Exploring the effects of photon correlations from thermal sources on bacterial photosynthesis

Science.gov (United States)

Manrique, Pedro D.; Caycedo-Soler, Felipe; De Mendoza, Adriana; Rodríguez, Ferney; Quiroga, Luis; Johnson, Neil F.

Thermal light sources can produce photons with strong spatial correlations. We study the role that these correlations might potentially play in bacterial photosynthesis. Our findings show a relationship between the transversal distance between consecutive absorptions and the efficiency of the photosynthetic process. Furthermore, membranes where the clustering of core complexes (so-called RC-LH1) is high, display a range where the organism profits maximally from the spatial correlation of the incoming light. By contrast, no maximum is found for membranes with low core-core clustering. We employ a detailed membrane model with state-of-the-art empirical inputs. Our results suggest that the organization of the membrane's antenna complexes may be well-suited to the spatial correlations present in an natural light source. Future experiments will be needed to test this prediction.

Airborne bacterial assemblage in a zero carbon building: A case study.

Science.gov (United States)

Leung, M H Y; Tong, X; Tong, J C K; Lee, P K H

2018-01-01

Currently, there is little information pertaining to the airborne bacterial communities of green buildings. In this case study, the air bacterial community of a zero carbon building (ZCB) in Hong Kong was characterized by targeting the bacterial 16S rRNA gene. Bacteria associated with the outdoor environment dominated the indoor airborne bacterial assemblage, with a modest contribution from bacteria associated with human skin. Differences in overall community diversity, membership, and composition associated with short (day-to-day) and long-term temporal properties were detected, which may have been driven by specific environmental genera and taxa. Furthermore, time-decay relationships in community membership (based on unweighted UniFrac distances) and composition (based on weighted UniFrac distances) differed depending on the season and sampling location. A Bayesian source-tracking approach further supported the importance of adjacent outdoor air bacterial assemblage in sourcing the ZCB indoor bioaerosol. Despite the unique building attributes, the ZCB microbial assemblage detected and its temporal characteristics were not dissimilar to that of conventional built environments investigated previously. Future controlled experiments and microbial assemblage investigations of other ZCBs will undoubtedly uncover additional knowledge related to how airborne bacteria in green buildings may be influenced by their distinctive architectural attributes. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Investigation of bacterial communities in peat land of the Gahai Lake natural conservation area

Science.gov (United States)

Bai, Yani; Wang, Jinchang; Zhan, Zhigao; Guan, Limei; Jin, Liang; Zheng, Guohua

2017-10-01

Peat is involved in the global carbon cycle and water conservation; therefore, it is implicated in global environmental change. Microorganisms play an important role in the function of peat. To investigate the bacterial communities in peat of Gahai Lake, different locations and depths were sampled and Illumina Miseq sequencing was used to analyze the microbial community. Chemical properties of peat samples were analyzed by China state standard methods (GB methods). The results showed that bacterial communities were affected by depth, with bacterial diversity and community structure at 90 and 120 cm significantly different from that at 10, 30 and 50 cm depth from the peat surface. Chemical properties of peat land including organic matter, total nitrogen and humus content did not significantly influence bacterial community structure in peat, with only one group from genus Rhizomicrobium that was significantly correlated with total nitrogen. A substantial proportion of the bacterial sequences were unclassified (1.4%), which indicates the great application potential of peat in the Gahai Lake natural conservation area in the future.

Investigation on Ion Source Parameters

CERN Document Server

M. Cheikh Mhamed, S. Essabaa, C. Lau

The EURISOL multi-mega-watt target station requires dedicated radioactive ion sources. Notably, they must be capable of operating under extremely hard radiations and with a larger fission target producing over 1014 fissions/s. The realisation of next-generation ion sources suitable for such operating conditions needs exhaustive studies and developments. In order to take up such a challenge, a review on radioactive ion sources was achieved and the investigation on ion source parameters was in particular focused on a plasma ion source through a R&D program.

Investigation of multimodal forward scatter phenotyping from bacterial colonies

Science.gov (United States)

Kim, Huisung

A rapid, label-free, and elastic light scattering (ELS) based bacterial colony phenotyping technology, bacterial rapid detection using optical scattering technology (BARDOT) provides a successful classification of several bacterial genus and species. For a thorough understanding of the phenomena and overcoming the limitations of the previous design, five additional modalities from a bacterial colony: 3D morphology, spatial optical density (OD) distribution, spectral forward scattering pattern, spectral OD, and surface backward reflection pattern are proposed to enhance the classification/identification ratio, and the feasibilities of each modality are verified. For the verification, three different instruments: integrated colony morphology analyzer (ICMA), multi-spectral BARDOT (MS-BARDOT) , and multi-modal BARDOT (MM-BARDOT) are proposed and developed. The ICMA can measure 3D morphology and spatial OD distribution of the colony simultaneously. A commercialized confocal displacement meter is used to measure the profiles of the bacterial colonies, together with a custom built optical density measurement unit to interrogate the biophysics behind the collective behavior of a bacterial colony. The system delivers essential information related to the quantitative growth dynamics (height, diameter, aspect ratio, optical density) of the bacterial colony, as well as, a relationship in between the morphological characteristics of the bacterial colony and its forward scattering pattern. Two different genera: Escherichia coli O157:H7 EDL933, and Staphylococcus aureus ATCC 25923 are selected for the analysis of the spatially resolved growth dynamics, while, Bacillus spp. such as B. subtilis ATCC 6633, B. cereus ATCC 14579, B. thuringiensis DUP6044, B. polymyxa B719W, and B. megaterium DSP 81319, are interrogated since some of the Bacillus spp. provides strikingly different characteristics of ELS patterns, and the origin of the speckle patterns are successfully correlated with

Exploring the effects of photon correlations from thermal sources on bacterial photosynthesis

Directory of Open Access Journals (Sweden)

Pedro D. Manrique

Full Text Available Thermal light sources can produce photons with strong spatial correlations. We study the role that these correlations might potentially play in bacterial photosynthesis. Our findings show a relationship between the transversal distance between consecutive absorptions and the efficiency of the photosynthetic process. Furthermore, membranes where the clustering of core complexes (so-called RC-LH1 is high, display a range where the organism profits maximally from the spatial correlation of the incoming light. By contrast, no maximum is found for membranes with low core-core clustering. We employ a detailed membrane model with state-of-the-art empirical inputs. Our results suggest that the organization of the membrane’s antenna complexes may be well-suited to the spatial correlations present in an natural light source. Future experiments will be needed to test this prediction. Keywords: Photo-bunching, Spatial correlation, Photosynthesis, Purple bacteria

Sequencing-based analysis of the bacterial and fungal composition of kefir grains and milks from multiple sources.

Directory of Open Access Journals (Sweden)

Alan J Marsh

Full Text Available Kefir is a fermented milk-based beverage to which a number of health-promoting properties have been attributed. The microbes responsible for the fermentation of milk to produce kefir consist of a complex association of bacteria and yeasts, bound within a polysaccharide matrix, known as the kefir grain. The consistency of this microbial population, and that present in the resultant beverage, has been the subject of a number of previous, almost exclusively culture-based, studies which have indicated differences depending on geographical location and culture conditions. However, culture-based identification studies are limited by virtue of only detecting species with the ability to grow on the specific medium used and thus culture-independent, molecular-based techniques offer the potential for a more comprehensive analysis of such communities. Here we describe a detailed investigation of the microbial population, both bacterial and fungal, of kefir, using high-throughput sequencing to analyse 25 kefir milks and associated grains sourced from 8 geographically distinct regions. This is the first occasion that this technology has been employed to investigate the fungal component of these populations or to reveal the microbial composition of such an extensive number of kefir grains or milks. As a result several genera and species not previously identified in kefir were revealed. Our analysis shows that the bacterial populations in kefir are dominated by 2 phyla, the Firmicutes and the Proteobacteria. It was also established that the fungal populations of kefir were dominated by the genera Kazachstania, Kluyveromyces and Naumovozyma, but that a variable sub-dominant population also exists.

Sequencing-Based Analysis of the Bacterial and Fungal Composition of Kefir Grains and Milks from Multiple Sources

Science.gov (United States)

Marsh, Alan J.; O’Sullivan, Orla; Hill, Colin; Ross, R. Paul; Cotter, Paul D.

2013-01-01

Kefir is a fermented milk-based beverage to which a number of health-promoting properties have been attributed. The microbes responsible for the fermentation of milk to produce kefir consist of a complex association of bacteria and yeasts, bound within a polysaccharide matrix, known as the kefir grain. The consistency of this microbial population, and that present in the resultant beverage, has been the subject of a number of previous, almost exclusively culture-based, studies which have indicated differences depending on geographical location and culture conditions. However, culture-based identification studies are limited by virtue of only detecting species with the ability to grow on the specific medium used and thus culture-independent, molecular-based techniques offer the potential for a more comprehensive analysis of such communities. Here we describe a detailed investigation of the microbial population, both bacterial and fungal, of kefir, using high-throughput sequencing to analyse 25 kefir milks and associated grains sourced from 8 geographically distinct regions. This is the first occasion that this technology has been employed to investigate the fungal component of these populations or to reveal the microbial composition of such an extensive number of kefir grains or milks. As a result several genera and species not previously identified in kefir were revealed. Our analysis shows that the bacterial populations in kefir are dominated by 2 phyla, the Firmicutes and the Proteobacteria. It was also established that the fungal populations of kefir were dominated by the genera Kazachstania, Kluyveromyces and Naumovozyma, but that a variable sub-dominant population also exists. PMID:23894461

Sequencing-based analysis of the bacterial and fungal composition of kefir grains and milks from multiple sources.

Science.gov (United States)

Marsh, Alan J; O'Sullivan, Orla; Hill, Colin; Ross, R Paul; Cotter, Paul D

2013-01-01

Kefir is a fermented milk-based beverage to which a number of health-promoting properties have been attributed. The microbes responsible for the fermentation of milk to produce kefir consist of a complex association of bacteria and yeasts, bound within a polysaccharide matrix, known as the kefir grain. The consistency of this microbial population, and that present in the resultant beverage, has been the subject of a number of previous, almost exclusively culture-based, studies which have indicated differences depending on geographical location and culture conditions. However, culture-based identification studies are limited by virtue of only detecting species with the ability to grow on the specific medium used and thus culture-independent, molecular-based techniques offer the potential for a more comprehensive analysis of such communities. Here we describe a detailed investigation of the microbial population, both bacterial and fungal, of kefir, using high-throughput sequencing to analyse 25 kefir milks and associated grains sourced from 8 geographically distinct regions. This is the first occasion that this technology has been employed to investigate the fungal component of these populations or to reveal the microbial composition of such an extensive number of kefir grains or milks. As a result several genera and species not previously identified in kefir were revealed. Our analysis shows that the bacterial populations in kefir are dominated by 2 phyla, the Firmicutes and the Proteobacteria. It was also established that the fungal populations of kefir were dominated by the genera Kazachstania, Kluyveromyces and Naumovozyma, but that a variable sub-dominant population also exists.

