Culture collections.

Science.gov (United States)

Smith, David

2012-01-01

Culture collections no matter their size, form, or institutional objectives play a role in underpinning microbiology, supplying the resources for study, innovation, and discovery. Their basic roles include providing a mechanism for ex situ conservation of organisms; they are repositories for strains subject to publication, taking in safe, confidential, and patent deposits from researchers. They supply strains for use; therefore, the microorganisms provided must be authentic and preserved well, and any associated information must be valid and sufficient to facilitate the confirmation of their identity and to facilitate their use. The organisms must be collected in compliance with international conventions, international and national legislation and distributed to users indicating clearly the terms and conditions under which they are received and can be used. Collections are harmonizing approaches and characterizing strains to meet user needs. No one single collection can carry out this task alone, and therefore, it is important that output and strategy are coordinated to ensure culture collections deliver the basic resources and services microbiological innovation requires. This chapter describes the types of collection and how they can implement quality management systems and operate to deliver their basic functions. The links to information sources given not only provide support for the practitioners within collections but also provide guidance to users on accessing the huge resource available and how they can help ensure microbiology has the resources and a solid platform for future development. Copyright © 2012 Elsevier Inc. All rights reserved.

Novel co-culture plate enables growth dynamic-based assessment of contact-independent microbial interactions.

Directory of Open Access Journals (Sweden)

Thomas J Moutinho

Full Text Available Interactions between microbes are central to the dynamics of microbial communities. Understanding these interactions is essential for the characterization of communities, yet challenging to accomplish in practice. There are limited available tools for characterizing diffusion-mediated, contact-independent microbial interactions. A practical and widely implemented technique in such characterization involves the simultaneous co-culture of distinct bacterial species and subsequent analysis of relative abundance in the total population. However, distinguishing between species can be logistically challenging. In this paper, we present a low-cost, vertical membrane, co-culture plate to quantify contact-independent interactions between distinct bacterial populations in co-culture via real-time optical density measurements. These measurements can be used to facilitate the analysis of the interaction between microbes that are physically separated by a semipermeable membrane yet able to exchange diffusible molecules. We show that diffusion across the membrane occurs at a sufficient rate to enable effective interaction between physically separate cultures. Two bacterial species commonly found in the cystic fibrotic lung, Pseudomonas aeruginosa and Burkholderia cenocepacia, were co-cultured to demonstrate how this plate may be implemented to study microbial interactions. We have demonstrated that this novel co-culture device is able to reliably generate real-time measurements of optical density data that can be used to characterize interactions between microbial species.

Production of microbial biomass protein by sequential culture fermentation of Arachniotus sp., and Candida utilis

International Nuclear Information System (INIS)

Ahmed, S.; Ahmad, F.; Hashmi, A.S.

2010-01-01

Sequential culture fermentation by Arachniotus sp. at 35 deg. C for 72 h and followed by Candida utilis fermentation at 35 deg. C for 72 h more resulted in higher production of microbial biomass protein. 6% (w/v) corn stover, 0.0075% CaCl/sub 2/.2H/sub 2/O, 0.005% MgSO/sub 4/.7H/sub 2/O, 0.01% KH/sub 2/PO/sub 4/, C:N ratio of 30:1 and 1% molasses gave higher microbial biomass protein production by the sequential culture fermentation of Arachniotus sp., and C. utilis. The mixed microbial biomass protein produced in the 75-L fermentor contained 16.41%, 23.51%, 10.9%, 12.11% and 0.12% true protein, crude protein, crude fiber, ash and RNA content, respectively. The amino acid profile of final mixed microbial biomass protein showed that it was enriched with essential amino acids. Thus, the potential utilization of corn stover can minimize the cost for growth of these microorganisms and enhance microbial biomass protein production by sequential culture fermentation. (author)

KACC: An identification and characterization for microbial resources ...

African Journals Online (AJOL)

Korean Agricultural Culture Collection (KACC) is an authorized organizer and the official depository for microbial resources in Korea. The KACC has developed a web-based database system to provide integrated information about microbial resources. It includes not only simple text information on individual microbe but ...

Functional implications of the microbial community structure of undefined mesophilic starter cultures

NARCIS (Netherlands)

Smid, E.J.; Erkus, O.; Spus, M.; Wolkers-Rooijackers, J.C.M.; Alexeeva, S.V.; Kleerebezem, M.

2014-01-01

This review describes the recent advances made in the studies of the microbial community of complex and undefined cheese starter cultures. We report on work related to the composition of the cultures at the level of genetic lineages, on the presence and activity of bacteriophages and on the

77 FR 52610 - Pesticides; Microbial Pesticide Definitions and Applicability; Clarification and Availability of...

Science.gov (United States)

2012-08-30

... corrections to words and references. Finally, EPA is announcing the availability of a final microbial... nationally recognized culture collection. Collectively, the final rule clarifications and revisions, as well... sample in a nationally recognized culture collection, did not have an accompanying test guideline and...

A common basis for facilitated legitimate exchange of biological materials proposed by the European Culture Collections' Organisation

Directory of Open Access Journals (Sweden)

Dagmar Fritze

2009-12-01

Full Text Available Being charged with the task of accessioning and supplying of living microbiological material, microbial culture collections are institutions that play a central role between the interests of a variety of user communities. On the one side are the providers of living microbiological material, such as individual scientists, institutions and countries of origin and on the other side are the various kinds of recipients/users of cultures of microorganisms from academia and industry. Thus, providing access to high quality biological material and scientific services while at the same time observing donor countries' rights, intellectual property rights, biosafety and biosecurity aspects poses demanding challenges. E.g. donor countries rights relate to Article 15 of the Convention on Biological Diversity: "Contracting parties …. recognize the sovereign rights of states over their natural resources …. shall facilitate access to resources … and not impose restrictions that run counter to the aims of the Convention. Access to natural resources shall be by mutually agreed terms and subject to prior informed consent ..." The use of a proposed standard contract by culture collections is discussed as a way of contractually safeguarding the existing research commons, while observing the new rights established in the Convention on Biological Diversity as well as other existing and new legislation impacting on the accessibility of living microbial material.

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

Science.gov (United States)

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

Culture-dependent and -independent investigations of microbial diversity on urinary catheters

DEFF Research Database (Denmark)

Xu, Yijuan; Moser, Claus Ernst; Abu Al-Soud, Waleed

2012-01-01

Catheter-associated urinary tract infection is caused by bacteria, which ascend the catheter along its external or internal surface to the bladder and subsequently develop into biofilms on the catheter and uroepithelium. Antibiotic-treated bacteria and bacteria residing in biofilm can be difficult...... to culture. In this study we used culture-based and 16S rRNA gene-based culture-independent methods (fingerprinting, cloning, and pyrosequencing) to determine the microbial diversity of biofilms on 24 urinary catheters. Most of the patients were catheterized for...

Culture-dependent and -independent approaches establish the complexity of a PAH-degrading microbial consortium

Energy Technology Data Exchange (ETDEWEB)

Vinas, M.; Sabate, J.; Solanas, A.M. [Barcelona Univ., Barcelona (Spain). Dept. of Microbiology; Guasp, C.; Lalucat, J. [Illes Balears Univ., Palma de Mallorca (Spain). Dept. of Biology

2005-11-15

Microbial consortia are used in the decontamination of polluted environmental sites. A microbial consortium obtained by batch enrichment culture is a closed system with controlled conditions in which micro-organisms with a potentially high growth rate are selected and become dominant. The aim of this study was to identify the members of consortium AM, in which earlier batch enrichment work had shown high biodegradation rates of the aromatic fraction of polycyclic aromatic hydrocarbon (PAH). The AM consortium was obtained by sequential enrichment in liquid culture with a PAH mixture of 3- and 4- ringed PAHs as the sole source of carbon and energy. The consortium was examined using a triple approach method based on various cultivation strategies, denaturing gradient electrophoresis (DGGE) and the screening of 16S and 18S rRNA gene clone libraries. Eleven different sequences by culture-dependent techniques and 7 by both DGGE and clone libraries were obtained, yielding 19 different microbial components. Proteobacteria were the dominant group, representing 83 per cent of the total, while the Cytophaga-Flexibactor-Bacteroides group (CFB) was 11 per cent, and Ascomycota fungi were 6 per cent. It was determined that {beta}-Proteobacteria were predominant in the DGGE and clone library methods, whereas they were a minority in culturable strains. The highest diversity and number of noncoincident sequences was achieved by the cultivation method that showed members of the {alpha},{beta}, and {gamma}-Proteobacteria, CFB bacterial group, and Ascomycota fungi. Only 6 of the 11 strains isolated showed PAH-degrading capability. The bacterial strain (AMS7) and the fungal strain (AMF1) achieved the greatest PAH depletion. Results indicated that polyphasic assessment is necessary for a proper understanding of the composition of a microbial consortium. It was concluded that microbial consortia are more complex than previously realized. 54 refs., 3 tabs., 3 figs.

Benzoate-driven dehalogenation of chlorinated ethenes in microbial cultures from a contaminated aquifer

Energy Technology Data Exchange (ETDEWEB)

Bunge, M.; Kleikemper, J.; Miniaci, C.; Duc, L.; Muusse, M.G.; Zeyer, J. [Swiss Federal Institute of Technology (ETH), Zurich (Switzerland). Inst. of Biogeochemistry and Pollutant Dynamics, Soil Biology; Hause, G. [Halle-Wittenberg Univ., Halle (Germany). Biocenter

2007-10-15

Microbial dehalogenation of tetrachloroethene (PCE) and cis-dichloroethene (cis-DCE) was studied in cultures from a continuous stirred tank reactor initially inoculated with aquifer material from a PCE-contaminated site. Cultures amended with hydrogen and acetate readily dechlorinated PCE and cis-DCE; however, this transformation was incomplete and resulted in the accumulation of chlorinated intermediates and only small amounts of ethene within 60 days of incubation. Conversely, microbial PCE and cis-DCE dechlorination in cultures with benzoate and acetate resulted in the complete transformation to ethene within 30 days. Community fingerprinting by denaturing gradient gel electrophoresis (DGGE) revealed the predominance of phylotypes closely affiliated with Desulfitobacterium, Dehalococcoides, and Syntrophus species. The Dehalococcoides culture VZ, obtained from small whitish colonies in cis-DCE dechlorinating agarose cultures, revealed an irregular cell diameter between 200 and 500 nm, and a spherical or biconcave disk-shaped morphology. These organisms were identified as responsible for the dechlorination of cis-DCE to ethene in the PCE-dechlorinating consortia, operating together with the Desulfitobacterium as PCE-to-cis-DCE dehalogenating bacterium and with a Syntrophus species as potential hydrogen-producing partner in cultures with benzoate. (orig.)

Functional implications of the microbial community structure of undefined mesophilic starter cultures.

Science.gov (United States)

Smid, Eddy J; Erkus, Oylum; Spus, Maciej; Wolkers-Rooijackers, Judith C M; Alexeeva, Svetlana; Kleerebezem, Michiel

2014-08-29

This review describes the recent advances made in the studies of the microbial community of complex and undefined cheese starter cultures. We report on work related to the composition of the cultures at the level of genetic lineages, on the presence and activity of bacteriophages and on the population dynamics during cheese making and during starter culture propagation. Furthermore, the link between starter composition and starter functionality will be discussed. Finally, recent advances in predictive metabolic modelling of the multi-strain cultures will be discussed in the context of microbe-microbe interactions.

Investment into the future of microbial resources: culture collection funding models and BRC business plans for biological resource centres.

Science.gov (United States)

Smith, David; McCluskey, Kevin; Stackebrandt, Erko

2014-01-01

Through their long history of public service, diverse microbial Biological Resource Centres (mBRCs) have made myriad contributions to society and science. They have enabled the maintenance of specimens isolated before antibiotics, made available strains showing the development and change of pathogenicity toward animals, humans and plants, and have maintained and provided reference strains to ensure quality and reproducibility of science. However, this has not been achieved without considerable financial commitment. Different collections have unique histories and their support is often tied to their origins. However many collections have grown to serve large constituencies and need to develop novel funding mechanisms. Moreover, several international initiatives have described mBRCs as a factor in economic development and have led to the increased professionalism among mBRCs.

Microbial community dynamics in thermophilic undefined milk starter cultures.

Science.gov (United States)

Parente, Eugenio; Guidone, Angela; Matera, Attilio; De Filippis, Francesca; Mauriello, Gianluigi; Ricciardi, Annamaria

2016-01-18

Model undefined thermophilic starter cultures were produced from raw milk of nine pasta-filata cheesemaking plants using a selective procedure based on pasteurization and incubation at high temperature with the objective of studying the microbial community dynamics and the variability in performances under repeated (7-13) reproduction cycles with backslopping. The traditional culture-dependent approach, based on random isolation and molecular characterization of isolates was coupled to the determination of pH and the evaluation of the ability to produce acid and fermentation metabolites. Moreover, a culture-independent approach based on amplicon-targeted next-generation sequencing was employed. The microbial diversity was evaluated by 16S rRNA gene sequencing (V1-V3 regions), while the microdiversity of Streptococcus thermophilus populations was explored by using novel approach based on sequencing of partial amplicons of the phosphoserine phosphatase gene (serB). In addition, the occurrence of bacteriophages was evaluated by qPCR and by multiplex PCR. Although it was relatively easy to select for a community dominated by thermophilic lactic acid bacteria (LAB) within a single reproduction cycle, final pH, LAB populations and acid production activity fluctuated over reproduction cycles. Both culture-dependent and -independent methods showed that the cultures were dominated by either S. thermophilus or Lactobacillus delbrueckii subsp. lactis or by both species. Nevertheless, subdominant mesophilic species, including lactococci and spoilage organisms, persisted at low levels. A limited number of serB sequence types (ST) were present in S. thermophilus populations. L. delbrueckii and Lactococcus lactis bacteriophages were below the detection limit of the method used and high titres of cos type S. thermophilus bacteriophages were detected in only two cases. In one case a high titre of bacteriophages was concurrent with a S. thermophilus biotype shift in the culture

Leveraging culture collections for the discovery and development of microbial biological control agents

Science.gov (United States)

The incorporation of living microbial biological control agents into integrated pest management programs is highly desirable because it reduces the use of chemical insecticides harmful to livestock, humans and the environment. In addition, it provides an alternative means to combat resistance to che...

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

Science.gov (United States)

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.

Experimental Investigation Of Microbially Induced Corrosion Of Test Samples And Effect Of Self-assembled Hydrophobic Monolayers. Exposure Of Test Samples To Continuous Microbial Cultures, Chemical Analysis, And Biochemical Studies

CERN Document Server

Laurinavichius, K S

1998-01-01

Experimental Investigation Of Microbially Induced Corrosion Of Test Samples And Effect Of Self-assembled Hydrophobic Monolayers. Exposure Of Test Samples To Continuous Microbial Cultures, Chemical Analysis, And Biochemical Studies

The mind-body-microbial continuum

OpenAIRE

Gonzalez, Antonio; Stombaugh, Jesse; Lozupone, Catherine; Turnbaugh, Peter J.; Gordon, Jeffrey I.; Knight, Rob

2011-01-01

Our understanding of the vast collection of microbes that live on and inside us (microbiota) and their collective genes (microbiome) has been revolutionized by culture-independent ?metagenomic? techniques and DNA sequencing technologies. Most of our microbes live in our gut, where they function as a metabolic organ and provide attributes not encoded in our human genome. Metagenomic studies are revealing shared and distinctive features of microbial communities inhabiting different humans. A ce...

Culture-Dependent and -Independent Methods Capture Different Microbial Community Fractions in Hydrocarbon-Contaminated Soils

OpenAIRE

Stefani, Franck O. P.; Bell, Terrence H.; Marchand, Charlotte; de la Providencia, Ivan E.; El Yassimi, Abdel; St-Arnaud, Marc; Hijri, Mohamed

2015-01-01

Bioremediation is a cost-effective and sustainable approach for treating polluted soils, but our ability to improve on current bioremediation strategies depends on our ability to isolate microorganisms from these soils. Although culturing is widely used in bioremediation research and applications, it is unknown whether the composition of cultured isolates closely mirrors the indigenous microbial community from contaminated soils. To assess this, we paired culture-independent (454-pyrosequenci...

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

Science.gov (United States)

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.

Microbial dynamics in anaerobic enrichment cultures degrading di-n-butyl phthalic acid ester

DEFF Research Database (Denmark)

Trably, Eric; Batstone, Damien J.; Christensen, Nina

2008-01-01

losses were observed in the sterile controls (20-22%), substantial DBP biodegradation was found in the enrichment cultures (90-99%). In addition, significant population changes were observed. The dominant bacterial species in the DBP-degrading cultures was affiliated to Soehngenia saccharolytica...... in enrichment cultures degrading phthalic acid esters under methanogenic conditions. A selection pressure was applied by adding DBP at 10 and 200 mg L(-1) in semi-continuous anaerobic reactors. The microbial dynamics were monitored using single strand conformation polymorphism (SSCP). While only limited abiotic...

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

Science.gov (United States)

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.

Culture-Dependent and -Independent Methods Capture Different Microbial Community Fractions in Hydrocarbon-Contaminated Soils.

Directory of Open Access Journals (Sweden)

Franck O P Stefani

Full Text Available Bioremediation is a cost-effective and sustainable approach for treating polluted soils, but our ability to improve on current bioremediation strategies depends on our ability to isolate microorganisms from these soils. Although culturing is widely used in bioremediation research and applications, it is unknown whether the composition of cultured isolates closely mirrors the indigenous microbial community from contaminated soils. To assess this, we paired culture-independent (454-pyrosequencing of total soil DNA with culture-dependent (isolation using seven different growth media techniques to analyse the bacterial and fungal communities from hydrocarbon-contaminated soils. Although bacterial and fungal rarefaction curves were saturated for both methods, only 2.4% and 8.2% of the bacterial and fungal OTUs, respectively, were shared between datasets. Isolated taxa increased the total recovered species richness by only 2% for bacteria and 5% for fungi. Interestingly, none of the bacteria that we isolated were representative of the major bacterial OTUs recovered by 454-pyrosequencing. Isolation of fungi was moderately more effective at capturing the dominant OTUs observed by culture-independent analysis, as 3 of 31 cultured fungal strains ranked among the 20 most abundant fungal OTUs in the 454-pyrosequencing dataset. This study is one of the most comprehensive comparisons of microbial communities from hydrocarbon-contaminated soils using both isolation and high-throughput sequencing methods.

Culture-Dependent and -Independent Methods Capture Different Microbial Community Fractions in Hydrocarbon-Contaminated Soils.

Science.gov (United States)

Stefani, Franck O P; Bell, Terrence H; Marchand, Charlotte; de la Providencia, Ivan E; El Yassimi, Abdel; St-Arnaud, Marc; Hijri, Mohamed

2015-01-01

Bioremediation is a cost-effective and sustainable approach for treating polluted soils, but our ability to improve on current bioremediation strategies depends on our ability to isolate microorganisms from these soils. Although culturing is widely used in bioremediation research and applications, it is unknown whether the composition of cultured isolates closely mirrors the indigenous microbial community from contaminated soils. To assess this, we paired culture-independent (454-pyrosequencing of total soil DNA) with culture-dependent (isolation using seven different growth media) techniques to analyse the bacterial and fungal communities from hydrocarbon-contaminated soils. Although bacterial and fungal rarefaction curves were saturated for both methods, only 2.4% and 8.2% of the bacterial and fungal OTUs, respectively, were shared between datasets. Isolated taxa increased the total recovered species richness by only 2% for bacteria and 5% for fungi. Interestingly, none of the bacteria that we isolated were representative of the major bacterial OTUs recovered by 454-pyrosequencing. Isolation of fungi was moderately more effective at capturing the dominant OTUs observed by culture-independent analysis, as 3 of 31 cultured fungal strains ranked among the 20 most abundant fungal OTUs in the 454-pyrosequencing dataset. This study is one of the most comprehensive comparisons of microbial communities from hydrocarbon-contaminated soils using both isolation and high-throughput sequencing methods.

Microbial acetate oxidation in horizontal rotating tubular bioreactor

Indian Academy of Sciences (India)

Unknown

shaped partition walls that served as carriers for micro- bial biomass. Mixing ... from soil sample collected from Zagreb mountain. This microbial culture was ... HRTB was made of a plastic tube 1⋅8 m long with an inner diameter of 0⋅25 m.

Microalgae Culture Collection: 1984-1985

Energy Technology Data Exchange (ETDEWEB)

1984-09-01

The Microalgae Culture Collection at the Solar Energy Research Institute has been established for the maintenance and distribution of strains that have been characterized for biomass fuel applications.

A fermented meat model system for studies of microbial aroma formation

DEFF Research Database (Denmark)

Tjener, Karsten; Stahnke, Louise Heller; Andersen, L.

2003-01-01

A fermented meat model system was developed, by which microbial formation of volatiles could be examined The model was evaluated against dry, fermented sausages with respect to microbial growth, pH and volatile profiles. Fast and slowly acidified sausages and models were produced using the starte......H, microbial growth and volatile profiles was similar to sausage production. Based on these findings, the model system was considered valid for studies of aroma formation of meat cultures for fermented sausage.......A fermented meat model system was developed, by which microbial formation of volatiles could be examined The model was evaluated against dry, fermented sausages with respect to microbial growth, pH and volatile profiles. Fast and slowly acidified sausages and models were produced using the starter...... cultures Pediococcus pentosaceus and Staphylococcus xylosus. Volatiles were collected and analysed by dynamic headspace sampling and GC MS. The analysis was primarily focused on volatiles arising from amino acid degradation and a total of 24 compounds, of which 19 were quantified, were used...

The binning of metagenomic contigs for microbial physiology of mixed cultures.

Science.gov (United States)

Strous, Marc; Kraft, Beate; Bisdorf, Regina; Tegetmeyer, Halina E

2012-01-01

So far, microbial physiology has dedicated itself mainly to pure cultures. In nature, cross feeding and competition are important aspects of microbial physiology and these can only be addressed by studying complete communities such as enrichment cultures. Metagenomic sequencing is a powerful tool to characterize such mixed cultures. In the analysis of metagenomic data, well established algorithms exist for the assembly of short reads into contigs and for the annotation of predicted genes. However, the binning of the assembled contigs or unassembled reads is still a major bottleneck and required to understand how the overall metabolism is partitioned over different community members. Binning consists of the clustering of contigs or reads that apparently originate from the same source population. In the present study eight metagenomic samples from the same habitat, a laboratory enrichment culture, were sequenced. Each sample contained 13-23 Mb of assembled contigs and up to eight abundant populations. Binning was attempted with existing methods but they were found to produce poor results, were slow, dependent on non-standard platforms or produced errors. A new binning procedure was developed based on multivariate statistics of tetranucleotide frequencies combined with the use of interpolated Markov models. Its performance was evaluated by comparison of the results between samples with BLAST and in comparison to existing algorithms for four publicly available metagenomes and one previously published artificial metagenome. The accuracy of the new approach was comparable or higher than existing methods. Further, it was up to a 100 times faster. It was implemented in Java Swing as a complete open source graphical binning application available for download and further development (http://sourceforge.net/projects/metawatt).

The binning of metagenomic contigs for microbial physiology of mixed cultures

Directory of Open Access Journals (Sweden)

Marc eStrous

2012-12-01

Full Text Available So far, microbial physiology has dedicated itself mainly to pure cultures. In nature, cross feeding and competition are important aspects of microbial physiology and these can only be addressed by studying complete communities such as enrichment cultures. Metagenomic sequencing is a powerful tool to characterize such mixed cultures. In the analysis of metagenomic data, well established algorithms exist for the assembly of short reads into contigs and for the annotation of predicted genes. However, the binning of the assembled contigs or unassembled reads is still a major bottleneck and required to understand how the overall metabolism is partitioned over different community members. Binning consists of the clustering of contigs or reads that apparently originate from the same source population.In the present study eight metagenomic samples originating from the same habitat, a laboratory enrichment culture, were sequenced. Each sample contained 13-23 Mb of assembled contigs and up to eight abundant populations. Binning was attempted with existing methods but they were found to produce poor results, were slow, dependent on non-standard platforms or produced errors. A new binning procedure was developed based on multivariate statistics of tetranucleotide frequencies combined with the use of interpolated Markov models. Its performance was evaluated by comparison of the results between samples with BLAST and in comparison to exisiting algorithms for four publicly available metagenomes and one previously published artificial metagenome. The accuracy of the new approach was comparable or higher than existing methods. Further, it was up to a hunderd times faster. It was implemented in Java Swing as a complete open source graphical binning application available for download and further development (http://sourceforge.net/projects/metawatt.

Microbial diversity of a Camembert-type cheese using freeze-dried Tibetan kefir coculture as starter culture by culture-dependent and culture-independent methods.

Directory of Open Access Journals (Sweden)

Jun Mei

Full Text Available The biochemical changes occurring during cheese ripening are directly and indirectly dependent on the microbial associations of starter cultures. Freeze-dried Tibetan kefir coculture was used as a starter culture in the Camembert-type cheese production for the first time. Therefore, it's necessary to elucidate the stability, organization and identification of the dominant microbiota presented in the cheese. Bacteria and yeasts were subjected to culture-dependent on selective media and culture-independent polymerase chain reaction (PCR-denaturing gradient gel electrophoresis (DGGE analysis and sequencing of dominant bands to assess the microbial structure and dynamics through ripening. In further studies, kefir grains were observed using scanning electron microscopy (SEM methods. A total of 147 bacteria and 129 yeasts were obtained from the cheese during ripening. Lactobacillus paracasei represents the most commonly identified lactic acid bacteria isolates, with 59 of a total of 147 isolates, followed by Lactococcus lactis (29 isolates. Meanwhile, Kazachstania servazzii (51 isolates represented the mainly identified yeast isolate, followed by Saccharomyces cerevisiae (40 isolates. However, some lactic acid bacteria detected by sequence analysis of DGGE bands were not recovered by plating. The yeast S. cerevisiae and K. servazzii are described for the first time with kefir starter culture. SEM showed that the microbiota were dominated by a variety of lactobacilli (long and curved cells growing in close association with a few yeasts in the inner portion of the grain and the short lactobacilli were observed along with yeast cells on the exterior portion. Results indicated that conventional culture method and PCR-DGGE should be combined to describe in maximal detail the microbiological composition in the cheese during ripening. The data could help in the selection of appropriate commercial starters for Camembert-type cheese.

Microbial Diversity of a Camembert-Type Cheese Using Freeze-Dried Tibetan Kefir Coculture as Starter Culture by Culture-Dependent and Culture-Independent Methods

Science.gov (United States)

Mei, Jun; Guo, Qizhen; Wu, Yan; Li, Yunfei

2014-01-01

The biochemical changes occurring during cheese ripening are directly and indirectly dependent on the microbial associations of starter cultures. Freeze-dried Tibetan kefir coculture was used as a starter culture in the Camembert-type cheese production for the first time. Therefore, it's necessary to elucidate the stability, organization and identification of the dominant microbiota presented in the cheese. Bacteria and yeasts were subjected to culture-dependent on selective media and culture-independent polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) analysis and sequencing of dominant bands to assess the microbial structure and dynamics through ripening. In further studies, kefir grains were observed using scanning electron microscopy (SEM) methods. A total of 147 bacteria and 129 yeasts were obtained from the cheese during ripening. Lactobacillus paracasei represents the most commonly identified lactic acid bacteria isolates, with 59 of a total of 147 isolates, followed by Lactococcus lactis (29 isolates). Meanwhile, Kazachstania servazzii (51 isolates) represented the mainly identified yeast isolate, followed by Saccharomyces cerevisiae (40 isolates). However, some lactic acid bacteria detected by sequence analysis of DGGE bands were not recovered by plating. The yeast S. cerevisiae and K. servazzii are described for the first time with kefir starter culture. SEM showed that the microbiota were dominated by a variety of lactobacilli (long and curved) cells growing in close association with a few yeasts in the inner portion of the grain and the short lactobacilli were observed along with yeast cells on the exterior portion. Results indicated that conventional culture method and PCR-DGGE should be combined to describe in maximal detail the microbiological composition in the cheese during ripening. The data could help in the selection of appropriate commercial starters for Camembert-type cheese. PMID:25360757

Microbial diversity of a Camembert-type cheese using freeze-dried Tibetan kefir coculture as starter culture by culture-dependent and culture-independent methods.

Science.gov (United States)

Mei, Jun; Guo, Qizhen; Wu, Yan; Li, Yunfei

2014-01-01

The biochemical changes occurring during cheese ripening are directly and indirectly dependent on the microbial associations of starter cultures. Freeze-dried Tibetan kefir coculture was used as a starter culture in the Camembert-type cheese production for the first time. Therefore, it's necessary to elucidate the stability, organization and identification of the dominant microbiota presented in the cheese. Bacteria and yeasts were subjected to culture-dependent on selective media and culture-independent polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) analysis and sequencing of dominant bands to assess the microbial structure and dynamics through ripening. In further studies, kefir grains were observed using scanning electron microscopy (SEM) methods. A total of 147 bacteria and 129 yeasts were obtained from the cheese during ripening. Lactobacillus paracasei represents the most commonly identified lactic acid bacteria isolates, with 59 of a total of 147 isolates, followed by Lactococcus lactis (29 isolates). Meanwhile, Kazachstania servazzii (51 isolates) represented the mainly identified yeast isolate, followed by Saccharomyces cerevisiae (40 isolates). However, some lactic acid bacteria detected by sequence analysis of DGGE bands were not recovered by plating. The yeast S. cerevisiae and K. servazzii are described for the first time with kefir starter culture. SEM showed that the microbiota were dominated by a variety of lactobacilli (long and curved) cells growing in close association with a few yeasts in the inner portion of the grain and the short lactobacilli were observed along with yeast cells on the exterior portion. Results indicated that conventional culture method and PCR-DGGE should be combined to describe in maximal detail the microbiological composition in the cheese during ripening. The data could help in the selection of appropriate commercial starters for Camembert-type cheese.

Title: Effect of abiotic stress on reduction of microbial contamination ...

African Journals Online (AJOL)

TERI

2016-03-23

Mar 23, 2016 ... to 36% reduced microbial contamination in aseptic culture establishment ... collected from farmer's field of Assam, India. .... Average weight loss (%) ± SE. 0 .... Asian J. Plant Sci. 6:496-501. Holdgate DP, Zandvoort EA (1997).

The maturing of microbial ecology.

Science.gov (United States)

Schmidt, Thomas M

2006-09-01

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

Microbial flora analysis for the degradation of beta-cypermethrin.

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Science.gov (United States)

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.

Science.gov (United States)

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.

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

Science.gov (United States)

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

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

Science.gov (United States)

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.

Digital Extension of Music Memory Music as a Collective Cultural Memory

Directory of Open Access Journals (Sweden)

Dimitrije Buzarovski

2014-11-01

Full Text Available Artistic works represent a very important part of collective cultural memory. Every artistic work, by definition, can confirm its existence only through the presence in collective cultural memory. The migration from author’s individual memory to common collective cultural memory forms the cultural heritage. This equally applies to tangible and intangible cultural artifacts. Being part of collective cultural memory, music reflects the spatial (geographic and temporal (historic dimensions of this memory. Until the appearance of written signs (scores music was preserved only through collective cultural memory. Scores have facilitated further distribution of music artifacts. The appearance of different means for audio, and later audio/video recordings have greatly improved the distribution of music. The transition from analog to digital recording and carriers has been a revolutionary step which substantially extended the chances for the survival of music artifacts in collective memory.

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

Science.gov (United States)

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.

Role of collective self-esteem on youth violence in a collective culture.

Science.gov (United States)

Lim, Lena L; Chang, Weining C

2009-02-01

Youth violence involvement has always been the focus of significant research attention. However, as most of the studies on youth violence have been conducted in Western cultures, little is known about the antecedents of violence in the Asian context. Researchers have suggested that collectivism might be the reason for the lower violent crime rates in Asia. Nevertheless, the present study proposes an alternative approach to the collectivistic orientation and violence relationship: The possibility that allocentrism (collectivist tendency at the individual difference level) might shape the meaning of and the attitudes towards violence; thus not all aspects of a collectivist culture serve as deterrents for violence. Instead of viewing it as a random individual act, violence in a collective cultural context could be seen, under certain circumstances, as a social obligation to one's in-group (especially when one's in-group is supportive of violence) and as an internalization of the norms and values of the culture. Thus, the present study investigates the relationship between allocentrism and its relation to violence in a highly collectivist Asian culture, Singapore. We further hypothesized that collective self-esteem might serve as the mediator between allocentrism and the values of violence. Using a sample of 149 incarcerated Singaporean male adolescents, results support the proposed theoretical model whereby collective self-esteem was found to mediate between allocentrism and the culture's norms and attitudes of violence, which eventually lead to physical violence behaviours.

75 FR 42818 - Agency Information Collection; Activity Under OMB Review; Collection of Safety Culture Data for...

Science.gov (United States)

2010-07-22

... Collection; Activity Under OMB Review; Collection of Safety Culture Data for Program Evaluation AGENCY... . SUPPLEMENTARY INFORMATION: Title: Collection of Safety Culture Data for Program Evaluation. Type of Request... data on the nation's transportation system is an important component of BTS' responsibility to the...

Growth of microbial mixed cultures under anaerobic, alkaline conditions

International Nuclear Information System (INIS)

Wenk, M.

1993-09-01

Cement and concrete are the most important engineered barrier materials in a repository for low- and intermediate-level waste and thus represent the most significant component of the total disposal inventory. Based on the chemical composition of the concrete used in the repository and the groundwater fluxes in the modelled host rock, it is to be expected that the pH in the near vicinity of the repository could exceed a value of 10.5 for more than a million years. The groundwater in the repository environment also has a limited carbon concentration. Since microorganisms will be present in a repository and can even find suitable living conditions within the waste itself, investigations were carried out in order to establish the extent to which microbial activity is possible under the extreme conditions of the repository near-field. For the investigations, alkalophilic cultures were enriched from samples from alkaline habitats and from Valanginian Marl. Anaerobic bacteria with fermentative, sulfate-reducing and methanogenic metabolism were selected. The growth and activity of the mixed cultures were studied under alkaline conditions and the dependence on pH and carbon concentration determined. All the mixed cultures investigated are alkalophilic. The optimum growth range for the cultures is between pH 9.0 and pH 10.0. The activity limit for the fermentative mixed culture is at pH 12, for the sulfate-reducers at pH 11 and for the methanogens at pH 10.5. Given the limited supply of carbon, the mixed cultures can only grow under slightly alkaline conditions. Only the fermentative cultures are capable of surviving with limited carbon supply at pH 13. (author) 24 figs., 18 tabs., 101 refs

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

Science.gov (United States)

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 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.

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

Science.gov (United States)

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.

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

Science.gov (United States)

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 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.

An Autonomous System for Experimental Evolution of Microbial Cultures: Test Results Using Ultraviolet-C Radiation and Escherichia Coli.

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Electrospinning of microbial polyester for cell culture

Energy Technology Data Exchange (ETDEWEB)

Kwon, Oh Hyeong [Department of Polymer Science and Engineering, Kumoh National Institute of Technology, 1 Yangho-dong, Gumi, Gyeongbuk 730-701 (Korea, Republic of); Lee, Ik Sang [Department of Polymer Science and Engineering, Kumoh National Institute of Technology, 1 Yangho-dong, Gumi, Gyeongbuk 730-701 (Korea, Republic of); Ko, Young-Gwang [Department of Polymer Science and Engineering, Kumoh National Institute of Technology, 1 Yangho-dong, Gumi, Gyeongbuk 730-701 (Korea, Republic of); Meng, Wan [Department of Polymer Science, Kyungpook National University, 1370 Sankyuk-dong, Buk-gu, Daegu 702-701 (Korea, Republic of); Jung, Kyung-Hye [Department of Polymer Science, Kyungpook National University, 1370 Sankyuk-dong, Buk-gu, Daegu 702-701 (Korea, Republic of); Kang, Inn-Kyu [Department of Polymer Science, Kyungpook National University, 1370 Sankyuk-dong, Buk-gu, Daegu 702-701 (Korea, Republic of); Ito, Yoshihiro [Kanagawa Academy of Science and Technology, KSP East 309, Sakado 3-2-1, Takatsu-ku, Kawasaki 213-0012 (Japan)

2007-03-01

Biodegradable and biocompatible poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV), a copolymer of microbial polyester, was fabricated as a nanofibrous mat by electrospinning. The specific surface area and the porosity of electrospun PHBV nanofibrous mat were determined. When the mechanical properties of flat film and electrospun PHBV nanofibrous mats were investigated, both the tensile modulus and strength of electrospun PHBV were less than those of cast PHBV film. However, the elongation ratio of nanofiber mat was higher than that of the cast film. The structure of electrospun nanofibers using PHBV-trifluoroethanol solutions depended on the solution concentrations. When x-ray diffraction patterns of bulk PHBV before and after electrospinning were compared, the crystallinity of PHBV was not significantly affected by the electrospinning process. Chondrocytes adhered and grew on the electrospun PHBV nanofibrous mat better than on the cast PHBV film. Therefore, the electrospun PHBV was considered to be suitable for cell culture.

Culturable microbial groups and thallium-tolerant fungi in soils with high thallium contamination.

Science.gov (United States)

Sun, Jialong; Zou, Xiao; Ning, Zengping; Sun, Min; Peng, Jingquan; Xiao, Tangfu

2012-12-15

Thallium (Tl) contamination in soil exerts a significant threat to the ecosystem health due to its high toxicity. However, little is known about the effect of Tl on the microbial community in soil. The present study aimed at characterizing the culturable microbial groups in soils which experience for a long time high Tl contamination and elevated Hg and As. The contamination originates from As, Hg and Tl sulfide mineralization and the associated mining activities in the Guizhou Province, Southwest China. Our investigation showed the existence of culturable bacteria, filamentous fungi and actinomyces in long-term Tl-contaminated soils. Some fungal groups grow in the presence of high Tl level up to 1000 mg kg⁻¹. We have isolated and identified nine Tl-tolerant fungal strains based on the morphological traits and ITS analysis. The dominant genera identified were Trichoderma, Penicillium and Paecilomyces. Preliminary data obtained in this study suggested that certain microbes were able to face high Tl pollution in soil and maintain their metabolic activities and resistances. The highly Tl-tolerant fungi that we have isolated are potentially useful in the remediation of Tl-contaminated sites. Copyright © 2012 Elsevier B.V. All rights reserved.

Analysis of microbial community variation during the mixed culture fermentation of agricultural peel wastes to produce lactic acid.

Science.gov (United States)

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.

Degradation of polycyclic aromatic hydrocarbons by microbial consortia enriched from three soils using two different culture media

International Nuclear Information System (INIS)

Wu, Manli; Chen, Liming; Tian, Yongqiang; Ding, Yi; Dick, Warren A.

2013-01-01

A consortium composed of many different bacterial species is required to efficiently degrade polycyclic aromatic hydrocarbons (PAH) in oil-contaminated soil. We obtained six PAH-degrading microbial consortia from three oil-contaminated soils using two different isolation culture media. Denaturing gradient gel electrophoresis (DGGE) and sequence analyses of amplified 16s rRNA genes confirmed the bacterial community was greatly affected by both the culture medium and the soil from which the consortia were enriched. Three bacterial consortia enriched using malt yeast extract (MYE) medium showed higher degradation rates of PAHs than consortia enriched using Luria broth (LB) medium. Consortia obtained from a soil and then added back to that same soil was more effective in degrading PAHs than adding, to the same soil, consortia isolated from other, unrelated soils. This suggests that inoculum used for bioremediation should be from the same, or very similar nearby soils, as the soil that is actually being bioremediated. -- Highlights: •Six PAH-degrading microbial consortia were isolated from three oil-contaminated soils. •The bacterial community by 16s rRNA genes was affected by culture media and source soil. •Inoculum should be from the same or similar soil as the soil being bioremediated. -- Bioremediation of oil-contaminated soils was most effective when using inoculum of microbial consortia from the same or similar soil as the soil being bioremediated

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

Science.gov (United States)

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.

Selection and screening of microbial consortia for efficient and ecofriendly degradation of plastic garbage collected from urban and rural areas of Bangalore, India.

Science.gov (United States)

Skariyachan, Sinosh; Megha, M; Kini, Meghna Niranjan; Mukund, Kamath Manali; Rizvi, Alya; Vasist, Kiran

2015-01-01

Industrialization and urbanization have led to massive accumulation of plastic garbage all over India. The persistence of plastic in soil and aquatic environment has become ecological threat to the metropolitan city such as Bangalore, India. Present study investigates an ecofriendly, efficient and cost-effective approach for plastic waste management by the screening of novel microbial consortia which are capable of degrading plastic polymers. Plastic-contaminated soil and water samples were collected from six hot spots of urban and rural areas of Bangalore. The plastic-degrading bacteria were enriched, and degradation ability was determined by zone of clearance method. The percentage of polymer degradation was initially monitored by weight loss method, and the main isolates were characterized by standard microbiology protocols. These isolates were used to form microbial consortia, and the degradation efficiency of the consortia was compared with individual isolate and known strains obtained from the Microbial Type Culture Collection (MTCC) and Gene Bank, India. One of the main enzymes responsible for polymer degradation was identified, and the biodegradation mechanism was hypothesized by bioinformatics studies. From this study, it is evident that the bacteria utilized the plastic polymer as a sole source of carbon and showed 20-50% weight reduction over a period of 120 days. The two main bacteria responsible for the degradation were microbiologically characterized to be Pseudomonas spp. These bacteria could grow optimally at 37 °C in pH 9.0 and showed 35-40% of plastic weight reduction over 120 days. These isolates were showed better degradation ability than known strains from MTCC. The current study further revealed that the microbial consortia formulated by combining Psuedomonas spp. showed 40 plastic weight reduction over a period of 90 days. Further, extracellular lipase, one of the main enzymes responsible for polymer degradation, was identified. The

Effect of changing temperature on anaerobic hydrogen production and microbial community composition in an open-mixed culture bioreactor

Energy Technology Data Exchange (ETDEWEB)

Karadag, Dogan; Puhakka, Jaakko A. [Department of Chemistry and Bioengineering, Tampere University of Technology, Tampere (Finland)

2010-10-15

The temperature effect (37-65 C) on H{sub 2} production from glucose in an open-mixed culture bioreactor using an enrichment culture from a hot spring was studied. The dynamics of microbial communities was investigated by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). At 45 and 60 C the H{sub 2} production was the highest i.e. 1.71 and 0.85 mol H{sub 2}/mol glucose, respectively. No H{sub 2} was produced at temperatures 50 and 55 C. At 37-45 C, H{sub 2} production was produced by butyrate type fermentation while fermentation mechanism changed to ethanol type at 60 C. Clostridium species were dominant at 37-45 C while at 50-55 C and 60 C the culture was dominated by Bacillus coagulans and Thermoanaerobacterium, respectively. In the presence of B. Coagulans the metabolism was directed to lactate production. The results show that the mixed culture had two optima for H{sub 2} production and that the microbial communities and metabolic patterns promptly changed according to changing temperatures. (author)

Microbial ecology and starter culture technology in coffee processing.

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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.

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

Science.gov (United States)

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 reduction of uranium(VI) in sediments of different lithologies collected from Sellafield

International Nuclear Information System (INIS)

Newsome, Laura; Morris, Katherine; Trivedi, Divyesh; Atherton, Nick; Lloyd, Jonathan R.

