems Biology of Microbial Exopolysaccharides Production.

PubMed

Ates, Ozlem

2015-01-01

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

Systems Biology of Microbial Exopolysaccharides Production

PubMed Central

Ates, Ozlem

2015-01-01

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

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.

Molecular ecology of hydrothermal vent microbial communities.

PubMed

Jeanthon, C

2000-02-01

The study of the structure and diversity of hydrothermal vent microbial communities has long been restricted to the morphological description of microorganisms and the use of enrichment culture-based techniques. Until recently the identification of the culturable fraction required the isolation of pure cultures followed by testing for multiple physiological and biochemical traits. However, peculiar inhabitants of the hydrothermal ecosystem such as the invertebrate endosymbionts and the dense microbial mat filaments have eluded laboratory cultivation. Substantial progress has been achieved in recent years in techniques for the identification of microorganisms in natural environments. Application of molecular approaches has revealed the existence of unique and previously unrecognized microorganisms. These have provided fresh insight into the ecology, diversity and evolution of mesophilic and thermophilic microbial communities from the deep-sea hydrothermal ecosystem. This review reports the main discoveries made through the introduction of these powerful techniques in the study of deep-sea hydrothermal vent microbiology.

Microbial oxidation of pyrrhotites in coal chars

USGS Publications Warehouse

Miller, K.W.; Risatti, J.B.

1988-01-01

The ability of Thiobacillus ferrooxidans to oxidize pyrrhotite minerals occurring in coal chars was investigated, to evaluate the feasibility of microbial char desulphurization. Bio-oxidation of pyrrhotites in chars produced by two different processes was demonstrated conclusively. Microbial removal of sulphur from a char and its parent coal proceeded at the rate of 3.5% and 12% day-1, respectively with a total of 48% and 81% removal after 27 days. The pH of shake flask cultures containing the coal dropped naturally to a final value of 2.2, while the pH of cultures containing the corresponding char rose and had to be lowered artificially with additional acid. Amending char cultures with elemental sulphur to increase acidity upon bio-oxidation and prevent precipitation of ferric iron was successful; however, the extent of pyrrhotite removal, as demonstated by X-ray diffraction analysis, was not improved. As yet, there is no explanation for the failure of microbial removal of pyrrhotitic sulphur to go to completion. ?? 1988.

TSCA Section 5(a)(3)(C) Determination for Microbial Commercial Activity Notice (MCAN) J-16-0011, J-16-0012, J-16-0013, J-16-0014, J-16-0015, and J-16-0016

EPA Pesticide Factsheets

This document describes EPA's Microbial Commercial Activity Notice (MCAN) review determination under amended TSCA for J-16-0011, J-16-0012, J-16-0013, J-16-0014, J-16-0015, and J-16-0016, a biofuel producing organism.

Pathogen and biological contamination management in plant tissue culture: phytopathogens, vitro pathogens, and vitro pests.

PubMed

Cassells, Alan C

2012-01-01

The ability to establish and grow plant cell, organ, and tissue cultures has been widely exploited for basic and applied research, and for the commercial production of plants (micro-propagation). Regardless of whether the application is for research or commerce, it is essential that the cultures be established in vitro free of biological contamination and be maintained as aseptic cultures during manipulation, growth, and storage. The risks from microbial contamination are spurious experimental results due to the effects of latent contaminants or losses of valuable experimental or commercial cultures. Much of the emphasis in culture contamination management historically focussed on the elimination of phytopathogens and the maintenance of cultures free from laboratory contamination by environmental bacteria, fungi (collectively referred to as "vitro pathogens", i.e. pathogens or environmental micro-organisms which cause culture losses), and micro-arthropods ("vitro pests"). Microbial contamination of plant tissue cultures is due to the high nutrient availability in the almost universally used Murashige and Skoog (Physiol Plant 15:473-497, 1962) basal medium or variants of it. In recent years, it has been shown that many plants, especially perennials, are at least locally endophytically colonized intercellularly by bacteria. The latter, and intracellular pathogenic bacteria and viruses/viroids, may pass latently into culture and be spread horizontally and vertically in cultures. Growth of some potentially cultivable endophytes may be suppressed by the high salt and sugar content of the Murashige and Skoog basal medium and suboptimal temperatures for their growth in plant tissue growth rooms. The management of contamination in tissue culture involves three stages: disease screening (syn. disease indexing) of the stock plants with disease and endophyte elimination where detected; establishment and pathogen and contaminant screening of established initial cultures

Facilitation as Attenuating of Environmental Stress among Structured Microbial Populations.

PubMed

Martins, Suzana Cláudia Silveira; Santaella, Sandra Tédde; Martins, Claudia Miranda; Martins, Rogério Parentoni

2016-01-01

There is currently an intense debate in microbial societies on whether evolution in complex communities is driven by competition or cooperation. Since Darwin, competition for scarce food resources has been considered the main ecological interaction shaping population dynamics and community structure both in vivo and in vitro. However, facilitation may be widespread across several animal and plant species. This could also be true in microbial strains growing under environmental stress. Pure and mixed strains of Serratia marcescens and Candida rugosa were grown in mineral culture media containing phenol. Growth rates were estimated as the angular coefficients computed from linearized growth curves. Fitness index was estimated as the quotient between growth rates computed for lineages grown in isolation and in mixed cultures. The growth rates were significantly higher in associated cultures than in pure cultures and fitness index was greater than 1 for both microbial species showing that the interaction between Serratia marcescens and Candida rugosa yielded more efficient phenol utilization by both lineages. This result corroborates the hypothesis that facilitation between microbial strains can increase their fitness and performance in environmental bioremediation.

Changes in Microbial Communities, Including both Uncultured and Culturable Bacteria, with Mid-Ocean Ballast-Water Exchange during a Voyage from Japan to Australia

PubMed Central

Tomaru, Akiko; Kawachi, Masanobu; Demura, Mikihide; Fukuyo, Yasuwo

2014-01-01

We assessed changes in the microbial communities in ballast water during a trans-Pacific voyage from Japan to Australia that included a mid-ocean ballast-water exchange. Uncultured (i.e., total) and culturable bacteria were counted and were characterized by using denaturing gradient gel electrophoresis (DGGE). There was a clear decrease over time in numbers of uncultured microorganisms, except for heterotrophic nanoflagellates, whereas the abundance of culturable bacteria initially decreased after the ballast-water exchange but then increased. The increase, however, was only up to 5.34% of the total number of uncultured bacteria. Cluster analysis showed that the DGGE profiles of uncultured bacteria clearly changed after the exchange. In contrast, there was no clear change in the DGGE profiles of culturable bacteria after the exchange. Multidimensional scaling analysis showed changes in microbial communities over the course of the voyage. Although indicator microbes as defined by the International Convention for the Control and Management of Ships' Ballast Water and Sediments were occasionally detected, no coliform bacteria were detected after the exchange. PMID:24817212

Microbial contamination and disinfection methods of pacifiers.

PubMed

Nelson-Filho, Paulo; Louvain, Márcia Costa; Macari, Soraia; Lucisano, Marília Pacífico; Silva, Raquel Assed Bezerra da; Queiroz, Alexandra Mussolino de; Gaton-Hernández, Patrícia; Silva, Léa Assed Bezerra da

2015-10-01

To evaluate the microbial contamination of pacifiers by Mutans Streptococci(MS) and the efficacy of different methods for their disinfection. Twenty-eight children were assigned to a 4-stage changeover system with a 1-week interval. In each stage, children received a new pacifier and the parents were instructed to maintain their normal habits for 1 week. After this time, the pacifiers were subjected to the following 4 disinfection methods: spraying with 0.12% chlorhexidine solution, Brushtox or sterile tap water, and immersion in boiling tap water for 15 minutes. Microbiological culture for MS and Scanning Electron Microscopy (SEM) were performed. The results were analyzed statistically by Friedman's non-parametric test (a=0.05). The 0.12% chlorhexidine spray was statistically similar to the boiling water (p>0.05) and more effective than the Brushtox spray and control (p<0.05). The analysis of SEM showed the formation of a cariogenic biofilm in all groups with positive culture. Pacifiers become contaminated by MS after their use by children and should be disinfected routinely. Spraying with a 0.12% chlorhexidine solution and immersion in boiling water promoted better disinfection of the pacifiers compared with a commercial antiseptic toothbrush cleanser (Brushtox).

Enhanced polyhydroxyalkanoate production by mixed microbial culture with extended cultivation strategy.

PubMed

Huang, Long; Chen, Zhiqiang; Wen, Qinxue; Lee, Duu-Jong

2017-10-01

Low biomass output is a crucial reason for low polyhydroxyalkanoate (PHA) production in mixed microbial cultures (MMCs) PHA process. In this research, an extended cultivation strategy was proposed to rapidly expand the biomass yield of PHA accumulating MMCs and conserve the PHA accumulating ability simultaneously. High PHA content of the cultivated MMCs of 71.4% and 66.7% (higher than 62.1% of the seed biomass) in batch assays and biomass magnification of 43 and 52 were obtained after 10days of extended cultivation with and without sludge discharge, respectively. By embedding the extended cultivation process into the production process, a highly competitive PHA production performance in terms of overall PHA storage yield (0.49g CODPHA/gCODVFA) and volumetric productivity (1.21gPHA/L/d with final cell density of 17.22g/L) was achieved. The proposed PHA production process based on the extended cultivation can be a promising choice in industrial scale practice. Copyright © 2017 Elsevier Ltd. All rights reserved.

Microbial populations in contaminant plumes

USGS Publications Warehouse

Haack, S.K.; Bekins, B.A.

2000-01-01

Efficient biodegradation of subsurface contaminants requires two elements: (1) microbial populations with the necessary degradative capabilities, and (2) favorable subsurface geochemical and hydrological conditions. Practical constraints on experimental design and interpretation in both the hydrogeological and microbiological sciences have resulted in limited knowledge of the interaction between hydrogeological and microbiological features of subsurface environments. These practical constraints include: (1) inconsistencies between the scales of investigation in the hydrogeological and microbiological sciences, and (2) practical limitations on the ability to accurately define microbial populations in environmental samples. However, advances in application of small-scale sampling methods and interdisciplinary approaches to site investigations are beginning to significantly improve understanding of hydrogeological and microbiological interactions. Likewise, culture-based and molecular analyses of microbial populations in subsurface contaminant plumes have revealed significant adaptation of microbial populations to plume environmental conditions. Results of recent studies suggest that variability in subsurface geochemical and hydrological conditions significantly influences subsurface microbial-community structure. Combined investigations of site conditions and microbial-community structure provide the knowledge needed to understand interactions between subsurface microbial populations, plume geochemistry, and contaminant biodegradation.

Implementing high-temperature short-time media treatment in commercial-scale cell culture manufacturing processes.

PubMed

Pohlscheidt, Michael; Charaniya, Salim; Kulenovic, Fikret; Corrales, Mahalia; Shiratori, Masaru; Bourret, Justin; Meier, Steven; Fallon, Eric; Kiss, Robert

2014-04-01

The production of therapeutic proteins by mammalian cell culture is complex and sets high requirements for process, facility, and equipment design, as well as rigorous regulatory and quality standards. One particular point of concern and significant risk to supply chain is the susceptibility to contamination such as bacteria, fungi, mycoplasma, and viruses. Several technologies have been developed to create barriers for these agents to enter the process, e.g. filtration, UV inactivation, and temperature inactivation. However, if not implemented during development of the manufacturing process, these types of process changes can have significant impact on process performance if not managed appropriately. This article describes the implementation of the high-temperature short-time (HTST) treatment of cell culture media as an additional safety barrier against adventitious agents during the transfer of a large-scale commercial cell culture manufacturing process. The necessary steps and experiments, as well as subsequent results during qualification runs and routine manufacturing, are shown.

Radioisotopic, Culture-Based, and Oligonucleotide Microchip Analyses of Thermophilic Microbial Communities in a Continental High-Temperature Petroleum Reservoir†

PubMed Central

Bonch-Osmolovskaya, Elizaveta A.; Miroshnichenko, Margarita L.; Lebedinsky, Alexander V.; Chernyh, Nikolai A.; Nazina, Tamara N.; Ivoilov, Valery S.; Belyaev, Sergey S.; Boulygina, Eugenia S.; Lysov, Yury P.; Perov, Alexander N.; Mirzabekov , Andrei D.; Hippe, Hans; Stackebrandt, Erko; L'Haridon, Stéphane; Jeanthon, Christian

2003-01-01

Activity measurements by radioisotopic methods and cultural and molecular approaches were used in parallel to investigate the microbial biodiversity and its physiological potential in formation waters of the Samotlor high-temperature oil reservoir (Western Siberia, Russia). Sulfate reduction with rates not exceeding 20 nmol of H2S liter−1 day−1 occurred at 60 and 80°C. In upper horizons (AB, A, and B), methanogenesis (lithotrophic and/or acetoclastic) was detected only in wells in which sulfate reduction did not occur. In some of the wells from deeper (J) horizons, high-temperature sulfate reduction and methanogenesis occurred simultaneously, the rate of lithotrophic methanogenesis exceeding 80 nmol of CH4 liter−1 day−1. Enrichment cultures indicated the presence of diverse physiological groups representing aerobic and anaerobic thermophiles and hyperthermophiles; fermentative organotrophs were predominant. Phylogenetic analyses of 15 isolates identified representatives of the genera Thermotoga, Thermoanaerobacter, Geobacillus, Petrotoga, Thermosipho, and Thermococcus, the latter four being represented by new species. Except for Thermosipho, the isolates were members of genera recovered earlier from similar habitats. DNA obtained from three samples was hybridized with a set of oligonucleotide probes targeting selected microbial groups encompassing key genera of thermophilic bacteria and archaea. Oligonucleotide microchip analyses confirmed the cultural data but also revealed the presence of several groups of microorganisms that escaped cultivation, among them representatives of the Aquificales/Desulfurobacterium-Thermovibrio cluster and of the genera Desulfurococcus and Thermus, up to now unknown in this habitat. The unexpected presence of these organisms suggests that their distribution may be much wider than suspected. PMID:14532074

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.

Microbial flora analysis for the degradation of beta-cypermethrin.

PubMed

Qi, Zhang; Wei, Zhang

2017-03-01

In the Xinjiang region of Eurasia, sustained long-term and continuous cropping of cotton over a wide expanse of land is practiced, which requires application of high levels of pyrethroid and other classes of pesticides-resulting in high levels of pesticide residues in the soil. In this study, soil samples were collected from areas of long-term continuous cotton crops with the aim of obtaining microbial resources applicable for remediation of pyrethroid pesticide contamination suitable for the soil type and climate of that area. Soil samples were first used to culture microbial flora capable of degrading beta-cypermethrin using an enrichment culture method. Structural changes and ultimate microbial floral composition during enrichment were analyzed by high-throughput sequencing. Four strains capable of degrading beta-cypermethrin were isolated and preliminarily classified. Finally, comparative rates and speeds of degradation of beta-cypermethrin between relevant microbial flora and single strains were determined. After continuous subculture for 3 weeks, soil sample microbial flora formed a new type of microbial flora by rapid succession, which showed stable growth by utilizing beta-cypermethrin as the sole carbon source (GXzq). This microbial flora mainly consisted of Pseudomonas, Hyphomicrobium, Dokdonella, and Methyloversatilis. Analysis of the microbial flora also permitted separation of four additional strains; i.e., GXZQ4, GXZQ6, GXZQ7, and GXZQ13 that, respectively, belonged to Streptomyces, Enterobacter, Streptomyces, and Pseudomonas. Under culture conditions of 37 °C and 180 rpm, the degradation rate of beta-cypermethrin by GXzq was as high as 89.84% within 96 h, which exceeded that achieved by the single strains GXZQ4, GXZQ6, GXZQ7, and GXZQ13 and their derived microbial flora GXh.

Microbial diversity in methanogenic hydrocarbon-degrading enrichment cultures isolated from a water-flooded oil reservoir (Dagang oil field, China)

NASA Astrophysics Data System (ADS)

Jiménez, Núria; Cai, Minmin; Straaten, Nontje; Yao, Jun; Richnow, Hans H.; Krüger, Martin

2015-04-01

Microbial transformation of oil to methane is one of the main degradation processes taking place in oil reservoirs, and it has important consequences as it negatively affects the quality and economic value of the oil. Nevertheless, methane could constitute a recovery method of carbon from exhausted reservoirs. Previous studies combining geochemical and isotopic analysis with molecular methods showed evidence for in situ methanogenic oil degradation in the Dagang oil field, China (Jiménez et al., 2012). However, the main key microbial players and the underlying mechanisms are still relatively unknown. In order to better characterize these processes and identify the main microorganisms involved, laboratory biodegradation experiments under methanogenic conditions were performed. Microcosms were inoculated with production and injection waters from the reservoir, and oil or 13C-labelled single hydrocarbons (e.g. n-hexadecane or 2-methylnaphthalene) were added as sole substrates. Indigenous microbiota were able to extensively degrade oil within months, depleting most of the n-alkanes in 200 days, and producing methane at a rate of 76 ± 6 µmol day-1 g-1 oil added. They could also produce heavy methane from 13C-labeled 2-methylnaphthalene, suggesting that further methanogenesis may occur from the aromatic and polyaromatic fractions of Dagang reservoir fluids. Microbial communities from oil and 2-methyl-naphthalene enrichment cultures were slightly different. Although, in both cases Deltaproteobacteria, mainly belonging to Syntrophobacterales (e.g. Syntrophobacter, Smithella or Syntrophus) and Clostridia, mostly Clostridiales, were among the most represented taxa, Gammaproteobacteria could be only identified in oil-degrading cultures. The proportion of Chloroflexi, exclusively belonging to Anaerolineales (e.g. Leptolinea, Bellilinea) was considerably higher in 2-methyl-naphthalene degrading cultures. Archaeal communities consisted almost exclusively of representatives of

Effects of cryopreservation on microbial-contaminated cord blood.

PubMed

Clark, Pamela; Trickett, Annette; Saffo, Sandra; Stark, Damien

2014-03-01

Cord blood units (CBUs) are associated with significant risk of exposure to microbial contamination during collection and processing; however, the survival of bacteria within a CBU is poorly understood. This study aimed to determine whether contaminating organisms in CBU survive the cryopreservation, frozen storage, and subsequent thawing conditions before infusion. A total of 134 CBUs rejected from banking due to known contamination were thawed and rescreened using blood culture bottles (BacT/ALERT, bioMérieux). An additional 61 fresh CBUs were deliberately spiked with a range of microbial organisms and evaluated both before freeze and after thaw. Microbial contaminants were detected after thaw in 63% of stored contaminated CBUs and 85% of spiked CBUs. Postthaw organism detection in spiked cord blood (CB) was higher in adult culture bottles (80%) than pediatric culture bottles (61%). Twenty percent of spiked organisms, particularly Bacillus subtilis, Escherichia coli, Clostridium sporogenes, and Propionibacterium acnes, were not detected in prefreeze samples but were detectable after thaw. This study demonstrates that the majority of contaminating organisms isolated in a prefreeze sample of CB have the ability to survive cryopreservation, frozen storage, and thawing. Further, CBUs reported as microbial free may contain microbial contamination, which could result in transplantation of contaminated CB and be potentially deleterious to a patient. © 2013 The Sydney Children's Hospital Network. Transfusion © 2013 American Association of Blood Banks.

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.

Microalgae-microbial fuel cell: A mini review.

PubMed

Lee, Duu-Jong; Chang, Jo-Shu; Lai, Juin-Yih

2015-12-01

Microalgae-microbial fuel cells (mMFCs) are a device that can convert solar energy to electrical energy via biological pathways. This mini-review lists new research and development works on microalgae processes, microbial fuel cell (MFC) processes, and their combined version, mMFC. The substantial improvement and technological advancement are highlighted, with a discussion on the challenges and prospects for possible commercialization of mMFC technologies. Copyright © 2015 Elsevier Ltd. All rights reserved.

Biotechnological potential of microbial consortia and future perspectives.

PubMed

Bhatia, Shashi Kant; Bhatia, Ravi Kant; Choi, Yong-Keun; Kan, Eunsung; Kim, Yun-Gon; Yang, Yung-Hun

2018-05-15

Design of a microbial consortium is a newly emerging field that enables researchers to extend the frontiers of biotechnology from a pure culture to mixed cultures. A microbial consortium enables microbes to use a broad range of carbon sources. It provides microbes with robustness in response to environmental stress factors. Microbes in a consortium can perform complex functions that are impossible for a single organism. With advancement of technology, it is now possible to understand microbial interaction mechanism and construct consortia. Microbial consortia can be classified in terms of their construction, modes of interaction, and functions. Here we discuss different trends in the study of microbial functions and interactions, including single-cell genomics (SCG), microfluidics, fluorescent imaging, and membrane separation. Community profile studies using polymerase chain-reaction denaturing gradient gel electrophoresis (PCR-DGGE), amplified ribosomal DNA restriction analysis (ARDRA), and terminal restriction fragment-length polymorphism (T-RFLP) are also reviewed. We also provide a few examples of their possible applications in areas of biopolymers, bioenergy, biochemicals, and bioremediation.

Single-cell transcriptomics for microbial eukaryotes.

PubMed

Kolisko, Martin; Boscaro, Vittorio; Burki, Fabien; Lynn, Denis H; Keeling, Patrick J

2014-11-17

One of the greatest hindrances to a comprehensive understanding of microbial genomics, cell biology, ecology, and evolution is that most microbial life is not in culture. Solutions to this problem have mainly focused on whole-community surveys like metagenomics, but these analyses inevitably loose information and present particular challenges for eukaryotes, which are relatively rare and possess large, gene-sparse genomes. Single-cell analyses present an alternative solution that allows for specific species to be targeted, while retaining information on cellular identity, morphology, and partitioning of activities within microbial communities. Single-cell transcriptomics, pioneered in medical research, offers particular potential advantages for uncultivated eukaryotes, but the efficiency and biases have not been tested. Here we describe a simple and reproducible method for single-cell transcriptomics using manually isolated cells from five model ciliate species; we examine impacts of amplification bias and contamination, and compare the efficacy of gene discovery to traditional culture-based transcriptomics. Gene discovery using single-cell transcriptomes was found to be comparable to mass-culture methods, suggesting single-cell transcriptomics is an efficient entry point into genomic data from the vast majority of eukaryotic biodiversity. Copyright © 2014 Elsevier Ltd. All rights reserved.

Homogeneous Matrix Deposition on Dried Agar for MALDI Imaging Mass Spectrometry of Microbial Cultures

NASA Astrophysics Data System (ADS)

Hoffmann, Thomas; Dorrestein, Pieter C.

2015-11-01

Matrix deposition on agar-based microbial colonies for MALDI imaging mass spectrometry is often complicated by the complex media on which microbes are grown. This Application Note demonstrates how consecutive short spray pulses of a matrix solution can form an evenly closed matrix layer on dried agar. Compared with sieving dry matrix onto wet agar, this method supports analyte cocrystallization, which results in significantly more signals, higher signal-to-noise ratios, and improved ionization efficiency. The even matrix layer improves spot-to-spot precision of measured m/z values when using TOF mass spectrometers. With this technique, we established reproducible imaging mass spectrometry of myxobacterial cultures on nutrient-rich cultivation media, which was not possible with the sieving technique.

Fermentation by the human large intestine microbial community in an in vitro semicontinuous culture system.

PubMed Central

Miller, T L; Wolin, M J

1981-01-01

A semicontinuous culture of the microbial community of the human large intestine that was maintained over 81 days is described. The initial inoculum was feces, and about 200 ml of nutrient suspension was fed to 500 ml of fermentor contents once or twice daily. The nutrient suspension contained comminuted fibrous food, sodium deoxycholate, urea, acid-hydrolyzed casein, vitamins, and salts. The fermentation was monitored, and the major products were acetate, propionate, butyrate, methane, hydrogen, and carbon dioxide. The concentration of anaerobic bacteria was 2 X 10(9) per ml of culture contents and was 100 times that of fecal coliforms. When the nutrient suspension contained lettuce, celery, carrots, and unsweetened applesauce, the predominant nonsporeforming anaerobes isolated were Bacteroides species. When carrots and applesauce were omitted, the predominant nonsporeforming isolates were Fusobacterium species. On both diets, clostridia were isolated that resembled Clostridium clostridiiforme. The fermentation and bacteriological analyses indicated that the in vitro ecosystem appears to be a reasonable facsimile of the large intestine ecosystem. Images PMID:7027952

Facilitation as Attenuating of Environmental Stress among Structured Microbial Populations

PubMed Central

Santaella, Sandra Tédde; Martins, Claudia Miranda; Martins, Rogério Parentoni

2016-01-01

There is currently an intense debate in microbial societies on whether evolution in complex communities is driven by competition or cooperation. Since Darwin, competition for scarce food resources has been considered the main ecological interaction shaping population dynamics and community structure both in vivo and in vitro. However, facilitation may be widespread across several animal and plant species. This could also be true in microbial strains growing under environmental stress. Pure and mixed strains of Serratia marcescens and Candida rugosa were grown in mineral culture media containing phenol. Growth rates were estimated as the angular coefficients computed from linearized growth curves. Fitness index was estimated as the quotient between growth rates computed for lineages grown in isolation and in mixed cultures. The growth rates were significantly higher in associated cultures than in pure cultures and fitness index was greater than 1 for both microbial species showing that the interaction between Serratia marcescens and Candida rugosa yielded more efficient phenol utilization by both lineages. This result corroborates the hypothesis that facilitation between microbial strains can increase their fitness and performance in environmental bioremediation. PMID:26904719

Breeding Strategy To Generate Robust Yeast Starter Cultures for Cocoa Pulp Fermentations

PubMed Central

Meersman, Esther; Steensels, Jan; Paulus, Tinneke; Struyf, Nore; Saels, Veerle; Mathawan, Melissa; Koffi, Jean; Vrancken, Gino

2015-01-01

Cocoa pulp fermentation is a spontaneous process during which the natural microbiota present at cocoa farms is allowed to ferment the pulp surrounding cocoa beans. Because such spontaneous fermentations are inconsistent and contribute to product variability, there is growing interest in a microbial starter culture that could be used to inoculate cocoa pulp fermentations. Previous studies have revealed that many different fungi are recovered from different batches of spontaneous cocoa pulp fermentations, whereas the variation in the prokaryotic microbiome is much more limited. In this study, therefore, we aimed to develop a suitable yeast starter culture that is able to outcompete wild contaminants and consistently produce high-quality chocolate. Starting from specifically selected Saccharomyces cerevisiae strains, we developed robust hybrids with characteristics that allow them to efficiently ferment cocoa pulp, including improved temperature tolerance and fermentation capacity. We conducted several laboratory and field trials to show that these new hybrids often outperform their parental strains and are able to dominate spontaneous pilot scale fermentations, which results in much more consistent microbial profiles. Moreover, analysis of the resulting chocolate showed that some of the cocoa batches that were fermented with specific starter cultures yielded superior chocolate. Taken together, these results describe the development of robust yeast starter cultures for cocoa pulp fermentations that can contribute to improving the consistency and quality of commercial chocolate production. PMID:26150457

Novel and Unexpected Microbial Diversity in Acid Mine Drainage in Svalbard (78° N), Revealed by Culture-Independent Approaches

PubMed Central

García-Moyano, Antonio; Austnes, Andreas Erling; Lanzén, Anders; González-Toril, Elena; Aguilera, Ángeles; Øvreås, Lise

2015-01-01

Svalbard, situated in the high Arctic, is an important past and present coal mining area. Dozens of abandoned waste rock piles can be found in the proximity of Longyearbyen. This environment offers a unique opportunity for studying the biological control over the weathering of sulphide rocks at low temperatures. Although the extension and impact of acid mine drainage (AMD) in this area is known, the native microbial communities involved in this process are still scarcely studied and uncharacterized. Several abandoned mining areas were explored in the search for active AMD and a culture-independent approach was applied with samples from two different runoffs for the identification and quantification of the native microbial communities. The results obtained revealed two distinct microbial communities. One of the runoffs was more extreme with regards to pH and higher concentration of soluble iron and heavy metals. These conditions favored the development of algal-dominated microbial mats. Typical AMD microorganisms related to known iron-oxidizing bacteria (Acidithiobacillus ferrivorans, Acidobacteria and Actinobacteria) dominated the bacterial community although some unexpected populations related to Chloroflexi were also significant. No microbial mats were found in the second area. The geochemistry here showed less extreme drainage, most likely in direct contact with the ore under the waste pile. Large deposits of secondary minerals were found and the presence of iron stalks was revealed by microscopy analysis. Although typical AMD microorganisms were also detected here, the microbial community was dominated by other populations, some of them new to this type of system (Saccharibacteria, Gallionellaceae). These were absent or lowered in numbers the farther from the spring source and they could represent native populations involved in the oxidation of sulphide rocks within the waste rock pile. This environment appears thus as a highly interesting field of potential

Microbial deterioration of vacuum-packaged chilled beef cuts and techniques for microbiota detection and characterization: a review.

PubMed

Hernández-Macedo, Maria Lucila; Barancelli, Giovana Verginia; Contreras-Castillo, Carmen Josefina

2011-01-01

Gas production from microbial deterioration in vacuum-packs of chilled meat leads to pack distension, which is commonly referred as blown pack. This phenomenon is attributed to some psychrophilic and psychrotrophic Clostridium species, as well as Enterobacteria. The ability of these microorganisms to grow at refrigeration temperatures makes the control by the meat industry a challenge. This type of deterioration has been reported in many countries including some plants in the Midwestern and Southeastern regions of Brazil. In addition to causing economic losses, spoilage negatively impacts the commercial product brand, thereby impairing the meat industry. In the case of strict anaerobes species they are difficult to grow and isolate using culture methods in conventional microbiology laboratories. Furthermore, conventional culture methods are sometimes not capable of distinguishing species or genera. DNA-based molecular methods are alternative strategies for detecting viable and non-cultivable microorganisms and strict anaerobic microorganisms that are difficult to cultivate. Here, we review the microorganisms and mechanisms involved in the deterioration of vacuum-packaged chilled meat and address the use of molecular methods for detecting specific strict anaerobic microorganisms and microbial communities in meat samples.

Detection of microbial contamination during human islet isolation.

PubMed

Kin, Tatsuya; Rosichuk, Shawn; Shapiro, A M James; Lakey, Jonathan R T

2007-01-01

Current good manufacturing practice (cGMP) islet processing facilities provide an ultraclean environment for the safe production of clinical grade islets for transplantation into immunosuppressed diabetic recipients. The objective of this study was to monitor the rate of microbial contamination in islet products after implementation of good manufacturing practice conditions. Fluid samples for microbial contamination were collected at the following steps: from the pancreas transport solution upon arrival of the organ (n=157), after surface decontamination of the pancreas with antiseptic agents (n=89), from islet supernatant at the end of the isolation (n=104), and from islet supernatant as a final transplantable product after culture (n=53). Bacterial, fungal, and mycoplasma cultures were conducted for 2, 2, and 3 weeks, respectively. Microbial contamination was detected in 31% of transport solution. The contamination was not associated with the presence of the duodenum during the preservation, cold ischemia time, or procurement team (local vs. distant). Surface decontamination of the pancreas resulted in clearance of 92% of the microbial contamination. Six preparations at the end of the isolation revealed microbial growth. All were de novo contamination during the processing. Fifty-three preparations that met our release criteria in terms of product sterility were transplanted into type 1 diabetic patients. In two instances, positive culture of the islet preparation was reported after transplantation had occurred. No patient showed any clinical findings suggestive of infection or any radiological abnormalities suggestive of abscess; a single dose of antibiotic coverage was given routinely to recipients prior to islet infusion. Although transport solution carries a high risk of microbial contamination, most contaminants become undetectable during islet processing. Microbial contamination in final products is rare, but de novo contamination still occurs during

Detection of Microbial Contamination during Human Islet Isolation.

PubMed

Kin, Tatsuya; Rosichuk, Shawn; Shapiro, A M James; Lakey, Jonathan R T

2007-01-01

Current good manufacturing practice (cGMP) islet processing facilities provide an ultraclean environment for the safe production of clinical grade islets for transplantation into immunosuppressed diabetic recipients. The objective of this study was to monitor the rate of microbial contamination in islet products after implementation of good manufacturing practice conditions. Fluid samples for microbial contamination were collected at the following steps: from the pancreas transport solution upon arrival of the organ (n = 157), after surface decontamination of the pancreas with antiseptic agents (n = 89), from islet supernatant at the end of the isolation (n = 104), and from islet supernatant as a final transplantable product after culture (n = 53). Bacterial, fungal, and mycoplasma cultures were conducted for 2, 2, and 3 weeks, respectively. Microbial contamination was detected in 31% of transport solution. The contamination was not associated with the presence of the duodenum during the preservation, cold ischemia time, or procurement team (local vs. distant). Surface decontamination of the pancreas resulted in clearance of 92% of the microbial contamination. Six preparations at the end of the isolation revealed microbial growth. All were de novo contamination during the processing. Fifty-three preparations that met our release criteria in terms of product sterility were transplanted into type 1 diabetic patients. In two instances, positive culture of the islet preparation was reported after transplantation had occurred. No patient showed any clinical findings suggestive of infection or any radiological abnormalities suggestive of abscess; a single dose of antibiotic coverage was given routinely to recipients prior to islet infusion. Although transport solution carries a high risk of microbial contamination, most contaminants become undetectable during islet processing. Microbial contamination in final products is rare, but de novo contamination still occurs

Molybdenum limitation of microbial nitrogen assimilation in aquatic ecosystems and pure cultures.

PubMed

Glass, Jennifer B; Axler, Richard P; Chandra, Sudeep; Goldman, Charles R

2012-01-01

Molybdenum (Mo) is an essential micronutrient for biological assimilation of nitrogen gas and nitrate because it is present in the cofactors of nitrogenase and nitrate reductase enzymes. Although Mo is the most abundant transition metal in seawater (107 nM), it is present in low concentrations in most freshwaters, typically <20 nM. In 1960, it was discovered that primary productivity was limited by Mo scarcity (2-4 nM) in Castle Lake, a small, meso-oligotrophic lake in northern California. Follow up studies demonstrated that Mo also limited primary productivity in lakes in New Zealand, Alaska, and the Sierra Nevada. Research in the 1970s and 1980s showed that Mo limited primary productivity and nitrate uptake in Castle Lake only during periods of the growing season when nitrate concentrations were relatively high because ammonium assimilation does not require Mo. In the years since, research has shifted to investigate whether Mo limitation also occurs in marine and soil environments. Here we review studies of Mo limitation of nitrogen assimilation in natural microbial communities and pure cultures. We also summarize new data showing that the simultaneous addition of Mo and nitrate causes increased activity of proteins involved in nitrogen assimilation in the hypolimnion of Castle Lake when ammonium is scarce. Furthermore, we suggest that meter-scale Mo and oxygen depth profiles from Castle Lake are consistent with the hypothesis that nitrogen-fixing cyanobacteria in freshwater periphyton communities have higher Mo requirements than other microbial communities. Finally, we present topics for future research related to Mo bioavailability through time and with changing oxidation state.

Hydrogen production from microbial strains

DOEpatents

Harwood, Caroline S; Rey, Federico E

2012-09-18

The present invention is directed to a method of screening microbe strains capable of generating hydrogen. This method involves inoculating one or more microbes in a sample containing cell culture medium to form an inoculated culture medium. The inoculated culture medium is then incubated under hydrogen producing conditions. Once incubating causes the inoculated culture medium to produce hydrogen, microbes in the culture medium are identified as candidate microbe strains capable of generating hydrogen. Methods of producing hydrogen using one or more of the microbial strains identified as well as the hydrogen producing strains themselves are also disclosed.

Efficacy of a commercial probiotic relative to oxytetracycline as Gram-negative bacterial control agents in a rotifer (Brachionus plicatilis) batch culture

USDA-ARS?s Scientific Manuscript database

Two trials were conducted to evaluate two gram-negative bacterial control strategies in batch cultures of the rotifer Brachionus plicatilis. In the first trial, rotifers at an initial density of 47/mL were cultured for 5 d and dosed with a 10-mg/L solution of either oxytetracycline or a commercial p...

A Moderately Thermophilic Mixed Microbial Culture for Bioleaching of Chalcopyrite Concentrate at High Pulp Density

PubMed Central

Wang, Yuguang; Zeng, Weimin; Qiu, Guanzhou; Chen, Xinhua

2014-01-01

Three kinds of samples (acid mine drainage, coal mine wastewater, and thermal spring) derived from different sites were collected in China. Thereafter, these samples were combined and then inoculated into a basal salts solution in which different substrates (ferrous sulfate, elemental sulfur, and chalcopyrite) served as energy sources. After that, the mixed cultures growing on different substrates were pooled equally, resulting in a final mixed culture. After being adapted to gradually increasing pulp densities of chalcopyrite concentrate by serial subculturing for more than 2 years, the final culture was able to efficiently leach the chalcopyrite at a pulp density of 20% (wt/vol). At that pulp density, the culture extracted 60.4% of copper from the chalcopyrite in 25 days. The bacterial and archaeal diversities during adaptation were analyzed by denaturing gradient gel electrophoresis and constructing clone libraries of the 16S rRNA gene. The results show that the culture consisted mainly of four species, including Leptospirillum ferriphilum, Acidithiobacillus caldus, Sulfobacillus acidophilus, and Ferroplasma thermophilum, before adapting to a pulp density of 4%. However, L. ferriphilum could not be detected when the pulp density was greater than 4%. Real-time quantitative PCR was employed to monitor the microbial dynamics during bioleaching at a pulp density of 20%. The results show that A. caldus was the predominant species in the initial stage, while S. acidophilus rather than A. caldus became the predominant species in the middle stage. F. thermophilum accounted for the greatest proportion in the final stage. PMID:24242252

An EXAFS study of zinc coordination in microbial cells.

PubMed

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

2001-03-01

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

Dynamic flux balance modeling of microbial co-cultures for efficient batch fermentation of glucose and xylose mixtures.

PubMed

Hanly, Timothy J; Henson, Michael A

2011-02-01

Sequential uptake of pentose and hexose sugars that compose lignocellulosic biomass limits the ability of pure microbial cultures to efficiently produce value-added bioproducts. In this work, we used dynamic flux balance modeling to examine the capability of mixed cultures of substrate-selective microbes to improve the utilization of glucose/xylose mixtures and to convert these mixed substrates into products. Co-culture simulations of Escherichia coli strains ALS1008 and ZSC113, engineered for glucose and xylose only uptake respectively, indicated that improvements in batch substrate consumption observed in previous experimental studies resulted primarily from an increase in ZSC113 xylose uptake relative to wild-type E. coli. The E. coli strain ZSC113 engineered for the elimination of glucose uptake was computationally co-cultured with wild-type Saccharomyces cerevisiae, which can only metabolize glucose, to determine if the co-culture was capable of enhanced ethanol production compared to pure cultures of wild-type E. coli and the S. cerevisiae strain RWB218 engineered for combined glucose and xylose uptake. Under the simplifying assumption that both microbes grow optimally under common environmental conditions, optimization of the strain inoculum and the aerobic to anaerobic switching time produced an almost twofold increase in ethanol productivity over the pure cultures. To examine the effect of reduced strain growth rates at non-optimal pH and temperature values, a break even analysis was performed to determine possible reductions in individual strain substrate uptake rates that resulted in the same predicted ethanol productivity as the best pure culture. © 2010 Wiley Periodicals, Inc.

21 CFR 173.150 - Milk-clotting enzymes, microbial.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 21 Food and Drugs 3 2012-04-01 2012-04-01 false Milk-clotting enzymes, microbial. 173.150 Section... HUMAN CONSUMPTION Enzyme Preparations and Microorganisms § 173.150 Milk-clotting enzymes, microbial. Milk-clotting enzyme produced by pure-culture fermentation process may be safely used in the production...

21 CFR 173.150 - Milk-clotting enzymes, microbial.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 21 Food and Drugs 3 2013-04-01 2013-04-01 false Milk-clotting enzymes, microbial. 173.150 Section... HUMAN CONSUMPTION Enzyme Preparations and Microorganisms § 173.150 Milk-clotting enzymes, microbial. Milk-clotting enzyme produced by pure-culture fermentation process may be safely used in the production...

21 CFR 173.150 - Milk-clotting enzymes, microbial.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 3 2014-04-01 2014-04-01 false Milk-clotting enzymes, microbial. 173.150 Section... (CONTINUED) SECONDARY DIRECT FOOD ADDITIVES PERMITTED IN FOOD FOR HUMAN CONSUMPTION Enzyme Preparations and Microorganisms § 173.150 Milk-clotting enzymes, microbial. Milk-clotting enzyme produced by pure-culture...

21 CFR 173.150 - Milk-clotting enzymes, microbial.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 3 2011-04-01 2011-04-01 false Milk-clotting enzymes, microbial. 173.150 Section... HUMAN CONSUMPTION Enzyme Preparations and Microorganisms § 173.150 Milk-clotting enzymes, microbial. Milk-clotting enzyme produced by pure-culture fermentation process may be safely used in the production...