Bacterial biofilms investigated by atomic force microscopy and electrochemistry

DEFF Research Database (Denmark)

Hu, Yifan

Bacterial biofilms are aggregates of microorganisms in which cells adhere to each other and adhere to a solid surface or an animal host cavity. Bacterial biofilms play important roles in human life, and cause serious harm for human society and huge economic losses. The complex composition of bact...

Production of bacterial cellulose using different carbon sources and culture media.

Science.gov (United States)

Mohammadkazemi, Faranak; Azin, Mehrdad; Ashori, Alireza

2015-03-06

In this work, the effects of carbon sources and culture media on the production and structural properties of bacterial cellulose (BC) have been studied. BC nanofibers were synthesized using Gluconacetobacter xylinus strain PTCC 1734. Media used were Hestrin-Schramm (H), Yamanaka (Y), and Zhou (Z). Five different carbon sources, namely date syrup, glucose, mannitol, sucrose, and food-grade sucrose were used in these media. All the produced BC pellicles were characterized in terms of dry weight production, biomass yield, thermal stability, crystallinity and morphology by thermogravimetric analysis (TGA), x-ray diffraction (XRD), and field emission scanning electron microscopy (FE-SEM). The obtained results showed that mannitol lead to the highest yield, followed by sucrose. The highest production efficiency of mannitol might be due to the nitrogen source, which plays an important role. The maximum improvement on the thermal stability of the composites was achieved when mannitol was used in H medium. In addition, the crystallinity was higher in BC formed in H medium compared to other media. FE-SEM micrographs illustrated that the BC pellicles, synthesized in the culture media H and Z, were stable, unlike those in medium Y that were unstable. The micrographs of BC produced in media containing mannitol and sucrose provided evidence of the strong interfacial adhesion between the BC fibers without noticeable aggregates. Copyright © 2014 Elsevier Ltd. All rights reserved.

Electrical conductivity measurements of bacterial nanowires from Pseudomonas aeruginosa

International Nuclear Information System (INIS)

Maruthupandy, Muthusamy; Anand, Muthusamy; Beevi, Akbar Sait Hameedha; Priya, Radhakrishnan Jeeva; Maduraiveeran, Govindhan

2015-01-01

The extracellular appendages of bacteria (flagella) that transfer electrons to electrodes are called bacterial nanowires. This study focuses on the isolation and separation of nanowires that are attached via Pseudomonas aeruginosa bacterial culture. The size and roughness of separated nanowires were measured using transmission electron microscopy (TEM) and atomic force microscopy (AFM), respectively. The obtained bacterial nanowires indicated a clear image of bacterial nanowires measuring 16 nm in diameter. The formation of bacterial nanowires was confirmed by microscopic studies (AFM and TEM) and the conductivity nature of bacterial nanowire was investigated by electrochemical techniques. Cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS), which are nondestructive voltammetry techniques, suggest that bacterial nanowires could be the source of electrons—which may be used in various applications, for example, microbial fuel cells, biosensors, organic solar cells, and bioelectronic devices. Routine analysis of electron transfer between bacterial nanowires and the electrode was performed, providing insight into the extracellular electron transfer (EET) to the electrode. CV revealed the catalytic electron transferability of bacterial nanowires and electrodes and showed excellent redox activities. CV and EIS studies showed that bacterial nanowires can charge the surface by producing and storing sufficient electrons, behave as a capacitor, and have features consistent with EET. Finally, electrochemical studies confirmed the development of bacterial nanowires with EET. This study suggests that bacterial nanowires can be used to fabricate biomolecular sensors and nanoelectronic devices. (paper)

Isolation of bacterial cellulose nanocrystalline from pineapple peel waste: Optimization of acid concentration in the hydrolysis method

Science.gov (United States)

Anwar, Budiman; Rosyid, Nurul Huda; Effendi, Devi Bentia; Nandiyanto, Asep Bayu Dani; Mudzakir, Ahmad; Hidayat, Topik

2016-02-01

Isolation of needle-shaped bacterial cellulose nanocrystalline with a diameter of 16-64 nm, a fiber length of 258-806 nm, and a degree of crystallinity of 64% from pineapple peel waste using an acid hydrolysis process was investigated. Experimental showed that selective concentration of acid played important roles in isolating the bacterial cellulose nanocrystalline from the cellulose source. To achieve the successful isolation of bacterial cellulose nanocrystalline, various acid concentrations were tested. To confirm the effect of acid concentration on the successful isolation process, the reaction conditions were fixed at a temperature of 50°C, a hydrolysis time of 30 minutes, and a bacterial cellulose-to-acid ratio of 1:50. Pineapple peel waste was used as a model for a cellulose source because to the best of our knowledge, there is no report on the use of this raw material for producing bacterial cellulose nanocrystalline. In fact, this material can be used as an alternative for ecofriendly and cost-free cellulose sources. Therefore, understanding in how to isolate bacterial cellulose nanocrystalline from pineapple peel waste has the potential for large-scale production of inexpensive cellulose nanocrystalline.

Manganese oxidation and bacterial diversity on different filter media coatings during the start-up of drinking water biofilters

DEFF Research Database (Denmark)

Breda, I. L.; Ramsay, L.; Roslev, P.

2017-01-01

Manganese removal is a typical concern in drinking water production. Biofiltration may be used when treating groundwater sources but the onset of manganese removal in virgin biofilters can vary considerably. The aim of this study was to investigate the effect of different filter media on manganese...... by manganese oxide, while 48, 57 and 72 days were required by virgin quartz, calcium carbonate and polystyrene, respectively. The bacterial community was investigated using DAPI staining, quantitative polymerase chain reaction (qPCR), 16S rRNA gene pyrosequencing, and bacterial enrichments. Bacterial abundance...

Investigation of 6-[¹⁸F]-fluoromaltose as a novel PET tracer for imaging bacterial infection.

Directory of Open Access Journals (Sweden)

Gayatri Gowrishankar

Full Text Available Despite advances in the field of nuclear medicine, the imaging of bacterial infections has remained a challenge. The existing reagents suffer from poor sensitivity and specificity. In this study we investigate the potential of a novel PET (positron emission tomography tracer that overcomes these limitations.6-[¹⁸F]-fluoromaltose was synthesized. Its behavior in vitro was evaluated in bacterial and mammalian cultures. Detailed pharmacokinetic and biodistribution profiles for the tracer were obtained from a murine model.6-[¹⁸F]-fluoromaltose is taken up by multiple strains of pathogenic bacteria. It is not taken up by mammalian cancer cell lines. 6-[¹⁸F]-fluoromaltose is retained in infected muscles in a murine model of bacterial myositis. It does not accumulate in inflamed tissue.We have shown that 6-[¹⁸F]-fluoromaltose can be used to image bacterial infection in vivo with high specificity. We believe that this class of agents will have a significant impact on the clinical management of patients.

Investigation Of Information Sources And Communication Channels ...

African Journals Online (AJOL)

Investigation Of Information Sources And Communication Channels In Ipm Rice ... the information accessibility of farmer groups seems as empowerment strategy. ... information sources and communication channels, in order of importance, ...

Investigation of Solar and Solar-Gas Thermal Energy Sources

OpenAIRE

Ivan Herec; Jan Zupa

2003-01-01

The article deals with the investigation of solar thermal sources of electrical and heat energy as well as the investigation of hybrid solar-gas thermal sources of electrical and heat energy (so called photothermal sources). Photothermal sources presented here utilize computer-controlled injection of the conversion fluid into special capillary porous substance that is adjusted to direct temperature treatment by the concentrated thermal radiation absorption.

Nanoindentation of Pseudomonas aeruginosa bacterial biofilm using atomic force microscopy

International Nuclear Information System (INIS)

Baniasadi, Mahmoud; Xu, Zhe; Du, Yingjie; Lu, Hongbing; Minary-Jolandan, Majid; Gandee, Leah; Zimmern, Philippe

2014-01-01

Bacterial biofilms are a source of many chronic infections. Biofilms and their inherent resistance to antibiotics are attributable to a range of health issues including affecting prosthetic implants, hospital-acquired infections, and wound infection. Mechanical properties of biofilm, in particular, at micro- and nano-scales, are governed by microstructures and porosity of the biofilm, which in turn may contribute to their inherent antibiotic resistance. We utilize atomic force microscopy (AFM)-based nanoindentation and finite element simulation to investigate the nanoscale mechanical properties of Pseudomonas aeruginosa bacterial biofilm. This biofilm was derived from human samples and represents a medically relevant model. (paper)

Corn cob biochar increases soil culturable bacterial abundance without enhancing their capacities in utilizing carbon sources in Biolog Eco-plates

Institute of Scientific and Technical Information of China (English)

JIANG Lin-lin; HAN Guang-ming; LAN Yu; LIU Sai-nan; GAO Ji-ping; YANG Xu; MENG Jun; CHEN Wen-fu

2017-01-01

Biochar has been shown to influence soil microbial communities in terms of their abundance and diversity.However,the relationship among microbial abundance,structure and C metabolic traits is not well studied under biochar application.Here it was hypothesized that the addition of biochar with intrinsic properties (i.e.,porous structure) could affect the proliferation of culturable microbes and the genetic structure of soil bacterial communities.In the meantime,the presence of available organic carbon in biochar may influence the C utilization capacities of microbial community in Biolog Eco-plates.A pot experiment was conducted with differenct biochar application (BC) rates:control (0 t ha-1),BC1 (20 t ha-1) and BC2 (40 t ha-1).Culturable microorganisms were enumerated via the plate counting method.Bacterial diversity was examined using denaturing gradient gel electrophoresis (DGGE).Microbial capacity in using C sources was assessed using Biolog Eco-plates.The addition of biochar stimulated the growth of actinomyces and bacteria,especially the ammonifying bacteria and azotobacteria,but had no significant effect on fungi proliferation.The phylogenetic distribution of the operational taxonomic units could be divided into the following groups with the biochar addition:Firmicutes,Acidobacteria,Gemmatimonadetes,Actinobacteria,Cyanobacteria and α-,β-,γ-and δ-Proteobacteria (average similarity ＞95％).Biochar application had a higher capacity utilization for L-asparagine,Tween 80,D-mannitol,L-serine,γ-hydroxybutyric acid,N-acetyI-D-glucosamine,glycogen,itaconic acid,glycyl-L-glutamic acid,α-ketobutyricacid and putrescine,whereas it had received decreased capacities in using the other 20 carbon sources in Biolog Eco-plates.Redundancy analysis (RDA) revealed that the physico-chemical properties,indices of bacterial diversity,and C metabolic traits were positively correlated with the appearance of novel sequences under BC2 treatment.Our study indicates that the

Non-thermal effects of 94 GHz radiation on bacterial metabolism

Science.gov (United States)

Raitt, Brittany J.