2014-01-01

Highlights: • U(VI) (aq) mobility can be controlled by stimulating biogeochemical interactions. • Indigenous microbes in varied sediments reduced U(VI) to insoluble U(IV). • Sediment cell numbers and amount of bioavailable Fe(III) could limit this process. - Abstract: The presence of uranium in groundwater at nuclear sites can be controlled by microbial processes. Here we describe the results from stimulating microbial reduction of U(VI) in sediment samples obtained from a nuclear-licensed site in the UK. A variety of different lithology sediments were selected to represent the heterogeneity of the subsurface at a site underlain by glacial outwash deposits and sandstone. The natural sediment microbial communities were stimulated via the addition of an acetate/lactate electron donor mix and were monitored for changes in geochemistry and molecular ecology. Most sediments facilitated the removal of 12 ppm U(VI) during the onset of Fe(III)-reducing conditions; this was reflected by an increase in the proportion of known Fe(III)- and U(VI)-reducing species. However U(VI) remained in solution in two sediments and Fe(III)-reducing conditions did not develop. Sequential extractions, addition of an Fe(III)-enrichment culture and most probable number enumerations revealed that a lack of bioavailable iron or low cell numbers of Fe(III)-reducing bacteria may be responsible. These results highlight the potential for stimulation of microbial U(VI)-reduction to be used as a bioremediation strategy at UK nuclear sites, and they emphasise the importance of both site-specific and borehole-specific investigations to be completed prior to implementation

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

Science.gov (United States)

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.

Dynamics of culturable soil microbial communities during ...

African Journals Online (AJOL)

Ecological zones impacted significantly (P < 0.05) on bacterial proliferation, but not on fungal growth. Sampling period significantly (P < 0.05) affected microbial density and the semi-arid agroecozone was more supportive of microbial proliferation than the arid zone. A total of nine predominant fungal species belonging to ...

Classical Pop: Documenting Popular Musical Culture in Library Audio Collections.

Science.gov (United States)

Tarakan, Sheldon Lewis

1983-01-01

Discusses the library's role in developing a classical pop collection (defined as that music which is best representative of an era, event, or recognizable cultural trend). Popular culture, establishing the collection, funding, and archives are highlighted. A 230-item discography, addresses of five record companies, and 14 references are appended.…

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

Science.gov (United States)

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

Microbial Fuel Cells using Mixed Cultures of Wastewater for Electricity Generation

International Nuclear Information System (INIS)

Zain, S.M; Roslani, N.S.; Hashim, R.; Anuar, N.; Suja, F.; Basi, N.E.A.; Anuar, N.; Daud, W.R.W.

2011-01-01

Fossil fuels (petroleum, natural gas and coal) are the main resources for generating electricity. However, they have been major contributors to environmental problems. One potential alternative to explore is the use of microbial fuel cells (MFCs), which generate electricity using microorganisms. MFCs uses catalytic reactions activated by microorganisms to convert energy preserved in the chemical bonds between organic molecules into electrical energy. MFC has the ability to generate electricity during the wastewater treatment process while simultaneously treating the pollutants. This study investigated the potential of using different types of mixed cultures (raw sewage, mixed liquor from the aeration tank and return waste activated sludge) from an activated sludge treatment plant in MFCs for electricity generation and pollutant removals (COD and total kjeldahl nitrogen, TKN). The MFC in this study was designed as a dual-chambered system, in which the chambers were separated by a Nafion TM membrane using a mixed culture of wastewater as a bio catalyst. The maximum power density generated using activated sludge was 9.053 mW/ cm 2 , with 26.8 % COD removal and 40 % TKN removal. It is demonstrated that MFC offers great potential to optimize power generation using mixed cultures of wastewater. (author)

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

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Peng Chen

2015-01-01

Full Text Available BACKGROUND: 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. RESULTS: 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 m

75 FR 11988 - Notice of Request for Approval To Collect New Information: Collection of Safety Culture Data

Science.gov (United States)

2010-03-12

..., information about changes to the safety culture of the affected workplaces will be used as one of several data...: RITA-2008-0002] Notice of Request for Approval To Collect New Information: Collection of Safety Culture.... mail to Federal offices in Washington, DC, we recommend that persons consider an alternative method...

Microbial electrosynthetic cells

Energy Technology Data Exchange (ETDEWEB)

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.

Comparative analysis and culturing of the microbial community of Aiptasia pallida, A Sea Anemone Model for Coral Biology

KAUST Repository

Binsarhan, Mohammad

2016-01-01

Recent works has highlighted the contribution of microbes to animal function. In this regard, the microbial community associated with corals has become a growing field of research in order to understand how microbes contribute to the host organisms’ response to environmental changes. It has been shown that microbes associated with corals have important functions in the coral holobiont such as immunity and nutrient assimilation. However, corals are notoriously difficult to work with. To this end, the sea anemone Aiptasia is becoming a model organism for coral symbiosis. Given the importance of host-­microbiome interactions, the topic of this thesis is to assess microbial structure of Aiptasia, culture prominent bacterial members, and compare bacterial community structure to corals. Different molecular methods have been applied using 16S rRNA bacterial gene fragments to characterize the microbial composition of Aiptasia. 16S rRNA gene sequence derived from cultured bacteria was compared to 16S rRNA gene sequences retrieved from native Red Sea Aiptasia. Inter-­individual as well as methodological differences were found to account for variance in microbiome composition. However, all approaches showed a highly abundant microbial taxon belonging to the genus Alteromonas in all samples. The Alteromonas species was successfully isolated for further research targeting microbiome selection mechanisms in Aiptasia. Future investigations by using different molecular tools will help to define the functions and relationship between the Aiptasia and its complex microbiome.

Influence of Culture Media on Microbial Fingerprints Using Raman Spectroscopy.

Science.gov (United States)

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.

Synthetic Microbial Ecology: Engineering Habitats for Modular Consortia.

Science.gov (United States)

Ben Said, Sami; Or, Dani

2017-01-01

potential applications. We briefly review existing tools to engineer such assemblies and optimize potential benefits resulting from the collective activity of their members. Prospective microbial consortia and proposed spatial configurations will be illustrated and preliminary calculations highlighting the advantages of SLMC over co-cultures will be presented, followed by a discussion of challenges and opportunities for moving forward with some designs.

LIIS: A web-based system for culture collections and sample annotation

Directory of Open Access Journals (Sweden)

Matthew S Forster

2014-04-01

Full Text Available The Lab Information Indexing System (LIIS is a web-driven database application for laboratories looking to store their sample or culture metadata on a central server. The design was driven by a need to replace traditional paper storage with an easier to search format, and extend current spreadsheet storage methods. The system supports the import and export of CSV spreadsheets, and stores general metadata designed to complement the environmental packages provided by the Genomic Standards Consortium. The goals of the LIIS are to simplify the storage and archival processes and to provide an easy to access library of laboratory annotations. The program will find utility in microbial ecology laboratories or any lab that needs to annotate samples/cultures.

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

Science.gov (United States)

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.

Microbial lipid production by oleaginous yeast Cryptococcus sp. in the batch cultures using corncob hydrolysate as carbon source

International Nuclear Information System (INIS)

Chang, Yi-Huang; Chang, Ku-Shang; Lee, Ching-Fu; Hsu, Chuan-Liang; Huang, Cheng-Wei; Jang, Hung-Der

2015-01-01

To realize the feasibility of biodiesel production from high-lipid cell culture, microbial lipid production by the oleaginous yeasts was studied using glucose and sucrose as carbon source. Among the tested strains, Cryptococcus sp. SM5S05 accumulated the highest levels of intracellular lipids. The crude lipid contents of Cryptococcus sp. cultured in yeast malt agar reached 30% on a dry weight basis. The accumulation of lipids strongly depended on carbon/nitrogen ratio and nitrogen concentration. The highest content of lipids, measured at a carbon/nitrogen ratio of 60–90 and at a nitrogen concentration of 0.2%, was 60–57% lipids in the dry biomass. Batch cultures using corncob hydrolysate demonstrated that there was minimal inhibitory effect with a reducing sugar concentration of 60 g l −1 or higher. Batch cultures of Cryptococcus sp. SM5S05 in the corncob hydrolysate medium with 60 g l −1 glucose resulted in a dry biomass, lipid yields, and content of 12.6 g l −1 , 7.6 g l −1 , and 60.2%, respectively. The lipids contained mainly long-chain saturated and unsaturated fatty acids with 16 and 18 carbon atoms. The fatty acid profile of Cryptococcus oils was quite similar to that of conventional vegetable oil. The cost of lipid production could be further reduced with corncob hydrolysate being utilized as the raw material for the oleaginous yeast. The results showed that the microbial lipid from Cryptococcus sp. was a potential alternative resource for biodiesel production. - Highlights: • Microbial oil production from oleaginous yeast Cryptococcus sp. was studied. • Accumulation of lipid strongly depended on C/N ratio and nitrogen concentration. • Cultures in hydrolysate medium with 60 g/l glucose resulted in maximum lipid yields. • Maximal lipid content in the Cryptococcus sp. were 60.2% on dried weight basis

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

Science.gov (United States)

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).

Molecular characterization of some lignicolous species from fungal culture collection

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Stević Nevena

2014-01-01

Full Text Available Culture collections of microorganisms, including fungi, are strain deposits recognised as Biological Resource Centers (BRCs with a great importance in science, industry and education. Their objective is to preserve the purity, viability and genomic integrity of every single strain as a member of such collection. Since improvement of molecular methods nowadays brought many novel approaches in manipulation with strains of microorganisms, they can also be useful for characterization of existing stored strains. ITS1 region in nuclear DNA is preferred barcoding marker for taxon identification, which can be explained by its great inter-species variability. This paper presents results from analysing ITS1 region sequences (17 obtained from fungal DNA of culture collection of autochthonous, lignicolous genera Piptoporus, Pleurotus, Ganoderma and Schizophyllum cultured on malt agar plates for 14 days at 25°C. BLAST (Basic Local Alignment Search Tool was used for comparison with online databases, while alignment of sequences was made with MEGA 5.10 software. Morphological determination of species or genus was confirmed for 13 cultures, while the others were disproved. The resulting alignment indicated small intra-species variability of ITS1 region and pointed to it as an ideal marker for verification of fungal culture collections' authenticity. [Projekat Ministarstva nauke Republike Srbije, br. III43002 and by the Provincial Secretariat for Science and Technological Development, Vojvodina, Serbia APV 114-4513592/2013-03: Molecular and phenotypic diversity of taxa of economical and epidemiological importance, and endangered and endemic species in Europe

Microbial Fe(III) Oxide Reduction in Chocolate Pots Hot Springs, Yellowstone National Park

Science.gov (United States)

Fortney, N. W.; Roden, E. E.; Boyd, E. S.; Converse, B. J.

2014-12-01

Previous work on dissimilatory iron reduction (DIR) in Yellowstone National Park (YNP) has focused on high temperature, low pH environments where soluble Fe(III) is utilized as an electron acceptor for respiration. Much less attention has been paid to DIR in lower temperature, circumneutral pH environments, where solid phase Fe(III) oxides are the dominant forms of Fe(III). This study explored the potential for DIR in the warm (ca. 40-50°C), circumneutral pH Chocolate Pots hot springs (CP) in YNP. Most probable number (MPN) enumerations and enrichment culture studies confirmed the presence of endogenous microbial communities that reduced native CP Fe(III) oxides. Enrichment cultures demonstrated sustained DIR coupled to acetate and lactate oxidation through repeated transfers over ca. 450 days. Pyrosequencing of 16S rRNA genes indicated that the dominant organisms in the enrichments were closely affiliated with the well known Fe(III) reducer Geobacter metallireducens. Additional taxa included relatives of sulfate reducing bacterial genera Desulfohalobium and Thermodesulfovibrio; however, amendment of enrichments with molybdate, an inhibitor of sulfate reduction, suggested that sulfate reduction was not a primary metabolic pathway involved in DIR in the cultures. A metagenomic analysis of enrichment cultures is underway in anticipation of identifying genes involved in DIR in the less well-characterized dominant organisms. Current studies are aimed at interrogating the in situ microbial community at CP. Core samples were collected along the flow path (Fig. 1) and subdivided into 1 cm depth intervals for geochemical and microbiological analysis. The presence of significant quantities of Fe(II) in the solids indicated that DIR is active in situ. A parallel study investigated in vitro microbial DIR in sediments collected from three of the coring sites. DNA was extracted from samples from both studies for 16S rRNA gene and metagenomic sequencing in order to obtain a

Dynamics of the Content of Lactobacilli, Microbial Metabolites and Antimicrobial Activity of Growing Culture of Lactobacillus Plantarum 8P-A3

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I. Yu. Chicherin

2013-01-01

Full Text Available The dynamics of the content of lactobacilli, microbial metabolites and antimicrobial activity of growing cultures of Lactobacillus plantarum 8Р-А3 was studied. Lactobacilli L. plantarum 8Р-А3 and test microorganisms isolated from the intestinal contents of patients with dysbacteriosis were used in experiments. Study of the component composition of growing culture supernatant of lactobacilli was carried out by gas liquid chromatography with mass selective detection. By 54 h of cultivation the content of viable microbial cells in the native culture of Lactobacillus achieves 3,0·109 in 1 mL without further increase during the cultivation. The principal component of lactobacilli culture medium possessing antibacterial activity is lactic acid. In addition to lactic acid, which accounts for 70% of the total metabolites, the culture medium and the supernatant contain salts of phosphoric acid (14% as well as amino acids, carboxylic acids, fatty acids, sugars and polyhydric alcohol constituting of up to 16% of the total metabolites. It is found that during the cultivation in liquid medium lactobacilli produce metabolites which possess antibacterial activity against pathogenic bacteria that cause intestinal infections.

Examination of a Culturable Microbial Population from the Gastrointestinal Tract of the Wood-Eating Loricariid Catfish Panaque nigrolineatus

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Harold J. Schreier

2013-08-01

Full Text Available Fish play a critical role in nutrient cycling and organic matter flow in aquatic environments. However, little is known about the microbial diversity within the gastrointestinal tracts that may be essential in these degradation activities. Panaque nigrolineatus is a loricariid catfish found in the Neotropics that have a rare dietary strategy of consuming large amounts of woody material in its natural environment. As a consequence, the gastrointestinal (GI tract of P. nigrolineatus is continually exposed to high levels of cellulose and other recalcitrant wood compounds and is, therefore, an attractive, uncharacterized system to study microbial community diversity. Our previous 16S rRNA gene surveys demonstrated that the GI tract microbial community includes phylotypes having the capacity to degrade cellulose and fix molecular nitrogen. In the present study we verify the presence of a resident microbial community by fluorescence microscopy and focus on the cellulose-degrading members by culture-based and 13C-labeled cellulose DNA stable-isotope probing (SIP approaches. Analysis of GI tract communities generated from anaerobic microcrystalline cellulose enrichment cultures by 16S rRNA gene analysis revealed phylotypes sharing high sequence similarity to known cellulolytic bacteria including Clostridium, Cellulomonas, Bacteroides, Eubacterium and Aeromonas spp. Related bacteria were identified in the SIP community, which also included nitrogen-fixing Azospirillum spp. Our ability to enrich for specialized cellulose-degrading communities suggests that the P. nigrolineatus GI tract provides a favorable environment for this activity and these communities may be involved in providing assimilable carbon under challenging dietary conditions.

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

Science.gov (United States)

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.

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

Energy Technology Data Exchange (ETDEWEB)

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 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.

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

Energy Technology Data Exchange (ETDEWEB)

Anderton, Christopher R.; Chu, Rosalie K.; Tolic, Nikola; Creissen, Alain V.; Pasa-Tolic, Ljiljana

2016-01-07

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 where 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.

Microbial characterization of bee pollen from the Vesuvius area collected by using three different traps

Science.gov (United States)

De Prisco, Annachiara; Di Prisco, Gennaro; La Storia, Antonietta; Caprio, Emilio

2017-01-01

Flower pollen is collected by honeybee foragers, adhered on their rear legs and transported into the hives in the form of pellets. Once in the hives, bee pollen is moisturised with nectar and bee mouth secretions and due to enzymatically modifications it becomes the so-called bee-bread, the protein reservoir of young bees. Bee pollen can be artificially removed from bee legs and collected by using specific systems, the bee pollen traps. Bee pollen is commercialized for human consumption as fresh product and after freezing or drying. Although bee pollen is nowadays largely consumed in developed countries, as food or food supplement according to local legislation, little is known on its safety related to microbiological hazards. In this work, we aimed to characterize for the first time the microbiological profile of Italian bee pollen in fresh, frozen and dried form collected along an entire harvesting season. Moreover, monthly microbiological analyses were performed on frozen (storage at -18°C) and dried (storage at room temperature) bee pollen over a 4 months period. Further aim of this work was the evaluation of the possible impact on production level of three different traps used for pollen collection. Our results on microbial contamination of fresh and frozen bee pollen show that a more comprehensive microbiological risk assessment of bee pollen is required. On the other side, dried pollen showed very low microbial contamination and no pathogen survived after the drying process and during storage. PMID:28934240

Data management and database structure at the ARS Culture Collection

Science.gov (United States)

The organization and management of collection data for the 96,000 strains held in the ARS Culture Collection has been an ongoing process. Originally, the records for the four separate collections were maintained by individual curators in notebooks and/or card files and subsequently on the National C...

Application of the Lyapunov exponent to detect noise-induced chaos in oscillating microbial cultures

International Nuclear Information System (INIS)

Patnaik, P.R.

2005-01-01

Oscillating microbial processes can, under certain conditions, gravitate into chaotic behavior induced by external noise. Detection and control of chaos are important for the survival of the microorganisms and to operate a process usefully. In this study the largest Lyapunov exponent is recommended as a convenient and reliable index of chaos in continuous oscillating cultures. For the growth of Saccharomyces cerevisiae as a model system, the exponents increase with the oxygen mass transfer coefficient and decrease as the dilution rate increases. By comparing with the corresponding time-domain oscillations determined earlier, it is inferred that weakly oscillating cultures are less likely to be driven to chaotic behavior. The main carbon source, glucose, is quite robust to chaotic destabilization, thus enhancing its suitability as a manipulated variable for bioreactor control

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

Science.gov (United States)

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 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 leucine with ammonia. Comparisons of bacterial community structure in the fermenter effluent samples using PCR amplicons

Iron oxyhydroxide mineralization on microbial extracellular polysaccharides

Energy Technology Data Exchange (ETDEWEB)

Chan, Clara S.; Fakra, Sirine C.; Edwards, David C.; Emerson, David; Banfield, Jillian F.

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 isolated 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.

International Marine Biotechnology Culture Collection (IMBCC)

Energy Technology Data Exchange (ETDEWEB)

Zaborsky, O.R.; Baker, K. [Univ. of Hawaii at Manoa, Honolulu, HI (United States)

1996-10-01

The objective of this project is to establish a premier culture collection of tropical marine microorganisms able to generate hydrogen from water or organic substances. Both eukaryotic and prokaryotic microorganisms will serve as the biological reservoir or {open_quotes}library{close_quotes} for other DOE Hydrogen Program contractors, the biohydrogen research community and industry. This project consists of several tasks: (a) transfer of the Mitsui-Miami strains to Hawaii`s International Marine Biotechnology Culture Collection (IMBCC) housed at the Hawaii Natural Energy Institute (HNEI); (b) maintain and distribute Mitsui-Miami strains; (c) characterize key strains by traditional and advanced biotechnological techniques; (d) expand Hawaii`s IMBCC; and (e) establish and operate an information resource (database). The project was initiated only late in the summer of 1995 but progress has been made on all tasks. Of the 161 cyanobacterial strains imported, 147 survived storage and importation and 145 are viable. with most exhibiting growth. Of the 406 strains of other photosynthetic bacteria imported, 392 survived storage and importation and 353 are viable, with many exhibiting growth. This project is linked to cooperative efforts being supported by the Japanese Ministry of International Trade and Industry (MITI) through its Marine Biotechnology Institute (MBI) and Research Institute of Innovative Technology for the Earth (RITE).

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

Science.gov (United States)

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

Establishment of a Quality Management System Based on ISO 9001 Standard in a Public Service Fungal Culture Collection

Science.gov (United States)

Simões, Marta F.; Dias, Nicolina; Santos, Cledir; Lima, Nelson

2016-01-01

Collaborations between different Microbiological Resource Centres (mBRCs) and ethical sourcing practices are mandatory to guarantee biodiversity conservation, successful and sustainable preservation and fair share of benefits that arise from the use of genetic resources. Since microbial Culture Collections (CCs) are now engaged in meeting high quality operational standards, they are facing the challenge of establishing quality control criteria to certify their biological materials. The authentication/certification of strains is nowadays a demand from the bioeconomy sector for the global operation of mBRCs. The achievement of consistent quality assurance and trust within the mBRCs and microbial CCs context is a dynamic and never-ending process. A good option to facilitate that process is to implement a Quality Management System (QMS) based on the ISO 9001 standard. Here, we report a detailed description of all the steps taken for the QMS implementation at the Portuguese CC of filamentous fungi: Micoteca da Universidade do Minho (MUM). Our aim is to provide guidelines for the certification of other CCs, so that they can also enhance the search and choice of the most consistent, reliable, and effective operating methods, with assured procedures and validation of preservation; and guarantee trustworthy relations with all stakeholders. PMID:27681915

Establishment of a Quality Management System Based on ISO 9001 Standard in a Public Service Fungal Culture Collection

KAUST Repository

Simoes, Marta

2016-06-22

Collaborations between different Microbiological Resource Centres (mBRCs) and ethical sourcing practices are mandatory to guarantee biodiversity conservation, successful and sustainable preservation and fair share of benefits that arise from the use of genetic resources. Since microbial Culture Collections (CCs) are now engaged in meeting high quality operational standards, they are facing the challenge of establishing quality control criteria to certify their biological materials. The authentication/certification of strains is nowadays a demand from the bioeconomy sector for the global operation of mBRCs. The achievement of consistent quality assurance and trust within the mBRCs and microbial CCs context is a dynamic and never-ending process. A good option to facilitate that process is to implement a Quality Management System (QMS) based on the ISO 9001 standard. Here, we report a detailed description of all the steps taken for the QMS implementation at the Portuguese CC of filamentous fungi: Micoteca da Universidade do Minho (MUM). Our aim is to provide guidelines for the certification of other CCs, so that they can also enhance the search and choice of the most consistent, reliable, and effective operating methods, with assured procedures and validation of preservation; and guarantee trustworthy relations with all stakeholders.

Establishment of a Quality Management System Based on ISO 9001 Standard in a Public Service Fungal Culture Collection.

Science.gov (United States)

Simões, Marta F; Dias, Nicolina; Santos, Cledir; Lima, Nelson

2016-06-22

Collaborations between different Microbiological Resource Centres (mBRCs) and ethical sourcing practices are mandatory to guarantee biodiversity conservation, successful and sustainable preservation and fair share of benefits that arise from the use of genetic resources. Since microbial Culture Collections (CCs) are now engaged in meeting high quality operational standards, they are facing the challenge of establishing quality control criteria to certify their biological materials. The authentication/certification of strains is nowadays a demand from the bioeconomy sector for the global operation of mBRCs. The achievement of consistent quality assurance and trust within the mBRCs and microbial CCs context is a dynamic and never-ending process. A good option to facilitate that process is to implement a Quality Management System (QMS) based on the ISO 9001 standard. Here, we report a detailed description of all the steps taken for the QMS implementation at the Portuguese CC of filamentous fungi: Micoteca da Universidade do Minho (MUM). Our aim is to provide guidelines for the certification of other CCs, so that they can also enhance the search and choice of the most consistent, reliable, and effective operating methods, with assured procedures and validation of preservation; and guarantee trustworthy relations with all stakeholders.

Reconciling long-term cultural diversity and short-term collective social behavior.

Science.gov (United States)

Valori, Luca; Picciolo, Francesco; Allansdottir, Agnes; Garlaschelli, Diego

2012-01-24

An outstanding open problem is whether collective social phenomena occurring over short timescales can systematically reduce cultural heterogeneity in the long run, and whether offline and online human interactions contribute differently to the process. Theoretical models suggest that short-term collective behavior and long-term cultural diversity are mutually excluding, since they require very different levels of social influence. The latter jointly depends on two factors: the topology of the underlying social network and the overlap between individuals in multidimensional cultural space. However, while the empirical properties of social networks are intensively studied, little is known about the large-scale organization of real societies in cultural space, so that random input specifications are necessarily used in models. Here we use a large dataset to perform a high-dimensional analysis of the scientific beliefs of thousands of Europeans. We find that interopinion correlations determine a nontrivial ultrametric hierarchy of individuals in cultural space. When empirical data are used as inputs in models, ultrametricity has strong and counterintuitive effects. On short timescales, it facilitates a symmetry-breaking phase transition triggering coordinated social behavior. On long timescales, it suppresses cultural convergence by restricting it within disjoint groups. Moreover, ultrametricity implies that these results are surprisingly robust to modifications of the dynamical rules considered. Thus the empirical distribution of individuals in cultural space appears to systematically optimize the coexistence of short-term collective behavior and long-term cultural diversity, which can be realized simultaneously for the same moderate level of mutual influence in a diverse range of online and offline settings.

Microbial ecology of artisanal italian cheese: Molecular microbial characterization by culture-independent method

International Nuclear Information System (INIS)

Colombo, E.; Scarpellini, M.; Franzatti, L.; Dioguardi, L.

2009-01-01

Present study will treat the next topics: ecology of the natural and man made environments and functional diversity of bacteria. The microbial communities in artisanal goat cheeses produced in mountain pastures (typical farms) in Piemonte mountain (North of Italy) change a lot during precessing and ripening time. Moreover cheese microbial ecosystems are different in each small dairy because adventitious microflora can come from the environment and contamination the milk before the cheese making process and the product during manufacture and ripening. (Author)

Microbial ecology of artisanal italian cheese: Molecular microbial characterization by culture-independent method

Energy Technology Data Exchange (ETDEWEB)

Colombo, E.; Scarpellini, M.; Franzatti, L.; Dioguardi, L.

2009-07-01

Present study will treat the next topics: ecology of the natural and man made environments and functional diversity of bacteria. The microbial communities in artisanal goat cheeses produced in mountain pastures (typical farms) in Piemonte mountain (North of Italy) change a lot during precessing and ripening time. Moreover cheese microbial ecosystems are different in each small dairy because adventitious microflora can come from the environment and contamination the milk before the cheese making process and the product during manufacture and ripening. (Author)

Culture Media and Individual Hosts Affect the Recovery of Culturable Bacterial Diversity from Amphibian Skin.

Science.gov (United States)

Medina, Daniel; Walke, Jenifer B; Gajewski, Zachary; Becker, Matthew H; Swartwout, Meredith C; Belden, Lisa K

2017-01-01

One current challenge in microbial ecology is elucidating the functional roles of the large diversity of free-living and host-associated bacteria identified by culture-independent molecular methods. Importantly, the characterization of this immense bacterial diversity will likely require merging data from culture-independent approaches with work on bacterial isolates in culture. Amphibian skin bacterial communities have become a recent focus of work in host-associated microbial systems due to the potential role of these skin bacteria in host defense against the pathogenic fungus Batrachochytrium dendrobatidis (Bd), which is associated with global amphibian population declines and extinctions. As there is evidence that some skin bacteria may inhibit growth of Bd and prevent infection in some cases, there is interest in using these bacteria as probiotic therapy for conservation of at-risk amphibians. In this study, we used skin swabs from American toads ( Anaxyrus americanus ) to: (1) assess the diversity and community structure of culturable amphibian skin bacteria grown on high and low nutrient culture media, (2) determine which culture media recover the highest proportion of the total skin bacterial community of individual toads relative to culture-independent data, and (3) assess whether the plated communities from the distinct media types vary in their ability to inhibit Bd growth in in-vitro assays. Overall, we found that culture media with low nutrient concentrations facilitated the growth of more diverse bacterial taxa and grew distinct communities relative to media with higher nutrient concentrations. Use of low nutrient media also resulted in culturing proportionally more of the bacterial diversity on individual toads relative to the overall community defined using culture-independent methods. However, while there were differences in diversity among media types, the variation among individual hosts was greater than variation among media types, suggesting

Effectiveness of a Novel Specimen Collection System in Reducing Blood Culture Contamination Rates.

Science.gov (United States)

Bell, Mary; Bogar, Catherine; Plante, Jessica; Rasmussen, Kristen; Winters, Sharon

2018-04-20

False-positive blood-culture results due to skin contamination of samples remain a persistent problem for health care providers. Our health system recognized that our rates of contamination across the 4 emergency department campuses were above the national average. A unique specimen collection system was implemented throughout the 4 emergency departments and became the mandatory way to collect adult blood cultures. The microbiology laboratory reported contamination rates weekly to manage potential problems; 7 months of data are presented here. There was an 82.8% reduction in false positives with the unique specimen collection system compared with the standard method (chi-squared test with Yates correction, 2-tailed, P = 0.0001). Based on the historical 3.52% rate of blood-culture contamination for our health facilities, 2.92 false positives were prevented for every 100 blood cultures drawn, resulting from adoption of the unique specimen collection system as the standard of care. This unique collection system can reduce the risk of blood culture contamination significantly and is designed to augment, rather than replace, the standard phlebotomy protocol already in use in most health care settings. Copyright © 2018 Elsevier Inc. All rights reserved.

Microbial Diversity in Sulfate-Reducing Marine Sediment Enrichment Cultures Associated with Anaerobic Biotransformation of Coastal Stockpiled Phosphogypsum (Sfax, Tunisia

Directory of Open Access Journals (Sweden)

Hana Zouch

2017-08-01

Full Text Available 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.

Characterizing microbial diversity and damage in mural paintings.

Science.gov (United States)

Rosado, Tânia; Mirão, José; Candeias, António; Caldeira, Ana Teresa

2015-02-01

Mural paintings are some of the oldest and most important cultural expressions of mankind and play an important role for the understanding of societies and civilizations. These cultural assets have high economic and cultural value and therefore their degradation has social and economic impact. The present work presents a novel microanalytical approach to understand the damages caused by microbial communities in mural paintings. This comprises the characterization and identification of microbial diversity and evaluation of damage promoted by their biological activity. Culture-dependent methods and DNA-based approaches like denaturing gradient gel electrophoresis (DGGE) and pyrosequencing are important tools in the isolation and identification of the microbial communities allowing characterization of the biota involved in the biodeterioration phenomena. Raman microspectrometry, infrared spectrometry, and variable pressure scanning electron microscopy coupled with energy-dispersive X-ray spectrometry are also useful tools for evaluation of the presence of microbial contamination and detection of the alteration products resulting from metabolic activity of the microorganisms. This study shows that the degradation status of mural paintings can be correlated to the presence of metabolically active microorganisms.

Acting and Collecting: Imagining Asia through material culture and musical theatre

OpenAIRE

Peter Thorley

2015-01-01

This paper explores the link between Asian-inspired material culture and musical theatre through the collections of Anglo-Australian performer Herbert Browne (1895-1975). Brown played lead roles in 1920s Australian musical theatre productions of The Mikado and Chu Chin Chow and re-lived his connection with oriental theatre by collecting and responding to objects performatively in the Chinoiserie room of his Melbourne home. Oriental musical theatre blended exotic cultures and locales in visual...

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

Science.gov (United States)

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.

Microbial community analysis of ambient temperature anaerobic digesters

Energy Technology Data Exchange (ETDEWEB)

Ciotola, R. [Ohio State Univ., Columbus, OH (United States). Dept. of Food, Agriculture and Biological Engineering

2010-07-01

This paper reported on a study in which designs for Chinese and Indian fixed-dome anaerobic digesters were modified in an effort to produce smaller and more affordable digesters. While these types of systems are common in tropical regions of developing countries, they have not been used in colder climates because of the low biogas yield during the winter months. Although there is evidence that sufficient biogas production can be maintained in colder temperatures through design and operational changes, there is a lack of knowledge about the seasonal changes in the composition of the microbial communities in ambient temperature digesters. More knowledge is needed to design and operate systems for maximum biogas yield in temperate climates. The purpose of this study was to cultivate a microbial community that maximizes biogas production at psychrophilic temperatures. The study was conducted on a 300 gallon experimental anaerobic digester on the campus of Ohio State University. Culture-independent methods were used on weekly samples collected from the digester in order to examine microbial community response to changes in ambient temperature. Microbial community profiles were established using universal bacterial and archaeal primers that targeted the 16S rRNA gene. In addition to the methanogenic archaea, this analysis also targeted some of the other numerically and functionally important microbial taxa in anaerobic digesters, such as hydrolytic, fermentative, acetogenic and sulfate reducing bacteria. According to preliminary results, the composition of the microbial community shifts with changes in seasonal temperature.

Utilization of Alternate Chirality Enantiomers in Microbial Communities

Science.gov (United States)

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.

Acting and Collecting: Imagining Asia through material culture and musical theatre

Directory of Open Access Journals (Sweden)

Peter Thorley

2015-07-01

Full Text Available This paper explores the link between Asian-inspired material culture and musical theatre through the collections of Anglo-Australian performer Herbert Browne (1895-1975. Brown played lead roles in 1920s Australian musical theatre productions of The Mikado and Chu Chin Chow and re-lived his connection with oriental theatre by collecting and responding to objects performatively in the Chinoiserie room of his Melbourne home. Oriental musical theatre blended exotic cultures and locales in visually spectacular productions which bore little resemblance to reality. The taste for escapist fiction in the theatre took place against a backdrop of museum collecting which aimed to reproduce authentic Asian and Other cultures. In this paper, I draw on French philosopher Merleau-Ponty’s observations on the relationship between thought and the body’s interaction with space to interpret the influence of Browne’s theatricality on collecting choices. From this perspective, objects materialize particular understandings of the world which originate in the body and the body’s performative engagement with space.

The ARS Culture Collection and Developments in Biotechnology

Science.gov (United States)

The ARS Culture Collection (NRRL) has played a prominent role in the development of biotechnology since its founding in 1940 when the Northern Regional Research Laboratory opened. Early discoveries included selection of production strains for penicillin, dextran blood extender, xanthan gum and the v...

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

Science.gov (United States)

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.

Onshore Wind Speed Modulates Microbial Aerosols along an Urban Waterfront

Directory of Open Access Journals (Sweden)

M. Elias Dueker

2017-11-01

Full Text Available Wind blowing over aquatic and terrestrial surfaces produces aerosols, which include microbial aerosols. We studied the effect of onshore wind speeds on aerosol concentrations as well as total and culturable microbial aerosols (bacterial and viral at an urban waterfront (New York, NY, United States of America. We used two distinct methods to characterize microbial aerosol responses to wind speed: A culture-based exposure-plate method measuring viable bacterial deposition near-shore (CFU accumulation rate; and a culture-independent aerosol sampler-based method measuring total bacterial and viral aerosols (cells m−3 air. While ambient coarse (>2 µm and fine (0.3–2 µm aerosol particle number concentrations (regulated indicators of air quality decreased with increasing onshore wind speeds, total and depositing culturable bacterial aerosols and total viral aerosols increased. Taxonomic identification of the 16S rDNA of bacterial aerosol isolates suggested both terrestrial and aquatic sources. Wind appears to increase microbial aerosol number concentrations in the near-shore environment by onshore transport at low wind speeds (<4 m s−1, and increased local production and transport of new microbial aerosols from adjacent water surfaces at higher wind speeds (>4 m s−1. This study demonstrates a wind-modulated microbial connection between water and air in the coastal urban environment, with implications for public health management and urban microbial ecology.

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

Science.gov (United States)

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.

[Preservation of high risk fungal cultures of Histoplasma and Cryptococcus].

Science.gov (United States)

Fernández Andreu, C Carlos Manuel; Díaz Suárez, Luis Alberto; Ilnait Zaragozi, María Teresa; Aragonés López, Carlos; Martínez Machín, Gerardo; Perurena Lancha, Mayda R

2012-01-01

culture collections are responsible for providing the microbial resources for development of biological sciences. Storage in distilled water is one of the easiest and least expensive method for long-term fungal preservation. to evaluate the usefulness of this preservation method in fungal culture of Histoplasma and Cryptococcus. the preservation condition of the highest biological risk species from Histoplasma y Cryptococcus genera, included in the fungal culture collection of "Pedro Kouri" Institute of Tropical Medicine in Havana, was evaluated in this study. One hundred and two strains stored in distilled water, 92% of which had been preserved for more than 10 years, were analyzed. the percentages of recovered strains from H. capsulatum, C. neoformans and C. gattii were 64.3%; 79.1% and 100% respectively. This method of preservation proved to be satisfactory for fungal culture in labs with limited financial resources. A web-based database with interesting information about the collection was made. The importance of strict compliance with the biosafety measures in these collections, particularly with high risk pathogens. preservation of fungal cultures in distilled water is a very useful method for laboratories with limited resources. Culture collections should be assumed as an essential activity in order to solve increasing challenges in the development of biomedical sciences.

Producing health, producing safety. Developing a collective safety culture in radiotherapy

International Nuclear Information System (INIS)

Nascimento, Adelaide

2009-01-01

This research thesis aims at a better understanding of safety management in radiotherapy and at proposing improvements for patient safety through the development of a collective safety culture. A first part presents the current context in France and abroad, addresses the transposition of other safety methods to the medical domain, and discusses the peculiarities of radiotherapy in terms of risks and the existing quality-assurance approaches. The second part presents the theoretical framework by commenting the intellectual evolution with respect to system safety and the emergence of the concept of safety culture, and by presenting the labour collective aspects and their relationship with system safety. The author then comments the variety of safety cultures among the different professions present in radiotherapy, highlights the importance of the collective dimension in correcting discrepancies at the end of the treatment process, and highlights how physicians take their colleagues work into account. Recommendations are made to improve patient safety in radiotherapy

Dose-effect curves for electron-beam irradiation of some collection microbial strains

International Nuclear Information System (INIS)

Ferdes, O.; Dumitru, E.; Catargiu, L.; Ferdes, M.; Minea, R.; Oproiu, C.; Niculescu, A.

1994-01-01

There were electron-beam irradiated some microbial strains of B.subtilis ICA I-60 both in germination and in sporulated forms. The irradiation were performed at the IPTRD's electron accelerator at 6 MeV, and in the dose range between 0.1-5.0 kGy, at different dose-rate varying from 50 Gy/minute to 100 Gy/minute. The dosimetry was carried out by a PTW medical dosemeter. There were established the dose-effect relationships and curves, the inactivation dose (factor) and the optimum domain for electron-beam mutagenesis. There were obtained some mutant strains with 2-3.5 higher biosynthesis potential, which are in the IFC's collection. (Author)

76 FR 33395 - 30-Day Notice of Proposed Information Collections: ECA Sports & Culture Evaluation Surveys

Science.gov (United States)

2011-06-08

... Information Collection: Sports & Culture Evaluation, Sports Envoys Survey. OMB Control Number: None. Type of... Evaluation, Sports Surveys. OMB Control Number: None. Type of Request: New Collection. Originating Office...: Sports & Culture Evaluation, Kennedy Center (KC) Cultural Visitors Survey. OMB Control Number: None. Type...

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

Science.gov (United States)

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.

Treatment and electricity harvesting from sulfate/sulfide-containing wastewaters using microbial fuel cell with enriched sulfate-reducing mixed culture

International Nuclear Information System (INIS)

Lee, Duu-Jong; Lee, Chin-Yu; Chang, Jo-Shu

2012-01-01

Highlights: ► We started up microbial fuel cell (MFC) using enriched sulfate-reducing mixed culture. ► Sulfate-reducing bacteria and anode-respiring bacteria were enriched in anodic biofilms. ► The MFC effectively remove sulfate to elementary sulfur in the presence of lactate. ► The present device can treat sulfate laden wastewaters with electricity harvesting. - Abstract: Anaerobic treatment of sulfate-laden wastewaters can produce excess sulfide, which is corrosive to pipelines and is toxic to incorporated microorganisms. This work started up microbial fuel cell (MFC) using enriched sulfate-reducing mixed culture as anodic biofilms and applied the so yielded MFC for treating sulfate or sulfide-laden wastewaters. The sulfate-reducing bacteria in anodic biofilm effectively reduced sulfate to sulfide, which was then used by neighboring anode respiring bacteria (ARB) as electron donor for electricity production. The presence of organic carbons enhanced MFC performance since the biofilm ARB were mixotrophs that need organic carbon to grow. The present device introduces a route for treating sulfate laden wastewaters with electricity harvesting.

Treatment and electricity harvesting from sulfate/sulfide-containing wastewaters using microbial fuel cell with enriched sulfate-reducing mixed culture

Energy Technology Data Exchange (ETDEWEB)

Lee, Duu-Jong, E-mail: cedean@mail.ntust.edu.tw [Department of Chemical Engineering, National Taiwan University, Taipei, Taiwan (China); Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei, Taiwan (China); Lee, Chin-Yu [Department of Chemical Engineering, National Taiwan University, Taipei, Taiwan (China); Chang, Jo-Shu [Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan (China); Center for Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan (China); Research Center for Energy Technology and Strategy, National Cheng Kung University, Tainan, Taiwan (China)

2012-12-15

Highlights: Black-Right-Pointing-Pointer We started up microbial fuel cell (MFC) using enriched sulfate-reducing mixed culture. Black-Right-Pointing-Pointer Sulfate-reducing bacteria and anode-respiring bacteria were enriched in anodic biofilms. Black-Right-Pointing-Pointer The MFC effectively remove sulfate to elementary sulfur in the presence of lactate. Black-Right-Pointing-Pointer The present device can treat sulfate laden wastewaters with electricity harvesting. - Abstract: Anaerobic treatment of sulfate-laden wastewaters can produce excess sulfide, which is corrosive to pipelines and is toxic to incorporated microorganisms. This work started up microbial fuel cell (MFC) using enriched sulfate-reducing mixed culture as anodic biofilms and applied the so yielded MFC for treating sulfate or sulfide-laden wastewaters. The sulfate-reducing bacteria in anodic biofilm effectively reduced sulfate to sulfide, which was then used by neighboring anode respiring bacteria (ARB) as electron donor for electricity production. The presence of organic carbons enhanced MFC performance since the biofilm ARB were mixotrophs that need organic carbon to grow. The present device introduces a route for treating sulfate laden wastewaters with electricity harvesting.

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

Science.gov (United States)

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.

[Neuroscience and collective memory: memory schemas linking brain, societies and cultures].

Science.gov (United States)

Legrand, Nicolas; Gagnepain, Pierre; Peschanski, Denis; Eustache, Francis

2015-01-01

During the last two decades, the effect of intersubjective relationships on cognition has been an emerging topic in cognitive neurosciences leading through a so-called "social turn" to the formation of new domains integrating society and cultures to this research area. Such inquiry has been recently extended to collective memory studies. Collective memory refers to shared representations that are constitutive of the identity of a group and distributed among all its members connected by a common history. After briefly describing those evolutions in the study of human brain and behaviors, we review recent researches that have brought together cognitive psychology, neuroscience and social sciences into collective memory studies. Using the reemerging concept of memory schema, we propose a theoretical framework allowing to account for collective memories formation with a specific focus on the encoding process of historical events. We suggest that (1) if the concept of schema has been mainly used to describe rather passive framework of knowledge, such structure may also be implied in more active fashions in the understanding of significant collective events. And, (2) if some schema researches have restricted themselves to the individual level of inquiry, we describe a strong coherence between memory and cultural frameworks. Integrating the neural basis and properties of memory schema to collective memory studies may pave the way toward a better understanding of the reciprocal interaction between individual memories and cultural resources such as media or education. © Société de Biologie, 2016.

EVA Suit Microbial Leakage Investigation

Data.gov (United States)

National Aeronautics and Space Administration — The objective of this project is to collect microbial samples from various EVA suits to determine how much microbial contamination is typically released during...