Composition of Hydrothermal Vent Microbial Communities as Revealed by Analyses of Signature Lipids, Stable Carbon Isotopes and Aquificales Cultures

NASA Technical Reports Server (NTRS)

Jahnke, Linda L.; Edger, Wolfgang; Huber, Robert; Hinrichs, Kai-Uwe; Hayes, John M.; DesMarais, David J.; Cady, Sherry; Hope, Janet M.; Summons, Roger E.; DeVincenzi, Donald L. (Technical Monitor)

2001-01-01

Extremely thermophilic microbial communities associated with the siliceous vent walls and outflow channel of Octopus Spring, Yellowstone National Park, have been examined for lipid biomarkers and carbon isotopic signatures. These data were compared with that obtained from representatives of three Aquificales genera. Thermocrinis ruber. "Thermocrinis sp. HI", Hydrogenobacter thermophilus TK-6, Aquifex pyrophilus and Aquifex aeolicus all contained phospholipids composed not only of the usual ester-linked fatty acids, but also ether-linked alkyls. The fatty acids of all cultured organisms were dominated by a very distinct pattern of n-C-20:1 and cy-C-21 compounds. The alkyl glycerol ethers were present primarily as CIS() monoethers with the expection of the Aquifex spp. in which dialkyl glycerol ethers with a boarder carbon-number distribution were also present. These Aquificales biomarker lipids were the major constituents in the lipid extracts of the Octopus Spring microbial samples. Two natural samples, a microbial biofilm growing in association with deposition of amorphous silica on the vent walls at 92 C, and the well-known 'pink-streamers community' (PSC), siliceous filaments of a microbial consortia growing in the upper outflow channel at 87 C were analyzed. Both the biofilm and PSC samples contained mono and dialkyl glycerol ethers with a prevalence of C-18 and C-20 alkyls. Phospholipid fatty acids were comprised of both the characteristic Aquificales n-C-20:1 and cy-C-21, and in addition, a series of iso-branched fatty acids from i-C-15:0 to i-C-21:0, With i-C-17:0 dominant in the PSC and i-C-19:0 in the biofilm, suggesting the presence of two major bacterial groups. Bacteriohopanepolyols were absent and the minute quantities of archaeol detected showed that Archaea were only minor constituents. Carbon isotopic compositions of the PSC yielded information about community structure and likely physiology. Biomass was C-13-depleted (10.9%) relative to available

Homogeneous matrix deposition on dried agar for MALDI imaging mass spectrometry of microbial cultures.

PubMed

Hoffmann, Thomas; Dorrestein, Pieter C

2015-11-01

Matrix deposition on agar-based microbial colonies for MALDI imaging mass spectrometry is often complicated by the complex media on which microbes are grown. This Application Note demonstrates how consecutive short spray pulses of a matrix solution can form an evenly closed matrix layer on dried agar. Compared with sieving dry matrix onto wet agar, this method supports analyte cocrystallization, which results in significantly more signals, higher signal-to-noise ratios, and improved ionization efficiency. The even matrix layer improves spot-to-spot precision of measured m/z values when using TOF mass spectrometers. With this technique, we established reproducible imaging mass spectrometry of myxobacterial cultures on nutrient-rich cultivation media, which was not possible with the sieving technique. Graphical Abstract ᅟ.

Detection of periodontopathogenic bacteria in pregnant women by traditional anaerobic culture method and by a commercial molecular genetic method.

PubMed

Urbán, Edit; Terhes, Gabriella; Radnai, Márta; Gorzó, István; Nagy, Elisabeth

2010-06-01

To culture facultative and strict anaerobic bacteria is a well-established method for analyzing subgingival plaque samples. Micro-IDent and micro-IDent Plus (HAIN Lifescience GmbH, Nehren, Germany) tests are two commercially available rapid PCR-based methods for the identification and quantification of putative periodontopathogen bacteria. In this study, we compared these commercial PCR-based hybridization methods with conventional anaerobic culture technique. A total of 36 subgingival plaque samples were collected from periodontal pockets of pregnant women with chronic localized periodontitis. Aliquots of these samples were evaluated with species-specific probes provided by micro-IDent and micro-IDent Plus tests simultaneously, and from the same samples anaerobic and capnophylic bacteria were cultured on selective media. The overall agreement between both methods was excellent for Eubacterium nodatum, Tannerella forsythia and Porphyromonas gingivalis (97-92%), fair for Capnocytophaga sp, Eikenella corrodens, Actinobacillus actinomycetemcomitans, and Prevotella intermedia (91-89%) and poor for Fusobacterium nucleatum, Parvimonas micra (Micromonas micros), and Campylobacter rectus (86-78%). Discrepancies in the results may be explained by inability of culture method to distinguish between closely related taxa (e.i P. intermedia/Prevotella. nigrescens), and problems of keeping periodontopathogen bacteria viable, which is required for successful detection by standard culture method. Nucleic acid-based methods may replace cultivation method as frequently used methods in microbiological diagnosis of progressive periodontitis, thus micro-IDent and micro-IDent Plus tests can be recommended where culture of periodontopathogenic bacteria is not performed in routine microbiology laboratories to analyze subgingival plaque samples. 2010 Elsevier Ltd. All rights reserved.

Therapeutic Potential of Plants as Anti-microbials for Drug Discovery

PubMed Central

Perumal Samy, Ramar

2010-01-01

The uses of traditional medicinal plants for primary health care have steadily increased worldwide in recent years. Scientists are in search of new phytochemicals that could be developed as useful anti-microbials for treatment of infectious diseases. Currently, out of 80% of pharmaceuticals derived from plants, very few are now being used as anti-microbials. Plants are rich in a wide variety of secondary metabolites that have found anti-microbial properties. This review highlights the current status of traditional medicine, its contribution to modern medicine, recent trends in the evaluation of anti-microbials with a special emphasis upon some tribal medicine, in vitro and in vivo experimental design for screening, and therapeutic efficacy in safety and human clinical trails for commercial outlet. Many of these commercially available compounds are crude preparations administered without performing human clinical trials. Recent methods are useful to standardize the extraction for scientific investigation of new phytochemicals and anti-microbials of traditionally used plants. It is concluded that once the local ethnomedical preparations of traditional sources are scientifically evaluated before dispensing they should replace existing drugs commonly used for the therapeutic treatment of infection. This method should be put into practice for future investigations in the field of ethnopharmacology, phytochemistry, ethnobotany and other biological fields for drug discovery. PMID:18955349

Microbial degradation of the herbicide molinate by defined cultures and in the environment.

PubMed

Nunes, Olga C; Lopes, Ana R; Manaia, Célia M

2013-12-01

Molinate is a thiocarbamate herbicide used worldwide in rice crop protection. As with other pesticides, molinate is a recognized environmental pollutant, detected in soils, irrigation water, or rivers and bio-accumulated by some wildlife forms. For this reason, and in spite of its low toxicity to humans, environmental protection measures, which include reduction of use and/or remediation processes, are recommended. Due to its physic-chemical properties, molinate can easily disperse and react in the environment, originating diverse transformation products, some with increased toxicity. In spite of being a xenobiotic compound, molinate can also suffer microbial transformation by bacteria or fungi, sometimes serving as nutrient and energy source. In an attempt to isolate microorganisms to be used in the bioremediation of molinate-contaminated sites, a mixed culture, dominated by the actinobacterium Gulosibacter molinativorax ON4(T), was recovered from the runoff of a molinate-producing plant. Beyond a promising tool to decontaminate molinate-polluted sites, this culture also brought interesting insights into the biology of the degradation of this herbicide. In this review, an overview of the distribution and properties of molinate as environmental contaminant, the capability of microorganisms to transform this herbicide, and some reflections about possible bioremediation approaches are made.

Defining functional diversity for lignocellulose degradation in a microbial community using multi-omics studies.

PubMed

Alessi, Anna M; Bird, Susannah M; Oates, Nicola C; Li, Yi; Dowle, Adam A; Novotny, Etelvino H; deAzevedo, Eduardo R; Bennett, Joseph P; Polikarpov, Igor; Young, J Peter W; McQueen-Mason, Simon J; Bruce, Neil C

2018-01-01

Lignocellulose is one of the most abundant forms of fixed carbon in the biosphere. Current industrial approaches to the degradation of lignocellulose employ enzyme mixtures, usually from a single fungal species, which are only effective in hydrolyzing polysaccharides following biomass pre-treatments. While the enzymatic mechanisms of lignocellulose degradation have been characterized in detail in individual microbial species, the microbial communities that efficiently breakdown plant materials in nature are species rich and secrete a myriad of enzymes to perform "community-level" metabolism of lignocellulose. Single-species approaches are, therefore, likely to miss important aspects of lignocellulose degradation that will be central to optimizing commercial processes. Here, we investigated the microbial degradation of wheat straw in liquid cultures that had been inoculated with wheat straw compost. Samples taken at selected time points were subjected to multi-omics analysis with the aim of identifying new microbial mechanisms for lignocellulose degradation that could be applied in industrial pre-treatment of feedstocks. Phylogenetic composition of the community, based on sequenced bacterial and eukaryotic ribosomal genes, showed a gradual decrease in complexity and diversity over time due to microbial enrichment. Taxonomic affiliation of bacterial species showed dominance of Bacteroidetes and Proteobacteria and high relative abundance of genera Asticcacaulis , Leadbetterella and Truepera . The eukaryotic members of the community were enriched in peritrich ciliates from genus Telotrochidium that thrived in the liquid cultures compared to fungal species that were present in low abundance. A targeted metasecretome approach combined with metatranscriptomics analysis, identified 1127 proteins and showed the presence of numerous carbohydrate-active enzymes extracted from the biomass-bound fractions and from the culture supernatant. This revealed a wide array of

Composition of Hydrothermal Vent Microbial Communities as Revealed by Analyses of Signature Lipids, Stable Carbon Isotopes and Aquificales Cultures

NASA Technical Reports Server (NTRS)

Jahnke, Linda L.; Eder, Wolfgang; Huber, Robert; Hinrichs, Kai-Uwe; Hayes, John M.; Cady, Sherry L.; DesMarais, David J.; Hope, Janet M.; Summons, Roger E.

2001-01-01

Extremely thermophilic microbial communities associated with the siliceous vent walls and outflow channel of Octopus Spring, Yellowstone National Park, have been examined for lipid biomarker and carbon isotopic signatures. These data were compared with that obtained from representatives of three Aquificales genera. Thermocrinis ruber, Thermocrinis sp. HI, Hydrogenobacter thermophilus, Aquifex pyrophilus and Aquifex aeolicus all contained phospholipids composed not only of the usual ester-linked fatty acids, but also ether-linked alkyl moieties. The fatty acids of all cultured organisms were dominated by very distinct pattern of n-C-20:1 and cy-C-21 compounds. The alkyl glycerol ethers were present primarily as C-18:0 monoethers with the exception of the Aquifex spp. in which dialkyl glycerol ethers with a boarder carbon-number distribution were also present. These Aquificales biomarker lipids were the major constituents in the lipid extracts of the Octopus Spring microbial samples. Two natural samples, a microbial biofilm growing in association with deposition of amorphous silica on the vent walls at 92 C, and the well-known "pink-streamer community" (PSC), siliceous filaments of a microbial consortia growing in the outflow channel at 87 C were analyzed. Both the biofilm and PSC samples contained mono- and dialkyl glycerol ethers with a prevalence of C-18 and C-20 alkyls. Phospholipid fatty acids were comprised of both the characteristic. Additional information is contained in the original extended abstract.

Microbial Resources and Enological Significance: Opportunities and Benefits

PubMed Central

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

2017-01-01

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

Microbial contamination and disinfection methods of pacifiers

PubMed Central

NELSON, Paulo; LOUVAIN, Márcia Costa; MACARI, Soraia; LUCISANO, Marília Pacífico; da SILVA, Raquel Assed Bezerra; de QUEIROZ, Alexandra Mussolino; GATON-HERNÁNDEZ, Patrícia; da SILVA, Léa Assed Bezerra

2015-01-01

Objectives To evaluate the microbial contamination of pacifiers by Mutans Streptococci (MS) and the efficacy of different methods for their disinfection. Methods Twenty-eight children were assigned to a 4-stage changeover system with a 1-week interval. In each stage, children received a new pacifier and the parents were instructed to maintain their normal habits for 1 week. After this time, the pacifiers were subjected to the following 4 disinfection methods: spraying with 0.12% chlorhexidine solution, Brushtox® or sterile tap water, and immersion in boiling tap water for 15 minutes. Microbiological culture for MS and Scanning Electron Microscopy (SEM) were performed. The results were analyzed statistically by Friedman’s non-parametric test (a=0.05). Results The 0.12% chlorhexidine spray was statistically similar to the boiling water (p>0.05) and more effective than the Brushtox® spray and control (p<0.05). The analysis of SEM showed the formation of a cariogenic biofilm in all groups with positive culture. Conclusions Pacifiers become contaminated by MS after their use by children and should be disinfected routinely. Spraying with a 0.12% chlorhexidine solution and immersion in boiling water promoted better disinfection of the pacifiers compared with a commercial antiseptic toothbrush cleanser (Brushtox®). PMID:26537723

Culture-based indicators of fecal contamination and molecular microbial indicators rarely correlate with Campylobacter spp. in recreational waters.

PubMed

Hellein, Kristen N; Battie, Cynthia; Tauchman, Eric; Lund, Deanna; Oyarzabal, Omar A; Lepo, Joe Eugene

2011-12-01

Campylobacter spp. are the leading cause of gastroenteritis worldwide. Most human infections result from contaminated food; however, infections are also caused by recreational waterway contamination. Campylobacter culture is technically challenging and enumeration by culture-based methods is onerous. Thus, we employed qPCR to quantify Campylobacter spp. in fresh- and marine-water samples, raw sewage and animal feces. Multiplex PCR determined whether Campylobacter jejuni or C. coli, most commonly associated with human disease, were present in qPCR-positive samples. Campylobacters were detected in raw sewage, and in feces of all avian and mammalian species tested. Campylobacter-positive concentrations ranged from 68 to 2.3 × 10⁶ cells per 500 mL. Although C. jejuni and C. coli were rare in waterways, they were prevalent in sewage and feces. Campylobacter-specific qPCR screening of environmental waters did not correlate with the regulatory EPA method 1600 (Enterococcus culture), nor with culture-independent, molecular-based microbial source tracking indicators, such as human polyomavirus, human Bacteroidales and Methanobrevibacter smithii. Our results suggest that neither the standard EPA method nor the newly proposed culture-independent methods are appropriate surrogates for Campylobacter contamination in water. Thus, assays for specific pathogens may be necessary to protect human health, especially in waters that are contaminated with sewage and animal feces.

Modes of action of microbially-produced phytotoxins.

PubMed

Duke, Stephen O; Dayan, Franck E

2011-08-01

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

Molybdenum limitation of microbial nitrogen assimilation in aquatic ecosystems and pure cultures

PubMed Central

Glass, Jennifer B.; Axler, Richard P.; Chandra, Sudeep; Goldman, Charles R.

2012-01-01

Molybdenum (Mo) is an essential micronutrient for biological assimilation of nitrogen gas and nitrate because it is present in the cofactors of nitrogenase and nitrate reductase enzymes. Although Mo is the most abundant transition metal in seawater (107 nM), it is present in low concentrations in most freshwaters, typically <20 nM. In 1960, it was discovered that primary productivity was limited by Mo scarcity (2–4 nM) in Castle Lake, a small, meso-oligotrophic lake in northern California. Follow up studies demonstrated that Mo also limited primary productivity in lakes in New Zealand, Alaska, and the Sierra Nevada. Research in the 1970s and 1980s showed that Mo limited primary productivity and nitrate uptake in Castle Lake only during periods of the growing season when nitrate concentrations were relatively high because ammonium assimilation does not require Mo. In the years since, research has shifted to investigate whether Mo limitation also occurs in marine and soil environments. Here we review studies of Mo limitation of nitrogen assimilation in natural microbial communities and pure cultures. We also summarize new data showing that the simultaneous addition of Mo and nitrate causes increased activity of proteins involved in nitrogen assimilation in the hypolimnion of Castle Lake when ammonium is scarce. Furthermore, we suggest that meter-scale Mo and oxygen depth profiles from Castle Lake are consistent with the hypothesis that nitrogen-fixing cyanobacteria in freshwater periphyton communities have higher Mo requirements than other microbial communities. Finally, we present topics for future research related to Mo bioavailability through time and with changing oxidation state. PMID:22993512

Increased bacterial cell density and recombinant protein yield using a commercial microbial cultivation system.

PubMed

Peck, Grantley R; Bowden, Timothy R; Shiell, Brian J; Michalski, Wojtek P

2014-01-01

EnBase (BioSilta, Finland) is a microbial cultivation system that replicates fed-batch systems through sustained release of glucose by enzymatic degradation of a polymeric substrate. Achievable bacterial cell densities and recombinant capripoxvirus protein expression levels, solubility, and antigenicity using the EnBase system were assessed. BL21-AI Escherichia coli expressing capripoxvirus proteins achieved up to eightfold higher cell densities when grown in EnBase media compared with standard media. Greater yields of capripoxvirus proteins were attained using EnBase media, either through increases in the amount of expressed protein per cell in conjunction with higher cell density or through the increase in cell density alone. Addition of EnBase booster enhanced protein yield for one of the proteins tested but reduced yield for the other. However, the amount of soluble forms of the capripoxvirus proteins tested was not different from that observed from cultures grown under standard conditions. Purified capripoxvirus proteins expressed using EnBase or standard media were assessed for their performance by enzyme-linked immunosorbent assay (ELISA) and were shown to be equally capable of specifically binding capripoxvirus antibodies.

Genome engineering for microbial natural product discovery.

PubMed

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

2018-03-03

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

Use of a commercial probiotic supplement in meat goats.

PubMed

Whitley, N C; Cazac, D; Rude, B J; Jackson-O'Brien, D; Parveen, S

2009-02-01

Sixty-three Boer crossbred goats were used in 5 separate experiments (Exp. 1 to 5) to evaluate the effects of a commercial probiotic supplement on growth performance (Exp. 1 to 4), diet digestibility (Exp. 5), carcass traits (Exp. 3), and fecal bacterial populations (Exp. 4). Goats were either fed a commercially pelleted concentrate diet and supplemented with a commercial probiotic (PRO) that had shown anecdotal positive effects on goat growth and performance according to local goat producers, or they remained as controls. The dose of PRO used was within the labeled dose for sheep for all studies. For Exp. 1, goat BW and feed intake were measured and G:F was calculated every 7 d for 56 d. For Exp. 2 to 4, BW and feed intake were measured and G:F was calculated every 14 d. The first day of supplementation was considered d 0. Carcass traits were also collected at slaughter on d 57 for Exp. 3, and fecal samples were collected every 14 d for microbial culture for Exp. 4. For Exp. 5, which was a digestibility trial that lasted for 10 d, animals were placed in metabolic pens for collection of feces and orts. Growth performance of goats was not affected by probiotic supplementation, with the exception of performance in Exp. 2, in which ADG and G:F were improved (P < 0.03) in PRO goats compared with control goats on d 56 only (treatment x day interaction; P < 0.05), averaging 0.21 +/- 0.02 kg/d for PRO goats and 0.11 +/- 0.02 kg/d for control goats for ADG and 0.17 +/- 0.02 for PRO goats and 0.10 +/- 0.02 for control goats for G:F. Carcass weights and weights of fabricated cuts (shoulder, loin, leg, rack, shank, and total parts) as well as carcass length, leg circumference, loin eye area, and backfat were not influenced by PRO supplementation. Apparent digestibilities of OM, DM, NDF, ADF, CP, and GE (on a DM basis) were similar for the PRO and control treatments. Fecal culture analysis of Escherichia coli and coliforms, Lactobacillus, and Bifidobacterium populations were

Breeding Strategy To Generate Robust Yeast Starter Cultures for Cocoa Pulp Fermentations.

PubMed

Meersman, Esther; Steensels, Jan; Paulus, Tinneke; Struyf, Nore; Saels, Veerle; Mathawan, Melissa; Koffi, Jean; Vrancken, Gino; Verstrepen, Kevin J

2015-09-01

Cocoa pulp fermentation is a spontaneous process during which the natural microbiota present at cocoa farms is allowed to ferment the pulp surrounding cocoa beans. Because such spontaneous fermentations are inconsistent and contribute to product variability, there is growing interest in a microbial starter culture that could be used to inoculate cocoa pulp fermentations. Previous studies have revealed that many different fungi are recovered from different batches of spontaneous cocoa pulp fermentations, whereas the variation in the prokaryotic microbiome is much more limited. In this study, therefore, we aimed to develop a suitable yeast starter culture that is able to outcompete wild contaminants and consistently produce high-quality chocolate. Starting from specifically selected Saccharomyces cerevisiae strains, we developed robust hybrids with characteristics that allow them to efficiently ferment cocoa pulp, including improved temperature tolerance and fermentation capacity. We conducted several laboratory and field trials to show that these new hybrids often outperform their parental strains and are able to dominate spontaneous pilot scale fermentations, which results in much more consistent microbial profiles. Moreover, analysis of the resulting chocolate showed that some of the cocoa batches that were fermented with specific starter cultures yielded superior chocolate. Taken together, these results describe the development of robust yeast starter cultures for cocoa pulp fermentations that can contribute to improving the consistency and quality of commercial chocolate production. Copyright © 2015, American Society for Microbiology. 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

Proteomic profiling of an undefined microbial consortium cultured in fermented dairy manure: Methods development.

PubMed

Hanson, Andrea J; Paszczynski, Andrzej J; Coats, Erik R

2016-03-01

The production of polyhydroxyalkanoates (PHA; bioplastics) from waste or surplus feedstocks using mixed microbial consortia (MMC) and aerobic dynamic feeding (ADF) is a growing field within mixed culture biotechnology. This study aimed to optimize a 2DE workflow to investigate the proteome dynamics of an MMC synthesizing PHA from fermented dairy manure. To mitigate the challenges posed to effective 2DE by this complex sample matrix, the bacterial biomass was purified using Accudenz gradient centrifugation (AGC) before protein extraction. The optimized 2DE method yielded high-quality gels suitable for quantitative comparative analysis and subsequent protein identification by LC-MS/MS. The optimized 2DE method could be adapted to other proteomic investigations involving MMC in complex organic or environmental matrices. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Rapid assessment of viable but non-culturable Bacillus coagulans MTCC 5856 in commercial formulations using Flow cytometry.

PubMed

Majeed, Muhammed; Majeed, Shaheen; Nagabhushanam, Kalyanam; Punnapuzha, Ardra; Philip, Sheena; Mundkur, Lakshmi

2018-01-01

Accurate enumeration of bacterial count in probiotic formulation is imperative to ensure that the product adheres to regulatory standards and citation in consumer product label. Standard methods like plate count, can enumerate only replicating bacterial population under selected culture conditions. Viable but non culturable bacteria (VBNC) retain characteristics of living cells and can regain cultivability by a process known as resuscitation. This is a protective mechanism adapted by bacteria to evade stressful environmental conditions. B. coagulans MTCC 5856(LactoSpore®) is a probiotic endospore which can survive for decades in hostile environments without dividing. In the present study, we explored the use of flow cytometry to enumerate the viable count of B. coagulans MTCC 5856 under acidic and alkaline conditions, high temperature and in commercial formulations like compressed tablets and capsules. Flow cytometry (FCM) was comparable to plate count method when the spores were counted at physiological conditions. We show that VBNC state is induced in B. coagulans MTCC 5856by high temperature and acidic pH. The cells get resuscitated under physiological conditions and FCM was sensitive to detect the VBNC spores. Flow cytometry showed excellent ability to assess the viable spore count in commercial probiotic formulations of B. coagulans MTCC 5856. The results establish Flow cytometry as a reliable method to count viable bacteria in commercial probiotic preparations. Sporulation as well as existence as VBNC could contribute to the extreme stability of B. coagulans MTCC 5856.

Rapid assessment of viable but non-culturable Bacillus coagulans MTCC 5856 in commercial formulations using Flow cytometry

PubMed Central

Majeed, Muhammed; Majeed, Shaheen; Nagabhushanam, Kalyanam; Punnapuzha, Ardra; Philip, Sheena

2018-01-01

Accurate enumeration of bacterial count in probiotic formulation is imperative to ensure that the product adheres to regulatory standards and citation in consumer product label. Standard methods like plate count, can enumerate only replicating bacterial population under selected culture conditions. Viable but non culturable bacteria (VBNC) retain characteristics of living cells and can regain cultivability by a process known as resuscitation. This is a protective mechanism adapted by bacteria to evade stressful environmental conditions. B. coagulans MTCC 5856(LactoSpore®) is a probiotic endospore which can survive for decades in hostile environments without dividing. In the present study, we explored the use of flow cytometry to enumerate the viable count of B. coagulans MTCC 5856 under acidic and alkaline conditions, high temperature and in commercial formulations like compressed tablets and capsules. Flow cytometry (FCM) was comparable to plate count method when the spores were counted at physiological conditions. We show that VBNC state is induced in B. coagulans MTCC 5856by high temperature and acidic pH. The cells get resuscitated under physiological conditions and FCM was sensitive to detect the VBNC spores. Flow cytometry showed excellent ability to assess the viable spore count in commercial probiotic formulations of B. coagulans MTCC 5856. The results establish Flow cytometry as a reliable method to count viable bacteria in commercial probiotic preparations. Sporulation as well as existence as VBNC could contribute to the extreme stability of B. coagulans MTCC 5856. PMID:29474436

When micro meets macro: microbial lipid analysis and ecosystem ecology

NASA Astrophysics Data System (ADS)

Balser, T.; Gutknecht, J.

2008-12-01

There is growing interest in linking soil microbial community composition and activity with large-scale field studies of nutrient cycling or plant community response to disturbances. And while analysis of microbial communities has moved rapidly in the past decade from culture-based to non-culture based techniques, still it must be asked what have we gained from the move? How well does the necessarily micro-scale of microbial analysis allow us to address questions of interest at the macro-scale? Several challenges exist in bridging the scales, and foremost is the question of methodological feasibility. Past microbiological methodologies have not been readily adaptable to the large sample sizes necessary for ecosystem-scale research. As a result, it has been difficult to generate compatible microbial and ecosystem data sets. We describe the use of a modified lipid extraction method to generate microbial community data sets that allow us to match landscape-scale or long-term ecological studies with microbial community data. We briefly discuss the challenges and advantages associated with lipid analysis as an approach to addressing ecosystem ecological studies, and provide examples from our research in ecosystem restoration and recovery following disturbance and climate change.

Biosynthesis and derivatization of microbial glycolipids and their potential application in tribology

USDA-ARS?s Scientific Manuscript database

Microbial-produced glycolipids are biobased products with immense potential for commercial applications. Advances in the production process have led to the lowering of production cost and the appearance of commercial products in niche markets. The ability to manipulate the molecular structure by f...

Biodiesels from microbial oils: Opportunity and challenges.

PubMed

Ma, Yingqun; Gao, Zhen; Wang, Qunhui; Liu, Yu

2018-05-08

Although biodiesel has been extensively explored as an important renewable energy source, the raw materials-associated cost poses a serious challenge on its large-scale commercial production. The first and second generations of biodiesel are mainly produced from usable raw materials, e.g. edible oils, crops etc. Such a situation inevitably imposes higher demands on land and water usage, which in turn compromise future food and water supply. Obviously, there is an urgent need to explore alternative feedstock, e.g. microbial oils which can be produced by many types of microorganisms including microalgae, fungi and bacteria with the advantages of small footprint, high lipid content and efficient uptake of carbon dioxide. Therefore, this review offers a comprehensive picture of microbial oil-based technology for biodiesel production. The perspectives and directions forward are also outlined for future biodiesel production and commercialization. Copyright © 2018 Elsevier Ltd. All rights reserved.

Potential of Zimbabwean commercial probiotic products and strains of Lactobacillus plantarum as prophylaxis and therapy against diarrhoea caused by Escherichia coli in children.

PubMed

Chingwaru, Walter; Vidmar, Jerneja

2017-01-01

To evaluate the potential of commercial fermented products sold in the country, and strains of Lactobacillus plantarum (L. plantarum) as prophylaxis and therapy against diarrhoea in children. The antimicrobial potential of cultures of lactobacilli enriched from 4 Zimbabwean commercial food/beverage products: Dairibord Lacto sour milk (DLSM), Probrand sour milk (PSM), Kefalos Vuka cheese (KVC) and Chibuku opaque beer (COB); and four strains of L. plantarum obtained from Balkan traditional cheeses against clinical strains of Escherichia coli (E. coli) was assayed using the well diffusion method. Three commercial paediatric antidiarrhoeal drug products: Biogaia (BG), Prolife (PL) and Probio Junior (PJ) and a mutant strain of E. coli [strain 11105 (ATCC) - a vitamin B-12 auxotroph and penicillin G acylase-producing strain] were used as controls. An agar diffusion assay and a competitive exclusion assay were carried out on Mueller Hinton agar. Crude cultures of putative lactobacillus strains obtained from Zimbabwean dairy products (Probrand sour milk, Kefalos Vuka vuka cheese and Chibuku opaque beer) had significantly higher antimicrobial activities against clinical strains of E. coli than strains of L. plantarum isolated from Balkan cheeses (CLP1, CLP2 or CLP3) and crude microbial cultures from commercial paediatric probiotic products (BG, PJ and PL) of a culture of Lactobacillus rhamnosus LGG (P < 0.05). The putative Lactobacilli from four commercial Zimbabwean dairy products (Probrand sour milk, Kefalos Vuka vuka cheese and Chibuku opaque beer), and three strains of L. plantarum from Balkan cheeses (CLP1, CLP2 or CLP3) exhibited high antibacterial activities that can be harnessed to control paediatric diarrhoea that is caused by pathogenic strains of E. coli. Studies to characterise the probiotic potential of the live cultures in the products and the new strains of L. plantarum are underway. Copyright © 2017 Hainan Medical University. Production and

The pig gut microbial diversity: Understanding the pig gut microbial ecology through the next generation high throughput sequencing.

PubMed

Kim, Hyeun Bum; Isaacson, Richard E

2015-06-12

The importance of the gut microbiota of animals is widely acknowledged because of its pivotal roles in the health and well being of animals. The genetic diversity of the gut microbiota contributes to the overall development and metabolic needs of the animal, and provides the host with many beneficial functions including production of volatile fatty acids, re-cycling of bile salts, production of vitamin K, cellulose digestion, and development of immune system. Thus the intestinal microbiota of animals has been the subject of study for many decades. Although most of the older studies have used culture dependent methods, the recent advent of high throughput sequencing of 16S rRNA genes has facilitated in depth studies exploring microbial populations and their dynamics in the animal gut. These culture independent DNA based studies generate large amounts of data and as a result contribute to a more detailed understanding of the microbiota dynamics in the gut and the ecology of the microbial populations. Of equal importance, is being able to identify and quantify microbes that are difficult to grow or that have not been grown in the laboratory. Interpreting the data obtained from this type of study requires using basic principles of microbial diversity to understand importance of the composition of microbial populations. In this review, we summarize the literature on culture independent studies of the pig gut microbiota with an emphasis on its succession and alterations caused by diverse factors. Copyright © 2015 Elsevier B.V. All rights reserved.

Modes of Action of Microbially-Produced Phytotoxins

PubMed Central

Duke, Stephen O.; Dayan, Franck E.

2011-01-01

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

Community proteomics provides functional insight into polyhydroxyalkanoate production by a mixed microbial culture cultivated on fermented dairy manure.

PubMed

Hanson, Andrea J; Guho, Nicholas M; Paszczynski, Andrzej J; Coats, Erik R

2016-09-01

Polyhydroxyalkanoates (PHAs) are bio-based, biodegradable polyesters that can be produced from organic-rich waste streams using mixed microbial cultures (MMCs). To maximize PHA production, MMCs are enriched for bacteria with a high polymer storage capacity through the application of aerobic dynamic feeding (ADF) in a sequencing batch reactor (SBR), which consequently induces a feast-famine metabolic response. Though the feast-famine response is generally understood empirically at a macro-level, the molecular level is less refined. The objective of this study was to investigate the microbial community composition and proteome profile of an enriched MMC cultivated on fermented dairy manure. The enriched MMC exhibited a feast-famine response and was capable of producing up to 40 % (wt. basis) PHA in a fed-batch reactor. High-throughput 16S rRNA gene sequencing revealed a microbial community dominated by Meganema, a known PHA-producing genus not often observed in high abundance in enrichment SBRs. The application of the proteomic methods two-dimensional electrophoresis and LC-MS/MS revealed PHA synthesis, energy generation, and protein synthesis prominently occurring during the feast phase, corroborating bulk solution variable observations and theoretical expectations. During the famine phase, nutrient transport, acyl-CoA metabolism, additional energy generation, and housekeeping functions were more pronounced, informing previously under-determined MMC functionality under famine conditions. During fed-batch PHA production, acetyl-CoA acetyltransferase and PHA granule-bound phasin proteins were in increased abundance relative to the SBR, supporting the higher PHA content observed. Collectively, the results provide unique microbial community structural and functional insight into feast-famine PHA production from waste feedstocks using MMCs.

Rapid Microbial Sample Preparation from Blood Using a Novel Concentration Device

PubMed Central

Boardman, Anna K.; Campbell, Jennifer; Wirz, Holger; Sharon, Andre; Sauer-Budge, Alexis F.

2015-01-01

Appropriate care for bacteremic patients is dictated by the amount of time needed for an accurate diagnosis. However, the concentration of microbes in the blood is extremely low in these patients (1–100 CFU/mL), traditionally requiring growth (blood culture) or amplification (e.g., PCR) for detection. Current culture-based methods can take a minimum of two days, while faster methods like PCR require a sample free of inhibitors (i.e., blood components). Though commercial kits exist for the removal of blood from these samples, they typically capture only DNA, thereby necessitating the use of blood culture for antimicrobial testing. Here, we report a novel, scaled-up sample preparation protocol carried out in a new microbial concentration device. The process can efficiently lyse 10 mL of bacteremic blood while maintaining the microorganisms’ viability, giving a 30‑μL final output volume. A suite of six microorganisms (Staphylococcus aureus, Streptococcus pneumoniae, Escherichia coli, Haemophilus influenzae, Pseudomonas aeruginosa, and Candida albicans) at a range of clinically relevant concentrations was tested. All of the microorganisms had recoveries greater than 55% at the highest tested concentration of 100 CFU/mL, with three of them having over 70% recovery. At the lowest tested concentration of 3 CFU/mL, two microorganisms had recoveries of ca. 40–50% while the other four gave recoveries greater than 70%. Using a Taqman assay for methicillin-sensitive S. aureus (MSSA)to prove the feasibility of downstream analysis, we show that our microbial pellets are clean enough for PCR amplification. PCR testing of 56 spiked-positive and negative samples gave a specificity of 0.97 and a sensitivity of 0.96, showing that our sample preparation protocol holds great promise for the rapid diagnosis of bacteremia directly from a primary sample. PMID:25675242

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

PubMed

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

2005-02-01

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

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.

Microbial enzymes with special characteristics for biotechnological applications.

PubMed

Nigam, Poonam Singh

2013-08-23

This article overviews the enzymes produced by microorganisms, which have been extensively studied worldwide for their isolation, purification and characterization of their specific properties. Researchers have isolated specific microorganisms from extreme sources under extreme culture conditions, with the objective that such isolated microbes would possess the capability to bio-synthesize special enzymes. Various Bio-industries require enzymes possessing special characteristics for their applications in processing of substrates and raw materials. The microbial enzymes act as bio-catalysts to perform reactions in bio-processes in an economical and environmentally-friendly way as opposed to the use of chemical catalysts. The special characteristics of enzymes are exploited for their commercial interest and industrial applications, which include: thermotolerance, thermophilic nature, tolerance to a varied range of pH, stability of enzyme activity over a range of temperature and pH, and other harsh reaction conditions. Such enzymes have proven their utility in bio-industries such as food, leather, textiles, animal feed, and in bio-conversions and bio-remediations.

Research and application of microbial enzymes--India's contribution.

PubMed

Chand, Subhash; Mishra, Prashant

2003-01-01

Enzymes have attracted the attention of scientists world over due to their wide range of physiological, analytical and industrial applications. Although enzymes have been isolated, purified and studied from microbial, animal and plant sources, microorganisms represent the most common source of enzymes due to their broad biochemical diversity, feasibility of mass culture and ease of genetic manipulation. With the advent of molecular biology techniques, a number of genes of industrially important enzymes has been cloned and expressed in order to improve the production of enzymes, substrate utilization and other commercially useful properties. Special attention has been focused on enzymes isolated from thermophiles due to their inherent stability and industrial applications. In addition, a variety of methods have been employed to modify enzymes for their industrial usage including strain improvement, chemical modifications, modification of reaction environment, immobilization and protein engineering. A wide range of applications of enzymes in different bioprocess industries is discussed.

Characterizing the risk of infection from Mycobacterium tuberculosis in commercial passenger aircraft using quantitative microbial risk assessment.

PubMed

Jones, Rachael M; Masago, Yoshifumi; Bartrand, Timothy; Haas, Charles N; Nicas, Mark; Rose, Joan B

2009-03-01

Quantitative microbial risk assessment was used to predict the likelihood and spatial organization of Mycobacterium tuberculosis (Mtb) transmission in a commercial aircraft. Passenger exposure was predicted via a multizone Markov model in four scenarios: seated or moving infectious passengers and with or without filtration of recirculated cabin air. The traditional exponential (k = 1) and a new exponential (k = 0.0218) dose-response function were used to compute infection risk. Emission variability was included by Monte Carlo simulation. Infection risks were higher nearer and aft of the source; steady state airborne concentration levels were not attained. Expected incidence was low to moderate, with the central 95% ranging from 10(-6) to 10(-1) per 169 passengers in the four scenarios. Emission rates used were low compared to measurements from active TB patients in wards, thus a "superspreader" emitting 44 quanta/h could produce 6.2 cases or more under these scenarios. Use of respiratory protection by the infectious source and/or susceptible passengers reduced infection incidence up to one order of magnitude.

Bayesian Integrated Microbial Forensics

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

Jarman, Kristin H.; Kreuzer-Martin, Helen W.; Wunschel, David S.

2008-06-01

In the aftermath of the 2001 anthrax letters, researchers have been exploring ways to predict the production environment of unknown source microorganisms. Different mass spectral techniques are being developed to characterize components of a microbe’s culture medium including water, carbon and nitrogen sources, metal ions added, and the presence of agar. Individually, each technique has the potential to identify one or two ingredients in a culture medium recipe. However, by integrating data from multiple mass spectral techniques, a more complete characterization is possible. We present a Bayesian statistical approach to integrated microbial forensics and illustrate its application on spores grownmore » in different culture media.« less

Microbial biofilms on facial prostheses.

PubMed

Ariani, Nina; Vissink, Arjan; van Oort, Robert P; Kusdhany, Lindawati; Djais, Ariadna; Rahardjo, Tri Budi W; van der Mei, Henny C; Krom, Bastiaan P

2012-01-01

The composition of microbial biofilms on silicone rubber facial prostheses was investigated and compared with the microbial flora on healthy and prosthesis-covered skin. Scanning electron microscopy showed the presence of mixed bacterial and yeast biofilms on and deterioration of the surface of the prostheses. Microbial culturing confirmed the presence of yeasts and bacteria. Microbial colonization was significantly increased on prosthesis-covered skin compared to healthy skin. Candida spp. were exclusively isolated from prosthesis-covered skin and from prostheses. Biofilms from prostheses showed the least diverse band-profile in denaturing gradient gel electrophoresis (DGGE) whereas prosthesis-covered skin showed the most diverse band-profile. Bacterial diversity exceeded yeast diversity in all samples. It is concluded that occlusion of the skin by prostheses creates a favorable niche for opportunistic pathogens such as Candida spp. and Staphylococcus aureus. Biofilms on healthy skin, skin underneath the prosthesis and on the prosthesis had a comparable composition, but the numbers present differed according to the microorganism.

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

PubMed

Zhang, Haoran; Wang, Xiaonan

2016-09-01

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

Microbial ecology: new insights into the great wide-open culture independent sea

USDA-ARS?s Scientific Manuscript database

Microbial communities are the basis for most, if not all, biochemical or biogeochemical functions in the environment. These environments are vastly different with respect to matrix, function, and biodiversity, and as such, present minute to stark differences in their respective microbial communities...

Microbial communities affecting albumen photography heritage: a methodological survey

NASA Astrophysics Data System (ADS)

Puškárová, Andrea; Bučková, Mária; Habalová, Božena; Kraková, Lucia; Maková, Alena; Pangallo, Domenico

2016-02-01

This study is one of the few investigations which analyze albumen prints, perhaps the most important photographic heritage of the late 19th and early 20th centuries. The chemical composition of photographic samples was assessed using Fourier-transform infrared spectroscopy and X-ray fluorescence. These two non-invasive techniques revealed the complex nature of albumen prints, which are composed of a mixture of proteins, cellulose and salts. Microbial sampling was performed using cellulose nitrate membranes which also permitted the trapped microflora to be observed with a scanning electron microscope. Microbial analysis was performed using the combination of culture-dependent (cultivation in different media, including one 3% NaCl) and culture-independent (bacterial and fungal cloning and sequencing) approaches. The isolated microorganisms were screened for their lipolytic, proteolytic, cellulolytic, catalase and peroxidase activities. The combination of the culture-dependent and -independent techniques together with enzymatic assays revealed a substantial microbial diversity with several deteriogen microorganisms from the genera Bacillus, Kocuria, Streptomyces and Geobacillus and the fungal strains Acrostalagmus luteoalbus, Bjerkandera adusta, Pleurotus pulmonarius and Trichothecium roseum.