Bacillus subtilis, Escherichia coli, Staphylococcus aureus, and Klebsiella pneumoniae were used to investigate the non-thermal effects of terahertz (THz) radiation exposure on bacterial cells. The THz source used was a 94 GHz (0.94 THz) Millitech Gunn Diode Oscillator with a power density of 1.3 mW/cm2. The cultures were placed in the middle sixty wells of two 96-well microplates, one serving as the experimental plate and one serving as a control. The experimental plate was placed on the radiation source for either two, eighteen, or twenty-four hours and the metabolism of the cells was measured in a spectrophotometer using the tetrazolium dye XTT. The results showed no consistent significant differences in either the growth rates or the metabolism of any of the bacterial species at this frequency and power density.

Postviral Complications: Bacterial Pneumonia.

Science.gov (United States)

Prasso, Jason E; Deng, Jane C

2017-03-01

Secondary bacterial pneumonia after viral respiratory infection remains a significant source of morbidity and mortality. Susceptibility is mediated by a variety of viral and bacterial factors, and complex interactions with the host immune system. Prevention and treatment strategies are limited to influenza vaccination and antibiotics/antivirals respectively. Novel approaches to identifying the individuals with influenza who are at increased risk for secondary bacterial pneumonias are urgently needed. Given the threat of further pandemics and the heightened prevalence of these viruses, more research into the immunologic mechanisms of this disease is warranted with the hope of discovering new potential therapies. Published by Elsevier Inc.

Gene calling and bacterial genome annotation with BG7.

Science.gov (United States)

Tobes, Raquel; Pareja-Tobes, Pablo; Manrique, Marina; Pareja-Tobes, Eduardo; Kovach, Evdokim; Alekhin, Alexey; Pareja, Eduardo

2015-01-01

New massive sequencing technologies are providing many bacterial genome sequences from diverse taxa but a refined annotation of these genomes is crucial for obtaining scientific findings and new knowledge. Thus, bacterial genome annotation has emerged as a key point to investigate in bacteria. Any efficient tool designed specifically to annotate bacterial genomes sequenced with massively parallel technologies has to consider the specific features of bacterial genomes (absence of introns and scarcity of nonprotein-coding sequence) and of next-generation sequencing (NGS) technologies (presence of errors and not perfectly assembled genomes). These features make it convenient to focus on coding regions and, hence, on protein sequences that are the elements directly related with biological functions. In this chapter we describe how to annotate bacterial genomes with BG7, an open-source tool based on a protein-centered gene calling/annotation paradigm. BG7 is specifically designed for the annotation of bacterial genomes sequenced with NGS. This tool is sequence error tolerant maintaining their capabilities for the annotation of highly fragmented genomes or for annotating mixed sequences coming from several genomes (as those obtained through metagenomics samples). BG7 has been designed with scalability as a requirement, with a computing infrastructure completely based on cloud computing (Amazon Web Services).

Response of soil bacterial communities to lead and zinc pollution revealed by Illumina MiSeq sequencing investigation.

Science.gov (United States)

Xu, Xihui; Zhang, Zhou; Hu, Shunli; Ruan, Zhepu; Jiang, Jiandong; Chen, Chen; Shen, Zhenguo

2017-01-01

Soil provides a critical environment for microbial community development. However, microorganisms may be sensitive to substances such as heavy metals (HMs), which are common soil contaminants. This study investigated bacterial communities using 16S ribosomal RNA (rRNA) gene fragment sequencing in geographic regions with and without HM pollution to elucidate the effects of soil properties and HMs on bacterial communities. No obvious changes in the richness or diversity of bacterial communities were observed between samples from mining and control areas. Significant differences in bacterial richness and diversity were detected between samples from different geographic regions, indicating that the basic soil characteristics were the most important factors affecting bacterial communities other than HMs. However, the abundances of several phyla and genera differed significantly between mining and control samples, suggesting that Zn and Pb pollution may impact the soil bacterial community composition. Moreover, regression analyses showed that the relative abundances of these phyla and genera were correlated significantly with the soil-available Zn and Pb contents. Redundancy analysis indicated that the soil K, ammoniacal nitrogen (NH 4 + -N), total Cu, and available Zn and Cu contents were the most important factors. Our results not only suggested that the soil bacteria were sensitive to HM stresses but also indicated that other soil properties may affect soil microorganisms to a greater extent.

Investigation of the bacterial communities associated with females of Lutzomyia sand fly species from South America.

Directory of Open Access Journals (Sweden)

Mauricio R V Sant'Anna

Full Text Available Phlebotomine sand flies are vectors of Leishmania that are acquired by the female sand fly during blood feeding on an infected mammal. Leishmania parasites develop exclusively in the gut lumen during their residence in the insect before transmission to a suitable host during the next blood feed. Female phlebotomine sand flies are blood feeding insects but their life style of visiting plants as well as animals, and the propensity for larvae to feed on detritus including animal faeces means that the insect host and parasite are exposed to a range of microorganisms. Thus, the sand fly microbiota may interact with the developing Leishmania population in the gut. The aim of the study was to investigate and identify the bacterial diversity associated with wild adult female Lutzomyia sand flies from different geographical locations in the New World. The bacterial phylotypes recovered from 16S rRNA gene clone libraries obtained from wild caught adult female Lutzomyia sand flies were estimated from direct band sequencing after denaturing gradient gel electrophoresis of bacterial 16 rRNA gene fragments. These results confirm that the Lutzomyia sand flies contain a limited array of bacterial phylotypes across several divisions. Several potential plant-related bacterial sequences were detected including Erwinia sp. and putative Ralstonia sp. from two sand fly species sampled from 3 geographically separated regions in Brazil. Identification of putative human pathogens also demonstrated the potential for sand flies to act as vectors of bacterial pathogens of medical importance in addition to their role in Leishmania transmission.

Bacterial Species and Biochemical Characteristic Investigations of Nostoc flagelliforme Concentrates during its Storage.

Science.gov (United States)

Yue, Lifang; Lv, Hexin; Zhen, Jing; Jiang, Shengping; Jia, Shiru; Shen, Shigang; Gao, Lu; Dai, Yujie

2016-04-28

Preservation of fresh algae plays an important role in algae seed subculture and aquaculture. The determination and examination of the changes of cell viability, composition, and bacterial species during storage would help to take suitable preservation methods to prolong the preservation time of fresh algae. Nostoc flagelliforme is a kind of edible cyanobacterium with important herbal and dietary values. This article investigated the changes of bacterial species and biochemical characteristics of fresh N. flagelliforme concentrate during natural storage. It was found that the viability of cells decreased along with the storage time. Fourteen bacteria strains in the algae concentrate were identified by PCR-DGGE and were grouped into four phyla, including Cyanobacteria, Firmicutes, Proteobacteria, and Bacteroidetes. Among them, Enterococcus viikkiensis may be a concern in the preservation. Eleven volatile organic compounds were identified from N. flagelliforme cells, in which geosmin could be treated as an indicator of the freshness of N. flagelliforme. The occurrence of indole compound may be an indicator of the degradation of cells.

An investigation of total bacterial communities, culturable antibiotic-resistant bacterial communities and integrons in the river water environments of Taipei city.

Science.gov (United States)

Yang, Chu-Wen; Chang, Yi-Tang; Chao, Wei-Liang; Shiung, Iau-Iun; Lin, Han-Sheng; Chen, Hsuan; Ho, Szu-Han; Lu, Min-Jheng; Lee, Pin-Hsuan; Fan, Shao-Ning

2014-07-30

The intensive use of antibiotics may accelerate the development of antibiotic-resistant bacteria (ARB). The global geographical distribution of environmental ARB has been indicated by many studies. However, the ARB in the water environments of Taiwan has not been extensively investigated. The objective of this study was to investigate the communities of ARB in Huanghsi Stream, which presents a natural acidic (pH 4) water environment. Waishuanghsi Stream provides a neutral (pH 7) water environment and was thus also monitored to allow comparison. The plate counts of culturable bacteria in eight antibiotics indicate that the numbers of culturable carbenicillin- and vancomycin-resistant bacteria in both Huanghsi and Waishuanghsi Streams are greater than the numbers of culturable bacteria resistant to the other antibiotics tested. Using a 16S rDNA sequencing approach, both the antibiotic-resistant bacterial communities (culture-based) and the total bacterial communities (metagenome-based) in Waishuanghsi Stream exhibit a higher diversity than those in Huanghsi Stream were observed. Of the three classes of integron, only class I integrons were identified in Waishuanghsi Stream. Our results suggest that an acidic (pH 4) water environment may not only affect the community composition of antibiotic-resistant bacteria but also the horizontal gene transfer mediated by integrons. Copyright © 2013 Elsevier B.V. All rights reserved.

Persistence of antibiotic resistance genes and bacterial community changes in drinking water treatment system: From drinking water source to tap water.

Science.gov (United States)

Su, Hao-Chang; Liu, You-Sheng; Pan, Chang-Gui; Chen, Jun; He, Liang-Ying; Ying, Guang-Guo

2018-03-01

As emerging contaminants, antibiotic resistance genes (ARGs) have become a public concern. This study aimed to investigate the occurrence and diversity of ARGs, and variation in the composition of bacterial communities in source water, drinking water treatment plants, and tap water in the Pearl River Delta region, South China. Various ARGs were present in the different types of water. Among the 27 target ARGs, floR and sul1 dominated in source water from three large rivers in the region. Pearson correlation analysis suggested that sul1, sul2, floR, and cmlA could be potential indicators for ARGs in water samples. The total abundance of the detected ARGs in tap water was much lower than that in source water. Sand filtration and sedimentation in drinking water treatment plants could effectively remove ARGs; in contrast, granular activated carbon filtration increased the abundance of ARGs. It was found that Pseudomonas may be involved in the proliferation and dissemination of ARGs in the studied drinking water treatment system. Bacteria and ARGs were still present in tap water after treatment, though they were significantly reduced. More research is needed to optimize the water treatment process for ARG removal. Copyright © 2017 Elsevier B.V. All rights reserved.

A New Experimental Design for Bacterial Microleakage Investigation at the Implant-Abutment Interface: An In Vitro Study.

Science.gov (United States)

Zipprich, Holger; Miatke, Sven; Hmaidouch, Rim; Lauer, Hans-Christoph

2016-01-01

regarding the bacterial seal of different implant systems. Conical IACs offer a better bacterial seal compared with flat IACs, which showed increased microleakage after dynamic loading. IAC design plays a crucial role in terms of bacterial colonization. Taking samples of the implant interior without abutment disconnection eliminates an error source.

Bacterial diversity among four healthcare-associated institutes in Taiwan.