Dark fermentative hydrogen production by defined mixed microbial cultures immobilized on ligno-cellulosic waste materials

Energy Technology Data Exchange (ETDEWEB)

Patel, Sanjay K.S. [Microbial Biotechnology and Genomics, Institute of Genomics and Integrative Biology (IGIB), CSIR, Delhi University Campus, Mall Road, Delhi 110007 (India); Department of Biotechnology, University of Pune, Pune 411007 (India); Purohit, Hemant J. [Environmental Genomics Unit, National Environmental Engineering Research Institute (NEERI), CSIR, Nehru Marg, Nagpur 440020 (India); Kalia, Vipin C. [Microbial Biotechnology and Genomics, Institute of Genomics and Integrative Biology (IGIB), CSIR, Delhi University Campus, Mall Road, Delhi 110007 (India)

2010-10-15

Mixed microbial cultures (MMCs) based on 11 isolates belonging to Bacillus spp. (Firmicutes), Bordetella avium, Enterobacter aerogenes and Proteus mirabilis (Proteobacteria) were employed to produce hydrogen (H{sub 2}) under dark fermentative conditions. Under daily fed culture conditions (hydraulic retention time of 2 days), MMC6 and MMC4, immobilized on ligno-cellulosic wastes - banana leaves and coconut coir evolved 300-330 mL H{sub 2}/day. Here, H{sub 2} constituted 58-62% of the total biogas evolved. It amounted to a H{sub 2} yield of 1.54-1.65 mol/mol glucose utilized over a period of 60 days of fermentation. The involvement of various Bacillus spp. -Bacillus sp., Bacillus cereus, Bacillus megaterium, Bacillus pumilus and Bacillus thuringiensis as components of the defined MMCs for H{sub 2} production has been reported here for the first time. (author)

Electrochemical evaluation of Ti/TiO{sub 2}-polyaniline anodes for microbial fuel cells using hypersaline microbial consortia for synthetic-wastewater treatment

Energy Technology Data Exchange (ETDEWEB)

Benetton, X.D.; Navarro-Avila, S.G. [Univ. Autonoma de Yucatan, Yucatan (Mexico). Biotecnologia y Bioingenieria; Carrera-Figueiras, C. [Univ. Autonoma de Yucatan, Yucatan (Mexico). Quimica Fundamental y Aplicada

2010-07-01

This paper described the development of a titanium (Ti/TiO{sub 2}) polyaniline composite electrode. The electrode was designed for use with a microbial fuel cell (MFC) that generated electricity through the microbial biodegradation of organic compounds. A modified NBAF medium was used with a 20 mM acetate as an electron donor and 53 mM fumarate as an electron acceptor for a period of 96 hours at 37 degrees C. Strains were cultured under strict anaerobic conditions. Two microbial cultures were used: (1) pure cultures of Geobacter sulfur-reducens; and (2) an uncharacterized stable microbial consortia isolated from hypersaline swamp sediments. The anodes were made with an emeraldine form of PANI deposited over Ti/TiO{sub 2} electrodes. Electrochemical impedance spectroscopy (EIS) monitoring was used to determine the open circuit potential of the MFC. Negative real impedances were obtained and reproduced in all systems studied with the Ti/TiO{sub 2}-PANI anodes. The highest power density was obtained using the Geobacter sulfur-reducens culture. Further research is needed to study the mechanisms that contribute to the occurrence of negative real impedances. 23 refs., 1 tab., 5 figs.

Visualising Cultures: The "European Picture Book Collection" Moves "Down Under"

Science.gov (United States)

Cotton, Penni; Daly, Nicola

2015-01-01

The potential for picture books in national collections to act as mirrors reflecting the reader's cultural identity, is widely accepted. This paper shows that the books in a New Zealand Picture Book Collection can also become windows into unfamiliar worlds for non-New Zealand readers, giving them the opportunity to learn more about a context in…

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

Science.gov (United States)

Larsen, Peter; Gilbert, Jack

2013-01-01

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

The Legal Status of Microbial Food Cultures in the European Union

DEFF Research Database (Denmark)

Herody, Caroline; Soyeux, Y; Hansen, Egon Bech

2010-01-01

The production of fermented foods is one of the oldest food processing technologies known to man. Since the dawn of civilisation, methods for the fermentation of milks, meats, fish and vegetables have been used to produce safe foods with distinctive organoleptic properties. Microbial food cultures...... (MFC) with a technological impact on food are called “starter cultures”. They may be present as natural microflora in the food, or as a result of the intentional addition of the microorganisms in an industrial food fermentation process. MFC that are used for their beneficial effect on consumers’ health...... are called probiotics. Probiotics are always intentionally added to the food as they have been carefully selected and studied to guarantee that they provide a proven beneficial effect to consumers. They may be used in both fermented and non-fermented foods such as food supplements. This paper aims to provide...

Phylogenetic & Physiological Profiling of Microbial Communities of Contaminated Soils/Sediments: Identifying Microbial consortia...

Energy Technology Data Exchange (ETDEWEB)

Terence L. Marsh

2004-05-26

The goals of this study were: (1) survey the microbial community in soil samples from a site contaminated with heavy metals using new rapid molecular techniques that are culture-independent; (2) identify phylogenetic signatures of microbial populations that correlate with metal ion contamination; and (3) cultivate these diagnostic strains using traditional as well as novel cultivation techniques in order to identify organisms that may be of value in site evaluation/management or bioremediation.

Microbial consortia of gorgonian corals from the Aleutian islands.

Science.gov (United States)

Gray, Michael A; Stone, Robert P; McLaughlin, Molly R; Kellogg, Christina A

2011-04-01

Gorgonians make up the majority of corals in the Aleutian archipelago and provide critical fish habitat in areas of economically important fisheries. The microbial ecology of the deep-sea gorgonian corals Paragorgea arborea, Plumarella superba, and Cryogorgia koolsae was examined with culture-based and 16S rRNA gene-based techniques. Six coral colonies (two per species) were collected. Samples from all corals were cultured, and clone libraries were constructed from P. superba and C. koolsae. Cultured bacteria were dominated by the Gammaproteobacteria, especially Vibrionaceae, with other phyla comprising libraries showed dramatically different bacterial communities between corals of the same species collected at different sites, with no clear pattern of conserved bacterial consortia. Two of the clone libraries (one from each coral species) were dominated by Tenericutes, with Alphaproteobacteria dominating the remaining sequences. The other libraries were more diverse and had a more even distribution of bacterial phyla, showing more similarity between genera than within coral species. Here we report the first microbiological characterization of P. arborea, P. superba, and C. koolsae. FEMS Microbiology Ecology © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. No claim to original US government works.

77 FR 74048 - Culturally Significant Object Imported for Exhibition Determinations: “Connecting Collections...

Science.gov (United States)

2012-12-12

... determine that the object to be included in the exhibition ``Connecting Collections: Collecting Connections... DEPARTMENT OF STATE [Public Notice 8112] Culturally Significant Object Imported for Exhibition Determinations: ``Connecting Collections: Collecting Connections. 50 Years of Pre-Columbian Art at Dumbarton Oaks...

Survival of microbial cultures on mineral while passing dense layers of the atmosphere

Science.gov (United States)

Viacheslav, Ilyin; Novikova, Nataliya; Deshevaya, Elena; Polikarpov, Nikolay; Slobodkin, Alexander; Gavrilov, Sergey; Ionov, Viktor; Morozova, Julia

The purpose of the experiment is to study the possibility of extremophilic microorganisms survival in meteorite-like mineral while passing through the dense layers of the atmosphere. For this purpose cultures of bacteria were placed into the holes made in basalt pieces fixed to the outer wall of the spacecraft Bion M1. Control: similar materials placed in the outer container, prevented from overheating in the dense layers of the atmosphere by lid. In the flight experiment five strains of thermophilic bacteria and 2 strains of hyperthermophilic archaea from the collection of the Institute of Microbiology, RAS were used. In addition, microorganisms were selected from the collection of the Institute of Biomedical Problems, isolated from the environment objects of ISS: 10 fungal cultures and a culture of bacteria Bacillus pumilus. For thermophiles and hyperthermophiles the ability to redox interactions with minerals is considered as a priority physiological property. Ability of thermophiles to anaerobic growth also meets the conditions of the experiment - testing cell survival of microorganisms in the conditions of extraterrestrial space and ancient anaerobic atmosphere of the Earth. After 30-days flight in orbit control all spore-forming microorganisms have been successfully survived. Hyperthermophilic archaea growth in all control was significantly less intensive. Meanwhile, in one experimental samples there was obtained signs of survival of spore forming bacteria culture Carboxydocella ferrireducens. However, the maximum concentration of cells was 2 orders of magnitude below the values characteristic of an actively growing culture of the microorganism. Due to damage of holes in the stone, this result was obtained only in one replicate and for final prove of survival of C. ferrireducens when returning through the dense layers of the atmosphere it is necessary to repeat the experiment It should be noted that an important indicator of the possibility of survival of C

Reducing unnecessary culturing: a systems approach to evaluating urine culture ordering and collection practices among nurses in two acute care settings

Directory of Open Access Journals (Sweden)

Robert Redwood

2018-01-01

Full Text Available Abstract Background Inappropriate ordering and acquisition of urine cultures leads to unnecessary treatment of asymptomatic bacteriuria (ASB. Treatment of ASB contributes to antimicrobial resistance particularly among hospital-acquired organisms. Our objective was to investigate urine culture ordering and collection practices among nurses to identify key system-level and human factor barriers and facilitators that affect optimal ordering and collection practices. Methods We conducted two focus groups, one with ED nurses and the other with ICU nurses. Questions were developed using the Systems Engineering Initiative for Patient Safety (SEIPS framework. We used iterative categorization (directed content analysis followed by summative content analysis to code and analyze the data both deductively (using SEIPS domains and inductively (emerging themes. Results Factors affecting optimal urine ordering and collection included barriers at the person, process, and task levels. For ED nurses, barriers included patient factors, physician communication, reflex culture protocols, the electronic health record, urinary symptoms, and ED throughput. For ICU nurses, barriers included physician notification of urinalysis results, personal protective equipment, collection technique, patient body habitus, and Foley catheter issues. Conclusions We identified multiple potential process barriers to nurse adherence with evidence-based recommendations for ordering and collecting urine cultures in the ICU and ED. A systems approach to identifying barriers and facilitators can be useful to design interventions for improving urine ordering and collection practices.

The Microbial DNA Index System (MiDIS): A tool for microbial pathogen source identification

Energy Technology Data Exchange (ETDEWEB)

Velsko, S. P. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

2010-08-09

The microbial DNA Index System (MiDIS) is a concept for a microbial forensic database and investigative decision support system that can be used to help investigators identify the sources of microbial agents that have been used in a criminal or terrorist incident. The heart of the proposed system is a rigorous method for calculating source probabilities by using certain fundamental sampling distributions associated with the propagation and mutation of microbes on disease transmission networks. This formalism has a close relationship to mitochondrial and Y-chromosomal human DNA forensics, and the proposed decision support system is somewhat analogous to the CODIS and SWGDAM mtDNA databases. The MiDIS concept does not involve the use of opportunistic collections of microbial isolates and phylogenetic tree building as a basis for inference. A staged approach can be used to build MiDIS as an enduring capability, beginning with a pilot demonstration program that must meet user expectations for performance and validation before evolving into a continuing effort. Because MiDIS requires input from a a broad array of expertise including outbreak surveillance, field microbial isolate collection, microbial genome sequencing, disease transmission networks, and laboratory mutation rate studies, it will be necessary to assemble a national multi-laboratory team to develop such a system. The MiDIS effort would lend direction and focus to the national microbial genetics research program for microbial forensics, and would provide an appropriate forensic framework for interfacing to future national and international disease surveillance efforts.

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

Directory of Open Access Journals (Sweden)

Peter Larsen

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

Microbial diversity of western Canadian subsurface coal beds and methanogenic coal enrichment cultures

Energy Technology Data Exchange (ETDEWEB)

Penner, Tara J.; Foght, Julia M. [Department of Biological Sciences, University of Alberta, Edmonton, Alberta (Canada); Budwill, Karen [Carbon and Energy Management, Alberta Innovates-Technology Futures, 250 Karl Clark Road, Edmonton, Alberta (Canada)

2010-05-01

Coalbed methane is an unconventional fuel source associated with certain coal seams. Biogenic methane can comprise a significant portion of the gas found in coal seams, yet the role of microbes in methanogenesis in situ is uncertain. The purpose of this study was to detect and identify major bacterial and archaeal species associated with coal sampled from sub-bituminous methane-producing coal beds in western Canada, and to examine the potential for methane biogenesis from coal. Enrichment cultures of coal samples were established to determine how nutrient amendment influenced the microbial community and methane production in the laboratory. 16S rRNA gene clone libraries were constructed using DNA extracted and amplified from uncultured coal samples and from methanogenic coal enrichment cultures. Libraries were screened using restriction fragment length polymorphism, and representative clones were sequenced. Most (> 50%) of the bacterial sequences amplified from uncultured coal samples were affiliated with Proteobacteria that exhibit nitrate reduction, nitrogen fixation and/or hydrogen utilization activities, including Pseudomonas, Thauera and Acidovorax spp., whereas enrichment cultures were dominated by Bacteroidetes, Clostridia and/or Lactobacillales. Archaeal 16S rRNA genes could not be amplified from uncultured coal, suggesting that methanogens are present in coal below the detection levels of our methods. However, enrichment cultures established with coal inocula produced significant volumes of methane and the archaeal clone libraries were dominated by sequences closely affiliated with Methanosarcina spp. Enrichment cultures incubated with coal plus organic nutrients produced more methane than either nutrient or coal supplements alone, implying that competent methanogenic consortia exist in coal beds but that nutrient limitations restrict their activity in situ. This report adds to the scant literature on coal bed microbiology and suggests how microbes may be

Elucidating Microbial Adaptation Dynamics via Autonomous Exposure and Sampling

Science.gov (United States)

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

2013-01-01

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

Microbial contamination of the Tzu-Chi Cord Blood Bank from 2005 to 2006.

Science.gov (United States)

Chen, Shu-Huey; Zheng, Ya-Jun; Yang, Shang-Hsien; Yang, Kuo-Liang; Shyr, Ming-Hwang; Ho, Yu-Huai

2008-01-01

In total, 4502 units of cord blood (CB) were collected during a 2-year period from 2005 to 2006 by the Buddhist Tzu-Chi Stem Cells Center. The aim of this study was to analyze the incidence of microbial contamination and type of organism present in the cord blood. The clinical impact of microbial contamination on hematopoietic progenitor cell (HPC) grafts used for HPC transplantation is also discussed. First and second specimens were obtained for microbial assessment. These were collected in laboratory after cord blood collection and after cord blood unit manipulation, respectively. The samples were cultured and the results reviewed. The overall incidence of microbiological contamination was 1.8% (82/4502). Three CB units were contaminated with two different organisms. Infectious organisms comprised 9.4% (8/85) of total isolated microbes. These infectious microorganisms were beta-Streptococci group B, Candida tropicalis and Staphylococcus aureus which were isolated in 6, 1 and 1 of CB units respectively. Escherichia coli, Bacteroides fragilis, Lactobacillus spp., Enterococcus, beta-Streptococcus Group B, Bacteroides valgatus, Corynebacterium spp., Klebsiella pneumonia and Peptococcus spp. were the most frequently encountered microorganisms. A higher contamination rate of the CB units was noted after vaginal delivery (2.16%) compared to caesarian section (0.85%) (p bank, we use a closed system but an in utero method. Similar to other studies, most of microorganisms reported here as contaminants are non-pathogenic.

Comparison of Uriswab to alternative methods for urine culture collection and transport: confirmation of standard culture methodology for investigation of urinary tract infections.

Science.gov (United States)

Rennie, Robert P; Turnbull, Lee-Ann; Gauchier-Pitts, Kaylee; Bennett, Tracy; Dyrland, Debbie; Blonski, Susan

2016-08-01

The ability to isolate and identify causative agents of urinary tract infections relies primarily on the quality of the urine sample that is submitted to the microbiology. The most important factors are the method of collection, the maintenance of viability of the potential pathogens during transport, and standardization of the culturing of the urine sample. This report is a composite of several investigations comparing collection and transport on urine culture paddles, with a preservative urine sponge (Uriswab), and a comparison of Uriswab with the BD preservative transport tube as methods of preservation of urinary pathogens. Primary studies showed that Uriswab maintained significantly more urinary pathogens than the urine culture paddle with fewer mixed or contaminated cultures. The two preservative transport systems were comparable for maintenance of viability of the pathogens, but there were fewer mixed cultures when samples were collected with Uriswab. This study confirms the importance of a standard volume of 1 μL of urine for culture. Copyright © 2016 Elsevier Inc. All rights reserved.

The microbial community of the cystic fibrosis airway is disrupted in early life.

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Julie Renwick

Full Text Available Molecular techniques have uncovered vast numbers of organisms in the cystic fibrosis (CF airways, the clinical significance of which is yet to be determined. The aim of this study was to describe and compare the microbial communities of the lower airway of clinically stable children with CF and children without CF.Bronchoalveolar lavage (BAL fluid and paired oropharyngeal swabs from clinically stable children with CF (n = 13 and BAL from children without CF (n = 9 were collected. DNA was isolated, the 16S rRNA regions amplified, fragmented, biotinylated and hybridised to a 16S rRNA microarray. Patient medical and demographic information was recorded and standard microbiological culture was performed.A diverse bacterial community was detected in the lower airways of children with CF and children without CF. The airway microbiome of clinically stable children with CF and children without CF were significantly different as measured by Shannon's Diversity Indices (p = 0.001; t test and Principle coordinate analysis (p = 0.01; Adonis test. Overall the CF airway microbial community was more variable and had a less even distribution than the microbial community in the airways of children without CF. We highlighted several bacteria of interest, particularly Prevotella veroralis, CW040 and a Corynebacterium, which were of significantly differential abundance between the CF and non-CF lower airways. Both Pseudomonas aeruginosa and Streptococcus pneumoniae culture abundance were found to be associated with CF airway microbial community structure. The CF upper and lower airways were found to have a broadly similar microbial milieu.The microbial communities in the lower airways of stable children with CF and children without CF show significant differences in overall diversity. These discrepancies indicate a disruption of the airway microflora occurring early in life in children with CF.

Microbial Transport, Survival, and Succession in a Sequence of Buried Sediments

International Nuclear Information System (INIS)

Kieft, T.L.; Murphy, E.M.; Haldeman, D.L.; Amy, P.S.; Bjornstad, B.N.; McDonald, E.V.; Ringelberg, D.B.; White, D.C.; Stair, J.; Griffiths, R.P.; Gsell, T.C.; Holben, W.E.; Boone, D.R.

1995-01-01

Two chronosequence of unsaturated buried loess sediments ranging in age from and lt;10,000 years to and gt;1 million years were investigated to reconstruct patterns of microbial ecological succession that have occurred since sediment burial. The relative importance of microbial transport and survival to succession were inferred from sediment ages, porewater ages, patterns of abundance (measured by direct counts, counts of culturable cells, and total phospholipid fatty acids), activities (measured by radiotracer and enzyme assays), and community composition (measured by phospholipid fatty acid patterns and Biolog substrate usage). Samples were collected by coring at two sites 40 km apart in the Palouse region of eastern Washington State near the towns of Washtucna and Winona. The Washtucna site was flooded multiple times during the Pleistocene by glacial outburst floods; the elevation of the Winona site is above flood stage. Sediments at the Washtucna site were collected from near surface to 14.9 m depth, where the sediment age was(approx)250 ka and the porewater age was 3700 years; sample intervals at the Winona site ranged from near surface to 38 m (sediment age:(approx)1 Ma; porewater age: 1200 years). Microbial abundance and activities declined with depth at both sites; however, even the deepest, oldest sediments showed evidence of viable microorganisms. Sediments of equivalent age had equal quantities of microorganisms, but differing community types. Differences in community make-up between the two sites can be attributed to differences in groundwater recharge and paleoflooding. Estimates of the ages of the microbial communities can be constrained by porewater and sediment ages. In the shallower sediments ( and lt;9 m at Washtucna, and lt;12 m at Winona), the microbial communities are likely similar in age to the groundwater; thus, microbial succession has been influenced by recent transport of microorganisms from the surface. In the deeper sediments, the

Microbial Transport, Survival, and Succession in a Sequence of Buried Sediments

Energy Technology Data Exchange (ETDEWEB)

Kieft, T.L.; Murphy, E.M.; Haldeman, D.L.; Amy, P.S.; Bjornstad, B.N.; McDonald, E.V.; Ringelberg, D.B.; White, D.C.; Stair, J.; Griffiths, R.P.; Gsell, T.C.; Holben, W.E.; Boone, D.R.

1995-01-05

Two chronosequence of unsaturated buried loess sediments ranging in age from <10,000 years to >1 million years were investigated to reconstruct patterns of microbial ecological succession that have occurred since sediment burial. The relative importance of microbial transport and survival to succession were inferred from sediment ages, porewater ages, patterns of abundance (measured by direct counts, counts of culturable cells, and total phospholipid fatty acids), activities (measured by radiotracer and enzyme assays), and community composition (measured by phospholipid fatty acid patterns and Biolog substrate usage). Samples were collected by coring at two sites 40 km apart in the Palouse region of eastern Washington State near the towns of Washtucna and Winona. The Washtucna site was flooded multiple times during the Pleistocene by glacial outburst floods; the elevation of the Winona site is above flood stage. Sediments at the Washtucna site were collected from near surface to 14.9 m depth, where the sediment age was {approx}250 ka and the porewater age was 3700 years; sample intervals at the Winona site ranged from near surface to 38 m (sediment age: {approx}1 Ma; porewater age: 1200 years). Microbial abundance and activities declined with depth at both sites; however, even the deepest, oldest sediments showed evidence of viable microorganisms. Sediments of equivalent age had equal quantities of microorganisms, but differing community types. Differences in community make-up between the two sites can be attributed to differences in groundwater recharge and paleoflooding. Estimates of the ages of the microbial communities can be constrained by porewater and sediment ages. In the shallower sediments (<9 m at Washtucna, <12 m at Winona), the microbial communities are likely similar in age to the groundwater; thus, microbial succession has been influenced by recent transport of microorganisms from the surface. In the deeper sediments, the populations may be

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

Science.gov (United States)

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

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

Energy Technology Data Exchange (ETDEWEB)

Zhang, Fan; Zhang, Xiao-Tao; Hou, Du-Jie [China Univ. of Geosciences, Beijing (China). The Key Lab. of Marine Reservoir Evolution and Hydrocarbon Accumulation Mechanism; She, Yue-Hui [Yangtze Univ., Jingzhou, Hubei (China). College of Chemistry and Environmental Engineering; Huazhong Univ. of Science and Technology, Wuhan (China). College of Life Science and Technology; Li, Hua-Min [Beijing Bioscience Research Center (China); Shu, Fu-Chang; Wang, Zheng-Liang [Yangtze Univ., Jingzhou, Hubei (China). College of Chemistry and Environmental Engineering; Yu, Long-Jiang [Huazhong Univ. of Science and Technology, Wuhan (China). College of Life Science and Technology

2012-08-15

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. (orig.)

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

Science.gov (United States)

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.

Bacterial diversity analysis of larvae and adult midgut microflora using culture-dependent and culture-independent methods in lab-reared and field-collected Anopheles stephensi-an Asian malarial vector

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Adak Tridibesh

2009-05-01

Full Text Available Abstract Background Mosquitoes are intermediate hosts for numerous disease causing organisms. Vector control is one of the most investigated strategy for the suppression of mosquito-borne diseases. Anopheles stephensi is one of the vectors of malaria parasite Plasmodium vivax. The parasite undergoes major developmental and maturation steps within the mosquito midgut and little is known about Anopheles-associated midgut microbiota. Identification and characterization of the mosquito midgut flora is likely to contribute towards better understanding of mosquito biology including longevity, reproduction and mosquito-pathogen interactions that are important to evolve strategies for vector control mechanisms. Results Lab-reared and field-collected A. stephensi male, female and larvae were screened by "culture-dependent and culture-independent" methods. Five 16S rRNA gene library were constructed form lab and field-caught A. stephensi mosquitoes and a total of 115 culturable isolates from both samples were analyzed further. Altogether, 68 genera were identified from midgut of adult and larval A. stephensi, 53 from field-caught and 15 from lab-reared mosquitoes. A total of 171 and 44 distinct phylotypes having 85 to 99% similarity with the closest database matches were detected among field and lab-reared A. stephensi midgut, respectively. These OTUs had a Shannon diversity index value of 1.74–2.14 for lab-reared and in the range of 2.75–3.49 for field-caught A. stephensi mosquitoes. The high species evenness values of 0.93 to 0.99 in field-collected adult and larvae midgut flora indicated the vastness of microbial diversity retrieved by these approaches. The dominant bacteria in field-caught adult male A. stephensi were uncultured Paenibacillaceae while in female and in larvae it was Serratia marcescens, on the other hand in lab-reared mosquitoes, Serratia marcescens and Cryseobacterium meninqosepticum bacteria were found to be abundant. Conclusion

The Chinese-Indonesian collections in the National Museum of World Cultures, the Netherlands

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Francine Brinkgreve

2017-05-01

Full Text Available Among the more than 130,000 objects from Indonesia in the Dutch National Museum of World Cultures, many once belonged to or were used by the Chinese population of Indonesia. In this article, the authors provide an overview of these collections by presenting their collecting histories from the earliest acquisitions to the most recent collections and by highlighting a number of objects, which in their materials, techniques, motifs, colours or function show a combination of elements from both Chinese and Indonesian cultures. The authors pay particular attention to objects which play a role in the Chinese-Indonesian wedding ceremony.

Insect Cell Culture

NARCIS (Netherlands)

Oers, van M.M.; Lynn, D.E.

2010-01-01

Insect cell cultures are widely used in studies on insect cell physiology, developmental biology and microbial pathology. In particular, insect cell culture is an indispensable tool for the study of insect viruses. The first continuously growing insect cell cultures were established from

Connecting Local Cultural Heritage Collections with ICT: the Case of ZBORZBIRK

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Špela Ledinek Lozej

2014-12-01

Full Text Available AbstractPurpose: The article discusses the digitisation and inventory of 34 local cultural heritage collections in the border region between the Alps and the Karst, and the establishment of a network of owners, guardians of collections and professionals from the field of museology, ethnology, digital humanities and informatics.Methodology/approach: In the framework of the project “ZBORZBIRK – Cultural heritage between the Alps and the Karst” 34 collections of cultural heritage of different type and contents, until then inaccessible to the general public and experts, were catalogued, contextualised and presented to the general and expert public in different media and on the project website.Results: A unified repository with metadata on objects (units was established containing also digital photographs and scans of images and textual objects (digital objects. There are 4583 units and 5190 digital objects in the repository. It is designed for researchers, experts and students from the fields of ethnology, cultural anthropology, history, linguistics as well for the general public, and above all to achieve greater recognisability of the region.Research limitation: The research and the results were limited by the material itself, i.e. the collections included into the project, as well as by different aspirations of collectors and various levels of specialised skills of registrars and recorders who documented and digitised the units and entered the data in the metadata database. The project addresses a wide scope of potential users thus the implementation of different solutions gave rise to the conflict of interests among target groups. The question was whether it should serve as a virtual museum or as a research archival repository. More attention was focused on archival and research standards than on presentation technologies.Originality/practical implications: The project ZBORZBIRK is one of the first projects in the Italian and Slovenian

Cyanobacterial diversity held in microbial biological resource centers as a biotechnological asset: the case study of the newly established LEGE culture collection.

Science.gov (United States)

Ramos, Vitor; Morais, João; Castelo-Branco, Raquel; Pinheiro, Ângela; Martins, Joana; Regueiras, Ana; Pereira, Ana L; Lopes, Viviana R; Frazão, Bárbara; Gomes, Dina; Moreira, Cristiana; Costa, Maria Sofia; Brûle, Sébastien; Faustino, Silvia; Martins, Rosário; Saker, Martin; Osswald, Joana; Leão, Pedro N; Vasconcelos, Vitor M

2018-01-01

Cyanobacteria are a well-known source of bioproducts which renders culturable strains a valuable resource for biotechnology purposes. We describe here the establishment of a cyanobacterial culture collection (CC) and present the first version of the strain catalog and its online database (http://lege.ciimar.up.pt/). The LEGE CC holds 386 strains, mainly collected in coastal (48%), estuarine (11%), and fresh (34%) water bodies, for the most part from Portugal (84%). By following the most recent taxonomic classification, LEGE CC strains were classified into at least 46 genera from six orders (41% belong to the Synechococcales), several of them are unique among the phylogenetic diversity of the cyanobacteria. For all strains, primary data were obtained and secondary data were surveyed and reviewed, which can be reached through the strain sheets either in the catalog or in the online database. An overview on the notable biodiversity of LEGE CC strains is showcased, including a searchable phylogenetic tree and images for all strains. With this work, 80% of the LEGE CC strains have now their 16S rRNA gene sequences deposited in GenBank. Also, based in primary data, it is demonstrated that several LEGE CC strains are a promising source of extracellular polymeric substances (EPS). Through a review of previously published data, it is exposed that LEGE CC strains have the potential or actual capacity to produce a variety of biotechnologically interesting compounds, including common cyanotoxins or unprecedented bioactive molecules. Phylogenetic diversity of LEGE CC strains does not entirely reflect chemodiversity. Further bioprospecting should, therefore, account for strain specificity of the valuable cyanobacterial holdings of LEGE CC.

Digital Collections, Digital Libraries & the Digitization of Cultural Heritage Information.

Science.gov (United States)

Lynch, Clifford

2002-01-01

Discusses digital collections and digital libraries. Topics include broadband availability; digital rights protection; content, both non-profit and commercial; digitization of cultural content; sustainability; metadata harvesting protocol; infrastructure; authorship; linking multiple resources; data mining; digitization of reference works;…

Hydrogen production from microbial strains

Science.gov (United States)

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.

Isolation and characterization of the microbial community of a freshwater distribution system

International Nuclear Information System (INIS)

Balamurugan, P.; Subba Rao, T.

2015-01-01

This investigation provides generic information on culturable and non-culturable microbial community of a freshwater distribution system. Culture based and culture independent (16S rRNA gene sequencing) techniques were used to identify the resident microbial community of the system. Selective isolation of the fouling bacteria such as biofilm formers and corrosion causing bacteria was also attempted. Denaturing gradient gel electrophoresis (DGGE) was carried out and the bands were sequenced to obtain the diversity of the total bacterial types. Pseudomonas aeruginosa was predominantly observed in most of the samples. A variety of bacteria, related to groups such as Cyanobacteria, Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes were identified. The study highlights the relevance of the observed microbial diversity with respect to material deterioration in a freshwater distribution system, which can aid in designing effective control methods. (author)

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

Science.gov (United States)

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.

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

Science.gov (United States)

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

Microbial incorporation of nitrogen in stream detritus

Science.gov (United States)

Diane M. Sanzone; Jennifer L. Tank; Judy L. Meyer; Patrick J. Mulholland; Stuart E.G. Findlay

2001-01-01

We adapted the chloroform fumigation method to determine microbial nitrogen (N) and microbial incorporation of 15N on three common substrates [leaves, wood and fine benthic organic matter (FBOM)] in three forest streams. We compared microbial N and 15 content of samples collected during a 6-week15N-NH...

Assessment of Microbial Contamination of Surfaces and Medical Equipment in Wards of the Panjom Azar Hospital of Gorgan in 2014

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Roghaye Noroozi

2014-06-01

Full Text Available Methods: In this cross-sectional study, different wards of panjom Azar educational hospital including ICU, dialysis and surgery room were investigated. Samples were collected randomly, for three months from July to September 2014, from beds, oxygen masks, oxygen manometer, patient table, covers of the patient's medical records, nurse's desk, border walls and water tap.  Samples were then cultured on blood agar and EMB agar. In order to determine the bacteria type, specific culture media with specific biochemical tests and diagnostic disks were used. Results: Results showed that from 216 samples collected from the levels, the 190 cases (88% had microbial contamination. Most of the recognized bacteria were Staphylococcus saprophyticus, Staphylococcus epidermidis, Staphylococcus aureus, Bacillus subtilis, Pseudomonas aeruginosa, Escherichia coli, Enterobacter and klebsiela. Results of microbial culture of equipments and levels were positive in case of bacterial contamination and maximum contamination was observed in the dialysis ward of the hospital. Conclusion: Due to the relatively high detected contamination, contamination control of levels and patient care equipments could considered as an effective action in reducing nosocomial infections. Thus, using appropriate disinfectant equipment, monitoring the disinfectants preparation, continuous monitoring and detection of common microorganisms are the most important ways for infection control in hospitals.

Microbial Resources and Enological Significance: Opportunities and Benefits

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Leonardo Petruzzi

2017-06-01

Full Text Available 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.

Microbial Resources and Enological Significance: Opportunities and Benefits

Science.gov (United States)

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

COMPARATIVE EVALUATION OF CULTURE MEDIA FOR PATHOGEN ISOLATION OF PURULENT BACTERIAL MENINGITIS

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Ya. V. Podkopaev

2016-01-01

Full Text Available The State Research Center for Applied Microbiology and Biotechnology has designed two nutrient media — chocolate agar and PBM-agar to isolate pathogens of purulent bacterial meningitis (PBM. In our previous research using collected microbial strains the media were shown to be highly susceptible and to provide the growth of Neisseria meningiti-dis, Streptococcus pneumoniae and Haemophilus influenzae strains, when inoculated with microbial suspensions containing single cells. When isolating Haemophilus influenzae, meningococci, and pneumococci the use of selective additives in both media assures selective isolation of required microorganisms, inhibiting contaminants. The objective of this research was to assess the media in bacteriological tests of clinical samples collected from the upper and lower respiratory tract in humans. The bacteriological plating of throat smear specimens (n = 90 from children and adults at the age of 0 to 66 with disorder of the upper respiratory tract on chocolate agar, PBM-agar and on a control medium in the absence of selective additives resulted in the equal amount of microbial cultures isolated. Of 154 isolated cultures 2, 23 and 9 were attributed to Neisseria meningitidis, Streptococcus pneumoniae and Haemophilus influenzae, respectively. The plating of throat smears (n = 10 from healthy people at the age of 30 to 55 on the analyzable and control media in the presence of additives allowed us to selectively isolate Haemophilus influenzae and Streptococcus pneumoniae cultures without a quantitative loss, with contaminants inhibited. By their growth characteristics chocolate agar and PBM-agar were highly competitive with reference media being used in clinical practice for isolating main causative agents of purulent bacterial meningitis.

Genome engineering for microbial natural product discovery.

Science.gov (United States)

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.

Microbial metabolomics in open microscale platforms

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Barkal, Layla J.; Theberge, Ashleigh B.; Guo, Chun-Jun; Spraker, Joe; Rappert, Lucas; Berthier, Jean; Brakke, Kenneth A.; Wang, Clay C. C.; Beebe, David J.; Keller, Nancy P.; Berthier, Erwin

2016-01-01

The microbial secondary metabolome encompasses great synthetic diversity, empowering microbes to tune their chemical responses to changing microenvironments. Traditional metabolomics methods are ill-equipped to probe a wide variety of environments or environmental dynamics. Here we introduce a class of microscale culture platforms to analyse chemical diversity of fungal and bacterial secondary metabolomes. By leveraging stable biphasic interfaces to integrate microculture with small molecule isolation via liquid–liquid extraction, we enable metabolomics-scale analysis using mass spectrometry. This platform facilitates exploration of culture microenvironments (including rare media typically inaccessible using established methods), unusual organic solvents for metabolite isolation and microbial mutants. Utilizing Aspergillus, a fungal genus known for its rich secondary metabolism, we characterize the effects of culture geometry and growth matrix on secondary metabolism, highlighting the potential use of microscale systems to unlock unknown or cryptic secondary metabolites for natural products discovery. Finally, we demonstrate the potential for this class of microfluidic systems to study interkingdom communication between fungi and bacteria. PMID:26842393

Association of high mortality with extended-spectrum β-lactamase (ESBL) positive cultures in community acquired infections.

Science.gov (United States)

Ray, Sumit; Anand, Dimple; Purwar, Sankalp; Samanta, Arijit; Upadhye, Kaustubh V; Gupta, Prasoon; Dhar, Debashis

2018-04-01

Infections due to multidrug resistant organisms have become a serious health concern worldwide. The present study was conducted to investigate the spectrum of microbial resistance pattern in the community and their effects on mortality. A retrospective review and analysis of prospectively collected data was done of all patients admitted with diagnosis of sepsis in two tertiary care ICU's for a period of two years. Demographics, culture positivity, microbial spectrum, resistance pattern and outcome data were collected. Out of 5309 patients enrolled; 3822 had suspected clinical infection on admission with 1452 patients growing positive microbial cultures. Among these, 201 bacterial strains were isolated from patients who had community acquired infections. 73% were Gram negative bacilli, commonest being E. coli (63%). 63.4% E. coli and 60.7% Klebsiella isolates were ESBL producers. The mortality in ESBL positive infections was significantly higher as compared to ESBL negative infections (Odds ratio 2.756). Moreover, ESBL positive patients empirically treated with Beta Lactams+Beta Lactamase inhibitors (BL+BLI) had significantly higher mortality as compared to patients treated with carbapenems. More data from multiple centres need to be gathered to formulate appropriate antibiotic policy for critically ill patients admitted from the community. Copyright © 2017 Elsevier Inc. All rights reserved.

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

Science.gov (United States)

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.

Recent advances in molecular techniques to study microbial communities in food-associated matrices and processes

NARCIS (Netherlands)

Justé, A.; Thomma, B.P.H.J.; Lievens, B.

2008-01-01

In the last two decades major changes have occurred in how microbial ecologists study microbial communities. Limitations associated with traditional culture-based methods have pushed for the development of culture-independent techniques, which are primarily based on the analysis of nucleic acids.

Selection of culturable environmental microbial strains for cellular ...

African Journals Online (AJOL)

Environmental pollution by organic compounds is a global problem. Biological treatment methods are used to restore polluted environments. Microbial immobilization on abiotic surfaces is a recent strategy to improve the efficiency of these processes. In this technique, cell adhesion is a fundamental step for subsequent ...

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

Science.gov (United States)

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.

76 FR 16030 - 60-Day Notice of Proposed Information Collection: Bureau of Educational and Cultural Affairs...

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2011-03-22

... and Cultural Affairs, Office of Policy and Evaluation, Evaluation Division: Sports & Culture... collection clearance will allow ECA/P/V as part of their larger Sports and Culture Evaluation to conduct a... of Educational and Cultural Affairs, Office of Policy and Evaluation, Evaluation Division: Sports...

76 FR 16032 - 60-Day Notice of Proposed Information Collection: Bureau of Educational and Cultural Affairs...

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2011-03-22

... Cultural Affairs, Office of Policy and Evaluation, Evaluation Division: Sports & Culture Evaluation IWP... collection clearance will allow ECA/P/V as part of their larger Sports and Culture Evaluation to conduct a... of Educational and Cultural Affairs, Office of Policy and Evaluation, Evaluation Division: Sports...

Environmental controls on microbial communities in continental serpentinite fluids

Directory of Open Access Journals (Sweden)

Melitza eCrespo-Medina

2014-11-01

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

Sequential enrichment of microbial population exhibiting enhanced biodegradation of crude oil

International Nuclear Information System (INIS)

Venkateswaran, Kasthuri; Harayama, Shigeaki.

1995-01-01

The distribution of oil-degrading bacteria in the coastal waters and sediments of Hokkaido, Japan, was surveyed. It was found that the potential of mixed microbial populations to degrade weathered crude oil was not confined to any ecological components (water or sediment) nor to the sampling stations. One microbial culture that was stable during repeated subculturing degraded 45% of the saturates and 20% of the aromatics present in crude oil in 10 days during the initial screening. The residual hydrocarbons in this culture were extracted by chloroform and dispersed in a fresh seawater-based medium and subsequently inoculated with microorganisms from the first culture. After full growth of the second culture, the residual hydrocarbons were extracted and dispersed in a fresh medium in which microorganisms from the second culture had been inoculated. This sequential process was carried out six times to enrich those microorganisms that grew on the recalcitrant components of crude oil. After repeated exposure of the residual crude oil to the enriched microorganisms, about 80% of the initially added crude oil was degraded. The cultures obtained after each enrichment cycle were kept, and the degradation of fresh crude oil by the enriched microorganisms was monitored. The degrading activity of the enriched cultures increased as the number of enrichment cycles increased. A microbial population that had been selected six times on the residual crude oil could degrade 70% of the saturates and 30% of the aromatics of crude oil, indicating that growth of a microbial population on residual crude oil improved its ability to biodegrade crude oil. 21 refs., 2 tabs., 7 figs

Digital Collections, Digital Libraries and the Digitization of Cultural Heritage Information.

Science.gov (United States)

Lynch, Clifford

2002-01-01

Discusses the development of digital collections and digital libraries. Topics include digitization of cultural heritage information; broadband issues; lack of compelling content; training issues; types of materials being digitized; sustainability; digital preservation; infrastructure; digital images; data mining; and future possibilities for…

Collective Pedagogical Teacher Culture and Mathematics Achievement: Differences by Race, Ethnicity, and Socioeconomic Status

Science.gov (United States)

Moller, Stephanie; Mickelson, Roslyn Arlin; Stearns, Elizabeth; Banerjee, Neena; Bottia, Martha Cecilia

2013-01-01

Scholars have not adequately assessed how organizational cultures in schools differentially influence students' mathematics achievement by race and socioeconomic status (SES). We focus on what we term "collective pedagogical teacher culture", highlighting the role of professional communities and teacher collaboration in influencing…

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

Science.gov (United States)

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

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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...

Linkage of microbial ecology to phenotype: correlation of rumen microbial ecology to cattle's feed efficiency.

Science.gov (United States)

Guan, Le Luo; Nkrumah, Joshua D; Basarab, John A; Moore, Stephen S

2008-11-01

Linkage of rumen microbial structure to host phenotypical traits may enhance the understanding of host-microbial interactions in livestock species. This study used culture-independent PCR-denaturing gradient gel electrophoresis (PCR-DGGE) to investigate the microbial profiles in the rumen of cattle differing in feed efficiency. The analysis of detectable bacterial PCR-DGGE profiles showed that the profiles generated from efficient steers clustered together and were clearly separated from those obtained from inefficient steers, indicating that specific bacterial groups may only inhabit in efficient steers. In addition, the bacterial profiles were more likely clustered within a certain breed, suggesting that host genetics may play an important role in rumen microbial structure. The correlations between the concentrations of volatile fatty acids and feed efficiency traits were also observed. Significantly higher concentrations of butyrate (P < 0.001) and valerate (P = 0.006) were detected in the efficient steers. Our results revealed potential associations between the detectable rumen microbiota and its fermentation parameters with the feed efficiency of cattle.

Degradation of polycyclic aromatic hydrocarbons by microbial consortia enriched from three soils using two different culture media.

Science.gov (United States)

Wu, Manli; Chen, Liming; Tian, Yongqiang; Ding, Yi; Dick, Warren A

2013-07-01

A consortium composed of many different bacterial species is required to efficiently degrade polycyclic aromatic hydrocarbons (PAH) in oil-contaminated soil. We obtained six PAH-degrading microbial consortia from three oil-contaminated soils using two different isolation culture media. Denaturing gradient gel electrophoresis (DGGE) and sequence analyses of amplified 16s rRNA genes confirmed the bacterial community was greatly affected by both the culture medium and the soil from which the consortia were enriched. Three bacterial consortia enriched using malt yeast extract (MYE) medium showed higher degradation rates of PAHs than consortia enriched using Luria broth (LB) medium. Consortia obtained from a soil and then added back to that same soil was more effective in degrading PAHs than adding, to the same soil, consortia isolated from other, unrelated soils. This suggests that inoculum used for bioremediation should be from the same, or very similar nearby soils, as the soil that is actually being bioremediated. Copyright © 2013 Elsevier Ltd. All rights reserved.

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

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Community Structure Comparisons of Hydrothermal Vent Microbial Mats Along the Mariana Arc and Back-arc

Science.gov (United States)

Hager, K. W.; Fullerton, H.; Moyer, C. L.