Microbial communities affecting albumen photography heritage: a methodological survey.

PubMed

Puškárová, Andrea; Bučková, Mária; Habalová, Božena; Kraková, Lucia; Maková, Alena; Pangallo, Domenico

2016-02-11

This study is one of the few investigations which analyze albumen prints, perhaps the most important photographic heritage of the late 19(th) and early 20(th) centuries. The chemical composition of photographic samples was assessed using Fourier-transform infrared spectroscopy and X-ray fluorescence. These two non-invasive techniques revealed the complex nature of albumen prints, which are composed of a mixture of proteins, cellulose and salts. Microbial sampling was performed using cellulose nitrate membranes which also permitted the trapped microflora to be observed with a scanning electron microscope. Microbial analysis was performed using the combination of culture-dependent (cultivation in different media, including one 3% NaCl) and culture-independent (bacterial and fungal cloning and sequencing) approaches. The isolated microorganisms were screened for their lipolytic, proteolytic, cellulolytic, catalase and peroxidase activities. The combination of the culture-dependent and -independent techniques together with enzymatic assays revealed a substantial microbial diversity with several deteriogen microorganisms from the genera Bacillus, Kocuria, Streptomyces and Geobacillus and the fungal strains Acrostalagmus luteoalbus, Bjerkandera adusta, Pleurotus pulmonarius and Trichothecium roseum.

Evaluation of Mixed Probiotic Starter Cultures Isolated from Kimchi on Physicochemical and Functional Properties, and Volatile Compounds of Fermented Hams.

PubMed

Kim, Young Joo; Park, Sung Yong; Lee, Hong Chul; Yoo, Seung Seok; Oh, Sejong; Kim, Kwang Hyun; Chin, Koo Bok

2016-01-01

The objective of this study was to investigate the effects of mixed starter cultures isolated from kimchi on physicochemical properties, functionality and flavors of fermented ham. Physicochemical properties, microbial counts, shear force, cholesterol contents and volatile compounds of fermented ham were investigated during processing (curing and ripening time). Curing process for 7 d increased saltiness, however, decreased hunter color values (L, a, and b values). Ripening process for 21 d increased most parameters, such as saltiness, color values, weight loss, shear force and cholesterol content due to the drying process. The mixed starter culture had higher lactic acid bacteria than the commercial one. While eight volatile compounds were identified from fermented hams during curing process, total fiftyeight volatile compounds were identified from fermented hams during ripening process. The main volatile compounds were alcohols, esters and furans. However, no differences in volatile compounds were observed between two batches. Fermented hams (batch B) manufactured with probiotic starter culture (LPP) had higher sensory score in texture, color and overall acceptability than counterparts (batch A), while the opposite trend was observed in flavor. Therefore, mixed probiotic starter culture isolated from kimchi might be used as a starter culture to be able to replace with commercial starter culture (LK-30 plus) for the manufacture of fermented ham.

Evaluation of Mixed Probiotic Starter Cultures Isolated from Kimchi on Physicochemical and Functional Properties, and Volatile Compounds of Fermented Hams

PubMed Central

Yoo, Seung Seok

2016-01-01

The objective of this study was to investigate the effects of mixed starter cultures isolated from kimchi on physicochemical properties, functionality and flavors of fermented ham. Physicochemical properties, microbial counts, shear force, cholesterol contents and volatile compounds of fermented ham were investigated during processing (curing and ripening time). Curing process for 7 d increased saltiness, however, decreased hunter color values (L, a, and b values). Ripening process for 21 d increased most parameters, such as saltiness, color values, weight loss, shear force and cholesterol content due to the drying process. The mixed starter culture had higher lactic acid bacteria than the commercial one. While eight volatile compounds were identified from fermented hams during curing process, total fiftyeight volatile compounds were identified from fermented hams during ripening process. The main volatile compounds were alcohols, esters and furans. However, no differences in volatile compounds were observed between two batches. Fermented hams (batch B) manufactured with probiotic starter culture (LPP) had higher sensory score in texture, color and overall acceptability than counterparts (batch A), while the opposite trend was observed in flavor. Therefore, mixed probiotic starter culture isolated from kimchi might be used as a starter culture to be able to replace with commercial starter culture (LK-30 plus) for the manufacture of fermented ham. PMID:27499673

A flexible microbial co-culture platform for simultaneous utilization of methane and carbon dioxide from gas feedstocks

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

Hill, Eric A.; Chrisler, William B.; Beliaev, Alex S.

A new co-cultivation technology is presented that converts greenhouse gasses, CH 4 and CO 2, into microbial biomass. The methanotrophic bacterium, Methylomicrobium alcaliphilum 20z, was coupled to a cyanobacterium, Synechococcus PCC 7002 via oxygenic photosynthesis. The system exhibited robust growth on diverse gas mixtures ranging from biogas to those representative of a natural gas feedstock. A continuous processes was developed on a synthetic natural gas feed that achieved steady-state by imposing coupled light and O 2 limitations on the cyanobacterium and methanotroph, respectively. Continuous co-cultivation resulted in an O 2 depleted reactor and does not require CH 4/O 2 mixturesmore » to be fed into the system, thereby enhancing process safety considerations over traditional methanotroph mono-culture platforms. This co-culture technology is scalable with respect to its ability to utilize different gas streams and its biological components constructed from model bacteria that can be metabolically customized to produce a range of biofuels and bioproducts.« less

A flexible microbial co-culture platform for simultaneous utilization of methane and carbon dioxide from gas feedstocks

DOE PAGES

Hill, Eric A.; Chrisler, William B.; Beliaev, Alex S.; ...

2017-01-03

A new co-cultivation technology is presented that converts greenhouse gasses, CH 4 and CO 2, into microbial biomass. The methanotrophic bacterium, Methylomicrobium alcaliphilum 20z, was coupled to a cyanobacterium, Synechococcus PCC 7002 via oxygenic photosynthesis. The system exhibited robust growth on diverse gas mixtures ranging from biogas to those representative of a natural gas feedstock. A continuous processes was developed on a synthetic natural gas feed that achieved steady-state by imposing coupled light and O 2 limitations on the cyanobacterium and methanotroph, respectively. Continuous co-cultivation resulted in an O 2 depleted reactor and does not require CH 4/O 2 mixturesmore » to be fed into the system, thereby enhancing process safety considerations over traditional methanotroph mono-culture platforms. This co-culture technology is scalable with respect to its ability to utilize different gas streams and its biological components constructed from model bacteria that can be metabolically customized to produce a range of biofuels and bioproducts.« less

Integration of microbial biopesticides in greenhouse floriculture: The Canadian experience.

PubMed

Brownbridge, Michael; Buitenhuis, Rose

2017-11-28

Historically, greenhouse floriculture has relied on synthetic insecticides to meet its pest control needs. But, growers are increasingly faced with the loss or failure of synthetic chemical pesticides, declining access to new chemistries, stricter environmental/health and safety regulations, and the need to produce plants in a manner that meets the 'sustainability' demands of a consumer driven market. In Canada, reports of thrips resistance to spinosad (Success™) within 6-12 months of its registration prompted a radical change in pest management philosophy and approach. Faced with a lack of registered chemical alternatives, growers turned to biological control out of necessity. Biological control now forms the foundation for pest management programs in Canadian floriculture greenhouses. Success in a biocontrol program is rarely achieved through the use of a single agent, though. Rather, it is realized through the concurrent use of biological, cultural and other strategies within an integrated plant production system. Microbial insecticides can play a critical supporting role in biologically-based integrated pest management (IPM) programs. They have unique modes of action and are active against a range of challenging pests. As commercial microbial insecticides have come to market, research to generate efficacy data has assisted their registration in Canada, and the development and adaptation of integrated programs has promoted uptake by floriculture growers. This review documents some of the work done to integrate microbial insecticides into chrysanthemum and poinsettia production systems, outlines current use practices, and identifies opportunities to improve efficacy in Canadian floriculture crops. Copyright © 2017 Elsevier Inc. All rights reserved.

Effects of cinnamaldehyde and garlic oil on rumen microbial fermentation in a dual flow continuous culture.

PubMed

Busquet, M; Calsamiglia, S; Ferret, A; Cardozo, P W; Kamel, C

2005-07-01

Eight continuous culture fermentors inoculated with ruminal liquor from heifers fed a 50:50 alfalfa hay:concentrate diet (17.6% crude protein, 28.0% neutral detergent fiber) were used in 3 replicated periods to study the effects of cinnamaldehyde (CIN) and garlic oil (GAR) on rumen microbial fermentation. Treatments were no additive (negative control); 1.25 mg/L (MON) and 12.5 mg/L (MON10) of the ionophore antibiotic monensin (positive control); 31.2 mg/L CIN (CIN) and 312 mg/L (CIN10) of CIN; and 31.2 mg/L GAR (GAR) and 312 mg/L (GAR10) of GAR (Allium sativa). The MON10 caused expected changes in microbial fermentation patterns (a decrease in fiber digestion, ammonia N concentration, and proportions of acetate and butyrate; an increase in the proportion of propionate; and a trend to increase small peptide plus AA N concentration). The CIN decreased the proportion of acetate and branch-chained volatile fatty acids (VFA) and increased the proportion of propionate; CIN10 decreased the proportion of acetate and increased the proportion of butyrate compared with the control. The GAR10 increased the proportion of propionate and butyrate and decreased the proportion of acetate and branch-chained VFA compared with the control. The GAR10 also increased the small peptide plus amino acid N concentration, although no effects were observed on large peptides or ammonia N concentrations. The CIN and GAR10 resulted in similar effects as monensin, with the exception of the effects on the molar proportion of butyrate, which suggests that they might have a different mode of action in affecting in vitro microbial fermentation.

Engineering microbial fatty acid metabolism for biofuels and biochemicals.

PubMed

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

2018-04-01

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

Microbial diversity in an Armenian geothermal spring assessed by molecular and culture-based methods.

PubMed

Panosyan, Hovik; Birkeland, Nils-Kåre

2014-11-01

The phylogenetic diversity of the prokaryotic community thriving in the Arzakan hot spring in Armenia was studied using molecular and culture-based methods. A sequence analysis of 16S rRNA gene clone libraries demonstrated the presence of a diversity of microorganisms belonging to the Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Epsilonproteobacteria, Firmicutes, Bacteroidetes phyla, and Cyanobacteria. Proteobacteria was the dominant group, representing 52% of the bacterial clones. Denaturing gradient gel electrophoresis profiles of the bacterial 16S rRNA gene fragments also indicated the abundance of Proteobacteria, Bacteroidetes, and Cyanobacteria populations. Most of the sequences were most closely related to uncultivated microorganisms and shared less than 96% similarity with their closest matches in GenBank, indicating that this spring harbors a unique community of novel microbial species or genera. The majority of the sequences of an archaeal 16S rRNA gene library, generated from a methanogenic enrichment, were close relatives of members of the genus Methanoculleus. Aerobic endospore-forming bacteria mainly belonging to Bacillus and Geobacillus were detected only by culture-dependent methods. Three isolates were successfully obtained having 99, 96, and 96% 16S rRNA gene sequence similarities to Arcobacter sp., Methylocaldum sp., and Methanoculleus sp., respectively. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

High-Throughput Sequencing and Metagenomics: Moving Forward in the Culture-Independent Analysis of Food Microbial Ecology

PubMed Central

2013-01-01

Following recent trends in environmental microbiology, food microbiology has benefited from the advances in molecular biology and adopted novel strategies to detect, identify, and monitor microbes in food. An in-depth study of the microbial diversity in food can now be achieved by using high-throughput sequencing (HTS) approaches after direct nucleic acid extraction from the sample to be studied. In this review, the workflow of applying culture-independent HTS to food matrices is described. The current scenario and future perspectives of HTS uses to study food microbiota are presented, and the decision-making process leading to the best choice of working conditions to fulfill the specific needs of food research is described. PMID:23475615

Teaching the Microbial Growth Curve Concept Using Microalgal Cultures and Flow Cytometry

ERIC Educational Resources Information Center

Forget, Nathalie; Belzile, Claude; Rioux, Pierre; Nozais, Christian

2010-01-01

The microbial growth curve is widely studied within microbiology classes and bacteria are usually the microbial model used. Here, we describe a novel laboratory protocol involving flow cytometry to assess the growth dynamics of the unicellular microalgae "Isochrysis galbana." The algal model represents an appropriate alternative to…

Prediction of Microbial Infection of Cultured Cells Using DNA Microarray Gene-Expression Profiles of Host Responses

PubMed Central

Park, Yu Rang; Chung, Tae Su; Lee, Young Joo; Song, Yeong Wook; Lee, Eun Young; Sohn, Yeo Won; Song, Sukgil; Park, Woong Yang

2012-01-01

Infection by microorganisms may cause fatally erroneous interpretations in the biologic researches based on cell culture. The contamination by microorganism in the cell culture is quite frequent (5% to 35%). However, current approaches to identify the presence of contamination have many limitations such as high cost of time and labor, and difficulty in interpreting the result. In this paper, we propose a model to predict cell infection, using a microarray technique which gives an overview of the whole genome profile. By analysis of 62 microarray expression profiles under various experimental conditions altering cell type, source of infection and collection time, we discovered 5 marker genes, NM_005298, NM_016408, NM_014588, S76389, and NM_001853. In addition, we discovered two of these genes, S76389, and NM_001853, are involved in a Mycolplasma-specific infection process. We also suggest models to predict the source of infection, cell type or time after infection. We implemented a web based prediction tool in microarray data, named Prediction of Microbial Infection (http://www.snubi.org/software/PMI). PMID:23091307

Petroleum storage tank cleaning using commercial microbial culture products

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

Schneider, D.R.; Entzeroth, L.C.; Timmis, A.

1995-12-31

The removal of paraffinic bottom accumulations from refinery storage tanks represents an increasingly costly area of petroleum storage management. Microorganisms can be used to reduce paraffinic bottoms by increasing the solubility of bottom material and by increasing the wax-carrying capacity of carrier oil used in the cleaning process. The economic savings of such treatments are considerable. The process is also intrinsically safer than alternative methods, as it reduces and even eliminates the need for personnel to enter the tank during the cleaning process. Both laboratory and field sample analyses can be used to document changes in tank material during themore » treatment process. These changes include increases in volatile content and changes in wax distribution. Several case histories illustrating these physical and chemical changes are presented along with the economics of treatment.« less

Kinetics of nitrate and sulfate removal using a mixed microbial culture with or without limited-oxygen fed.

PubMed

Xu, Xi-Jun; Chen, Chuan; Wang, Ai-Jie; Guo, Hong-Liang; Yuan, Ye; Lee, Duu-Jong; Ren, Nan-Qi

2014-07-01

The biological degradation of nitrate and sulfate was investigated using a mixed microbial culture and lactate as the carbon source, with or without limited-oxygen fed. It was found that sulfate reduction was slightly inhibited by nitrate, since after nitrate depletion the sulfate reduction rate increased from 0.37 mg SO4 (2-)/mg VSS d to 0.71 mg SO4 (2-)/mg VSS d, and the maximum rate of sulfate reduction in the presence of nitrate corresponded to 56 % of the non-inhibited sulfate reduction rate determined after nitrate depleted. However, simultaneous but not sequential reduction of both oxy-anions was observed in this study, unlike some literature reports in which sulfate reduction starts only after depletion of nitrate, and this case might be due to the fact that lactate was always kept above the limiting conditions. At limited oxygen, the inhibited effect on sulfate reduction by nitrate was relieved, and the sulfate reduction rate seemed relatively higher than that obtained without limited-oxygen fed, whereas kept almost constant (0.86-0.89 mg SO4 (2-)/mg VSS d) cross the six ROS states. In contrast, nitrate reduction rates decreased substantially with the increase in the initial limited-oxygen fed, showing an inhibited effect on nitrate reduction by oxygen. Kinetic parameters determined for the mixed microbial culture showed that the maximum specific sulfate utilization rate obtained (0.098 ± 0.022 mg SO4 (2-)/(mg VSS h)) was similar to the reported typical value (0.1 mg SO4 (2-)/(mg VSS h)), also indicating a moderate inhibited effect by nitrate.

Evaluation of the microbial community in industrial rye sourdough upon continuous back-slopping propagation revealed Lactobacillus helveticus as the dominant species.

PubMed

Viiard, E; Mihhalevski, A; Rühka, T; Paalme, T; Sarand, I

2013-02-01

To assess the structure and stability of a dominant lactic acid bacteria (LAB) population during the propagation of rye sourdough in an industrial semi-fluid production over a period of 7 months. The sourdough was started from a 6-year-old freeze-dried sourdough originating from the same bakery. A unique microbial consortium consisting mainly of bacteria belonging to species Lactobacillus helveticus, Lactobacillus panis and Lactobacillus pontis was identified based on culture-dependent (Rep-PCR) and culture-independent [denaturing gradient gel electrophoresis (DGGE)] methods. Three of the isolated Lact. helveticus strains showed remarkable adaptation to the sourdough conditions. They differed from the type strain by the ability to ferment compounds specific to plant material, like salicin, cellobiose and sucrose, but did not ferment lactose. We showed remarkable stability of a LAB consortium in rye sourdough started from lyophilized sourdough and propagated in a large bakery for 7 months. Lactobacillus helveticus was detected as the dominant species in the consortium and was shown to be metabolically adapted to the sourdough environment. The use of an established and adapted microbial consortium as a starter is a good alternative to commercial starter strains. © 2012 The Society for Applied Microbiology.

Aerobic microbial mineralization of dichloroethene as sole carbon substrate

USGS Publications Warehouse

Bradley, P.M.; Chapelle, F.H.

2000-01-01

Microorganisms indigenous to the bed sediments of a black- water stream utilized 1,2-dichloroethene (1,2-DCE) as a sole carbon substrate for aerobic metabolism. Although no evidence of growth was observed in the minimal salts culture media used in this study, efficient aerobic microbial mineralization of 1,2-DCE as sole carbon substrate was maintained through three sequential transfers (107 final dilution) of the original environmental innoculum. These results indicate that 1,2-DCE can be utilized as a primary substrate to support microbial metabolism under aerobic conditions.Microorganisms indigenous to the bed sediments of a black-water stream utilized 1,2-dichloroethene (1,2-DCE) as a sole carbon substrate for aerobic metabolism. Although no evidence of growth was observed in the minimal salts culture media used in this study, efficient aerobic microbial mineralization of 1,2-DCE as sole carbon substrate was maintained through three sequential transfers (107 final dilution) of the original environmental innoculum. These results indicate that 1,2-DCE can be utilized as a primary substrate to support microbial metabolism under aerobic conditions.

Recent advances in microbial fermentation for dairy and health

PubMed Central

Arendt, Elke; Hill, Colin; Stanton, Catherine; Ross, R Paul

2017-01-01

Microbial fermentation has been used historically for the preservation of foods, the health benefits of which have since come to light. Early dairy fermentations depended on the spontaneous activity of the indigenous microbiota of the milk. Modern fermentations rely on defined starter cultures with desirable characteristics to ensure consistency and commercial viability. The selection of defined starters depends on specific phenotypes that benefit the product by guaranteeing shelf life and ensuring safety, texture, and flavour. Lactic acid bacteria can produce a number of bioactive metabolites during fermentation, such as bacteriocins, biogenic amines, exopolysaccharides, and proteolytically released peptides, among others. Prebiotics are added to food fermentations to improve the performance of probiotics. It has also been found that prebiotics fermented in the gut can have benefits that go beyond helping probiotic growth. Studies are now looking at how the fermentation of prebiotics such as fructo-oligosaccharides can help in the prevention of diseases such as osteoporosis, obesity, and colorectal cancer. The potential to prevent or even treat disease through the fermentation of food is a medically and commercially attractive goal and is showing increasing promise. However, the stringent regulation of probiotics is beginning to detrimentally affect the field and limit their application. PMID:28649371

Engineering microbial fuels cells: recent patents and new directions.

PubMed

Biffinger, Justin C; Ringeisen, Bradley R

2008-01-01

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

Potential for microbial oxidation of ferrous iron in basaltic glass.

PubMed

Xiong, Mai Yia; Shelobolina, Evgenya S; Roden, Eric E

2015-05-01

Basaltic glass (BG) is an amorphous ferrous iron [Fe(II)]-containing material present in basaltic rocks, which are abundant on rocky planets such as Earth and Mars. Previous research has suggested that Fe(II) in BG can serve as an energy source for chemolithotrophic microbial metabolism, which has important ramifications for potential past and present microbial life on Mars. However, to date there has been no direct demonstration of microbially catalyzed oxidation of Fe(II) in BG. In this study, three different culture systems were used to investigate the potential for microbial oxidation of Fe(II) in BG, including (1) the chemolithoautotrophic Fe(II)-oxidizing, nitrate-reducing "Straub culture"; (2) the mixotrophic Fe(II)-oxidizing, nitrate-reducing organism Desulfitobacterium frappieri strain G2; and (3) indigenous microorganisms from a streambed Fe seep in Wisconsin. The BG employed consisted of clay and silt-sized particles of freshly quenched lava from the TEB flow in Kilauea, Hawaii. Soluble Fe(II) or chemically reduced NAu-2 smectite (RS) were employed as positive controls to verify Fe(II) oxidation activity in the culture systems. All three systems demonstrated oxidation of soluble Fe(II) and/or structural Fe(II) in RS, whereas no oxidation of Fe(II) in BG material was observed. The inability of the Straub culture to oxidize Fe(II) in BG was particularly surprising, as this culture can oxidize other insoluble Fe(II)-bearing minerals such as biotite, magnetite, and siderite. Although the reason for the resistance of the BG toward enzymatic oxidation remains unknown, it seems possible that the absence of distinct crystal faces or edge sites in the amorphous glass renders the material resistant to such attack. These findings have implications with regard to the idea that Fe(II)-Si-rich phases in basalt rocks could provide a basis for chemolithotrophic microbial life on Mars, specifically in neutral-pH environments where acid-promoted mineral dissolution and

From Metchnikoff to Monsanto and beyond: the path of microbial control.

PubMed

Lord, Jeffrey C

2005-05-01

In 125 years since Metchnikoff proposed the use of Metarhizium anisopliae to control the wheat cockchafer and brought about the first field trials, microbial control has progressed from the application of naturalists' observations to biotechnology and precision delivery. This review highlights major milestones in its evolution and presents a perspective on its current direction. Fungal pathogens, the most eye-catching agents, dominated the early period, but major mycological control efforts for chinch bugs and citrus pests in the US had questionable success, and interest waned. The discoveries of Bacillus popilliae and Bacillus thuringiensis began the era of practical and commercially viable microbial control. A program to control the Japanese beetle in the US led to the discovery of both B. popilliae and Steinernema glaseri, the first nematode used as a microbial control agent. Viral insect control became practical in the latter half of the 20th century, and the first registration was obtained with the Heliothis nuclear polyhedrosis virus in 1975. Now strategies are shifting for microbial control. While Bt transgenic crops are now planted on millions of hectares, the successes of more narrowly defined microbial control are mainly in small niches. Commercial enthusiasm for traditional microbial control agents has been unsteady in recent years. The prospects of microbial insecticide use on vast areas of major crops are now viewed more realistically. Regulatory constraints, activist resistance, benign and efficacious chemicals, and limited research funding all drive changes in focus. Emphasis is shifting to monitoring, conservation, integration with chemical pesticides, and selection of favorable venues such as organic agriculture and countries that have low costs, mild regulatory climates, modest chemical inputs, and small scale farming.

Benchmarking of commercially available CHO cell culture media for antibody production.

PubMed

Reinhart, David; Damjanovic, Lukas; Kaisermayer, Christian; Kunert, Renate

2015-06-01

In this study, eight commercially available, chemically defined Chinese hamster ovary (CHO) cell culture media from different vendors were evaluated in batch culture using an IgG-producing CHO DG44 cell line as a model. Medium adaptation revealed that the occurrence of even small aggregates might be a good indicator of cell growth performance in subsequent high cell density cultures. Batch experiments confirmed that the culture medium has a significant impact on bioprocess performance, but high amino acid concentrations alone were not sufficient to ensure superior cell growth and high antibody production. However, some key amino acids that were limiting in most media could be identified. Unbalanced glucose and amino acids led to high cell-specific lactate and ammonium production rates. In some media, persistently high glucose concentrations probably induced the suppression of respiration and oxidative phosphorylation, known as Crabtree effect, which resulted in high cell-specific glycolysis rates along with a continuous and high lactate production. In additional experiments, two of the eight basal media were supplemented with feeds from two different manufacturers in six combinations, in order to understand the combined impact of media and feeds on cell metabolism in a CHO fed-batch process. Cell growth, nutrient consumption and metabolite production rates, antibody production, and IgG quality were evaluated in detail. Concentrated feed supplements boosted cell concentrations almost threefold and antibody titers up to sevenfold. Depending on the fed-batch strategy, fourfold higher peak cell concentrations and eightfold increased IgG titers (up to 5.8 g/L) were achieved. The glycolytic flux was remarkably similar among the fed-batches; however, substantially different specific lactate production rates were observed in the different media and feed combinations. Further analysis revealed that in addition to the feed additives, the basal medium can make a considerable

Immunological evaluation of polystyrene and poly(ether imide) cell culture inserts with different roughness.

PubMed

Roch, Toralf; Krüger, Anne; Kratz, Karl; Ma, Nan; Jung, Friedrich; Lendlein, Andreas

2012-01-01

For the successful clinical and biological application of polymers, their interaction with cells, tissues, and body fluids has to be well characterized. In order to investigate how the physical, chemical, and mechanical properties of candidate biomaterials influence cell behaviours, the testing sample is usually placed in commercially available cell culture plates. Thus, not only the testing sample itself but also the culture dish material might influence the cell behaviour. Therefore, an insert system was created to exclude this influence and allow investigations of the testing material solely. In this study micropatterned inserts prepared from polystyrene (PS) as well as from poly(ether imide) (PEI) with three different roughness levels of i) Rq = 0.29 μm (PS) and 0.23 μm (PEI); ii) Rq = 3.47 μm (PS) and 3.92 μm (PEI); and iii) Rq = 22.16 μm [corrected] (PS) and 22.65 μm (PEI) were explored with regard of their immuno-compatibility including the determination of potential contaminations with endotoxins or other microbial products. The endotoxin levels of the inserts were determined to be less than 0.07 EU/mL, which is well below the U.S. Food and Drug Administration limit of 0.5 EU/mL and the survival of murine macrophages cultured in the inserts was not impaired. Activation of early immune mechanisms such as complement activation and the generation of reactive oxygen species could not be observed. All tested materials had no influence on the cytokine secretion from cells of whole human blood. The investigated inserts were immuno-compatible and apparently free of contaminations with microbial products. The roughness of the inserts had no stimulatory or inhibitory effect on early immune mechanisms. Conclusively, the 24-well plate insert systems introduced in this study allow investigating the interactions of tailored surface properties such as roughness with many other cell types, without the disadvantage of the standard commercially available culture

Microbial β-glucosidases from cow rumen metagenome enhance the saccharification of lignocellulose in combination with commercial cellulase cocktail

PubMed Central

2012-01-01

Background A complete saccharification of plant polymers is the critical step in the efficient production of bio-alcohols. Beta-glucosidases acting in the degradation of intermediate gluco-oligosaccharides produced by cellulases limit the yield of the final product. Results In the present work, we have identified and then successfully cloned, expressed, purified and characterised 4 highly active beta-glucosidases from fibre-adherent microbial community from the cow rumen. The enzymes were most active at temperatures 45–55°C and pH 4.0-7.0 and exhibited high affinity and activity towards synthetic substrates such as p-nitrophenyl-beta-D-glucopyranoside (pNPbetaG) and pNP-beta-cellobiose, as well as to natural cello-oligosaccharides ranging from cellobiose to cellopentaose. The apparent capability of the most active beta-glucosidase, herein named LAB25g2, was tested for its ability to improve, at low dosage (31.25 units g-1 dry biomass, using pNPbetaG as substrate), the hydrolysis of pre-treated corn stover (dry matter content of 20%; 350 g glucan kg-1 dry biomass) in combination with a beta-glucosidase-deficient commercial Trichoderma reseei cellulase cocktail (5 units g-1 dry biomass in the basis of pNPbetaG). LAB25g2 increased the final hydrolysis yield by a factor of 20% (44.5 ± 1.7% vs. 34.5 ± 1.5% in control conditions) after 96–120 h as compared to control reactions in its absence or in the presence of other commercial beta-glucosidase preparations. The high stability (half-life higher than 5 days at 50°C and pH 5.2) and 2–38000 fold higher (as compared with reported beta-glucosidases) activity towards cello-oligosaccharides may account for its performance in supplementation assays. Conclusions The results suggest that beta-glucosidases from yet uncultured bacteria from animal digestomes may be of a potential interest for biotechnological processes related to the effective bio-ethanol production in combination with low dosage of commercial cellulases

Microbial communities associated with wet flue gas desulfurization systems

PubMed Central

Brown, Bryan P.; Brown, Shannon R.; Senko, John M.

2012-01-01

Flue gas desulfurization (FGD) systems are employed to remove SOx gasses that are produced by the combustion of coal for electric power generation, and consequently limit acid rain associated with these activities. Wet FGDs represent a physicochemically extreme environment due to the high operating temperatures and total dissolved solids (TDS) of fluids in the interior of the FGD units. Despite the potential importance of microbial activities in the performance and operation of FGD systems, the microbial communities associated with them have not been evaluated. Microbial communities associated with distinct process points of FGD systems at several coal-fired electricity generation facilities were evaluated using culture-dependent and -independent approaches. Due to the high solute concentrations and temperatures in the FGD absorber units, culturable halothermophilic/tolerant bacteria were more abundant in samples collected from within the absorber units than in samples collected from the makeup waters that are used to replenish fluids inside the absorber units. Evaluation of bacterial 16S rRNA genes recovered from scale deposits on the walls of absorber units revealed that the microbial communities associated with these deposits are primarily composed of thermophilic bacterial lineages. These findings suggest that unique microbial communities develop in FGD systems in response to physicochemical characteristics of the different process points within the systems. The activities of the thermophilic microbial communities that develop within scale deposits could play a role in the corrosion of steel structures in FGD systems. PMID:23226147

Diversity of Extremely Halophilic Archaeal and Bacterial Communities from Commercial Salts.

PubMed

Gibtan, Ashagrie; Park, Kyounghee; Woo, Mingyeong; Shin, Jung-Kue; Lee, Dong-Woo; Sohn, Jae Hak; Song, Minjung; Roh, Seong Woon; Lee, Sang-Jae; Lee, Han-Seung

2017-01-01

Salting is one of the oldest food preservation techniques. However, salt is also the source of living halophilic microorganisms that may affect human health. In order to determine the microbial communities of commercial salts, an investigation were done using amplicon sequencing approach in four commercial salts: Ethiopian Afdera salt (EAS), Ethiopian rock salt (ERS), Korean Jangpan salt (KJS), and Korean Topan salt (KTS). Using domain-specific primers, a region of the 16S rRNA gene was amplified and sequenced using a Roche 454 instrument. The results indicated that these microbial communities contained 48.22-61.4% Bacteria, 37.72-51.26% Archaea, 0.51-0.86% Eukarya, and 0.005-0.009% unclassified reads. Among bacteria, the communities in these salts were dominated by the phyla Proteobacteria, Bacteroidetes, Actinobacteria , and Firmicutes . Of the archaea, 91.58% belonged to the class Halobacteria , whereas the remaining 7.58, 0.83, and 0.01% were Nanoarchaea, Methanobacteria , and Thermococci , respectively. This comparison of microbial diversity in salts from two countries showed the presence of many archaeal and bacterial genera that occurred in salt samples from one country but not the other. The bacterial genera Enterobacter and Halovibrio were found only in Korean and Ethiopian salts, respectively. This study indicated the occurrence and diversity of halophilic bacteria and archaea in commercial salts that could be important in the gastrointestinal tract after ingestion.

Microbiota of high-pressure-processed Serrano ham investigated by culture-dependent and culture-independent methods.

PubMed

Martínez-Onandi, N; Castioni, A; San Martín, E; Rivas-Cañedo, A; Nuñez, M; Torriani, S; Picon, A

2017-01-16

The microbiota of Serrano dry-cured ham of different chemical composition, subjected or not to high-pressure processing (HPP), was investigated using culture-dependent and culture-independent methods. Microbial counts were submitted to analysis of variance with physicochemical parameters (a w , NaCl concentration, salt-in-lean ratio and intramuscular fat content) or HPP as main effects. In untreated hams, physicochemical parameters significantly affected counts of aerobic mesophiles, psychrotrophs, and moulds and yeasts. NaCl concentration and fat content influenced the levels of four and three of the five studied microbial groups, respectively, whereas no influence of a w was stated. The HPP treatment had a significant effect on counts of all investigated microbial groups. Culture-independent methods showed the presence of bacteria such as Staphylococcus equorum, Staphylococcus succinus, Bacillus subtilis and Cellulosimicrobium sp., moulds like Penicillium commune, Aspergillus fumigatus, Sclerotinia sclerotiorum, Eurotium athecium and Moniliella mellis, and yeasts like Debaryomyces hansenii and Candida glucosophila. Absence of B. subtilis bands and weaker bands of E. athecium were recorded for HPP-treated hams. The higher microbial levels found in lean ham might result in a quicker deterioration. HPP treatment confirmed its suitability as a procedure to control spoilage microorganisms. DGGE did not seem to be sensitive enough to highlight changes caused by HPP treatment in the microbiota of ham, but contributed to the detection of microbial species not previously found in ham. Copyright © 2016 Elsevier B.V. All rights reserved.

Comparison of microbially enhanced compost extracts produced from composted cattle rumen content material and from commercially available inocula.

PubMed

Shrestha, Karuna; Adetutu, Eric M; Shrestha, Pramod; Walsh, Kerry B; Harrower, Keith M; Ball, Andrew S; Midmore, David J

2011-09-01

A comparative study was performed on compost extracts prepared from cattle rumen content composted for three and nine months, nine month old compost inoculated with a Nutri-Life 4/20™ inoculum, and two commercial preparations (LivingSoil™ and Nutri-Life 4/20™), all incubated for 48h. Nutri-Life 4/20™ had the highest concentrations of NO(3)(-)-N and K(+)-K, while rumen compost extract had higher humic and fulvic acids concentration. The bacterial and fungal community level functional diversity of three month old compost extract and of LivingSoil™, assessed with Biolog™, were higher than that of nine month old rumen compost extract, with or without Nutri-Life 4/20™ inoculum, or Nutri-Life 4/20™. No difference in fungal diversity was observed between treatments, as indicated by Denaturing Gradient Gel Electrophoresis (DGGE) analysis, however, bacterial diversity was higher in all compost extracts and LivingSoil™ compared to the Nutri-Life 4/20™. Criteria for judging the quality of a microbially enhanced extract are discussed. Copyright © 2011 Elsevier Ltd. All rights reserved.

Addition of high concentration of inorganic selenium in orchardgrass (Dactylis glomerata L.) hay diet does not interfere with microbial fermentation in mixed ruminal microorganisms in continuous cultures

USDA-ARS?s Scientific Manuscript database

The current literature lacks information on ruminal microbial metabolism in response to high selenium (Se) concentration in the diet. We investigated changes in ruminal fermentation when high concentration of Se was administered in mixed ruminal cultures in fermentors. Two mature beef cows, 'tted wi...

Rapid System to Quantitatively Characterize the Airborne Microbial Community

NASA Technical Reports Server (NTRS)

Macnaughton, Sarah J.

1998-01-01

Bioaerosols have been linked to a wide range of different allergies and respiratory illnesses. Currently, microorganism culture is the most commonly used method for exposure assessment. Such culture techniques, however, generally fail to detect between 90-99% of the actual viable biomass. Consequently, an unbiased technique for detecting airborne microorganisms is essential. In this Phase II proposal, a portable air sampling device his been developed for the collection of airborne microbial biomass from indoor (and outdoor) environments. Methods were evaluated for extracting and identifying lipids that provide information on indoor air microbial biomass, and automation of these procedures was investigated. Also, techniques to automate the extraction of DNA were explored.

Biodegradation of oil tank bottom sludge using microbial consortia.

PubMed

Gallego, José Luis R; García-Martínez, María Jesús; Llamas, Juan F; Belloch, Carmen; Peláez, Ana I; Sánchez, Jesús

2007-06-01

We present a rationale for the selection of a microbial consortia specifically adapted to degrade toxic components of oil refinery tank bottom sludge (OTBS). Sources such as polluted soils, petrochemical waste, sludge from refinery-wastewater plants, and others were used to obtain a collection of eight microorganisms, which were individually tested and characterized to analyze their degradative capabilities on different hydrocarbon families. After initial experiments using mixtures of these strains, we developed a consortium consisting of four microorganisms (three bacteria and one yeast) selected in the basis of their cometabolic effects, emulsification properties, colonization of oil components, and degradative capabilities. Although the specific contribution each of the former parameters makes is not clearly understood, the activity of the four-member consortium had a strong impact not only on linear alkane degradation (100%), but also on the degradation of cycloalkanes (85%), branched alkanes (44%), and aromatic and sulphur-aromatic compounds (31-55%). The effectiveness of this consortium was significantly superior to that obtained by individual strains, commercial inocula or an undefined mixture of culturable and non-culturable microorganisms obtained from OTBS-polluted soil. However, results were similar when another consortium of four microorganisms, previously isolated in the same OTBS-polluted soil, was assayed.

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

PubMed Central

Zou, Wei; Zhao, Changqing; Luo, Huibo

2018-01-01

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

Microbial Engineering for Aldehyde Synthesis

PubMed Central

Kunjapur, Aditya M.

2015-01-01

Aldehydes are a class of chemicals with many industrial uses. Several aldehydes are responsible for flavors and fragrances present in plants, but aldehydes are not known to accumulate in most natural microorganisms. In many cases, microbial production of aldehydes presents an attractive alternative to extraction from plants or chemical synthesis. During the past 2 decades, a variety of aldehyde biosynthetic enzymes have undergone detailed characterization. Although metabolic pathways that result in alcohol synthesis via aldehyde intermediates were long known, only recent investigations in model microbes such as Escherichia coli have succeeded in minimizing the rapid endogenous conversion of aldehydes into their corresponding alcohols. Such efforts have provided a foundation for microbial aldehyde synthesis and broader utilization of aldehydes as intermediates for other synthetically challenging biochemical classes. However, aldehyde toxicity imposes a practical limit on achievable aldehyde titers and remains an issue of academic and commercial interest. In this minireview, we summarize published efforts of microbial engineering for aldehyde synthesis, with an emphasis on de novo synthesis, engineered aldehyde accumulation in E. coli, and the challenge of aldehyde toxicity. PMID:25576610

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

Overproduction of laccase and pectinase by microbial associations in solid substrate fermentation.

PubMed

Stoilova, Ivanka; Krastanov, Albert

2008-04-01

The growth and the enzymatic production of two microbial fungal associations were studied: Aspergillus niger and Fusarium moniliforme and Trametes versicolor and Aspergillus niger. The synergistic interrelations between the species of the first mixed culture increased the biosynthesis of alpha-amylase and pectinase. T. versicolor and A. niger proved to be compatible partners in the overproduction of the enzyme laccase, whose synthesis surpassed 8.4 times the enzymatic level in the monoculture, with both of the mixed microbial populations cocultivation facilitating the amplified synthesis of enzymes rather than their growth acceleration. A further proof of the presence of synergism established by the cultures was the enzyme volumetric productivities in both of the mixed microbial cultures, which increased parallel to the rise in the combined biomass synthesis. The competent selection of compatible partners can adjust the desired enzymatic levels and compositions in mixed fungal systems aimed at a number of specified designations. Thus, a very high level of laccase production (97,600 IU/g dry weight) was achieved. The chosen fungal strains produce a variety of different enzymes, but first microbial association produces mainly amylase and pectinase, necessary for their growth, and second association produces mainly laccase and pectinase.

Design of a microbial fuel cell and its transition to microbial electrolytic cell for hydrogen production by electrohydrogenesis.