Science.gov (United States)

Chen, Chang-Hua; Lin, Yaw-Ling; Chen, Kuan-Hsueh; Chen, Wen-Pei; Chen, Zhao-Feng; Kuo, Han-Yueh; Hung, Hsueh-Fen; Tang, Chuan Yi; Liou, Ming-Li

2017-08-15

Indoor microbial communities have important implications for human health, especially in health-care institutes (HCIs). The factors that determine the diversity and composition of microbiomes in a built environment remain unclear. Herein, we used 16S rRNA amplicon sequencing to investigate the relationships between building attributes and surface bacterial communities among four HCIs located in three buildings. We examined the surface bacterial communities and environmental parameters in the buildings supplied with different ventilation types and compared the results using a Dirichlet multinomial mixture (DMM)-based approach. A total of 203 samples from the four HCIs were analyzed. Four bacterial communities were grouped using the DMM-based approach, which were highly similar to those in the 4 HCIs. The α-diversity and β-diversity in the naturally ventilated building were different from the conditioner-ventilated building. The bacterial source composition varied across each building. Nine genera were found as the core microbiota shared by all the areas, of which Acinetobacter, Enterobacter, Pseudomonas, and Staphylococcus are regarded as healthcare-associated pathogens (HAPs). The observed relationship between environmental parameters such as core microbiota and surface bacterial diversity suggests that we might manage indoor environments by creating new sanitation protocols, adjusting the ventilation design, and further understanding the transmission routes of HAPs.

Hospital effluents are one of several sources of metal, antibiotic resistance genes and bacterial markers disseminated in Sub-Saharan urban rivers

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Amandine Laffite

2016-07-01

Full Text Available Data concerning the occurrence of emerging biological contaminants such as antibiotic resistance genes (ARGs and fecal indicator bacteria (FIB in aquatic environments in Sub-Saharan African countries is limited. On the other hand, antibiotic resistance remains a worldwide problem which may pose serious potential risks to human and animal health. Consequently, there is a growing number of reports concerning the prevalence and dissemination of these contaminants into various environmental compartments. Sediments provide the opportunity to reconstruct the pollution history and evaluate impacts so this study investigates the abundance and distribution of toxic metals, FIB, and ARGs released from hospital effluent wastewaters and their presence in river sediments receiving systems. ARGs (blaTEM, blaCTX-M, blaSHV, and aadA, total bacterial load, and selected bacterial species FIB (E. coli, Enterococcus (ENT and Pseudomonas species (Psd were quantified by targeting species specific genes using quantitative PCR (qPCR in total DNA extracted from the sediments recovered from 4 hospital outlet pipes (HOP and their river receiving systems in the City of Kinshasa in the Democratic Republic of the Congo. The results highlight the great concentration of toxic metals in HOP, reaching the values (in mg kg-1 of 47.9 (Cr, 213.6 (Cu, 1434.4 (Zn, 2.6 (Cd, 281.5 (Pb, and 13.6 (Hg. The results also highlight the highest (P˂0.05 values of 16S rRNA, FIB, and ARGs copy numbers in all sampling sites including upstream (control site, discharge point, and downstream of receiving rivers, indicating that the hospital effluent water is not an exclusive source of the biological contaminants entering the urban rivers. Significant correlation were observed between (i all analyzed ARGs and total bacterial load (16S rRNA 0.51 to 0.72 (p<0.001, n=65; (ii ARGs (except blaTEM and FIB and Psd 0.57 < r < 0.82 (p<0.001, n=65; and (iii ARGs (except blaTEM and toxic metals (Cd, Cr, Cu

Bacterial contaminations of informally marketed raw milk in Ghana ...

African Journals Online (AJOL)

Background: Milk has an outstanding nutritional quality but is also an excellent medium for bacterial growth and an important source of bacterial infection when consumed without pasteurization. Objective: To estimate the bacterial health risk of milk consumption in Accra and Kumasi, the twomajor cities in Ghana. Method: A ...

Bacterial Prostatitis: Bacterial Virulence, Clinical Outcomes, and New Directions.

Science.gov (United States)

Krieger, John N; Thumbikat, Praveen

2016-02-01

Four prostatitis syndromes are recognized clinically: acute bacterial prostatitis, chronic bacterial prostatitis, chronic prostatitis/chronic pelvic pain syndrome, and asymptomatic prostatitis. Because Escherichia coli represents the most common cause of bacterial prostatitis, we investigated the importance of bacterial virulence factors and antimicrobial resistance in E. coli strains causing prostatitis and the potential association of these characteristics with clinical outcomes. A structured literature review revealed that we have limited understanding of the virulence-associated characteristics of E. coli causing acute prostatitis. Therefore, we completed a comprehensive microbiological and molecular investigation of a unique strain collection isolated from healthy young men. We also considered new data from an animal model system suggesting certain E. coli might prove important in the etiology of chronic prostatitis/chronic pelvic pain syndrome. Our human data suggest that E. coli needs multiple pathogenicity-associated traits to overcome anatomic and immune responses in healthy young men without urological risk factors. The phylogenetic background and accumulation of an exceptional repertoire of extraintestinal pathogenic virulence-associated genes indicate that these E. coli strains belong to a highly virulent subset of uropathogenic variants. In contrast, antibiotic resistance confers little added advantage to E. coli strains in these healthy outpatients. Our animal model data also suggest that certain pathogenic E. coli may be important in the etiology of chronic prostatitis/chronic pelvic pain syndrome through mechanisms that are dependent on the host genetic background and the virulence of the bacterial strain.

Microbial ecology of bacterially mediated PCB biodegradation

International Nuclear Information System (INIS)

Pettigrew, C.A. Jr.

1989-01-01

The roles of plasmid mediated and consortia mediated polychlorinated biphenyl (PCB) biodegradation by bacterial populations isolated from PCB contaminated freshwater sediments were investigated. PCB degrading bacteria were isolated by DNA:DNA colony hybridization, batch enrichments, and chemostat enrichment. Analysis of substrate removal and metabolite production were done using chlorinated biphenyl spray plates, reverse phase high pressure liquid chromatography, Cl - detection, and 14 C-labeled substrate mineralization methods. A bacterial consortium, designated LPS10, involved in a concerted metabolic attack on chlorinated biphenyls, was shown to mineralize 4-chlorobiphenyl (4CB) and 4,4'-dichlorobiphenyl (4,4' CB). The LPS10 consortium was isolated by both batch and chemostat enrichment using 4CB and biphenyl (BP) as sole carbon source and was found to have tree bacterial isolates that predominated; these included: Pseudomonas, testosteroni LPS10A which mediated the breakdown of 4CB and 4,4' CB to the putative meta-cleavage product and subsequently to 4-chlorobenzoic acid (4CBA), an isolate tentatively identified as an Arthrobacter sp. LPS10B which mediated 4CBA degradation, and Pseudomonas putida by A LPS10C whose role in the consortium has not been determined

Bacterial-Fungal Interactions: Hyphens between Agricultural, Clinical, Environmental, and Food Microbiologists

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Frey-Klett, P.; Burlinson, P.; Deveau, A.; Barret, M.; Tarkka, M.; Sarniguet, A.

2011-01-01

Summary: Bacteria and fungi can form a range of physical associations that depend on various modes of molecular communication for their development and functioning. These bacterial-fungal interactions often result in changes to the pathogenicity or the nutritional influence of one or both partners toward plants or animals (including humans). They can also result in unique contributions to biogeochemical cycles and biotechnological processes. Thus, the interactions between bacteria and fungi are of central importance to numerous biological questions in agriculture, forestry, environmental science, food production, and medicine. Here we present a structured review of bacterial-fungal interactions, illustrated by examples sourced from many diverse scientific fields. We consider the general and specific properties of these interactions, providing a global perspective across this emerging multidisciplinary research area. We show that in many cases, parallels can be drawn between different scenarios in which bacterial-fungal interactions are important. Finally, we discuss how new avenues of investigation may enhance our ability to combat, manipulate, or exploit bacterial-fungal complexes for the economic and practical benefit of humanity as well as reshape our current understanding of bacterial and fungal ecology. PMID:22126995

Dark fermentative biohydrogen production by mesophilic bacterial consortia isolated from riverbed sediments

Energy Technology Data Exchange (ETDEWEB)

Singh, Sneha; Sudhakaran, Anu K.; Sarma, Priyangshu Manab; Subudhi, Sanjukta; Mandal, Ajoy Kumar; Lal, Banwari [Environmental and Industrial Biotechnology Division, The Energy and Resources Institute (TERI), Habitat Place, Darbari Seth Block, Lodhi Road, New Delhi 110003 (India); Gandham, Ganesh [Hindustan Petroleum Corporation Limited, Mumbai Refinery, B. D. Patil Marg, Mahul, Mumbai 400074 (India)

2010-10-15

Dark fermentative bacterial strains were isolated from riverbed sediments and investigated for hydrogen production. A series of batch experiments were conducted to study the effect of pH, substrate concentration and temperature on hydrogen production from a selected bacterial consortium, TERI BH05. Batch experiments for fermentative conversion of sucrose, starch, glucose, fructose, and xylose indicated that TERI BH05 effectively utilized all the five sugars to produce fermentative hydrogen. Glucose was the most preferred carbon source indicating highest hydrogen yields of 22.3 mmol/L. Acetic and butyric acid were the major soluble metabolites detected. Investigation on optimization of pH, temperature, and substrate concentration revealed that TERI BH05 produced maximum hydrogen at 37 C, pH 6 with 8 g/L of glucose supplementation and maximum yield of hydrogen production observed was 2.0-2.3 mol H{sub 2}/mol glucose. Characterization of TERI BH05 revealed the presence of two different bacterial strains showing maximum homology to Clostridium butyricum and Clostridium bifermentans. (author)

Seaweed as source of energy. I: effect of a specific bacterial strain on biogas production

Energy Technology Data Exchange (ETDEWEB)

Rao, P.S.; Tarwade, S.J.; Sarma, K.S.R.

1980-01-01

Biogas was produced from seaweed by making use of alginate-digesting marine bacteria that were isolated from decomposing seaweed and can digest seaweed carbohydrates (agar and alginic acid). Laboratory digesters containing 100 g seaweed were inoculated with 50 mL broth cultures of different seaweed-derived bacterial strains, and the maximum amount of degradation obtained was 28% (compared with 13% for a bacteria-free digestion). Cow dung was added as a source of methanogenic bacteria, and the amount of biogas produced was more than double the amount obtained when seaweed and cow dung were digested in the absence of the seaweed-derived bacteria. Adding a small amount of Ulva to the seaweed digester increased the production of biogas.

Comparison of Bacterial Cellulose Production among Different Strains and Fermented Media

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Maryam Jalili Tabaii

2015-12-01

Full Text Available The effect of different carbon sources on bacterial cellulose production by Gluconacetobacter xylinus (PTCC 1734 and two newly isolated strains (from vinegar under static culture conditions was studied. The production of bacterial cellulose was examined in modified Hestrin-Shramm medium by replacing D-glucose with other carbon sources. The results showed that the yield and characteristics of bacterial cellulose were influenced by the type of carbon source. Glycerol gave the highest yield in all of the studied strains (6%, 9.7% and 3.8% for S, A2 strain and Gluconacetobacter xylinus (PTCC 1734, respectively. The maximum dry bacterial cellulose weight in the glycerol containing medium is due to A2 strain (1.9 g l-1 in comparison to Gluconacetobacter xylinus as reference strain (0.76 g l-1. Although all of the studied strains were in Gluconacetobacter family, each used different sugars for maximum production after glycerol (mannitol and fructose for two newly isolated strains and glucose for Gluconacetobacter xylinus. The maximum moisture content was observed when sucrose and food-grade sucrose were used as carbon source. Contrary to expectations, while the maximum thickness of bacterial cellulose membrane was attained when glycerol was used, bacterial cellulose from glycerol had less moisture content than the others. The oxidized cellulose showed antibacterial activities, which makes it as a good candidate for food-preservatives.