2015-12-01

Hydrothermal vents along the Mariana Arc and back-arc represent a hotspot of microbial diversity that has not yet been fully recognized. The Mariana Arc and back-arc contain hydrothermal vents with varied vent effluent chemistry and temperature, which translates to diverse community composition. We have focused on iron-rich sites where the dominant primary producers are iron oxidizing bacteria. Because microbes from these environments have proven elusive in culturing efforts, we performed culture independent analysis among different microbial communities found at these hydrothermal vents. Terminal-restriction fragment length polymorphism (T-RFLP) and Illumina sequencing of small subunit ribosomal gene amplicons were used to characterize community members and identify samples for shotgun metagenomics. Used in combination, these methods will better elucidate the composition and characteristics of the bacterial communities at these hydrothermal vent systems. The overarching goal of this study is to evaluate and compare taxonomic and metabolic diversity among different communities of microbial mats. We compared communities collected on a fine scale to analyze the bacterial community based on gross mat morphology, geography, and nearby vent effluent chemistry. Taxa richness and evenness are compared with rarefaction curves to visualize diversity. As well as providing a survey of diversity this study also presents a juxtaposition of three methods in which ribosomal small subunit diversity is compared with T-RFLP, next generation amplicon sequencing, and metagenomic shotgun sequencing.

Microbial keratitis in West and East Malaysia

OpenAIRE

Vanitha Ratnalingam; Thiageswari Umapathy; Kala Sumugam; Hanida Hanafi; Shamala Retnasabapathy

2017-01-01

AIM: To evaluate the epidemiological and etiological factors of microbial keratitis seen in tertiary hospitals in West and East Malaysia.METHODS: A total of 207 patients were enrolled. Patients referred for microbial keratitis to Sungai Buloh Hospital and Kuala Lumpur Hospital in West Malaysia and Queen Elizabeth Hospital and Kuching General Hospital in East Malaysia were recruited. Risk factors were documented. Corneal scrapings for microscopy and culture were performed.RESULTS: The most com...

Awe, the diminished self, and collective engagement: Universals and cultural variations in the small self.

Science.gov (United States)

Bai, Yang; Maruskin, Laura A; Chen, Serena; Gordon, Amie M; Stellar, Jennifer E; McNeil, Galen D; Peng, Kaiping; Keltner, Dacher

2017-08-01

Awe has been theorized as a collective emotion, one that enables individuals to integrate into social collectives. In keeping with this theorizing, we propose that awe diminishes the sense of self and shifts attention away from individual interests and concerns. In testing this hypothesis across 6 studies (N = 2137), we first validate pictorial and verbal measures of the small self; we then document that daily, in vivo, and lab experiences of awe, but not other positive emotions, diminish the sense of the self. These findings were observed across collectivist and individualistic cultures, but also varied across cultures in magnitude and content. Evidence from the last 2 studies showed that the influence of awe upon the small self accounted for increases in collective engagement, fitting with claims that awe promotes integration into social groups. Discussion focused on how the small self might mediate the effects of awe on collective cognition and behavior, the need to study more negatively valenced varieties of awe, and other potential cultural variations of the small self. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

An assessment of microbial communities associated with surface mining-disturbed overburden.

Science.gov (United States)

Poncelet, Dominique M; Cavender, Nicole; Cutright, Teresa J; Senko, John M

2014-03-01

To assess the microbiological changes that occur during the maturation of overburden that has been disturbed by surface mining of coal, a surface mining-disturbed overburden unit in southeastern Ohio, USA was characterized. Overburden from the same unit that had been disturbed for 37 and 16 years were compared to undisturbed soil from the same region. Overburden and soil samples were collected as shallow subsurface cores from each subregion of the mined area (i.e., land 16 years and 37 years post-mining, and unmined land). Chemical and mineralogical characteristics of overburden samples were determined, as were microbial respiration rates. The composition of microbial communities associated with overburden and soil were determined using culture-independent, nucleic acid-based approaches. Chemical and mineralogical evaluation of overburden suggested that weathering of disturbed overburden gave rise to a setting with lower pH and more oxidized chemical constituents. Overburden-associated microbial biomass and respiration rates increased with time after overburden disturbance. Evaluation of 16S rRNA gene libraries that were produced by "next-generation" sequencing technology revealed that recently disturbed overburden contained an abundance of phylotypes attributable to sulfur-oxidizing Limnobacter spp., but with increasing time post-disturbance, overburden-associated microbial communities developed a structure similar to that of undisturbed soil, but retained characteristics of more recently disturbed overburden. Our results indicate that over time, the biogeochemical weathering of disturbed overburden leads to the development of geochemical conditions and microbial communities that approximate those of undisturbed soil, but that this transition is incomplete after 37 years of overburden maturation.

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

Science.gov (United States)

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

2017-05-01

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

Long-term oil contamination causes similar changes in microbial communities of two distinct soils.

Science.gov (United States)

Liao, Jingqiu; Wang, Jie; Jiang, Dalin; Wang, Michael Cai; Huang, Yi

2015-12-01

Since total petroleum hydrocarbons (TPH) are toxic and persistent in environments, studying the impact of oil contamination on microbial communities in different soils is vital to oil production engineering, effective soil management and pollution control. This study analyzed the impact of oil contamination on the structure, activity and function in carbon metabolism of microbial communities of Chernozem soil from Daqing oil field and Cinnamon soil from Huabei oil field through both culture-dependent techniques and a culture-independent technique-pyrosequencing. Results revealed that pristine microbial communities in these two soils presented disparate patterns, where Cinnamon soil showed higher abundance of alkane, (polycyclic aromatic hydrocarbons) PAHs and TPH degraders, number of cultivable microbes, bacterial richness, bacterial biodiversity, and stronger microbial activity and function in carbon metabolism than Chernozem soil. It suggested that complicated properties of microbes and soils resulted in the difference in soil microbial patterns. However, the changes of microbial communities caused by oil contamination were similar in respect of two dominant phenomena. Firstly, the microbial community structures were greatly changed, with higher abundance, higher bacterial biodiversity, occurrence of Candidate_division_BRC1 and TAO6, disappearance of BD1-5 and Candidate_division_OD1, dominance of Streptomyces, higher percentage of hydrocarbon-degrading groups, and lower percentage of nitrogen-transforming groups. Secondly, microbial activity and function in carbon metabolism were significantly enhanced. Based on the characteristics of microbial communities in the two soils, appropriate strategy for in situ bioremediation was provided for each oil field. This research underscored the usefulness of combination of culture-dependent techniques and next-generation sequencing techniques both to unravel the microbial patterns and understand the ecological impact of

Growth-arresting Activity of Acmella Essential Oil and its Isolated Component D-Limonene (1, 8 P-Mentha Diene) against Trichophyton rubrum (Microbial Type Culture Collection 296).

Science.gov (United States)

Padhan, Diptikanta; Pattnaik, Smaranika; Behera, Ajaya Kumar

2017-10-01

Spilanthes acmella is used as a remedy in toothache complaints by the tribal people of Western part of Odisha, India. The objective of this study was to study the growth-arresting activity of an indigenous Acmella essential oil (EO) ( S. acmella Murr, Asteraceae ) and its isolated component, d-limonene against Trichophyton rubrum (microbial type culture collection 296). The EO was extracted from flowers of indigenous S. acmella using Clevenger's apparatus and analyzed by gas chromatography-mass spectrometry (GC-MS). High pressure liquid chromatography (HPLC) was carried out to isolate the major constituent. The isolated fraction was subjected to fourier transform infrared spectroscopy (FTIR) and nuclear magnetic resonance (NMR). The antidermatophytic activity was screened for using "disc diffusion" and "slant dilution" method followed by optical, scanning electron microscopy (SEM), and transmission electron microscopy (TEM) studies. The molecular dockings were made between d-limonene with cell wall synthesis-related key enzymes (14 methyl deaminase and monooxygenase). The GC-MS analysis EO had inferred the presence of 7 number of major (≥2%) components. The component with highest peak area (%) was found to be 41.02. The HPLC-isolated fraction was identified as d-limonene (1,8 p-Mentha-diene) by FTIR and NMR. Qualitative and quantitative assays had suggested the growth inhibitory activity of Acmella EO and its component. Shrinkage, evacuation, cell wall puncture, and leakage of cellular constituents by the activity of Acmella oil and d-limonene were evidenced from optical, SEM, and TEM studies. The computer simulation had predicted the binding strengths of d-limonene and fluconazole with dermatophyte cell wall enzymes. There could have been synergistic action of all or some of compounds present in indigenous Acmella EO. There was presence of seven number of (d-limonene, ocimene, β-myrcene, cyclohexene, 3-(1, 5-dimethyl-4-hexenyl)-6-methylene, �

Characterization of mixed-culture biofilms established in microbial fuel cells

International Nuclear Information System (INIS)

Yang, Suling; Du, Fangzhou; Liu, Hong

2012-01-01

For the successful operation of a microbial fuel cell, it is important to characterize the biofilm on the anode. The behavior of MFCs during initial biofilm growth and characterization of anodic biofilm were studied using two-chamber MFCs with activated sludge as inoculum. After three times' replacement of the anodic growth medium, the biofilms were well developed, and a maximum closed circuit potential of 0.41 V and 0.37 V (1000 Ω resistor) was achieved using acetate and glucose, respectively. Electron microscopy revealed that there were rod-shaped cells 0.2–0.3 μm wide by 1.5–2.5 μm long in the anode biofilm in the acetate-fed MFC, and these cells were mainly arranged by monolayer. The biofilm in the glucose-fed MFC was made of cocci-shaped cells in chains and a thick matrix. Both using acetate and glucose, the anodic bacterial communities were different than those of the activated sludge. Cyclic voltammograms suggested that extracellular electron transfer in these MFCs was accomplished mainly by the biofilms on the anode and not by bacteria-produced mediators. -- Highlights: ► The mixed-culture biofilms established in MFCs were characterized. ► The possible electron transfer mechanism was presented. ► In these MFCs the anodic area should be much larger.

Potential for microbial oxidation of ferrous iron in basaltic glass.

Science.gov (United States)

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

Evaluation of microbial biofilm communities from an Alberta oil sands tailings pond.

Science.gov (United States)

Golby, Susanne; Ceri, Howard; Gieg, Lisa M; Chatterjee, Indranil; Marques, Lyriam L R; Turner, Raymond J

2012-01-01

Bitumen extraction from the oil sands of Alberta has resulted in millions of cubic meters of waste stored on-site in tailings ponds. Unique microbial ecology is expected in these ponds, which may be key to their bioremediation potential. We considered that direct culturing of microbes from a tailings sample as biofilms could lead to the recovery of microbial communities that provide good representation of the ecology of the tailings. Culturing of mixed species biofilms in vitro using the Calgary Biofilm Device (CBD) under aerobic, microaerobic, and anaerobic growth conditions was successful both with and without the addition of various growth nutrients. Denaturant gradient gel electrophoresis and 16S rRNA gene pyrotag sequencing revealed that unique mixed biofilm communities were recovered under each incubation condition, with the dominant species belonging to Pseudomonas, Thauera, Hydrogenophaga, Rhodoferax, and Acidovorax. This work used an approach that allowed organisms to grow as a biofilm directly from a sample collected of their environment, and the biofilms cultivated in vitro were representative of the endogenous environmental community. For the first time, representative environmental mixed species biofilms have been isolated and grown under laboratory conditions from an oil sands tailings pond environment and a description of their composition is provided.

Bottoms Up! Secrets to Overcoming Cultural Barriers for Data Collection in Vietnam

DEFF Research Database (Denmark)

Phi, Giang

2018-01-01

Qualitative data collection in remote areas of Asia can be rather challenging, especially when the researchers come from very different cultural backgrounds to the participants and the research topics centre on sensitive issues such as poverty....

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

DEFF Research Database (Denmark)

Friis-Holm, Lotte Bjerrum; Engberg, R.M.; Leser, T.D.

2006-01-01

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 ...% 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...

Digital Forensics and Born-Digital Content in Cultural Heritage Collections. CLIR Publication No. 149

Science.gov (United States)

Kirschenbaum, Matthew G.; Ovenden, Richard; Redwine, Gabriela

2010-01-01

The purpose of this report is twofold: first, to introduce the field of digital forensics to professionals in the cultural heritage sector; and second, to explore some particular points of convergence between the interests of those charged with collecting and maintaining born-digital cultural heritage materials and those charged with collecting…

Characterization of indigenous oil field microorganisms for microbially enhanced oil recovery (MEOR)

Energy Technology Data Exchange (ETDEWEB)

Sitte, J.; Krueger, M. [Bundesanstalt fuer Geowissenschaften und Rohstoffe (BGR), Hannover (Germany); Biegel, E.; Herold, A. [BASF SE, Ludwigshafen (Germany); Alkan, H. [Wintershall Holding GmbH, Kassel (Germany)

2013-08-01

Microbial activities and their resulting metabolites became a focus of attention for enhanced oil recovery (MEOR, microbial enhanced oil recovery) in the recent years. In order to develop a strategy for a MEOR application in a German oil field operated by Wintershall experiments were performed to investigate different sampling strategies and the microbial communities found in these samples. The objectives of this study were (1) to characterize the indigenous microbial communities, (2) to investigate the dependency of microbial activity/diversity on the different sampling strategies, and (3) to study the influence of the in situ pressure on bacterial growth and metabolite production. Fluids were sampled at the well head (surface) and in situ in approx. 785 m depth to collect uncontaminated production water directly from the reservoir horizon and under the in situ pressure of 31 bar (subsurface). In the lab the pressure was either released quickly or slowly to assess the sensitivity of microorganisms to rapid pressure changes. Quantitative PCR resulted in higher microbial cell numbers in the subsurface than in the surface sample. Biogenic CO{sub 2} and CH{sub 4} formation rates were determined under atmospheric and high pressure conditions in the original fluids, with highest rates found in the surface fluid. Interestingly, no methane was formed in the native fluid samples. While nitrate reduction was exclusively detected in the surface samples, sulfide formation also occurred in the subsurface fluids. Increased CO{sub 2} formation was measured after addition of a variety of substrates in the surface fluids, while only fructose and glucose showed a stimulating effect on CO{sub 2} production for the subsurface sample. Stable enrichment cultures were obtained in complex medium inoculated with the subsurface fluid, both under atmospheric and in situ pressure. Growth experiments with constant or changing pressure, and subsequent DGGE analysis of bacterial 16S rRNA genes

Study on chromosome aberrations test determinated by micro-whole blood culture in vacuum blood collection tube

International Nuclear Information System (INIS)

Zhong Zhihong; Han Fang'an; Ge Qinjuan; Wu Xiao; Chen Juan

2006-01-01

Objective: To develop an easier and efficient method of culturing the chromosome and analyzing the aberrations in peripheral lymphocytes. Methods: Micro whole was cultured for 54 hours in home-made vacuum blood collection tube, and then collection, slice-making, microscopy detection for the chromosome aberrations was done. The difference of the results was analysed by comparing with the common method. Results: For 60 radiologists and 30 contrasts, the chromosome aberrations in peripheral lymphocytes were examed by this system, the lymphocytes and chromosome were clear and alive and easier to analyse. Compared with the common method, there was no significantly difference between the two analyzing results. Conclusion: The chromosome aberrations test by micro whole blood culture in vacuum blood collection tube is easier and efficient, and is worthy of being widely popularized. (authors)

Microbial Contamination on Used Surgical Masks among Hospital Personnel and Microbial Air Quality in their Working Wards: A Hospital in Bangkok.

Science.gov (United States)

Luksamijarulkul, Pipat; Aiempradit, Natkitta; Vatanasomboon, Pisit

2014-09-01

To assess the relationship of bacterial and fungal contamination on used surgical masks worn by the hospital personnel and microbial air quality in their working wards. This is a cross-sectional study of 230 used surgical masks collected from 214 hospital personnel, and 215 indoor air samples collected from their working wards to culture for bacterial and fungal counts. This study was carried out at the hospital in Bangkok. Group or genus of isolated bacteria and fungi were preliminarily identified by Gram's stain and lacto-phenol cotton blue. Data were analyzed using paired t-test and Pearson's correlation coefficient at the significant level of pcontamination on inside area of the used masks were 47 ± 56 and 15 ± 9 cfu/ml/piece, and on outside area were 166 ± 199 and 34 ± 18 cfu/ml/piece, respectively, pcontamination on used masks from hospital personnel working in the male and female medical wards and out-patient department, as well as the bacterial and fungal counts of the indoor air sample collected from the same area were relatively higher than the other wards. The predominant isolated bacteria and fungi contaminated on inside and outside areas of the used masks and air samples were similar (Staphylococcus spp. and Aspergillus spp.; respectively). For its relationship, results found that bacterial and fungal counts in air samples showed significantly positive correlation with the bacterial contamination load on outside area of the used masks, r=0.16, p=0.018 and r=0.21, p=0.003, respectively. High bacterial contamination on outside area of the used masks was demonstrated, and it showed a significant correlation with microbial air quality of working wards.

Assessment of the Deepwater Horizon oil spill impact on Gulf coast microbial communities

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Regina eLamendella

2014-04-01

Full Text Available One of the major environmental concerns of the Deepwater Horizon oil spill in the Gulf of Mexico was the ecological impact of the oil that reached shorelines of the Gulf Coast. Here we investigated the impact of the oil on the microbial composition in beach samples collected in June 2010 along a heavily impacted shoreline near Grand Isle, Louisiana. Successional changes in the microbial community structure due to the oil contamination were determined by deep sequencing of 16S rRNA genes. Metatranscriptomics was used to determine expression of functional genes involved in hydrocarbon degradation processes. In addition, potential hydrocarbon-degrading Bacteria were obtained in culture. The 16S data revealed that highly contaminated samples had higher abundances of Alpha- and Gammaproteobacteria sequences. Successional changes in these classes were observed over time, during which the oil was partially degraded. The metatranscriptome data revealed that PAH, n-alkane, and toluene degradation genes were expressed in the contaminated samples, with high homology to genes from Alteromonadales, Rhodobacterales, and Pseudomonales. Notably, Marinobacter (Gammaproteobacteria had the highest representation of expressed genes in the samples. A Marinobacter isolated from this beach was shown to have potential for transformation of hydrocarbons in incubation experiments with oil obtained from the Mississippi Canyon Block 252 (MC252 well; collected during the Deepwater Horizon spill. The combined data revealed a response of the beach microbial community to oil contaminants, including prevalence of Bacteria endowed with the functional capacity to degrade oil.

Microbial stratification and microbially catalyzed processes along a hypersaline chemocline

Science.gov (United States)

Hyde, A.; Joye, S. B.; Teske, A.

2017-12-01

Orca Basin is the largest deep hypersaline anoxic basin in the world, covering over 400 km2. Located at the bottom of the Gulf of Mexico, this body of water reaches depths of 200 meters and is 8 times denser (and more saline) than the overlying seawater. The sharp pycnocline prevents any significant vertical mixing and serves as a particle trap for sinking organic matter. These rapid changes in salinity, oxygen, organic matter, and other geochemical parameters present unique conditions for the microbial communities present. We collected samples in 10m intervals throughout the chemocline. After filtering the water, we used high-throughput bacterial and archaeal 16S rRNA gene sequencing to characterize the changing microbial community along the Orca Basin chemocline. The results reveal a dominance of microbial taxa whose biogeochemical function is entirely unknown. We then used metagenomic sequencing and reconstructed genomes for select samples, revealing the potential dominant metabolic processes in the Orca Basin chemocline. Understanding how these unique geochemical conditions shape microbial communities and metabolic capabilities will have implications for the ocean's biogeochemical cycles and the consequences of expanding oxygen minimum zones.

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

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Wei Zou

2018-04-01

Full Text Available 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.

Application of Sequence-based Methods in Human MicrobialEcology

Energy Technology Data Exchange (ETDEWEB)

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 to 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.

GeoChip-based insights into the microbial functional gene repertoire of marine sponges (high microbial abundance, low microbial abundance) and seawater

KAUST Repository

Bayer, Kristina

2015-01-08

The GeoChip 4.2 gene array was employed to interrogate the microbial functional gene repertoire of sponges and seawater collected from the Red Sea and the Mediterranean. Complementary amplicon sequencing confirmed the microbial community composition characteristic of high microbial abundance (HMA) and low microbial abundance (LMA) sponges. By use of GeoChip, altogether 20 273 probes encoding for 627 functional genes and representing 16 gene categories were identified. Minimum curvilinear embedding analyses revealed a clear separation between the samples. The HMA/LMA dichotomy was stronger than any possible geographic pattern, which is shown here for the first time on the level of functional genes. However, upon inspection of individual genes, very few specific differences were discernible. Differences were related to microbial ammonia oxidation, ammonification, and archaeal autotrophic carbon fixation (higher gene abundance in sponges over seawater) as well as denitrification and radiation-stress-related genes (lower gene abundance in sponges over seawater). Except for few documented specific differences the functional gene repertoire between the different sources appeared largely similar. This study expands previous reports in that functional gene convergence is not only reported between HMA and LMA sponges but also between sponges and seawater.

GeoChip-based insights into the microbial functional gene repertoire of marine sponges (high microbial abundance, low microbial abundance) and seawater

KAUST Repository

Bayer, Kristina; Moitinho-Silva, Lucas; Brü mmer, Franz; Cannistraci, Carlo V.; Ravasi, Timothy; Hentschel, Ute

2015-01-01

The GeoChip 4.2 gene array was employed to interrogate the microbial functional gene repertoire of sponges and seawater collected from the Red Sea and the Mediterranean. Complementary amplicon sequencing confirmed the microbial community composition characteristic of high microbial abundance (HMA) and low microbial abundance (LMA) sponges. By use of GeoChip, altogether 20 273 probes encoding for 627 functional genes and representing 16 gene categories were identified. Minimum curvilinear embedding analyses revealed a clear separation between the samples. The HMA/LMA dichotomy was stronger than any possible geographic pattern, which is shown here for the first time on the level of functional genes. However, upon inspection of individual genes, very few specific differences were discernible. Differences were related to microbial ammonia oxidation, ammonification, and archaeal autotrophic carbon fixation (higher gene abundance in sponges over seawater) as well as denitrification and radiation-stress-related genes (lower gene abundance in sponges over seawater). Except for few documented specific differences the functional gene repertoire between the different sources appeared largely similar. This study expands previous reports in that functional gene convergence is not only reported between HMA and LMA sponges but also between sponges and seawater.

Characterization of bacteriophages infecting clinical isolates of Pseudomonas aeruginosa stored in a culture collection

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C.C.S. Zanetti

2013-08-01

Full Text Available Some clinical isolates of Pseudomonas aeruginosa stored in our culture collection did not grow or grew poorly and showed lysis on the culture plates when removed from the collection and inoculated on MacConkey agar. One hypothesis was that bacteriophages had infected and killed those clinical isolates. To check the best storage conditions to maintain viable P. aeruginosa for a longer time, clinical isolates were stored at various temperatures and were grown monthly. We investigated the presence of phage in 10 clinical isolates of P. aeruginosa stored in our culture collection. Four strains of P. aeruginosa were infected by phages that were characterized by electron microscopy and isolated to assess their ability to infect. The best condition to maintain the viability of the strains during storage was in water at room temperature. Three Siphoviridae and two Myoviridae phages were visualized and characterized by morphology. We confirmed the presence of bacteriophages infecting clinical isolates, and their ability to infect and lyse alternative hosts. Strain PAO1, however, did not show lysis to any phage. Mucoid and multidrug resistant strains of P. aeruginosa showed lysis to 50% of the phages tested.

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

Science.gov (United States)

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 extremophiles from the 2008 Schirmacher Oasis Expedition: preliminary results

Science.gov (United States)

Hoover, Richard B.; Pikuta, Elena V.; Townsend, Alisa; Anthony, Joshua; Guisler, Melissa; McDaniel, Jasmine; Bej, Asim; Storrie-Lombardi, Michael

2008-08-01

Among the most interesting targets for Astrobiology research are the polar ice caps and the permafrost of Mars and the ice and liquid water bodies that may lie beneath the frozen crusts of comets, the icy moons of Jupiter (Europa, Io and Ganymede) and Saturn (Titan and Enceladus). The permanently ice-covered lakes of Antarctica, such as Lake Vostok and Lake Untersee, provide some of the best terrestrial analogues for these targets. The 2008 International Tawani Schirmacher Oasis/Lake Untersee Expeditions have been organized to conduct studies of novel microbial extremophiles and investigate the biodiversity of the glaciers and ice-covered lakes of Dronning Maud Land, East Antarctica. This paper describes the preliminary analysis of the anaerobic microbial extremophiles isolated from samples collected during the 2008 International Schirmacher Oasis Antarctica Reconnaissance Expedition. These samples showed great diversity of psychrophlic and psychrotolerant bacteria. Six new anaerobic strains have been isolated in pure cultures and partially characterized. Two of them (strains ARHSd-7G and ARHSd-9G) were isolated from a small tidal pool near the colony of African Penguins Spheniscus demersus. Strain ARHSd-7G was isolated on mineral anaerobic medium with 3 % NaCl, pH 7 and D-glucose, it has motile, vibrion shape cells, and is Gram variable. Strain ARHSd-9G grew on anaerobic, alkaline medium with pH 9 and 1 % NaCl at 3°C. The substrate was D-glucose supplemented with yeast extract (0.05 %). Cells of strain ARHSd-9G had morphology of straight or slightly curved elongated rods and demonstrated unusual optical effects under dark-field visible light microscopy. The cells were spore-forming and Gram positive. From the mat sample collected near Lake Zub, the new strain LZ-3 was isolated in pure culture at 3°C. Strain LZ-3 was anaerobic and grew on 0.5 % NaCl mineral medium with Dglucose as a substrate. The gram positive cells were spore-forming. They exhibited a

Examination of gutta-percha cones for microbial contamination during chemical use

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Guven Kayaoglu

2009-06-01

Full Text Available OBJECTIVE: The aim of this study was to evaluate the degree of microbial contamination in packaged gutta-percha cones before and during use in clinical conditions. MATERIAL AND METHODS: Sealed packages of #15-40 gutta-percha cones were opened under aseptic laboratory conditions. Two gutta-percha cones from each size were randomly drawn and added to tubes containing glass beads and 750 µL of saline. The tubes were vortexed, serially diluted and samples of 250 µL were cultured on agar plates. The plates were incubated at 37ºC for 3 days and colonies were counted. The initially sampled packages were distributed to 12 final year dental students. The packages were collected at the end of the first and the third clinical practice days and sampled as described above. RESULTS: Baseline microbial counts did not exceed 3 CFU. At the end of the first and the third day, additional contamination was found in five and three of the packages, respectively. The ratio of contaminated packages at the first day and the third day was not significantly different (z-test; p > 0.05. The numbers of microorganisms cultured at the first day (8 ± 9.9 CFU and the third day (4.5 ± 8.3 CFU were not significantly different (Wilcoxon signed-rank test; p > 0.05. No significant correlation was found between the number of filled root canals and cultured microorganisms at either the first day (Spearman's rho; r = 0.481, p = 0.113 or the third day (r = -0.034, p = 0.917. CONCLUSIONS: Gutta-percha cones taken directly from manufacturer's sealed package harbored microorganisms. Clinical use of the packages has been found to be associated with additional contamination of the gutta-percha cones. The counts of cultured microorganisms did not correlate well with the number of filled root canals.

Biorremediación de los efluentes de cultivo del camarón Litopenaeus vannamei (Boone, 1931 utilizando tapetes microbianos en un sistema de recirculación Bioremediacion of effluents ones of the culture of Litopenaeus vannamei (Boone, 1931 using microbial mats in a recirculating system

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Carlos Lezama-Cervantes

2010-01-01

Full Text Available Se desarrolló un sistema de recirculación (SR integrando el cultivo del camarón con tapetes microbianos buscando mitigar los impactos ambientales de los subproductos del cultivo del camarón y avanzar hacia la biorremediación del agua de cultivo. Los consorcios microbianos obtenidos de ambientes naturales (TaM estuvieron constituidos por bacterias (55,6%, cianófitas (18,4%, diatomeas (9%, nemátodos (5,6% y clorófitas (1,4%, entre los grupos taxonómicos principales. La remoción de nutrientes y sólidos se evaluó en un SR (2 ciclos/hora conteniendo (n = 3 60 y 120 ind m-2 de Litopenaeus vannamei. Los resultados demostraron que los TaM redujeron los niveles de nitrógeno amoniacal por encima del 71% diariamente; la demanda bioquímica de oxígeno (DBO5 se redujo más de 68% y los sólidos suspendidos (SST hasta en 62% al compararse con los sistemas control (p 0,05. El agua bio-remediada tiene un efecto positivo en el cultivo de Litopenaeus vannamei, y promueve el crecimiento y sobrevivencia en presencia de TaM en el SR.We developed a recirculating system integrating shrimp culture with microbial mats aiming to mitigate the environmental impacts of by-products from shrimp culture and to advance toward the bioremediation of the shrimp culture water. The microbial consortia collected from natural environments (TaM was constituted by bacteria (55.6%, Cyanophyte (18.4%, diatoms (9%, nematods (5.6% and Chlorophyte algae (1.4% among the major taxonomic groups. The removal of nutrients and solids by these mats was assessed in a recirculating system (2 cycles/hour (n = 3 containing 60 and 120 ind m-2 of Litopenaeus vannamei. Results showed that the microbial mat reduces daily up to 71% of ammonia nitrogen, decreases around 68% of the biochemical oxygen demand (DBO5 and up to 62% of suspended solids (SST when comparing to the control systems (p 0.05. The Bioremediated culture water had a positive effect on the culture of Litopenaeus vannamei, and

[Prokaryotic community of subglacial bottom sediments of Antarctic Lake Untersee: detection by cultural and direct microscopic techniques].

Science.gov (United States)

Muliukin, A L; Demkina, E V; Manucharova, N A; Akimov, V N; Andersen, D; McKay, C; Gal'chenko, V F

2014-01-01

The heterotrophic mesophilic component was studied in microbial communities of the samples of frozen regolith collected from the glacier near Lake Untersee collected in 2011 during the joint Russian-American expedition to central Dronning Maud Land (Eastern Antarctica). Cultural techniques revealed high bacterial numbers in the samples. For enumeration of viable cells, the most probable numbers (MPN) method proved more efficient than plating on agar media. Fluorescent in situ hybridization with the relevant oligonucleotide probes revealed members of the groups Eubacteria (Actinobacteria, Firmicutes) and Archaea. Application of the methods of cell resuscitation, such as the use of diluted media and prevention of oxidative stress, did not result in a significant increase in the numbers of viable cells retrieved form subglacial sediment samples. Our previous investigations demonstrated the necessity for special procedures for efficient reactivation of the cells from microbial communities of preserved fossil soil and permafrost samples collected in the Arctic zone. The differences in response to the special resuscitation procedures may reflect the differences in the physiological and morphological state of bacterial cells in microbial communities subject to continuous or periodic low temperatures and dehydration.

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

Science.gov (United States)

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...

Seasonality in ocean microbial communities.

Science.gov (United States)

Giovannoni, Stephen J; Vergin, Kevin L

2012-02-10

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

Microbial Life of North Pacific Oceanic Crust

Science.gov (United States)

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

Deciphering Diversity Indices for a Better Understanding of Microbial Communities.

Science.gov (United States)

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 content of abattoir wastewater and its contaminated soil in ...

African Journals Online (AJOL)

Microbial content of wastewater in two abattoirs and the impact on microbial population of receiving soil was studied in Agege and Ojo Local Government Areas in Lagos State, Nigeria. Wastewater samples were collected from each of the abattoirs over three months period and examined for microbial content. Soil samples ...

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

Science.gov (United States)

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.

The Study about the Influence of the Pop Culture for the Japanese Fashion　：　The Historical Materials Collection about the Connection of Japanese Fashion and Pop Cultures after World War II

OpenAIRE

田中, 里尚; 中村, 仁; 梅原, 宏司; 齋木, 吉隆; 古賀, 令子

2010-01-01

The purpose of this research collect and arrange documents and historical materials to determine how pop culture influenced the fashion in Japan after World War II. In 2010, we firstly collected previous fashion and popular culture studies done in foreign countries. We found many intriguing studies, but we came upon one which was particularly noteworthy. As a means of clarifying the relationship between fashion and pop culture, we collected books written by Angela McRobbie. Second, we collect...

Farm Deployable Microbial Bioreactor for Fuel Ethanol Production

Energy Technology Data Exchange (ETDEWEB)

Okeke, Benedict [Auburn Univ., Montgomery AL (United States)

2016-03-30

Research was conducted to develop a farm and field deployable microbial bioreactor for bioethanol production from biomass. Experiments were conducted to select the most efficient microorganisms for conversion of plant fiber to sugars for fermentation to ethanol. Mixtures of biomass and surface soil samples were collected from selected sites in Alabama black belt counties (Macon, Sumter, Choctaw, Dallas, Montgomery, Lowndes) and other areas within the state of Alabama. Experiments were conducted to determine the effects of culture parameters on key biomass saccharifying enzymes (cellulase, beta-glucosidase, xylanase and beta-xylosidase). A wide-scale sampling of locally-grown fruits in Central Alabama was embarked to isolate potential xylose fermenting microorganisms. Yeast isolates were evaluated for xylose fermentation. Selected microorganisms were characterized by DNA based methods. Factors affecting enzyme production and biomass saccharification were examined and optimized in the laboratory. Methods of biomass pretreatment were compared. Co-production of amylolytic enzymes with celluloytic-xylanolytic enzymes was evaluated; and co-saccharification of a combination of biomass, and starch-rich materials was examined. Simultaneous saccharification and fermentation with and without pre-saccharifcation was studied. Whole culture broth and filtered culture broth simultaneous saccahrifcation and fermentation were compared. A bioreactor system was designed and constructed to employ laboratory results for scale up of biomass saccharification.

Collection methods and quality assessment for Esche-richia coli, water quality, and microbial source tracking data within Tumacácori National Historical Park and the upper Santa Cruz River, Arizona, 2015-16

Science.gov (United States)

Paretti, Nicholas; Coes, Alissa L.; Kephart, Christopher M.; Mayo, Justine

2018-03-05

Tumacácori National Historical Park protects the culturally important Mission, San José de Tumacácori, while also managing a portion of the ecologically diverse riparian corridor of the Santa Cruz River. This report describes the methods and quality assurance procedures used in the collection of water samples for the analysis of Escherichia coli (E. coli), microbial source tracking markers, suspended sediment, water-quality parameters, turbidity, and the data collection for discharge and stage; the process for data review and approval is also described. Finally, this report provides a quantitative assessment of the quality of the E. coli, microbial source tracking, and suspended sediment data.The data-quality assessment revealed that bias attributed to field and laboratory contamination was minimal, with E. coli detections in only 3 out of 33 field blank samples analyzed. Concentrations in the field blanks were several orders of magnitude lower than environmental concentrations. The microbial source tracking (MST) field blank was below the detection limit for all MST markers analyzed. Laboratory blanks for E. coli at the USGS Arizona Water Science Center and laboratory blanks for MST markers at the USGS Ohio Water Microbiology Laboratory were all below the detection limit. Irreplicate data for E. coli and suspended sediment indicated that bias was not introduced to the data by combining samples collected using discrete sampling methods with samples collected using automatic sampling methods.The split and sequential E. coli replicate data showed consistent analytical variability and a single equation was developed to explain the variability of E. coli concentrations. An additional analysis of analytical variability for E. coli indicated analytical variability around 18 percent relative standard deviation and no trend was observed in the concentration during the processing and analysis of multiple split-replicates. Two replicate samples were

Comparing the effect of echinacea and chlorhexidine mouthwash on the microbial flora of intubated patients admitted to the intensive care unit

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Mehdi Safarabadi

2017-01-01

Full Text Available Background: Providing intubated patients admitted to the intensive care units with oral healthcare is one of the main tasks of nurses in order to prevent Ventilator-Associated Pneumonia (VAP. This study aimed at comparing the effects of two mouthwash solutions (echinacea and chlorhexidine on the oral microbial flora of patients hospitalized in the intensive care units. Materials and Methods: In this clinical trial, 70 patients aged between18 and 65 years undergoing tracheal intubation through the mouth in three hospitals in Arak, were selected using simple random sampling and were randomly divided into two groups: the intervention group and the control group. The oral health checklist was used to collect the data (before and after the intervention. The samples were obtained from the orally intubated patients and were then cultured in selective media. Afterwards, the aerobic microbial growth was investigated in all culture media. The data were analyzed using SPSS software. Results: The microbial flora in the echinacea group significantly decreased after the intervention (p < 0.0001 and it was also the case withmicrobial flora of the patients in the chlorhexidine group (p < 0.001. After 4 days, the oral microbial flora of the patients in the intervention group was lower than that of the patients in the control group (p < 0.001. Conclusions: The results showed that the echinacea solution was more effective in decreasing the oral microbial flora of patients in the intensive care unit. Given the benefits of the components of the herb Echinacea, it can be suggested as a viable alternative to chlorhexidine.

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

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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...

Collective animal navigation and migratory culture: from theoretical models to empirical evidence

Science.gov (United States)

Dell, Anthony I.

2018-01-01

Animals often travel in groups, and their navigational decisions can be influenced by social interactions. Both theory and empirical observations suggest that such collective navigation can result in individuals improving their ability to find their way and could be one of the key benefits of sociality for these species. Here, we provide an overview of the potential mechanisms underlying collective navigation, review the known, and supposed, empirical evidence for such behaviour and highlight interesting directions for future research. We further explore how both social and collective learning during group navigation could lead to the accumulation of knowledge at the population level, resulting in the emergence of migratory culture. This article is part of the theme issue ‘Collective movement ecology’. PMID:29581394

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

OpenAIRE

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

2014-01-01

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 chara...

Language model: Extension to solve inconsistency, incompleteness, and short query in cultural heritage collection

Science.gov (United States)

Tan, Kian Lam; Lim, Chen Kim

2017-10-01

With the explosive growth of online information such as email messages, news articles, and scientific literature, many institutions and museums are converting their cultural collections from physical data to digital format. However, this conversion resulted in the issues of inconsistency and incompleteness. Besides, the usage of inaccurate keywords also resulted in short query problem. Most of the time, the inconsistency and incompleteness are caused by the aggregation fault in annotating a document itself while the short query problem is caused by naive user who has prior knowledge and experience in cultural heritage domain. In this paper, we presented an approach to solve the problem of inconsistency, incompleteness and short query by incorporating the Term Similarity Matrix into the Language Model. Our approach is tested on the Cultural Heritage in CLEF (CHiC) collection which consists of short queries and documents. The results show that the proposed approach is effective and has improved the accuracy in retrieval time.

From Field to Laboratory: A New Database Approach for Linking Microbial Field Ecology with Laboratory Studies

Science.gov (United States)

Bebout, Leslie; Keller, R.; Miller, S.; Jahnke, L.; DeVincenzi, D. (Technical Monitor)

2002-01-01

The Ames Exobiology Culture Collection Database (AECC-DB) has been developed as a collaboration between microbial ecologists and information technology specialists. It allows for extensive web-based archiving of information regarding field samples to document microbial co-habitation of specific ecosystem micro-environments. Documentation and archiving continues as pure cultures are isolated, metabolic properties determined, and DNA extracted and sequenced. In this way metabolic properties and molecular sequences are clearly linked back to specific isolates and the location of those microbes in the ecosystem of origin. Use of this database system presents a significant advancement over traditional bookkeeping wherein there is generally little or no information regarding the environments from which microorganisms were isolated. Generally there is only a general ecosystem designation (i.e., hot-spring). However within each of these there are a myriad of microenvironments with very different properties and determining exactly where (which microenvironment) a given microbe comes from is critical in designing appropriate isolation media and interpreting physiological properties. We are currently using the database to aid in the isolation of a large number of cyanobacterial species and will present results by PI's and students demonstrating the utility of this new approach.

Microbial ecosystem constructed in water for successful organic hydroponics

OpenAIRE

Makoto Shinohara; Hiromi Ohmori; Yoichi Uehara

2008-01-01

Conventional hydroponics systems generally use only chemical fertilisers, not organic ones, since there are no microbial ecosystems present in such systems to mineralise organic compounds to inorganic nutrients. Addition of organic compounds to the hydroponic solution generally has phytotoxic effects and causes poor plant growth. We developed a novel hydroponic culture method using organic fertiliser. A microbial ecosystem was constructed in hydroponic solution by regulating the amounts of or...

Microbial diversity in the floral nectar of Linaria vulgaris along an urbanization gradient.

Science.gov (United States)

Bartlewicz, Jacek; Lievens, Bart; Honnay, Olivier; Jacquemyn, Hans

2016-03-30

Microbes are common inhabitants of floral nectar and are capable of influencing plant-pollinator interactions. All studies so far investigated microbial communities in floral nectar in plant populations that were located in natural environments, but nothing is known about these communities in nectar of plants inhabiting urban environments. However, at least some microbes are vectored into floral nectar by pollinators, and because urbanization can have a profound impact on pollinator communities and plant-pollinator interactions, it can be expected that it affects nectar microbes as well. To test this hypothesis, we related microbial diversity in floral nectar to the degree of urbanization in the late-flowering plant Linaria vulgaris. Floral nectar was collected from twenty populations along an urbanization gradient and culturable bacteria and yeasts were isolated and identified by partially sequencing the genes coding for small and large ribosome subunits, respectively. A total of seven yeast and 13 bacterial operational taxonomic units (OTUs) were found at 3 and 1% sequence dissimilarity cut-offs, respectively. In agreement with previous studies, Metschnikowia reukaufii and M. gruessi were the main yeast constituents of nectar yeast communities, whereas Acinetobacter nectaris and Rosenbergiella epipactidis were the most frequently found bacterial species. Microbial incidence was high and did not change along the investigated urbanization gradient. However, microbial communities showed a nested subset structure, indicating that species-poor communities were a subset of species-rich communities. The level of urbanization was putatively identified as an important driver of nestedness, suggesting that environmental changes related to urbanization may impact microbial communities in floral nectar of plants growing in urban environments.

Quantitative comparison of the in situ microbial communities in different biomes

Energy Technology Data Exchange (ETDEWEB)

White, D.C. [Tennessee Univ., Knoxville, TN (United States)]|[Oak Ridge National Lab., TN (United States); Ringelberg, D.B.; Palmer, R.J. [Tennessee Univ., Knoxville, TN (United States). Center for Environmental Biotechnology

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 repeatedly 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 chromatography/

Microbial Contamination on Used Surgical Masks among Hospital Personnel and Microbial Air Quality in their Working Wards: A Hospital in Bangkok

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Pipat Luksamijarulkul

2014-09-01

Full Text Available Objective: To assess the relationship of bacterial and fungal contamination on used surgical masks worn by the hospital personnel and microbial air quality in their working wards. Methods: This is a cross-sectional study of 230 used surgical masks collected from 214 hospital personnel, and 215 indoor air samples collected from their working wards to culture for bacterial and fungal counts. This study was carried out at the hospital in Bangkok. Group or genus of isolated bacteria and fungi were preliminarily identified by Gram’s stain and lacto-phenol cotton blue. Data were analyzed using paired t-test and Pearson’s correlation coefficient at the significant level of p<0.050. Results: Means and standard deviation of bacterial and fungal contamination on inside area of the used masks were 47 ± 56 and 15 ± 9 cfu/ml/piece, and on outside area were 166 ± 199 and 34 ± 18 cfu/ml/piece, respectively, p<0.001. The bacterial and fungal contamination on used masks from hospital personnel working in the male and female medical wards and out-patient department, as well as the bacterial and fungal counts of the indoor air sample collected from the same area were relatively higher than the other wards. The predominant isolated bacteria and fungi contaminated on inside and outside areas of the used masks and air samples were similar (Staphylococcus spp. and Aspergillus spp.; respectively. For its relationship, results found that bacterial and fungal counts in air samples showed significantly positive correlation with the bacterial contamination load on outside area of the used masks, r=0.16, p=0.018 and r=0.21, p=0.003, respectively. Conclusion: High bacterial contamination on outside area of the used masks was demonstrated, and it showed a significant correlation with microbial air quality of working wards.