PubMed

Gupta, Pratima; Parkhey, Piyush; Joshi, Komal; Mahilkar, Anjali

2013-10-01

Anaerobic bacteria were isolated from industrial wastewater and soil samples and tested for exoelectrogenic activity by current production in double chambered microbial fuel cell (MFC), which was further transitioned into a single chambered microbial electrolytic cell to test hydrogen production by electrohydrogenesis. Of all the cultures, the isolate from industrial water sample showed the maximum values for current = 0.161 mA, current density = 108.57 mA/m2 and power density = 48.85 mW/m2 with graphite electrode. Maximum voltage across the cell, however, was reported by the isolate from sewage water sample (506 mv) with copper as electrode. Tap water with KMnO4 was the best cathodic electrolyte as the highest values for all the measured MFC parameters were reported with it. Once the exoelectrogenic activity of the isolates was confirmed by current production, these were tested for hydrogen production in a single chambered microbial electrolytic cell (MEC) modified from the MFC. Hydrogen production was reported positive from co-culture of isolates of both the water samples and co-culture of one soil and one water sample. The maximum rate and yield of hydrogen production was 0.18 m3H2/m3/d and 3.2 mol H2/mol glucose respectively with total hydrogen production of 42.4 mL and energy recovery of 57.4%. Cumulative hydrogen production for a five day cycle of MEC operation was 0.16 m3H2/m3/d.

Microbial synthesis of chalcogenide semiconductor nanoparticles: a review.

PubMed

Jacob, Jaya Mary; Lens, Piet N L; Balakrishnan, Raj Mohan

2016-01-01

Chalcogenide semiconductor quantum dots are emerging as promising nanomaterials due to their size tunable optoelectronic properties. The commercial synthesis and their subsequent integration for practical uses have, however, been contorted largely due to the toxicity and cost issues associated with the present chemical synthesis protocols. Accordingly, there is an immediate need to develop alternative environment-friendly synthesis procedures. Microbial factories hold immense potential to achieve this objective. Over the past few years, bacteria, fungi and yeasts have been experimented with as eco-friendly and cost-effective tools for the biosynthesis of semiconductor quantum dots. This review provides a detailed overview about the production of chalcogen-based semiconductor quantum particles using the inherent microbial machinery. © 2015 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Electricity production and microbial biofilm characterization in cellulose-fed microbial fuel cells.

PubMed

Ren, Z; Steinberg, L M; Regan, J M

2008-01-01

Converting biodegradable materials into electricity, microbial fuel cells (MFCs) present a promising technology for renewable energy production in specific applications. Unlike typical soluble substrates that have been used as electron donors in MFC studies, cellulose is unique because it requires a microbial consortium that can metabolize both an insoluble electron donor (cellulose) and electron acceptor (electrode). In this study, electricity generation and the microbial ecology of cellulose-fed MFCs were analyzed using a defined co-culture of Clostridium cellulolyticum and Geobacter sulfurreducens. Fluorescent in situ hybridization and quantitative PCR showed that when particulate MN301 cellulose was used as sole substrate, most Clostridium cells were found adhered to cellulose particles in suspension, while most Geobacter cells were attached to the electrode. By comparison, both bacteria resided in suspension and biofilm samples when soluble carboxymethyl cellulose was used. This distinct function-related distribution of the bacteria suggests an opportunity to optimize reactor operation by settling cellulose and decanting supernatant to extend cellulose hydrolysis and improve cellulose-electricity conversion. (c) IWA Publishing 2008.

Dynamic assessment of microbial ecology (DAME): A shiny app for analysis and visualization of microbial sequencing data

USDA-ARS?s Scientific Manuscript database

A new renaissance in knowledge about the role of commensal microbiota in health and disease is well underway facilitated by culture-independent sequencing technologies; however, microbial sequencing data poses new challenges (e.g., taxonomic hierarchy, overdispersion) not generally seen in more trad...

Unconditioned commercial embryo culture media contain a large variety of non-declared proteins: a comprehensive proteomics analysis.

PubMed

Dyrlund, Thomas F; Kirkegaard, Kirstine; Poulsen, Ebbe Toftgaard; Sanggaard, Kristian W; Hindkjær, Johnny J; Kjems, Jørgen; Enghild, Jan J; Ingerslev, Hans Jakob

2014-11-01

Which non-declared proteins (proteins not listed on the composition list of the product data sheet) are present in unconditioned commercial embryo culture media? A total of 110 non-declared proteins were identified in unconditioned media and between 6 and 8 of these were quantifiable and therefore represent the majority of the total protein in the media samples. There are no data in the literature on what non-declared proteins are present in unconditioned (fresh media in which no embryos have been cultured) commercial embryo media. The following eight commercial embryo culture media were included in this study: G-1 PLUS and G-2 PLUS G5 Series from Vitrolife, Sydney IVF Cleavage Medium and Sydney IVF Blastocyst Medium from Cook Medical and EmbryoAssist, BlastAssist, Sequential Cleav and Sequential Blast from ORIGIO. Two batches were analyzed from each of the Sydney IVF media and one batch from each of the other media. All embryo culture media are supplemented by the manufacturers with purified human serum albumin (HSA 5 mg/ml). The purified HSA (HSA-solution from Vitrolife) and the recombinant human albumin supplement (G-MM from Vitrolife) were also analyzed. For protein quantification, media samples were in-solution digested with trypsin and analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). For in-depth protein identification, media were albumin depleted, dialyzed and concentrated before sodium dodecyl sulfate polyacrylamide gel electrophoresis. The gel was cut into 14 slices followed by in-gel trypsin digestion, and analysis by LC-MS/MS. Proteins were further investigated using gene ontology (GO) terms analysis. Using advanced mass spectrometry and high confidence criteria for accepting proteins (P < 0.01), a total of 110 proteins other than HSA were identified. The average HSA content was found to be 94% (92-97%) of total protein. Other individual proteins accounted for up to 4.7% of the total protein. Analysis of purified HSA strongly

Synthetic Microbial Ecology: Engineering Habitats for Modular Consortia.

PubMed

Ben Said, Sami; Or, Dani

2017-01-01

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

Culture-independent phylogenetic analysis of the microbial community in industrial sugarcane bagasse feedstock piles.

PubMed

Rattanachomsri, Ukrit; Kanokratana, Pattanop; Eurwilaichitr, Lily; Igarashi, Yasuo; Champreda, Verawat

2011-01-01

Sugarcane bagasse is an important lignocellulosic by-product with potential for conversion to biofuels and chemicals in biorefinery. As a step towards an understanding of microbial diversity and the processes existing in bagasse collection sites, the microbial community in industrial bagasse feedstock piles was investigated. Molecular biodiversity analysis of 16S rDNA sequences revealed the presence of a complex bacterial community. A diverse group of mainly aerobic and facultative anaerobic bacteria was identified reflecting the aerobic and high temperature microenvironmental conditions under the pile surface. The major bacterial taxa present were identified as Firmicutes, Alpha- and Gammaproteobacteria, Acidobacteria, Bacteroidetes, and Actinobacteria. Analysis of the eukaryotic microbial assemblage based on an internal transcribed spacer revealed the predominance of diverse cellulolytic and hemicellulolytic ascomycota. A microbial interaction model is proposed, focusing on lignocellulose degradation and methane metabolism. The insights into the microbial community in this study provide a basis for efficient utilization of bagasse in lignocellulosic biomass-based industries.

Microbial Life of North Pacific Oceanic Crust

NASA Astrophysics Data System (ADS)

Schumann, G.; Koos, R.; Manz, W.; Reitner, J.

2003-12-01

Information on the microbiology of the deep subsurface is necessary in order to understand the factors controlling the rate and extent of the microbially catalyzed reactions that influence the geophysical properties of these environments. Drilling into 45-Ma oceanic basaltic crust in a deepwater environment during ODP Leg 200 provided a promising opportunity to explore the abundance, diversity and activity of micro-organisms. The combined use of culture-independent molecular phylogenetic analyses and enrichment culture techniques is an advantageous approach in investigating subsurface microbial ecosystems. Enrichment culture methods allow the evaluation of potential activities and functions. Microbiological investigations revealed few aerobic cultivable, in part hitherto unknown, micro-organisms in deep submarine sediments and basaltic lava flows. 16S rDNA sequencing of isolates from sediment revealed the next relatives to be members of the genera Halomonas, Pseudomonas, and Lactobacillus. Within the Pseudomonadaceae the closest relative is Acinetobacter sp., which was isolated from a deep subsurface environment. The next phylogenetical relatives within the Halomonadaceae are bacteria typically isolated from Soda lakes, which are considered as model of early life conditions. Interestingly, not only sediment bacteria could be obtained in pure culture. Aerobic strains could also be successfully isolated from the massive tholeiitic basalt layer at a depth of 76.16 mbsf (46 m below the sediment/basement contact). These particular isolates are gram-positive with low G+C content of DNA, phylogenetically affiliated to the phylum Firmicutes. The closest neighbors are e.g. a marine Bacillus isolated from the Gulf of Mexico and a low G+C gram-positive bacterium, which belongs to the microbial flora in the deepest sea mud of the Mariana Trench, isolated from a depth of 10,897 m. Based on the similarity values, the isolates represent hitherto undescribed species of the deep

Production of microbial glycolipid biosurfactants and their antimicrobial activity

USDA-ARS?s Scientific Manuscript database

Microbial glycolipids produced by bacteria or yeast as secondary metabolites, such as sophorolipids (SLs), rhamnolipids (RLs) and mannosylerythritol lipids (MELs) are “green” biosurfactants desirable in a bioeconomy. High cost of production is a major hurdle toward widespread commercial use of bios...

Deciphering Diversity Indices for a Better Understanding of Microbial Communities.

PubMed

Kim, Bo-Ra; Shin, Jiwon; Guevarra, Robin; Lee, Jun Hyung; Kim, Doo Wan; Seol, Kuk-Hwan; Lee, Ju-Hoon; Kim, Hyeun Bum; Isaacson, Richard

2017-12-28

The past decades have been a golden era during which great tasks were accomplished in the field of microbiology, including food microbiology. In the past, culture-dependent methods have been the primary choice to investigate bacterial diversity. However, using cultureindependent high-throughput sequencing of 16S rRNA genes has greatly facilitated studies exploring the microbial compositions and dynamics associated with health and diseases. These culture-independent DNA-based studies generate large-scale data sets that describe the microbial composition of a certain niche. Consequently, understanding microbial diversity becomes of greater importance when investigating the composition, function, and dynamics of the microbiota associated with health and diseases. Even though there is no general agreement on which diversity index is the best to use, diversity indices have been used to compare the diversity among samples and between treatments with controls. Tools such as the Shannon- Weaver index and Simpson index can be used to describe population diversity in samples. The purpose of this review is to explain the principles of diversity indices, such as Shannon- Weaver and Simpson, to aid general microbiologists in better understanding bacterial communities. In this review, important questions concerning microbial diversity are addressed. Information from this review should facilitate evidence-based strategies to explore microbial communities.

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

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

Sharma, M.M.; Georgiou, G.

1992-12-31

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

Effects of carbon sources on the enrichment of halophilic polyhydroxyalkanoate-storing mixed microbial culture in an aerobic dynamic feeding process

PubMed Central

Cui, You-Wei; Zhang, Hong-Yu; Lu, Peng-Fei; Peng, Yong-Zhen

2016-01-01

Microbial polyhydroxyalkanoate (PHA) production serves as a substitute for petroleum-based plastics. Enriching mixed microbial cultures (MMCs) with the capacity to store PHA is a key precursor for low-cost PHA production. This study investigated the impact of carbon types on enrichment outcomes. Three MMCs were separately fed by acetate sodium, glucose, and starch as an enriching carbon source, and were exposed to long-term aerobic dynamic feeding (ADF) periods. The PHA production capacity, kinetics and stoichiometry of the enrichments, the PHA composition, and the microbial diversity and community composition were explored to determine carbon and enrichment correlations. After 350-cycle enriching periods under feast-famine (F-F) regimes, the MMCs enriched by acetate sodium and glucose contained a maximum PHA content of 64.7% and 60.5% cell dry weight (CDW). The starch-enriched MMC only had 27.3% CDW of PHA. High-throughput sequencing revealed that non-PHA bacteria survived alongside PHA storing bacteria, even under severe F-F selective pressure. Genus of Pseudomonas and Stappia were the possible PHA accumulating bacteria in acetate-enriched MMC. Genus of Oceanicella, Piscicoccus and Vibrio were found as PHA accumulating bacteria in glucose-enriched MMC. Vibrio genus was the only PHA accumulating bacteria in starch-enriched MMC. The community diversity and composition were regulated by the substrate types. PMID:27485896

Effects of carbon sources on the enrichment of halophilic polyhydroxyalkanoate-storing mixed microbial culture in an aerobic dynamic feeding process

NASA Astrophysics Data System (ADS)

Cui, You-Wei; Zhang, Hong-Yu; Lu, Peng-Fei; Peng, Yong-Zhen

2016-08-01

Microbial polyhydroxyalkanoate (PHA) production serves as a substitute for petroleum-based plastics. Enriching mixed microbial cultures (MMCs) with the capacity to store PHA is a key precursor for low-cost PHA production. This study investigated the impact of carbon types on enrichment outcomes. Three MMCs were separately fed by acetate sodium, glucose, and starch as an enriching carbon source, and were exposed to long-term aerobic dynamic feeding (ADF) periods. The PHA production capacity, kinetics and stoichiometry of the enrichments, the PHA composition, and the microbial diversity and community composition were explored to determine carbon and enrichment correlations. After 350-cycle enriching periods under feast-famine (F-F) regimes, the MMCs enriched by acetate sodium and glucose contained a maximum PHA content of 64.7% and 60.5% cell dry weight (CDW). The starch-enriched MMC only had 27.3% CDW of PHA. High-throughput sequencing revealed that non-PHA bacteria survived alongside PHA storing bacteria, even under severe F-F selective pressure. Genus of Pseudomonas and Stappia were the possible PHA accumulating bacteria in acetate-enriched MMC. Genus of Oceanicella, Piscicoccus and Vibrio were found as PHA accumulating bacteria in glucose-enriched MMC. Vibrio genus was the only PHA accumulating bacteria in starch-enriched MMC. The community diversity and composition were regulated by the substrate types.

Effects of carbon sources on the enrichment of halophilic polyhydroxyalkanoate-storing mixed microbial culture in an aerobic dynamic feeding process.

PubMed

Cui, You-Wei; Zhang, Hong-Yu; Lu, Peng-Fei; Peng, Yong-Zhen

2016-08-03

Microbial polyhydroxyalkanoate (PHA) production serves as a substitute for petroleum-based plastics. Enriching mixed microbial cultures (MMCs) with the capacity to store PHA is a key precursor for low-cost PHA production. This study investigated the impact of carbon types on enrichment outcomes. Three MMCs were separately fed by acetate sodium, glucose, and starch as an enriching carbon source, and were exposed to long-term aerobic dynamic feeding (ADF) periods. The PHA production capacity, kinetics and stoichiometry of the enrichments, the PHA composition, and the microbial diversity and community composition were explored to determine carbon and enrichment correlations. After 350-cycle enriching periods under feast-famine (F-F) regimes, the MMCs enriched by acetate sodium and glucose contained a maximum PHA content of 64.7% and 60.5% cell dry weight (CDW). The starch-enriched MMC only had 27.3% CDW of PHA. High-throughput sequencing revealed that non-PHA bacteria survived alongside PHA storing bacteria, even under severe F-F selective pressure. Genus of Pseudomonas and Stappia were the possible PHA accumulating bacteria in acetate-enriched MMC. Genus of Oceanicella, Piscicoccus and Vibrio were found as PHA accumulating bacteria in glucose-enriched MMC. Vibrio genus was the only PHA accumulating bacteria in starch-enriched MMC. The community diversity and composition were regulated by the substrate types.

Biogeochemistry of microbial coal-bed methane

USGS Publications Warehouse

Strc, D.; Mastalerz, Maria; Dawson, K.; MacAlady, J.; Callaghan, A.V.; Wawrik, B.; Turich, C.; Ashby, M.

2011-01-01

Microbial methane accumulations have been discovered in multiple coal-bearing basins over the past two decades. Such discoveries were originally based on unique biogenic signatures in the stable isotopic composition of methane and carbon dioxide. Basins with microbial methane contain either low-maturity coals with predominantly microbial methane gas or uplifted coals containing older, thermogenic gas mixed with more recently produced microbial methane. Recent advances in genomics have allowed further evaluation of the source of microbial methane, through the use of high-throughput phylogenetic sequencing and fluorescent in situ hybridization, to describe the diversity and abundance of bacteria and methanogenic archaea in these subsurface formations. However, the anaerobic metabolism of the bacteria breaking coal down to methanogenic substrates, the likely rate-limiting step in biogenic gas production, is not fully understood. Coal molecules are more recalcitrant to biodegradation with increasing thermal maturity, and progress has been made in identifying some of the enzymes involved in the anaerobic degradation of these recalcitrant organic molecules using metagenomic studies and culture enrichments. In recent years, researchers have attempted lab and subsurface stimulation of the naturally slow process of methanogenic degradation of coal. Copyright ?? 2011 by Annual Reviews. All rights reserved.

Culture and molecular identification of fungal contaminants in edible bird nests.

PubMed

Chen, Jennifer Xiao Jing; Wong, Shew Fung; Lim, Patricia Kim Chooi; Mak, Joon Wah

2015-01-01

Widespread food poisoning due to microbial contamination has been a major concern for the food industry, consumers and governing authorities. This study is designed to determine the levels of fungal contamination in edible bird nests (EBNs) using culture and molecular techniques. Raw EBNs were collected from five house farms, and commercial EBNs were purchased from five Chinese traditional medicine shops (companies A-E) in Peninsular Malaysia. The fungal contents in the raw and commercial EBNs, and boiled and unboiled EBNs were determined. Culturable fungi were isolated and identified. In this study, the use of these methods revealed that all EBNs had fungal colony-forming units (CFUs) that exceeded the limit set by Standards and Industrial Research Institute of Malaysia (SIRIM) for yeast and moulds in EBNs. There was a significant difference (p < 0.05) in the number of types of fungi isolated from raw and commercial EBNs, but no significant difference in the reduction of the number of types of fungi after boiling the EBNs (p > 0.05). The types of fungi isolated from the unboiled raw EBNs were mainly soil, plant and environmental fungi, while the types of fungi isolated from the boiled raw EBNs, unboiled and boiled commercial EBNs were mainly environmental fungi. Aspergillus sp., Candida sp., Cladosporium sp., Neurospora sp. and Penicillum sp. were the most common fungi isolated from the unboiled and boiled raw and commercial EBNs. Some of these fungi are mycotoxin producers and cause opportunistic infections in humans. Further studies to determine the mycotoxin levels and methods to prevent or remove these contaminations from EBNs for safe consumption are necessary. The establishment and implementation of stringent regulations for the standards of EBNs should be regularly updated and monitored to improve the quality of the EBNs and consumer safety.

Characterization and performance of anodic mixed culture biofilms in submersed microbial fuel cells.

PubMed

Saba, Beenish; Christy, Ann D; Yu, Zhongtang; Co, Anne C; Islam, Rafiq; Tuovinen, Olli H

2017-02-01

Microbial fuel cells (MFCs) were designed for laboratory scale experiments to study electroactive biofilms in anodic chambers. Anodic biofilms and current generation during biofilm growth were examined using single chambered MFCs submersed in algal catholyte. A culture of the marine green alga Nanochloropsis salina was used as a biocatholyte, and a rumen fluid microbiota was the anodic chamber inoculum. Electrical impedance spectroscopy was performed under varying external resistance once a week to identify mass transport limitations at the biofilm-electrolyte interface during the four-week experiment. The power generation increased from 249 to 461mWm -2 during the time course. Confocal laser scanning microscopy imaging showed that the depth of the bacterial biofilm on the anode was about 65μm. There were more viable bacteria on the biofilm surface and near the biofilm-electrolyte interface as compared to those close to the anode surface. The results suggest that biofilm growth on the anode creates a conductive layer, which can help overcome mass transport limitations in MFCs. Copyright © 2016 Elsevier B.V. All rights reserved.

The Microbial Fecal Indicator Paradigm: Tools in the Toolbox Applications in Recreational Waters

EPA Science Inventory

Summary of ORD’s recent research to develop tools for assessing microbial water quality in recreational waters. Methods discussed include the development of health associations between microbial fecal indicators and the development of culture, and molecular methods for fec...

Census of the bacterial community of the gypsy moth larval midgut by using culturing and culture-independent methods.

PubMed

Broderick, Nichole A; Raffa, Kenneth F; Goodman, Robert M; Handelsman, Jo

2004-01-01

Little is known about bacteria associated with Lepidoptera, the large group of mostly phytophagous insects comprising the moths and butterflies. We inventoried the larval midgut bacteria of a polyphagous foliivore, the gypsy moth (Lymantria dispar L.), whose gut is highly alkaline, by using traditional culturing and culture-independent methods. We also examined the effects of diet on microbial composition. Analysis of individual third-instar larvae revealed a high degree of similarity of microbial composition among insects fed on the same diet. DNA sequence analysis indicated that most of the PCR-amplified 16S rRNA genes belong to the gamma-Proteobacteria and low G+C gram-positive divisions and that the cultured members represented more than half of the phylotypes identified. Less frequently detected taxa included members of the alpha-Proteobacterium, Actinobacterium, and Cytophaga/Flexibacter/Bacteroides divisions. The 16S rRNA gene sequences from 7 of the 15 cultured organisms and 8 of the 9 sequences identified by PCR amplification diverged from previously reported bacterial sequences. The microbial composition of midguts differed substantially among larvae feeding on a sterilized artificial diet, aspen, larch, white oak, or willow. 16S rRNA analysis of cultured isolates indicated that an Enterococcus species and culture-independent analysis indicated that an Entbacter sp. were both present in all larvae, regardless of the feeding substrate; the sequences of these two phylotypes varied less than 1% among individual insects. These results provide the first comprehensive description of the microbial diversity of a lepidopteran midgut and demonstrate that the plant species in the diet influences the composition of the gut bacterial community.

Microbial community structures differentiated in a single-chamber air-cathode microbial fuel cell fueled with rice straw hydrolysate.

PubMed

Wang, Zejie; Lee, Taekwon; Lim, Bongsu; Choi, Chansoo; Park, Joonhong

2014-01-17

The microbial fuel cell represents a novel technology to simultaneously generate electric power and treat wastewater. Both pure organic matter and real wastewater can be used as fuel to generate electric power and the substrate type can influence the microbial community structure. In the present study, rice straw, an important feedstock source in the world, was used as fuel after pretreatment with diluted acid method for a microbial fuel cell to obtain electric power. Moreover, the microbial community structures of anodic and cathodic biofilm and planktonic culturewere analyzed and compared to reveal the effect of niche on microbial community structure. The microbial fuel cell produced a maximum power density of 137.6 ± 15.5 mW/m2 at a COD concentration of 400 mg/L, which was further increased to 293.33 ± 7.89 mW/m2 through adjusting the electrolyte conductivity from 5.6 mS/cm to 17 mS/cm. Microbial community analysis showed reduction of the microbial diversities of the anodic biofilm and planktonic culture, whereas diversity of the cathodic biofilm was increased. Planktonic microbial communities were clustered closer to the anodic microbial communities compared to the cathodic biofilm. The differentiation in microbial community structure of the samples was caused by minor portion of the genus. The three samples shared the same predominant phylum of Proteobacteria. The abundance of exoelectrogenic genus was increased with Desulfobulbus as the shared most abundant genus; while the most abundant exoelectrogenic genus of Clostridium in the inoculum was reduced. Sulfate reducing bacteria accounted for large relative abundance in all the samples, whereas the relative abundance varied in different samples. The results demonstrated that rice straw hydrolysate can be used as fuel for microbial fuel cells; microbial community structure differentiated depending on niches after microbial fuel cell operation; exoelectrogens were enriched; sulfate from rice straw

Microbial community structures differentiated in a single-chamber air-cathode microbial fuel cell fueled with rice straw hydrolysate

PubMed Central

2014-01-01

Background The microbial fuel cell represents a novel technology to simultaneously generate electric power and treat wastewater. Both pure organic matter and real wastewater can be used as fuel to generate electric power and the substrate type can influence the microbial community structure. In the present study, rice straw, an important feedstock source in the world, was used as fuel after pretreatment with diluted acid method for a microbial fuel cell to obtain electric power. Moreover, the microbial community structures of anodic and cathodic biofilm and planktonic culturewere analyzed and compared to reveal the effect of niche on microbial community structure. Results The microbial fuel cell produced a maximum power density of 137.6 ± 15.5 mW/m2 at a COD concentration of 400 mg/L, which was further increased to 293.33 ± 7.89 mW/m2 through adjusting the electrolyte conductivity from 5.6 mS/cm to 17 mS/cm. Microbial community analysis showed reduction of the microbial diversities of the anodic biofilm and planktonic culture, whereas diversity of the cathodic biofilm was increased. Planktonic microbial communities were clustered closer to the anodic microbial communities compared to the cathodic biofilm. The differentiation in microbial community structure of the samples was caused by minor portion of the genus. The three samples shared the same predominant phylum of Proteobacteria. The abundance of exoelectrogenic genus was increased with Desulfobulbus as the shared most abundant genus; while the most abundant exoelectrogenic genus of Clostridium in the inoculum was reduced. Sulfate reducing bacteria accounted for large relative abundance in all the samples, whereas the relative abundance varied in different samples. Conclusion The results demonstrated that rice straw hydrolysate can be used as fuel for microbial fuel cells; microbial community structure differentiated depending on niches after microbial fuel cell operation; exoelectrogens were

Characterization of two diesel fuel degrading microbial consortia enriched from a non acclimated, complex source of microorganisms

PubMed Central

2010-01-01

Background The bioremediation of soils impacted by diesel fuels is very often limited by the lack of indigenous microflora with the required broad substrate specificity. In such cases, the soil inoculation with cultures with the desired catabolic capabilities (bioaugmentation) is an essential option. The use of consortia of microorganisms obtained from rich sources of microbes (e.g., sludges, composts, manure) via enrichment (i.e., serial growth transfers) on the polluting hydrocarbons would provide bioremediation enhancements more robust and reproducible than those achieved with specialized pure cultures or tailored combinations (co-cultures) of them, together with none or minor risks of soil loading with unrelated or pathogenic allocthonous microorganisms. Results In this work, two microbial consortia, i.e., ENZ-G1 and ENZ-G2, were enriched from ENZYVEBA (a complex commercial source of microorganisms) on Diesel (G1) and HiQ Diesel (G2), respectively, and characterized in terms of microbial composition and hydrocarbon biodegradation capability and specificity. ENZ-G1 and ENZ-G2 exhibited a comparable and remarkable biodegradation capability and specificity towards n-C10 to n-C24 linear paraffins by removing about 90% of 1 g l-1 of diesel fuel applied after 10 days of aerobic shaken flask batch culture incubation at 30°C. Cultivation dependent and independent approaches evidenced that both consortia consist of bacteria belonging to the genera Chryseobacterium, Acinetobacter, Psudomonas, Stenotrophomonas, Alcaligenes and Gordonia along with the fungus Trametes gibbosa. However, only the fungus was found to grow and remarkably biodegrade G1 and G2 hydrocarbons under the same conditions. The biodegradation activity and specificity and the microbial composition of ENZ-G1 and ENZ-G2 did not significantly change after cryopreservation and storage at -20°C for several months. Conclusions ENZ-G1 and ENZ-G2 are very similar highly enriched consortia of bacteria and a

Characterization of two diesel fuel degrading microbial consortia enriched from a non acclimated, complex source of microorganisms.

PubMed

Zanaroli, Giulio; Di Toro, Sara; Todaro, Daniela; Varese, Giovanna C; Bertolotto, Antonio; Fava, Fabio

2010-02-16

The bioremediation of soils impacted by diesel fuels is very often limited by the lack of indigenous microflora with the required broad substrate specificity. In such cases, the soil inoculation with cultures with the desired catabolic capabilities (bioaugmentation) is an essential option. The use of consortia of microorganisms obtained from rich sources of microbes (e.g., sludges, composts, manure) via enrichment (i.e., serial growth transfers) on the polluting hydrocarbons would provide bioremediation enhancements more robust and reproducible than those achieved with specialized pure cultures or tailored combinations (co-cultures) of them, together with none or minor risks of soil loading with unrelated or pathogenic allocthonous microorganisms. In this work, two microbial consortia, i.e., ENZ-G1 and ENZ-G2, were enriched from ENZYVEBA (a complex commercial source of microorganisms) on Diesel (G1) and HiQ Diesel (G2), respectively, and characterized in terms of microbial composition and hydrocarbon biodegradation capability and specificity. ENZ-G1 and ENZ-G2 exhibited a comparable and remarkable biodegradation capability and specificity towards n-C10 to n-C24 linear paraffins by removing about 90% of 1 g l-1 of diesel fuel applied after 10 days of aerobic shaken flask batch culture incubation at 30 degrees C. Cultivation dependent and independent approaches evidenced that both consortia consist of bacteria belonging to the genera Chryseobacterium, Acinetobacter, Psudomonas, Stenotrophomonas, Alcaligenes and Gordonia along with the fungus Trametes gibbosa. However, only the fungus was found to grow and remarkably biodegrade G1 and G2 hydrocarbons under the same conditions. The biodegradation activity and specificity and the microbial composition of ENZ-G1 and ENZ-G2 did not significantly change after cryopreservation and storage at -20 degrees C for several months. ENZ-G1 and ENZ-G2 are very similar highly enriched consortia of bacteria and a fungus capable of

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

PubMed

Wang, Gang; Or, Dani

2014-10-24

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

Quantitative comparison of the in situ microbial communities in different biomes

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

White, D.C.; Ringelberg, D.B.; Palmer, R.J.

1995-12-31

A system to define microbial communities in different biomes requires the application of non-traditional methodology. Classical microbiological methods have severe limitations for the analysis of environmental samples. Pure-culture isolation, biochemical testing, and/or enumeration by direct microscopic counting are not well suited for the estimation of total biomass or the assessment of community composition within environmental samples. Such methods provide little insight into the in situ phenotypic activity of the extant microbiota since these techniques are dependent on microbial growth and thus select against many environmental microorganisms which are non- culturable under a wide range of conditions. It has been repeatedlymore » documented in the literature that viable counts or direct counts of bacteria attached to sediment grains are difficult to quantitative and may grossly underestimate the extent of the existing community. The traditional tests provide little indication of the in situ nutritional status or for evidence of toxicity within the microbial community. A more recent development (MIDI Microbial Identification System), measure free and ester-linked fatty acids from isolated microorganisms. Bacterial isolates are identified by comparing their fatty acid profiles to the MIKI database which contains over 8000 entries. The application of the MIKI system to the analysis of environmental samples however, has significant drawbacks. The MIDI system was developed to identify clinical microorganisms and requires their isolation and culture on trypticase soy agar at 27{degrees}C. Since many isolates are unable to grow at these restrictive growth conditions, the system does not lend itself to identification of some environmental organisms. A more applicable methodology for environmental microbial analysis is based on the liquid extrication and separation of microbial lipids from environmental samples, followed by quantitative analysis using gas

MICROBIAL SOURCE TRACKING: DIFFERENT USES AND APPROACHES

EPA Science Inventory

Microbial Source Tracking (MST) methods are used to determine the origin of fecal pollution impacting natural water systems. Several methods require the isolation of pure cultures in order to develop phenotypic or genotypic fingerprint libraries of both source and water bacterial...

Longitudinal analysis of microbiota in microalga Nannochloropsis salina cultures

DOE PAGES

Geng, Haifeng; Sale, Kenneth L.; Tran-Gyamfi, Mary Bao; ...

2016-03-08

Here, large-scale open microalgae cultivation has tremendous potential to make a significant contribution to replacing petroleum-based fuels with biofuels. Open algal cultures are unavoidably inhabited with a diversity of microbes that live on, influence, and shape the fate of these ecosystems. However, there is little understanding of the resilience and stability of the microbial communities in engineered semicontinuous algal systems. To evaluate the dynamics and resilience of the microbial communities in microalgae biofuel cultures, we conducted a longitudinal study on open systems to compare the temporal profiles of the microbiota from two multigenerational algal cohorts, which include one seeded withmore » the microbiota from an in-house culture and the other exogenously seeded with a natural-occurring consortia of bacterial species harvested from the Pacific Ocean. From these month-long, semicontinuous open microalga Nannochloropsis salina cultures, we sequenced a time-series of 46 samples, yielding 8804 operational taxonomic units derived from 9,160,076 high-quality partial 16S rRNA sequences. We provide quantitative evidence that clearly illustrates the development of microbial community is associated with microbiota ancestry. In addition, N. salina growth phases were linked with distinct changes in microbial phylotypes. Alteromonadeles dominated the community in the N. salina exponential phase whereas Alphaproteobacteria and Flavobacteriia were more prevalent in the stationary phase. We also demonstrate that the N. salina-associated microbial community in open cultures is diverse, resilient, and dynamic in response to environmental perturbations. This knowledge has general implications for developing and testing design principles of cultivated algal systems.« less

Culture-independent Profiling of the Fecal Microbiome to Identify Microbial Species Associated with a Diarrheal Outbreak in Immunocompromised Mice.

PubMed

Misic, Ana M; Miedel, Emily L; Brice, Angela K; Cole, Stephen; Zhang, Grace F; Dyer, Cecilia D; Secreto, Anthony; Smith, Abigail L; Danet-Desnoyers, Gwenn; Beiting, Daniel P

2018-06-13

Immunocompromised mice are used frequently in biomedical research, in part because they accommodate the engraftmentandstudy of primary human cells within a mouse model; however, these animals are susceptible to opportunistic infectionsand require special husbandry considerations. In 2015, an outbreak marked by high morbidity but low mortality swept througha colony of immunocompromised mice; this outbreak rapidly affected 75% of the colony and ultimately required completedepopulation of the barrier suite. Conventional microbiologic and molecular diagnostics were unsuccessful in determiningthe cause; therefore, we explored culture-independent methods to broadly profile the microbial community in the feces of affected animals. This approach identified 4 bacterial taxa-Candidatus Arthromitus, Clostridium celatum, Clostridiales bacterium VE202-01, and Bifidobacterium pseudolongum strain PV8-2- that were significantly enriched in the affected mice. Based on these results, specific changes were made to the animal husbandry procedures for immunocompromised mice. This case report highlights the utility of culture-independent methods in laboratory animal diagnostics.

Polyhydroxybutyrate synthesis on biodiesel wastewater using mixed microbial consortia.

PubMed

Dobroth, Zachary T; Hu, Shengjun; Coats, Erik R; McDonald, Armando G

2011-02-01

Crude glycerol (CG), a by-product of biodiesel production, is an organic carbon-rich substrate with potential as feedstock for polyhydroxyalkanoate (PHA) production. PHA is a biodegradable thermoplastic synthesized by microorganisms as an intracellular granule. In this study we investigated PHA production on CG using mixed microbial consortia (MMC) and determined that the enriched MMC produced exclusively polyhydroxybutyrate (PHB) utilizing the methanol fraction. PHB synthesis appeared to be stimulated by a macronutrient deficiency. Intracellular concentrations remained relatively constant over an operational cycle, with microbial growth occurring concurrent with polymer synthesis. PHB average molecular weights ranged from 200-380 kDa, while thermal properties compared well with commercial PHB. The resulting PHB material properties and characteristics would be suitable for many commercial uses. Considering full-scale process application, it was estimated that a 38 million L (10 million gallon) per year biodiesel operation could potentially produce up to 19 metric ton (20.9t on) of PHB per year. Copyright © 2010 Elsevier Ltd. All rights reserved.

Short communication: The effects of frozen storage on the survival of probiotic microorganisms found in traditionally and commercially manufactured kefir.

PubMed

O'Brien, K V; Aryana, K J; Prinyawiwatkul, W; Ordonez, K M Carabante; Boeneke, C A

2016-09-01

Kefir is a fermented milk traditionally made from a unique starter culture, which consists of numerous bacteria and yeast species bound together in an exopolysaccharide matrix produced by certain lactic acid bacteria. Many health benefits are associated with traditionally produced kefir; however, bulging and leaking packaging, caused by secondary yeast fermentation during storage, has limited large-scale manufacture. Commercial kefir products have been designed to reduce these effects by using a pure starter culture consisting of a mixture of bacteria and yeast species that give a flavor similar to traditional kefir, but some health benefits may be lost in commercial production due to reduced microbial diversity and lack of beneficial exopolysaccharides. In this study, traditional and commercial kefir was frozen to study the effects of frozen storage on the viability of probiotic bacteria over time. Traditional kefir was prepared by inoculating 1L of pasteurized whole goat milk with approximately 30g of kefir grains. Commercial kefir was prepared by inoculating 1L of full-fat, pasteurized goat milk with a commercial kefir starter. The milk was allowed to ferment at room temperature (24-28°C) until pH 4.6 was reached. Samples were frozen (-8 to -14°C) immediately following the completion of fermentation and were thawed and plated for lactobacilli, lactococci, and yeasts on d 0, 7, 14, and 30 of frozen storage. Lactobacilli, lactococci, and yeasts were significantly reduced in number during frozen storage; however, the traditionally produced kefir was shown to have significantly higher counts of bacteria and yeast at each sampling. We concluded that frozen storage and the development of frozen kefir products could eliminate most packaging concerns associated with the large-scale manufacture of traditionally produced kefir, resulting in increased production and marketability of this healthful product. Copyright © 2016 American Dairy Science Association. Published

Rapid culture-independent microbial analysis aboard the International Space Station (ISS).

PubMed

Maule, Jake; Wainwright, Norm; Steele, Andrew; Monaco, Lisa; Morris, Heather; Gunter, Daniel; Damon, Michael; Wells, Mark

2009-10-01

A new culture-independent system for microbial monitoring, called the Lab-On-a-Chip Application Development Portable Test System (LOCAD-PTS), was operated aboard the International Space Station (ISS). LOCAD-PTS was launched to the ISS aboard Space Shuttle STS-116 on December 9, 2006, and has since been used by ISS crews to monitor endotoxin on cabin surfaces. Quantitative analysis was performed within 15 minutes, and sample return to Earth was not required. Endotoxin (a marker of Gram-negative bacteria) was distributed throughout the ISS, despite previous indications that mostbacteria on ISS surfaces were Gram-positive [corrected].Endotoxin was detected at 24 out of 42 surface areas tested and at every surface site where colony-forming units (cfu) were observed, even at levels of 4-120 bacterial cfu per 100 cm(2), which is below NASA in-flight requirements (<10,000 bacterial cfu per 100 cm(2)). Absent to low levels of endotoxin (<0.24 to 1.0 EU per 100 cm(2); defined in endotoxin units, or EU) were found on 31 surface areas, including on most panels in Node 1 and the US Lab. High to moderate levels (1.01 to 14.7 EU per 100 cm(2)) were found on 11 surface areas, including at exercise, hygiene, sleeping, and dining facilities. Endotoxin was absent from airlock surfaces, except the Extravehicular Hatch Handle (>3.78 EU per 100 cm(2)). Based upon data collected from the ISS so far, new culture-independent requirements (defined in EU) are suggested, which are verifiable in flight with LOCAD-PTS yet high enough to avoid false alarms. The suggested requirements are intended to supplement current ISS requirements (defined in cfu) and would serve a dual purpose of safeguarding crew health (internal spacecraft surfaces <20 EU per 100 cm(2)) and monitoring forward contamination during Constellation missions (surfaces periodically exposed to the external environment, including the airlock and space suits, <0.24 EU per 100 cm(2)).

Rapid Culture-Independent Microbial Analysis Aboard the International Space Station (ISS)

NASA Astrophysics Data System (ADS)

Maule, Jake; Wainwright, Norm; Steele, Andrew; Monaco, Lisa; Morris, Heather; Gunter, Daniel; Damon, Michael; Wells, Mark

2009-10-01

A new culture-independent system for microbial monitoring, called the Lab-On-a-Chip Application Development Portable Test System (LOCAD-PTS), was operated aboard the International Space Station (ISS). LOCAD-PTS was launched to the ISS aboard Space Shuttle STS-116 on December 9, 2006, and has since been used by ISS crews to monitor endotoxin on cabin surfaces. Quantitative analysis was performed within 15 minutes, and sample return to Earth was not required. Endotoxin (a marker of Gram-negative bacteria and fungi) was distributed throughout the ISS, despite previous indications that most bacteria on ISS surfaces were Gram-positive. Endotoxin was detected at 24 out of 42 surface areas tested and at every surface site where colony-forming units (cfu) were observed, even at levels of 4-120 bacterial cfu per 100 cm2, which is below NASA in-flight requirements (<10,000 bacterial cfu per 100 cm2). Absent to low levels of endotoxin (<0.24 to 1.0 EU per 100 cm2; defined in endotoxin units, or EU) were found on 31 surface areas, including on most panels in Node 1 and the US Lab. High to moderate levels (1.01 to 14.7 EU per 100 cm2) were found on 11 surface areas, including at exercise, hygiene, sleeping, and dining facilities. Endotoxin was absent from airlock surfaces, except the Extravehicular Hatch Handle (>3.78 EU per 100 cm2). Based upon data collected from the ISS so far, new culture-independent requirements (defined in EU) are suggested, which are verifiable in flight with LOCAD-PTS yet high enough to avoid false alarms. The suggested requirements are intended to supplement current ISS requirements (defined in cfu) and would serve a dual purpose of safeguarding crew health (internal spacecraft surfaces <20 EU per 100 cm2) and monitoring forward contamination during Constellation missions (surfaces periodically exposed to the external environment, including the airlock and space suits, <0.24 EU per 100 cm2).