Micro Corona Ionizer as an Ozone Source for Bacterial Cell Lysis

Science.gov (United States)

Lee, Eun-Hee; Lim, Hyun Jeong; Chua, Beelee; Son, Ahjeong

2015-04-01

DNA extraction is a critical process of DNA assays including polymerase chain reaction (PCR), microarrays, molecular cloning, and DNA hybridization which has been well established and can be implemented by commercial kits. DNA extraction involves cell lysis, precipitation, and purification through the combination of physical and chemical processes. Cell lysis is essential to high DNA recovery yield which can be achieved via a variety of physical, chemical, and enzymatic methods. However, these methods were originally developed for bioassays that were labor intensive, time consuming, and vulnerable to contamination and inhibition. Here, we proposed to employ a micro corona ionizer as an ozone source to lyse bacterial cells. Ozone has been well known and used as a disinfectant which allows cell lysis and DNA extraction. Previously, we have shown that a micro corona ionizer is capable of generating a significant amount of ozone. In this study, we employed the micro corona ionizer for the bacterial cell lysis which consists of a 50 μm diameter cantilever wire as the discharge cathode and a 50 μm thick copper foil as anode. Applied voltages varied from 1900 to 2200 V with corresponding corona currents from 16 to 28 μA. The resultant ozone (concentration > 0.14 ppm) generated from the micro corona ionizer was bubbled into the sample via a miniature pump. We demonstrated the cell lysis of Pseudomonas putida as the target bacterium using the micro corona ionizer. At a flow rate of 38 ml/min and applied corona voltage of 2000 V, 98.5 ± 0.2% lysis (normalized to sonication result) was achieved after 10 min. In comparison, untreated and air-treated samples showed normalized % lysis of 11.9 ± 2.4 and 36.1 ± 1.7%, respectively. We also showed that the cell lysis efficiency could be significantly increased by increasing the flow rate and the applied corona voltage. By comparing the experimental results for continuous and pulsed treatment, we verified that the percentage of

Investigation of the Rate of the Bacterial Contamination of the Ice Factories in Bandar Abbas, Iran

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Nahid Moradi

2016-09-01

Full Text Available Background: Pollution of drinking water and ice is one of the most serious ways of water borne diseases spread. The purpose of this study was to investigate the bacterial contamination of the ice produced by ice factories in Bandar Abbas. Methods: In this descriptive ,cross-sectional study samples were collected from seven ice factories in Bandar Abbas. Sampling was done by standard method. Amount of the Contamination of ice and water to coliforms was investigated by the Multiple Tube method to determine the MPN, isolate bacteria and identify the microorganisms using conventional bacteriological techniques and counting the total count of bacteria by the Plate Count method on a nutrient agar medium. The data was analyzed by the SPSS software. Results: In this study, a total of 84 samples were investigated. Gram-positive bacteria (65.5% and gram-negative bacteria(34.5% were separated from each other. The MPN rate in samples and total count of bacteria were 0->1100 and 2×101×104 CFU/mL, respectively. Conclusion: The results suggest that necessary precautions be taken by environmental health specialists and other public health authorities in production, transportation and distribution of the ice blocks to reduce the rate of bacterial contamination.

Investigation of hydraulic transmission noise sources

Science.gov (United States)

Klop, Richard J.

Advanced hydrostatic transmissions and hydraulic hybrids show potential in new market segments such as commercial vehicles and passenger cars. Such new applications regard low noise generation as a high priority, thus, demanding new quiet hydrostatic transmission designs. In this thesis, the aim is to investigate noise sources of hydrostatic transmissions to discover strategies for designing compact and quiet solutions. A model has been developed to capture the interaction of a pump and motor working in a hydrostatic transmission and to predict overall noise sources. This model allows a designer to compare noise sources for various configurations and to design compact and inherently quiet solutions. The model describes dynamics of the system by coupling lumped parameter pump and motor models with a one-dimensional unsteady compressible transmission line model. The model has been verified with dynamic pressure measurements in the line over a wide operating range for several system structures. Simulation studies were performed illustrating sensitivities of several design variables and the potential of the model to design transmissions with minimal noise sources. A semi-anechoic chamber has been designed and constructed suitable for sound intensity measurements that can be used to derive sound power. Measurements proved the potential to reduce audible noise by predicting and reducing both noise sources. Sound power measurements were conducted on a series hybrid transmission test bench to validate the model and compare predicted noise sources with sound power.

Diversity and biological activities of the bacterial community associated with the marine sponge Phorbas tenacior (Porifera, Demospongiae).

Science.gov (United States)

Dupont, S; Carré-Mlouka, A; Descarrega, F; Ereskovsky, A; Longeon, A; Mouray, E; Florent, I; Bourguet-Kondracki, M L

2014-01-01

The diversity of the cultivable microbiota of the marine sponge Phorbas tenacior frequently found in the Mediterranean Sea was investigated, and its potential as a source of antimicrobial, antioxidant and antiplasmodial compounds was evaluated. The cultivable bacterial community was studied by isolation, cultivation and 16S rRNA gene sequencing. Twenty-three bacterial strains were isolated and identified in the Proteobacteria (α or γ classes) and Actinobacteria phyla. Furthermore, three different bacterial morphotypes localized extracellularly within the sponge tissues were revealed by microscopic observations. Bacterial strains were assigned to seven different genera, namely Vibrio, Photobacterium, Shewanella, Pseudomonas, Ruegeria, Pseudovibrio and Citricoccus. The strains affiliated to the same genus were differentiated according to their genetic dissimilarities using random amplified polymorphic DNA (RAPD) analyses. Eleven bacterial strains were selected for evaluation of their bioactivities. Three isolates Pseudovibrio P1Ma4, Vibrio P1MaNal1 and Citricoccus P1S7 revealed antimicrobial activity; Citricoccus P1S7 and Vibrio P1MaNal1 isolates also exhibited antiplasmodial activity, while two Vibrio isolates P1Ma8 and P1Ma5 displayed antioxidant activity. These data confirmed the importance of Proteobacteria and Actinobacteria associated with marine sponges as a reservoir of bioactive compounds. This study presents the first report on the diversity of the cultivable bacteria associated with the marine sponge Phorbas tenacior, frequently found in the Mediterranean Sea. Evaluation of the antiplasmodial, antimicrobial and antioxidant activities of the isolates has been investigated and allowed to select bacterial strains, confirming the importance of Proteobacteria and Actinobacteria as sources of bioactive compounds. © 2013 The Society for Applied Microbiology.

Evaluating bacterial gene-finding HMM structures as probabilistic logic programs.

Science.gov (United States)

Mørk, Søren; Holmes, Ian

2012-03-01

Probabilistic logic programming offers a powerful way to describe and evaluate structured statistical models. To investigate the practicality of probabilistic logic programming for structure learning in bioinformatics, we undertook a simplified bacterial gene-finding benchmark in PRISM, a probabilistic dialect of Prolog. We evaluate Hidden Markov Model structures for bacterial protein-coding gene potential, including a simple null model structure, three structures based on existing bacterial gene finders and two novel model structures. We test standard versions as well as ADPH length modeling and three-state versions of the five model structures. The models are all represented as probabilistic logic programs and evaluated using the PRISM machine learning system in terms of statistical information criteria and gene-finding prediction accuracy, in two bacterial genomes. Neither of our implementations of the two currently most used model structures are best performing in terms of statistical information criteria or prediction performances, suggesting that better-fitting models might be achievable. The source code of all PRISM models, data and additional scripts are freely available for download at: http://github.com/somork/codonhmm. Supplementary data are available at Bioinformatics online.

Performance of improved bacterial cellulose application in the production of functional paper.

Science.gov (United States)

Basta, A H; El-Saied, H

2009-12-01

The purpose of this work was to study the feasibility of producing economic flame retardant bacterial cellulose (BC) and evaluating its behaviour in paper production. This type of BC was prepared by Gluconacetobacter subsp. xylinus and substituting the glucose in the cultivation medium by glucose phosphate as a carbon source; as well as using corn steep liquor as a nitrogen source. The investigated processing technique did not dispose any toxic chemicals that pollute the surroundings or cause unacceptable effluents, making the process environmentally safe. The fire retardant behaviour of the investigated BC has been studied by non-isothermal thermogravimetric analysis (TGA & DTGA). The activation energy of each degradation stage and the order of degradation were estimated using the Coats-Redfern equation and the least square method. Strength, optical properties, and thermogravimetric analysis of BC-phosphate added paper sheets were also tested. The study confirmed that the use of glucose phosphate along with glucose was significant in the high yield production of phosphate containing bacterial cellulose (PCBC1); more so than the use of glucose phosphate alone (PCBC2). Incorporating 5% of the PCBC with wood pulp during paper sheet formation was found to significantly improve kaolin retention, strength, and fire resistance properties as compared to paper sheets produced from incorporating bacterial cellulose (BC). This modified BC is a valuable product for the preparation of specialized paper, in addition to its function as a fillers aid.

Bacterial growth kinetics

International Nuclear Information System (INIS)

Boonkitticharoen, V.; Ehrhardt, J.C.; Kirchner, P.T.

1989-01-01

Quantitative measurement of bacterial growth may be made using a radioassay technique. This method measures, by scintillation counting, the 14 CO 2 derived from the bacterial metabolism of a 14 C-labeled substrate. Mathematical growth models may serve as reliable tools for estimation of the generation rate constant (or slope of the growth curve) and provide a basis for evaluating assay performance. Two models, i.e., exponential and logistic, are proposed. Both models yielded an accurate fit to the data from radioactive measurement of bacterial growth. The exponential model yielded high precision values of the generation rate constant, with an average relative standard deviation of 1.2%. Under most conditions the assay demonstrated no changes in the slopes of growth curves when the number of bacteria per inoculation was changed. However, the radiometric assay by scintillation method had a growth-inhibiting effect on a few strains of bacteria. The source of this problem was thought to be hypersensitivity to trace amounts of toluene remaining on the detector

Water Sources and Their Protection from the Impact of Microbial Contamination in Rural Areas of Beijing, China

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Hairong Li

2013-03-01

Full Text Available Bacterial contamination of drinking water is a major public health problem in rural China. To explore bacterial contamination in rural areas of Beijing and identify possible causes of bacteria in drinking water samples, water samples were collected from wells in ten rural districts of Beijing, China. Total bacterial count, total coliforms and Escherichia coli in drinking water were then determined and water source and wellhead protection were investigated. The bacterial contamination in drinking water was serious in areas north of Beijing, with the total bacterial count, total coliforms and Escherichia coli in some water samples reaching 88,000 CFU/mL, 1,600 MPN/100 mL and 1,600 MPN/100 mL, respectively. Water source types, well depth, whether the well was adequately sealed and housed, and whether wellhead is above or below ground were the main factors influencing bacterial contamination levels in drinking water. The bacterial contamination was serious in the water of shallow wells and wells that were not closed, had no well housing or had a wellhead below ground level. The contamination sources around wells, including village dry toilets and livestock farms, were well correlated with bacterial contamination. Total bacterial counts were affected by proximity to sewage ditches and polluting industries, however, proximity to landfills did not influence the microbial indicators.