Starter cultures for cereal based foods.

Science.gov (United States)

Brandt, Markus J

2014-02-01

Fermented cereals play a significant role in human nutrition in all parts of the world where cereals grow. These fermentations are started spontaneously or there have been traditional techniques developed in order to keep starter cultures for these processes alive. With the growing impact of industrial microbiology during 20th century this traditional starter culture propagation was replaced often, especially in the dairy industry, by the use of pure, frozen or freeze-dried cultures grown on microbial media. In contrast to the production of ethanol from cereals, in sourdough a pasteurization step before inoculation is avoided due to gelatinization of starch and inactivation of endogenous enzymes. Therefore cultures must be competitive to the relatively high microbial load of the cereal raw materials and well adapted to the specific ecology determined by the kind of cereal and the process conditions. Less adapted cultures could be used, but then the process of back-slopping of cultures is limited. Although cereal fermentations take the biggest volume among fermented foods, only for sourdoughs commercial cultures are available. Copyright © 2013 Elsevier Ltd. All rights reserved.

Teachers' Collective Efficacy, Job Satisfaction, and Job Stress in Cross-Cultural Context

Science.gov (United States)

Klassen, Robert M.; Usher, Ellen L.; Bong, Mimi

2010-01-01

This study examines how teachers' collective efficacy (TCE), job stress, and the cultural dimension of collectivism are associated with job satisfaction for 500 teachers from Canada, Korea (South Korea or Republic of Korea), and the United States. Multigroup path analysis revealed that TCE predicted job satisfaction across settings. Job stress was…

The Epidemiological And Susceptibility Study Of Inpatient Blood Cultures In Amir Alam Hospital 1998 - 2000

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Karimi Shahidi M

2002-07-01

Full Text Available Sepsis is one of the most critical medical emergency situations. Treatment with anti microbial drugs should be initiated as soon as samples of blood and other relevant sites have been cultured. Available information about patterns of anti microbial Susceptibility among bacterial isolates from the community, the hospital, and the patient should be taken in to account. It is important, pending culture results, to initiate empirical anti microbial therapy."nMaterials and methods: In a descriptive study during 3 years (1377-1379, microbial and anti microbial susceptibility patterns evaluated in Amir alam clinical laboratory on 2000 specimen of blood culture received from 765 hospitalized patients at Amir Alam hospital wards."nResults: 113 specimens from 77 patient (10 percent were positive for microbial growth. Enterobacter, S. aureus, S.epidermidis, Pneumococci, Ecoli, and Pseudomonas were the most common isolated etiologic agents(80 percent . The most common organism was Entenobacter in 1377, S.aureus in 1378 and pseudomonas in 1379 There were significant change in patlern of organisms, increase resistance to some important available antibiotics and change in antibiotic susceptibility pattern during three years (disc diffusion method."nConclusions: According to Results of this study due to change in pattern of organism and their antibiotic susceptibility, dynamic microbiological study provide important data for Ordering empirical and culture oriented treatment of patients with bacteremia, Sepsis, anti microbial Chemotherapy, anti microbial susceptibility empirical anti microbial therapy, microbial pattern.

Effects of concentrate replacement by feed blocks on ruminal fermentation and microbial growth in goats and single-flow continuous-culture fermenters.

Science.gov (United States)

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 fermenters, the diet affected pH (Por= 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 (Pfermenter contents and effluent were similar (P=0.05). Differences (Pfermentation 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 efficiency. Differences between the results obtained in vivo and in vitro indicate a need to identify conditions in fermenters that allow better simulation of fermentation, microbial growth, and bacterial pellet composition in vivo. Reduced feeding cost could be achieved with the inclusion of FB in the diets of unproductive goats without altering rumen fermentation.

Metabarcoding of the kombucha microbial community grown in different microenvironments.

Science.gov (United States)

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.

Pathogenic bacteria and heavy metals toxicity assessments in evaluating unpasteurized raw milk quality through biochemical tests collected from dairy cows

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Hamid Iqbal

2016-11-01

Full Text Available Objective: To evaluate the hygienic quality by determining the presence of predominant pathogenic microbial contaminants (contagious or environmental and indiscriminate heavy metals contained in unpasteurized milk samples collected from cattle specie of cow. Methods: Raw milk samples were collected in October, 2014 from different regions of District Kohat, Khyber Pakhtunkhwa, Pakistan and cultured on the selective media plates according to the manufacturer instructions to observe pathogenic microbial flora and confirm it with relevant biochemical tests to specify bacterial specie. Results: Milk samples analyzed on MacConkey and nutrient agar media were found contaminated mostly with coliform, Staphylococcus aureus, Enterobacter aerogenes and Proteus vulgaris. Similarly, result of the heavy metals analysis performed using atomic absorption spectrophotometer flame photometry showed that raw milk contains heavy metals residues of lead and cadmium contents at higher levels while copper, zinc and chromium were observed lower than permissible limits whereas manganese within specified recommended values. Conclusions: Microbial contamination of milk and toxic metals is mainly accredited to the scrupulous unhygienic measures during processing of milk exhibiting a wide array of hazardous impacts on human health.

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

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Igor Magalhães da Veiga Moreira

2017-05-01

Full Text Available 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.

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

Science.gov (United States)

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.

Relationships among Contrasting Measurements of Microbial Dynamics in Pasture and Organic Farm Soils

International Nuclear Information System (INIS)

Edenborn, S.L; Sexstone, A.J; Sutanto, Y; Chapman, J.A

2011-01-01

Soil bacteria exhibit short-term variations in community structure, providing an indication of anthropogenic disturbances. In this study, microbial biomass carbon (MBC), potentially mineralizable nitrogen (PMN), community level physiological profiling (CLPP), and culture-dependent DGGE (CD DGGE) fingerprinting of the 16 S r RNA gene were used to compare microbial communities in organic farm and pasture soils subjected to differing agronomic treatments. Correlation analyses revealed significant relationships between MBC, PMN, and data derived from microbial community analyses. All measures separated soil types but varied in their ability to distinguish among treatments within a soil type. Overall, MBC, PMN, and CLPP were most responsive to compost and manure amendments, while CD DGGE resolved differences in legume cropping and inorganic fertilization. The results support the hypothesis that culturable soil bacteria are a responsive fraction of the total microbial community, sensitive to agronomic perturbations and amenable to further studies aimed at linking community structure with soil functions.

A Cultural Psychological Analysis of Collective Memory as Mediated Action: Constructions of Indian History

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Sahana Mukherjee

2018-01-01

Full Text Available The present research applies a cultural psychological perspective on collective memory as mediated action to examine how constructions of a national past serve as tools that both reflect and shape national identity concerns. We employ a situation-sampling method to investigate collective memory in a series of studies concerning intergroup relations in the Indian context. In Study 1, participants (N = 55 generated three historical events that they considered important/relevant for Indian history. In Study 2, participants (N = 95 rated the importance and relevance of these events in a within-participant design. Illuminating the psychological constitution of cultural reality, frequency of recall (Study 1 and ratings of importance/relevance (Study 2 were greater for nation-glorifying events celebrating ingroup triumph than for typically silenced, critical events acknowledging ingroup wrongdoing. Moreover, these patterns were stronger among participants who scored higher in national identification. In Studies 3 (N = 65 and 4 (N = 160, we exposed participants to different categories of events in a between-participants design. Illuminating the cultural constitution of psychological experience, participants exposed to typically silenced, critical events reported lower national identification and greater perception of injustice against marginalized groups than did participants exposed to nation-glorifying events. Together, results illuminate a conception of collective memory as mediated action. Producers invest memory products with an identity-interested charge that directs subsequent intergroup relations toward identity-consistent ends.

Constraint-based modeling in microbial food biotechnology

Science.gov (United States)

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

Bacterial community profiling of milk samples as a means to understand culture-negative bovine clinical mastitis.

Science.gov (United States)

Kuehn, Joanna S; Gorden, Patrick J; Munro, Daniel; Rong, Ruichen; Dong, Qunfeng; Plummer, Paul J; Wang, Chong; Phillips, Gregory J

2013-01-01

Inflammation and infection of bovine mammary glands, commonly known as mastitis, imposes significant losses each year in the dairy industry worldwide. While several different bacterial species have been identified as causative agents of mastitis, many clinical mastitis cases remain culture negative, even after enrichment for bacterial growth. To understand the basis for this increasingly common phenomenon, the composition of bacterial communities from milk samples was analyzed using culture independent pyrosequencing of amplicons of 16S ribosomal RNA genes (16S rDNA). Comparisons were made of the microbial community composition of culture negative milk samples from mastitic quarters with that of non-mastitic quarters from the same animals. Genomic DNA from culture-negative clinical and healthy quarter sample pairs was isolated, and amplicon libraries were prepared using indexed primers specific to the V1-V2 region of bacterial 16S rRNA genes and sequenced using the Roche 454 GS FLX with titanium chemistry. Evaluation of the taxonomic composition of these samples revealed significant differences in the microbiota in milk from mastitic and healthy quarters. Statistical analysis identified seven bacterial genera that may be mainly responsible for the observed microbial community differences between mastitic and healthy quarters. Collectively, these results provide evidence that cases of culture negative mastitis can be associated with bacterial species that may be present below culture detection thresholds used here. The application of culture-independent bacterial community profiling represents a powerful approach to understand long-standing questions in animal health and disease.

The Effect of Therapeutic Clowning on Handwashing Technique and Microbial Colonization in Preschool Children.

Science.gov (United States)

Arıkan, Duygu; Gürarslan Baş, Nazan; Kurudirek, Fatma; Baştopcu, Ayşe; Uslu, Hakan

2018-05-15

This study aimed to determine the effect of therapeutic clowning on handwashing technique and microbial colonization in preschool children. This randomized controlled trial was conducted using pre-test and post-test experimental and control groups. The study was conducted between March and June 2016 in two kindergartens in eastern Turkey. The study was completed with a total of 195 students, including 90 students in the experimental group and 105 students in the control group. A questionnaire was used for data collection. This questionnaire included sections about the subjects' descriptive characteristics and the results of the bacterial cultures of their hand swabs. For the collection of these swabs, the subjects were informed in advance, and samples were collected at predetermined times. The swabs were analyzed to determine the bacterial colonization of the subjects' hands. Clowns and video activities were used as intervention tools in the study. In the post-test, the microbial growth was ≤10 3 in 68.9% and >10 3 in 31.1% of the subjects in the experimental group. In contrast, the growth was ≤10 3 in 34.3% and >10 3 in 65.7% of the control group subjects. The difference in the post-test microbial growths of the two groups was statistically significant (p < .000). The hygienic handwashing technique taught in the therapeutic clowning and videos reduced the bacterial colonization on the preschool children's hands by 50%. Moreover, this method was effective in reducing the growth rate of coliform bacteria that indicate undesirable, poor hygiene of the hands. Considering these results, we recommend that pediatric healthcare professionals use entertaining methods such as those involving clowns to teach and guide children regarding hygienic handwashing techniques. © 2018 Sigma Theta Tau International.

Microbial Stereoselective One-Step Conversion of Diols to Chiral Lactones in Yeast Cultures

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Filip Boratyński

2015-12-01

Full Text Available It has been shown that whole cells of different strains of yeast catalyze stereoselective oxidation of meso diols to the corresponding chiral lactones. Among screening-scale experiments, Candida pelliculosa ZP22 was selected as the most effective biocatalyst for the oxidation of monocyclic diols 3a–b with respect to the ratio of high conversion to stereoselectivity. This strain was used in the preparative oxidation, affording enantiomerically-enriched isomers of lactones: (+-(3aR,7aS-cis-hexahydro-1(3H -isobenzofuranone (2a and (+-(3aS,4,7,7aR-cis-tetrahydro-1(3H-isobenzofuranone (2b. Scaling up the culture growth, as well as biotransformation conditions has been successfully accomplished. Among more bulky substrates, bicyclic diol 3d was totally converted into enantiomerically-pure exo-bridged (+-(3aR,4S,7R,7aS-cis-tetrahydro-4,7-methanoisobenzofuran -1(3H-one (2d by Yarrovia lipolytica AR71. Microbial oxidation of diol 3f by Candida sake AM908 and Rhodotorula rubra AM4 afforded optically-pure cis-3-butylhexahydro-1(3H -isobenzofuranone (2f, however with low conversion.

Microbial effects on colloidal agglomeration

International Nuclear Information System (INIS)

Hersman, L.

1995-11-01

Colloidal particles are known to enhance the transport of radioactive metals through soil and rock systems. This study was performed to determine if a soil microorganism, isolated from the surface samples collected at Yucca Mountain, NV, could affect the colloidal properties of day particles. The agglomeration of a Wyoming bentonite clay in a sterile uninoculated microbial growth medium was compared to the agglomeration in the medium inoculated with a Pseudomonas sp. In a second experiment, microorganisms were cultured in the succinate medium for 50 h and removed by centrifugation. The agglomeration of the clay in this spent was compared to sterile uninoculated medium. In both experiments, the agglomeration of the clay was greater than that of the sterile, uninoculated control. Based on these results, which indicate that this microorganism enhanced the agglomeration of the bentonite clay, it is possible to say that in the presence of microorganisms colloidal movement through a rock matrix could be reduced because of an overall increase in the size of colloidal particle agglomerates. 32 refs

The impact of culture collections on molecular identification, taxonomy, and solving real problems

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Among the fungi, Fusarium has stood out as a major focus for culture collection resource development over the last century. This has facilitated unprecedented molecular taxonomic advancements, which in turn has led to problem solving in plant pathology, mycotoxicology, medical mycology, and basic re...

Microbial hydrogen production from sewage sludge bioaugmented with a constructed microbial consortium

Energy Technology Data Exchange (ETDEWEB)

Kotay, Shireen Meher; Das, Debabrata [Department of Biotechnology, Indian Institute of Technology, Kharagpur 721302 (India)

2010-10-15

A constructed microbial consortium was formulated from three facultative H{sub 2}-producing anaerobic bacteria, Enterobacter cloacae IIT-BT 08, Citrobacter freundii IIT-BT L139 and Bacillus coagulans IIT-BT S1. This consortium was tested as the seed culture for H{sub 2} production. In the initial studies with defined medium (MYG), E. cloacae produced more H{sub 2} than the other two strains and it also was found to be the dominant member when consortium was used. On the other hand, B. coagulans as a pure culture gave better H{sub 2} yield (37.16 ml H{sub 2}/g COD{sub consumed}) than the other two strains using sewage sludge as substrate. The pretreatment of sludge included sterilization (15% v/v), dilution and supplementation with 0.5% w/v glucose, which was found to be essential to screen out the H{sub 2} consuming bacteria and ameliorate the H{sub 2} production. Considering (1:1:1) defined consortium as inoculum, COD reduction was higher and yield of H{sub 2} was recorded to be 41.23 ml H{sub 2}/g COD{sub reduced}. Microbial profiling of the spent sludge showed that B. coagulans was the dominant member in the constructed consortium contributing towards H{sub 2} production. Increase in H{sub 2} yield indicated that in consortium, the substrate utilization was significantly higher. The H{sub 2} yield from pretreated sludge (35.54 ml H{sub 2}/g sludge) was comparatively higher than that reported in literature (8.1-16.9 ml H{sub 2}/g sludge). Employing formulated microbial consortium for biohydrogen production is a successful attempt to augment the H{sub 2} yield from sewage sludge. (author)

The U.S. Culture Collection Network Responding to the Requirements of the Nagoya Protocol on Access and Benefit Sharing

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Kevin McCluskey

2017-08-01

Full Text Available The U.S. Culture Collection Network held a meeting to share information about how culture collections are responding to the requirements of the recently enacted Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization to the Convention on Biological Diversity (CBD. The meeting included representatives of many culture collections and other biological collections, the U.S. Department of State, U.S. Department of Agriculture, Secretariat of the CBD, interested scientific societies, and collection groups, including Scientific Collections International and the Global Genome Biodiversity Network. The participants learned about the policies of the United States and other countries regarding access to genetic resources, the definition of genetic resources, and the status of historical materials and genetic sequence information. Key topics included what constitutes access and how the CBD Access and Benefit-Sharing Clearing-House can help guide researchers through the process of obtaining Prior Informed Consent on Mutually Agreed Terms. U.S. scientists and their international collaborators are required to follow the regulations of other countries when working with microbes originally isolated outside the United States, and the local regulations required by the Nagoya Protocol vary by the country of origin of the genetic resource. Managers of diverse living collections in the United States described their holdings and their efforts to provide access to genetic resources. This meeting laid the foundation for cooperation in establishing a set of standard operating procedures for U.S. and international culture collections in response to the Nagoya Protocol.

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

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Elizabeth A Dinsdale

Full Text Available 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

Microbial Ecology of Four Coral Atolls in the Northern Line Islands

Science.gov (United States)

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

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

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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

Science.gov (United States)

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

Effects of refrigerating preinoculated Vitek cards on microbial physiology and antibiotic susceptibility

Science.gov (United States)

Skweres, Joyce A.; Bassinger, Virginia J.; Mishra, S. K.; Pierson, Duane L.

1992-01-01

Reference cultures of 16 microorganisms obtained from the American Type Culture Collection and four clinical isolates were used in standardized solutions to inoculate 60 cards for each test strain. A set of three ID and three susceptibility cards was processed in the Vitek AutoMicrobic System (AMS) immediately after inoculation. The remaining cards were refrigerated at 4 C, and sets of six cards were removed and processed periodically for up to 17 days. The preinoculated AMS cards were evaluated for microorganism identification, percent probability of correct identification, length of time required for final result, individual substrate reactions, and antibiotic minimal inhibitory/concentration (MIC) values. Results indicate that 11 of the 20 microbes tested withstood refrigerated storage up to 17 days without detectable changes in delineating characteristics. MIC results appear variable, but certain antibiotics proved to be more stable than others. The results of these exploratory studies will be used to plan a microgravity experiment designed to study the effect of microgravity on microbial physiology and antibiotic sensitivity.

International Depository Authority and its Role in Microorganism's Deposition.

Science.gov (United States)

Parashar, Abhishek

2017-08-01

After the World Trade Organization's agreement on Trade Related Aspect of Intellectual Property Right, patents have come into major play. Patenting of work related to live organisms that have medical, agricultural and other uses is always a tedious, complicated and controversial job. In view of this an agreement called as Budapest Treaty was passed in 1977 for deposition of microorganisms in culture collection centers for patent purpose. To make a culture collection center an IDA the culture center has to follow rules and regulations made in Budapest Treaty. Today several culture collection centers are working as International Depository Authority (IDA) in India and abroad that are storing microorganisms for patent purpose. India has two IDA units; one is Microbial Culture Collection in National Centre for Cell Science Pune, India, and second one is Microbial Type Culture Collection and Gene Bank at Institute of Microbial Technology Chandigarh, India. IDA units are important for valuable sample depositions, supply of cultures, characterization of samples and conservation of biological materials.

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

Science.gov (United States)

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.

Effect of electrokinetic remediation on indigenous microbial activity and community within diesel contaminated soil.

Science.gov (United States)

Kim, Seong-Hye; Han, Hyo-Yeol; Lee, You-Jin; Kim, Chul Woong; Yang, Ji-Won

2010-07-15

Electrokinetic remediation has been successfully used to remove organic contaminants and heavy metals within soil. The electrokinetic process changes basic soil properties, but little is known about the impact of this remediation technology on indigenous soil microbial activities. This study reports on the effects of electrokinetic remediation on indigenous microbial activity and community within diesel contaminated soil. The main removal mechanism of diesel was electroosmosis and most of the bacteria were transported by electroosmosis. After 25 days of electrokinetic remediation (0.63 mA cm(-2)), soil pH developed from pH 3.5 near the anode to pH 10.8 near the cathode. The soil pH change by electrokinetics reduced microbial cell number and microbial diversity. Especially the number of culturable bacteria decreased significantly and only Bacillus and strains in Bacillales were found as culturable bacteria. The use of EDTA as an electrolyte seemed to have detrimental effects on the soil microbial activity, particularly in the soil near the cathode. On the other hand, the soil dehydrogenase activity was enhanced close to the anode and the analysis of microbial community structure showed the increase of several microbial populations after electrokinetics. It is thought that the main causes of changes in microbial activities were soil pH and direct electric current. The results described here suggest that the application of electrokinetics can be a promising soil remediation technology if soil parameters, electric current, and electrolyte are suitably controlled based on the understanding of interaction between electrokinetics, contaminants, and indigenous microbial community. Copyright 2010 Elsevier B.V. All rights reserved.

Microbial pattern of pressure ulcer in pediatric patients

Science.gov (United States)

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%).

Differential Microbial Diversity in Drosophila melanogaster: Are Fruit Flies Potential Vectors of Opportunistic Pathogens?

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Luis A. Ramírez-Camejo

2017-01-01

Full Text Available Drosophila melanogaster has become a model system to study interactions between innate immunity and microbial pathogens, yet many aspects regarding its microbial community and interactions with pathogens remain unclear. In this study wild D. melanogaster were collected from tropical fruits in Puerto Rico to test how the microbiota is distributed and to compare the culturable diversity of fungi and bacteria. Additionally, we investigated whether flies are potential vectors of human and plant pathogens. Eighteen species of fungi and twelve species of bacteria were isolated from wild flies. The most abundant microorganisms identified were the yeast Candida inconspicua and the bacterium Klebsiella sp. The yeast Issatchenkia hanoiensis was significantly more common internally than externally in flies. Species richness was higher in fungi than in bacteria, but diversity was lower in fungi than in bacteria. The microbial composition of flies was similar internally and externally. We identified a variety of opportunistic human and plant pathogens in flies such as Alcaligenes faecalis, Aspergillus flavus, A. fumigatus, A. niger, Fusarium equiseti/oxysporum, Geotrichum candidum, Klebsiella oxytoca, Microbacterium oxydans, and Stenotrophomonas maltophilia. Despite its utility as a model system, D. melanogaster can be a vector of microorganisms that represent a potential risk to plant and public health.

Microbial Contamination of Pastry Cream: Evidence from Iran

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Mohamadreza Pajohi-alamoti

2016-07-01

Full Text Available Background & Aims of the Study: Given the importance of microbial contamination in creating food-borne diseases, this study was conducted to assess level of microbial contamination of pastry creams in Hamedan, Iran. Materials and Methods: Totally, 80 samples were randomly collected from the confectioneries and analyzed for microbial contamination according to Iranian national standard microbial tests. Results: Data indicated that 49 (61.2% samples were contaminated, mostly comprised of Coliforms (92.5%. Moreover, the infection was seen to be higher in jelly roll compared to puff pastry. Yeast contamination was about 82.5 percent, which could accelerate the decay of such products. However, yeast contamination of puff pastries was higher than jelly roll. The microbial contamination with Staphylococcus aureus, total viable count and molds were 57.5%, 35% and 37.5%; respectively. Conclusion: Nevertheless, Salmonella, Escherichia coli and Listeria monocytogenes were not found in any of the samples. Abundance of microbial contamination in the puff pastry samples might put consumer’s health at risk.

Characterization of microbial communities in pest colonized books by molecular biology tools

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Franco Palla

2011-08-01

Full Text Available This work presents the identification of bacteria and fungi colonies in insect infesting books, by cultural-independent methodologies based on molecular biology techniques. Microbial genomic DNA extraction, in vitro amplification of specific target sequences by polymerase chain reactions (PCR, sequencing and sequence analysis were performed. These procedures minimized the samples amount, optimized the diagnostic studies on bacteria and fungi colonization and allowed the identification of many species also in complex microbial consortia. The molecular techniques for sure accomplish and integrate the microbiological standard methods (in vitro culture and morphological analyses (OM, SEM, CLSM, in order to understand the role of microorganisms in bio-deterioration of cultural assets. This monitoring is also indispensable to shed light on the risk for visitors and/or professionals to contract potential illnesses within indoor environments.

Culture-dependent and culture-independent characterization of microbial assemblages associated with high-temperature petroleum reservoirs.

Science.gov (United States)

Orphan, V J; Taylor, L T; Hafenbradl, D; Delong, E F

2000-02-01

Recent investigations of oil reservoirs in a variety of locales have indicated that these habitats may harbor active thermophilic prokaryotic assemblages. In this study, we used both molecular and culture-based methods to characterize prokaryotic consortia associated with high-temperature, sulfur-rich oil reservoirs in California. Enrichment cultures designed for anaerobic thermophiles, both autotrophic and heterotrophic, were successful at temperatures ranging from 60 to 90 degrees C. Heterotrophic enrichments from all sites yielded sheathed rods (Thermotogales), pleomorphic rods resembling Thermoanaerobacter, and Thermococcus-like isolates. The predominant autotrophic microorganisms recovered from inorganic enrichments using H(2), acetate, and CO(2) as energy and carbon sources were methanogens, including isolates closely related to Methanobacterium, Methanococcus, and Methanoculleus species. Two 16S rRNA gene (rDNA) libraries were generated from total community DNA collected from production wellheads, using either archaeal or universal oligonucleotide primer sets. Sequence analysis of the universal library indicated that a large percentage of clones were highly similar to known bacterial and archaeal isolates recovered from similar habitats. Represented genera in rDNA clone libraries included Thermoanaerobacter, Thermococcus, Desulfothiovibrio, Aminobacterium, Acidaminococcus, Pseudomonas, Halomonas, Acinetobacter, Sphingomonas, Methylobacterium, and Desulfomicrobium. The archaeal library was dominated by methanogen-like rDNAs, with a lower percentage of clones belonging to the Thermococcales. Our results strongly support the hypothesis that sulfur-utilizing and methane-producing thermophilic microorganisms have a widespread distribution in oil reservoirs and the potential to actively participate in the biogeochemical transformation of carbon, hydrogen, and sulfur in situ.

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

Science.gov (United States)

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 control of the dark end of the biological pump

NARCIS (Netherlands)

Herndl, G.J.; Reinthaler, T.

2013-01-01

A fraction of the carbon captured by phytoplankton in the sunlit surface ocean sinks to depth as dead organic matter and faecal material. The microbial breakdown of this material in the subsurface ocean generates carbon dioxide. Collectively, this microbially mediated flux of carbon from the

Microbial characterization of toluene-degrading denitrifying consortia obtained from terrestrial and marine ecosystems.

Science.gov (United States)

An, Y-J; Joo, Y-H; Hong, I-Y; Ryu, H-W; Cho, K-S

2004-10-01

The degradation characteristics of toluene coupled to nitrate reduction were investigated in enrichment culture and the microbial communities of toluene-degrading denitrifying consortia were characterized by denaturing gradient gel electrophoresis (DGGE) technique. Anaerobic nitrate-reducing bacteria were enriched from oil-contaminated soil samples collected from terrestrial (rice field) and marine (tidal flat) ecosystems. Enriched consortia degraded toluene in the presence of nitrate as a terminal electron acceptor. The degradation rate of toluene was affected by the initial substrate concentration and co-existence of other hydrocarbons. The types of toluene-degrading denitrifying consortia depended on the type of ecosystem. The clone RS-7 obtained from the enriched consortium of the rice field was most closely related to a toluene-degrading and denitrifying bacterium, Azoarcus denitrificians (A. tolulyticus sp. nov.). The clone TS-11 detected in the tidal flat enriched consortium was affiliated to Thauera sp. strain S2 (T. aminoaromatica sp. nov.) that was able to degrade toluene under denitrifying conditions. This indicates that environmental factors greatly influence microbial communities obtained from terrestrial (rice field) and marine (tidal flat) ecosystems.

Microbial and heavy metal contamination of pineapple products ...

African Journals Online (AJOL)

SAM

3Department of Social Sciences, University of Rwanda, P.O. Box 117 Butare, ... pineapple processing Enterprises (SMEs) over a storage duration of 12 months. .... The results were measured against ... analyzed for microbial contamination using International Organization ... All culture media used were manufactured by.

Next-generation approaches to the microbial ecology of food fermentations

Directory of Open Access Journals (Sweden)

Nicholas A. Bokulich1,2,3 & David A. Mills1,2,3*

2012-07-01

Full Text Available Food fermentations have enhanced human health since the dawnof time and remain a prevalent means of food processing andpreservation. Due to their cultural and nutritional importance,many of these foods have been studied in detail using moleculartools, leading to enhancements in quality and safety. Furthermore,recent advances in high-throughput sequencing technologyare revolutionizing the study of food microbial ecology,deepening insight into complex fermentation systems. Thisreview provides insight into novel applications of selectmolecular techniques, particularly next-generation sequencingtechnology, for analysis of microbial communities in fermentedfoods. We present a guideline for integrated molecular analysis offood microbial ecology and a starting point for implementingnext-generation analysis of food systems.

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

Science.gov (United States)

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.

Culture collection of fungi (CCF) in Prague – original isolates accessed during 2003-05

Czech Academy of Sciences Publication Activity Database

Kubátová, A.; Kolařík, Miroslav

2006-01-01

Roč. 18, č. 5 (2006), s. 1-15 ISSN 0862-5158 R&D Projects: GA ČR GA522/02/1206 Institutional research plan: CEZ:AV0Z50200510 Keywords : ccf * culture collection * microscopic fungi Subject RIV: EE - Microbiology, Virology

Central role of the cell in microbial ecology.

Science.gov (United States)

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.

The influence of fish culture in floating net cages on microbial indicators of water quality

Directory of Open Access Journals (Sweden)

K. Gorlach-Lira

Full Text Available This work was carried out to analyse the microbiological parameters of the water quality of a reservoir used for the irrigation and culture of tilapia (Oreochromis niloticus in floating net cages. The physico-chemical parameters, counts of mesophilic total aerobic bacteria, total and thermotolerant coliforms and fecal streptococci, and the presence of Escherichia coli in samples of water collected in three sites of the reservoir (pre-culture site, culture site, post-culture site were analysed. The levels of ammonia (0.047-0.059 mg/L, nitrite (0.001-0.021 mg/L and total phosphorus (0.050-0.355 mg/L in the water did not show significant differences (p > 0.05 between sampling sites. The levels of total bacteria in the water varied between 1.3 x 104 and 67.3 x 104 CFU/100 mL. The MPN values of thermotolerant coliforms (< 930 MPN/100 mL were within values recommended for water used for fish culture and/or irrigation. The presence of E. coli and fecal streptococci were verified in 48% and 56% of analysed samples, respectively. The site with floating net cages showed more samples contaminated with E. coli and fecal streptococci than other sampling points.

Electricity production and microbial characterization of thermophilic microbial fuel cells.

Science.gov (United States)

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.

Optimization of culture conditions and electricity generation using Geobacter sulfurreducens in a dual-chambered microbial fuel-cell

Energy Technology Data Exchange (ETDEWEB)

Kim, Mi-Sun; Lee, Yu-jin [Bioenergy Research Center, Korea Institute of Energy Research, Daejeon 305-343 (Korea, Republic of)

2010-12-15

The promise of generating electricity from the oxidation of organic substances using metal-reducing bacteria is drawing attention as an alternate form of bio-technology with positive environmental implications. In this study, we examined various experimental factors to obtain the maximum power output in a dual-chamber mediator-less microbial fuel-cell (MFC) using Geobacter sulfurreducens and acetate as an electron donor in a semi-continuous mode. The G. sulfurreducens culture conditions were optimized in a nutrient buffer containing 20 mM of acetate and 50 mM of fumarate at pH 6.8 and 30 C. For use in the MFC system, electrodes were made with carbon paper (area: 11.5 cm{sup 2}) and spaced 1.5 cm apart. Once the MFC was inoculated with the pre-cultured G. sulfurreducens in the anode chamber and while air was continuously sparged to the cathode chamber, the cells produced electricity stably over 60 days with the regular addition of 20 mM acetate, generating the maximum power density of 7 mW/m{sup 2} with a 5000 and ohm; load. The current output was significantly increased, by 1.6 times after 20 days of incubation under the same experimental conditions, when the carbon-paper anode was coated with carbon nanotubes. (author)

Microbial activity of trench leachates from shallow-land, low-level radioactive waste disposal sites

International Nuclear Information System (INIS)

Francis, A.J.; Dobbs, S.; Nine, B.J.

1980-01-01

Trench leachate samples collected anoxically from shallow-land, low-level radioactive waste disposal sites were analyzed for total aerobic and anaerobic populations, sulfate reducers, denitrifiers, and methanogens. Among the several aerobic and anaerobic bacteria isolated, only Bacillus sp., Pseudomonas sp., Citrobacter sp., and Clostridium sp. were identified. Mixed bacterial cultures isolated from the trench leachates were able to grow anaerobically in trench leachates, which indicates that the radionuclides and organic chemicals present were not toxic to these bacteria. Changes in concentrations of several of the organic constituents of the waste leachate samples were observed due to anaerobic microbial activity. Growth of a mixed culture of trench-water bacteria in media containing a mixture of radionuclides, 60 Co, 85 Sr, and 134 137 Cs, was not affected at total activity concentrations of 2.6 x 10 2 and 2.7 x 10 3 pCi/ml

Microbial diversity in firework chemical exposed soil and water samples collected in Virudhunagar district, Tamil Nadu, India.

Science.gov (United States)

Dhasarathan, P; Theriappan, P; Ashokraja, C

2010-03-01

Microbial diversity of soil and water samples collected from pyrochemicals exposed areas of Virdhunagar district (Tamil Nadu, India) was studied. Soil and water samples from cultivable area, waste land and city area of the same region were also studied for a comparative acount. There is a remarkable reduction in total heterotrophic bacterial population (THB) in pyrochemicals exposed soil and water samples (42 × 10(4) CFU/g and 5.6 × 10(4) CFU/ml respectively), compared to the THB of cultivable area soil and water samples (98 × 10(7) CFU/g and 38.6 × 10(7) CFU/ml). The generic composition the THB of the pyrochemicals exposed samples too exhibited considerable change compared to other samples. Pseudomonas sp. was the predominant one (41.6%) followed by Achromobacter sp. (25%) in pyrochemical exposed soil and Pseudomonas sp. was the predominant one (25%) in pyrochemical exposed water samples followed by Bacillus sp. (25%) and Micrococcus sp. (16.6%). It was observed that Cornybacterium sp. and Micrococcus sp. were absent completely in pyrochemical exposed soil and Achromobacter sp. was missing in the pyrochemical exposed water samples, which were present in the other samples. The outcome of this study clearly demonstrates that pollutants such as chemicals used in pyrotechniques affect the microbial biodiversity and suitable measures have to be taken to control the pollution level and to save biodiversity.

Enhanced Tolerance to Cadmium in Bacterial-Fungal Co-Cultures as a Strategy for Metal Biorecovery from e-Waste

Directory of Open Access Journals (Sweden)

Geremia Losa

2018-03-01

Full Text Available We investigated a microbe-based approach to be used for the biorecovery of valuable metals from e-waste. E-waste is a heterogeneous matrix at the microbial scale. Therefore, this study aims at taking advantage of bacterial-fungal (BF interactions in order to mobilize and immobilize a selected metal present in e-waste. We used cadmium (Cd and a selection of Cd-tolerant microorganisms from our culture collection or isolated from a naturally cadmium-contaminated soil. Several experiments were designed in order to use the synergistic bioremediation capabilities of BF couples to mobilize and immobilize Cd from a culture medium. Initial results showed that the selected synergistic BF couples are more tolerant to Cd concentrations than the organisms alone. However, setting the conditions leading to effective immobilization of this toxic metal still need further work. Using microbial consortia rather than single species represents an innovative alternative to traditional bioremediation approaches for the development of new biotechnological approaches in urban mining.

Microbial analysis of the buffer/container experiment at AECL's Underground Research Laboratory

International Nuclear Information System (INIS)

Stroes-Gascoyne, S.; Hamon, C.J.; Haveman, S.A.; Delaney, T.L.

1996-05-01

The Buffer/Container experiment was carried out for 2.5 years to examine the in-situ performance of compacted buffer material in a single emplacement borehole under vault-relevant conditions. During decommissioning of this experiment, numerous samples were taken for microbial analysis to determine if the naturally present microbial population in buffer material survived to conditions and to determine which groups of microorganisms would be dominant in such a simulated vault environment. Microbial analyses were initiated within 24 hour of sampling for all types of samples taken. The culture results showed an almost universal disappearance of viable microorganisms in the samples taken from near the heater surface. The microbial activity measurements confirmed the lack of viable organisms with very weak or no activity measured in most of these samples. Generally, aerobic heterotrophic culture conditions gave the highest mean colony-forming units (CFU) values at both 25 and 50 C. Under anaerobic conditions, and especially at 50 C, lower mean CFU values were obtained. In all samples analyzed, numbers of sulfate reducing bacteria were less than 1000 CFU/g dry material. Methanogens were either not present or were found in very low numbers. Anaerobic sulfur oxidizing bacteria were found in higher numbers in most sample types with sufficient moisture. The statistical evaluation of the culture data demonstrated clearly that the water content was the variable limiting the viability of the bacteria present, and not the temperature. 68 refs, 35 figs, 37 tabs

Microbial Load of Some Medicinal Plants Sold in Some Local ...

African Journals Online (AJOL)

Microbial Load of Some Medicinal Plants Sold in Some Local Markets in Abeokuta, Nigeria. I MacDonald, S Omonigho, J Erhabor, H Efijuemue. Abstract. Purpose: To evaluate the microbial load on 17 randomly selected plant samples from 60 ethnobotanically collected medicinal plants from five local markets in Abeokuta, ...

Mineralogical Control on Microbial Diversity in a Weathered Granite?

Science.gov (United States)

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

Topological defects control collective dynamics in neural progenitor cell cultures

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Kawaguchi, Kyogo; Kageyama, Ryoichiro; Sano, Masaki

2017-04-01

Cultured stem cells have become a standard platform not only for regenerative medicine and developmental biology but also for biophysical studies. Yet, the characterization of cultured stem cells at the level of morphology and of the macroscopic patterns resulting from cell-to-cell interactions remains largely qualitative. Here we report on the collective dynamics of cultured murine neural progenitor cells (NPCs), which are multipotent stem cells that give rise to cells in the central nervous system. At low densities, NPCs moved randomly in an amoeba-like fashion. However, NPCs at high density elongated and aligned their shapes with one another, gliding at relatively high velocities. Although the direction of motion of individual cells reversed stochastically along the axes of alignment, the cells were capable of forming an aligned pattern up to length scales similar to that of the migratory stream observed in the adult brain. The two-dimensional order of alignment within the culture showed a liquid-crystalline pattern containing interspersed topological defects with winding numbers of +1/2 and -1/2 (half-integer due to the nematic feature that arises from the head-tail symmetry of cell-to-cell interaction). We identified rapid cell accumulation at +1/2 defects and the formation of three-dimensional mounds. Imaging at the single-cell level around the defects allowed us to quantify the velocity field and the evolving cell density; cells not only concentrate at +1/2 defects, but also escape from -1/2 defects. We propose a generic mechanism for the instability in cell density around the defects that arises from the interplay between the anisotropic friction and the active force field.

Do inactivated Microbial Preparations Improve Life History Traits of the Copepod Acartia tonsa?

DEFF Research Database (Denmark)

Drillet, Guillaume; Rabarimanantsoa, Tahina; Frouel, Stéphane

2011-01-01

We have tested a microbial preparation with probiotic effects (PSI; Sorbial A/S DANISCO) on the calanoid copepod Acartia tonsa (Dana) development time and reproduction effectiveness in culture. The hypotheses were that PSI increases the productivity and quality of copepods in culture (increased egg...

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

Science.gov (United States)

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

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

Science.gov (United States)

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.

Changes in microbial community structure in the wake of Hurricanes Katrina and Rita.

Science.gov (United States)

Amaral-Zettler, Linda A; Rocca, Jennifer D; Lamontagne, Michael G; Dennett, Mark R; Gast, Rebecca J

2008-12-15

Hurricanes have the potential to alter the structures of coastal ecosystems and generate pathogen-laden floodwaters thatthreaten public health. To examine the impact of hurricanes on urban systems, we compared microbial community structures in samples collected after Hurricane Katrina and before and after Hurricane Rita. We extracted environmental DNA and sequenced small-subunit rRNA (SSU rRNA) gene clone libraries to survey microbial communities in floodwater, water, and sediment samples collected from Lake Charles, Lake Pontchartrain, the 17th Street and Industrial Canals in New Orleans, and raw sewage. Correspondence analysis showed that microbial communities associated with sediments formed one cluster while communities associated with lake and Industrial Canal water formed a second. Communities associated with water from the 17th Street Canal and floodwaters collected in New Orleans showed similarity to communities in raw sewage and contained a number of sequences associated with possible pathogenic microbes. This suggests that a distinct microbial community developed in floodwaters following Hurricane Katrina and that microbial community structures as a whole might be sensitive indicators of ecosystem health and serve as "sentinels" of water quality in the environment.

Shotgun microbial profiling of fossil remains

DEFF Research Database (Denmark)

Der Sarkissian, Clio; Ermini, Luca; Jónsson, Hákon

2014-01-01

the specimen of interest, but instead reflect environmental organisms that colonized the specimen after death. Here, we characterize the microbial diversity recovered from seven c. 200- to 13 000-year-old horse bones collected from northern Siberia. We use a robust, taxonomy-based assignment approach...... to identify the microorganisms present in ancient DNA extracts and quantify their relative abundance. Our results suggest that molecular preservation niches exist within ancient samples that can potentially be used to characterize the environments from which the remains are recovered. In addition, microbial...... community profiling of the seven specimens revealed site-specific environmental signatures. These microbial communities appear to comprise mainly organisms that colonized the fossils recently. Our approach significantly extends the amount of useful data that can be recovered from ancient specimens using...

Viral coinfection is shaped by host ecology and virus-virus interactions across diverse microbial taxa and environments.

Science.gov (United States)

Díaz-Muñoz, Samuel L

2017-01-01

Infection of more than one virus in a host, coinfection, is common across taxa and environments. Viral coinfection can enable genetic exchange, alter the dynamics of infections, and change the course of viral evolution. Yet, a systematic test of the factors explaining variation in viral coinfection across different taxa and environments awaits completion. Here I employ three microbial data sets of virus-host interactions covering cross-infectivity, culture coinfection, and single-cell coinfection (total: 6,564 microbial hosts, 13,103 viruses) to provide a broad, comprehensive picture of the ecological and biological factors shaping viral coinfection. I found evidence that ecology and virus-virus interactions are recurrent factors shaping coinfection patterns. Host ecology was a consistent and strong predictor of coinfection across all three data sets: cross-infectivity, culture coinfection, and single-cell coinfection. Host phylogeny or taxonomy was a less consistent predictor, being weak or absent in the cross-infectivity and single-cell coinfection models, yet it was the strongest predictor in the culture coinfection model. Virus-virus interactions strongly affected coinfection. In the largest test of superinfection exclusion to date, prophage sequences reduced culture coinfection by other prophages, with a weaker effect on extrachromosomal virus coinfection. At the single-cell level, prophage sequences eliminated coinfection. Virus-virus interactions also increased culture coinfection with ssDNA-dsDNA coinfections >2× more likely than ssDNA-only coinfections. The presence of CRISPR spacers was associated with a ∼50% reduction in single-cell coinfection in a marine bacteria, despite the absence of exact spacer matches in any active infection. Collectively, these results suggest the environment bacteria inhabit and the interactions among surrounding viruses are two factors consistently shaping viral coinfection patterns. These findings highlight the role of

Conditioning biomass for microbial growth

Science.gov (United States)

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.

Accuracy of the cytopathology, bacterioscopy, and vaginal flora culture.