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.

Engineering microbial hosts for production of bacterial natural products.

PubMed

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

2016-08-27

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

Anti-inflammatory effect of microbial consortia during the utilization of dietary polysaccharides.

PubMed

Thomson, Pamela; Medina, Daniel A; Ortúzar, Verónica; Gotteland, Martín; Garrido, Daniel

2018-07-01

The gut microbiome has a significant impact on host health, especially at the metabolic level. Dietary compounds arriving at the colon have a large influence on the composition of the gut microbiome. High fiber diets have been associated to health benefits that are mediated in great part by short chain fatty acids (SCFA). Gut microbial interactions are relevant for the utilization of complex carbohydrates in the gut microbiome. In this work we characterized the utilization of two dietary polysaccharides by combinations of representative adult gut microbes, and the impact of their activities on a cellular inflammation model. Paired combinations of Bifidobacterium adolescentis, Bacteroides dorei, Lactobacillus plantarum, Escherichia coli and Clostridium symbiosum were grown in inulin or xylan as carbon source. Their relative abundance, substrate consumption and major SCFAs produced were determined. Higher cell growth was observed during inulin consumption, and B. adolescentis and L. plantarum were dominant in co-cultures. The co-culture of B. dorei and C. symbiosum was dominant in xylan. In several cases the combined bacterial growth was lower in co-cultures than monocultures, with a few exceptions of synergistic growth between microorganisms. Inulin fermentation resulted in larger acetate and lactate concentrations, and several combinations grown in xylan containing C. symbiosum were characterized by high amounts of butyrate. These microbial consortia were scaled to batch bioreactor fermentations reaching high cell densities and similar profiles to co-culture experiments. Interestingly, a microbial combination producing high amounts of butyrate was able to reduce IL-8 expression in HT-29 cells co-incubated with TNFα. In summary, this work shows that microbial interactions during the utilization of dietary polysaccharides are complex and substrate dependent. Moreover, certain combinations deploy potent anti-inflammatory effects, which are independent of individual

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

NASA Astrophysics Data System (ADS)

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

2014-12-01

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

7 CFR 58.433 - Cheese cultures.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 7 Agriculture 3 2011-01-01 2011-01-01 false Cheese cultures. 58.433 Section 58.433 Agriculture... Material § 58.433 Cheese cultures. Harmless microbial cultures used in the development of acid and flavor components in cheese shall have a pleasing and desirable taste and odor and shall have the ability to...

7 CFR 58.433 - Cheese cultures.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 3 2010-01-01 2010-01-01 false Cheese cultures. 58.433 Section 58.433 Agriculture... Material § 58.433 Cheese cultures. Harmless microbial cultures used in the development of acid and flavor components in cheese shall have a pleasing and desirable taste and odor and shall have the ability to...

A simple and cost effective liquid culture system for the micropropagation of two commercially important apple rootstocks.

PubMed

Mehta, Mohina; Ram, Raja; Bhattacharya, Amita

2014-07-01

The two commercially important apple rootstocks i.e., MM106 and B9 were micropropagated using a liquid culture system. Three different strengths of 0.8% agar solidified PGR free basal MS medium were first tested to optimize the culture media for both the rootstocks. Full strength medium (MS0) supported maximum in vitro growth, multiplication, rooting and survival under field conditions as opposed to quarter and half strength media. When three different volumes of liquid MS0 were tested, highest in vitro growth, multiplication, rooting and also survival under field conditions were achieved in 20 mL liquid MS0. The cost of one litre of liquid medium was also reduced by 8 times to Rs. 6.29 as compared to solid medium. The cost of 20 mL medium was further reduced to Rs. 0.125.

Application and microbial preparation of D-valine.

PubMed

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

2016-10-01

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

Associations among Wine Grape Microbiome, Metabolome, and Fermentation Behavior Suggest Microbial Contribution to Regional Wine Characteristics.

PubMed

Bokulich, Nicholas A; Collins, Thomas S; Masarweh, Chad; Allen, Greg; Heymann, Hildegarde; Ebeler, Susan E; Mills, David A

2016-06-14

Regionally distinct wine characteristics (terroir) are an important aspect of wine production and consumer appreciation. Microbial activity is an integral part of wine production, and grape and wine microbiota present regionally defined patterns associated with vineyard and climatic conditions, but the degree to which these microbial patterns associate with the chemical composition of wine is unclear. Through a longitudinal survey of over 200 commercial wine fermentations, we demonstrate that both grape microbiota and wine metabolite profiles distinguish viticultural area designations and individual vineyards within Napa and Sonoma Counties, California. Associations among wine microbiota and fermentation characteristics suggest new links between microbiota, fermentation performance, and wine properties. The bacterial and fungal consortia of wine fermentations, composed from vineyard and winery sources, correlate with the chemical composition of the finished wines and predict metabolite abundances in finished wines using machine learning models. The use of postharvest microbiota as an early predictor of wine chemical composition is unprecedented and potentially poses a new paradigm for quality control of agricultural products. These findings add further evidence that microbial activity is associated with wine terroir Wine production is a multi-billion-dollar global industry for which microbial control and wine chemical composition are crucial aspects of quality. Terroir is an important feature of consumer appreciation and wine culture, but the many factors that contribute to terroir are nebulous. We show that grape and wine microbiota exhibit regional patterns that correlate with wine chemical composition, suggesting that the grape microbiome may influence terroir In addition to enriching our understanding of how growing region and wine properties interact, this may provide further economic incentive for agricultural and enological practices that maintain regional

Immune modulation by Baccillus subtilis-based direct-fed microbials in commercial broiler chickens

USDA-ARS?s Scientific Manuscript database

Direct-fed microbials (DFMs), also known as probiotics have been successfully used to improve the balance of gut microflora. Spores of Bacillus subtilis (B. subtilis), have been used as DFMs for food animals and humans, and our previous studies showed that dietary supplementation of newly hatched br...

Metabarcoding of the kombucha microbial community grown in different microenvironments.

PubMed

Reva, Oleg N; Zaets, Iryna E; Ovcharenko, Leonid P; Kukharenko, Olga E; Shpylova, Switlana P; Podolich, Olga V; de Vera, Jean-Pierre; Kozyrovska, Natalia O

2015-12-01

Introducing of the DNA metabarcoding analysis of probiotic microbial communities allowed getting insight into their functioning and establishing a better control on safety and efficacy of the probiotic communities. In this work the kombucha poly-microbial probiotic community was analysed to study its flexibility under different growth conditions. Environmental DNA sequencing revealed a complex and flexible composition of the kombucha microbial culture (KMC) constituting more bacterial and fungal organisms in addition to those found by cultural method. The community comprised bacterial and yeast components including cultured and uncultivable microorganisms. Culturing the KMC under different conditions revealed the core part of the community which included acetobacteria of two genera Komagataeibacter (former Gluconacetobacter) and Gluconobacter, and representatives of several yeast genera among which Brettanomyces/Dekkera and Pichia (including former Issatchenkia) were dominant. Herbaspirillum spp. and Halomonas spp., which previously had not been described in KMC, were found to be minor but permanent members of the community. The community composition was dependent on the growth conditions. The bacterial component of KMC was relatively stable, but may include additional member-lactobacilli. The yeast species composition was significantly variable. High-throughput sequencing showed complexity and variability of KMC that may affect the quality of the probiotic drink. It was hypothesized that the kombucha core community might recruit some environmental bacteria, particularly lactobacilli, which potentially may contribute to the fermentative capacity of the probiotic drink. As many KMC-associated microorganisms cannot be cultured out of the community, a robust control for community composition should be provided by using DNA metabarcoding.

How commercial and ``violent'' video games can promote culturally sensitive science learning: some questions and challenges

NASA Astrophysics Data System (ADS)

Kwah, Helen

2012-12-01

In their paper, Muñoz and El-Hani propose to bring video games into science classrooms to promote culturally sensitive ethics and citizenship education. Instead of bringing "educational" games, Muñoz and El-Hani take a more creative route and include games such as Fallout 3® precisely because they are popular and they reproduce ideological and violent representations of gender, race, class, nationality, science and technology. However, there are many questions that arise in bringing these commercial video games into science classrooms, including the questions of how students' capacities for critical reflection can be facilitated, whether traditional science teachers can take on the role of using such games in their classrooms, and which video games would be most appropriate to use. In this response, I raise these questions and consider some of the challenges in order to further the possibility of implementing Muñoz and El-Hani's creative proposal for generating culturally sensitive science classrooms.

Successive DNA extractions improve characterization of soil microbial communities

PubMed Central

de Hollander, Mattias; Smidt, Hauke; van Veen, Johannes A.

2017-01-01

Currently, characterization of soil microbial communities relies heavily on the use of molecular approaches. Independently of the approach used, soil DNA extraction is a crucial step, and success of downstream procedures will depend on how well DNA extraction was performed. Often, studies describing and comparing soil microbial communities are based on a single DNA extraction, which may not lead to a representative recovery of DNA from all organisms present in the soil. The use of successive DNA extractions might improve soil microbial characterization, but the benefit of this approach has only been limitedly studied. To determine whether successive DNA extractions of the same soil sample would lead to different observations in terms of microbial abundance and community composition, we performed three successive extractions, with two widely used commercial kits, on a range of clay and sandy soils. Successive extractions increased DNA yield considerably (1–374%), as well as total bacterial and fungal abundances in most of the soil samples. Analysis of the 16S and 18S ribosomal RNA genes using 454-pyrosequencing, revealed that microbial community composition (taxonomic groups) observed in the successive DNA extractions were similar. However, successive DNA extractions did reveal several additional microbial groups. For some soil samples, shifts in microbial community composition were observed, mainly due to shifts in relative abundance of a number of microbial groups. Our results highlight that performing successive DNA extractions optimize DNA yield, and can lead to a better picture of overall community composition. PMID:28168105

Variables Influencing Extraction of Nucleic Acids from Microbial Plankton (Viruses, Bacteria, and Protists) Collected on Nanoporous Aluminum Oxide Filters

PubMed Central

Mueller, Jaclyn A.; Culley, Alexander I.

2014-01-01

Anodic aluminum oxide (AAO) filters have high porosity and can be manufactured with a pore size that is small enough to quantitatively capture viruses. These properties make the filters potentially useful for harvesting total microbial communities from water samples for molecular analyses, but their performance for nucleic acid extraction has not been systematically or quantitatively evaluated. In this study, we characterized the flux of water through commercially produced nanoporous (0.02 μm) AAO filters (Anotop; Whatman) and used isolates (a virus, a bacterium, and a protist) and natural seawater samples to test variables that we expected would influence the efficiency with which nucleic acids are recovered from the filters. Extraction chemistry had a significant effect on DNA yield, and back flushing the filters during extraction was found to improve yields of high-molecular-weight DNA. Using the back-flush protocol, the mass of DNA recovered from microorganisms collected on AAO filters was ≥100% of that extracted from pellets of cells and viruses and 94% ± 9% of that obtained by direct extraction of a liquid bacterial culture. The latter is a minimum estimate of the relative recovery of microbial DNA, since liquid cultures include dissolved nucleic acids that are retained inefficiently by the filter. In conclusion, we demonstrate that nucleic acids can be extracted from microorganisms on AAO filters with an efficiency similar to that achievable by direct extraction of microbes in suspension or in pellets. These filters are therefore a convenient means by which to harvest total microbial communities from multiple aqueous samples in parallel for subsequent molecular analyses. PMID:24747903

Microbial production of epoxides

DOEpatents

Clark, Thomas R.; Roberto, Francisco F.

2003-06-10

A method for microbial production of epoxides and other oxygenated products is disclosed. The method uses a biocatalyst of methanotrophic bacteria cultured in a biphasic medium containing a major amount of a non-aqueous polar solvent. Regeneration of reducing equivalents is carried out by using endogenous hydrogenase activity together with supplied hydrogen gas. This method is especially effective with gaseous substrates and cofactors that result in liquid products.

Impact of a Microbial Cocktail Used as a Starter Culture on Cocoa Fermentation and Chocolate Flavor.

PubMed

Magalhães da Veiga Moreira, Igor; de Figueiredo Vilela, Leonardo; da Cruz Pedroso Miguel, Maria Gabriela; Santos, Cledir; Lima, Nelson; Freitas Schwan, Rosane

2017-05-09

Chocolate production suffered a vast impact with the emergence of the "witches' broom" disease in cocoa plants. To recover cocoa production, many disease-resistant hybrid plants have been developed. However, some different cocoa hybrids produce cocoa beans that generate chocolate with variable quality. Fermentation of cocoa beans is a microbiological process that can be applied for the production of chocolate flavor precursors, leading to overcoming the problem of variable chocolate quality. The aim of this work was to use a cocktail of microorganisms as a starter culture on the fermentation of the ripe cocoa pods from PH15 cocoa hybrid, and evaluate its influence on the microbial communities present on the fermentative process on the compounds involved during the fermentation, and to perform the chocolate sensorial characterization. According to the results obtained, different volatile compounds were identified in fermented beans and in the chocolate produced. Bitterness was the dominant taste found in non-inoculated chocolate, while chocolate made with inoculated beans showed bitter, sweet, and cocoa tastes. 2,3-Butanediol and 2,3-dimethylpyrazine were considered as volatile compounds making the difference on the flavor of both chocolates. Saccharomyces cerevisiae UFLA CCMA 0200, Lactobacillus plantarum CCMA 0238, and Acetobacter pasteurianus CCMA 0241 are proposed as starter cultures for cocoa fermentation.

Immune modulation by Bacillus subtilus-based direct-fed microbials in commercial broiler chickens

USDA-ARS?s Scientific Manuscript database

Direct-fed microbials (DFMs), also known as probiotics, have been successfully used to improve the balance of gut microbiota. Spores of Bacillus subtilis, have been used as DFMs for food animals and humans and our previous studies showed that dietary supplementation of broiler chickens with a B. su...

Synthetic Microbial Ecology: Engineering Habitats for Modular Consortia

PubMed Central

Ben Said, Sami; Or, Dani

2017-01-01

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

Non-lethal inhibition of gut microbial trimethylamine production for the treatment of atherosclerosis

PubMed Central

Wang, Zeneng; Roberts, Adam B.; Buffa, Jennifer A.; Levison, Bruce S.; Zhu, Weifei; Org, Elin; Gu, Xiaodong; Huang, Ying; Zamanian-Daryoush, Maryam; Culley, Miranda K.; DiDonato, Anthony J.; Fu, Xiaoming; Hazen, Jennie E.; Krajcik, Daniel; DiDonato, Joseph A.; Lusis, Aldons J.; Hazen, Stanley L.

2016-01-01

SUMMARY Trimethylamine N-oxide (TMAO), a gut microbiota dependent metabolite, both enhances atherosclerosis in animal models and is associated with cardiovascular risks in clinical studies. Here we investigate the impact of targeted inhibition of the first step in TMAO generation, commensal microbial trimethylamine (TMA) production, on diet-induced atherosclerosis. A structural analogue of choline, 3,3-dimethyl-1-butanol (DMB), is shown to non-lethally inhibit TMA formation from cultured microbes, to inhibit distinct microbial TMA lyases, and to both inhibit TMA production from physiologic polymicrobial cultures (eg intestinal contents, human feces) and reduce TMAO levels in mice fed a high choline or carnitine diet. DMB inhibited choline diet-enhanced endogenous macrophage foam cell formation and atherosclerotic lesion development in apolipoprotein e−/− mice without alterations in circulating cholesterol levels. The present studies suggest gut microbial production of TMA specifically, and non-lethal microbial inhibitors in general, may serve as a potential therapeutic approach for the treatment of cardiometabolic diseases. PMID:26687352

Effects of heat shocks on microbial community structure and microbial activity of a methanogenic enrichment degrading benzoate.

PubMed

Mei, R; Narihiro, T; Nobu, M K; Liu, W-T

2016-11-01

In anaerobic digesters, temperature fluctuation could lead to process instability and failure. It is still not well understood how digester microbiota as a whole respond to heat shock, and what specific organisms are vulnerable to perturbation or responsible for process recovery after perturbation. To address these questions, a mesophilic benzoate-degrading methanogenic culture enriched from digester was subjected to different levels of heat shock. Three types of methane production profiles after perturbation were observed in comparison to the control: uninhibited, inhibited with later recovery, and inhibited without recovery. These responses were correlated with the microbial community compositions based on the analyses of 16S rRNA and 16S rRNA gene. Specifically, the primary benzoate-degrading syntroph was highly affected by heat shock, and its abundance and activity were both crucial to the restoration of benzoate degradation after heat shock. In contrast, methanogens were stable regardless whether methane production was inhibited. Populations related to 'Candidatus Cloacimonetes' and Firmicutes showed stimulated growth. These observations indicated distinct physiological traits and ecological niches associated with individual microbial groups. The results obtained after exposure to heat shock can be critical to more comprehensive characterization of digester ecology under perturbations. Anaerobic digestion is an essential step in municipal wastewater treatment owing to its striking capacity of reducing wasted sludge and recovering energy. However, as an elaborate microbial process, it requires constant temperature control and is sensitive to heat shock. In this study, we explored the microbial response to heat shock of a methanogenic culture enriched from anaerobic digester sludge. Microorganisms that were vulnerable to perturbation or responsible for process recovery after perturbation were identified. © 2016 The Society for Applied Microbiology.

Constraint-based modeling in microbial food biotechnology

PubMed Central

Rau, Martin H.

2018-01-01

Genome-scale metabolic network reconstruction offers a means to leverage the value of the exponentially growing genomics data and integrate it with other biological knowledge in a structured format. Constraint-based modeling (CBM) enables both the qualitative and quantitative analyses of the reconstructed networks. The rapid advancements in these areas can benefit both the industrial production of microbial food cultures and their application in food processing. CBM provides several avenues for improving our mechanistic understanding of physiology and genotype–phenotype relationships. This is essential for the rational improvement of industrial strains, which can further be facilitated through various model-guided strain design approaches. CBM of microbial communities offers a valuable tool for the rational design of defined food cultures, where it can catalyze hypothesis generation and provide unintuitive rationales for the development of enhanced community phenotypes and, consequently, novel or improved food products. In the industrial-scale production of microorganisms for food cultures, CBM may enable a knowledge-driven bioprocess optimization by rationally identifying strategies for growth and stability improvement. Through these applications, we believe that CBM can become a powerful tool for guiding the areas of strain development, culture development and process optimization in the production of food cultures. Nevertheless, in order to make the correct choice of the modeling framework for a particular application and to interpret model predictions in a biologically meaningful manner, one should be aware of the current limitations of CBM. PMID:29588387

Microbial study of meningitis and encephalitis cases.

PubMed

Selim, Heba S; El-Barrawy, Mohamed A; Rakha, Magda E; Yingst, Samuel L; Baskharoun, Magda F

2007-01-01

Meningitis and/or encephalitis can pose a serious public health problem especially during outbreaks. A rapid and accurate diagnosis is important for effective earlier treatment. This study aimed to identify the possible microbial causes of meningitis and/or encephalitis cases. CSF and serum samples were collected from 322 patients who had signs and symptoms suggestive of meningitis and/or encephalitis. Out of 250 cases with confirmed clinical diagnosis, 83 (33.2%) were definitely diagnosed as bacterial meningitis and/or encephalitis cases (by using CSF culture, biochemical tests, latex agglutination test, and CSF stain), 17 (6.8%) were definitely diagnosed as having viral causes ( by viral isolation on tissue culture, PCR and ELISA), and one (0.4%) was diagnosed as fungal meningitis case (by India ink stain, culture, and biochemical tests). Also, there was one encephalitis case with positive serum ELISA IgM antibodies against Sandfly scilian virus. N. meningitidis, S. pneumonia and M. tuberculosis were the most frequently detected bacterial agents, while Enteroviruses, herpes simplex viruses and varicella zoster viruses were the most common viral agents encountered. Further studies are needed to assess the role of different microbial agents in CNS infections and their effective methods of diagnosis.

Television Commercials: Symbols, Myths and Metaphors.

ERIC Educational Resources Information Center

Feasley, Florence G.

Television commercials convey to the audience through symbols, metaphors, and myths the feelings and emotions deeply rooted in our culture. While commercials on one level are concerned with a representation of the product or service, they are on another level a symbol of a larger meaning: love, family, romance, motherhood, or hero worship. A can…

Comprehensive Analysis of Secondary Dental Root Canal Infections: A Combination of Culture and Culture-Independent Approaches Reveals New Insights

PubMed Central

Anderson, Annette Carola; Hellwig, Elmar; Vespermann, Robin; Wittmer, Annette; Schmid, Michael; Karygianni, Lamprini; Al-Ahmad, Ali

2012-01-01

Persistence of microorganisms or reinfections are the main reasons for failure of root canal therapy. Very few studies to date have included culture-independent methods to assess the microbiota, including non-cultivable microorganisms. The aim of this study was to combine culture methods with culture-independent cloning methods to analyze the microbial flora of root-filled teeth with periradicular lesions. Twenty-one samples from previously root-filled teeth were collected from patients with periradicular lesions. Microorganisms were cultivated, isolated and biochemically identified. In addition, ribosomal DNA of bacteria, fungi and archaea derived from the same samples was amplified and the PCR products were used to construct clone libraries. DNA of selected clones was sequenced and microbial species were identified, comparing the sequences with public databases. Microorganisms were found in 12 samples with culture-dependent and -independent methods combined. The number of bacterial species ranged from 1 to 12 in one sample. The majority of the 26 taxa belonged to the phylum Firmicutes (14 taxa), followed by Actinobacteria, Proteobacteria and Bacteroidetes. One sample was positive for fungi, and archaea could not be detected. The results obtained with both methods differed. The cloning technique detected several as-yet-uncultivated taxa. Using a combination of both methods 13 taxa were detected that had not been found in root-filled teeth so far. Enterococcus faecalis was only detected in two samples using culture methods. Combining the culture-dependent and –independent approaches revealed new candidate endodontic pathogens and a high diversity of the microbial flora in root-filled teeth with periradicular lesions. Both methods yielded differing results, emphasizing the benefit of combined methods for the detection of the actual microbial diversity in apical periodontitis. PMID:23152922

Distribution of culturable microorganisms in Fennoscandian Shield groundwater.

PubMed

Haveman, Shelley A; Pedersen, Karsten

2002-02-01

Microbial populations in 16 groundwater samples from six Fennoscandian Shield sites in Finland and Sweden were investigated. The average total cell number was 3.7x10(5) cells ml(-1), and there was no change in the mean of the total cell numbers to a depth of 1390 m. Culture media were designed based on the chemical composition of each groundwater sample and used successfully to culture anaerobic microorganisms from all samples between 65 and 1350 m depth. Between 0.0084 and 14.8% of total cells were cultured from groundwater samples. Sulfate-reducing bacteria, iron-reducing bacteria and heterotrophic acetogenic bacteria were cultured from groundwater sampled at 65-686 m depth in geographically distant sites. Different microbial populations were cultured from deeper, older and more saline groundwater from 863 to 1350 m depth. Principal component analysis of groundwater chemistry data showed that sulfate- and iron-reducing bacteria were not detected in the most saline groundwater. Iron-reducing bacteria and acetogens were cultured from deep groundwater that contained 0.35-3.5 mM sulfate, while methanogens and acetogens were cultured from deep sulfate-depleted groundwater. In one borehole from which autotrophic methanogens were cultured, dissolved inorganic carbon was enriched in (13)C compared to other Fennoscandian Shield groundwater samples, suggesting that autotrophs were active. It can be concluded that a diverse microbial community is present from the surface to over 1300 m depth in the Fennoscandian Shield.

Nitrogen availability of grape juice limits killer yeast growth and fermentation activity during mixed-culture fermentation with sensitive commercial yeast strains.

PubMed Central

Medina, K; Carrau, F M; Gioia, O; Bracesco, N

1997-01-01

The competition between selected or commercial killer strains of type K2 and sensitive commercial strains of Saccharomyces cerevisiae was studied under various conditions in sterile grape juice fermentations. The focus of this study was the effect of yeast inoculation levels and the role of assimilable nitrogen nutrition on killer activity. A study of the consumption of free amino nitrogen (FAN) by pure and mixed cultures of killer and sensitive cells showed no differences between the profiles of nitrogen assimilation in all cases, and FAN was practically depleted in the first 2 days of fermentation. The effect of the addition of assimilable nitrogen and the size of inoculum was examined in mixed killer and sensitive strain competitions. Stuck and sluggish wine fermentations were observed to depend on nitrogen availability when the ratio of killer to sensitive cells was low (1:10 to 1:100). A relationship between the initial assimilable nitrogen content of must and the proportion of killer cells during fermentation was shown. An indirect relationship was found between inoculum size and the percentage of killer cells: a smaller inoculum resulted in a higher proportion of killer cells in grape juice fermentations. In all cases, wines obtained with pure-culture fermentations were preferred to mixed-culture fermentations by sensory analysis. The reasons why killer cells do not finish fermentation under competitive conditions with sensitive cells are discussed. PMID:9212430

Duckweed diversity decreases heavy metal toxicity by altering the metabolic function of associated microbial communities.

PubMed

Zhao, Zhao; Shi, Huijuan; Liu, Cunqi; Kang, Xianjiang; Chen, Lingci; Liang, Xiaofei; Jin, Lei

2018-07-01

Mono-cultured and mix-cultured duckweed species were investigated with respect to the function of their associated microbial communities in heavy metal contaminated wastewater. Results show that the carbon source utilization patterns of the L. aequinoctialis- and S. polyrhiza-associated microbial communities were different. The relationships between microbial activity, antioxidant enzyme activity (CAT, GSH, and SOD) and growth was positive and significant. The microbial activity of L. aequinoctialis and S. polyrhiza in mixture was higher than in monoculture in low and high heavy metal, respectively, thereby altering the utilization of specific carbon source types and increasing duckweed growth and antioxidant enzyme activity, when compared to the monocultured duckweed. Furthermore, results indicate that duckweed species in mixture are protected from damage through regulation of the associated bacterial communities. Copyright © 2018 Elsevier Ltd. All rights reserved.

Microbial Ecology of Four Coral Atolls in the Northern Line Islands

PubMed Central

Smriga, Steven; Edwards, Robert A.; Angly, Florent; Wegley, Linda; Hatay, Mark; Hall, Dana; Brown, Elysa; Haynes, Matthew; Krause, Lutz; Sala, Enric; Sandin, Stuart A.; Thurber, Rebecca Vega; Willis, Bette L.; Azam, Farooq; Knowlton, Nancy; Rohwer, Forest

2008-01-01

Microbes are key players in both healthy and degraded coral reefs. A combination of metagenomics, microscopy, culturing, and water chemistry were used to characterize microbial communities on four coral atolls in the Northern Line Islands, central Pacific. Kingman, a small uninhabited atoll which lies most northerly in the chain, had microbial and water chemistry characteristic of an open ocean ecosystem. On this atoll the microbial community was equally divided between autotrophs (mostly Prochlorococcus spp.) and heterotrophs. In contrast, Kiritimati, a large and populated (∼5500 people) atoll, which is most southerly in the chain, had microbial and water chemistry characteristic of a near-shore environment. On Kiritimati, there were 10 times more microbial cells and virus-like particles in the water column and these microbes were dominated by heterotrophs, including a large percentage of potential pathogens. Culturable Vibrios were common only on Kiritimati. The benthic community on Kiritimati had the highest prevalence of coral disease and lowest coral cover. The middle atolls, Palmyra and Tabuaeran, had intermediate densities of microbes and viruses and higher percentages of autotrophic microbes than either Kingman or Kiritimati. The differences in microbial communities across atolls could reflect variation in 1) oceaonographic and/or hydrographic conditions or 2) human impacts associated with land-use and fishing. The fact that historically Kingman and Kiritimati did not differ strongly in their fish or benthic communities (both had large numbers of sharks and high coral cover) suggest an anthropogenic component in the differences in the microbial communities. Kingman is one of the world's most pristine coral reefs, and this dataset should serve as a baseline for future studies of coral reef microbes. Obtaining the microbial data set, from atolls is particularly important given the association of microbes in the ongoing degradation of coral reef ecosystems

Microbial ecology of four coral atolls in the Northern Line Islands.

PubMed

Dinsdale, Elizabeth A; Pantos, Olga; Smriga, Steven; Edwards, Robert A; Angly, Florent; Wegley, Linda; Hatay, Mark; Hall, Dana; Brown, Elysa; Haynes, Matthew; Krause, Lutz; Sala, Enric; Sandin, Stuart A; Thurber, Rebecca Vega; Willis, Bette L; Azam, Farooq; Knowlton, Nancy; Rohwer, Forest

2008-02-27

Microbes are key players in both healthy and degraded coral reefs. A combination of metagenomics, microscopy, culturing, and water chemistry were used to characterize microbial communities on four coral atolls in the Northern Line Islands, central Pacific. Kingman, a small uninhabited atoll which lies most northerly in the chain, had microbial and water chemistry characteristic of an open ocean ecosystem. On this atoll the microbial community was equally divided between autotrophs (mostly Prochlorococcus spp.) and heterotrophs. In contrast, Kiritimati, a large and populated ( approximately 5500 people) atoll, which is most southerly in the chain, had microbial and water chemistry characteristic of a near-shore environment. On Kiritimati, there were 10 times more microbial cells and virus-like particles in the water column and these microbes were dominated by heterotrophs, including a large percentage of potential pathogens. Culturable Vibrios were common only on Kiritimati. The benthic community on Kiritimati had the highest prevalence of coral disease and lowest coral cover. The middle atolls, Palmyra and Tabuaeran, had intermediate densities of microbes and viruses and higher percentages of autotrophic microbes than either Kingman or Kiritimati. The differences in microbial communities across atolls could reflect variation in 1) oceaonographic and/or hydrographic conditions or 2) human impacts associated with land-use and fishing. The fact that historically Kingman and Kiritimati did not differ strongly in their fish or benthic communities (both had large numbers of sharks and high coral cover) suggest an anthropogenic component in the differences in the microbial communities. Kingman is one of the world's most pristine coral reefs, and this dataset should serve as a baseline for future studies of coral reef microbes. Obtaining the microbial data set, from atolls is particularly important given the association of microbes in the ongoing degradation of coral reef

Impact of nitrogen feeding regulation on polyhydroxyalkanoates production by mixed microbial cultures.

PubMed

Silva, Fernando; Campanari, Sabrina; Matteo, Stefania; Valentino, Francesco; Majone, Mauro; Villano, Marianna

2017-07-25

A sequencing batch reactor (SBR) is typically used for selecting mixed microbial cultures (MMC) for polyhydroxyalkanoate (PHA) production. Since many waste streams suitable as process feedstock for PHA production are nitrogen-deficient, a nutrient supply in the SBR is typically required to allow for efficient microbial growth. The scope of this study was to devise a nitrogen feeding strategy which allows controlling the nitrogen levels during the feast and famine regime of a lab-scale SBR, thereby selecting for PHA-storing microorganisms. At the beginning of the cycle the reactor was fed with a synthetic mixture of acetic and propionic acids at an overall organic load rate of 8.5gCODL -1 d -1 (i.e. 260CmmolL -1 d -1 ), whereas nitrogen (in the form of ammonium sulphate) was added either simultaneously to the carbon feed (coupled feeding strategy) or after the end of the feast phase (uncoupled feeding strategy). As a main result, PHA production was more than doubled (up to about 1300±64mgCODL -1 ) when carbon and nitrogen were separately fed and the higher PHA production also corresponded to an 82% increase in the polymer HV content (up to 20±1%, wtwt -1 ). Three SBR runs were performed with the uncoupled carbon and nitrogen feeding at different carbon to nitrogen (C/N) ratios (of 14.3, 17.9, and 22.3CmolNmol -1 , respectively) which were varied by progressively reducing the concentration of the nitrogen feeding. In spite of a comparable PHA storage yield at 14.3 and 17.9CmolNmol -1 (0.41±0.05 gCOD PHA gCOD VFA -1 and 0.38±0.05 gCOD PHA gCOD VFA -1 , respectively), the storage response of the selected MMC significantly decreased when the C/N ratio was set at the highest investigated value. Notably, an increase in this parameter also resulted in a change in the HV content in the polymer regardless the composition of the organic acids solution. Copyright © 2016 Elsevier B.V. All rights reserved.

Simultaneous Transformation of Commingled Trichloroethylene, Tetrachloroethylene, and 1,4-Dioxane by a Microbially Driven Fenton Reaction in Batch Liquid Cultures.

PubMed

Sekar, Ramanan; Taillefert, Martial; DiChristina, Thomas J

2016-11-01

Improper disposal of 1,4-dioxane and the chlorinated organic solvents trichloroethylene (TCE) and tetrachloroethylene (also known as perchloroethylene [PCE]) has resulted in widespread contamination of soil and groundwater. In the present study, a previously designed microbially driven Fenton reaction system was reconfigured to generate hydroxyl (HO˙) radicals for simultaneous transformation of source zone levels of single, binary, and ternary mixtures of TCE, PCE, and 1,4-dioxane. The reconfigured Fenton reaction system was driven by fed batch cultures of the Fe(III)-reducing facultative anaerobe Shewanella oneidensis amended with lactate, Fe(III), and contaminants and exposed to alternating anaerobic and aerobic conditions. To avoid contaminant loss due to volatility, the Fe(II)-generating, hydrogen peroxide-generating, and contaminant transformation phases of the microbially driven Fenton reaction system were separated. The reconfigured Fenton reaction system transformed TCE, PCE, and 1,4-dioxane either as single contaminants or as binary and ternary mixtures. In the presence of equimolar concentrations of PCE and TCE, the ratio of the experimentally derived rates of PCE and TCE transformation was nearly identical to the ratio of the corresponding HO˙ radical reaction rate constants. The reconfigured Fenton reaction system may be applied as an ex situ platform for simultaneous degradation of commingled TCE, PCE, and 1,4-dioxane and provides valuable information for future development of in situ remediation technologies. A microbially driven Fenton reaction system [driven by the Fe(III)-reducing facultative anaerobe S. oneidensis] was reconfigured to transform source zone levels of TCE, PCE, and 1,4-dioxane as single contaminants or as binary and ternary mixtures. The microbially driven Fenton reaction may thus be applied as an ex situ platform for simultaneous degradation of at least three (and potentially more) commingled contaminants. Additional targets for

Simultaneous Transformation of Commingled Trichloroethylene, Tetrachloroethylene, and 1,4-Dioxane by a Microbially Driven Fenton Reaction in Batch Liquid Cultures

PubMed Central

Sekar, Ramanan; Taillefert, Martial

2016-01-01

ABSTRACT Improper disposal of 1,4-dioxane and the chlorinated organic solvents trichloroethylene (TCE) and tetrachloroethylene (also known as perchloroethylene [PCE]) has resulted in widespread contamination of soil and groundwater. In the present study, a previously designed microbially driven Fenton reaction system was reconfigured to generate hydroxyl (HO˙) radicals for simultaneous transformation of source zone levels of single, binary, and ternary mixtures of TCE, PCE, and 1,4-dioxane. The reconfigured Fenton reaction system was driven by fed batch cultures of the Fe(III)-reducing facultative anaerobe Shewanella oneidensis amended with lactate, Fe(III), and contaminants and exposed to alternating anaerobic and aerobic conditions. To avoid contaminant loss due to volatility, the Fe(II)-generating, hydrogen peroxide-generating, and contaminant transformation phases of the microbially driven Fenton reaction system were separated. The reconfigured Fenton reaction system transformed TCE, PCE, and 1,4-dioxane either as single contaminants or as binary and ternary mixtures. In the presence of equimolar concentrations of PCE and TCE, the ratio of the experimentally derived rates of PCE and TCE transformation was nearly identical to the ratio of the corresponding HO˙ radical reaction rate constants. The reconfigured Fenton reaction system may be applied as an ex situ platform for simultaneous degradation of commingled TCE, PCE, and 1,4-dioxane and provides valuable information for future development of in situ remediation technologies. IMPORTANCE A microbially driven Fenton reaction system [driven by the Fe(III)-reducing facultative anaerobe S. oneidensis] was reconfigured to transform source zone levels of TCE, PCE, and 1,4-dioxane as single contaminants or as binary and ternary mixtures. The microbially driven Fenton reaction may thus be applied as an ex situ platform for simultaneous degradation of at least three (and potentially more) commingled contaminants

Regulation mechanisms in mixed and pure culture microbial fermentation.

PubMed

Hoelzle, Robert D; Virdis, Bernardino; Batstone, Damien J

2014-11-01

Mixed-culture fermentation is a key central process to enable next generation biofuels and biocommodity production due to economic and process advantages over application of pure cultures. However, a key limitation to the application of mixed-culture fermentation is predicting culture product response, related to metabolic regulation mechanisms. This is also a limitation in pure culture bacterial fermentation. This review evaluates recent literature in both pure and mixed culture studies with a focus on understanding how regulation and signaling mechanisms interact with metabolic routes and activity. In particular, we focus on how microorganisms balance electron sinking while maximizing catabolic energy generation. Analysis of these mechanisms and their effect on metabolism dynamics is absent in current models of mixed-culture fermentation. This limits process prediction and control, which in turn limits industrial application of mixed-culture fermentation. A key mechanism appears to be the role of internal electron mediating cofactors, and related regulatory signaling. This may determine direction of electrons towards either hydrogen or reduced organics as end-products and may form the basis for future mechanistic models. © 2014 Wiley Periodicals, Inc.

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

NASA Technical Reports Server (NTRS)

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

2006-01-01

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

Using qPCR for Water Microbial Risk Assessments

EPA Science Inventory

Microbial risk assessment (MRA) has traditionally utilized microbiological data that was obtained by culture-based techniques that are expensive and time consuming. With the advent of PCR methods there is a realistic opportunity to conduct MRA studies economically, in less time,...

Prospects of microbial cell factories developed through systems metabolic engineering.

PubMed

Gustavsson, Martin; Lee, Sang Yup

2016-09-01

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

Cheese Microbial Risk Assessments — A Review

PubMed Central

Choi, Kyoung-Hee; Lee, Heeyoung; Lee, Soomin; Kim, Sejeong; Yoon, Yohan

2016-01-01

Cheese is generally considered a safe and nutritious food, but foodborne illnesses linked to cheese consumption have occurred in many countries. Several microbial risk assessments related to Listeria monocytogenes, Staphylococcus aureus, and Escherichia coli infections, causing cheese-related foodborne illnesses, have been conducted. Although the assessments of microbial risk in soft and low moisture cheeses such as semi-hard and hard cheeses have been accomplished, it has been more focused on the correlations between pathogenic bacteria and soft cheese, because cheese-associated foodborne illnesses have been attributed to the consumption of soft cheeses. As a part of this microbial risk assessment, predictive models have been developed to describe the relationship between several factors (pH, Aw, starter culture, and time) and the fates of foodborne pathogens in cheese. Predictions from these studies have been used for microbial risk assessment as a part of exposure assessment. These microbial risk assessments have identified that risk increased in cheese with high moisture content, especially for raw milk cheese, but the risk can be reduced by preharvest and postharvest preventions. For accurate quantitative microbial risk assessment, more data including interventions such as curd cooking conditions (temperature and time) and ripening period should be available for predictive models developed with cheese, cheese consumption amounts and cheese intake frequency data as well as more dose-response models. PMID:26950859

Integrated ‘omics analysis for studying the microbial community response to a pH perturbation of a cellulose-degrading bioreactor culture

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

Boaro, Amy A.; Kim, Young-Mo; Konopka, Allan E.

2015-01-05

Propionate accumulation is a common indicator of process imbalances in anaerobic bioreactor systems. The accumulation of propionate can occur due to low retention rates, hydrogen accumulation, or mechanical changes affecting the proximity between propionate oxidizers and partner species, thereby preventing necessary electron transfer. Few studies, however, have observed the changes in microbial community structure during propionate accumulation. We used 454 pyrosequencing of 16S rDNA to evaluate the community membership during propionate accumulations in replicate bioreactors with rumen based cultures. Half of the culture volume from a parent reactor was transferred to a sterile “daughter” reactor, and both systems were runmore » identically. Both reactors experienced a propionate accumulation after roughly 10 days, with the propionate accumulation being less pronounced in the parent reactor as compared to the daughter reactor. Non-metric multidimensional scaling (NMDS) was used to determine clustering patterns of the samples, and correlative methods were used to determine which OTUs were significantly associated with the movements of samples along the NMDS axes. The presence of Saccharofermentans characterized the position of early samples, whereas the presence of Ruminococcus and Succiniclasticum were more indicative of the positions of later samples. Hydrogen accumulation and low sequence counts indicated low methanogen activity. Although both reactor systems were closed to microbial inputs due to the sterilization of influent media, we recorded significant increases in reactor diversity over time. This suggests that changes in the abundances of dominant community members may affect the sequencing of rare taxa within samples.« less

Effect of biofilm and selective mixed culture on microbial fuel cell for the treatment of tempeh industrial wastewater

NASA Astrophysics Data System (ADS)

Arbianti, Rita; Surya Utami, Tania; Leondo, Vifki; Elisabeth; Andyah Putri, Syafira; Hermansyah, Heri

2018-03-01

Microbial Fuel Cell (MFC) provides a new alternative in the treatment of organic waste. MFC produces 50-90% less sludge to be disposed than other methods. MFC technology can utilize existing microorganisms in the waste as a catalyst to generate electricity and simultaneously also serves as a wastewater treatment unit itself. Tempeh wastewater is one of the abundant industrial wastewater which can be processed using MFC. Research using the selective mixed culture is very likely to do due to the good result on COD removals by adding mixed culture. Microorganisms in tempeh wastewater consist of bacteria gram positive and gram negative. This study focused on the aspects of waste treatment which is determined by decreased levels of COD and BOD. Variations in this study are the formation time of biofilm and the addition of selective gram. MFC operated for 50 hours. For a variation of biofilm formation, experiments were performed after incubation by replacing incubation substrates used in the formation of biofilms. Biofilm formation time in this study was 3 days, 5 days, 7 days and 14 days. Gram positive and gram negative bacteria were used in selective mixed culture experiments. Selective mixed culture added to the reactor by 1 mL and 5 mL. Selection of gram-positive or gram-negative bacteria carried by growing mixed culture on selective media. COD and BOD levels were measured in the wastewater before and after the experiment conducted in each variation. Biofilm formation optimum time is 7 days which decrease COD and BOD levels by 18.2% and 35.9%. The addition of gram negative bacteria decreases COD and BOD levels by 29.32% and 51.32%. Further research is needed in order to get a better result on decreasing levels of COD and BOD.