Prevalence of antibiotic resistance genes in bacterial communities associated with Cladophora glomerata mats along the nearshore of Lake Ontario.

Science.gov (United States)

Ibsen, Michael; Fernando, Dinesh M; Kumar, Ayush; Kirkwood, Andrea E

2017-05-01

The alga Cladophora glomerata can erupt in nuisance blooms throughout the lower Great Lakes. Since bacterial abundance increases with the emergence and decay of Cladophora, we investigated the prevalence of antibiotic resistance (ABR) in Cladophora-associated bacterial communities up-gradient and down-gradient from a large sewage treatment plant (STP) on Lake Ontario. Although STPs are well-known sources of ABR, we also expected detectable ABR from up-gradient wetland communities, since they receive surface run-off from urban and agricultural sources. Statistically significant differences in aquatic bacterial abundance and ABR were found between down-gradient beach samples and up-gradient coastal wetland samples (ANOVA, Holm-Sidak test, p Cladophora sampled near the STP had the highest bacterial densities overall, including on ampicillin- and vancomycin-treated plates. However, quantitative polymerase chain reaction analysis of the ABR genes ampC, tetA, tetB, and vanA from environmental communities showed a different pattern. Some of the highest ABR gene levels occurred at the 2 coastal wetland sites (vanA). Overall, bacterial ABR profiles from environmental samples were distinguishable between living and decaying Cladophora, inferring that Cladophora may control bacterial ABR depending on its life-cycle stage. Our results also show how spatially and temporally dynamic ABR is in nearshore aquatic bacteria, which warrants further research.

Glyphosate Utilization as the Source of Carbon: Isolation and Identification of new Bacteria

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M. Mohsen Nourouzi

2011-01-01

Full Text Available Mixed bacteria from oil palm plantation soil (OPS were isolated to investigate their ability to utilize glyphosate as carbon source. Results showed that approximately all of the glyphosate was converted to aminomethyl-phosphonic acid (AMPA (99.5%. It is worthy to note that mixed bacteria were able to degrade only 2% of AMPA to further metabolites. Two bacterial strains i.e. Stenotrophomonas maltophilia and Providencia alcalifaciens were obtained from enrichment culture. Bacterial isolates were cultured individually on glyphosate as a sole carbon source. It was observed that both isolates were able to convert glyphosate to AMPA.

Biodegradability of bacterial surfactants.

Science.gov (United States)

Lima, Tânia M S; Procópio, Lorena C; Brandão, Felipe D; Carvalho, André M X; Tótola, Marcos R; Borges, Arnaldo C

2011-06-01

This work aimed at evaluating the biodegradability of different bacterial surfactants in liquid medium and in soil microcosms. The biodegradability of biosurfactants by pure and mixed bacterial cultures was evaluated through CO(2) evolution. Three bacterial strains, Acinetobacter baumanni LBBMA ES11, Acinetobacter haemolyticus LBBMA 53 and Pseudomonas sp. LBBMA 101B, used the biosurfactants produced by Bacillus sp. LBBMA 111A (mixed lipopeptide), Bacillus subtilis LBBMA 155 (lipopeptide), Flavobacterium sp. LBBMA 168 (mixture of flavolipids), Dietzia Maris LBBMA 191(glycolipid) and Arthrobacter oxydans LBBMA 201(lipopeptide) as carbon sources in minimal medium. The synthetic surfactant sodium dodecyl sulfate (SDS) was also mineralized by these microorganisms, but at a lower rate. CO(2) emitted by a mixed bacterial culture in soil microcosms with biosurfactants was higher than in the microcosm containing SDS. Biosurfactant mineralization in soil was confirmed by the increase in surface tension of the soil aqueous extracts after incubation with the mixed bacterial culture. It can be concluded that, in terms of biodegradability and environmental security, these compounds are more suitable for applications in remediation technologies in comparison to synthetic surfactants. However, more information is needed on structure of biosurfactants, their interaction with soil and contaminants and scale up and cost for biosurfactant production.

Investigation of the effects of oleuropein rich diet on rat enteric bacterial flora.

Science.gov (United States)

Kiraz, A; Simsek, T; Tekin, S Z; Elmas, S; Tekin, M; Sahin, H; Altinisik, H B; Pala, C

2016-01-01

Oleuropein is a phenolic compound of olive leaves. Enteric bacterial flora is very important for human health and diet is a directly affecting factor of enteric bacterial flora composition. In this study, it was hypothesized that oleuropein could reduce total aerobic bacterial count in rat caecal flora. Twenty adult, male, Wistar albino rats were randomly divided into two groups. Group C (n=10) was fed with standard rat chow and water for 30 days. Group O (n=10) received olive leaf extract 20 mg/kg/day by intragastric gavage in addition to standard rat chow and water for 30 days. One gram of caecal content was collected from each rat and then consecutive 10-fold serial dilutions were prepared with a final concentration of 10-8. Then 0.1 ml of each dilution were spread onto the surfaces of Plate Count Agar and Violet Red Bile Glucose Agar to enumerate the aerobic enteric bacteria. Total aerobic bacterial counts of Group O were significantly lower than of Group C in all agar plates inoculated with ceacal samples for every dilution (pbacterial translocation by reducing enteric bacterial counts (Tab. 1, Ref. 32).

Investigation of In vitro Mineral Forming Bacterial Isolates from ...

African Journals Online (AJOL)

Aim: Although it is known that bacterial mechanisms are involved in dental calculus formation, which is a predisposing factor in periodontal diseases, there have been few studies of such associations, and therefore, information available is limited. The purpose of this study was to isolate and identify aerobic bacteria ...

Taxonomic profiling of bacterial community structure from coastal sediment of Alang-Sosiya shipbreaking yard near Bhavnagar, India.

Science.gov (United States)

Patel, Vilas; Munot, Hitendra; Shah, Varun; Shouche, Yogesh S; Madamwar, Datta

2015-12-30

The Alang-Sosiya shipbreaking yard (ASSBY) is considered the largest of its kind in the world, and a major source of anthropogenic pollutants. The aim of this study was to investigate the impact of shipbreaking activities on the bacterial community structure with a combination of culture-dependent and culture-independent approaches. In the culture-dependent approach, 200 bacterial cultures were isolated and analyzed by molecular fingerprinting and 16S ribosomal RNA (r-RNA) gene sequencing, as well as being studied for degradation of polycyclic aromatic hydrocarbons (PAHs). In the culture-independent approach, operational taxonomic units (OTUs) were related to eight major phyla, of which Betaproteobacteria (especially Acidovorax) was predominantly found in the polluted sediments of ASSBY and Gammaproteobacteria in the pristine sediment sample. The statistical approaches showed a significant difference in the bacterial community structure between the pristine and polluted sediments. To the best of our knowledge, this is the first study investigating the effect of shipbreaking activity on the bacterial community structure of the coastal sediment at ASSBY. Copyright © 2015. Published by Elsevier Ltd.

Molecular diagnosis of bacterial vaginosis: Does adjustment for total bacterial load or human cellular content improve diagnostic performance?

Science.gov (United States)

Plummer, E L; Garland, S M; Bradshaw, C S; Law, M G; Vodstrcil, L A; Hocking, J S; Fairley, C K; Tabrizi, S N

2017-02-01

We investigated the utility of quantitative PCR assays for diagnosis of bacterial vaginosis and found that while the best model utilized bacterial copy number adjusted for total bacterial load (sensitivity=98%, specificity=93%, AUC=0.95[95%CI=0.93,0.97]), adjusting for total bacterial or human cell load did not consistently increase the diagnostic performance of the assays. Copyright © 2017 Elsevier B.V. All rights reserved.

Bacterial indicator occurrence and the use of an F+ specific RNA coliphage assay to identify fecal sources in Homosassa Springs, Florida

Science.gov (United States)

Griffin, Dale W.; Stokes, Rodger; Rose, J.B.; Paul, J.H.

2000-01-01

A microbiological water quality study of Homosassa Springs State Wildlife Park (HSSWP) and surrounding areas was undertaken. Samples were collected in November of 1997 (seven sites) and again in November of 1998 (nine sites). Fecal bacterial concentrations (total and fecal coliforms, Clostridium perfringens, and enterococci) were measured as relative indicators of fecal contamination. F+-specific coliphage genotyping was performed to determine the source of fecal contamination at the study sites. Bacterial levels were considerably higher at most sites in the 1997 sampling compared to the 1998 sampling, probably because of the greater rainfall that year. In November of 1997, 2 of the 7 sites were in violation of all indicator standards and guidance levels. In November of 1998, 1 of 9 sites was in violation of all indicator standard and guidance levels. The highest concentrations of all fecal indicators were found at a station downstream of the animal holding pens in HSSWP. The lowest levels of indicators were found at the Homosassa Main Spring vent. Levels of fecal indicators downstream of HSSWP (near the point of confluence with the river) were equivalent to those found in the Southeastern Fork and areas upstream of the park influences. F+ specific RNA coliphage analysis indicated that fecal contamination at all sites that tested positive was from animal sources (mammals and birds). These results suggest that animal (indigenous and those in HSSWP) and not human sources influenced microbial water quality in the area of Homosassa River covered by this study.

Diversity of Bacterial Communities of Fitness Center Surfaces in a U.S. Metropolitan Area

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Nabanita Mukherjee

2014-12-01

Full Text Available Public fitness centers and exercise facilities have been implicated as possible sources for transmitting community-acquired bacterial infections. However, the overall diversity of the bacterial community residing on the surfaces in these indoor environments is still unknown. In this study, we investigated the overall bacterial ecology of selected fitness centers in a metropolitan area (Memphis, TN, USA utilizing culture-independent pyrosequencing of the 16S rRNA genes. Samples were collected from the skin-contact surfaces (e.g., exercise instruments, floor mats, handrails, etc. within fitness centers. Taxonomical composition revealed the abundance of Firmicutes phyla, followed by Proteobacter and Actinobacteria, with a total of 17 bacterial families and 25 bacterial genera. Most of these bacterial genera are of human and environmental origin (including, air, dust, soil, and water. Additionally, we found the presence of some pathogenic or potential pathogenic bacterial genera including Salmonella, Staphylococcus, Klebsiella, and Micrococcus. Staphylococcus was found to be the most prevalent genus. Presence of viable forms of these pathogens elevates risk of exposure of any susceptible individuals. Several factors (including personal hygiene, surface cleaning and disinfection schedules of the facilities may be the reasons for the rich bacterial diversity found in this study. The current finding underscores the need to increase public awareness on the importance of personal hygiene and sanitation for public gym users.

Effects of inoculation with organic-phosphorus-mineralizing bacteria on soybean (Glycine max) growth and indigenous bacterial community diversity.