Science.gov (United States)

Almeida, P Q; Pereira, M A P; Palomo, F S; Okazaki, C; Schimidt, M A; Speck, N M G; Ribalta, J C L

2013-01-01

An over-population of vaginal microorganisms causing inflammatory processes renders it difficult to properly assess the cytopathological exam that aims to screen precedent cervical lesions. On the contrary, the occurrence of the microbial flora saprophyte does not influence correct cythodiagnosis. To assess the composition of vaginal tract aerobic microorganisms of asymptomatic women in menacme and post-menopause, and to analyze the accuracy of cytopathologic, bacterioscopic exams, and culturing of the flora. The women were first submitted to a focused anamnestic interrogatory and then submitted to gynecological exam. A sample of the vaginal fluid was collected with a culture swab and a smear was made on two glass slides for stained bacterioscopic exam (GRAM). The collection of material was then compiled in a cytopathologic smear analysis. All women signed the free and informed consent letter and the project was approved by the Ethics Research Board of Hospital São Paulo - UNIFESP. Bacterioscopy and culture proved to be better than the cytopathologic exam in featuring the bacilli and cocci. The bacterioscopy provided a better detection of the presence of bacilli (p < 0.001); no statistical difference was seen between both exams with respect to the detected cocci. The beta-hemolytic Streptococcus group was of significance in post-menopausal women (p < 0.05). In this study, the bacterioscopic and culture exams of the vaginal fluid were more effective in assessing the vaginal flora and in the detection of bacilli, compared to the cytopathological exam.

ATP measurements for monitoring microbial drinking water quality

DEFF Research Database (Denmark)

Vang, Óluva Karin

Current standard methods for surveillance of microbial drinking water quality are culture based, which are laborious and time-consuming, where results not are available before one to three days after sampling. This means that the water may have been consumed before results on deteriorated water....... The overall aim of this PhD study was to investigate various methodological features of the ATP assay for a potential implementation on a sensor platform as a real-time parameter for continuous on-line monitoring of microbial drinking water quality. Commercial reagents are commonly used to determine ATP......, microbial quality in distributed water, detection of aftergrowth, biofilm formation etc. This PhD project demonstrated that ATP levels are relatively low and fairly stable in drinking water without chlorine residual despite different sampling locations, different drinking water systems and time of year...

Microbial transformation of citral by Penicillium sp..

Science.gov (United States)

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.

Microbial Diversity in Soil Treatment Systems for Wastewater

Science.gov (United States)

Van Cuyk, S.; Spear, J.; Siegrist, R.; Pace, N.

2002-05-01

There is an increasing awareness and concern over land based wastewater system performance with respect to the removal of bacteria and virus. The goal of this work is to describe and identify the organismal composition of the microbiota in the applied wastewater effluent, the rich biomat that develops at the infiltrative surface, and in the soil percolate in order to aid in the understanding of bacterial and virus purification in soil treatment systems. The traditional reliance on pure culture techniques to describe microbiota is circumvented by the employment of a molecular approach. Microbial community characterization is underway based on cloning and sequencing of 16S rRNA genes for phylogenetic analyses, to determine the nature and quantity of microbiota that constitute these ecosystems. Knowledge of the organisms naturally present can influence the design and treatment capacity of these widely used land based systems. Laboratory, intermediate and field scale systems are currently under study. Since human pathogens are known to exist in sewage effluents, their removal in wastewater infiltration systems and within the underlying soil are in need of a more fundamental understanding. The relationship between design parameters and environmental conditions, including a microbial characterization, is essential for the prevention of contamination in groundwater sources. Preliminary results indicate the presence of uncultured organisms and phylogenetic kinds that had not been detected in these systems using other methods. Acinetobacter johnsonii and Acrobacter cryaerophilus were the two dominant species found in septic tank effluent, comprising 20% and 11% of the library respectively. In soil samples collected from the infiltrative surface of a column dosed with STE, there was no dominant bacterial species present. Percolate samples collected from the outflow of the column showed that a tuber borchii symbiont, a common soil microorganism, dominated the bacterial

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

Science.gov (United States)

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.

[Engineering issues of microbial ecology in space agriculture].

Science.gov (United States)

Yamashita, Masamichi; Ishikawa, Yoji; Oshima, Tairo

2005-03-01

Closure of the materials recycle loop for water-foods-oxygen is the primary purpose of space agriculture on Mars and Moon. A microbial ecological system takes a part of agriculture to process our metabolic excreta and inedible biomass and convert them to nutrients and soil substrate for cultivating plants. If we extend the purpose of space agriculture to the creation and control of a healthy and pleasant living environment, we should realize that our human body should not be sterilized but exposed to the appropriate microbial environment. We are proposing a use of hyper-thermophilic aerobic composting microbial ecology in space agriculture. Japan has a broad historical and cultural background on this subject. There had been agriculture that drove a closed loop of materials between consuming cities and farming villages in vicinity. Recent environmental problems regarding garbage collection and processing in towns have motivated home electronics companies to innovate "garbage composting" machines with bacterial technology. Based on those matured technology, together with new insights on microbiology and microbial ecology, we have been developing a conceptual design of space agriculture on Moon and Mars. There are several issues to be answered in order to prove effectiveness of the use of microbial systems in space. 1) Can the recycled nutrients, processed by the hyper-thermal aerobic composting microbial ecology, be formed in the physical and chemical state or configuration, with which plants can uptake those nutrients? A possibility of removing any major components of fertilizer from its recycle loop is another item to be evaluated. 2) What are the merits of forming soil microbial ecology around the root system of plants? This might be the most crucial question. Recent researches exhibit various mutually beneficial relationships among soil microbiota and plants, and symbiotic ecology in composting bacteria. It is essential to understand those features, and define

Microbial and plant ecology of a long-term TNT-contaminated site

International Nuclear Information System (INIS)

Travis, Emma R.; Bruce, Neil C.; Rosser, Susan J.

2008-01-01

The contamination of the environment with explosive residues presents a serious ecological problem at sites across the world, with the highly toxic compound trinitrotoluene (TNT) the most widespread contaminant. This study examines the soil microbial community composition across a long-term TNT-contaminated site. It also investigates the extent of nitroaromatic contamination and its effect on vegetation. Concentrations of TNT and its metabolites varied across the site and this was observed to dramatically impact on the extent and diversity of the vegetation, with the most heavily contaminated area completely devoid of vegetation. Bryophytes were seen to be particularly sensitive to TNT contamination. The microbial population experienced both a reduction in culturable bacterial numbers and a shift in composition at the high concentrations of TNT. DGGE and community-level physiological profiling (CLPP) revealed a clear change in both the genetic and functional diversity of the soil when soil was contaminated with TNT. - Long-term contamination of soil with TNT reduces the extent and diversity of vegetation, decreases culturable bacterial numbers and shifts the microbial community composition

Near-IR laser-triggered target cell collection using a carbon nanotube-based cell-cultured substrate.

Science.gov (United States)

Sada, Takao; Fujigaya, Tsuyohiko; Niidome, Yasuro; Nakazawa, Kohji; Nakashima, Naotoshi

2011-06-28

Unique near-IR optical properties of single-walled carbon nanotube (SWNTs) are of interest in many biological applications. Here we describe the selective cell detachment and collection from an SWNT-coated cell-culture dish triggered by near-IR pulse laser irradiation. First, HeLa cells were cultured on an SWNT-coated dish prepared by a spraying of an aqueous SWNT dispersion on a glass dish. The SWNT-coated dish was found to show a good cell adhesion behavior as well as a cellular proliferation rate similar to a conventional glass dish. We discovered, by near-IR pulse laser irradiation (at the laser power over 25 mW) to the cell under optical microscopic observation, a quick single-cell detachment from the SWNT-coated surface. Shockwave generation from the irradiated SWNTs is expected to play an important role for the cell detachment. Moreover, we have succeeded in catapulting the target single cell from the cultured medium when the depth of the medium was below 150 μm and the laser power was stronger than 40 mW. The captured cell maintained its original shape. The retention of the genetic information of the cell was confirmed by the polymerase chain reaction (PCR) technique. A target single-cell collection from a culture medium under optical microscopic observation is significant in wide fields of single-cell studies in biological areas.

Fecal microbial diversity and putative function in captive western lowland gorillas (Gorilla gorilla gorilla), common chimpanzees (Pan troglodytes), Hamadryas baboons (Papio hamadryas) and binturongs (Arctictis binturong).

Science.gov (United States)

McKenney, Erin A; Ashwell, Melissa; Lambert, Joanna E; Fellner, Vivek

2014-11-01

Microbial populations in the gastrointestinal tract contribute to host health and nutrition. Although gut microbial ecology is well studied in livestock and domestic animals, little is known of the endogenous populations inhabiting primates or carnivora. We characterized microbial populations in fecal cultures from gorillas (Gorilla gorilla gorilla), common chimpanzees (Pan troglodytes), Hamadryas baboons (Papio hamadryas) and binturongs (Arctictis binturong) to compare the microbiomes associated with different gastrointestinal morphologies and different omnivorous feeding strategies. Each species was fed a distinct standardized diet for 2 weeks prior to fecal collection. All diets were formulated to reflect the species' feeding strategies in situ. Fresh fecal samples were pooled within species and used to inoculate in vitro batch cultures. Acetate, propionate, butyrate and valerate were measured after 24 h of incubation. Eubacterial DNA was extracted from individual fecal samples, pooled, and the cpn60 gene region was amplified and then sequenced to identify the major eubacterial constituents associated with each host species. Short chain fatty acids (P < 0.001) and methane (P < 0.001) were significantly different across species. Eubacterial profiles were consistent with fermentation data and suggest an increase in diversity with dietary fiber. © 2014 International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and Wiley Publishing Asia Pty Ltd.

Optimized cryopreservation of mixed microbial communities for conserved functionality and diversity.

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Frederiek-Maarten Kerckhof

Full Text Available The use of mixed microbial communities (microbiomes for biotechnological applications has steadily increased over the past decades. However, these microbiomes are not readily available from public culture collections, hampering their potential for widespread use. The main reason for this lack of availability is the lack of an effective cryopreservation protocol. Due to this critical need, we evaluated the functionality as well as the community structure of three different types of microbiomes before and after cryopreservation with two cryoprotective agents (CPA. Microbiomes were selected based upon relevance towards applications: (1 a methanotrophic co-culture (MOB, with potential for mitigation of greenhouse gas emissions, environmental pollutants removal and bioplastics production; (2 an oxygen limited autotrophic nitrification/denitrification (OLAND biofilm, with enhanced economic and ecological benefits for wastewater treatment, and (3 fecal material from a human donor, with potential applications for fecal transplants and pre/probiotics research. After three months of cryopreservation at -80 °C, we found that metabolic activity, in terms of the specific activity recovery of MOB, aerobic ammonium oxidizing bacteria (AerAOB and anaerobic AOB (AnAOB, anammox in the OLAND mixed culture, resumes sooner when one of our selected CPA [dimethyl sulfoxide (DMSO and DMSO plus trehalose and tryptic soy broth (DMSO+TT] was added. However, the activity of the fecal community was not influenced by the CPA addition, although the preservation of the community structure (as determined by 16S rRNA gene sequencing was enhanced by addition of CPA. In summary, we have evaluated a cryopreservation protocol that succeeded in preserving both community structure and functionality of value-added microbiomes. This will allow individual laboratories and culture collections to boost the use of microbiomes in biotechnological applications.

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

Science.gov (United States)

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

Directory of Open Access Journals (Sweden)

Brett A. Neilan

2013-08-01

Full Text Available 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.

Microbial Profiling Of Cyanobacteria From VIT Lake

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Swati Singh

2015-08-01

Full Text Available The application of molecular biological methods to study the diversity and ecology of micro-organisms in natural environments has been practice in mid-1980. The aim of our research is to access the diversity composition and functioning of complex microbial community found in VIT Lake. Molecular ecology is a new field in which microbes can be recognized and their function can be understood at the DNA or RNA level which is useful for constructing genetically modified microbes by recombinant DNA technology for reputed use in the environment. In this research first we will isolate cyanobacteria in lab using conventional methods like broth culture and spread plate method then we will analyze their morphology using various staining methods and DNA and protein composition using electrophoresis method. The applications of community profiling approaches will advance our understanding of the functional role of microbial diversity in VIT Lake controls on microbial community composition.

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

Science.gov (United States)

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.

study of oral and gingival microbial flora in institutionalized mentally

African Journals Online (AJOL)

boaz

from the mouth and gingiva of 138 institutionalized mentally retarded patients of Sari to culture in specific media to ... Key words: Oral and gingival microbial flora, Mental retardation, D%, Sari ... staphylococcus aureus and, in case of negative.

Microbial analysis of the buffer/container experiment at AECL`s Underground Research Laboratory

Energy Technology Data Exchange (ETDEWEB)

Stroes-Gascoyne, S; Hamon, C J; Haveman, S A; Delaney, T L [Atomic Energy of Canada Ltd., Pinawa, MB (Canada). Whiteshell Labs; Pedersen, K; Ekendahl, S; Jahromi, N; Arlinger, J; Hallbeck, L [Univ. of Goeteborg, (Sweden). Dept. of General and Marine Microbiology; Daumas, S; Dekeyser, K [Guiges Recherche Appliquee en Microbiologie, Aix-en-Provence, (France)

1996-05-01

The Buffer/Container experiment was carried out for 2.5 years to examine the in-situ performance of compacted buffer material in a single emplacement borehole under vault-relevant conditions. During decommissioning of this experiment, numerous samples were taken for microbial analysis to determine if the naturally present microbial population in buffer material survived to conditions and to determine which groups of microorganisms would be dominant in such a simulated vault environment. Microbial analyses were initiated within 24 hour of sampling for all types of samples taken. The culture results showed an almost universal disappearance of viable microorganisms in the samples taken from near the heater surface. The microbial activity measurements confirmed the lack of viable organisms with very weak or no activity measured in most of these samples. Generally, aerobic heterotrophic culture conditions gave the highest mean colony-forming units (CFU) values at both 25 and 50 C. Under anaerobic conditions, and especially at 50 C, lower mean CFU values were obtained. In all samples analyzed, numbers of sulfate reducing bacteria were less than 1000 CFU/g dry material. Methanogens were either not present or were found in very low numbers. Anaerobic sulfur oxidizing bacteria were found in higher numbers in most sample types with sufficient moisture. The statistical evaluation of the culture data demonstrated clearly that the water content was the variable limiting the viability of the bacteria present, and not the temperature. 68 refs, 35 figs, 37 tabs.

Bacterial diversity of autotrophic enriched cultures from remote, glacial Antarctic, Alpine and Andean aerosol, snow and soil samples

OpenAIRE

Gonzalez-Toril , E.; Amils , R.; J. Delmas , Robert; Petit , Jean-Robert; Komarek , J.; Elster , J.

2009-01-01

Four different communities and one culture of autotrophic microbial assemblages were obtained by incubation of samples collected from high elevation snow in the Alps (Mt. Blanc area) and the Andes (Nevado Illimani summit, Bolivia), from Antarctic aerosol (French station Dumont d'Urville) and a maritime Antarctic soil (King George Island, South Shetlands, Uruguay Station Artigas), in a minimal mineral (oligotrophic) media. Molecular analysis of more than 200 16S rRNA gene sequences showed...

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

Science.gov (United States)

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 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 surface ripened semi-hard cheeses. Copyright © 2015 Elsevier B.V. All rights reserved.

Influence of Calcium on Microbial Reduction of Solid Phase Uranium (VI)

International Nuclear Information System (INIS)

Liu, Chongxuan; Jeon, Byong-Hun; Zachara, John M.; Wang, Zheming

2007-01-01

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 reduction 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

Soil microbial diversity in the vicinity of desert shrubs.

Science.gov (United States)

Saul-Tcherkas, Vered; Unc, Adrian; Steinberger, Yosef

2013-04-01

Water and nutrient availability are the major limiting factors of biological activity in arid and semiarid ecosystems. Therefore, perennial plants have developed different ecophysiological adaptations to cope with harsh conditions. The chemical profile of the root exudates varies among plant species and this can induce variability in associated microbial populations. We examined the influence of two shrubs species, Artemisia sieberi and Noaea mucronata, on soil microbial diversity. Soil samples were collected monthly, from December 2006 to November 2007, near canopies of both shrubs (0-10-cm depth). Samples were used for abiotic tests and determination of soil bacterial diversity. No significant differences were found in the abiotic variables (soil moisture, total organic matter, and total soluble nitrogen (TSN)) between soil samples collected from under the two shrubs during the study period. No obvious differences in the Shannon-Weaver index, evenness values, or total phylogenetic distances were found for the soil microbial communities. However, detailed denaturing gradient gel electrophoresis (DGGE) clustering as well as taxonomic diversity analyses indicated clear shifts in the soil microbial community composition. These shifts were governed by seasonal variability in water availability and, significantly, by plant species type.

Corporate culture and the culture of the labor collective: the methodology of distinguishing

Directory of Open Access Journals (Sweden)

M. Y. Dmytrenko

2014-07-01

The author points out the content and characteristics of corporate culture and the culture of the staff. The culture of the staff in the Late Modern constellations as well as corporate culture has both similarities and differences. Their common features are due to the influence of mass culture, subculture of the information society, organizational culture. Their differences are primarily of historical and anthropological nature. Corporate culture is defined as the essence of material, spiritual and social values created by the employees of the companies in the course of their activities and which reflect the uniqueness and individuality of this company. The author grounds the statement about the importance of working out methodological criteria for their differentiation.

Antifungal Microbial Agents for Food Biopreservation-A Review.

Science.gov (United States)

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.

Bioelectricity Production from Microalgae-Microbial Fuel Cell Technology (MMFC

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da Costa Carlito

2018-01-01

Full Text Available Microbial fuel cell is an ecological innovative technology producing bioelectricity by utilizing microbes activity. Substituent energy is produced by changing the chemical energy to electrical energy through the catalytic reaction of microorganism. The research aims to find out the potency of bioelectricity produced by microalgae microbial fuel cell technology by utilizing the combination of tapioca wastewater and microalgae cultivation. This research is conducted through the ingredients preparation stage – microalgae culture, wastewater characterization, membrane and graphite activation, and the providing of other supporting equipment. The next stage is the MMFC arrangement, while the last one is bioelectricity measurement. The result of optimal bioelectricity production on the comparison of electrode 2 : 2, the power density is 44,33 mW/m2 on day 6, meanwhile, on that of 1 : 1, 20,18 mW/m2 power density on day 1 is obtained. It shows that bioelectricity can be produced from the combination of tapioca wastewater and microalgae culture through the microalgae-microbial fuel cell (MMFC technology.This research is expected to be a reference for the next research particularly the one that observes the utilizing of microalgae as the part of new and renewable energy sources.

Production of hydrogen by microbial fermentation

Energy Technology Data Exchange (ETDEWEB)

Roychowdhury, S.; Cox, D.; Levandowsky, M.

1988-01-01

Production of hydrogen by defined and undefined bacterial cultures was studied, using pure sugars (glucose and maltose) or natural sources rich in either pure sugars or polysaccharides. The latter included sugar cane juice, corn pulp (enzymatically treated or untreated), and enzymatically treated paper. Mixed microbial flora from sewage and landfill sediments, as well as pure and mixed cultures of known coliform bacteria produced mixtures of hydrogen and carbon dioxide at 37/sup 0/C and 55/sup 0/C, with hydrogen concentrations as high as 87%. In the case of the pure glucose substrate, an average yield of 0.7 mol hydrogen per mol glucose was obtained.

Polyphenol and Microbial Profile of On-farm Cocoa Beans Fermented with Selected Microbial Consortia

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Tochukwu Vincent Balogu

2017-09-01

Full Text Available Background and Objective: Quality and preference of cocoa as raw material for various mcocoa products primarily depend on fermentation techniques that modulate the resultant flavour and the phytochemical properties. This study investigated the combined effect of selected microbial consortia and bioreactors on phytochemical profiles of fermented cocoa beans.Material and Methods: Three microbial consortia labeled as Treatments (T-1, T-2, T-3 were used as starter culture (≈105cells ml-1 for on-farm cocoa fermentation on three chambers (basket, woodbox, and plastic for 7 days. These novel consortia were T-1, Staphylococcus spp + Pseudomonas spp+ Bacillus spp, T-2, Staphylococcus spp + Pseudomonas spp +L. lactis, and T-3, Bacillus spp+ Lactobacillus spp + Saccharomyces spp+ Torulopsis spp.Results and Conclusion: The microbial profile were significantly (P≤0.05 altered by all treatments (T-1, T-2, T-3 and microbial frequency was enhanced by 5 -22.5%. T-3 and T-1 significantly altered phenolic content in basket chamber. Tannin was significantly (p≤0.05 varied by T-1(basket, plastic, wood box and T-2(plastic. Tannin: polyphenol conversion ratio adopted as fermented cocoa bean quality benchmark was significantly enhanced by T-1 (basket, woodbox and T-2 (plastic, but was significantly suppressed by T-3 (basket. This study evidently concluded that the appropriate synergy of microbial flora and fermenting chambers could achieve good cocoa quality with low polyphenol content (best for cocoa beverages or high polyphenol content (best for pharmaceutical, confectionery and nutraceutical industries. These findings would avail an economic alternative to the expensive polyphenol reconstitution of cocoa butter used for various industrial products, thereby maximizing economic benefits for both cocoa farmers and industrialists.Conflict of interest: The authors declare no conflict of interest.

Current Microbial Pattern of Patients Presenting with Pre-Labour ...

African Journals Online (AJOL)

Current Microbial Pattern of Patients Presenting with Pre-Labour Rupture of Membranes (PROM) at Kenyatta National Hospital, Nairobi, Kenya. ... Subject: Fifty antenatal patients with premature Rapture of Membranes and 50 controls. Results: A total of 100 questionnaires and laboratory liquor microscopic culture and ...

Starting up microbial enhanced oil recovery.

Science.gov (United States)

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

Science.gov (United States)

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

Directory of Open Access Journals (Sweden)

Patrick Broyer

2018-05-01

Full Text Available 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 VirtuoTM 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

The microbial community characteristics of ancient painted sculptures in Maijishan Grottoes, China.

Science.gov (United States)

Duan, Yulong; Wu, Fasi; Wang, Wanfu; He, Dongpeng; Gu, Ji-Dong; Feng, Huyuan; Chen, Tuo; Liu, Guangxiu; An, Lizhe

2017-01-01

In this study, a culture-independent Illumina MiSeq sequencing strategy was applied to investigate the microbial communities colonizing the ancient painted sculptures of the Maijishan Grottoes, a famous World Cultural Heritage site listed by UNESCO in China. Four mixed samples were collected from Cave 4-4 of the Maijishan Grottoes, the so-called Upper Seven Buddha Pavilion, which was built during the Northern Zhou Dynasty (557-581AD). The 16/18S rRNA gene-based sequences revealed a rich bacterial diversity and a relatively low fungal abundance, including the bacterial groups Actinobacteria, Acidobacteria, Bacteroidetes, Cyanobacteria, Chloroflexi, Firmicutes, Proteobacteria and Verrucomicrobia and the fungal groups Ascomycota, Basidiomycota and Chytridiomycota. Among them, the bacteria genera of Pseudonocardia and Rubrobacter and unclassified fungi in the order of Capnodiales were dominant. The relative abundance of Pseudonocardia in the painted layer samples was higher than that in the dust sample, while Cyanobacteria dominated in the dust sample. Many of them have been discovered at other cultural heritage sites and associated with the biodeterioration of cultural relics. The presence and activity of these pioneering microorganisms may lead to an unexpected deterioration of the painted sculptures that are preserved in this heritage site. Thus, proper management strategies and potential risk monitoring should be used in the Maijishan Grottoes to improve the conservation of these precious painted sculptures.

Radiochemically-supported microbial communities. A potential mechanism for biocolloid production of importance to actinide transport

Energy Technology Data Exchange (ETDEWEB)

Moser, Duane P. [Desert Research Institute, Las Vegas, NV (United States); Hamilton-Brehm, Scott D. [Desert Research Institute, Las Vegas, NV (United States); Fisher, Jenny C. [Univ. of Wisconsin, Milwaukee, WI (United States); Bruckner, James C. [Desert Research Institute, Las Vegas, NV (United States); Kruger, Brittany [Desert Research Institute, Las Vegas, NV (United States); Sackett, Joshua [Desert Research Institute, Las Vegas, NV (United States); Russell, Charles E. [Desert Research Institute, Las Vegas, NV (United States); Onstott, Tullis C. [Princeton Univ., NJ (United States); Czerwinski, Ken [Univ. of Nevada, Las Vegas, NV (United States); Zavarin, Mavrik [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Campbell, James H. [Northwest Missouri State Univ., Maryville, MO (United States)

2015-03-20

The work described here revealed the presence of diverse microbial communities located across 19 subsurface sites at the NNSS/NTTR and nearby locations. Overall, the diversity of microorganisms was high for subsurface habitats and variable between sites. As of this writing, preparations are being made to combine the Illumina sequences and 16S rRNA clone libraries with other non-NNSS/NTTR well sites of Southern Nevada Regional Flow System for a publication manuscript describing our very broad landscape scale survey of subsurface microbial diversity. Isolates DRI-13 and DRI-14 remain to be fully characterized and named in accordance with the conventions established by Bergey's Manual of Systematic Bacteriology. In preparation to be published, these microorganisms will be submitted to the American Type Culture Collection (ATCC) and the Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ).It is anticipated that the data resulting from this study in combination with other data sets that will allow us to produce a number of publications that will be impactful to the subsurface microbiology community.

Plant pathogen culture collections: it takes a village to preserve these resources vital to the advancement of agricultural security and plant pathology.

Science.gov (United States)

Kang, Seogchan; Blair, Jaime E; Geiser, David M; Khang, Chang-Hyun; Park, Sook-Young; Gahegan, Mark; O'Donnell, Kerry; Luster, Douglas G; Kim, Seong H; Ivors, Kelly L; Lee, Yong-Hwan; Lee, Yin-Won; Grünwald, Niklaus J; Martin, Frank M; Coffey, Michael D; Veeraraghavan, Narayanan; Makalowska, Izabela

2006-09-01

ABSTRACT Plant pathogen culture collections are essential resources in our fight against plant disease and for connecting discoveries of the present with established knowledge of the past. However, available infrastructure in support of culture collections is in serious need of improvement, and we continually face the risk of losing many of these collections. As novel and reemerging plant pathogens threaten agriculture, their timely identification and monitoring depends on rapid access to cultures representing the known diversity of plant pathogens along with genotypic, phenotypic, and epidemiological data associated with them. Archiving such data in a format that can be easily accessed and searched is essential for rapid assessment of potential risk and can help track the change and movement of pathogens. The underexplored pathogen diversity in nature further underscores the importance of cataloguing pathogen cultures. Realizing the potential of pathogen genomics as a foundation for developing effective disease control also hinges on how effectively we use the sequenced isolate as a reference to understand the genetic and phenotypic diversity within a pathogen species. In this letter, we propose a number of measures for improving pathogen culture collections.

Developing Model Benchtop Systems for Microbial Experimental Evolution

Science.gov (United States)

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

Microbial Biofilm as a Smart Material

DEFF Research Database (Denmark)

Garde, Christian; Welch, Martin; Ferkinghoff-Borg, Jesper

2015-01-01

Microbial biofilm colonies will in many cases form a smart material capable of responding to external threats dependent on their size and internal state. The microbial community accordingly switches between passive, protective, or attack modes of action. In order to decide which strategy to employ......, it is essential for the biofilm community to be able to sense its own size. The sensor designed to perform this task is termed a quorum sensor, since it only permits collective behaviour once a sufficiently large assembly of microbes have been established. The generic quorum sensor construct involves two genes...

Soil Microbial Activity in Conventional and Organic Agricultural Systems

Directory of Open Access Journals (Sweden)

Romero F.V. Carneiro

2009-06-01

Full Text Available The aim of this study was to evaluate microbial activity in soils under conventional and organic agricultural system management regimes. Soil samples were collected from plots under conventional management (CNV, organic management (ORG and native vegetation (AVN. Soil microbial activity and biomass was significantly greater in ORG compared with CNV. Soil bulk density decreased three years after adoption of organic system. Soil organic carbon (SOC was higher in the ORG than in the CNV. The soil under organic agricultural system presents higher microbial activity and biomass and lower bulk density than the conventional agricultural system.

Microbial ecology of two hot springs of Sikkim: Predominate population and geochemistry.

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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

Science.gov (United States)

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

The role of microbial low-molecular-weight autoregulatory factors (alkylhydroxybenzenes) in resistance of microorganisms to radiation and heat shock

Science.gov (United States)

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.

PCR-DGGE fingerprints of microbial succession during a manufacture of traditional water buffalo mozzarella cheese.

Science.gov (United States)

Ercolini, D; Mauriello, G; Blaiotta, G; Moschetti, G; Coppola, S

2004-01-01

To monitor the process and the starter effectiveness recording a series of fingerprints of the microbial diversity occurring at different steps of mozzarella cheese manufacture and to investigate the involvement of the natural starter to the achievement of the final product. Samples of raw milk, natural whey culture (NWC) used as starter, curd after ripening and final product were collected during a mozzarella cheese manufacture. Total microbial DNA was directly extracted from the dairy samples as well as bulk colonies collected from the plates of appropriate culture media generally used for viable counts of mesophilic and thermophilic lactic acid bacteria (LAB) and used in polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) experiments. The analysis of the DGGE profiles showed a strong influence of the microflora of the NWC on the whole process because after the starter addition, the profile of all the dairy samples was identical to the one shown by the NWC. Simple indexes were calculated for the DGGE profiles to have an objective estimation of biodiversity and of technological importance of specific groups of organisms. LAB grown on Man Rogosa Sharp (MRS) and Rogosa agar at 30 degrees C showed high viable counts and the highest diversity in species indicating their importance in the cheese making, which had not been considered so far. Moreover, the NWC profiles were shown to be the most similar to the curd profile suggesting to be effective in manufacture. The PCR-DGGE analysis showed that in premium quality manufacture the NWC used as starter had a strong influence on the microflora responsible for process development. The molecular approach appeared to be valid as a tool to control process development, starter effectiveness and product identity as well as to rank cheese quality.

Effect of Saccharomyces boulardii and Mode of Delivery on the Early Development of the Gut Microbial Community in Preterm Infants.

Science.gov (United States)

Zeber-Lubecka, Natalia; Kulecka, Maria; Ambrozkiewicz, Filip; Paziewska, Agnieszka; Lechowicz, Milosz; Konopka, Ewa; Majewska, Urszula; Borszewska-Kornacka, Maria; Mikula, Michal; Cukrowska, Bozena; Ostrowski, Jerzy

2016-01-01

Recent advances in culture-independent approaches have enabled insights into the diversity, complexity, and individual variability of gut microbial communities. To examine the effect of oral administration of Saccharomyces (S.) boulardii and mode of delivery on the intestinal microbial community in preterm infants. Stool samples were collected from preterm newborns randomly divided into two groups: a probiotic-receiving group (n = 18) or a placebo group (n = 21). Samples were collected before probiotic intake (day 0), and after 2 and 6 weeks of supplementation. The composition of colonizing bacteria was assessed by 16S ribosomal RNA (rRNA) gene sequencing of fecal samples using the Ion 16S Metagenomics Kit and the Ion Torrent Personal Genome Machine platform. A total of 11932257 reads were generated, and were clustered into 459, 187, and 176 operational taxonomic units at 0 days, 2 weeks, and 6 weeks, respectively. Of the 17 identified phyla, Firmicutes Actinobacteria, Proteobacteria, and Bacteroidetes were universal. The microbial community differed at day 0 compared with at 2 weeks and 6 weeks. There was a tendency for increased bacterial diversity at 2 weeks and 6 weeks compared with day 0, and infants with a gestational age of 31 weeks or higher presented increased bacterial diversity prior to S. boulardii administration. Firmicutes and Proteobacteria remained stable during the observation period, whereas Actinobacteria and Bacteroidetes increased in abundance, the latter particularly more sharply in vaginally delivered infants. While the mode of delivery may influence the development of a microbial community, this study had not enough power to detect statistical differences between cohorts supplemented with probiotics, and in a consequence, to speculate on S. boulardii effect on gut microbiome composition in preterm newborns.

Integrated Approach to Reconstruction of Microbial Regulatory Networks

Energy Technology Data Exchange (ETDEWEB)

Rodionov, Dmitry A [Sanford-Burnham Medical Research Institute; Novichkov, Pavel S [Lawrence Berkeley National Laboratory

2013-11-04

This project had the goal(s) of development of integrated bioinformatics platform for genome-scale inference and visualization of transcriptional regulatory networks (TRNs) in bacterial genomes. The work was done in Sanford-Burnham Medical Research Institute (SBMRI, P.I. D.A. Rodionov) and Lawrence Berkeley National Laboratory (LBNL, co-P.I. P.S. Novichkov). The developed computational resources include: (1) RegPredict web-platform for TRN inference and regulon reconstruction in microbial genomes, and (2) RegPrecise database for collection, visualization and comparative analysis of transcriptional regulons reconstructed by comparative genomics. These analytical resources were selected as key components in the DOE Systems Biology KnowledgeBase (SBKB). The high-quality data accumulated in RegPrecise will provide essential datasets of reference regulons in diverse microbes to enable automatic reconstruction of draft TRNs in newly sequenced genomes. We outline our progress toward the three aims of this grant proposal, which were: Develop integrated platform for genome-scale regulon reconstruction; Infer regulatory annotations in several groups of bacteria and building of reference collections of microbial regulons; and Develop KnowledgeBase on microbial transcriptional regulation.

N-acyl homoserine lactone-degrading microbial enrichment cultures isolated from Penaeus vannamei shrimp gut and their probiotic properties in Brachionus plicatilis cultures.

Science.gov (United States)

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.

In situ exposure to low herbicide concentrations affects microbial population composition and catabolic gene frequency in an aerobic shallow aquifer

DEFF Research Database (Denmark)

de Lipthay, J.R.; Tuxen, Nina; Johnsen, Kaare

2003-01-01

and were analyzed for the presence of general microbial populations, Pseudomonas bacteria, and specific phenoxy acid degraders. Both culture-dependent and culture-independent methods were applied. The abundance of microbial phenoxy acid degraders (10(0) to 10(4) g(-1) sediment) was determined by most...... measured by either PCR or plating on selective agar media was higher in sediments subjected to high levels of phenoxy acid. Furthermore, high numbers of CFU compared to direct counting of 4',6-diamidino-2-phenylindole-stained cells in the microscope suggested an increased culturability of the indigenous...

Microbial ecology and genomics: A crossroads of opportunity

Energy Technology Data Exchange (ETDEWEB)

Stahl, David A. [University of Washington; Tiedje, James M. [Michigan State University

2002-08-30

Microbes have dominated life on Earth for most of its 4.5 billionyear history. They are the foundation of the biosphere, controlling the biogeochemical cycles and affecting geology, hydrology, and local and global climates. All life is completely dependent upon them. Humans cannot survive without the rich diversity of microbes, but most microbial species can survive without humans. Extraordinary advances in molecular technology have fostered an explosion of information in microbial biology. It is now known that microbial species in culture poorly represent their natural diversity—which dwarfs conventions established for the visible world. This was revealed over the last decade using newer molecular tools to explore environmental diversity and has sparked an explosive growth in microbial ecology and technologies that may profit from the bounty of natural biochemical diversity. Several colloquia and meetings have helped formulate policy recommendations to enable sustained research programs in these areas. One such colloquium organized by the American Academy of Microbiology (“The Microbial World: Foundation of the Biosphere,” 1997) made two key recommendations: (1) develop a more complete inventory of living organisms and the interagency cooperation needed to accomplish this goal, and (2) develop strategies to harvest this remarkable biological diversity for the benefit of science, technology, and society. Complete genome sequence information was identified as an essential part of strategy development, and the recommendation was made to sequence the genome of at least one species of each of the major divisions of microbial life.

Energy, ecology and the distribution of microbial life.

Science.gov (United States)

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.

Microbial Flocculant for Nature Soda

Energy Technology Data Exchange (ETDEWEB)

Qin, Peiyong; Zhang, Tong; Chen, Cuixian

2004-03-31

Microbial flocculant for nature soda has been studied. Lactobacillus TRJ21, which was able to produce an excellent biopolymer flocculant for nature soda, was obtained in our lab. The microbial flocculant was mainly produced when the bacteria laid in stationary growth phase. Fructose or glucose, as carbon sources, were more favorable for the bacterial growth and flocculant production. The bacteria was able to use ammonium sulfate or Urea as nitrogen to produce flocculant, but was not able to use peptone effectively. High C/N ratio was more favorable to Lactobacillus TRJ21 growth and flocculant production than low C/N ratio. The biopolymer flocculant was mainly composed of polysaccharide and protein with a molecular weight 1.38x106 by gel permeation chromatography. It was able to be easily purified from the culture medium by acetone. Protein in the flocculant was tested for the flocculating activity ingredient by heating the flocculant.

Exogenous Nitrogen Addition Reduced the Temperature Sensitivity of Microbial Respiration without Altering the Microbial Community Composition

Directory of Open Access Journals (Sweden)

Hui Wei

2017-12-01

Full Text Available Atmospheric nitrogen (N deposition is changing in both load quantity and chemical composition. The load effects have been studied extensively, whereas the composition effects remain poorly understood. We conducted a microcosm experiment to study how N chemistry affected the soil microbial community composition characterized by phospholipid fatty acids (PLFAs and activity indicated by microbial CO2 release. Surface and subsurface soils collected from an old-growth subtropical forest were supplemented with three N-containing materials (ammonium, nitrate, and urea at the current regional deposition load (50 kg ha-1 yr-1 and incubated at three temperatures (10, 20, and 30°C to detect the interactive effects of N deposition and temperature. The results showed that the additions of N, regardless of form, did not alter the microbial PLFAs at any of the three temperatures. However, the addition of urea significantly stimulated soil CO2 release in the early incubation stage. Compared with the control, N addition consistently reduced the temperature dependency of microbial respiration, implying that N deposition could potentially weaken the positive feedback of the warming-stimulated soil CO2 release to the atmosphere. The consistent N effects for the surface and subsurface soils suggest that the effects of N on soil microbial communities may be independent of soil chemical contents and stoichiometry.

Combination of image descriptors for the exploration of cultural photographic collections

Science.gov (United States)

Bhowmik, Neelanjan; Gouet-Brunet, Valérie; Bloch, Gabriel; Besson, Sylvain

2017-01-01

The rapid growth of image digitization and collections in recent years makes it challenging and burdensome to organize, categorize, and retrieve similar images from voluminous collections. Content-based image retrieval (CBIR) is immensely convenient in this context. A considerable number of local feature detectors and descriptors are present in the literature of CBIR. We propose a model to anticipate the best feature combinations for image retrieval-related applications. Several spatial complementarity criteria of local feature detectors are analyzed and then engaged in a regression framework to find the optimal combination of detectors for a given dataset and are better adapted for each given image; the proposed model is also useful to optimally fix some other parameters, such as the k in k-nearest neighbor retrieval. Three public datasets of various contents and sizes are employed to evaluate the proposal, which is legitimized by improving the quality of retrieval notably facing classical approaches. Finally, the proposed image search engine is applied to the cultural photographic collections of a French museum, where it demonstrates its added value for the exploration and promotion of these contents at different levels from their archiving up to their exhibition in or ex situ.

Metagenomic Sequencing of an In Vitro-Simulated Microbial Community

Energy Technology Data Exchange (ETDEWEB)

Morgan, Jenna L.; Darling, Aaron E.; Eisen, Jonathan A.

2009-12-01

Background: Microbial life dominates the earth, but many species are difficult or even impossible to study under laboratory conditions. Sequencing DNA directly from the environment, a technique commonly referred to as metagenomics, is an important tool for cataloging microbial life. This culture-independent approach involves collecting samples that include microbes in them, extracting DNA from the samples, and sequencing the DNA. A sample may contain many different microorganisms, macroorganisms, and even free-floating environmental DNA. A fundamental challenge in metagenomics has been estimating the abundance of organisms in a sample based on the frequency with which the organism's DNA was observed in reads generated via DNA sequencing. Methodology/Principal Findings: We created mixtures of ten microbial species for which genome sequences are known. Each mixture contained an equal number of cells of each species. We then extracted DNA from the mixtures, sequenced the DNA, and measured the frequency with which genomic regions from each organism was observed in the sequenced DNA. We found that the observed frequency of reads mapping to each organism did not reflect the equal numbers of cells that were known to be included in each mixture. The relative organism abundances varied significantly depending on the DNA extraction and sequencing protocol utilized. Conclusions/Significance: We describe a new data resource for measuring the accuracy of metagenomic binning methods, created by in vitro-simulation of a metagenomic community. Our in vitro simulation can be used to complement previous in silico benchmark studies. In constructing a synthetic community and sequencing its metagenome, we encountered several sources of observation bias that likely affect most metagenomic experiments to date and present challenges for comparative metagenomic studies. DNA preparation methods have a particularly profound effect in our study, implying that samples prepared with

Quality tests of culture medium for microbiological analysis of drinkable water

International Nuclear Information System (INIS)

Roncoroni, M.

2000-01-01

For each of the parameters considered, in accordance with the water's law standards concerning drinking water, they have compared various culture media produced by different manufacturers, in order to choose the products with best selectivity and quality. With this purpose, known microbial cultures (Atcc cultures specified in >) have been used at first, in order to verify the selectivity of soils and the type of growth related with the morphology of the colonies developed. Later, sowings of superficial water of Lake Como have been made, in which a mixed microbial population was present, in order to verify selectivity and possible interference in the execution of an analysis of a real sample [it

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

Science.gov (United States)

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.

Key players and team play: anaerobic microbial communities in hydrocarbon-contaminated aquifers.

Science.gov (United States)

Kleinsteuber, Sabine; Schleinitz, Kathleen M; Vogt, Carsten

2012-05-01

Biodegradation of anthropogenic pollutants in shallow aquifers is an important microbial ecosystem service which is mainly brought about by indigenous anaerobic microorganisms. For the management of contaminated sites, risk assessment and control of natural attenuation, the assessment of in situ biodegradation and the underlying microbial processes is essential. The development of novel molecular methods, "omics" approaches, and high-throughput techniques has revealed new insight into complex microbial communities and their functions in anoxic environmental systems. This review summarizes recent advances in the application of molecular methods to study anaerobic microbial communities in contaminated terrestrial subsurface ecosystems. We focus on current approaches to analyze composition, dynamics, and functional diversity of subsurface communities, to link identity to activity and metabolic function, and to identify the ecophysiological role of not yet cultured microbes and syntrophic consortia. We discuss recent molecular surveys of contaminated sites from an ecological viewpoint regarding degrader ecotypes, abiotic factors shaping anaerobic communities, and biotic interactions underpinning the importance of microbial cooperation for microbial ecosystem services such as contaminant degradation.

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

Science.gov (United States)

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

2017-12-01

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

Microbial syntrophy: interaction for the common good.

Science.gov (United States)

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.

Science.gov (United States)

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.

Investigating Microbial Habitats in Hydrothermal Chimneys using Ti-Thermocouple Arrays: Microbial Diversity

Science.gov (United States)

Pagé, A.; Tivey, M. K.; Stakes, D. S.; Bradley, A. M.; Seewald, J. S.; Wheat, C. G.; Reysenbach, A.