Biodegradability of carbon nanotube/polymer nanocomposites under aerobic mixed culture conditions.

PubMed

Phan, Duc C; Goodwin, David G; Frank, Benjamin P; Bouwer, Edward J; Fairbrother, D Howard

2018-10-15

The properties and commercial viability of biodegradable polymers can be significantly enhanced by the incorporation of carbon nanotubes (CNTs). The environmental impact and persistence of these carbon nanotube/polymer nanocomposites (CNT/PNCs) after disposal will be strongly influenced by their microbial interactions, including their biodegradation rates. At the end of consumer use, CNT/PNCs will encounter diverse communities of microorganisms in landfills, surface waters, and wastewater treatment plants. To explore CNT/PNC biodegradation under realistic environmental conditions, the effect of multi-wall CNT (MWCNT) incorporation on the biodegradation of polyhydroxyalkanoates (PHA) was investigated using a mixed culture of microorganisms from wastewater. Relative to unfilled PHA (0% w/w), the MWCNT loading (0.5-10% w/w) had no statistically significant effect on the rate of PHA matrix biodegradation. Independent of the MWCNT loading, the extent of CNT/PNC mass remaining closely corresponded to the initial mass of CNTs in the matrix suggesting a lack of CNT release. CNT/PNC biodegradation was complete in approximately 20 days and resulted in the formation of a compressed CNT mat that retained the shape of the initial CNT/PNC. This study suggests that although CNTs have been shown to be cytotoxic towards a range of different microorganisms, this does not necessarily impact the biodegradation of the surrounding polymer matrix in mixed culture, particularly in situations where the polymer type and/or microbial population favor rapid polymer biodegradation. Copyright © 2018 Elsevier B.V. All rights reserved.

Microbial pattern of pressure ulcer in pediatric patients

NASA Astrophysics Data System (ADS)

Paramita, D. A.; Khairina; Lubis, N. Z.

2018-03-01

Pressure ulcer (PU) is a localized trauma to the skin and or tissue beneath which lies in bony prominence due to pressure or pressure that combines with a sharp surface. Several studies have found that PU is a common problem in pediatrics population. Infection at the site of a PU is the most common complication in which the PU may host a resistant microorganism and may turn into a local infection that will be the source of bacteremia in hospitalized patients. To reveal which is the most common microbial species that underlie in pressure ulcer of pediatrics patients.A cross-sectional study was conducted in July-September 2017, involving 18 PU pediatric patients in Haji Adam Malik Hospital. To each subject, swab culture from the ulcer was madein microbial laboratory in Haji Adam Malik Hospital to determine the microbial pattern. This study found that the most common microbial pattern in pressure ulcers of pediatrics patient in Haji Adam Malik Hospital is Acinetobacter baumannii (22.2%).

Microbial healing of cracks in concrete: a review.

PubMed

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

2017-11-01

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

The influence of Staphylococcus aureus on gut microbial ecology in an in vitro continuous culture human colonic model system.

PubMed

Sannasiddappa, Thippeswamy H; Costabile, Adele; Gibson, Glenn R; Clarke, Simon R

2011-01-01

An anaerobic three-stage continuous culture model of the human colon (gut model), which represent different anatomical areas of the large intestine, was used to study the effect of S. aureus infection of the gut on the resident faecal microbiota. Studies on the development of the microbiota in the three vessels were performed and bacteria identified by culture independent fluorescence in situ hybridization (FISH). Furthermore, short chain fatty acids (SCFA), as principal end products of gut bacterial metabolism, were measured along with a quantitative assessment of the predominant microbiota. During steady state conditions, numbers of S. aureus cells stabilised until they were washed out, but populations of indigenous bacteria were transiently altered; thus S. aureus was able to compromise colonisation resistance by the colonic microbiota. Furthermore, the concentration of butyric acid in the vessel representing the proximal colon was significantly decreased by infection. Thus infection by S. aureus appears to be able to alter the overall structure of the human colonic microbiota and the microbial metabolic profiles. This work provides an initial in vitro model to analyse interactions with pathogens.

Microbial Growth under Supercritical CO2

PubMed Central

Peet, Kyle C.; Freedman, Adam J. E.; Hernandez, Hector H.; Britto, Vanya; Boreham, Chris; Ajo-Franklin, Jonathan B.

2015-01-01

Growth of microorganisms in environments containing CO2 above its critical point is unexpected due to a combination of deleterious effects, including cytoplasmic acidification and membrane destabilization. Thus, supercritical CO2 (scCO2) is generally regarded as a sterilizing agent. We report isolation of bacteria from three sites targeted for geologic carbon dioxide sequestration (GCS) that are capable of growth in pressurized bioreactors containing scCO2. Analysis of 16S rRNA genes from scCO2 enrichment cultures revealed microbial assemblages of varied complexity, including representatives of the genus Bacillus. Propagation of enrichment cultures under scCO2 headspace led to isolation of six strains corresponding to Bacillus cereus, Bacillus subterraneus, Bacillus amyloliquefaciens, Bacillus safensis, and Bacillus megaterium. Isolates are spore-forming, facultative anaerobes and capable of germination and growth under an scCO2 headspace. In addition to these isolates, several Bacillus type strains grew under scCO2, suggesting that this may be a shared feature of spore-forming Bacillus spp. Our results provide direct evidence of microbial activity at the interface between scCO2 and an aqueous phase. Since microbial activity can influence the key mechanisms for permanent storage of sequestered CO2 (i.e., structural, residual, solubility, and mineral trapping), our work suggests that during GCS microorganisms may grow and catalyze biological reactions that influence the fate and transport of CO2 in the deep subsurface. PMID:25681188

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

PubMed

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

2014-01-01

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

Microbial identification and automated antibiotic susceptibility testing directly from positive blood cultures using MALDI-TOF MS and VITEK 2.

PubMed

Wattal, C; Oberoi, J K

2016-01-01

The study addresses the utility of Matrix Assisted Laser Desorption/Ionisation Time-Of-Flight mass spectrometry (MALDI-TOF MS) using VITEK MS and the VITEK 2 antimicrobial susceptibility testing (AST) system for direct identification (ID) and timely AST from positive blood culture bottles using a lysis-filtration method (LFM). Between July and December 2014, a total of 140 non-duplicate mono-microbial blood cultures were processed. An aliquot of positive blood culture broth was incubated with lysis buffer before the bacteria were filtered and washed. Micro-organisms recovered from the filter were first identified using VITEK MS and its suspension was used for direct AST by VITEK 2 once the ID was known. Direct ID and AST results were compared with classical methods using solid growth. Out of the 140 bottles tested, VITEK MS resulted in 70.7 % correct identification to the genus and/ or species level. For the 103 bottles where identification was possible, there was agreement in 97 samples (94.17 %) with classical culture. Compared to the routine method, the direct AST resulted in category agreement in 860 (96.5 %) of 891 bacteria-antimicrobial agent combinations tested. The results of direct ID and AST were available 16.1 hours before those of the standard approach on average. The combined use of VITEK MS and VITEK 2 directly on samples from positive blood culture bottles using a LFM technique can result in rapid and reliable ID and AST results in blood stream infections to result in early institution of targeted treatment. The combination of LFM and AST using VITEK 2 was found to expedite AST more reliably.

Automated Microbial Metabolism Laboratory

NASA Technical Reports Server (NTRS)

1973-01-01

Development of the automated microbial metabolism laboratory (AMML) concept is reported. The focus of effort of AMML was on the advanced labeled release experiment. Labeled substrates, inhibitors, and temperatures were investigated to establish a comparative biochemical profile. Profiles at three time intervals on soil and pure cultures of bacteria isolated from soil were prepared to establish a complete library. The development of a strategy for the return of a soil sample from Mars is also reported.

Effects of Actinomycete Secondary Metabolites on Sediment Microbial Communities.

PubMed

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

2017-02-15

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

Microbial Cellulose Utilization: Fundamentals and Biotechnology

PubMed Central

Lynd, Lee R.; Weimer, Paul J.; van Zyl, Willem H.; Pretorius, Isak S.

2002-01-01

Fundamental features of microbial cellulose utilization are examined at successively higher levels of aggregation encompassing the structure and composition of cellulosic biomass, taxonomic diversity, cellulase enzyme systems, molecular biology of cellulase enzymes, physiology of cellulolytic microorganisms, ecological aspects of cellulase-degrading communities, and rate-limiting factors in nature. The methodological basis for studying microbial cellulose utilization is considered relative to quantification of cells and enzymes in the presence of solid substrates as well as apparatus and analysis for cellulose-grown continuous cultures. Quantitative description of cellulose hydrolysis is addressed with respect to adsorption of cellulase enzymes, rates of enzymatic hydrolysis, bioenergetics of microbial cellulose utilization, kinetics of microbial cellulose utilization, and contrasting features compared to soluble substrate kinetics. A biological perspective on processing cellulosic biomass is presented, including features of pretreated substrates and alternative process configurations. Organism development is considered for “consolidated bioprocessing” (CBP), in which the production of cellulolytic enzymes, hydrolysis of biomass, and fermentation of resulting sugars to desired products occur in one step. Two organism development strategies for CBP are examined: (i) improve product yield and tolerance in microorganisms able to utilize cellulose, or (ii) express a heterologous system for cellulose hydrolysis and utilization in microorganisms that exhibit high product yield and tolerance. A concluding discussion identifies unresolved issues pertaining to microbial cellulose utilization, suggests approaches by which such issues might be resolved, and contrasts a microbially oriented cellulose hydrolysis paradigm to the more conventional enzymatically oriented paradigm in both fundamental and applied contexts. PMID:12209002

Central role of the cell in microbial ecology.

PubMed

Zengler, Karsten

2009-12-01

Over the last few decades, advances in cultivation-independent methods have significantly contributed to our understanding of microbial diversity and community composition in the environment. At the same time, cultivation-dependent methods have thrived, and the growing number of organisms obtained thereby have allowed for detailed studies of their physiology and genetics. Still, most microorganisms are recalcitrant to cultivation. This review not only conveys current knowledge about different isolation and cultivation strategies but also discusses what implications can be drawn from pure culture work for studies in microbial ecology. Specifically, in the light of single-cell individuality and genome heterogeneity, it becomes important to evaluate population-wide measurements carefully. An overview of various approaches in microbial ecology is given, and the cell as a central unit for understanding processes on a community level is discussed.

Electricity production and microbial characterization of thermophilic microbial fuel cells.

PubMed

Dai, Kun; Wen, Jun-Li; Zhang, Fang; Ma, Xi-Wen; Cui, Xiang-Yu; Zhang, Qi; Zhao, Ting-Jia; Zeng, Raymond J

2017-11-01

Thermophilic microbial fuel cell (TMFC) offers many benefits, but the investigations on the diversity of exoelectrogenic bacteria are scarce. In this study, a two-chamber TMFC was constructed using ethanol as an electron donor, and the microbial dynamics were analyzed by high-throughput sequencing and 16S rRNA clone-library sequencing. The open-circuit potential of TMFC was approximately 650mV, while the maximum voltage was around 550mV. The maximum power density was 437mW/m 2 , and the columbic efficiency in this work was 20.5±6.0%. The Firmicutes bacteria, related to the uncultured bacterium clone A55_D21_H_B_C01 with a similarity of 99%, accounted for 90.9% of all bacteria in the TMFC biofilm. This unknown bacterium has the potential to become a new thermophilic exoelectrogenic bacterium that is yet to be cultured. The development of TMFC-involved biotechnologies will be beneficial for the production of valuable chemicals and generation of energy in the future. Copyright © 2017 Elsevier Ltd. All rights reserved.

Microbial ice nucleators are scavenged from the atmosphere during artificial rain events

NASA Astrophysics Data System (ADS)

Hanlon, Regina; Powers, Craig; Failor, Kevin; Vinatzer, Boris; Schmale, David

2016-04-01

Some microorganisms associated with rain may catalyze the nucleation of ice crystals at significantly warmer temperatures than would normally be required for ice formation, suggesting that they may play an important role in the onset of precipitation. Rain samples collected near the surface of the earth contain an array of microbial ice nucleators, but the little is known about their source(s) and life history. We conducted a series of field experiments to test the hypothesis that microbial ice nucleators are scavenged from the atmosphere by rainfall. Thirty three artificial rain events were conducted over four months (Nov 2014, Dec 2014, April 2015, and June 2015) off the side of the Smart Road Bridge in Blacksburg, VA, USA. In each event, sterile water was dispensed over the side of the bridge and recovered in sterile containers following gravitational settling from the bridge to an open fallow agricultural field below (a distance of ~55m). Microbes scavenged from the artificial rain events were cultured on six different types of agar media (R2A, TSA, CA; +/-cycloheximide), and the ice nucleation activity was examined for colonies cultured from the different media types. Mean CFUs scavenged by artificial rain ranged from 2 to 267 CFUs/mL. Microbial ice nucleators were cultured from 94% (31/33) of the simulated rain events, and represented 1.4% (121/8871) of the total number of colonies assayed. This percentage is similar to the percentage of culturable microbial ice nucleators occurring in about half of the natural rain events studied in Blacksburg, VA. Sequence-assisted identification of the repeatable microbial ice nucleators that were scavenged from the atmosphere showed a number of unique prokaryotic and eukaryotic taxa. This work expands our knowledge of the scavenging properties of rainfall, and suggests that at least some ice nucleators in natural precipitation events may have been scrubbed from the atmosphere during rainfall, and thus are not likely to be

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

USDA-ARS?s Scientific Manuscript database

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

Microbiome involved in microbial electrochemical systems (MESs): A review.

PubMed

Saratale, Rijuta Ganesh; Saratale, Ganesh Dattatraya; Pugazhendhi, Arivalagan; Zhen, Guangyin; Kumar, Gopalakrishnan; Kadier, Abudukeremu; Sivagurunathan, Periyasamy

2017-06-01

Microbial electrochemical systems (MESs) are an attracting technology for the disposal of wastewater treatment and simultaneous energy production. In MESs, at the anode microorganisms through the catalytic activity generates electrons that can be converted into electricity or other valuable chemical compounds. Microorganisms those having ability to donate and accept electrons to and from anode and cathode electrodes, respectively are recognized as 'exoelectrogens'. In the MESs, it renders an important function for its performance. In the present mini-review, we have discussed the role of microbiome including pure culture, enriched culture and mixed culture in different BESs application. The effects of operational and biological factors on microbiome development have been discussed. Further discussion about the molecular techniques for the evaluation of microbial community analysis is addressed. In addition different electrochemical techniques for extracellular electron transfer (EET) mechanism of electroactive biofilms have been discussed. This review highlights the importance of microbiome in the development of MESs, effective operational factors for exo-electrogens activities as well their key challenges and future technological aspects are also briefly discussed. Copyright © 2017 Elsevier Ltd. All rights reserved.

Microbial adhesion to silicone hydrogel lenses: a review.

PubMed

Willcox, Mark D P

2013-01-01

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

A microbial identification framework for risk assessment.

PubMed

Bernatchez, Stéphane; Anoop, Valar; Saikali, Zeina; Breton, Marie

2018-06-01

Micro-organisms are increasingly used in a variety of products for commercial uses, including cleaning products. Such microbial-based cleaning products (MBCP) are represented as a more environmentally-friendly alternative to chemically based cleaning products. The identity of the micro-organisms formulated into these products is often considered confidential business information and is not revealed or it is only partly revealed (i.e., identification to the genus, not to the species). That paucity of information complicates the evaluation of the risk associated with their use. The accurate taxonomic identification of those micro-organisms is important so that a suitable risk assessment of the products can be conducted. To alleviate difficulties associated with adequate identification of micro-organisms in MBCP and other products containing micro-organisms, a microbial identification framework for risk assessment (MIFRA) has been elaborated. It serves to provide guidance on a polyphasic tiered approach, combining the data obtained from the use of various methods (i.e., polyphasic approach) combined with the sequential selection of the methods (i.e., tiered) to achieve a satisfactory identity of the micro-organism to an acceptable taxonomic level. The MIFRA is suitable in various risk assessment contexts for micro-organisms used in any commercial product. Copyright © 2018. Published by Elsevier Ltd.

Patent protection for microbial technologies.

PubMed

Sherkow, Jacob S

2017-11-01

Microbial technologies often serve as the basis of fundamental research tools in molecular biology. These present a variety of ethical, legal and social issues concerning their patenting. This commentary presents several case studies of these issues across three major microbiological tools: CRISPR, viral vectors and antimicrobial resistance drugs. It concludes that the development of these technologies-both scientifically and commercially-depend, in part, on the patent regime available for each, and researchers' willingness to enforce those patents against others. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Abundance and diversity of microbial inhabitants in European spacecraft-associated clean rooms.

PubMed

Stieglmeier, Michaela; Rettberg, Petra; Barczyk, Simon; Bohmeier, Maria; Pukall, Rüdiger; Wirth, Reinhard; Moissl-Eichinger, Christine

2012-06-01

The determination of the microbial load of a spacecraft en route to interesting extraterrestrial environments is mandatory and currently based on the culturable, heat-shock-surviving portion of microbial contaminants. Our study compared these classical bioburden measurements as required by NASA's and ESA's guidelines for the microbial examination of flight hardware, with molecular analysis methods (16S rRNA gene cloning and quantitative PCR) to further develop our understanding of the diversity and abundance of the microbial communities of spacecraft-associated clean rooms. Three samplings of the Herschel Space Observatory and its surrounding clean rooms were performed in two different European facilities. Molecular analyses detected a broad diversity of microbes typically found in the human microbiome with three bacterial genera (Staphylococcus, Propionibacterium, and Brevundimonas) common to all three locations. Bioburden measurements revealed a low, but heterogeneous, abundance of spore-forming and other heat-resistant microorganisms. Total cell numbers estimated by quantitative real-time PCR were typically 3 orders of magnitude greater than those determined by viable counts, which indicates a tendency for traditional methods to underestimate the extent of clean room bioburden. Furthermore, the molecular methods allowed the detection of a much broader diversity than traditional culture-based methods.

Effects of 2-hydroxy-4-(methylthio) butanoic acid (HMB) on microbial growth in continuous culture.

PubMed

Noftsger, S M; St-Pierre, N R; Karnati, S K R; Firkins, J L

2003-08-01

2-Hydroxy-4-(methylthio) butanoic acid (HMB) positively affects milk composition and yield, potentially through ruminal actions. Four continuous culture fermenters were used to determine the optimal concentration of HMB for digestibility of organic matter (OM), neutral detergent fiber (NDF), acid detergent fiber (ADF), and hemicellulose and synthesis of microbial N. A highly degradable mix of hay and grain was used as a basal diet to simulate a typical lactation diet. Three concentrations of HMB (0, 0.055, and 0.110%) and one concentration of dl-Met (0.097%) were infused into the fermenters according to a 4 x 4 Latin square design. Digesta samples were collected during the last 3 d of each of the four 10-d experimental periods. Digestibility of OM, hemicellulose, and NDF was largely insensitive to treatment. Digestibility of ADF showed a quadratic effect to supplementation of HMB, with 0.055% having lower digestibility than 0 or 0.110%. Total production of VFA was not influenced by HMB supplementation, but differences in concentration and production of individual VFA were seen. Isobutyrate increased linearly with increasing HMB supplementation. Propionate concentration decreased linearly with increased HMB supplementation, but propionate production showed a quadratic trend (P = 0.13). A higher concentration of acetate was detected for dl-Met compared with the highest HMB concentration. There were trends (P < 0.15) for dl-Met to decrease the production of isobutyrate and to lower the concentration of butyrate when compared with HMB. Microbial efficiency was not different among treatments. The proportion of bacterial N produced from NH3-N decreased linearly with increasing HMB, and bacteria receiving dl-Met synthesized more N from NH3-N than those receiving HMB. These data suggest that supplementation of HMB may have a sparing effect on branched chain volatile fatty acids because the fatty acids are not needed to provide carbon for synthesis of valine, isoleucine and

Effects of combining microbial and chemical insecticides on mortality of the Pecan Weevil (Coleoptera: Curculionidae).

PubMed

Shapiro-Ilan, David I; Cottrell, Ted E; Wood, Bruce W

2011-02-01

The pecan weevil, Curculio caryae (Horn), is a key pest of pecan [Carya illinoinensis (Wangenh.) K. Koch]. Current control recommendations are based on chemical insecticide applications. Microbial control agents such as the entomopathogenic nematode, Steinernema carpocapsae (Weiser) and the fungus Beauveria bassiana (Balsamo) Vuillemin occur naturally in southeastern U.S. pecan orchards and have shown promise as alternative control agents for C. caryjae. Conceivably, the chemical and microbial agents occur simultaneously within pecan orchards or might be applied concurrently. The objective of this study was to determine the interactions between two chemical insecticides that are used in commercial C. caryae control (i.e., carbaryl and cypermethrin applied below field rates) and the microbial agents B. bassiana and S. carpocapsae. In laboratory experiments, pecan weevil larval or adult mortality was assessed after application of microbial or chemical treatments applied singly or in combination (microbial + chemical agent). The nature of interactions (antagonism, additivity, or synergy) in terms of weevil mortality was evaluated over 9 d (larvae) or 5 d (adults). Results for B. bassiana indicated synergistic activity with carbaryl and antagonism with cypermethrin in C. caryae larvae and adults. For S. carpocapsae, synergy was detected with both chemicals in C. caryae larvae, but only additive effects were detected in adult weevils. Our results indicate that the chemical-microbial combinations tested are compatible with the exception of B. bassiana and cypermethrin. In addition, combinations that exhibited synergistic interactions may provide enhanced C. caryae control in commercial field applications; thus, their potential merits further exploration.

Proton transfer in microbial electrolysis cells

DOE PAGES

Borole, Abhijeet P.; Lewis, Alex J.

2017-02-15

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

Proton transfer in microbial electrolysis cells

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

Borole, Abhijeet P.; Lewis, Alex J.

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

Mineralogical Control on Microbial Diversity in a Weathered Granite?

NASA Astrophysics Data System (ADS)

Gleeson, D.; Clipson, N.; McDermott, F.

2003-12-01

Mineral transformation reactions and the behaviour of metals in rock and soils are affected not only by physicochemical parameters but also by biological factors, particularly by microbial activity. Microbes inhabit a wide range of niches in surface and subsurface environments, with mineral-microbe interactions being generally poorly understood. The focus of this study is to elucidate the role of microbial activity in the weathering of common silicate minerals in granitic rocks. A site in the Wicklow Mountains (Ireland) has been identified that consists of an outcrop surface of Caledonian (ca. 400 million years old) pegmatitic granite from which large intact crystals of variably weathered muscovite, plagioclase, K-feldspar and quartz were sampled, together with whole-rock granite. Culture-based microbial approaches have been widely used to profile microbial communities, particularly from copiotrophic environments, but it is now well established that for oligotrophic environments such as those that would be expected on weathering faces, perhaps less than 1% of microbial diversity can be profiled by cultural means. A number of culture-independent molecular based approaches have been developed to profile microbial diversity and community structure. These rely on successfully isolating environmental DNA from a given environment, followed by the use of the polymerase chain reaction (PCR) to amplify the typically small quantities of extracted DNA. Amplified DNA can then be analysed using cloning based approaches as well as community fingerprinting systems such as denaturing gradient gel electrophoresis (DGGE), terminal restriction fragment length polymorphism (TRFLP) and ribosomal intergenic spacer analysis (RISA). Community DNA was extracted and the intergenic spacer region (ITS) between small (16S) and large (23S) bacterial subunit rRNA genes was amplified. RISA fragments were then electrophoresed on a non-denaturing polyacrylamide gel. Banding patterns suggest that

Temperature effects on microbial respiration assessed with CO2-exchange and continuous culture techniques

NASA Astrophysics Data System (ADS)

Lehmeier, C.; Min, K.; Song, C.; Ballantyne, F.; Billings, S. A.

2012-12-01

Recent work attempts to incorporate requirements of soil microorganisms for carbon and other resources, and how these requirements may respond to temperature, into theoretical concepts of soil organic matter decomposition and climate change. Because of the difficulties of measuring resource fluxes in natural soils, empirical data to guide these concepts remain scarce. Here, we present an experimental system that combines continuous culture techniques with CO2 measurements to study carbon fluxes through microbes in a reductionist, controlled environment amenable to experimental manipulation. In this pilot study, we quantified mass specific respiration rates (MSR) and δ13C of respired CO2 of Pseudomonas fluorescens, a Gram-negative bacterium common to soils, grown at 15°C and 25°C with otherwise identical environmental conditions. The microbes were grown in a 1.9 L bioreactor, in 0.9 L of nutrient medium with C:N:P atomic ratios of 100:10:3, and with 10 mM cellobiose as the carbon source. A peristaltic pump continuously supplied the bioreactor with sterile medium, and removed medium from the bioreactor, at a rate of 63 mL h-1. Both vessels were contained within a temperature incubator, and stir bars provided continuously well mixed volumes. CO2-free air was continuously bubbled through the reactor medium so to provide the microbes with O2; a cavity ring down spectrometer withdrew reactor headspace air and measured concentration and δ13C of the CO2. Air supply was regulated with a pressure/mass flow controller to approx. 27 mL min-1. In both temperature regimes, the pH of the bioreactor as well as concentration and δ13C of the CO2 in the head space air were constant over the course of 1 d, such that any imbalances in the CO2-H2CO3 equilibrium were considered negligible in the assessment of microbial respiration rates and the δ13C of respired CO2. After this time period, reactor medium was passed through a 0.22 μm filter and the filtrate dried for 24 h to obtain

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

Microbial Community Response of an Organohalide Respiring Enrichment Culture to Permanganate Oxidation.

PubMed

Sutton, Nora B; Atashgahi, Siavash; Saccenti, Edoardo; Grotenhuis, Tim; Smidt, Hauke; Rijnaarts, Huub H M

2015-01-01

While in situ chemical oxidation is often used to remediate tetrachloroethene (PCE) contaminated locations, very little is known about its influence on microbial composition and organohalide respiration (OHR) activity. Here, we investigate the impact of oxidation with permanganate on OHR rates, the abundance of organohalide respiring bacteria (OHRB) and reductive dehalogenase (rdh) genes using quantitative PCR, and microbial community composition through sequencing of 16S rRNA genes. A PCE degrading enrichment was repeatedly treated with low (25 μmol), medium (50 μmol), or high (100 μmol) permanganate doses, or no oxidant treatment (biotic control). Low and medium treatments led to higher OHR rates and enrichment of several OHRB and rdh genes, as compared to the biotic control. Improved degradation rates can be attributed to enrichment of (1) OHRB able to also utilize Mn oxides as a terminal electron acceptor and (2) non-dechlorinating community members of the Clostridiales and Deltaproteobacteria possibly supporting OHRB by providing essential co-factors. In contrast, high permanganate treatment disrupted dechlorination beyond cis-dichloroethene and caused at least a 2-4 orders of magnitude reduction in the abundance of all measured OHRB and rdh genes, as compared to the biotic control. High permanganate treatments resulted in a notably divergent microbial community, with increased abundances of organisms affiliated with Campylobacterales and Oceanospirillales capable of dissimilatory Mn reduction, and decreased abundance of presumed supporters of OHRB. Although OTUs classified within the OHR-supportive order Clostridiales and OHRB increased in abundance over the course of 213 days following the final 100 μmol permanganate treatment, only limited regeneration of PCE dechlorination was observed in one of three microcosms, suggesting strong chemical oxidation treatments can irreversibly disrupt OHR. Overall, this detailed investigation into dose

Detection of Biosignatures in Natural and Microbial Cultured Jarosites Using Laser- Desorption Fourier Transform Mass Spectrometry: Implications for Astrobiology

NASA Astrophysics Data System (ADS)

Kotler, J.; Hinman, N. W.; Yan, B.; Stoner, D. L.; Scott, J. R.

2006-12-01

The jarosite group minerals have received increasing attention since the discovery by the Mars Exploration Rover-Opportunity of jarosite on the Martian surface. The general chemical formula for jarosite is XFe3(SO4)2(OH)6 where the X represents both monovalent and divalent cations that can occupy the axial positions in the crystal structure. Commonly found ions include K+, Na+, H3O+, NH4+, and Pb2+ with reports of other large ions occupying this position in the literature. Modeling efforts have been performed to confirm that jarosite has the ability to incorporate a variety of "foreign" cations. The minerals unique ability to incorporate various large ions in its structure and its association with biological activity in terrestrial environments has lead to investigations regarding its use as an indicator of aqueous and/or biological activity. The use of laser desorption Fourier transform mass spectrometry (LD-FTMS) has revealed the presence of organic matter including the amino acid, glycine, in several jarosite samples from various worldwide locations. Iron precipitates derived from acidophilic microbial cultures were also analyzed. Using attenuated total reflectance infrared spectroscopy (ATR-IR), signals indicative of microbes or microbial exudates were weak and ambiguous. In contrast, LD-FTMS clearly detected bioorganic constituents in some desorption spots. However, the signals were sporadic and required the laser scanning/imaging capability of our laboratory built system to locate the microbial signatures in the heterogeneous samples. The ability to observe these bioorganic signatures in jarosite samples using the instrumental technique employed in this study furthers the goals of planetary geologists to determine whether signs of life (e.g., presence of biomolecules or biomolecule precursors) can be detected in the rock record of terrestrial and extraterrestrial samples.

Long-term operation of microbial electrosynthesis cell reducing CO2 to multi-carbon chemicals with a mixed culture avoiding methanogenesis.

PubMed

Bajracharya, Suman; Yuliasni, Rustiana; Vanbroekhoven, Karolien; Buisman, Cees J N; Strik, David P B T B; Pant, Deepak

2017-02-01

In microbial electrosynthesis (MES), CO 2 can be reduced preferably to multi-carbon chemicals by a biocathode-based process which uses electrochemically active bacteria as catalysts. A mixed anaerobic consortium from biological origin typically produces methane from CO 2 reduction which circumvents production of multi-carbon compounds. This study aimed to develop a stable and robust CO 2 reducing biocathode from a mixed culture inoculum avoiding the methane generation. An effective approach was demonstrated based on (i) an enrichment procedure involving inoculum pre-treatment and several culture transfers in H 2 :CO 2 media, (ii) a transfer from heterotrophic to autotrophic growth and (iii) a sequential batch operation. Biomass growth and gradual acclimation to CO 2 electro-reduction accomplished a maximum acetate production rate of 400mgL catholyte -1 d -1 at -1V (vs. Ag/AgCl). Methane was never detected in more than 300days of operation. Accumulation of acetate up to 7-10gL -1 was repeatedly attained by supplying (80:20) CO 2 :N 2 mixture at -0.9 to -1V (vs. Ag/AgCl). In addition, ethanol and butyrate were also produced from CO 2 reduction. Thus, a robust CO 2 reducing biocathode can be developed from a mixed culture avoiding methane generation by adopting the specific culture enrichment and operation procedures without the direct addition of chemical inhibitor. Copyright © 2016 Elsevier B.V. All rights reserved.

Biodegradation of commercial gasoline (24% ethanol added) in liquid medium by microorganisms isolated from a landfarming site.

PubMed

Oliveira, Núbia M; Bento, Fátima M; Camargo, Flávio A O; Knorst, Aline Jéssica; Dos Santos, Anai Loreiro; Pizzolato, Tania M; Peralba, Maria do Carmo R

2011-01-01

Isolation of soil microorganisms from a landfarming site with a 19-year history of petrochemical residues disposal was carried out. After isolation, the bacteria behavior in mineral medium with 1% commercial gasoline (24% ethanol) was evaluated. Parameters employed for microorganism evaluation and selection of those with the greatest degradation potential were: microbial growth; biosurfactant generation and compound reduction in commercial gasoline. Starting from bacteria that presented the best degradation results, consortiums formed by 4 distinct microorganisms were formed. A microbial growth in the presence of commercial gasoline was observed and, for most of the bacteria, degradations of compounds such as benzene, toluene and xylenes (BTX) as well as biosurfactant production was observed. Ethanol was partially degraded by the bacterial isolates although the data does not allow affirming that it was degraded preferentially to the aromatic hydrocarbons investigated. The analyzed consortiums present an efficiency of 95% to 98% for most of the commercial gasoline compounds and a preferential attack to ethanol under the essay condition was not observed within 72 h.

Application of culture-dependent and culture-independent methods for the identification of Lactobacillus kefiranofaciens in microbial consortia present in kefir grains.

PubMed

Hamet, Maria Fernanda; Londero, Alejandra; Medrano, Micaela; Vercammen, Elisabeth; Van Hoorde, Koenraad; Garrote, Graciela L; Huys, Geert; Vandamme, Peter; Abraham, Analía G

2013-12-01

The biological and technological characteristics of kefiran as well as its importance in grain integrity led us to analyze the microbial kefir grain consortium with focus on Lactobacillus kefiranofaciens. The presence of L. kefiranofaciens in the nine kefir grains studied was demonstrated by denaturing gradient gel electrophoresis. By culture dependent methods applying a methodology focused on the search of this species, 22 isolates with typical morphology were obtained and identified applying a combination of SDS-PAGE of whole cell proteins, (GTG)5-PCR and sequence analysis of the housekeeping gene encoding the α-subunit of bacterial phenylalanyl-tRNA synthase (pheS). This polyphasic approach allowed the reliable identification of 11 L. kefiranofaciens, 5 Lactobacillus paracasei, 4 Lactobacillus kefiri and 2 Lactobacillus parakefiri isolates. Isolated L. kefiranofaciens strains produced polysaccharide in strain-dependent concentrations and EPS produced by them also differed in the degree of polymerization. The isolation and accurate identification of L. kefiranofaciens is relevant taking into account the important role of this microorganism in the grain ecosystem as well as its potential application as starter in food fermentations. Copyright © 2013 Elsevier Ltd. All rights reserved.

MICROBIAL CHARACTERIZATION OF DRINKING WATER SYSTEMS RECEIVING GROUNDWATER AND SURFACE WATER AS THE PRIMARY SOURCES OF WATER

EPA Science Inventory

Earlier descriptions of water distribution systems (WDS) microbial communities have relied on culturing techniques. These techniques are known to be highly selective in nature, but more importantly, they tend to grossly underestimate the microbial diversity of most environments. ...

Metataxonomic profiling and prediction of functional behaviour of wheat straw degrading microbial consortia

PubMed Central

2014-01-01

Background Mixed microbial cultures, in which bacteria and fungi interact, have been proposed as an efficient way to deconstruct plant waste. The characterization of specific microbial consortia could be the starting point for novel biotechnological applications related to the efficient conversion of lignocellulose to cello-oligosaccharides, plastics and/or biofuels. Here, the diversity, composition and predicted functional profiles of novel bacterial-fungal consortia are reported, on the basis of replicated aerobic wheat straw enrichment cultures. Results In order to set up biodegradative microcosms, microbial communities were retrieved from a forest soil and introduced into a mineral salt medium containing 1% of (un)treated wheat straw. Following each incubation step, sequential transfers were carried out using 1 to 1,000 dilutions. The microbial source next to three sequential batch cultures (transfers 1, 3 and 10) were analyzed by bacterial 16S rRNA gene and fungal ITS1 pyrosequencing. Faith’s phylogenetic diversity values became progressively smaller from the inoculum to the sequential batch cultures. Moreover, increases in the relative abundances of Enterobacteriales, Pseudomonadales, Flavobacteriales and Sphingobacteriales were noted along the enrichment process. Operational taxonomic units affiliated with Acinetobacter johnsonii, Pseudomonas putida and Sphingobacterium faecium were abundant and the underlying strains were successfully isolated. Interestingly, Klebsiella variicola (OTU1062) was found to dominate in both consortia, whereas K. variicola-affiliated strains retrieved from untreated wheat straw consortia showed endoglucanase/xylanase activities. Among the fungal players with high biotechnological relevance, we recovered members of the genera Penicillium, Acremonium, Coniochaeta and Trichosporon. Remarkably, the presence of peroxidases, alpha-L-fucosidases, beta-xylosidases, beta-mannases and beta-glucosidases, involved in lignocellulose

Conditioning biomass for microbial growth

DOEpatents

Bodie, Elizabeth A; England, George

2015-03-31

The present invention relates to methods for improving the yield of microbial processes that use lignocellulose biomass as a nutrient source. The methods comprise conditioning a composition comprising lignocellulose biomass with an enzyme composition that comprises a phenol oxidizing enzyme. The conditioned composition can support a higher rate of growth of microorganisms in a process. In one embodiment, a laccase composition is used to condition lignocellulose biomass derived from non-woody plants, such as corn and sugar cane. The invention also encompasses methods for culturing microorganisms that are sensitive to inhibitory compounds in lignocellulose biomass. The invention further provides methods of making a product by culturing the production microorganisms in conditioned lignocellulose biomass.

The role of coastal fog in increased viability of marine microbial aerosols

NASA Astrophysics Data System (ADS)

Dueker, M.; O'Mullan, G. D.; Weathers, K. C.; Juhl, A. R.; Uriarte, M.

2011-12-01

Microbes in the atmosphere (microbial aerosols) play an important role in climate and provide an ecological and biogeochemical connection between oceanic, atmospheric, and terrestrial environments. Despite the ubiquity of these bacteria (concentration estimates range from 1 x 10^4 to 6 x 10^5 cells m-3), much is still being learned about their source, viability, and interactions with climatic controls. They can be attached to ambient aerosol particles or exist singly in the air. They affect climate by serving as ice, cloud, and fog nucleators, and have the metabolic potential to alter atmospheric chemistry. Fog presence in particular has been shown to greatly increase the deposition of viable microbial aerosols in both urban and coastal environments, but the mechanisms behind this are not fully understood. To address this gap, we examined the diversity of culturable microbial aerosols from a relatively pristine coastal environment in Maine (USA) and determined the effect of fog presence on viability and community composition of microbial aerosols. 16S rRNA sequencing of culturable ocean surface bacteria and depositing microbial aerosols (under clear and foggy conditions) resulted in the detection of 31 bacterial genera, with 5 dominant genera (Vibrio, Bacillus, Pseudoalteromonas, Psychrobacter, Salinibacterium) making up 66% of all sequences. Seventy-five percent of the viable microbial aerosols falling out under foggy conditions were most similar to GenBank-published sequences detected in marine environments. The fog and ocean surface sequence libraries were significantly more similar in microbial community composition than clear (non-foggy) and ocean surface libraries. These findings support a dual role for fog in enhancing the fallout of viable marine microbial aerosols via increased gravitational settling rates and decreased aerosolization stress on the organisms. The dominant presence of marine bacteria in coastal microbial aerosols provides a strong case for

Microbial transformation of citral by Penicillium sp..

PubMed

Esmaeili, Akbar; Tavassoli, Afsaneh

2010-01-01

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

Outgrowth of fibroblast cells from goat skin explants in three different culture media and the establishment of cell lines.

PubMed

Singh, Mahipal; Sharma, Anil K

2011-02-01

Three different commercially available media, known to support human and porcine-specific fibroblast cultures, were tested for their growth potential on goat skin explants. Although outgrowth of fibroblasts was observed in all media tested, irrespective of breed, porcine-specific media exhibited higher rate of growth. Using this media, three fibroblast cell lines (GSF289, GSF737, and GSF2010) from ear skin explants of normal healthy dairy goats of Kiko and Saanen breed were successfully established in culture. Liquid nitrogen stocks of these frozen cells had a viability rate of 96.2% in in vitro cultures. These cells were morphologically indistinguishable from the cell stocks prior to freezing. Analysis of the growth of a fifth passage culture revealed an 'S' shaped growth curve with a population doubling time of 25 h. The cell lines were found negative for microbial, fungal, and mycoplasma contaminations. These goat skin fibroblast lines and the simple method of their isolation and freezing with high rate of viability will provide additional tools to study molecular mechanisms that regulate fibroblast function and for genetic manipulation of small ruminants.