Science.gov (United States)

Sun, Wei; Qian, Xun; Gu, Jie; Wang, Xiao-Juan; Li, Yang; Duan, Man-Li

2017-05-01

Three different organic-phosphorus-mineralizing bacteria (OPMB) strains were inoculated to soil planted with soybean (Glycine max), and their effects on soybean growth and indigenous bacterial community diversity were investigated. Inoculation with Pseudomonas fluorescens Z4-1 and Brevibacillus agri L7-1 increased organic phosphorus degradation by 22% and 30%, respectively, compared with the control at the mature stage. Strains P. fluorescens Z4-1 and B. agri L7-1 significantly improved the soil alkaline phosphatase activity, average well color development, and the soybean root activity. Terminal restriction fragment length polymorphism analysis demonstrated that P. fluorescens Z4-1 and B. agri L7-1 could persist in the soil at relative abundances of 2.0%-6.4% throughout soybean growth. Thus, P. fluorescens Z4-1 and B. agri L7-1 could potentially be used in organic-phosphorus-mineralizing biofertilizers. OPMB inoculation altered the genetic structure of the soil bacterial communities but had no apparent influence on the carbon source utilization profiles of the soil bacterial communities. Principal components analysis showed that the changes in the carbon source utilization profiles of bacterial community depended mainly on the plant growth stages rather than inoculation with OPMB. The results help to understand the evolution of the soil bacterial community after OPMB inoculation.

Phase I Source Investigation, Heckathorn Superfund Site, Richmond, California

Energy Technology Data Exchange (ETDEWEB)

Kohn, Nancy P; Evans, Nathan R

2002-12-18

This report represents Phase I of a multi-phase approach to a source investigation of DDT at the Heckathorn Superfund Site, Richmond, California, the former site of a pesticide packaging plant, and the adjacent waterway, the Lauritzen Channel. Potential identified sources of contamination were from sloughed material from undredged areas (such as side banks) and from outfall pipes. Objectives of Phase I included the (1) evaluation of pesticide concentrations associated with discharge from outfalls, (2) identification of additional outfalls in the area, (3) identification of type, quantity, and distribution of sediment under the Levin pier, (4) quantification of pesticide concentrations in sediment under the pier, and (5) evaluation of sediment structure and slope stability under the pier. Field operations included the collection of sediment directly from inside the mouths of outfall pipes, when possible, or the deployment of specially designed particle traps where direct sampling was problematic. Passive water samplers were placed at the end of known outfall pipes and analyzed for DDT and other pesticides of concern. Underwater dive surveys were conducted beneath the Levin pier to document type, slope, and thickness of sediment. Samples were collected at locations of interest and analyzed for contaminants. Also sampled was soil from bank areas, which were suspected of potentially contributing to continued DDT contamination of the Lauritzen Channel through erosion and groundwater leaching. The Phase I Source Investigation was successful in identifying significant sources of DDT contamination to Lauritzen Channel sediment. Undredged sediment beneath the Levin pier that has been redistributed to the channel is a likely source. Two outfalls tested bear further investigation. Not as well-defined are the contributions of bank erosional material and groundwater leaching. Subsequent investigations will be based on the results of this first phase.

Heme Synthesis and Acquisition in Bacterial Pathogens

OpenAIRE

Choby, Jacob E.; Skaar, Eric P.

2016-01-01

Bacterial pathogens require the iron-containing cofactor heme to cause disease. Heme is essential to the function of hemoproteins, which are involved in energy generation by the electron transport chain, detoxification of host immune effectors, and other processes. During infection, bacterial pathogens must synthesize heme or acquire heme from the host; however, host heme is sequestered in high-affinity hemoproteins. Pathogens have evolved elaborate strategies to acquire heme from host source...

Risk of bacterial cross infection associated with inspiration through flow-based spirometers.

Science.gov (United States)

Bracci, Massimo; Strafella, Elisabetta; Croce, Nicola; Staffolani, Sara; Carducci, Annalaura; Verani, Marco; Valentino, Matteo; Santarelli, Lory

2011-02-01

Bacterial contamination of spirometers has been documented in water-sealed devices, mouthpieces, and connection tubes. Little information is available about bacterial contamination of flow-based apparatuses such as turbine-type spirometers and pneumotachographs. Inspiration through contaminated equipment is a potential source of cross infection. To investigate bacteria mobilization (ie, bacteria detachment and aerosolization from the instrument) during routine spirometric testing, 2 types of flow-based spirometers were used. Bacteria mobilization during artificial inspiration through in-line filters or cardboard mouthpieces was evaluated. Nine hundred workers undergoing periodic spirometric testing were enrolled at the occupational physician office in 30 sessions of 30 subjects each. The participants were asked to perform a forced vital capacity test in a turbine-type spirometer and in an unheated pneumotachograph fitted with disposable in-line filters or cardboard mouthpieces. To evaluate bacterial mobilization, an artificial inspiration was performed and bacterial growth determined. The bacterial growth analysis was assessed after the first and the thirtieth spirometric tests of each session without disinfecting the instruments between tests. In addition, instrument bacterial contamination was evaluated. No significant bacterial mobilization and instrument contamination were found in spirometric tests executed with in-line filters. Conversely, a significant bacterial mobilization and instrument contamination were observed in tests performed with cardboard mouthpieces. Differences between the 2 spirometers were not significant. In-line filters may effectively reduce the risk of bacterial cross infection. Inspiration through flow-based spirometers fitted with disposable cardboard mouthpieces is completely safe when combined with spirometer disinfection/sterilization between subjects. Copyright © 2011 Association for Professionals in Infection Control and

Effect of Different Carbon Sources on Bacterial Nanocellulose Production and Structure Using the Low pH Resistant Strain Komagataeibacter Medellinensis

Directory of Open Access Journals (Sweden)

Carlos Molina-Ramírez

2017-06-01

Full Text Available Bacterial cellulose (BC is a polymer obtained by fermentation with microorganism of different genera. Recently, new producer species have been discovered, which require identification of the most important variables affecting cellulose production. In this work, the influence of different carbon sources in BC production by a novel low pH-resistant strain Komagataeibacter medellinensis was established. The Hestrin-Schramm culture medium was used as a reference and was compared to other media comprising glucose, fructose, and sucrose, used as carbon sources at three concentrations (1, 2, and 3% w/v. The BC yield and dynamics of carbon consumption were determined at given fermentation times during cellulose production. While the carbon source did not influence the BC structural characteristics, different production levels were determined: glucose > sucrose > fructose. These results highlight considerations to improve BC industrial production and to establish the BC property space for applications in different fields.

Investigation of In vitro Mineral forming bacterial isolates from supragingival calculus.

Science.gov (United States)

Baris, O; Demir, T; Gulluce, M

2017-12-01

Although it is known that bacterial mechanisms are involved in dental calculus formation, which is a predisposing factor in periodontal diseases, there have been few studies of such associations, and therefore, information available is limited. The purpose of this study was to isolate and identify aerobic bacteria responsible for direct calcification from supragingival calculus samples. The study was conducted using supragingival calculus samples from patients with periodontal disease, which was required as part of conventional treatment. Isolations were performed by sampling the supragingival calculus with buffer and inoculating the samples on media on which crystallization could be observed. The 16S recombinant DNA of the obtained pure cultures was then amplified and sequenced. A few bacterial species that have not previously been associated with mineralization or identified on bacterial plaque or calculus were detected. The bacteria that caused mineralization an aerobic environment are identified as Neisseria flava, Aggregatibacter segnis, Streptococcus tigurinus, and Morococcus cerebrosus. These findings proved that bacteria potentially play a role in the etiopathology of supragingival calculus. The association between the effects of the identified bacteria on periodontal diseases and calculus formation requires further studies.

Bacterial contamination hypothesis: a new concept in endometriosis.

Science.gov (United States)

Khan, Khaleque N; Fujishita, Akira; Hiraki, Koichi; Kitajima, Michio; Nakashima, Masahiro; Fushiki, Shinji; Kitawaki, Jo

2018-04-01

Endometriosis is a multifactorial disease that mainly affects women of reproductive age. The exact pathogenesis of this disease is still debatable. The role of bacterial endotoxin (lipopolysaccharide, LPS) and Toll-like receptor 4 (TLR4) in endometriosis were investigated and the possible source of endotoxin in the pelvic environment was examined. The limulus amoebocyte lysate test was used to measure the endotoxin levels in the menstrual fluid and peritoneal fluid and their potential role in the growth of endometriosis was investigated. Menstrual blood and endometrial samples were cultured for the presence of microbes. The effect of gonadotrophin-releasing hormone agonist (GnRHa) treatment on intrauterine microbial colonization (IUMC) and the occurrence of endometritis was investigated. Lipopolysaccharide regulates the pro-inflammatory response in the pelvis and growth of endometriosis via the LPS/TLR4 cascade. The menstrual blood was highly contaminated with Escherichea coli and the endometrial samples were colonized with other microbes. A cross-talk between inflammation and ovarian steroids or the stress reaction also was observed in the pelvis. Treatment with GnRHa further worsens intrauterine microbial colonization, with the consequent occurrence of endometritis in women with endometriosis. For the first time, a new concept called the "bacterial contamination hypothesis" is proposed in endometriosis. This study's findings of IUMC in women with endometriosis could hold new therapeutic potential in addition to the conventional estrogen-suppressing agent.

Bacterial Diversity in Submarine Groundwater along the Coasts of the Yellow Sea

OpenAIRE

Ye, Qi; Liu, Jianan; Du, Jinzhou; Zhang, Jing

2016-01-01

Submarine groundwater (SGD) is one of the most significant pathways for the exchange of groundwater and/or source of nutrients, metals and carbon to the ocean, subsequently cause deleterious impacts on the coastal ecosystems. Microorganisms have been recognized as the important participators in the biogeochemical processes in the SGD. In this study, by utilizing 16S rRNA-based Illumina Miseq sequencing technology, we investigated bacterial diversity and distribution in both fresh well water a...

Bacterial Cellulose Production from Industrial Waste and by-Product Streams.

Science.gov (United States)

Tsouko, Erminda; Kourmentza, Constantina; Ladakis, Dimitrios; Kopsahelis, Nikolaos; Mandala, Ioanna; Papanikolaou, Seraphim; Paloukis, Fotis; Alves, Vitor; Koutinas, Apostolis

2015-07-01

The utilization of fermentation media derived from waste and by-product streams from biodiesel and confectionery industries could lead to highly efficient production of bacterial cellulose. Batch fermentations with the bacterial strain Komagataeibacter sucrofermentans DSM (Deutsche Sammlung von Mikroorganismen) 15973 were initially carried out in synthetic media using commercial sugars and crude glycerol. The highest bacterial cellulose concentration was achieved when crude glycerol (3.2 g/L) and commercial sucrose (4.9 g/L) were used. The combination of crude glycerol and sunflower meal hydrolysates as the sole fermentation media resulted in bacterial cellulose production of 13.3 g/L. Similar results (13 g/L) were obtained when flour-rich hydrolysates produced from confectionery industry waste streams were used. The properties of bacterial celluloses developed when different fermentation media were used showed water holding capacities of 102-138 g · water/g · dry bacterial cellulose, viscosities of 4.7-9.3 dL/g, degree of polymerization of 1889.1-2672.8, stress at break of 72.3-139.5 MPa and Young's modulus of 0.97-1.64 GPa. This study demonstrated that by-product streams from the biodiesel industry and waste streams from confectionery industries could be used as the sole sources of nutrients for the production of bacterial cellulose with similar properties as those produced with commercial sources of nutrients.