2004-12-01

In order to examine the changes that occur in the microbial community composition as a deep-sea hydrothermal vent chimney develops, we deployed Ti-thermocouple arrays over high temperature vents at two active sites of the Guaymas Basin Southern Trough. Chimney material that precipitated around the arrays was recovered after 4 and 72 days. Chimney material that precipitated prior to deployment of the arrays was also recovered at one of the sites (Busted Shroom). Culture-independent analysis based on the small subunit rRNA sequence (cloning and DGGE) was used to determine the microbial diversity associated with subsamples of each chimney. The original Busted Shroom chimney (BSO) was dominated by members of the Crenarchaeota Marine Group I, a group of cosmopolitan marine Archaea, ɛ -Proteobacteria, and γ -Proteobacteria, two divisions of Bacteria that are common to deep-sea vents. The 4 days old Busted Shroom chimney (BSD1) was dominated by members of the Methanocaldococcaceae, hyperthermophilic methanogens, and the 72 days old chimney (BSD2) by members of the Methanosarcinaceae, mesophilic and thermophilic methanogens. At the second site, Toadstool, the 72 days old chimney material that had precipitated around the array (TS) revealed the dominance of sequences from uncultured marine Archaea, the DHVE group I and II, and from the ɛ -Proteobacteria. Additionally, sequences belonging to the Methanocaldococcaceae and Desulfurococcaceae were recovered next to thermocouples that were at temperatures of 109° C (at Busted Shroom) and 116° C (at Toadstool), respectively. These temperatures are higher than the upper limit for growth of cultured representatives from each family.

Strategies for efficiently selecting PHA producing mixed microbial cultures using complex feedstocks: Feast and famine regime and uncoupled carbon and nitrogen availabilities.

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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

Hydrogen production profiles using furans in microbial electrolysis cells.

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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.

Effect of co-existing plant specie on soil microbial activity under heavy metal stress

International Nuclear Information System (INIS)

Nwuche, C. O.; Ugoji, E. O.

2010-01-01

The influence of plant primary compounds on the activity of soil microbial communities under heavy metal stress was studied in a pot-culture field experiment conducted in a green house. Amaranthus spinosus was cultivated in an agricultural soil previously amended in the laboratory with solutions of different trace elements in two separate treatment modes: singly and in combination. Culture-independent metabolism based indices such as the rate of carbon and nitrogen mineralization, microbial biomass carbon and soil basal respiration were monitored fortnightly over a period of six weeks. Result shows that plant detritus have significant modifying effect on soil microbe-metal interactions. Data on microbial and biochemical processes in the respective mesocosms did not vary from control; not even in mesocosms containing very high concentrations of copper, zinc and nickel. The soil microbial biomass carbon and the rate of carbon and nitrogen cycling were not impeded by the respective metal treatment while the respiration responses increased as a result of increase in metabolic activity of the soil microbes. The plant based substrates enabled the soil microflora to resist high metal contamination because of its tendency to absorb large amounts of inorganic cations.

Comparison of Different Strategies for Selection/Adaptation of Mixed Microbial Cultures Able to Ferment Crude Glycerol Derived from Second-Generation Biodiesel

Directory of Open Access Journals (Sweden)

C. Varrone

2015-01-01

Full Text Available 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.

Comparison of Different Strategies for Selection/Adaptation of Mixed Microbial Cultures Able to Ferment Crude Glycerol Derived from Second-Generation Biodiesel.

Science.gov (United States)

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.

A communal catalogue reveals Earth's multiscale microbial diversity.

Science.gov (United States)

Thompson, Luke R; Sanders, Jon G; McDonald, Daniel; Amir, Amnon; Ladau, Joshua; Locey, Kenneth J; Prill, Robert J; Tripathi, Anupriya; Gibbons, Sean M; Ackermann, Gail; Navas-Molina, Jose A; Janssen, Stefan; Kopylova, Evguenia; Vázquez-Baeza, Yoshiki; González, Antonio; Morton, James T; Mirarab, Siavash; Zech Xu, Zhenjiang; Jiang, Lingjing; Haroon, Mohamed F; Kanbar, Jad; Zhu, Qiyun; Jin Song, Se; Kosciolek, Tomasz; Bokulich, Nicholas A; Lefler, Joshua; Brislawn, Colin J; Humphrey, Gregory; Owens, Sarah M; Hampton-Marcell, Jarrad; Berg-Lyons, Donna; McKenzie, Valerie; Fierer, Noah; Fuhrman, Jed A; Clauset, Aaron; Stevens, Rick L; Shade, Ashley; Pollard, Katherine S; Goodwin, Kelly D; Jansson, Janet K; Gilbert, Jack A; Knight, Rob

2017-11-23

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.

Effects of dietary changes and yeast culture (Saccharomyces cerevisiae) on rumen microbial fermentation of Holstein heifers.

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Moya, D; Calsamiglia, S; Ferret, A; Blanch, M; Fandiño, J I; Castillejos, L; Yoon, I

2009-09-01

The effects of a dietary challenge to induce digestive upsets and supplementation with yeast culture on rumen microbial fermentation were studied using 12 Holstein heifers (277 +/- 28 kg of BW) fitted with a ruminal cannula, in a crossover design with 2 periods of 5 wk. In each period, after 3 wk of adaptation to a 100% forage diet, the dietary challenge consisted of increasing the amount of grain at a rate of 2.5 kg/d (as-fed basis) over a period of 4 d, until a 10:90 forage:concentrate diet was reached, and then it was maintained for 10 d. Between periods, animals were fed again the 100% forage diet without any treatment for 1 wk as a wash-out period. Treatments started the first day of each period, and they were a control diet (CL) or the same diet with addition of yeast culture (YC, Diamond V XPCLS). Digestive upsets were determined by visual observation of bloat or by a reduction in feed intake (as-fed basis) of 50% or more compared with intake on the previous day. Feed intake was determined daily at 24-h intervals during the adaptation period and daily at 2, 6, and 12 h postfeeding during the dietary challenge. Ruminal liquid samples were collected daily during the dietary challenge to determine ruminal pH at 0, 3, 6, and 12 h postfeeding, and total and individual VFA, lactic acid, ammonia-N, and rumen fluid viscosity at 0 and 6 h postfeeding. The 16s rRNA gene copies of Streptococcus bovis and Megasphaera elsdenii were determined by quantitative PCR. Foam height and strength of the rumen fluid were also determined the day after the digestive upset to evaluate potential foam production. A total of 20 cases (83.3%) of digestive upsets were recorded in both periods during the dietary challenge, all diagnosed due to a reduction in feed intake. Rumen fermentation profile at 0 h on the digestive upset day was characterized by low ruminal pH, which remained under 6.0 for 18 h, accompanied by elevated total VFA concentration and, in some cases, by elevated lactate

Microbial Biofilm as a Smart Material

Directory of Open Access Journals (Sweden)

Christian Garde

2015-02-01

Full Text Available Microbial biofilm colonies will in many cases form a smart material capable of responding to external threats dependent on their size and internal state. The microbial community accordingly switches between passive, protective, or attack modes of action. In order to decide which strategy to employ, it is essential for the biofilm community to be able to sense its own size. The sensor designed to perform this task is termed a quorum sensor, since it only permits collective behaviour once a sufficiently large assembly of microbes have been established. The generic quorum sensor construct involves two genes, one coding for the production of a diffusible signal molecule and one coding for a regulator protein dedicated to sensing the signal molecules. A positive feedback in the signal molecule production sets a well-defined condition for switching into the collective mode. The activation of the regulator involves a slow dimerization, which allows low-pass filtering of the activation of the collective mode. Here, we review and combine the model components that form the basic quorum sensor in a number of Gram-negative bacteria, e.g., Pseudomonas aeruginosa.

Does iron inhibit cryptoendolithic microbial communities?

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Johnston, C. G.; Vestal, J. R.; Friedmann, E. I. (Principal Investigator)

1988-01-01

Photosynthetic activity of three cryptoendolithic microbial communities was studied under controlled conditions in the laboratory. In two of these communities, the dominant organisms were lichens, collected from Linnaeus Terrace and from Battleship Promontory. The third community, dominated by cyanobacteria, was collected from Battleship Promontory. Both sites are in the ice-free valleys of southern Victoria Land. Previous efforts have shown how physical conditions can influence metabolic activity in endolithic communities (Kappen and Friedmann 1983; Kappen, Friedmann, and Garty 1981; Vestal, Federle, and Friedmann 1984). Biological activity can also be strongly influenced by the chemical environment. Inorganic nutrients such as nitrate, ammonia, and phosphate are often limiting factors, so their effects on photosynthetic carbon-14 bicarbonate incorporation were investigated. Iron and manganese are two metals present in Linnaeus Terrace and Battleship Promontory sandstones, and their effects on photosynthesis were also studied. The results may add to our understanding of biogeochemical interactions within this unique microbial community.

An Inquiry-Based Laboratory Design for Microbial Ecology

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Tessier, Jack T.; Penniman, Clayton A.

2006-01-01

There is a collective need to increase the use of inquiry-based instruction at the college level. This paper provides of an example of how inquiry was successfully used in the laboratory component of an undergraduate course in microbial ecology. Students were offered a collection of field and laboratory methods to choose from, and they developed a…

Acetaldehyde production and microbial colonization in oral squamous cell carcinoma and oral lichenoid disease.

Science.gov (United States)

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.

Susceptibility of green and conventional building materials to microbial growth.

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Mensah-Attipoe, J; Reponen, T; Salmela, A; Veijalainen, A-M; Pasanen, P

2015-06-01

Green building materials are becoming more popular. However, little is known about their ability to support or limit microbial growth. The growth of fungi was evaluated on five building materials. Two green, two conventional building materials and wood as a positive control were selected. The materials were inoculated with Aspergillus versicolor, Cladosporium cladosporioides and Penicillium brevicompactum, in the absence and presence of house dust. Microbial growth was assessed at four different time points by cultivation and determining fungal biomass using the N-acetylhexosaminidase (NAHA) enzyme assay. No clear differences were seen between green and conventional building materials in their susceptibility to support microbial growth. The presence of dust, an external source of nutrients, promoted growth of all the fungal species similarly on green and conventional materials. The results also showed a correlation coefficient ranging from 0.81 to 0.88 between NAHA activity and culturable counts. The results suggest that the growth of microbes on a material surface depends on the availability of organic matter rather than the classification of the material as green or conventional. NAHA activity and culturability correlated well indicating that the two methods used in the experiments gave similar trends for the growth of fungi on material surfaces. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Microbial genome-enabled insights into plant-microorganism interactions.

Science.gov (United States)

Guttman, David S; McHardy, Alice C; Schulze-Lefert, Paul

2014-12-01

Advances in genome-based studies on plant-associated microorganisms have transformed our understanding of many plant pathogens and are beginning to greatly widen our knowledge of plant interactions with mutualistic and commensal microorganisms. Pathogenomics has revealed how pathogenic microorganisms adapt to particular hosts, subvert innate immune responses and change host range, as well as how new pathogen species emerge. Similarly, culture-independent community profiling methods, coupled with metagenomic and metatranscriptomic studies, have provided the first insights into the emerging field of research on plant-associated microbial communities. Together, these approaches have the potential to bridge the gap between plant microbial ecology and plant pathology, which have traditionally been two distinct research fields.

Insights into environmental controls on microbial communities in a continental serpentinite aquifer using a microcosm-based approach.

Science.gov (United States)

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

2014-01-01

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

Interval scanning photomicrography of microbial cell populations.

Science.gov (United States)

Casida, L. E., Jr.

1972-01-01

A single reproducible area of the preparation in a fixed focal plane is photographically scanned at intervals during incubation. The procedure can be used for evaluating the aerobic or anaerobic growth of many microbial cells simultaneously within a population. In addition, the microscope is not restricted to the viewing of any one microculture preparation, since the slide cultures are incubated separately from the microscope.

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

NARCIS (Netherlands)

Sutton, N.B.; Atashgahi, S.; Saccenti, E.; Grotenhuis, J.T.C.; Smidt, H.; Rijnaarts, H.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

Genome-centric metatranscriptomes and ecological roles of the active microbial populations during cellulosic biomass anaerobic digestion.

Science.gov (United States)

Jia, Yangyang; Ng, Siu-Kin; Lu, Hongyuan; Cai, Mingwei; Lee, Patrick K H

2018-01-01

Although anaerobic digestion for biogas production is used worldwide in treatment processes to recover energy from carbon-rich waste such as cellulosic biomass, the activities and interactions among the microbial populations that perform anaerobic digestion deserve further investigations, especially at the population genome level. To understand the cellulosic biomass-degrading potentials in two full-scale digesters, this study examined five methanogenic enrichment cultures derived from the digesters that anaerobically digested cellulose or xylan for more than 2 years under 35 or 55 °C conditions. Metagenomics and metatranscriptomics were used to capture the active microbial populations in each enrichment culture and reconstruct their meta-metabolic network and ecological roles. 107 population genomes were reconstructed from the five enrichment cultures using a differential coverage binning approach, of which only a subset was highly transcribed in the metatranscriptomes. Phylogenetic and functional convergence of communities by enrichment condition and phase of fermentation was observed for the highly transcribed populations in the metatranscriptomes. In the 35 °C cultures grown on cellulose, Clostridium cellulolyticum -related and Ruminococcus -related bacteria were identified as major hydrolyzers and primary fermenters in the early growth phase, while Clostridium leptum -related bacteria were major secondary fermenters and potential fatty acid scavengers in the late growth phase. While the meta-metabolism and trophic roles of the cultures were similar, the bacterial populations performing each function were distinct between the enrichment conditions. Overall, a population genome-centric view of the meta-metabolism and functional roles of key active players in anaerobic digestion of cellulosic biomass was obtained. This study represents a major step forward towards understanding the microbial functions and interactions at population genome level during the

A fermented meat model system for studies of microbial aroma formation

DEFF Research Database (Denmark)

Tjener, Karsten; Stahnke, Louise Heller; Andersen, L.

2003-01-01

A fermented meat model system was developed, by which microbial formation of volatiles could be examined The model was evaluated against dry, fermented sausages with respect to microbial growth, pH and volatile profiles. Fast and slowly acidified sausages and models were produced using the starter......H, microbial growth and volatile profiles was similar to sausage production. Based on these findings, the model system was considered valid for studies of aroma formation of meat cultures for fermented sausage....... for multivariate data analysis. Growth of lactic acid bacteria was comparable for model and sausages, whereas survival of S. xylosus was better in the model. Multivariate analysis of volatiles showed that differences between fast and slowly acidified samples were identical for model and sausage. For both sausage...

Resistance to Cultural Intervention: Formation of Inhibitory Collective and children's Self-Defensive Regulation in a Chinese School.

Science.gov (United States)

Wu, Aruna; Li, Xiao-Wen; Zhou, Lihua; Zhang, Qian

2017-09-01

A sequel to the previous article "Roots of Excellence: The Releasing Effect of Individual Potentials through Educational Cultural Intervention in a Chinese School" (in press), the present study is on the unexpected reversal phenomena in the process of cultural intervention. The goal of the intervention is to construct the dynamics of Jiti (well-organized collective in Chinese) through creative activities to promote students' development. In the intervention, the releasing effect (Wu et al. 2016) emerged as well, but the teacher's concern about worsening discipline and academic performance evoked and reinforced his habitual notions and practices of education, turning the joint activities into a way of strengthening discipline. The energy that had been discharging at the beginning of the intervention was inhibited, so that many more problematic behaviors took shape. The whole class formed an inhibitory atmosphere, within which pupils formed self-defensive regulation strategies. By comparing with the productive collective in which intervention was effective and analyzing this unexpected reversal process, we can not only see pupils' self-construction status in the inhibitory culture but illuminate the formation of the teacher's resistance to educational and cultural transformation as well. Resistance is originated from teachers not being able to interpret pupils' inner developmental needs but instead anxious about the ongoing problems.

A highly diverse, desert-like microbial biocenosis on solar panels in a Mediterranean city.

Science.gov (United States)

Dorado-Morales, Pedro; Vilanova, Cristina; Peretó, Juli; Codoñer, Francisco M; Ramón, Daniel; Porcar, Manuel

2016-07-05

Microorganisms colonize a wide range of natural and artificial environments although there are hardly any data on the microbial ecology of one the most widespread man-made extreme structures: solar panels. Here we show that solar panels in a Mediterranean city (Valencia, Spain) harbor a highly diverse microbial community with more than 500 different species per panel, most of which belong to drought-, heat- and radiation-adapted bacterial genera, and sun-irradiation adapted epiphytic fungi. The taxonomic and functional profiles of this microbial community and the characterization of selected culturable bacteria reveal the existence of a diverse mesophilic microbial community on the panels' surface. This biocenosis proved to be more similar to the ones inhabiting deserts than to any human or urban microbial ecosystem. This unique microbial community shows different day/night proteomic profiles; it is dominated by reddish pigment- and sphingolipid-producers, and is adapted to withstand circadian cycles of high temperatures, desiccation and solar radiation.

Microbial biogeography of drinking water: patterns in phylogenetic diversity across space and time

NARCIS (Netherlands)

Roeselers, G.; Coolen, J.; Wielen, P.W. van der; Jaspers, M.C.; Atsma, A.; Graaf, B. de; Schuren, F.

2015-01-01

In this study, we collected water from different locations in 32 drinking water distribution networks in the Netherlands and analysed the spatial and temporal variation in microbial community composition by high-throughput sequencing of 16S rRNA gene amplicons. We observed that microbial community

Statistical analysis and modeling of pelletized cultivation of Mucor circinelloides for microbial lipid accumulation.

Science.gov (United States)

Xia, Chunjie; Wei, Wei; Hu, Bo

2014-04-01

Microbial oil accumulation via oleaginous fungi has some potential benefits because filamentous fungi can form pellets during cell growth and these pellets are easier to harvest from the culture broth than individual cells. This research studied the effect of various culture conditions on the pelletized cell growth of Mucor circinelloides and its lipid accumulation. The results showed that cell pelletization was positively correlated to biomass accumulation; however, pellet size was negatively correlated to the oil content of the fungal biomass, possibly due to the mass transfer barriers generated by the pellet structure. How to control the size of the pellet is the key to the success of the pelletized microbial oil accumulation process.

Characterization of fungi in office dust: Comparing results of microbial secondary metabolites, fungal internal transcribed spacer region sequencing, viable culture and other microbial indices.

Science.gov (United States)

Park, J-H; Sulyok, M; Lemons, A R; Green, B J; Cox-Ganser, J M

2018-05-04

Recent developments in molecular and chemical methods have enabled the analysis of fungal DNA and secondary metabolites, often produced during fungal growth, in environmental samples. We compared 3 fungal analytical methods by analysing floor dust samples collected from an office building for fungi using viable culture, internal transcribed spacer (ITS) sequencing and secondary metabolites using liquid chromatography-tandem mass spectrometry. Of the 32 metabolites identified, 29 had a potential link to fungi with levels ranging from 0.04 (minimum for alternariol monomethylether) to 5700 ng/g (maximum for neoechinulin A). The number of fungal metabolites quantified per sample ranged from 8 to 16 (average = 13/sample). We identified 216 fungal operational taxonomic units (OTUs) with the number per sample ranging from 6 to 29 (average = 18/sample). We identified 37 fungal species using culture, and the number per sample ranged from 2 to 13 (average = 8/sample). Agreement in identification between ITS sequencing and culturing was weak (kappa = -0.12 to 0.27). The number of cultured fungal species poorly correlated with OTUs, which did not correlate with the number of metabolites. These suggest that using multiple measurement methods may provide an improved understanding of fungal exposures in indoor environments and that secondary metabolites may be considered as an additional source of exposure. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

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

Science.gov (United States)

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

Smoking cessation alters subgingival microbial recolonization.

Science.gov (United States)

Fullmer, S C; Preshaw, P M; Heasman, P A; Kumar, P S

2009-06-01

Smoking cessation improves the clinical manifestations of periodontitis; however, its effect on the subgingival biofilm, the primary etiological agent of periodontitis, is unclear. The purpose of this study was to investigate, longitudinally, if smoking cessation altered the composition of the subgingival microbial community, by means of a quantitative, cultivation-independent assay for bacterial profiling. Subgingival plaque was collected at baseline, and 3, 6, and 12 months post-treatment from smokers who received root planing and smoking cessation counseling. The plaque was analyzed by terminal restriction fragment length polymorphism (t-RFLP). Microbial profiles differed significantly between smokers and quitters at 6 and 12 months following smoking cessation. The microbial community in smokers was similar to baseline, while quitters demonstrated significantly divergent profiles. Changes in bacterial levels contributed to this shift. These findings reveal a critical role for smoking cessation in altering the subgingival biofilm and suggest a mechanism for improved periodontal health associated with smoking cessation.

Evaluation of the microbial safety of child food of animal origin in Greece.

Science.gov (United States)

Liandris, Emmanouil; Gazouli, Maria; Taka, Styliani; Andreadou, Margarita; Vaiopoulou, Anna; Tzimotoudis, Nikolaos; Kasampalidis, Ioannis; Mpaseas, Dionysis; Fyliousis, George; Poltronieri, Palmiro; Poltrionieri, Palmiro; Cook, Nigel; Ikonomopoulos, John

2014-03-01

Foodborne illness is a major cause of morbidity and mortality especially for children, even in the developed world. The aim of this study was to assess the microbial safety of food of animal origin intended for consumption by children in Greece. Sampling involved 8 categories of retail products and was completed with a collection of 850 samples. These were tested by PCR and/or culture for Listeria monocytogenes, Campylobacter spp., Escherichia coli O157, Salmonella spp., Cronobacter sakazakii, Brucella spp., and Mycobacterium avium subsp paratuberculosis (MAP). The number of positive results recorded collectively for the pathogens under investigation over the total number of samples tested was 3.52% and 0.12% by PCR and culture, respectively. The most frequently detected pathogen was enterohemorrhagic E. coli (1.29%) followed by Brucella (0.82%) and Listeria (0.82%). DNA belonging to MAP was detected in 0.35% of samples, which was also the percentage of positivity recorded for Campylobacter. The percentage for Salmonella was 0.12%. It can be concluded from the results that there is no indication of noncompliance for the tested food samples. However, detection of DNA belonging to pathogens that are transmissible to humans through food is indicative that constant vigilance regarding food safety is an absolute necessity. © 2014 Institute of Food Technologists®

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

Science.gov (United States)

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

2017-04-15

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

Heavy metal levels, physicochemical properties and microbial ...

African Journals Online (AJOL)

Journal of Applied Sciences and Environmental Management ... out to assess the microbial, physicochemical and heavy metal characteristics of soil samples from five different waste collection sites within the University of Benin, Benin City and evaluated using standard analytical and classical microbiological methods.

Microbial Evaluation of Some Non-sterile Pharmaceutical ...

African Journals Online (AJOL)

Purpose: To determine the type and incidence of predominant microorganisms in certain non-sterile pharmaceuticals immediately after collection and one year later. Methods: All pharmaceutical samples were subjected to the following examinations: total bacterial count and presence of microbial pathogens, using ...

A review of gastrointestinal microbiology with special emphasis on molecular microbial ecology approaches

International Nuclear Information System (INIS)

Mackie, R.I.; Cann, I.K.O.

2005-01-01

All animals, including humans, are adapted to life in a microbial world. Large populations of micro-organisms inhabit the gastrointestinal tract of all animals and form a closely integrated ecological unit with the host. This complex, mixed, microbial culture can be considered the most metabolically adaptable and rapidly renewable organ of the body, which plays a vital role in the normal nutritional, physiological, immunological and protective functions of the host animal. Bacteria have traditionally been classified mainly on the basis of phenotypic properties. Despite the vast amount of knowledge generated for ruminal and other intestinal ecosystems using traditional techniques, the basic requisites for ecological studies, namely, enumeration and identification of all community members, have limitations. The two major problems faced by microbial ecologists are bias introduced by culture-based enumeration and characterization techniques, and the lack of a phylogenetically-based classification scheme. Modem molecular ecology techniques based on sequence comparisons of nucleic acids (DNA or RNA) can be used to provide molecular characterization while at the same time providing a classification scheme that predicts natural evolutionary relationships. These molecular methods provide results that are independent of growth conditions and media used. Also, using these techniques, bacteria can be classified and identified before they can be grown in pure culture. These nucleic acid-based techniques will enable gut microbiologists to answer the most difficult question in microbial ecology: namely, describing the exact role or function a specific bacterium plays in its natural environment and its quantitative contribution to the whole. However, rather than replacing the classical culture-based system, the new molecular-based techniques can be used in combination with the classical approach to improve cultivation, speciation and evaluation of diversity. The study of microbial

Dynamics of bacterial populations during bench-scale bioremediation of oily seawater and desert soil bioaugmented with coastal microbial mats.

Science.gov (United States)

Ali, Nidaa; Dashti, Narjes; Salamah, Samar; Sorkhoh, Naser; Al-Awadhi, Husain; Radwan, Samir

2016-03-01

This study describes a bench-scale attempt to bioremediate Kuwaiti, oily water and soil samples through bioaugmentation with coastal microbial mats rich in hydrocarbonoclastic bacterioflora. Seawater and desert soil samples were artificially polluted with 1% weathered oil, and bioaugmented with microbial mat suspensions. Oil removal and microbial community dynamics were monitored. In batch cultures, oil removal was more effective in soil than in seawater. Hydrocarbonoclastic bacteria associated with mat samples colonized soil more readily than seawater. The predominant oil degrading bacterium in seawater batches was the autochthonous seawater species Marinobacter hydrocarbonoclasticus. The main oil degraders in the inoculated soil samples, on the other hand, were a mixture of the autochthonous mat and desert soil bacteria; Xanthobacter tagetidis, Pseudomonas geniculata, Olivibacter ginsengisoli and others. More bacterial diversity prevailed in seawater during continuous than batch bioremediation. Out of seven hydrocarbonoclastic bacterial species isolated from those cultures, only one, Mycobacterium chlorophenolicum, was of mat origin. This result too confirms that most of the autochthonous mat bacteria failed to colonize seawater. Also culture-independent analysis of seawater from continuous cultures revealed high-bacterial diversity. Many of the bacteria belonged to the Alphaproteobacteria, Flavobacteria and Gammaproteobacteria, and were hydrocarbonoclastic. Optimal biostimulation practices for continuous culture bioremediation of seawater via mat bioaugmentation were adding the highest possible oil concentration as one lot in the beginning of bioremediation, addition of vitamins, and slowing down the seawater flow rate. © 2016 The Author. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Effect of Saccharomyces boulardii and Mode of Delivery on the Early Development of the Gut Microbial Community in Preterm Infants.

Directory of Open Access Journals (Sweden)

Natalia Zeber-Lubecka

Full Text Available Recent advances in culture-independent approaches have enabled insights into the diversity, complexity, and individual variability of gut microbial communities.To examine the effect of oral administration of Saccharomyces (S. boulardii and mode of delivery on the intestinal microbial community in preterm infants.Stool samples were collected from preterm newborns randomly divided into two groups: a probiotic-receiving group (n = 18 or a placebo group (n = 21. Samples were collected before probiotic intake (day 0, and after 2 and 6 weeks of supplementation. The composition of colonizing bacteria was assessed by 16S ribosomal RNA (rRNA gene sequencing of fecal samples using the Ion 16S Metagenomics Kit and the Ion Torrent Personal Genome Machine platform.A total of 11932257 reads were generated, and were clustered into 459, 187, and 176 operational taxonomic units at 0 days, 2 weeks, and 6 weeks, respectively. Of the 17 identified phyla, Firmicutes Actinobacteria, Proteobacteria, and Bacteroidetes were universal. The microbial community differed at day 0 compared with at 2 weeks and 6 weeks. There was a tendency for increased bacterial diversity at 2 weeks and 6 weeks compared with day 0, and infants with a gestational age of 31 weeks or higher presented increased bacterial diversity prior to S. boulardii administration. Firmicutes and Proteobacteria remained stable during the observation period, whereas Actinobacteria and Bacteroidetes increased in abundance, the latter particularly more sharply in vaginally delivered infants.While the mode of delivery may influence the development of a microbial community, this study had not enough power to detect statistical differences between cohorts supplemented with probiotics, and in a consequence, to speculate on S. boulardii effect on gut microbiome composition in preterm newborns.

Enhancement of electricity production by graphene oxide in soil microbial fuel cells and plant microbial fuel cells

Directory of Open Access Journals (Sweden)

Yuko eGoto

2015-04-01

Full Text Available The effects of graphene oxide (GO on electricity generation in soil microbial fuel cells (SMFCs and plant microbial fuel cell (PMFCs were investigated. GO at concentrations ranging from 0 to 1.9 g•kg-1 was added to soil and reduced for 10 days under anaerobic incubation. All SMFCs (GO-SMFCs utilizing the soils incubated with GO produced electricity at a greater rate and in higher quantities than the SMFCs which did not contain GO. In fed-batch operations, the overall average electricity generation in GO-SMFCs containing 1.0 g•kg-1 of GO was 40 ± 19 mW•m-2, which was significantly higher than the value of 6.6 ± 8.9 mW•m-2 generated from GO-free SMFCs (p -2 of electricity after 27 days of operation. Collectively, this study demonstrates that GO added to soil can be microbially reduced in soil, and facilitates electron transfer to the anode in both SMFCs and PMFCs.

Impact of electrokinetic remediation on microbial communities within PCP contaminated soil

International Nuclear Information System (INIS)

Lear, G.; Harbottle, M.J.; Sills, G.; Knowles, C.J.; Semple, K.T.; Thompson, I.P.

2007-01-01

Electrokinetic techniques have been used to stimulate the removal of organic pollutants within soil, by directing contaminant migration to where remediation may be more easily achieved. The effect of this and other physical remediation techniques on the health of soil microbial communities has been poorly studied and indeed, largely ignored. This study reports the impact on soil microbial communities during the application of an electric field within ex situ laboratory soil microcosms contaminated with pentachlorophenol (PCP; 100 mg kg -1 oven dry soil). Electrokinetics reduced counts of culturable bacteria and fungi, soil microbial respiration and carbon substrate utilisation, especially close to the acidic anode where PCP accumulated (36 d), perhaps exacerbated by the greater toxicity of PCP at lower soil pH. There is little doubt that a better awareness of the interactions between soil electrokinetic processes and microbial communities is key to improving the efficacy and sustainability of this remediation strategy. - Electrokinetics negatively impacted soil

Influences of dissolved oxygen concentration on biocathodic microbial communities in microbial fuel cells.

Science.gov (United States)

Rago, Laura; Cristiani, Pierangela; Villa, Federica; Zecchin, Sarah; Colombo, Alessandra; Cavalca, Lucia; Schievano, Andrea

2017-08-01

Dissolved oxygen (DO) at cathodic interface is a critical factor influencing microbial fuel cells (MFC) performance. In this work, three MFCs were operated with cathode under different DO conditions: i) air-breathing (A-MFC); ii) water-submerged (W-MFC) and iii) assisted by photosynthetic microorganisms (P-MFC). A plateau of maximum current was reached at 1.06±0.03mA, 1.48±0.06mA and 1.66±0.04mA, increasing respectively for W-MFC, P-MFC and A-MFC. Electrochemical and microbiological tools (Illumina sequencing, confocal microscopy and biofilm cryosectioning) were used to explore anodic and cathodic biofilm in each MFC type. In all cases, biocathodes improved oxygen reduction reaction (ORR) as compared to abiotic condition and A-MFC was the best performing system. Photosynthetic cultures in the cathodic chamber supplied high DO level, up to 16mg O2 L -1 , which sustained aerobic microbial community in P-MFC biocathode. Halomonas, Pseudomonas and other microaerophilic genera reached >50% of the total OTUs. The presence of sulfur reducing bacteria (Desulfuromonas) and purple non-sulfur bacteria in A-MFC biocathode suggested that the recirculation of sulfur compounds could shuttle electrons to sustain the reduction of oxygen as final electron acceptor. The low DO concentration limited the cathode in W-MFC. A model of two different possible microbial mechanisms is proposed which can drive predominantly cathodic ORR. Copyright © 2017 Elsevier B.V. All rights reserved.

Establishment of 3D culture and induction of osteogenic differentiation of pre-osteoblasts using wet-collected aligned scaffolds

Energy Technology Data Exchange (ETDEWEB)

Ding, Huifen [Hubei-MOSTKLOS & KLOBM, School and Hospital of Stomatology, Wuhan University, Wuhan 430079 (China); Chongqing Affiliated Hospital of Stomatology, Chongqing University of Medical Sciences, Chongqing 400015 (China); Zhong, Junwen [Wuhan National Laboratory for Optoelectronics, School of Optical and Electronic Information, Huazhong University of Science and Technology, Wuhan 430074 (China); Xu, Fei; Song, Fangfang; Yin, Miao; Wu, Yanru; Hu, Qiyi [Hubei-MOSTKLOS & KLOBM, School and Hospital of Stomatology, Wuhan University, Wuhan 430079 (China); Wang, Jiawei, E-mail: wangjwei@hotmail.com [Hubei-MOSTKLOS & KLOBM, School and Hospital of Stomatology, Wuhan University, Wuhan 430079 (China)

2017-02-01

Aligned fibrous scaffolds have attracted much interest in bone tissue engineering, because they are supposed to induce osteogenic differentiation. For the first time, aligned silk fibroin nanofibres were loosely packed using a novel wet-collection electrospinning method. Moreover, three-dimensional (3D) culture of MC3T3-E1 pre-osteoblasts was established on these fibrous scaffolds. Physicochemical properties of the scaffolds and the behaviour of MC3T3-E1 pre-osteoblasts on the scaffolds were analysed and compared with scaffolds obtained using traditional method. Ethanol bath improved the uniformity and alignment of the fibres and increased the thickness and porosity of the scaffolds. Structures of the fibres were well maintained after immediate crosslinking in ethanol. Cells on the wet-collected scaffolds exhibited more ordered arrangement and elongated morphology as well as faster and deeper infiltration. The ordered infiltration resulted in the establishment of the 3D culture of cells, promoting proliferation and osteogenic differentiation of the pre-osteoblasts. Thus, the wet-collected aligned scaffolds with improved topographical and physicochemical properties presents significant potential application in bone regeneration. - Highlights: • Aligned silk fibroin nanofibres were loosely packed using a novel wet-collection electrospinning method. • Structural properties of the aligned nanofibres were improved. • Three-dimensional culture of MC3T3-E1 pre-osteoblasts was established. • The arrangement, morphology, infiltration, proliferation and osteogenic differentiation of cells were enhanced.

Co-culture microorganisms with different initial proportions reveal the mechanism of chalcopyrite bioleaching coupling with microbial community succession.

Science.gov (United States)

Ma, Liyuan; Wang, Xingjie; Feng, Xue; Liang, Yili; Xiao, Yunhua; Hao, Xiaodong; Yin, Huaqun; Liu, Hongwei; Liu, Xueduan

2017-01-01

The effect of co-culture microorganisms with different initial proportions on chalcopyrite bioleaching was investigated. Communities were rebuilt by six typical strains isolated from the same habitat. The results indicated, by community with more sulfur oxidizers at both 30 and 40°C, the final copper extraction rate was 19.8% and 6.5% higher, respectively, than that with more ferrous oxidizers. The variations of pH, redox potential, ferrous and copper ions in leachate also provided evidences that community with more sulfur oxidizers was more efficient. Community succession of free and attached cells revealed that initial proportions played decisive roles on community dynamics at 30°C, while communities shared similar structures, not relevant to initial proportions at 40°C. X-ray diffraction analysis confirmed different microbial functions on mineral surface. A mechanism model for chalcopyrite bioleaching was established coupling with community succession. This will provide theoretical basis for reconstructing an efficient community in industrial application. Copyright © 2016 Elsevier Ltd. All rights reserved.

Pre-banking microbial contamination of donor conjunctiva and storage medium for penetrating keratoplasty.

Science.gov (United States)

Inomata, Takenori; Ono, Koichi; Matsuba, Tsuyoshi; Shiang, Tina; Di Zazzo, Antonio; Nakatani, Satoru; Yamaguchi, Masahiro; Ebihara, Nobuyuki; Murakami, Akira

2017-09-01

The aims of this study were to investigate the incidence of positive donor tissue cultures before transfer to preservation medium (Optisol™-GS) for penetrating keratoplasty, to verify the efficacy of antibiotics contained in Optisol™-GS by examining the drug susceptibility and to assess the relationship between the results of our microbial assessments as well as donor factors and the incidence of contamination. We conducted a retrospective, cross-sectional study using Juntendo Eye Bank records for all corneal transplantations. Two hundred donor conjunctiva harvestings and storage medium (EP-II ® ) cultures were performed between July 2008 and June 2011. We analyzed the associations between donor factors (age, gender, history of cataract surgery, death-to-preservation interval, cause of death) and contamination rates using multivariate analysis by the generalized estimating equation model. We obtained positive bacterial cultures from 154 of the 200 eyes (77.0%). The isolated bacteria were indigenous, such as coagulase-negative Staphylococci, Corynebacterium sp., and methicillin-resistant Staphylococcus aureus (MRSA). There was significant resistance to levofloxacin (18 eyes, 9.0%) and gentamicin (12 eyes, 6.0%), and no vancomycin-resistant bacteria were detected. The donor factors did not correlate with the prevalence of bacterial contamination in our criteria. Pre-banking microbial assessment allows for microbial detection, bacterial susceptibility and resistance testing. This is useful for developing preservation mediums containing effective spectrum antibiotic agents for high quality control of corneal banking.

Effect of Mg/Ca ratios on microbially induced carbonate precipitation

Science.gov (United States)

Balci, Nurgul; Demirel, Cansu; Seref Sonmez, M.; Kurt, M. Ali

2016-04-01

Influence of Mg/Ca ratios on microbially induced carbonate mineralogy were investigated by series of experiments carried out under various environmental conditions (Mg/Ca ratio, temperature and salinity). Halophilic bacterial cultures used for biomineralization experiments were isolated from hypersaline Lake Acıgöl (Denizli, SW Turkey), displaying extreme water chemistry with an average pH around 8.6 (Balci eta l.,2015). Enriched bacterial culture used in the experiments consisted of Halomonas saccharevitans strain AJ275, Halomonas alimentaria strain L7B; Idiomarina sp. TBZ29, 98% Idiomarina seosensis strain CL-SP19. Biomineralization experiments were set up using above enriched culture with Mg/Ca ratios of 0.05, 1, 4 and 15 and salinity of 8% and 15% experiments at 30oC and 10oC. Additionally, long-term biomineralization experiments were set up to last for a year, for Mg/Ca=4 and Mg/Ca=15 experiments at 30oC. For each experimental condition abiotic experiments were also conducted. Solution chemistry throughout incubation was monitored for Na, K, Mg, Ca, bicarbonate, carbonate, ammonium and phosphate for a month. At the end of the experiments, precipitates were collected and morphology and mineralogy of the biominerals were investigated and results were evaluated using the software DIFFRAC.SUITE EVA. Overall the preliminary results showed chemical precipitation of calcite, halite, hydromagnesite and sylvite. Results obtained from biological experiments indicate that, low Mg/Ca ratios (0.05 and 1) favor chlorapatite precipitation, whereas higher Mg/Ca ratios favor struvite precipitation. Biomineralization of dolomite, huntite and magnesite is favorable at high Mg/Ca ratios (4 and 15), in the presence of halophilic bacteria. Moreover, results indicate that supersaturation with respect to Mg (Mg/Ca=15) combined with NaCl (15%) inhibits biomineralization and forms chemical precipitates. 15% salinity is shown to favor chemical precipitation of mineral phases more than

A program to assess microbial impacts on nuclear waste containment

International Nuclear Information System (INIS)

Horn, J.; Meike, A.

1996-01-01

In this paper we discuss aspects of a comprehensive program to identify and bound potential effects of microorganisms on long-term nuclear waste containment, using as examples, studies conducted within the Yucca Mountain Project. A comprehensive program has been formulated which cuts across standard disciplinary lines to address the specific concerns of microbial activity in a radioactive waste repository. Collectively, this program provides bounding parameters of microbial activities that modify the ambient geochemistry and hydrology, modify corrosion rates, and transport and transform radionuclides under conditions expected to be encountered after geological waste emplacement. This program is intended to provide microbial reaction rates and bounding conditions in a form that can be integrated into existing chemical and hydrological models. The inclusion of microbial effects will allow those models to more accurately assess long term repository integrity

Distribution of the dominant microbial communities in marine sediments containing high concentrations of gas hydrates

Energy Technology Data Exchange (ETDEWEB)

Briggs, B.; Colwell, F.; Carini, P.; Torres, M. [Oregon State Univ., Corvallis, OR (United States); Hangsterfer, A.; Kastner, M. [California Univ., San Diego, CA (United States). Scripps Inst. of Oceanography; Brodie, E. [Lawrence Berkeley National Laboratory, Berkeley, CA (United States). Center for Environmental Biotechnology; Daly, R. [California Univ., Berkeley, CA (United States); Holland, M. [GeoTek, Daventry, Northants (United Kingdom); Long, P.; Schaef, H. [Pacific Northwest National Laboratory, Richland, WA (United States). Environmental Technology; Delwiche, M. [Idaho National Laboratory, Idaho Falls, ID (United States). Biotechnology; Winters, W. [United States Geological Survey, Woods Hole, MA (United States). Woods Hole Science Center; Riedel, M. [McGill Univ., Montreal, PQ (Canada). Dept. of Earth and Planetary Sciences

2008-07-01

Methane produced by microorganisms represents a large portion of the methane that occurs in marine sediments where gas hydrates are present. The diverse communities that populate these formations have been documented by cultures or through molecular traces. Previous studies have explored the biogeography of hydrate-bearing systems by comparing clone libraries developed from sediments where hydrates are abundant with those developed from sediments that lack hydrates. There is a distinct microbial community present in sediments that have methane hydrates. This paper presented an investigation into finer-scale biogeography, in order to determine how factors such as the presence or absence of hydrates, grain size, and the depositional environment in marine sediments may control the number, type and distribution of microbial communities in sediments. The purpose of the study was to understand the controls on the distribution and activity of all microbes that contribute to the conversion of organic matter to methane. To this aim, DNA was extracted from deep marine sediments cored from continental slope locations including offshore India and the Cascadia Margin. The data from the study was used to refine computational models that require biological rate terms that are consistent with sediment conditions in order to accurately describe the dynamics of this large methane reservoir. The paper discussed the materials and methods used for the study, including the sample site, sample collection and microbiological analysis. Results were presented in terms of DNA extractions; microbial diversity; and biofilm analyses. It was concluded that the findings from the study complemented previously reported studies which indicated the presence of diverse microbial communities in sediments containing methane hydrates. 9 refs., 5 figs.

Selective whole genome amplification for resequencing target microbial species from complex natural samples.

Science.gov (United States)

Leichty, Aaron R; Brisson, Dustin

2014-10-01

Population genomic analyses have demonstrated power to address major questions in evolutionary and molecular microbiology. Collecting populations of genomes is hindered in many microbial species by the absence of a cost effective and practical method to collect ample quantities of sufficiently pure genomic DNA for next-generation sequencing. Here we present a simple method to amplify genomes of a target microbial species present in a complex, natural sample. The selective whole genome amplification (SWGA) technique amplifies target genomes using nucleotide sequence motifs that are common in the target microbe genome, but rare in the background genomes, to prime the highly processive phi29 polymerase. SWGA thus selectively amplifies the target genome from samples in which it originally represented a minor fraction of the total DNA. The post-SWGA samples are enriched in target genomic DNA, which are ideal for population resequencing. We demonstrate the efficacy of SWGA using both laboratory-prepared mixtures of cultured microbes as well as a natural host-microbe association. Targeted amplification of Borrelia burgdorferi mixed with Escherichia coli at genome ratios of 1:2000 resulted in >10(5)-fold amplification of the target genomes with genomic extracts from Wolbachia pipientis-infected Drosophila melanogaster resulted in up to 70% of high-throughput resequencing reads mapping to the W. pipientis genome. By contrast, 2-9% of sequencing reads were derived from W. pipientis without prior amplification. The SWGA technique results in high sequencing coverage at a fraction of the sequencing effort, thus allowing population genomic studies at affordable costs. Copyright © 2014 by the Genetics Society of America.