Mineral Influence on Microbial Survival During Carbon Sequestration

NASA Astrophysics Data System (ADS)

Santillan, E. U.; Shanahan, T. M.; Wolfe, W. W.; Bennett, P.

2012-12-01

CO2 sequestered in a deep saline aquifer will perturb subsurface biogeochemistry by acidifying the groundwater and accelerating mineral diagenesis. Subsurface microbial communities heavily influence geochemistry through their metabolic processes, such as with dissimilatory iron reducing bacteria (DIRB). However, CO2 also acts as a sterilant and will perturb these communities. We investigated the role of mineralogy and its effect on the survival of microbes at high PCO2 conditions using the model DIRB Shewanella oneidensis MR-1. Batch cultures of Shewanella were grown to stationary phase and exposed to high PCO2 using modified Parr reactors. Cell viability was then determined by plating cultures after exposure. Results indicate that at low PCO2 (2 bar), growth and iron reduction are decreased and cell death occurs within 1 hour when exposed to CO2 pressures of 10 bar or greater. Further, fatty acid analysis indicates microbial lipid degradation with C18 fatty acids being the slowest lipids to degrade. When cultures were grown in the presence of rocks or minerals representative of the deep subsurface such as carbonates and silicates and exposed to 25 bar CO2, survival lasted beyond 2 hours. The most effective protecting substratum was quartz sandstone, with cultures surviving beyond 8 hours of CO2 exposure. Scanning electron microscope images reveal biofilm formation on the mineral surfaces with copious amounts of extracellular polymeric substances (EPS) present. EPS from these biofilms acts as a reactive barrier to the CO2, slowing the penetration of CO2 into cells and resulting in increased survival. When biofilm cultures were grown with Al and As to simulate the release of toxic metals from minerals such as feldspars and clays, survival time decreased, indicating mineralogy may also enhance microbial death. Biofilms were then grown on iron-coated quartz sand to determine conversely what influence biofilms may have on mineral dissolution during CO2 perturbation

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

Mapping microbial ecosystems and spoilage-gene flow in breweries highlights patterns of contamination and resistance

PubMed Central

Bokulich, Nicholas A; Bergsveinson, Jordyn; Ziola, Barry; Mills, David A

2015-01-01

Distinct microbial ecosystems have evolved to meet the challenges of indoor environments, shaping the microbial communities that interact most with modern human activities. Microbial transmission in food-processing facilities has an enormous impact on the qualities and healthfulness of foods, beneficially or detrimentally interacting with food products. To explore modes of microbial transmission and spoilage-gene frequency in a commercial food-production scenario, we profiled hop-resistance gene frequencies and bacterial and fungal communities in a brewery. We employed a Bayesian approach for predicting routes of contamination, revealing critical control points for microbial management. Physically mapping microbial populations over time illustrates patterns of dispersal and identifies potential contaminant reservoirs within this environment. Habitual exposure to beer is associated with increased abundance of spoilage genes, predicting greater contamination risk. Elucidating the genetic landscapes of indoor environments poses important practical implications for food-production systems and these concepts are translatable to other built environments. DOI: http://dx.doi.org/10.7554/eLife.04634.001 PMID:25756611

The renaissance of continuous culture in the post-genomics age.

PubMed

Bull, Alan T

2010-10-01

The development of continuous culture techniques 60 years ago and the subsequent formulation of theory and the diversification of experimental systems revolutionised microbiology and heralded a unique period of innovative research. Then, progressively, molecular biology and thence genomics and related high-information-density omics technologies took centre stage and microbial growth physiology in general faded from educational programmes and research funding priorities alike. However, there has been a gathering appreciation over the past decade that if the claims of systems biology are going to be realised, they will have to be based on rigorously controlled and reproducible microbial and cell growth platforms. This revival of continuous culture will be long lasting because its recognition as the growth system of choice is firmly established. The purpose of this review, therefore, is to remind microbiologists, particularly those new to continuous culture approaches, of the legacy of what I call the first age of continuous culture, and to explore a selection of researches that are using these techniques in this post-genomics age. The review looks at the impact of continuous culture across a comprehensive range of microbiological research and development. The ability to establish (quasi-) steady state conditions is a frequently stated advantage of continuous cultures thereby allowing environmental parameters to be manipulated without causing concomitant changes in the specific growth rate. However, the use of continuous cultures also enables the critical study of specified transition states and chemical, physical or biological perturbations. Such dynamic analyses enhance our understanding of microbial ecology and microbial pathology for example, and offer a wider scope for innovative drug discovery; they also can inform the optimization of batch and fed-batch operations that are characterized by sequential transitions states.

Microbial fuel cell (MFC) power performance improvement through enhanced microbial electrogenicity.

PubMed

Li, Ming; Zhou, Minghua; Tian, Xiaoyu; Tan, Chaolin; McDaniel, Cameron T; Hassett, Daniel J; Gu, Tingyue

Within the past 5 years, tremendous advances have been made to maximize the performance of microbial fuel cells (MFCs) for both "clean" bioenergy production and bioremediation. Most research efforts have focused on parameters including (i) optimizing reactor configuration, (ii) electrode construction, (iii) addition of redox-active, electron donating mediators, (iv) biofilm acclimation and feed nutrient adjustment, as well as (v) other parameters that contribute to enhanced MFC performance. To date, tremendous advances have been made, but further improvements are needed for MFCs to be economically practical. In this review, the diversity of electrogenic microorganisms and microbial community changes in mixed cultures are discussed. More importantly, different approaches including chemical/genetic modifications and gene regulation of exoelectrogens, synthetic biology approaches and bacterial community cooperation are reviewed. Advances in recent years in metagenomics and microbiomes have allowed researchers to improve bacterial electrogenicity of robust biofilms in MFCs using novel, unconventional approaches. Taken together, this review provides some important and timely information to researchers who are examining additional means to enhance power production of MFCs. Copyright © 2018 Elsevier Inc. All rights reserved.

Diversity and Biosynthetic Potential of Culturable Microbes Associated with Toxic Marine Animals

PubMed Central

Chau, Rocky; Kalaitzis, John A.; Wood, Susanna A.; Neilan, Brett A.

2013-01-01

Tetrodotoxin (TTX) is a neurotoxin that has been reported from taxonomically diverse organisms across 14 different phyla. The biogenic origin of tetrodotoxin is still disputed, however, TTX biosynthesis by host-associated bacteria has been reported. An investigation into the culturable microbial populations from the TTX-associated blue-ringed octopus Hapalochlaena sp. and sea slug Pleurobranchaea maculata revealed a surprisingly high microbial diversity. Although TTX was not detected among the cultured isolates, PCR screening identifiedsome natural product biosynthesis genes putatively involved in its assembly. This study is the first to report on the microbial diversity of culturable communities from H. maculosa and P. maculata and common natural product biosynthesis genes from their microbiota. We also reassess the production of TTX reported from three bacterial strains isolated from the TTX-containing gastropod Nassarius semiplicatus. PMID:23917066

Diversity and biosynthetic potential of culturable microbes associated with toxic marine animals.

PubMed

Chau, Rocky; Kalaitzis, John A; Wood, Susanna A; Neilan, Brett A

2013-08-02

Tetrodotoxin (TTX) is a neurotoxin that has been reported from taxonomically diverse organisms across 14 different phyla. The biogenic origin of tetrodotoxin is still disputed, however, TTX biosynthesis by host-associated bacteria has been reported. An investigation into the culturable microbial populations from the TTX-associated blue-ringed octopus Hapalochlaena sp. and sea slug Pleurobranchaea maculata revealed a surprisingly high microbial diversity. Although TTX was not detected among the cultured isolates, PCR screening identifiedsome natural product biosynthesis genes putatively involved in its assembly. This study is the first to report on the microbial diversity of culturable communities from H. maculosa and P. maculata and common natural product biosynthesis genes from their microbiota. We also reassess the production of TTX reported from three bacterial strains isolated from the TTX-containing gastropod Nassarius semiplicatus.

A new method for long-term storage of titred microbial standard solutions suitable for microbiologic quality control activities of pharmaceutical companies.

PubMed

Chiellini, Carolina; Mocali, Stefano; Fani, Renato; Ferro, Iolanda; Bruschi, Serenella; Pinzani, Alessandro

2016-08-01

Commercially available lyophilized microbial standards are expensive and subject to reduction in cell viability due to freeze-drying stress. Here we introduce an inexpensive and straightforward method for in-house microbial standard preparation and cryoconservation that preserves constant cell titre and cell viability over 14 months.

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

PubMed

Jagmann, Nina; Philipp, Bodo

2014-12-20

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

Effect of Pseudomonas sp. P7014 on the growth of edible mushroom Pleurotus eryngii in bottle culture for commercial production.

PubMed

Kim, Min Keun; Math, Renukaradhya K; Cho, Kye Man; Shin, Ki Jae; Kim, Jong Ok; Ryu, Jae San; Lee, Young Han; Yun, Han Dae

2008-05-01

Addition of bacterial culture strain P7014 and its supernatant to the mushroom growing media resulted in mushroom mycelia run faster. Mycelial growth rate of Pleurotus eryngii was increased up to 1.6 fold and primordial formation was induced one day earlier. Moreover, it was supposed that addition of bacteria had beneficial applications for commercial mushroom production, which appreciably reduced total number of days for cultivation of about 5+/-2 days compared with uninoculated, which took 55+/-2 days.

Iron oxyhydroxide mineralization on microbial extracellular polysaccharides

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

Chan, Clara S.; Fakra, Sirine C.; Edwards, David C.

2010-06-22

Iron biominerals can form in neutral pH microaerophilic environments where microbes both catalyze iron oxidation and create polymers that localize mineral precipitation. In order to classify the microbial polymers that influence FeOOH mineralogy, we studied the organic and mineral components of biominerals using scanning transmission X-ray microscopy (STXM), micro X-ray fluorescence ({mu}XRF) microscopy, and high-resolution transmission electron microscopy (HRTEM). We focused on iron microbial mat samples from a creek and abandoned mine; these samples are dominated by iron oxyhydroxide-coated structures with sheath, stalk, and filament morphologies. In addition, we characterized the mineralized products of an iron-oxidizing, stalk-forming bacterial culture isolatedmore » from the mine. In both natural and cultured samples, microbial polymers were found to be acidic polysaccharides with carboxyl functional groups, strongly spatially correlated with iron oxyhydroxide distribution patterns. Organic fibrils collect FeOOH and control its recrystallization, in some cases resulting in oriented crystals with high aspect ratios. The impact of polymers is particularly pronounced as the materials age. Synthesis experiments designed to mimic the biomineralization processes show that the polysaccharide carboxyl groups bind dissolved iron strongly but release it as mineralization proceeds. Our results suggest that carboxyl groups of acidic polysaccharides are produced by different microorganisms to create a wide range of iron oxyhydroxide biomineral structures. The intimate and potentially long-term association controls the crystal growth, phase, and reactivity of iron oxyhydroxide nanoparticles in natural systems.« less

The Commercialization of Youth: Channel One in Context.

ERIC Educational Resources Information Center

Wartella, Ellen

1995-01-01

Places Channel One controversy in broader context of commercialization of youth culture during past 20 years. Changes in child-oriented TV market since mid-1970s include rise of independent stations and cable networks, introduction of program-length commercials, and proliferation of new products aimed at children. Targeting marketing to child…

Effects of Phytoecdysteroids (PEDS) Extracted from Cyanotis arachnoidea on Rumen Fermentation, Enzyme Activity and Microbial Efficiency in a Continuous-Culture System.

PubMed

Li, Deyong; Zhang, Yawei; Cui, Zhenliang; He, Liwen; Chen, Wanbao; Meng, Qingxiang; Ren, Liping

2016-01-01

The objective of this study was to evaluate the effects of supplementation of phytoecdysteroids (PEDS) extracted from Cyanotis arachnoidea on rumen fermentation, enzymes activity and microbial efficiency in a dual flow continuous-culture system. A single-factor experimental design was used with twelve fermenters in 4 groups with 3 replicates each. Fermenters were incubated for a total of 7 days that included first 4 days for adaptation and last 3 days for sampling. PEDS was added at levels of zero (as control), 5, 10, and 15 mg/g of the substrate (DM). The results showed that increasing supplementation levels of PEDS resulted in incremental digestibility of dry matter (DMD) (quadratic, P = 0.001) and organic matter (OMD) (quadratic, P = 0.031), but unchanged digestibility of neutral detergent fiber (NDFD), crude protein (CPD) and acid detergent acid (ADFD). As supplementation levels of PEDS increased, there were decreased response in the concentration of ammonia nitrogen (NH3-N) (linear, P = 0.015) and increased response in molar proportions of butyrate (linear, P = 0.004), but unchanged response in total volatile fatty acid (TVFA) and the molar proportion of acetate and propionate, respectively. Increasing PEDS supplementation levels decreased the ratio of acetate to propionate (linear, P = 0.038), suggesting an alteration of rumen fermentation pattern occurring due to PEDS supplementation in the diet. Supplementation of PEDS significantly increased activities of glutamate dehydrogenase (quadratic, P = 0.001), alanine dehydrogenase (quadratic, P = 0.004), glutamate synthase (linear, P = 0.038), glutamine synthetase (quadratic, P = 0.011), respectively. There were no discernible differences in the activity of carboxymethyl cellulose (CMCase), xylanase and protease regardless of the treatments. The daily production of microbial nitrogen (linear, P = 0.002) and microbial efficiency (MOEEF) (linear, P = 0.001) increased linearly as supplementation levels of PEDS

Integrated omics for the identification of key functionalities in biological wastewater treatment microbial communities.

PubMed

Narayanasamy, Shaman; Muller, Emilie E L; Sheik, Abdul R; Wilmes, Paul

2015-05-01

Biological wastewater treatment plants harbour diverse and complex microbial communities which prominently serve as models for microbial ecology and mixed culture biotechnological processes. Integrated omic analyses (combined metagenomics, metatranscriptomics, metaproteomics and metabolomics) are currently gaining momentum towards providing enhanced understanding of community structure, function and dynamics in situ as well as offering the potential to discover novel biological functionalities within the framework of Eco-Systems Biology. The integration of information from genome to metabolome allows the establishment of associations between genetic potential and final phenotype, a feature not realizable by only considering single 'omes'. Therefore, in our opinion, integrated omics will become the future standard for large-scale characterization of microbial consortia including those underpinning biological wastewater treatment processes. Systematically obtained time and space-resolved omic datasets will allow deconvolution of structure-function relationships by identifying key members and functions. Such knowledge will form the foundation for discovering novel genes on a much larger scale compared with previous efforts. In general, these insights will allow us to optimize microbial biotechnological processes either through better control of mixed culture processes or by use of more efficient enzymes in bioengineering applications. © 2015 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Quantifying the metabolic activities of human-associated microbial communities across multiple ecological scales

PubMed Central

Maurice, Corinne Ferrier; Turnbaugh, Peter James

2013-01-01

Humans are home to complex microbial communities, whose aggregate genomes and their encoded metabolic activities are referred to as the human microbiome. Recently, researchers have begun to appreciate that different human body habitats and the activities of their resident microorganisms can be better understood in ecological terms, as a range of spatial scales encompassing single cells, guilds of microorganisms responsive to a similar substrate, microbial communities, body habitats, and host populations. However, the bulk of the work to date has focused on studies of culturable microorganisms in isolation or on DNA sequencing-based surveys of microbial diversity in small to moderately sized cohorts of individuals. Here, we discuss recent work that highlights the potential for assessing the human microbiome at a range of spatial scales, and for developing novel techniques that bridge multiple levels: for example, through the combination of single cell methods and metagenomic sequencing. These studies promise to not only provide a much-needed epidemiological and ecological context for mechanistic studies of culturable and genetically tractable microorganisms, but may also lead to the discovery of fundamental rules that govern the assembly and function of host-associated microbial communities. PMID:23550823

Antifungal Microbial Agents for Food Biopreservation-A Review.

PubMed

Leyva Salas, Marcia; Mounier, Jérôme; Valence, Florence; Coton, Monika; Thierry, Anne; Coton, Emmanuel

2017-07-08

Food spoilage is a major issue for the food industry, leading to food waste, substantial economic losses for manufacturers and consumers, and a negative impact on brand names. Among causes, fungal contamination can be encountered at various stages of the food chain (e.g., post-harvest, during processing or storage). Fungal development leads to food sensory defects varying from visual deterioration to noticeable odor, flavor, or texture changes but can also have negative health impacts via mycotoxin production by some molds. In order to avoid microbial spoilage and thus extend product shelf life, different treatments-including fungicides and chemical preservatives-are used. In parallel, public authorities encourage the food industry to limit the use of these chemical compounds and develop natural methods for food preservation. This is accompanied by a strong societal demand for 'clean label' food products, as consumers are looking for more natural, less severely processed and safer products. In this context, microbial agents corresponding to bioprotective cultures, fermentates, culture-free supernatant or purified molecules, exhibiting antifungal activities represent a growing interest as an alternative to chemical preservation. This review presents the main fungal spoilers encountered in food products, the antifungal microorganisms tested for food bioprotection, and their mechanisms of action. A focus is made in particular on the recent in situ studies and the constraints associated with the use of antifungal microbial agents for food biopreservation.

Assessing Commercial and Alternative Poultry Processing Methods using Microbiome Analyses

USDA-ARS?s Scientific Manuscript database

Assessing poultry processing methods/strategies has historically used culture-based methods to assess bacterial changes or reductions, both in terms of general microbial communities (e.g. total aerobic bacteria) or zoonotic pathogens of interest (e.g. Salmonella, Campylobacter). The advent of next ...

Effect of red blood cells on the growth of Porphyromonas endodontalis and microbial community development.

PubMed

Zerr, M A; Cox, C D; Johnson, W T; Drake, D R

1998-04-01

Establishment of a microbial community in the root canal system depends on numerous factors, of which nutrient availability may be one of the most important. We hypothesized that the presence of red blood cells or hemoglobin in this environment could cause shifts in microbial composition of communities, resulting in organisms such as Porphyromonas endodontalis becoming more dominant. An in vitro model system using mixed, batch cultures was performed with the bacteria P. endodontalis, Fusobacterium nucleatum, Peptostreptococcus micros and Campylobacter rectus. Bacteria were cultured in media with or without the addition of washed red blood cells, hemoglobin, or serum. Cyclic growth studies revealed that P. endodontalis was lost from the community of organisms after three cycles. However, inclusion of red blood cells resulted in establishment of this organism. Moreover, red blood cells added to pure cultures of P. endodontalis substantially enhanced growth and protected the organisms from oxygen. We conclude that the presence of red blood cells could result in shifts of microbial communities of organisms within the root canal system.

A Cross-Cultural Analysis of Advertisements from High-Context Cultures and Low-Context Cultures

ERIC Educational Resources Information Center

Bai, He

2016-01-01

With the development of economy and the change of social culture, advertisements have penetrated our life slowly and done a lot to the commercial markets. Advertisements have often been analyzed in a stylistic way for its unique language style. But language is an important part, as well as a carrier, of culture. Advertising language, as other…

Starting up microbial enhanced oil recovery.

PubMed

Siegert, Michael; Sitte, Jana; Galushko, Alexander; Krüger, Martin

2014-01-01

This chapter gives the reader a practical introduction into microbial enhanced oil recovery (MEOR) including the microbial production of natural gas from oil. Decision makers who consider the use of one of these technologies are provided with the required scientific background as well as with practical advice for upgrading an existing laboratory in order to conduct microbiological experiments. We believe that the conversion of residual oil into natural gas (methane) and the in situ production of biosurfactants are the most promising approaches for MEOR and therefore focus on these topics. Moreover, we give an introduction to the microbiology of oilfields and demonstrate that in situ microorganisms as well as injected cultures can help displace unrecoverable oil in place (OIP). After an initial research phase, the enhanced oil recovery (EOR) manager must decide whether MEOR would be economical. MEOR generally improves oil production but the increment may not justify the investment. Therefore, we provide a brief economical assessment at the end of this chapter. We describe the necessary state-of-the-art scientific equipment to guide EOR managers towards an appropriate MEOR strategy. Because it is inevitable to characterize the microbial community of an oilfield that should be treated using MEOR techniques, we describe three complementary start-up approaches. These are: (i) culturing methods, (ii) the characterization of microbial communities and possible bio-geochemical pathways by using molecular biology methods, and (iii) interfacial tension measurements. In conclusion, we hope that this chapter will facilitate a decision on whether to launch MEOR activities. We also provide an update on relevant literature for experienced MEOR researchers and oilfield operators. Microbiologists will learn about basic principles of interface physics needed to study the impact of microorganisms living on oil droplets. Last but not least, students and technicians trying to understand

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

An Automated Sample Preparation Instrument to Accelerate Positive Blood Cultures Microbial Identification by MALDI-TOF Mass Spectrometry (Vitek®MS).

PubMed

Broyer, Patrick; Perrot, Nadine; Rostaing, Hervé; Blaze, Jérome; Pinston, Frederic; Gervasi, Gaspard; Charles, Marie-Hélène; Dachaud, Fabien; Dachaud, Jacques; Moulin, Frederic; Cordier, Sylvain; Dauwalder, Olivier; Meugnier, Hélène; Vandenesch, Francois

2018-01-01

Sepsis is the leading cause of death among patients in intensive care units (ICUs) requiring an early diagnosis to introduce efficient therapeutic intervention. Rapid identification (ID) of a causative pathogen is key to guide directed antimicrobial selection and was recently shown to reduce hospitalization length in ICUs. Direct processing of positive blood cultures by MALDI-TOF MS technology is one of the several currently available tools used to generate rapid microbial ID. However, all recently published protocols are still manual and time consuming, requiring dedicated technician availability and specific strategies for batch processing. We present here a new prototype instrument for automated preparation of Vitek ® MS slides directly from positive blood culture broth based on an "all-in-one" extraction strip. This bench top instrument was evaluated on 111 and 22 organisms processed using artificially inoculated blood culture bottles in the BacT/ALERT ® 3D (SA/SN blood culture bottles) or the BacT/ALERT Virtuo TM system (FA/FN Plus bottles), respectively. Overall, this new preparation station provided reliable and accurate Vitek MS species-level identification of 87% (Gram-negative bacteria = 85%, Gram-positive bacteria = 88%, and yeast = 100%) when used with BacT/ALERT ® 3D and of 84% (Gram-negative bacteria = 86%, Gram-positive bacteria = 86%, and yeast = 75%) with Virtuo ® instruments, respectively. The prototype was then evaluated in a clinical microbiology laboratory on 102 clinical blood culture bottles and compared to routine laboratory ID procedures. Overall, the correlation of ID on monomicrobial bottles was 83% (Gram-negative bacteria = 89%, Gram-positive bacteria = 79%, and yeast = 78%), demonstrating roughly equivalent performance between manual and automatized extraction methods. This prototype instrument exhibited a high level of performance regardless of bottle type or BacT/ALERT system. Furthermore, blood culture workflow could potentially

Developing Model Benchtop Systems for Microbial Experimental Evolution

NASA Astrophysics Data System (ADS)

Gentry, D.; Wang, J.; Arismendi, D.; Alvarez, J.; Ouandji, C.; Blaich, J.

2017-12-01

Understanding how microbes impact an ecosystem has improved through advances of molecular and genetic tools, but creating complex systems that emulate natural biology goes beyond current technology. In fact, many chemical, biological, and metabolic pathways of even model organisms are still poorly characterized. Even then, standard laboratory techniques for testing microbial impact on environmental change can have many drawbacks; they are time-consuming, labor intensive, and are at risk of contamination. By having an automated process, many of these problems can be reduced or even eliminated. We are developing a benchtop system that can run for long periods of time without the need for human intervention, involve multiple environmental stressors at once, perform real-time adjustments of stressor exposure based on current state of the population, and minimize contamination risks. Our prototype device allows operators to generate an analogue of real world micro-scale ecosystems that can be used to model the effects of disruptive environmental change on microbial ecosystems. It comprises of electronics, mechatronics, and fluidics based systems to control, measure, and evaluate the before and after state of microbial cultures from exposure to environmental stressors. Currently, it uses four parallel growth chambers to perform tests on liquid cultures. To measure the population state, optical sensors (LED/photodiode) are used. Its primary selection pressure is UV-C radiation, a well-studied stressor known for its cell- and DNA- damaging effects and as a mutagen. Future work will involve improving the current growth chambers, as well as implementing additional sensors and environmental stressors into the system. Full integration of multiple culture testing will allow inter-culture comparisons. Besides the temperature and OD sensors, other types of sensors can be integrated such as conductivity, biomass, pH, and dissolved gasses such as CO2 and O2. Additional

Developing Model Benchtop Systems for Microbial Experimental Evolution

NASA Technical Reports Server (NTRS)

Wang, Jonathan; Arismendi, Dillon; Alvarez, Jennifer; Ouandji, Cynthia; Blaich, Justin; Gentry, Diana

2017-01-01

Understanding how microbes impact an ecosystem has improved through advances of molecular and genetic tools, but creating complex systems that emulate natural biology goes beyond current technology. In fact, many chemical, biological, and metabolic pathways of even model organisms are still poorly characterized. Even then, standard laboratory techniques for testing microbial impact on environmental change can have many drawbacks; they are time-consuming, labor intensive, and are at risk of contamination. By having an automated process, many of these problems can be reduced or even eliminated. We are developing a benchtop system that can run for long periods of time without the need for human intervention, involve multiple environmental stressors at once, perform real-time adjustments of stressor exposure based on current state of the population, and minimize contamination risks. Our prototype device allows operators to generate an analogue of real world micro-scale ecosystems that can be used to model the effects of disruptive environmental change on microbial ecosystems. It comprises of electronics, mechatronics, and fluidics based systems to control, measure, and evaluate the before and after state of microbial cultures from exposure to environmental stressors. Currently, it uses four parallel growth chambers to perform tests on liquid cultures. To measure the population state, optical sensors (LED/photodiode) are used. Its primary selection pressure is UV-C radiation, a well-studied stressor known for its cell- and DNA-damaging effects and as a mutagen. Future work will involve improving the current growth chambers, as well as implementing additional sensors and environmental stressors into the system. Full integration of multiple culture testing will allow inter-culture comparisons. Besides the temperature and OD sensors, other types of sensors can be integrated such as conductivity, biomass, pH, and dissolved gasses such as CO and O. Additional environmental

Abiotic factors shape microbial diversity in Sonoran Desert soils.

PubMed

Andrew, David R; Fitak, Robert R; Munguia-Vega, Adrian; Racolta, Adriana; Martinson, Vincent G; Dontsova, Katerina

2012-11-01

High-throughput, culture-independent surveys of bacterial and archaeal communities in soil have illuminated the importance of both edaphic and biotic influences on microbial diversity, yet few studies compare the relative importance of these factors. Here, we employ multiplexed pyrosequencing of the 16S rRNA gene to examine soil- and cactus-associated rhizosphere microbial communities of the Sonoran Desert and the artificial desert biome of the Biosphere2 research facility. The results of our replicate sampling approach show that microbial communities are shaped primarily by soil characteristics associated with geographic locations, while rhizosphere associations are secondary factors. We found little difference between rhizosphere communities of the ecologically similar saguaro (Carnegiea gigantea) and cardón (Pachycereus pringlei) cacti. Both rhizosphere and soil communities were dominated by the disproportionately abundant Crenarchaeota class Thermoprotei, which comprised 18.7% of 183,320 total pyrosequencing reads from a comparatively small number (1,337 or 3.7%) of the 36,162 total operational taxonomic units (OTUs). OTUs common to both soil and rhizosphere samples comprised the bulk of raw sequence reads, suggesting that the shared community of soil and rhizosphere microbes constitute common and abundant taxa, particularly in the bacterial phyla Proteobacteria, Actinobacteria, Planctomycetes, Firmicutes, Bacteroidetes, Chloroflexi, and Acidobacteria. The vast majority of OTUs, however, were rare and unique to either soil or rhizosphere communities and differed among locations dozens of kilometers apart. Several soil properties, particularly soil pH and carbon content, were significantly correlated with community diversity measurements. Our results highlight the importance of culture-independent approaches in surveying microbial communities of extreme environments.

Bio-mining the microbial treasures of the ocean: new natural products.

PubMed

Imhoff, Johannes F; Labes, Antje; Wiese, Jutta

2011-01-01

The biological resources of the oceans have been exploited since ancient human history, mainly by catching fish and harvesting algae. Research on natural products with special emphasis on marine animals and also algae during the last decades of the 20th century has revealed the importance of marine organisms as producers of substances useful for the treatment of human diseases. Though a large number of bioactive substances have been identified, some many years ago, only recently the first drugs from the oceans were approved. Quite astonishingly, the immense diversity of microbes in the marine environments and their almost untouched capacity to produce natural products and therefore the importance of microbes for marine biotechnology was realized on a broad basis by the scientific communities only recently. This has strengthened worldwide research activities dealing with the exploration of marine microorganisms for biotechnological applications, which comprise the production of bioactive compounds for pharmaceutical use, as well as the development of other valuable products, such as enzymes, nutraceuticals and cosmetics. While the focus in these fields was mainly on marine bacteria, also marine fungi now receive growing attention. Although culture-dependent studies continue to provide interesting new chemical structures with biological activities at a high rate and represent highly promising approaches for the search of new drugs, exploration and use of genomic and metagenomic resources are considered to further increase this potential. Many efforts are made for the sustainable exploration of marine microbial resources. Large culture collections specifically of marine bacteria and marine fungi are available. Compound libraries of marine natural products, even of highly purified substances, were established. The expectations into the commercial exploitation of marine microbial resources has given rise to numerous institutions worldwide, basic research facilities as

Microbial Community Response of an Organohalide Respiring Enrichment Culture to Permanganate Oxidation

PubMed Central

Sutton, Nora B.; Atashgahi, Siavash; Saccenti, Edoardo; Grotenhuis, Tim; Smidt, Hauke; Rijnaarts, Huub H. M.

2015-01-01

While in situ chemical oxidation is often used to remediate tetrachloroethene (PCE) contaminated locations, very little is known about its influence on microbial composition and organohalide respiration (OHR) activity. Here, we investigate the impact of oxidation with permanganate on OHR rates, the abundance of organohalide respiring bacteria (OHRB) and reductive dehalogenase (rdh) genes using quantitative PCR, and microbial community composition through sequencing of 16S rRNA genes. A PCE degrading enrichment was repeatedly treated with low (25 μmol), medium (50 μmol), or high (100 μmol) permanganate doses, or no oxidant treatment (biotic control). Low and medium treatments led to higher OHR rates and enrichment of several OHRB and rdh genes, as compared to the biotic control. Improved degradation rates can be attributed to enrichment of (1) OHRB able to also utilize Mn oxides as a terminal electron acceptor and (2) non-dechlorinating community members of the Clostridiales and Deltaproteobacteria possibly supporting OHRB by providing essential co-factors. In contrast, high permanganate treatment disrupted dechlorination beyond cis-dichloroethene and caused at least a 2–4 orders of magnitude reduction in the abundance of all measured OHRB and rdh genes, as compared to the biotic control. High permanganate treatments resulted in a notably divergent microbial community, with increased abundances of organisms affiliated with Campylobacterales and Oceanospirillales capable of dissimilatory Mn reduction, and decreased abundance of presumed supporters of OHRB. Although OTUs classified within the OHR-supportive order Clostridiales and OHRB increased in abundance over the course of 213 days following the final 100 μmol permanganate treatment, only limited regeneration of PCE dechlorination was observed in one of three microcosms, suggesting strong chemical oxidation treatments can irreversibly disrupt OHR. Overall, this detailed investigation into dose

Microbial ecology of two hot springs of Sikkim: Predominate population and geochemistry.

PubMed

Najar, Ishfaq Nabi; Sherpa, Mingma Thundu; Das, Sayak; Das, Saurav; Thakur, Nagendra

2018-10-01

Northeastern regions of India are known for their floral and faunal biodiversity. Especially the state of Sikkim lies in the eastern Himalayan ecological hotspot region. The state harbors many sulfur rich hot springs which have therapeutic and spiritual values. However, these hot springs are yet to be explored for their microbial ecology. The development of neo generation techniques such as metagenomics has provided an opportunity for inclusive study of microbial community of different environment. The present study describes the microbial diversity in two hot springs of Sikkim that is Polok and Borong with the assist of culture dependent and culture independent approaches. The culture independent techniques used in this study were next generation sequencing (NGS) and Phospholipid Fatty Acid Analysis (PLFA). Having relatively distinct geochemistry both the hot springs are thermophilic environments with the temperature range of 50-77 °C and pH range of 5-8. Metagenomic data revealed the dominance of bacteria over archaea. The most abundant phyla were Proteobacteria and Bacteroidetes although other phyla were also present such as Acidobacteria, Nitrospirae, Firmicutes, Proteobacteria, Parcubacteria and Spirochaetes. The PLFA studies have shown the abundance of Gram Positive bacteria followed by Gram negative bacteria. The culture dependent technique was correlative with PLFA studies. Most abundant bacteria as isolated and identified were Gram-positive genus Geobacillus and Anoxybacillus. The genus Geobacillus has been reported for the first time in North-Eastern states of India. The Geobacillus species obtained from the concerned hot springs were Geobacillus toebii, Geobacillus lituanicus, Geobacillus Kaustophillus and the Anoxybacillus species includes Anoxybacillus gonensis and Anoxybacillus Caldiproteolyticus. The distribution of major genera and their statistical correlation analyses with the geochemistry of the springs predicted that the temperature, p

Microbial diversity in the floral nectar of seven Epipactis (Orchidaceae) species

PubMed Central

Jacquemyn, Hans; Lenaerts, Marijke; Tyteca, Daniel; Lievens, Bart

2013-01-01

Abstract Floral nectar of animal-pollinated plants is commonly infested with microorganisms, yet little is known about the microorganisms inhabiting the floral nectar of orchids. In this study, we investigated microbial communities occurring in the floral nectar of seven Epipactis (Orchidaceae) species. Culturable bacteria and yeasts were isolated and identified by partially sequencing the small subunit (SSU) ribosomal RNA (rRNA) gene and the D1/D2 domains of the large subunit (LSU) rRNA gene, respectively. Using three different culture media, we found that bacteria were common inhabitants of the floral nectar of Epipactis. The most widely distributed bacterial operational taxonomic units (OTUs) in nectar of Epipactis were representatives of the family of Enterobacteriaceae, with an unspecified Enterobacteriaceae bacterium as the most common. In contrast to previous studies investigating microbial communities in floral nectar, very few yeast species (mainly of the genus Cryptococcus) were observed, and most of them occurred in very low densities. Total OTU richness (i.e., the number of bacterial and yeast OTUs per orchid species) varied between 4 and 20. Cluster analysis revealed that microbial communities of allogamous species differed from those of autogamous and facultatively autogamous species. This study extends previous efforts to identify microbial communities in floral nectar and indicates that the floral nectar of the orchids investigated mainly contained bacterial communities with moderate phylogenetic diversity. PMID:23836678

Microbial Diversity in Sulfate-Reducing Marine Sediment Enrichment Cultures Associated with Anaerobic Biotransformation of Coastal Stockpiled Phosphogypsum (Sfax, Tunisia)

PubMed Central

Zouch, Hana; Karray, Fatma; Armougom, Fabrice; Chifflet, Sandrine; Hirschler-Réa, Agnès; Kharrat, Hanen; Kamoun, Lotfi; Ben Hania, Wajdi; Ollivier, Bernard; Sayadi, Sami; Quéméneur, Marianne

2017-01-01

Anaerobic biotechnology using sulfate-reducing bacteria (SRB) is a promising alternative for reducing long-term stockpiling of phosphogypsum (PG), an acidic (pH ~3) by-product of the phosphate fertilizer industries containing high amounts of sulfate. The main objective of this study was to evaluate, for the first time, the diversity and ability of anaerobic marine microorganisms to convert sulfate from PG into sulfide, in order to look for marine SRB of biotechnological interest. A series of sulfate-reducing enrichment cultures were performed using different electron donors (i.e., acetate, formate, or lactate) and sulfate sources (i.e., sodium sulfate or PG) as electron acceptors. Significant sulfide production was observed from enrichment cultures inoculated with marine sediments, collected near the effluent discharge point of a Tunisian fertilizer industry (Sfax, Tunisia). Sulfate sources impacted sulfide production rates from marine sediments as well as the diversity of SRB species belonging to Deltaproteobacteria. When PG was used as sulfate source, Desulfovibrio species dominated microbial communities of marine sediments, while Desulfobacter species were mainly detected using sodium sulfate. Sulfide production was also affected depending on the electron donor used, with the highest production obtained using formate. In contrast, low sulfide production (acetate-containing cultures) was associated with an increase in the population of Firmicutes. These results suggested that marine Desulfovibrio species, to be further isolated, are potential candidates for bioremediation of PG by immobilizing metals and metalloids thanks to sulfide production by these SRB. PMID:28871244

Microbial quality and bioactive constituents of sweet peppers from sustainable production systems.

PubMed

Marín, Alicia; Gil, María I; Flores, Pilar; Hellín, Pilar; Selma, María V

2008-12-10

Integrated, organic, and soil-less production systems are the principal production practices that have emerged to encourage more sustainable agricultural practices and safer edible plants, reducing inputs of plaguicides, pesticides, and fertilizers. Sweet peppers grown commercially under integrated, organic, and soil-less production systems were compared to study the influence of these sustainable production systems on the microbial quality and bioactive constituents (vitamin C, individual and total carotenoids, hydroxycinnamic acids, and flavonoids). The antioxidant composition of peppers was analyzed at green and red maturity stages and at three harvest times (initial, middle, and late season). Irrigation water, manure, and soil were shown to be potential transmission sources of pathogens to the produce. Coliform counts of soil-less peppers were up to 2.9 log units lower than those of organic and integrated peppers. Soil-less green and red peppers showed maximum vitamin C contents of 52 and 80 mg 100 g(-1) fresh weight (fw), respectively, similar to those grown in the organic production system. Moreover, the highest content of total carotenoids was found in the soil-less red peppers, which reached a maximum of 148 mg 100 g(-1) fw, while slightly lower contents were found in integrated and organic red peppers. Hydroxycinnamic acids and flavonoids represented 15 and 85% of the total phenolic content, respectively. Total phenolic content, which ranged from 1.2 to 4.1 mg 100 g(-1) fw, was significantly affected by the harvest time but not by the production system assayed. Soil-less peppers showed similar or even higher concentrations of bioactive compounds (vitamin C, provitamin A, total carotenoid, hydroxycinnamic acids, and flavonoids) than peppers grown under organic and integrated practices. Therefore, in the commercial conditions studied, soil-less culture was a more suitable alternative than organic or integrated practices, because it improved the microbial

The role of microbial low-molecular-weight autoregulatory factors (alkylhydroxybenzenes) in resistance of microorganisms to radiation and heat shock

NASA Astrophysics Data System (ADS)

El-Registan, Galina I.; Mulyukin, Andrey L.; Nikolaev, Yuri A.; Stepanenko, Irina Yu.; Kozlova, Alla N.; Martirosova, Elena I.; Shanenko, Elena F.; Strakhovskaya, Marina G.; Revina, Aleksandra A.

Low-molecular-weight cell-to-cell communication factors are produced by various pro- and eukaryotes and involved in autoregulation of the growth and development of microbial cultures. As for some bacterial and yeast species, these factors were identified as isomers and homologues of alkylhydroxybenzenes (AHB). Depending on the concentration, they participate in controlling the transition to stationary phase, entering the resting state, and stress resistance of vegetative cells to gamma-irradiation, photooxidation (singlet oxygen), and heat shock. Chemical analogues of microbial AHB protected microbial cultures from stressful situations and exerted (1) the stabilizing activity toward macromolecules and (2) the ability to scavenge active oxygen species. The stabilizing effect of AHBs resulted from their complex formation with protected macromolecules due to intermolecular hydrogen bonds, hydrophobic and electrostatic interactions and was demonstrated on models of individual enzymes (trypsin). Particularly, AHBs protected the yeast from the action of (a) active oxygen species formed during gamma-irradiation (500 Gy, 1.96 Gy/s) or (b) singlet oxygen generated in cells photosensitized by chlorin e 6 (10 μg/L). It is important that microbial AHBs were not species-specific and defended cultured microbial and animal cells from the action of organic toxicants. The use of AHBs as protectants and adaptogens is discussed as well as perspectives of further investigations.

Anti-microbial Activity of Urine after Ingestion of Cranberry: A Pilot Study.

PubMed

Lee, Yee Lean; Najm, Wadie I; Owens, John; Thrupp, Laurie; Baron, Sheryl; Shanbrom, Edward; Cesario, Thomas

2010-06-01

We explore the anti-microbial activity of urine specimens after the ingestion of a commercial cranberry preparation. Twenty subjects without urinary infection, off antibiotics and all supplements or vitamins were recruited. The study was conducted in two phases: in phase 1, subjects collected the first morning urine prior to ingesting 900 mg of cranberry and then at 2, 4 and 6 h. In phase 2, subjects collected urine on 2 consecutive days: on Day 1 no cranberry was ingested (control specimens), on Day 2, cranberry was ingested. The pH of all urine specimens were adjusted to the same pH as that of the first morning urine specimen. Aliquots of each specimen were independently inoculated with Escherichia coli, Klebsiella pneumoniae or Candida albicans. After incubation, colony forming units/ml (CFU ml(-1)) in the control specimen was compared with CFU ml(-1) in specimens collected 2, 4 and 6 h later. Specimens showing ≥50% reduction in CFU ml(-1) were considered as having 'activity' against the strains tested. In phase 1, 7/20 (35%) subjects had anti-microbial activity against E. coli, 13/20 (65%) against K. pneumoniae and 9/20 (45%) against C. albicans in specimens collected 2-6 h after ingestion of cranberry. In phase 2, 6/9 (67%) of the subjects had activity against K. pneumoniae. This pilot study demonstrates weak anti-microbial activity in urine specimens after ingestion of a single dose of commercial cranberry. Anti-microbial activity was noted only against K. pneumoniae 2-6 h after ingestion of the cranberry preparation.

Microbial responses to microgravity and other low-shear environments.

PubMed

Nickerson, Cheryl A; Ott, C Mark; Wilson, James W; Ramamurthy, Rajee; Pierson, Duane L

2004-06-01

Microbial adaptation to environmental stimuli is essential for survival. While several of these stimuli have been studied in detail, recent studies have demonstrated an important role for a novel environmental parameter in which microgravity and the low fluid shear dynamics associated with microgravity globally regulate microbial gene expression, physiology, and pathogenesis. In addition to analyzing fundamental questions about microbial responses to spaceflight, these studies have demonstrated important applications for microbial responses to a ground-based, low-shear stress environment similar to that encountered during spaceflight. Moreover, the low-shear growth environment sensed by microbes during microgravity of spaceflight and during ground-based microgravity analogue culture is relevant to those encountered during their natural life cycles on Earth. While no mechanism has been clearly defined to explain how the mechanical force of fluid shear transmits intracellular signals to microbial cells at the molecular level, the fact that cross talk exists between microbial signal transduction systems holds intriguing possibilities that future studies might reveal common mechanotransduction themes between these systems and those used to sense and respond to low-shear stress and changes in gravitation forces. The study of microbial mechanotransduction may identify common conserved mechanisms used by cells to perceive changes in mechanical and/or physical forces, and it has the potential to provide valuable insight for understanding mechanosensing mechanisms in higher organisms. This review summarizes recent and future research trends aimed at understanding the dynamic effects of changes in the mechanical forces that occur in microgravity and other low-shear environments on a wide variety of important microbial parameters.

Microbial Responses to Microgravity and Other Low-Shear Environments

NASA Technical Reports Server (NTRS)

Nickerson, Cheryl A.; Ott, C. Mark; Wilson, James W.; Ramamurthy, Rajee; Pierson, Duane L.

2004-01-01

Microbial adaptation to environmental stimuli is essential for survival. While several of these stimuli have been studied in detail, recent studies have demonstrated an important role for a novel environmental parameter in which microgravity and the low fluid shear dynamics associated with microgravity globally regulate microbial gene expression, physiology, and pathogenesis. In addition to analyzing fundamental questions about microbial responses to spaceflight, these studies have demonstrated important applications for microbial responses to a ground-based, low-shear stress environment similar to that encountered during spaceflight. Moreover, the low-shear growth environment sensed by microbes during microgravity of spaceflight and during ground-based microgravity analogue culture is relevant to those encountered during their natural life cycles on Earth. While no mechanism has been clearly defined to explain how the mechanical force of fluid shear transmits intracellular signals to microbial cells at the molecular level, the fact that cross talk exists between microbial signal transduction systems holds intriguing possibilities that future studies might reveal common mechanotransduction themes between these systems and those used to sense and respond to low-shear stress and changes in gravitation forces. The study of microbial mechanotransduction may identify common conserved mechanisms used by cells to perceive changes in mechanical and/or physical forces, and it has the potential to provide valuable insight for understanding mechanosensing mechanisms in higher organisms. This review summarizes recent and future research trends aimed at understanding the dynamic effects of changes in the mechanical forces that occur in microgravity and other low-shear environments on a wide variety of important microbial parameters.

Community structure and PAH ring-hydroxylating dioxygenase genes of a marine pyrene-degrading microbial consortium.

PubMed

Gallego, Sara; Vila, Joaquim; Tauler, Margalida; Nieto, José María; Breugelmans, Philip; Springael, Dirk; Grifoll, Magdalena

2014-07-01

Marine microbial consortium UBF, enriched from a beach polluted by the Prestige oil spill and highly efficient in degrading this heavy fuel, was subcultured in pyrene minimal medium. The pyrene-degrading subpopulation (UBF-Py) mineralized 31 % of pyrene without accumulation of partially oxidized intermediates indicating the cooperation of different microbial components in substrate mineralization. The microbial community composition was characterized by culture dependent and PCR based methods (PCR-DGGE and clone libraries). Molecular analyses showed a highly stable community composed by Alphaproteobacteria (84 %, Breoghania, Thalassospira, Paracoccus, and Martelella) and Actinobacteria (16 %, Gordonia). The members of Thalasosspira and Gordonia were not recovered as pure cultures, but five additional strains, not detected in the molecular analysis, that classified within the genera Novosphingobium, Sphingopyxis, Aurantimonas (Alphaproteobacteria), Alcanivorax (Gammaproteobacteria) and Micrococcus (Actinobacteria), were isolated. None of the isolates degraded pyrene or other PAHs in pure culture. PCR amplification of Gram-positive and Gram-negative dioxygenase genes did not produce results with any of the cultured strains. However, sequences related to the NidA3 pyrene dioxygenase present in mycobacterial strains were detected in UBF-Py consortium, suggesting the representative of Gordonia as the key pyrene degrader, which is consistent with a preeminent role of actinobacteria in pyrene removal in coastal environments affected by marine oil spills.

N-acyl homoserine lactone-degrading microbial enrichment cultures isolated from Penaeus vannamei shrimp gut and their probiotic properties in Brachionus plicatilis cultures.

PubMed

Tinh, Nguyen Thi Ngoc; Asanka Gunasekara, R A Y S; Boon, Nico; Dierckens, Kristof; Sorgeloos, Patrick; Bossier, Peter

2007-10-01

Three bacterial enrichment cultures (ECs) were isolated from the digestive tract of Pacific white shrimp Penaeus vannamei, by growing the shrimp microbial communities in a mixture of N-acyl homoserine lactone (AHL) molecules. The ECs, characterized by denaturing gradient gel electrophoresis analysis and subsequent rRNA sequencing, degraded AHL molecules in the degradation assays. Apparently, the resting cells of the ECs also degraded one of the three types of quorum-sensing signal molecules produced by Vibrio harveyi in vitro [i.e. harveyi autoinducer 1 (HAI-1)]. The most efficient AHL-degrading ECs, EC5, was tested in Brachionus experiments. EC5 degraded the V. harveyi HAI-1 autoinducer in vivo, neutralizing the negative effect of V. harveyi autoinducer 2 (AI-2) mutant, in which only the HAI-1- and CAI-1-mediated components of the quorum-sensing system are functional on the growth of Brachionus. This suggests that EC5 interferes with HAI-1-regulated metabolism in V. harveyi. These AHL-degrading ECs need to be tested in other aquatic systems for their probiotic properties, preferably in combination with specific AI-2-degrading bacteria.

MOLECULAR DIVERSITY OF DRINKING WATER MICROBIAL COMMUNITIES: A PHYLOGENETIC APPROACH

EPA Science Inventory

The microbiological quality of drinking water is assessed using culture-based methods that are highly selective and that tend to underestimate the densities and diversity of microbial populations inhabiting distribution systems. In order to better understand the effect of differe...

Microbial Community Analysis in the Roots of Aquatic Plants and Isolation of Novel Microbes Including an Organism of the Candidate Phylum OP10

PubMed Central

Tanaka, Yasuhiro; Tamaki, Hideyuki; Matsuzawa, Hiroaki; Nigaya, Masahiro; Mori, Kazuhiro; Kamagata, Yoichi

2012-01-01

A number of molecular ecological studies have revealed complex and unique microbial communities in various terrestrial plant roots; however, little is known about the microbial communities of aquatic plant roots in spite of their potential use for water quality improvement in aquatic environments (e.g. floating treatment wetland system). Here, we report the microbial communities inhabiting the roots of emerged plants, reed (Phragmites australis) and Japanese loosestrife (Lythrum anceps), collected from a floating treatment wetland in a pond by both culture-independent and culture-dependent approaches. Culture-independent analysis based on 16S rRNA gene sequences revealed that the microbial compositions between the two aquatic plant roots were clearly different (e.g. the predominant microbe was Betaproteobacteria for reed and Alphaproteobacteria for Japanese loosestrife). In comparisons of microbial communities between the plant roots and pond water taken from near the plants, the microbial diversity in the plant roots (e.g. 4.40–4.26 Shannon-Weiner index) were higher than that of pond water (e.g. 3.15 Shannon-Weiner index). Furthermore, the plant roots harbored 2.5–3.5 times more phylogenetically novel clone phylotypes than pond water. The culture-dependent approach also revealed differences in the microbial composition and diversity among the two plant roots and pond water. More importantly, compared to pond water, we succeeded in isolating approximately two times more novel isolate phylotypes, including a bacterium of candidate phylum OP10 (recently named Armatimonadetes) from the plant roots. These findings suggest that aquatic plants roots are significant sources for a variety of novel organisms. PMID:22791047

Microbial Diversity of Impact-Generated Habitats

NASA Astrophysics Data System (ADS)

Pontefract, Alexandra; Osinski, Gordon R.; Cockell, Charles S.; Southam, Gordon; McCausland, Phil J. A.; Umoh, Joseph; Holdsworth, David W.

2016-10-01

Impact-generated lithologies have recently been identified as viable and important microbial habitats, especially within cold and arid regions such as the polar deserts on Earth. These unique habitats provide protection from environmental stressors, such as freeze-thaw events, desiccation, and UV radiation, and act to trap aerially deposited detritus within the fissures and pore spaces, providing necessary nutrients for endoliths. This study provides the first culture-independent analysis of the microbial community structure within impact-generated lithologies in a Mars analog environment, involving the analysis of 44,534 16S rRNA sequences from an assemblage of 21 rock samples that comprises three shock metamorphism categories. We find that species diversity increases (H = 2.4-4.6) with exposure to higher shock pressures, which leads to the development of three distinct populations. In each population, Actinobacteria were the most abundant (41%, 65%, and 59%), and the dominant phototrophic taxa came from the Chloroflexi. Calculated porosity (a function of shock metamorphism) for these samples correlates (R2 = 0.62) with inverse Simpson indices, accounting for overlap in populations in the higher shock levels. The results of our study show that microbial diversity is tied to the amount of porosity in the target substrate (as a function of shock metamorphism), resulting in the formation of distinct microbial populations.

Energy, ecology and the distribution of microbial life.

PubMed

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

2013-07-19

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

Energy, ecology and the distribution of microbial life

PubMed Central

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

2013-01-01

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

Nonacid meat decontamination technologies: model studies and commercial applications.

PubMed

Sofos, J N; Smith, G C

1998-11-10

Increased consumer awareness and concern about microbial foodborne diseases has resulted in intensified efforts to reduce contamination of raw meat, as evidenced by new meat and poultry inspection regulations being implemented in the United States. In addition to requiring operation of meat and poultry slaughtering and processing plants under the principles of the hazard analysis critical control point (HACCP) system, the new regulations have established microbiological testing criteria for Escherichia coli and Salmonella, as a means of evaluating plant performance. These developments have renewed and intensified interest in the development and commercial application of meat and poultry decontamination procedures. Technologies developed and evaluated for decontamination include live animal cleaning/washing, chemical dehairing, carcass knife-trimming to remove physical contaminants, steam/hot water-vacuuming for spot-cleaning/decontamination of carcasses, spray washing/rinsing of carcasses with water of low or high pressures and temperatures or chemical solutions, and exposure of carcass sides to pressurized steam. Under appropriate conditions, the technologies applied to carcasses may reduce mean microbiological counts by approximately one-three log colony forming units (cfu)/cm2, and some of them have been approved and are employed in commercial applications (i.e., steam-vacuuming; carcass spray-washing with water, chlorine, organic acid or trisodium phosphate solutions; hot water deluging/spraying/rinsing, and pressurized steam). The contribution of these decontamination technologies to the enhancement of food safety will be determined over the long term, as surveillance data on microbial foodborne illness are collected. This review examines carcass decontamination technologies, other than organic acids, with emphasis placed on recent advances and commercial applications.

Microbial Activity and Silica Degradation in Rice Straw

NASA Astrophysics Data System (ADS)

Kim, Esther Jin-kyung

Abundantly available agricultural residues like rice straw have the potential to be feedstocks for bioethanol production. Developing optimized conditions for rice straw deconstruction is a key step toward utilizing the biomass to its full potential. One challenge associated with conversion of rice straw to bioenergy is its high silica content as high silica erodes machinery. Another obstacle is the availability of enzymes that hydrolyze polymers in rice straw under industrially relevant conditions. Microbial communities that colonize compost may be a source of enzymes for bioconversion of lignocellulose to products because composting systems operate under thermophilic and high solids conditions that have been shown to be commercially relevant. Compost microbial communities enriched on rice straw could provide insight into a more targeted source of enzymes for the breakdown of rice straw polysaccharides and silica. Because rice straw is low in nitrogen it is important to understand the impact of nitrogen concentrations on the production of enzyme activity by the microbial community. This study aims to address this issue by developing a method to measure microbial silica-degrading activity and measure the effect of nitrogen amendment to rice straw on microbial activity and extracted enzyme activity during a high-solids, thermophilic incubation. An assay was developed to measure silica-degrading enzyme or silicase activity. This process included identifying methods of enzyme extraction from rice straw, identifying a model substrate for the assay, and optimizing measurement techniques. Rice straw incubations were conducted with five different levels of nitrogen added to the biomass. Microbial activity was measured by respiration and enzyme activity. A microbial community analysis was performed to understand the shift in community structure with different treatments. With increased levels of nitrogen, respiration and cellulose and hemicellulose degrading activity

Antioxidant and antimicrobial activity of commercial propolis extract in beef patties.

PubMed

Vargas-Sánchez, Rey D; Torrescano-Urrutia, Gastón R; Acedo-Félix, Evelia; Carvajal-Millán, Elizabeth; González-Córdova, Aarón F; Vallejo-Galland, Belinda; Torres-Llanez, María J; Sánchez-Escalante, Armida

2014-08-01

The objective of this study was to evaluate the efficacy of propolis extract (PE) to reduce lipid oxidation and microbial growth on beef patties during refrigerated storage. Beef patties were manufactured by incorporating PE in 4 different treatments: (1) Control (no PE addition); (2) commercial propolis 1 (2% w/w; CP1); (3) commercial propolis 2 (2% w/w; CP2); and (4) noncommercial propolis (2% w/w; NCP). Raw patties were wrapped with polyvinyl chloride and stored at 2 °C for 8 d. Total phenolic content (TPC), free-radical scavenging activity (FRS), and polyphenolic content of the PE were evaluated using high-performance liquid chromatography (HPLC). Lipid oxidation (thiobarbituric acid-reactive substances (TBARS), conjugated dienes (CnDs), metmyoglobin (MetMb%), pH variation, and color (L*, a*, b*, C*, and h*), and microbial growth (mesophilic and psychrotrophic bacteria) of patty samples were measured. NCP treatment demonstrated the highest FRS (64.8% at 100 μg/mL), which correlated with TPC and the presence of polyphenolic compounds. Lipid oxidation (78.54%, TBARS; 45.53%, CnD; 58.57%, MetMb) and microbial mesophilic and psychrotrophic growth (19.75 and 27.03%, respectively) values were reduced by NCP treatment in refrigerated samples after 8 d. These results indicate that PE has great potential as a natural antioxidant and antimicrobial additive to extend the shelf life of beef patties. © 2014 Institute of Food Technologists®

Characterization of microbial current production as a function of microbe-electrode-interaction.

PubMed

Dolch, Kerstin; Danzer, Joana; Kabbeck, Tobias; Bierer, Benedikt; Erben, Johannes; Förster, Andreas H; Maisch, Jan; Nick, Peter; Kerzenmacher, Sven; Gescher, Johannes

2014-04-01

Microbe-electrode-interactions are keys for microbial fuel cell technology. Nevertheless, standard measurement routines to analyze the interplay of microbial physiology and material characteristics have not been introduced yet. In this study, graphite anodes with varying surface properties were evaluated using pure cultures of Shewanella oneidensis and Geobacter sulfurreducens, as well as defined and undefined mixed cultures. The evaluation routine consisted of a galvanostatic period, a current sweep and an evaluation of population density. The results show that surface area correlates only to a certain extent with population density and anode performance. Furthermore, the study highlights a strain-specific microbe-electrode-interaction, which is affected by the introduction of another microorganism. Moreover, evidence is provided for the possibility of translating results from pure culture to undefined mixed species experiments. This is the first study on microbe-electrode-interaction that systematically integrates and compares electrochemical and biological data. Copyright © 2014 Elsevier Ltd. All rights reserved.

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.

Effects of concentrate replacement by feed blocks on ruminal fermentation and microbial growth in goats and single-flow continuous-culture fermenters.

PubMed

Molina-Alcaide, E; Pascual, M R; Cantalapiedra-Hijar, G; Morales-García, E Y; Martín-García, A I

2009-04-01

The effect of replacing concentrate with 2 different feed blocks (FB) on ruminal fermentation and microbial growth was evaluated in goats and in single-flow continuous-culture fermenters. Diets consisted of alfalfa hay plus concentrate and alfalfa hay plus concentrate with 1 of the 2 studied FB. Three trials were carried out with 6 rumen-fistulated Granadina goats and 3 incubation runs in 6 single-flow continuous-culture fermenters. Experimental treatments were assigned randomly within each run, with 2 repetitions for each diet. At the end of each in vivo trial, the rumen contents were obtained for inoculating the fermenters. For each incubation run, the fermenters were inoculated with ruminal fluid from goats fed the same diet supplied to the corresponding fermenter flask. The average pH values, total and individual VFA, and NH(3)-N concentrations, and acetate:propionate ratios in the rumen of goats were not affected (P >or= 0.10) by diet, whereas the microbial N flow (MNF) and efficiency were affected (P or= 0.05), and total (P=0.02), NH(3) (P=0.005), and non-NH(3) (P=0.02) N flows, whereas the efficiency of VFA production was not affected (P=0.75). The effect of diet on MNF and efficiency depended on the bacterial pellet used as a reference. An effect (P<0.05) of diet on the composition of solid- and liquid-associated bacteria was observed. The compositions of liquid-associated bacteria in the fermenter contents and effluent were similar (P=0.05). Differences (P<0.001) between in vivo and in vitro values for most fermentation variables and bacterial pellet compositions were found. Partial replacement of the concentrate with FB did not greatly compromise carbohydrate fermentation in unproductive goats. However, this was not the case for MNF and

Bioelectricity generation in microbial fuel cell using natural microflora and isolated pure culture bacteria from anaerobic palm oil mill effluent sludge.

PubMed

Nor, Muhamad Hanif Md; Mubarak, Mohd Fahmi Muhammad; Elmi, Hassan Sh Abdirahman; Ibrahim, Norahim; Wahab, Mohd Firdaus Abdul; Ibrahim, Zaharah

2015-08-01

A double-chambered membrane microbial fuel cell (MFC) was constructed to investigate the potential use of natural microflora anaerobic palm oil mill effluent (POME) sludge and pure culture bacteria isolated from anaerobic POME sludge as inoculum for electricity generation. Sterilized final discharge POME was used as the substrate with no addition of nutrients. MFC operation using natural microflora anaerobic POME sludge showed a maximum power density and current density of 85.11mW/m(2) and 91.12mA/m(2) respectively. Bacterial identification using 16S rRNA analysis of the pure culture isolated from the biofilm on the anode MFC was identified as Pseudomonas aeruginosa strain ZH1. The electricity generated in MFC using P. aeruginosa strain ZH1 showed maximum power density and current density of 451.26mW/m(2) and 654.90mA/m(2) respectively which were five times higher in power density and seven times higher in current density compared to that of MFC using anaerobic POME sludge. Copyright © 2015 Elsevier Ltd. All rights reserved.

Identification and microbial production of a terpene-based advanced biofuel

PubMed Central

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

2011-01-01

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

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

PubMed

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

2014-11-15

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

Microbial syntrophy: interaction for the common good.

PubMed

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

2013-05-01

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

Application of molecular techniques for the assessment of microorganism diversity on cultural heritage objects.

PubMed

Otlewska, Anna; Adamiak, Justyna; Gutarowska, Beata

2014-01-01

As a result of their unpredictable ability to adapt to varying environmental conditions, microorganisms inhabit different types of biological niches on Earth. Owing to the key role of microorganisms in many biogeochemical processes, trends in modern microbiology emphasize the need to know and understand the structure and function of complex microbial communities. This is particularly important if the strategy relates to microbial communities that cause biodeterioration of materials that constitute our cultural heritage. Until recently, the detection and identification of microorganisms inhabiting objects of cultural value was based only on cultivation-dependent methods. In spite of many advantages, these methods provide limited information because they identify only viable organisms capable of growth under standard laboratory conditions. However, in order to carry out proper conservation and renovation, it is necessary to know the complete composition of microbial communities and their activity. This paper presents and characterizes modern techniques such as genetic fingerprinting and clone library construction for the assessment of microbial diversity based on molecular biology. Molecular methods represent a favourable alternative to culture-dependent methods and make it possible to assess the biodiversity of microorganisms inhabiting technical materials and cultural heritage objects.

Microbial innovations in the world of food.

PubMed

Kawasaki, Hisashi; Ueda, Kenji

2017-01-01

Technological developments in Japan based on the results of microbial research were a major pillar supporting the postwar industrial revolution. The wellspring of these advancements was the sophisticated technology used in traditional brewing, a foundation of the characteristic Japanese food culture. In this manuscript, we will describe the fermentative production of amino acids and nucleic acids following the discovery of the umami component so distinct in Japanese cuisine, which finally revealed the true power of microbial production. Thereafter, we will describe acetic acid production stemming from brewed vinegar production and the fermentative production of some other organic acids. Finally, we will delve into the massive scale of innovations achieved by the discovery of valuable micro-organisms and how they have affected the field of food.

Strategies for efficiently selecting PHA producing mixed microbial cultures using complex feedstocks: Feast and famine regime and uncoupled carbon and nitrogen availabilities.

PubMed

Oliveira, Catarina S S; Silva, Carlos E; Carvalho, Gilda; Reis, Maria A

2017-07-25

Production of polyhydroxyalkanoates (PHAs) by open mixed microbial cultures (MMCs) has been attracting increasing interest as an alternative technology to PHA production by pure cultures, due to the potential for lower costs associated with the use of open systems (eliminating the requirement for sterile conditions) and the utilisation of cheap feedstock (industrial and agricultural wastes). Such technology relies on the efficient selection of an MMC enriched in PHA-accumulating organisms. Fermented cheese whey, a protein-rich complex feedstock, has been used previously to produce PHA using the feast and famine regime for selection of PHA accumulating cultures. While this selection strategy was found efficient when operated at relatively low organic loading rate (OLR, 2g-CODL -1 d -1 ), great instability and low selection efficiency of PHA accumulating organisms were observed when higher OLR (ca. 6g-CODL -1 d -1 ) was applied. High organic loading is desirable as a means to enhance PHA productivity. In the present study, a new selection strategy was tested with the aim of improving selection for high OLR. It was based on uncoupling carbon and nitrogen supply and was implemented and compared with the conventional feast and famine strategy. For this, two selection reactors were fed with fermented cheese whey applying an OLR of ca. 8.5g-CODL -1 (with 3.8g-CODL -1 resulting from organic acids and ethanol), and operated in parallel under similar conditions, except for the timing of nitrogen supplementation. Whereas in the conventional strategy nitrogen and carbon substrates were added simultaneously at the beginning of the cycle, in the uncoupled substrates strategy, nitrogen addition was delayed to the end of the feast phase (i.e. after exogenous carbon was exhausted). The two different strategies selected different PHA-storing microbial communities, dominated by Corynebacterium and a Xantomonadaceae, respectively with the conventional and the new approaches. The new

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

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

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

2007-06-27

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

Hydrogen production profiles using furans in microbial electrolysis cells.

PubMed

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

2017-06-01

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

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.

Single gene-based distinction of individual microbial genomes from a mixed population of microbial cells.

PubMed

Tamminen, Manu V; Virta, Marko P J

2015-01-01

Recent progress in environmental microbiology has revealed vast populations of microbes in any given habitat that cannot be detected by conventional culturing strategies. The use of sensitive genetic detection methods such as CARD-FISH and in situ PCR have been limited by the cell wall permeabilization requirement that cannot be performed similarly on all cell types without lysing some and leaving some nonpermeabilized. Furthermore, the detection of low copy targets such as genes present in single copies in the microbial genomes, has remained problematic. We describe an emulsion-based procedure to trap individual microbial cells into picoliter-volume polyacrylamide droplets that provide a rigid support for genetic material and therefore allow complete degradation of cellular material to expose the individual genomes. The polyacrylamide droplets are subsequently converted into picoliter-scale reactors for genome amplification. The amplified genomes are labeled based on the presence of a target gene and differentiated from those that do not contain the gene by flow cytometry. Using the Escherichia coli strains XL1 and MC1061, which differ with respect to the presence (XL1), or absence (MC1061) of a single copy of a tetracycline resistance gene per genome, we demonstrate that XL1 genomes present at 0.1% of MC1061 genomes can be differentiated using this method. Using a spiked sediment microbial sample, we demonstrate that the method is applicable to highly complex environmental microbial communities as a target gene-based screen for individual microbes. The method provides a novel tool for enumerating functional cell populations in complex microbial communities. We envision that the method could be optimized for fluorescence-activated cell sorting to enrich genetic material of interest from complex environmental samples.

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

Reflection on Molecular Approaches Influencing State-of-the-Art Bioremediation Design: Culturing to Microbial Community Fingerprinting to Omics

PubMed Central

Czaplicki, Lauren M.; Gunsch, Claudia K.

2017-01-01

Bioremediation is generally viewed as a cost effective and sustainable technology because it relies on microbes to transform pollutants into benign compounds. Advances in molecular biological analyses allow unprecedented microbial detection and are increasingly incorporated into bioremediation. Throughout history, state-of-the-art techniques have informed bioremediation strategies. However, the insights those techniques provided were not as in depth as those provided by recently developed omics tools. Advances in next generation sequencing (NGS) have now placed metagenomics and metatranscriptomics within reach of environmental engineers. As NGS costs decrease, metagenomics and metatranscriptomics have become increasingly feasible options to rapidly scan sites for specific degradative functions and identify microorganisms important in pollutant degradation. These omic techniques are capable of revolutionizing biological treatment in environmental engineering by allowing highly sensitive characterization of previously uncultured microorganisms. Omics enables the discovery of novel microorganisms for use in bioaugmentation and supports systematic optimization of biostimulation strategies. This review describes the omics journey from roots in biology and medicine to its current status in environmental engineering including potential future directions in commercial application. PMID:28348455

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

PubMed

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

2011-09-01

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

The biogeochemistry of microbial mats, stromatolites and the ancient biosphere

NASA Technical Reports Server (NTRS)

Desmarais, D. J.; Canfield, D. E.

1991-01-01

Stromatolites offer an unparalleled geologic record of early life, because they constitute the oldest and most abundant recognizable remains of microbial ecosystems. Microbial mats are living homologs of stromatolites; thus, the physiology of the microbiota as well as the processes which create those features of mats (e.g., biomarker organic compounds, elemental and stable isotopic compositions) which are preserved in the ancient record. Observations of the carbon isotopic composition (delta C-13) of stromatolites and microbial mats were made and are consistent with the hypothesis that atmospheric CO2 concentrations have declined by at least one to two orders of magnitude during the past 2.5 Ga. Whereas delta C-13 values of carbonate carbon average about 0 permil during both the early and mid-Proterozoic, the delta C-13 values of stromatolitic organic matter increase from an average of -35 between 2.0 and 2.6 Ga ago to an average of about -28 about 1.0 Ga ago. Modern microbial mats in hypersaline environments have delta C-13 values typically in the range of -5 to -9, relative to an inorganic bicarbonate source at 0 permil. Both microbial mats and pur cultures of cyanobacteria grown in waters in near equilibrium with current atmospheric CO2 levels exhibit minimal discrimination against C-13. In contrast, hot spring cyanobacterial mats or cyanobacterial cultures grown under higher CO2 levels exhibit substantially greater discrimination. If care is taken to compare modern mats with stromatolites from comparable environments, it might be possible to estimate ancient levels of atmospheric CO2. In modern microbial mats, a tight coupling exists between photosynthetic organic carbon production and subsequent carbon oxidation, mostly by sulfate reduction. The rate of one process fuels a high rate of the other, with much of the sulfate reduction occurring within the same depth interval as oxygenic photosynthesis. Other aspects of this study are presented.

Maximizing efficiency of rumen microbial protein production

PubMed Central

Hackmann, Timothy J.; Firkins, Jeffrey L.

2015-01-01

Rumen microbes produce cellular protein inefficiently partly because they do not direct all ATP toward growth. They direct some ATP toward maintenance functions, as long-recognized, but they also direct ATP toward reserve carbohydrate synthesis and energy spilling (futile cycles that dissipate heat). Rumen microbes expend ATP by vacillating between (1) accumulation of reserve carbohydrate after feeding (during carbohydrate excess) and (2) mobilization of that carbohydrate thereafter (during carbohydrate limitation). Protozoa account for most accumulation of reserve carbohydrate, and in competition experiments, protozoa accumulated nearly 35-fold more reserve carbohydrate than bacteria. Some pure cultures of bacteria spill energy, but only recently have mixed rumen communities been recognized as capable of the same. When these communities were dosed glucose in vitro, energy spilling could account for nearly 40% of heat production. We suspect that cycling of glycogen (a major reserve carbohydrate) is a major mechanism of spilling; such cycling has already been observed in single-species cultures of protozoa and bacteria. Interconversions of short-chain fatty acids (SCFA) may also expend ATP and depress efficiency of microbial protein production. These interconversions may involve extensive cycling of intermediates, such as cycling of acetate during butyrate production in certain butyrivibrios. We speculate this cycling may expend ATP directly or indirectly. By further quantifying the impact of reserve carbohydrate accumulation, energy spilling, and SCFA interconversions on growth efficiency, we can improve prediction of microbial protein production and guide efforts to improve efficiency of microbial protein production in the rumen. PMID:26029197

Microbial ranking of porous packaging materials (exposure chamber method), ASTM method: collaborative study.

PubMed

Placencia, A M; Peeler, J T

1999-01-01

A collaborative study involving 11 laboratories was conducted to measure the microbial barrier effectiveness of porous medical packaging. Two randomly cut samples from each of 6 commercially available porous materials and one positive and one negative control were tested by one operator in each of 11 laboratories. Microbial barrier effectiveness was measured in terms of logarithm reduction value (LRV), which reflects the log10 microbial penetration of the material being tested. The logarithm of the final concentration is subtracted from that of the initial concentration to obtain the LRV. Thus the higher the LRV, the better the barrier. Repeatability standard deviations ranged from 6.42 to 16.40; reproducibility standard deviations ranged from 15.50 to 22.70. Materials B(53), C(50), D(CT), and E(45MF) differ significantly from the positive control. The microbial ranking of porous packaging materials (exposure chamber method), ASTM method, has been adopted First Action by AOAC INTERNATIONAL.

Microbial response to single-cell protein production and brewery wastewater treatment

PubMed Central

Lee, Jackson Z; Logan, Andrew; Terry, Seth; Spear, John R

2015-01-01

As global fisheries decline, microbial single-cell protein (SCP) produced from brewery process water has been highlighted as a potential source of protein for sustainable animal feed. However, biotechnological investigation of SCP is difficult because of the natural variation and complexity of microbial ecology in wastewater bioreactors. In this study, we investigate microbial response across a full-scale brewery wastewater treatment plant and a parallel pilot bioreactor modified to produce an SCP product. A pyrosequencing survey of the brewery treatment plant showed that each unit process selected for a unique microbial community. Notably, flow equalization basins were dominated by Prevotella, methanogenesis effluent had the highest levels of diversity, and clarifier wet-well samples were sources of sequences for the candidate bacterial phyla of TM7 and BD1-5. Next, the microbial response of a pilot bioreactor producing SCP was tracked over 1 year, showing that two different production trials produced two different communities originating from the same starting influent. However, SCP production resulted generally in enrichment of several clades of rhizospheric diazotrophs of Alphaproteobacteria and Betaproteobacteria in the bioreactor and even more so in the final product. These diazotrophs are potentially useful as the basis of a SCP product for commercial feed production. PMID:24837420

Testosterone-mineralizing culture enriched from swine manure: characterization of degradation pathways and microbial community composition.

PubMed

Yang, Yun-Ya; Pereyra, Luciana P; Young, Robert B; Reardon, Kenneth F; Borch, Thomas

2011-08-15

Environmental releases and fate of steroid sex hormones from livestock and wastewater treatment plants are of increasing regulatory concern. Despite the detection of these hormones in manures, biosolids, and the environment, little attention has been paid to characterization of fecal bacteria capable of hormone degradation. The enrichments of (swine) manure-borne bacteria capable of aerobic testosterone degradation were prepared and the testosterone mineralization pathway was elucidated. Six DNA sequences of bacteria from the Proteobacteria phylum distributed among the genera Acinetobacter, Brevundimonas, Comamonas, Sphingomonas, Stenotrophomonas, and Rhodobacter were identified in a testosterone-degrading enriched culture with testosterone as the sole carbon source. Three degradation products of testosterone were identified as androstenedione, androstadienedione, and dehydrotestosterone using commercially available reference standards, liquid chromatography-UV diode array detection, and liquid chromatography-time-of-flight mass spectrometry (LC-TOF/MS). Three additional degradation products of testosterone were tentatively identified as 9α-hydroxytestosterone, 9α-hydroxyandrostadienedione or 3-hydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione, and 9α-hydroxydehydrotestosterone or 9α-hydroxyandrostenedione using LC-TOF/MS. When (14)C-testosterone was introduced to the enriched culture, 49-68% of the added (14)C-testosterone was mineralized to (14)CO(2) within 8 days of incubation. The mineralization of (14)C-testosterone followed pseudo-first-order reaction kinetics in the enriched culture with half-lives (t(1/2)) of 10-143 h. This work suggests that Proteobacteria play an important environmental role in degradation of steroid sex hormones and that androgens have the potential to be mineralized during aerobic manure treatment or after land application to agricultural fields by manure-borne bacteria.

Identification and Characterization of Lactic Acid Bacteria in a Commercial Probiotic Culture

PubMed Central

MENCONI, Anita; KALLAPURA, Gopala; LATORRE, Juan D.; MORGAN, Marion J.; PUMFORD, Neil R.; HARGIS, Billy M.; TELLEZ, Guillermo

2014-01-01

The aim of the present study was to describe the identification and characterization (physiological properties) of two strains of lactic acid bacteria (LAB 18 and 48) present in a commercial probiotic culture, FloraMax®-B11. Isolates were characterized morphologically, and identified biochemically. In addition, the MIDI System ID, the Biolog ID System, and 16S rRNA sequence analyses for identification of LAB 18 and LAB 48 strains were used to compare the identification results. Tolerance and resistance to acidic pH, high osmotic concentration of NaCl, and bile salts were tested in broth medium. In vitro assessment of antimicrobial activity against enteropathogenic bacteria and susceptibility to antibiotics were also tested. The results obtained in this study showed tolerance of LAB 18 and LAB 48 to pH 3.0, 6.5% NaCl and a high bile salt concentration (0.6%). Both strains evaluated showed in vitro antibacterial activity against Salmonella enterica serovar Enteritidis, Escherichia coli (O157:H7), and Campylobacter jejuni. These are important characteristics of lactic acid bacteria that should be evaluated when selecting strains to be used as probiotics. Antimicrobial activity of these effective isolates may contribute to efficacy, possibly by direct antimicrobial activity in vivo. PMID:24936379

Cell culture contamination.

PubMed

Stacey, Glyn N

2011-01-01

Microbial contamination is a major issue in cell culture, but there are a range of procedures which can be adopted to prevent or eliminate contamination. Contamination may arise from the operator and the laboratory environment, from other cells used in the laboratory, and from reagents. Some infections may present a risk to laboratory workers: containment and aseptic technique are the key defence against such risks. Remedial management of suspected infection may simply mean discarding a single potentially infected culture. However, if a more widespread problem is identified, then all contaminated cultures and associated unused media that have been opened during this period should be discarded, equipment should be inspected and cleaned, cell culture operations reviewed, and isolation from other laboratories instituted until the problem is solved. Attention to training of staff, laboratory layout, appropriate use of quarantine for new cultures or cell lines, cleaning and maintenance, and quality control are important factors in preventing contamination in cell culture laboratories.

Utilization of Alternate Chirality Enantiomers in Microbial Communities

NASA Technical Reports Server (NTRS)

Pikuta, Elena V.; Hoover, Richard B.

2010-01-01

Our previous study of chirality led to interesting findings for some anaerobic extremophiles: the ability to metabolize substrates with alternate chirality enantiomers of amino acids and sugars. We have subsequently found that not just separate microbial species or strains but entire microbial communities have this ability. The functional division within a microbial community on proteo- and sugarlytic links was also reflected in a microbial diet with L-sugars and D-amino acids. Several questions are addressed in this paper. Why and when was this feature developed in a microbial world? Was it a secondary de novo adaptation in a bacterial world? Or is this a piece of genetic information that has been left in modern genomes as an atavism? Is it limited exclusively to prokaryotes, or does this ability also occur in eukaryotes? In this article, we have used a broader approach to study this phenomenon using anaerobic extremophilic strains from our laboratory collection. A series of experiments were performed on physiologically different groups of extremophilic anaerobes (pure and enrichment cultures). The following characteristics were studied: 1) the ability to grow on alternate chirality enantiomers -- L-sugars and D- amino acids; 2) Growth-inhibitory effect of alternate chirality enantiomers; 3) Stickland reaction with alternate chirality amino acids. The results of this research are presented in this paper.

Acetaldehyde production and microbial colonization in oral squamous cell carcinoma and oral lichenoid disease.

PubMed

Marttila, Emilia; Uittamo, Johanna; Rusanen, Peter; Lindqvist, Christian; Salaspuro, Mikko; Rautemaa, Riina

2013-07-01

The main aim of this prospective study was to explore the ability of the oral microbiome to produce acetaldehyde in ethanol incubation. A total of 90 patients [30 oral squamous cell carcinoma (OSCC); 30 oral lichenoid disease (OLD); 30 healthy controls (CO)] were enrolled in the study. Microbial samples were taken from the mucosa using a filter paper method. The density of microbial colonization was calculated and the spectrum analyzed. Microbial acetaldehyde production was measured by gas chromatography. The majority (68%) of cultures produced carcinogenic levels of acetaldehyde (>100 μM) when incubated with ethanol (22 mM). The mean acetaldehyde production by microbes cultured from smoker samples was significantly higher (213 μM) than from non-smoker samples (141 μM) (P=.0326). The oral microbiota from OSCC, OLD patients and healthy individuals are able to produce carcinogenic levels of acetaldehyde. The present provisional study suggests smoking may increase the production of acetaldehyde. Copyright © 2013 Elsevier Inc. All rights reserved.

Influence of calcium on microbial reduction of solid phase uranium(VI).

PubMed

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

2007-08-15

The effect of calcium on the dissolution and microbial reduction of a representative solid phase uranyl [U(VI)], sodium boltwoodite (NaUO(2)SiO(3)OH . 1.5H(2)O), was investigated to evaluate the rate-limiting step of microbial reduction of the solid phase U(VI). Microbial reduction experiments were performed in a culture of a dissimilatory metal-reducing bacterium (DMRB), Shewanella oneidensis strain MR-1, in a bicarbonate medium with lactate as electron donor at pH 6.8 buffered with PIPES. Calcium increased the rate of Na-boltwoodite dissolution and U(VI) bioavailability by increasing its solubility through the formation of a ternary aqueous calcium-uranyl-carbonate species. The ternary species, however, decreased the rates of microbial reduction of aqueous U(VI). Laser-induced fluorescence spectroscopy (LIFS) and transmission electron microscopy (TEM) collectively revealed that microbial reduction of solid phase U(VI) was a sequentially coupled process of Na-boltwoodite dissolution, U(VI) aqueous speciation, and microbial reduction of dissolved U(VI) to U(IV) that accumulated on bacterial surfaces/periplasm. Under studied experimental conditions, the overall rate of microbial reduction of solid phase U(VI) was limited by U(VI) dissolution reactions in solutions without calcium and limited by microbial reduction in solutions with calcium. Generally, the overall rate of microbial reduction of solid phase U(VI) was determined by the coupling of solid phase U(VI) dissolution, U(VI) aqueous speciation, and microbial reduction of dissolved U(VI) that were all affected by calcium. (c) 2007 Wiley Periodicals, Inc.