Culture-Independent Molecular Tools for Soil and Rhizosphere Microbiology

Directory of Open Access Journals (Sweden)

Peer M. Schenk

2013-08-01

Full Text Available Soil microbial communities play an important role in plant health and soil quality. Researchers have developed a wide range of methods for studying the structure, diversity, and activity of microbes to better understand soil biology and plant-microbe interactions. Functional microbiological analyses of the rhizosphere have given new insights into the role of microbial communities in plant nutrition and plant protection against diseases. In this review, we present the most commonly used traditional as well as new culture-independent molecular methods to assess the diversity and function of soil microbial communities. Furthermore, we discuss advantages and disadvantages of these techniques and provide a perspective on emerging technologies for soil microbial community profiling.

Screening of biofilm formation by beneficial vaginal lactobacilli and influence of culture media components.

Science.gov (United States)

Terraf, M C Leccese; Juárez Tomás, M S; Nader-Macías, M E F; Silva, C

2012-12-01

To assess the ability of vaginal lactobacilli to form biofilm under different culture conditions and to determine the relationship between their growth and the capability of biofilm formation by selected strains. Fifteen Lactobacillus strains from human vagina were tested for biofilm formation by crystal violet staining. Only Lactobacillus rhamnosus Centro de Referencia para Lactobacilos Culture Collection (CRL) 1332, Lact. reuteri CRL 1324 and Lact. delbrueckii CRL 1510 were able to grow and form biofilm in culture media without Tween 80. However, Lact. gasseri CRL 1263 (a non-biofilm-forming strain) did not grow in these media. Scanning electron microscopy showed that Lact. rhamnosus CRL 1332 and Lact. reuteri CRL 1324 formed a highly structured biofilm, but only Lact. reuteri CRL 1324 showed a high amount of extracellular material in medium without Tween. Biofilm formation was significantly influenced by the strain, culture medium, inoculum concentration, microbial growth and chemical nature of the support used for the assay. The results allow the selection of biofilm-forming vaginal Lactobacillus strains and the conditions and factors that affect this phenomenon. © 2012 The Society for Applied Microbiology.

Effects of microbial inhibitors on anaerobic degradation of DDT

Energy Technology Data Exchange (ETDEWEB)

Wang, Y.S.; Chiu, T.C.; Yen, J.H. [National Taiwan Univ., Taipei (Taiwan)

2004-09-15

Chlorinated insecticide DDT [1,1,1-trichloro-2,2-bis(p-chlorophenyl)ethane] was extensively used for controlling pests in the agricultural field and human-being living environments in the past several decades. Due to the chemical stability, DDT was extremely persistent and recalcitrant in soils and sediments and it was banned by nations. Microorganisms usually play important roles in reducing organochlorine compounds in the environments. Under low-oxygen conditions, microbial dechlorination is thought as the onset of highly chlorinated compounds. Methanogenic and sulfate-reducing bacteria participate in microbial dechlorination under anaerobic condition has been reported. In this study, a mixed anaerobic culture enabling to dechlorinate DDT was obtained from river sediment in Taiwan. In order to understand the effect of these microorganisms on DDT dechlorination, microbial inhibitors BESA (2-bromoethanesulfonate) and molybdate, for inhibiting methanogenic and sulfate-reducing bacteria, respectively, were chosen to investigate the interaction between specific microbial communities and their degradation activities. Besides, a molecular technique, denaturing gradient gel electrophoresis (DGGE), based on analyzing the 16S rDNA of bacteria, was used for monitoring the bacterial community structure in this study.

Bioaugmentation for Electricity Generation from Corn Stover Biomass Using Microbial Fuel Cells

KAUST Repository

Wang, Xin; Feng, Yujie; Wang, Heming; Qu, Youpeng; Yu, Yanling; Ren, Nanqi; Li, Nan; Wang, Elle; Lee, He; Logan, Bruce E.

2009-01-01

of microbial consortia specifically acclimated for biomass breakdown. A mixed culture that was developed to have a high saccharification rate with corn stover was added to singlechamber, air-cathode MFCs acclimated for power production using glucose. The MFC

Selective sweeps in growing microbial colonies

International Nuclear Information System (INIS)

Korolev, Kirill S; Müller, Melanie J I; Murray, Andrew W; Nelson, David R; Karahan, Nilay; Hallatschek, Oskar

2012-01-01

Evolutionary experiments with microbes are a powerful tool to study mutations and natural selection. These experiments, however, are often limited to the well-mixed environments of a test tube or a chemostat. Since spatial organization can significantly affect evolutionary dynamics, the need is growing for evolutionary experiments in spatially structured environments. The surface of a Petri dish provides such an environment, but a more detailed understanding of microbial growth on Petri dishes is necessary to interpret such experiments. We formulate a simple deterministic reaction–diffusion model, which successfully predicts the spatial patterns created by two competing species during colony expansion. We also derive the shape of these patterns analytically without relying on microscopic details of the model. In particular, we find that the relative fitness of two microbial strains can be estimated from the logarithmic spirals created by selective sweeps. The theory is tested with strains of the budding yeast Saccharomyces cerevisiae for spatial competitions with different initial conditions and for a range of relative fitnesses. The reaction–diffusion model also connects the microscopic parameters like growth rates and diffusion constants with macroscopic spatial patterns and predicts the relationship between fitness in liquid cultures and on Petri dishes, which we confirmed experimentally. Spatial sector patterns therefore provide an alternative fitness assay to the commonly used liquid culture fitness assays. (paper)

Selective sweeps in growing microbial colonies

Science.gov (United States)

Korolev, Kirill S.; Müller, Melanie J. I.; Karahan, Nilay; Murray, Andrew W.; Hallatschek, Oskar; Nelson, David R.

2012-04-01

Evolutionary experiments with microbes are a powerful tool to study mutations and natural selection. These experiments, however, are often limited to the well-mixed environments of a test tube or a chemostat. Since spatial organization can significantly affect evolutionary dynamics, the need is growing for evolutionary experiments in spatially structured environments. The surface of a Petri dish provides such an environment, but a more detailed understanding of microbial growth on Petri dishes is necessary to interpret such experiments. We formulate a simple deterministic reaction-diffusion model, which successfully predicts the spatial patterns created by two competing species during colony expansion. We also derive the shape of these patterns analytically without relying on microscopic details of the model. In particular, we find that the relative fitness of two microbial strains can be estimated from the logarithmic spirals created by selective sweeps. The theory is tested with strains of the budding yeast Saccharomyces cerevisiae for spatial competitions with different initial conditions and for a range of relative fitnesses. The reaction-diffusion model also connects the microscopic parameters like growth rates and diffusion constants with macroscopic spatial patterns and predicts the relationship between fitness in liquid cultures and on Petri dishes, which we confirmed experimentally. Spatial sector patterns therefore provide an alternative fitness assay to the commonly used liquid culture fitness assays.

Characterization of multiple antibiotic resistance of culturable microorganisms and metagenomic analysis of total microbial diversity of marine fish sold in retail shops in Mumbai, India.

Science.gov (United States)

Naik, Onkar A; Shashidhar, Ravindranath; Rath, Devashish; Bandekar, Jayant R; Rath, Archana

2018-03-01

Marine fish species were analyzed for culturable and total metagenomic microbial diversity, antibiotic resistance (AR) pattern, and horizontal gene transfer in culturable microorganisms. We observed a high AR microbial load of 3 to 4 log CFU g -1 . Many fish pathogens like Providencia, Staphylococcus, Klebsiella pneumoniae, Enterobacter, Vagococcus, and Aeromonas veronii were isolated. Photobacterium and Vibrio were two major fish and human pathogens which were identified in the fish metagenome. Other pathogens that were identified were Shewanella, Acinetobacter, Psychrobacter, and Flavobacterium. Most of these pathogens were resistant to multiple antibiotics such as erythromycin, kanamycin, neomycin, streptomycin, penicillin, cefotaxime, bacitracin, rifampicin, trimethoprim, ciprofloxacin, and doxycycline with a high multiple antibiotic resistance index of 0.54-0.77. The fish microflora showed high prevalence of AR genes like bla TEM , Class I integron, tetA, aph(3')-IIIa, ermB, aadA, and sul1. Nineteen of 26 AR isolates harbored Class I integrons showing high co-resistance to trimethoprim, kanamycin, doxycycline, and cefotaxime. Mobile R-plasmids from 6 of the 12 AR pathogens were transferred to recipient E. coli after conjugation. The transconjugants harbored the same R-plasmid carrying bla CTX-M , dfr1, tetA, bla TEM , and cat genes. This study confirms that fish is a potential carrier of AR pathogens which can enter the human gut via food chain. To the best of our knowledge, this is the first study in the Indian subcontinent reporting a direct evidence of spread of AR pathogens to humans from specific marine fish consumption.

Smoking Impact on the Microbial Load of Clarias gariepinus ...

African Journals Online (AJOL)

Effects of different smoking methods on microbial load on freshly collected freshwater mud fish, Clarias gariepinus samples from Oyo State Fisheries Department, Ibadan in South-Western Nigeria was carried out. Seventy-two C. gariepinus (505 ± 0.45g and 25.5 ± 1.30cm) were collected and sorted into 4 groups. 10 fish ...

Microbial uptake of uranium, cesium, and radium

Energy Technology Data Exchange (ETDEWEB)

Strandberg, G.W.; Shumate, S.E. II; Parrott, J.R. Jr.; McWhirter, D.A.

1980-01-01

The ability of diverse microbial species to concentrate uranium, cesium, and radium was examined. Saccharomyces cerevisiae, Pseudomonas aeruginosa, and a mixed culture of denitrifying bacteria accumulated uranium to 10 to 15% of the dry cell weight. Only a fraction of the cells in a given population had visible uranium deposits in electron micrographs. While metabolism was not required for uranium uptake, mechanistic differences in the metal uptake process were indicated. Uranium accumulated slowly (hours) on the surface of S. cerevisiae and was subject to environmental factors (i.e., temperature, pH, interfering cations and anions). In contrast, P. aeruginosa and the mixed culture of denitrifying bacteria accumulated uranium rapidly (minutes) as dense, apparently random, intracellular deposits. This very rapid accumulation has prevented us from determining whether the uptake rate during the transient between the initial and equilibrium distribution of uranium is affected by environmental conditions. However, the final equilibrium distributions are not affected by those conditions which affect uptake by S. cerevisiae. Cesium and radium were concentrated to a considerably lesser extent than uranium by the several microbial species tested. The potential utility of microorganisms for the removal and concentration of these metals from nuclear processing wastes and several bioreactor designs for contacting microorganisms with contaminated waste streams will be discussed.

The role of microbial low-molecular-weight autoregulatory factors (alkylhydroxybenzenes) in resistance of microorganisms to radiation

Science.gov (United States)

El-Registan, G. I.; Mulyukin, A. L.; Nikolaev, Yu. A.; Stepanenko, I. Yu.; Shanenko, E. A.; Strakhovskaya, M. G.; Revina, A. 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 homologs of alkylhydroxybenzenes (AHBs). 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), heat shock. Chemical analogs of microbial AHBs protected microbial cultures from stressful situations and prolonged starvation and exerted (1) the stabilizing activity toward biomacromolecules and supermolecular structures (cell membranes) and (2) the ability to scavenge active oxygen species. The stabilizing effect of AHBs as chemical chaperones 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, amylase, etc.). The action of AHBs as active oxygen species scavengers was related to their oxidative conversion to water-insoluble polymeric products. Particularly, AHBs protected the yeast from the action of (a) active oxygen species formed during gamma-irradiation (50 krad, 196 rad/sec) or (b) singlet oxygen generated in cells photosensitized by chlorin e6 (10 mkg/L). It is important that microbial AHBs were not species-specific and defended cultured animal cells (ras-transformed fibroblasts) from the action of organic toxicants. The use of AHBs as protectants and adaptogens will be discussed as well as perspectives of further investigations.

Psychrophiles and astrobiology: microbial life of frozen worlds

Science.gov (United States)

Pikuta, Elena V.; Hoover, Richard B.

2003-01-01

Most bodies of our Solar System are "Frozen Worlds" where the prevailing surface temperature remains at or below freezing. On Earth there are vast permanently frozen regions of permafrost, polar ice sheets, and glaciers and the deep oceans and deep-sea marine sediments have remained at 2 - 4°C for eons. Psychrophilic and psychrotrophic microbiota that inhabit these regimes provide analogs for microbial life that might inhabit ice sheets and permafrost of Mars, comets, or the ice/water interfaces or sediments deep beneath the icy crusts of Europa, Callisto, or Ganymede. Cryopreserved micro-organisms can remain viable (in a deep anabiotic state) for millions of years frozen in permafrost and ice. Psychrophilic and psychrotrophic (cold-loving) microbes can carry out metabolic processes in water films and brine, acidic, or alkaline chanels in permafrost or ice at temperatures far below 0°C. These microbes of the cryosphere help define the thermal and temporal limits of life on Earth and may provide clues to where and how to search for evidence of life elsewhere in the Cosmos. Astrobiologists at the NASA Marshall Space Flight Center have collected microbial extremophiles from the Pleistocene ice wedges and frozen thermokarst ponds from the Fox Permafrost Tunnel of Alaska. Microbes have also been isolated from samples of Magellanic Penguin guano from Patagonia; deep-sea marine muds near hydrothermal vents; snow and permafrost from Siberia, and deep ice cores, ice-bubble and cryoconite rocks of the Central Antarctic Ice Sheet. These samples have yielded microbial extremophiles representing a wide variety of anaerobic bacteria and archaea. These microbes have been isolated, cultured, characterized and analyzed by phylogenetic and genomic methods. Images were obtained by Phase Contrast, Environmental, Field Emission Scanning and Transmission Electron Microscopes to study the ultra-microstructure and elemental distribution in the composition of these micro-organisms. We

Clinical Presentation and Antibiotic Susceptibility of Contact Lens Associated Microbial Keratitis

Directory of Open Access Journals (Sweden)

Hesam Hedayati

2015-01-01

Full Text Available Introduction. In recent years, the number of contact lens wearers has dramatically increased in Iran, particularly in youngsters. The purpose of current study was to assess the clinical presentation and antibiotic susceptibility of contact lens related microbial keratitis in Ahvaz, southwest of Iran. Methodology. A cross-sectional investigation of 26 patients (33 eyes with contact lens induced corneal ulcers who were admitted to Imam Khomeini Hospital, Ahwaz City, from June 2012 to June 2013 was done. In order to study microbial culture and susceptibility of corneal ulcers, all of them were scraped. Results. Eight samples were reported as sterile. Pseudomonas aeruginosa (80% in positive cultures was the most widely recognized causative organism isolated. This is followed by Staphylococcus aureus 12% and Enterobacter 8%. The results showed that 84% of the microorganism cases were sensitive to ciprofloxacin, while imipenem, meropenem, and ceftazidime were the second most effective antibiotics (76%. Conclusion. Results of current study show the importance of referring all contact lens wearers with suspected corneal infection to ophthalmologists for more cure. The corneal scraping culture and contact lens solution should be performed to guide antibiotic therapy.

Characterization of Microbial Communities in Chinese Rice Wine Collected at Yichang City and Suzhou City in China.

Science.gov (United States)

Lü, Yucai; Gong, Yanli; Li, Yajie; Pan, Zejiang; Yao, Yi; Li, Ning; Guo, Jinling; Gong, Dachun; Tian, Yihong; Peng, Caiyun

2017-08-28

Two typical microbial communities from Chinese rice wine fermentation collected in Yichang city and Suzhou city in China were investigated. Both communities could ferment glutinous rice to rice wine in 2 days. The sugar and ethanol contents were 198.67 and 14.47 mg/g, respectively, for rice wine from Yichang city, and 292.50 and 12.31 mg/g, respectively, for rice wine from Suzhou city. Acetic acid and lactic acid were the most abundant organic acids. Abundant fungi and bacteria were detected in both communities by high-throughput sequencing. Saccharomycopsis fibuligera and Rhizopus oryzae were the dominant fungi in rice wine from Suzhou city, compared with R. oryzae , Wickerhamomyces anomalus, Saccharomyces cerevisiae, Mucor indicus , and Rhizopus microsporus in rice wine from Yichang city. Bacterial diversity was greater than fungal diversity in both communities. Citrobacter was the most abundant genus. Furthermore, Exiguobacterium, Aeromonas, Acinetobacter, Pseudomonas, Enterobacter, Bacillus , and Lactococcus were highly abundant in both communities.

Cultural commons and cultural evolution

OpenAIRE

Bravo, Giangiacomo

2010-01-01

Culture evolves following a process that is akin to biological evolution, although with some significant differences. At the same time culture has often a collective good value for human groups. This paper studies culture in an evolutionary perspective, with a focus on the implications of group definition for the coexistence of different cultures. A model of cultural evolution is presented where agents interacts in an artificial environment. The belonging to a specific memetic group is a majo...

Taxonomia e potencial antimicrobiano de fungos depositados no acervo de pesquisa da Central de Recursos Microbianos da UNESP

OpenAIRE

Polezel, Danilo Augusto [UNESP

2015-01-01

Culture collections are keystones in the preservation, cataloging and exploration of microbial diversity. In order to meet international standards of deposit and supply of biological materials, the UNESP-Microbial Resources Center (CRM-UNESP) started their suitability for functioning and management to reach international standards; which include taxonomic authentication of cultures preserved in the collection. Using an adapted molecular screening protocol (microsatellites) coupled with morpho...

The role of acid incubation in rapid immobilization of hydrogen-producing culture in anaerobic upflow column reactors

Energy Technology Data Exchange (ETDEWEB)

Zhang, Zhen-Peng; Tay, Joo-Hwa [School of Civil and Environmental Engineering, Nanyang Technological University (Singapore); Institute of Environmental Science and Engineering, Nanyang Technological University (Singapore); Show, Kuan-Yeow [Faculty of Science, Engineering and Technology, University Tunku Abdul Rahman, 31900 Kampar, Perak (Malaysia); Liang, David Tee [Institute of Environmental Science and Engineering, Nanyang Technological University (Singapore); Lee, Duu-Jong [Department of Chemical Engineering, National Taiwan University, Taipei 10617 (China); Su, Ay [Department of Mechanical Engineering, Fuel Cell Center, Yuan-Ze University, Taoyuan 320 (China)

2008-10-15

An approach of acidification was examined on formation of hydrogen-producing granules and biofilms in upflow column-shaped reactors. The reactors were fed with synthetic glucose wastewater and operated at 37 C and pH 5.5. The acclimated anaerobic culture was inoculated in four reactors designated R1, R2, R3 and R4, with R3 and R4 filled with granular activated carbon as support medium. To unveil the roles of acidification, microbial culture in R2 and R3 was subject to an acid incubation for 24 h by shifting the culture pH from 5.5 to 2.0. The experimental results suggested that the acidification substantially accelerated microbial granulation, but not biofilm formation. Microbial activities were inhibited by the acid incubation for about 78 h, resulting in the retarded formation of biofilms of the acidified culture. Reducing culture pH resulted in improvement in cell surface physicochemical properties favoring microbial adhesion and immobilization. Zeta potential increased from -25.3 mV to 11.9 mV, hydrophobicity in terms of contact angle improved from 31 to 38 and production of extracellular polymers increased from 66 mg/g-VSS to 136 mg/g-VSS. As a result of the formation of granules and biofilms, high hydrogen production rates of 6.98 and 7.49 L/L h were achieved in granule-based and biofilm-based reactors, respectively. It is concluded that acid incubation is an efficient means to initiate the rapid formation of granules by regulating the surface characteristics of microbial culture. The use of support media as starting nuclei may result in rapid formation of biofilms without the acidification. (author)

The role of acid incubation in rapid immobilization of hydrogen-producing culture in anaerobic upflow column reactors

International Nuclear Information System (INIS)

Zhang, Zhen-Peng; Tay, Joo-Hwa; Show, Kuan-Yeow; Liang, David Tee; Lee, Duu-Jong; Su, Ay

2008-01-01

An approach of acidification was examined on formation of hydrogen-producing granules and biofilms in upflow column-shaped reactors. The reactors were fed with synthetic glucose wastewater and operated at 37 C and pH 5.5. The acclimated anaerobic culture was inoculated in four reactors designated R1, R2, R3 and R4, with R3 and R4 filled with granular activated carbon as support medium. To unveil the roles of acidification, microbial culture in R2 and R3 was subject to an acid incubation for 24 h by shifting the culture pH from 5.5 to 2.0. The experimental results suggested that the acidification substantially accelerated microbial granulation, but not biofilm formation. Microbial activities were inhibited by the acid incubation for about 78 h, resulting in the retarded formation of biofilms of the acidified culture. Reducing culture pH resulted in improvement in cell surface physicochemical properties favoring microbial adhesion and immobilization. Zeta potential increased from -25.3 mV to 11.9 mV, hydrophobicity in terms of contact angle improved from 31 to 38 and production of extracellular polymers increased from 66 mg/g-VSS to 136 mg/g-VSS. As a result of the formation of granules and biofilms, high hydrogen production rates of 6.98 and 7.49 L/L h were achieved in granule-based and biofilm-based reactors, respectively. It is concluded that acid incubation is an efficient means to initiate the rapid formation of granules by regulating the surface characteristics of microbial culture. The use of support media as starting nuclei may result in rapid formation of biofilms without the acidification. (author)

Synthetic microbial ecology and the dynamic interplay between microbial genotypes.

Science.gov (United States)

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

2016-11-01

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

Comparison of Different Strategies for Selection/Adaptation of Mixed Microbial Cultures Able to Ferment Crude Glycerol Derived from Second-Generation Biodiesel

DEFF Research Database (Denmark)

Varrone, Cristiano; Heggeset, T. M. B.; Le, S. B.

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...... 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...

Mixed Cultures Fermentation for the Production of Poly-ß-hydroxybutyrate

Directory of Open Access Journals (Sweden)

Thomas Shalin

2014-10-01

Full Text Available Poly-ß-hydroxybutyrate (PHB is a biodegradable intracellular microbial product produced by many bacteria and it is comparable to some of the petrochemical derived thermoplastics such as polypropylene. One of the main barriers for the commercial exploitation is the high cost of the substrate for the production of biopolymer. The utilization of mixed microbial cultures facilitates the use of complex substrates thereby reducing the cost of PHB production. In the present study, mixed culture systems were evaluated for PHB production. Bacillus firmus NII 0830 was used for the production of PHB since it accumulates a large amount of PHB and a second organism Lactobacillus delbrueckii NII 0925 was used to provide lactic acid. FTIR and 1H NMR analyses revealed that the PHB extracted from pure culture and mixed culture showed exact match to that of standard PHB. Biodegradation studies of the PHB blends showed 87% degradation. It was also found that a consortium of organisms degraded the films faster than a single organism.

Dynamics of Cocoa Bean Pulp Degradation during Cocoa Bean Fermentation: Effects of Yeast Starter Culture Addition

Directory of Open Access Journals (Sweden)

Laras Cempaka

2014-07-01

Full Text Available Fermentation is a crucial step in the post-harvest processing of cocoa beans. This process comprises mixed culture microbial activities on the cocoa bean pulp, producing metabolites that act as important precursors for cocoa flavour development. Variations in the microbial population dynamics during the fermentation process may induce changes in the overall process. Thus, the introduction of a specific microbial starter culture may improve the quality of the fermentation. This article discusses the effects ofthe addition of Saccharomyces cerevisae var. Chevalieri starter culture on cocoa bean fermentation. The dynamics in the yeast concentration, sugary pulp compounds and metabolic products were measured during fermentation. The alterations in the dynamic metabolite profile were significant, although only a slight difference was observed in the yeast population. A higher fermentation index was measured for the cocoa bean fermentation with yeast starter culture, 1.13 compared to 0.84. In conclusion, this method can potentially be applied to shorten the cocoa bean fermentation time.

Direct identification of microorganisms from positive blood cultures using the lysis-filtration technique and matrix assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS): a multicentre study.

Science.gov (United States)

Farina, Claudio; Arena, Fabio; Casprini, Patrizia; Cichero, Paola; Clementi, Massimo; Cosentino, Marina; Degl'Innocenti, Roberto; Giani, Tommaso; Luzzaro, Francesco; Mattei, Romano; Mauri, Carola; Nardone, Maria; Rossolini, Gian Maria; Serna Ortega, Paula Andrea; Vailati, Francesca

2015-04-01

Microbial identification from blood cultures is essential to institute optimal antibiotic therapy and improve survival possibilities. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been successfully applied to identify bacteria and yeasts from positive blood cultures broths. The aim of this multicentre study was to evaluate the reliability of the lysis-filtration technique associated with MALDI-TOF MS to directly identify microorganisms from 765 positive blood cultures collected in six Italian hospitals. Overall, 675/765 (78.1%) blood isolates were correctly identified at the species level, with significant differences between Gram-negative and Gram-positive bacteria (92.6%, and 69.8%, respectively). Some difficulties arise in identifying Streptococcus pneumoniae, Staphylococcus aureus, yeasts and anaerobes. The lysis-filtration protocol is a suitable procedure in terms of performance in identifying microorganisms, but it is quite expensive and technically time-consuming since the time of filtration is not regular for all the samples. The application of the MALDI-TOF MS technique to the direct microbial identification from positive blood cultures is a very promising approach, even if more experience must be gained to minimize errors and costs.

Discovery of novel enzymes with industrial potential from a cold and alkaline environment by a combination of functional metagenomics and culturing.

Science.gov (United States)

Vester, Jan Kjølhede; Glaring, Mikkel Andreas; Stougaard, Peter

2014-05-20

The use of cold-active enzymes has many advantages, including reduced energy consumption and easy inactivation. The ikaite columns of SW Greenland are permanently cold (4-6°C) and alkaline (above pH 10), and the microorganisms living there and their enzymes are adapted to these conditions. Since only a small fraction of the total microbial diversity can be cultured in the laboratory, a combined approach involving functional screening of a strain collection and a metagenomic library was undertaken for discovery of novel enzymes from the ikaite columns. A strain collection with 322 cultured isolates was screened for enzymatic activities identifying a large number of enzyme producers, with a high re-discovery rate to previously characterized strains. A functional expression library established in Escherichia coli identified a number of novel cold-active enzymes. Both α-amylases and β-galactosidases were characterized in more detail with respect to temperature and pH profiles and one of the β-galactosidases, BGalI17E2, was able to hydrolyze lactose at 5°C. A metagenome sequence of the expression library indicated that the majority of enzymatic activities were not detected by functional expression. Phylogenetic analysis showed that different bacterial communities were targeted with the culture dependent and independent approaches and revealed the bias of multiple displacement amplification (MDA) of DNA isolated from complex microbial communities. Many cold- and/or alkaline-active enzymes of industrial relevance were identified in the culture based approach and the majority of the enzyme-producing isolates were closely related to previously characterized strains. The function-based metagenomic approach, on the other hand, identified several enzymes (β-galactosidases, α-amylases and a phosphatase) with low homology to known sequences that were easily expressed in the production host E. coli. The β-galactosidase BGalI17E2 was able to hydrolyze lactose at low

Conditional Dependence in Microbial Forensic Assays - A Primer

Energy Technology Data Exchange (ETDEWEB)

Velsko, Stephan P. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

2013-11-08

This report provides an introduction to the topic of conditional dependence in the context of microbial forensic assays. Conditional dependence between two items of evidence E1 and E2 occurs when they are both used to support a hypothesis, but E1 affects the probability of E2 and vice versa. Ignoring this dependence can lead to very large errors in estimating the diagnosticity of the combined evidence. To introduce readers to this concept, a number of definitions of conditional dependence that have been used by authors in the past have been collected together and compared. Formal mathematical relationships that constrain conditional dependence are summarized. There are several specific scenarios in which unrecognized conditional dependence can arise in microbial forensic contexts. This report provides some notional examples that illustrate dramatic effects of conditional dependence on the weight of microbial forensic evidence, and discusses the relevance of these observations for the validation of microbial forensic assays. A two-­parameter model that describes the transition between various limiting forms of conditional dependence relations is provided in an appendix.

Microbial mutualism at a distance: The role of geometry in diffusive exchanges

Science.gov (United States)

Peaudecerf, François J.; Bunbury, Freddy; Bhardwaj, Vaibhav; Bees, Martin A.; Smith, Alison G.; Goldstein, Raymond E.; Croze, Ottavio A.

2018-02-01

The exchange of diffusive metabolites is known to control the spatial patterns formed by microbial populations, as revealed by recent studies in the laboratory. However, the matrices used, such as agarose pads, lack the structured geometry of many natural microbial habitats, including in the soil or on the surfaces of plants or animals. Here we address the important question of how such geometry may control diffusive exchanges and microbial interaction. We model mathematically mutualistic interactions within a minimal unit of structure: two growing reservoirs linked by a diffusive channel through which metabolites are exchanged. The model is applied to study a synthetic mutualism, experimentally parametrized on a model algal-bacterial co-culture. Analytical and numerical solutions of the model predict conditions for the successful establishment of remote mutualisms, and how this depends, often counterintuitively, on diffusion geometry. We connect our findings to understanding complex behavior in synthetic and naturally occurring microbial communities.

The language of cheese-ripening cultures

DEFF Research Database (Denmark)

Gori, Klaus; Jespersen, Lene

2010-01-01

Microbial interactions are of importance for the establishment and growth of cheese ripening cultures. An interesting aspect of microbial interactions is cell-cell communication, often referred to as quorum sensing; the process in which micro-organisms communicate with signalling molecules and co......-ordinate gene expression in a cell density dependent manner. Little is known about quorum sensing in foods. However, as quorum sensing is expected to be a general phenomenon in micro-organisms, it is likely to be of importance for micro-organisms in foods. An example of a food product where quorum sensing could...... be of importance is surface ripened cheeses. The present review focuses on our findings on quorum sensing systems in cheese ripening cultures. The main focus is on the group of bacterial non-species-specific signalling molecules referred to as autoinducer-2 (AI-2) in smear bacteria as well as alcohol...

Transvaginal Drainage of Pelvic Abscesses and Collections Using Transabdominal Ultrasound Guidance.

Science.gov (United States)

Ching, Kevin C; Sumkin, Jules H

2015-01-01

Objectives. To evaluate clinical outcomes following transvaginal catheter placement using transabdominal ultrasound guidance for management of pelvic fluid collections. Methods. A retrospective review was performed for all patients who underwent transvaginal catheter drainage of pelvic fluid collections utilizing transabdominal ultrasound guidance between July 2008 and July 2013. 24 consecutive patients were identified and 24 catheters were placed. Results. The mean age of patients was 48.1 years (range = 27-76 y). 88% of collections were postoperative (n = 21), 8% were from pelvic inflammatory disease (n = 2), and 4% were idiopathic (n = 1). Of the 24 patients, 83% of patients (n = 20) had previously undergone a hysterectomy and 1 patient (4%) was pregnant at the time of drainage. The mean volume of initial drainage was 108 mL (range = 5 to 570). Catheters were left in place for an average of 4.3 days (range = 1-17 d). Microbial sampling was performed in all patients with 71% (n = 17) returning a positive culture. All collections were successfully managed percutaneously. There were no technical complications. Conclusions. Transvaginal catheter drainage of pelvic fluid collections using transabdominal ultrasound guidance is a safe and clinically effective procedure. Appropriate percutaneous management can avoid the need for surgery.

[Oxidation of sulfur-containing substrates by aboriginal and experimentally designed microbial communities].

Science.gov (United States)

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

2012-01-01

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

Cultural Understanding Through Cross-Cultural Analysis.

Science.gov (United States)

Briere, Jean-Francois

1986-01-01

A college course used an explicit intercultural approach and collective research activities to compare French and American cultures and to examine the reasons for cultural attitudes and culture conflict. Class assignments dealt with contrastive analyses of American and French institutions like advertising, cinema, feminism, etc. (MSE)

Egypt’s Red Sea Coast: Phylogenetic analysis of cultured microbial consortia in industrialized sites

Directory of Open Access Journals (Sweden)

Ghada A. Mustafa

2014-08-01

Full Text Available The Red Sea has a unique geography and ecosystem and its shores are very rich in mangrove, macro-algae and coral reefs. Different sources of pollution are affecting the Red Sea shores and waters which impacts biological life including microbial life. We assessed the effects of industrialization, along the Egyptian Red Sea coast in eight coastal sites and two lakes, on microbial life. The bacterial community in sediment samples was analyzed using bacterial 16S rDNApyrosequencing of V6-V4 hypervariable regions. Taxonomical assignment of 131,402 significant reads to major bacterial taxa revealed five main bacterial phyla dominating the sampled Red Sea sites. This includes Proteobacteria (68%, Firmicutes (13%, Fusobacteria (12%, Bacteriodetes (6% and Spirochetes (0.03%. Further analysis revealed distinct bacterial consortium formed mainly of: 1 marine Vibrio’s- suggesting a Marine Vibrio phenomenon 2 potential human pathogens and 3 oil-degrading bacteria. We discuss a distinct microbial consortium in Solar Lake West near Taba/Eilat and Saline Lake in Ras Muhammad; revealing the highest abundance of human pathogens versus no pathogens, respectively. Our results draw attention to the affects of industrialization on the Red Sea, and suggest further analysis to overcome hazardous affects on the impacted sites.

Determination of lactic microflora of kefir grains and kefir beverage by using culture-dependent and culture-independent methods.

Science.gov (United States)

Kesmen, Zülal; Kacmaz, Nazife

2011-01-01

In this study, we investigated the bacterial compositions of kefir grains and kefir beverages collected from different regions of Turkey by using culture-independent and culture-dependent methods. In the culture-independent detection, 10 different species of bacteria were detected in total by using the polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis of the 16S rRNA gene V3 region. Among these species, Lactobacillus kefiranofaciens was the most dominant one in the kefir grains, while Lactococcus lactis was found to be significantly prevalent in the kefir beverages. In the culture-dependent detection, the primary differentiation and grouping of the isolates from kefir beverages and kefir grains were performed using repetitive sequence-based PCR (rep-PCR) fingerprinting, and the results were validated by 16S rDNA full-length sequencing. According to the results of culture-dependent methods, the most frequently isolated species were L. lactis, Leuconostoc mesenteroides, and Lactobacillus kefiri, respectively. Only 3 species, which are L. lactis, Lactobacillus acidophilus, and Streptococcus thermophilus, were detected with both culture-dependent and culture-independent methods. This study showed that the combination of both methods is necessary for a detailed and reliable investigation of microbial communities in kefir grains and kefir beverages. Due to their artisan- and region-dependent microflora, kefir products can be a source of interesting lactic acid bacteria, either new taxa or strains with specific functional properties, which might be used for the development of new starter cultures and innovative food products. Therefore, an increasing demand exists for new strains that show desirable effects on the product characteristics Artisan dairy products are a candidate source of such microorganisms. For this reason, in this study, the bacterial compositions of kefir grains and kefir beverages obtained from

Web-based experiments for the study of collective social dynamics in cultural markets.

Science.gov (United States)

Salganik, Matthew J; Watts, Duncan J

2009-07-01

Social scientists are often interested in understanding how the dynamics of social systems are driven by the behavior of individuals that make up those systems. However, this process is hindered by the difficulty of experimentally studying how individual behavioral tendencies lead to collective social dynamics in large groups of people interacting over time. In this study, we investigate the role of social influence, a process well studied at the individual level, on the puzzling nature of success for cultural products such as books, movies, and music. Using a "multiple-worlds" experimental design, we are able to isolate the causal effect of an individual-level mechanism on collective social outcomes. We employ this design in a Web-based experiment in which 2,930 participants listened to, rated, and downloaded 48 songs by up-and-coming bands. Surprisingly, despite relatively large differences in the demographics, behavior, and preferences of participants, the experimental results at both the individual and collective levels were similar to those found in Salganik, Dodds, and Watts (2006). Further, by comparing results from two distinct pools of participants, we are able to gain new insights into the role of individual behavior on collective outcomes. We conclude with a discussion of the strengths and weaknesses of Web-based experiments to address questions of collective social dynamics. Copyright © 2009 Cognitive Science Society, Inc.

Culturable bioaerosols along an urban waterfront are primarily associated with coarse particles

Directory of Open Access Journals (Sweden)

Angel Montero

2016-12-01

Full Text Available The source, characteristics and transport of viable microbial aerosols in urban centers are topics of significant environmental and public health concern. Recent studies have identified adjacent waterways, and especially polluted waterways, as an important source of microbial aerosols to urban air. The size of these aerosols influences how far they travel, their resistance to environmental stress, and their inhalation potential. In this study, we utilize a cascade impactor and aerosol particle monitor to characterize the size distribution of particles and culturable bacterial and fungal aerosols along the waterfront of a New York City embayment. We seek to address the potential contribution of bacterial aerosols from local sources and to determine how their number, size distribution, and taxonomic identity are affected by wind speed and wind direction (onshore vs. offshore. Total culturable microbial counts were higher under offshore winds (average of 778 CFU/m3 ± 67, with bacteria comprising the majority of colonies (58.5%, as compared to onshore winds (580 CFU/m3 ± 110 where fungi were dominant (87.7%. The majority of cultured bacteria and fungi sampled during both offshore winds (88% and onshore winds (72% were associated with coarse aerosols (>2.1 µm, indicative of production from local sources. There was a significant correlation (p < 0.05 of wind speed with both total and coarse culturable microbial aerosol concentrations. Taxonomic analysis, based on DNA sequencing, showed that Actinobacteria was the dominant phylum among aerosol isolates. In particular, Streptomyces and Bacillus, both spore forming genera that are often soil-associated, were abundant under both offshore and onshore wind conditions. Comparisons of bacterial communities present in the bioaerosol sequence libraries revealed that particle size played an important role in microbial aerosol taxonomy. Onshore and offshore coarse libraries were found to be most similar

The Indigo V Indian Ocean Expedition: a prototype for citizen microbial oceanography

DEFF Research Database (Denmark)

Lauro, Frederico; Senstius, Svend Jacob; Cullen, Jay

2014-01-01

Microbial Oceanography has long been an extremely expensive discipline, requiring ship time for sample collection and thereby economically constraining the number of samples collected. This is especially true for under-sampled water bodies such as the Indian Ocean. Specialised scientific equipmen...

Use of a Burkholderia cenocepacia ABTS Oxidizer in a Microbial Fuel Cell

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Microbial fuel cells (MFCs) often use biological processes to generate electrons from organic material contained in the anode chamber and abiotic processes employing atmospheric oxygen as the oxidant in the cathode chamber. This study investigated the accumulation of an oxidant in bacterial cultures...

Use of Dehydrated Agar to Estimate Microbial Water Quality for Horticulture Irrigation.

Science.gov (United States)

Meador, Dustin P; Fisher, Paul R; Guy, Charles L; Harmon, Philip F; Peres, Natalia A; Teplitski, Max

2016-07-01

Petrifilms are dehydrated agar culture plates that have been used to quantify colony forming units (CFU) mL of either aerobic bacteria (Petrifilm-AC) or fungus (Petrifilm-YM), depending on substrate composition. Microbes in irrigation systems can indicate biofilm risk and potential clogging of irrigation emitters. The research objective was to compare counts on Petrifilms versus traditional, hydrated-agar plates using samples collected from recirculated irrigation waters and cultures of isolated known species. The estimated count (in CFU mL) from a recirculated irrigation sample after 7 d of incubation on Petrifilm-YM was only 5.5% of the count quantified using sabouraud dextrose agar (SDA) with chloramphenicol after 14 d. In a separate experiment with a known species, Petrifilm-YM did not successfully culture zoospores of . Isolates of viable zoospores were cultured successfully on potato-dextrose agar (PDA), with comparable counts with a vegetable juice medium supplemented with the antibiotics pimaricin, ampicillin, rifamycin, pentochloronitrobenzene and hymexazol (PARP-H). The quantification of pv. Begoniaceae on Petrifilm-AC was not significantly different ( < 0.05) than on PDA, but was lower than on Reasoner and Goldrich agar (R2A) or with a hemocytometer. The current formulation of Petrifilm-YM is unlikely to be a useful monitoring method for plant pathogens in irrigation water because of the inability to successfully culture oomycetes. However, Petrifilm-AC was an effective method to quantify bacteria and can provide an easy-to-use on-farm tool to monitor biofilm risk and microbial density. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

Culture independent PCR: an alternative enzyme discovery strategy

DEFF Research Database (Denmark)

Jacobsen, Jonas; Lydolph, Magnus; Lange, Lene

2005-01-01

Degenerate primers were designed for use in a culture-independent PCR screening of DNA from composite fungal communities, inhabiting residues of corn stovers and leaves. According to similarity searches and alignments amplified clone sequences affiliated with glycosyl hydrolase family 7 and glyco...... the value of culture-independent PCR in microbial diversity studies and could add to development of a new enzyme screening technology....

Marine snow microbial communities: scaling of abundances with aggregate size

DEFF Research Database (Denmark)

Kiørboe, Thomas

2003-01-01

Marine aggregates are inhabited by diverse microbial communities, and the concentration of attached microbes typically exceeds concentrations in the ambient water by orders of magnitude. An extension of the classical Lotka-Volterra model, which includes 3 trophic levels (bacteria, flagellates...... are controlled by flagellate grazing, while flagellate and ciliate populations are governed by colonization and detachment. The model also suggests that microbial populations are turned over rapidly (1 to 20 times d-1) due to continued colonization and detachment. The model overpredicts somewhat the scaling...... of microbial abundances with aggregate size observed in field-collected aggregates. This may be because it disregards the aggregation/disaggregation dynamics of aggregates, as well as interspecific interactions between bacteria....

Overview: Microbial amendment of remediated soils for effective recycling

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Kim Soo-Bin

2017-01-01

Full Text Available In recent years, various methods are being considered with appropriate amendments, not with conventional reclamation to recycle deteriorated soils after remediation as agricultural addition, backfilling and construction materials etc. Among these amendments, microbial amendments with effective microorganism(EMs are known to improve soil qualities such as fertility, strength and toxicity to be recycled into possible utilizations. This study indicates the possibility of recycling the remediated soils by using these EMs most efficiently. Soil samples will be collected from contaminated sites with either heavy metals or petroleum and will be remediated by bench-scale soil washing and thermal desorption. And then the remediated soils will be treated with easily obtainable inocula, substrates (culture media near our life and they are compared with commercial EM products in terms of the cost and efficiency. Also, after treating with a number of mixing ratios, soil properties of (1 fresh, (2 contaminated, (3 remediated (4 amended soils will be evaluated based on soil quality indicators depending on demands and the optimal mixing ratios which are effective than commercial EM products will be determined. The ratio derived from pre-tests could be applied on the remediated soils with pilot-scale in order to assess suitability for recycling and characterize correlation between soil properties and microbial amendments regarding contaminants and remediation, and furthermore for modelling. In conclusion, application of the established models on recycling remediated soils may help to dispose the remediated soils in future, including environmental and ecological values as well as economical values.

Taxonomic evaluation of unidentified Streptomyces isolates in the ARS Culture Collection (NRRL) using multi-locus sequence analysis

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The ARS Culture Collection (NRRL) currently contains 7569 strains within the family Streptomycetaceae but 4368 of them have not been characterized to the species level. A gene sequence database using the Bacterial Isolate Genomic Sequence Database package (BIGSdb) (Jolley & Maiden, 2010) is availabl...

Limitations of ATP as a measure of microbial biomass

African Journals Online (AJOL)

limits the use of ATP as a measure of microbial biomass. S. AIr. J. Zool. 1982, 17: 93 - 95. Beraming van die totale .... only micro-organisms present in the experimental culture, but these were later succeeded by a large ... a value of 49: I by the last day of the experiment. Estimates of the total living biomass of the heterotro-.

Mineralogical controls on surface colonization by sulfur-metabolizing microbial communities

Science.gov (United States)

Jones, A. A.; Bennett, P.

2012-12-01