Investigation of an incident due to orphan sources in Iran

Energy Technology Data Exchange (ETDEWEB)

Mehdizadeh, S. [Shiraz Univ. (Iran, Islamic Republic of); Kardan, M.R.; Abdollah Miangi, F.; Rastkhah, N. [National Radiation Protection Dept., Tehran (Iran, Islamic Republic of)

2006-07-01

This paper discusses an incident occurred in one of the radiation application centers in Iran, and follow up investigations as well as lessons learnt. In January 2004 the Regulatory Authority was informed through Shiraz University R.P.O. of an incident regarding orphan radioactive sources which belonged to a Radiation Application Center (R.A.C.) in Shiraz. In this incident a metallic box containing a neutron emitting and three gamma emitting sources belonging to the above mentioned center were unearthed from a burial site outside of Shiraz by some person or persons and the box was eventually set on fire. Investigations conducted later on, showed that despite the melting of the paraffin shield of neutron emitting source, the capsules containing sources were intact and unharmed, and no radioactive leaking had occurred. Further investigations showed that this box contained one Am-Be source and three Cs-137 sources which had been given to the above mentioned center, long time before by a foreign well logging company from former Czech Republic and without notifying the Regulatory Authority. Follow up measurements indicated the maximum dose rate of 111 GBq Am-Be and 3.7 GBq Cs-137 sources to be 13 mSv/h and 7 mSv/hr accordingly. Therefore the maximum dose for the people involved in this incident is estimated to have been about 100 mSv, consequently no severe deterministic effects to individuals is expected: the findings showed that the main reasons for the incident were as follows: 1. Lack of professionalism in working with radioactive materials. 2. Violation of obligation under Radiation protection act and related regulations by the owner of the sources which was a well logging foreign company. 3. Leaving the sources in an improper storage condition. 4. Unauthorized access to the radiation sources in the owner center. 5. Lack of an effective national register system in the Regulatory Authority. 6. Lack of a well scheduled and risk base inspection program for the

An investigation into the bacterial contamination of goniolenses in use in clinical practice.

Science.gov (United States)

Grundon, Rachael; Scurrell, Emma; Mould, John; Hayton-Lee, Emma; Heinrich, Christine

2017-12-18

Objectives To report the incidence and evaluate the clinical significance of goniolens bacterial contamination in clinical use in dogs with three different usage protocols and one with an added cleaning protocol. Animals Studied and Methods Three groups of twenty dogs undergoing gonioscopy at a private practice in the UK had the goniolenses swabbed for bacteriology culture and identification prior to placement on the cornea. Three protocols of lens use, with 2 different types of goniolens, were studied. One protocol was then repeated with 21 dogs with a lens cleaning protocol prior to storage. Results Low levels of bacterial contamination were found in all 3 initial groups (10-15%). No correlation was found between usage protocol used and rate of contamination and no correlation was found between length of storage between use and contamination. All bacteria cultured were considered naturally occurring commensals for the canine eye and environment. The group with a cleaning protocol had a 4.7% contamination rate. This was not statistically different from the non-cleaning groups. Conclusions The rate of bacterial contamination of goniolenses in clinical practice is low and the bacterial contaminants consist of commensal bacteria, unlikely to be of detriment to the eye. Minimal contamination of the goniolenses was found and this did not appear to be of clinical significance. The introduction of a simple cleaning protocol did not produce a statistically significant reduction in bacterial contamination. © 2017 American College of Veterinary Ophthalmologists.

A New Phylogenetic Approach to Investigate the Intestinal Bacterial Composition

DEFF Research Database (Denmark)

Hermann-Bank, Marie Louise; Mølbak, Lars

literature, meaning their use had already been verified. DNA from reference bacteria and DNA from faecal samples were used to check specificity and sensitivity of the assay when analysing bacterial communities. The heat map showed nice dilution colour series consistent with the diluted sample concentrations...... reactions in a few hours. Subsequently the 16S rDNA amplicons can be harvested and used for next generation sequencing. The experimental setup was designed so that the primers represented a phylogenetic overview of the biggest groups of intestinal bacteria. Primers were mainly chosen from published...... ranging from 50 to 0.005 ng/μl and in agreement to the expected results. This implies that the AA48.48 is a useful tool when examining the bacterial composition of faeces and maybe superior to competitive methods, as it gives a quantitative measurement of the bacteria in the sample and afterwards...

Investigating Primary Source Literacy

Science.gov (United States)

Archer, Joanne; Hanlon, Ann M.; Levine, Jennie A.

2009-01-01

Primary source research requires students to acquire specialized research skills. This paper presents results from a user study testing the effectiveness of a Web guide designed to convey the concepts behind "primary source literacy". The study also evaluated students' strengths and weaknesses when conducting primary source research. (Contains 3…

Rifaximin has minor effects on bacterial composition, inflammation and bacterial translocation in cirrhosis

DEFF Research Database (Denmark)

Kimer, Nina; Pedersen, Julie S.; Tavenier, Juliette

2018-01-01

.4), and MELD score 12 (±3.9). Patients received rifaximin 550 mg BD (n=36) or placebo BD (n=18). Blood and faecal (n=15) sampling were conducted at baseline and after four weeks. Bacterial DNA in blood was determined by real-time qPCR 16S rRNA gene quantification. Bacterial composition in faeces was analysed......BACKGROUND & AIMS: Decompensated cirrhosis is characterized by disturbed haemodynamics, immune dysfunction, and high risk of infections. Translocation of viable bacteria and bacterial products from the gut to the blood is considered a key driver in this process. Intestinal decontamination...... with rifaximin may reduce bacterial translocation (BT) and decrease inflammation. In a randomized, placebo-controlled trial investigated the effects of rifaximin on inflammation and BT in decompensated cirrhosis. METHODS: Fifty-four out-patients with cirrhosis and ascites were randomized, mean age 56 years (±8...

Coal fly ash impairs airway antimicrobial peptides and increases bacterial growth.

Science.gov (United States)

Borcherding, Jennifer A; Chen, Haihan; Caraballo, Juan C; Baltrusaitis, Jonas; Pezzulo, Alejandro A; Zabner, Joseph; Grassian, Vicki H; Comellas, Alejandro P

2013-01-01

Air pollution is a risk factor for respiratory infections, and one of its main components is particulate matter (PM), which is comprised of a number of particles that contain iron, such as coal fly ash (CFA). Since free iron concentrations are extremely low in airway surface liquid (ASL), we hypothesize that CFA impairs antimicrobial peptides (AMP) function and can be a source of iron to bacteria. We tested this hypothesis in vivo by instilling mice with Pseudomonas aeruginosa (PA01) and CFA and determine the percentage of bacterial clearance. In addition, we tested bacterial clearance in cell culture by exposing primary human airway epithelial cells to PA01 and CFA and determining the AMP activity and bacterial growth in vitro. We report that CFA is a bioavailable source of iron for bacteria. We show that CFA interferes with bacterial clearance in vivo and in primary human airway epithelial cultures. Also, we demonstrate that CFA inhibits AMP activity in vitro, which we propose as a mechanism of our cell culture and in vivo results. Furthermore, PA01 uses CFA as an iron source with a direct correlation between CFA iron dissolution and bacterial growth. CFA concentrations used are very relevant to human daily exposures, thus posing a potential public health risk for susceptible subjects. Although CFA provides a source of bioavailable iron for bacteria, not all CFA particles have the same biological effects, and their propensity for iron dissolution is an important factor. CFA impairs lung innate immune mechanisms of bacterial clearance, specifically AMP activity. We expect that identifying the PM mechanisms of respiratory infections will translate into public health policies aimed at controlling, not only concentration of PM exposure, but physicochemical characteristics that will potentially cause respiratory infections in susceptible individuals and populations.

Bacterial contamination of street vending food in Kumasi, Ghana ...

African Journals Online (AJOL)

Street vending foods are readily available sources of meals for many people but the biological safe-ty of such food is always in doubt. The aim of this study is to ascertain bacterial isolate and deter-mine total counts of bacterial species responsible for the contamination of the street vending food in Kumasi so as to determine ...

Reproducible Biofilm Cultivation of Chemostat-Grown Escherichia coli and Investigation of Bacterial Adhesion on Biomaterials Using a Non-Constant-Depth Film Fermenter

Science.gov (United States)

Lüdecke, Claudia; Jandt, Klaus D.; Siegismund, Daniel; Kujau, Marian J.; Zang, Emerson; Rettenmayr, Markus; Bossert, Jörg; Roth, Martin

2014-01-01

Biomaterials-associated infections are primarily initiated by the adhesion of microorganisms on the biomaterial surfaces and subsequent biofilm formation. Understanding the fundamental microbial adhesion mechanisms and biofilm development is crucial for developing strategies to prevent such infections. Suitable in vitro systems for biofilm cultivation and bacterial adhesion at controllable, constant and reproducible conditions are indispensable. This study aimed (i) to modify the previously described constant-depth film fermenter for the reproducible cultivation of biofilms at non-depth-restricted, constant and low shear conditions and (ii) to use this system to elucidate bacterial adhesion kinetics on different biomaterials, focusing on biomaterials surface nanoroughness and hydrophobicity. Chemostat-grown Escherichia coli were used for biofilm cultivation on titanium oxide and investigating bacterial adhesion over time on titanium oxide, poly(styrene), poly(tetrafluoroethylene) and glass. Using chemostat-grown microbial cells (single-species continuous culture) minimized variations between the biofilms cultivated during different experimental runs. Bacterial adhesion on biomaterials comprised an initial lag-phase I followed by a fast adhesion phase II and a phase of saturation III. With increasing biomaterials surface nanoroughness and increasing hydrophobicity, adhesion rates increased during phases I and II. The influence of materials surface hydrophobicity seemed to exceed that of nanoroughness during the lag-phase I, whereas it was vice versa during adhesion phase II. This study introduces the non-constant-depth film fermenter in combination with a chemostat culture to allow for a controlled approach to reproducibly cultivate biofilms and to investigate bacterial adhesion kinetics at constant and low shear conditions. The findings will support developing and adequate testing of biomaterials surface modifications eventually preventing biomaterial

Investigation of rf plasma light sources for dye laser excitation

International Nuclear Information System (INIS)

Kendall, J.S.; Jaminet, J.F.

1975-06-01

Analytical and experimental studies were performed to assess the applicability of radio frequency (rf) induction heated plasma light sources for potential excitation of continuous dye lasers. Experimental efforts were directed toward development of a continuous light source having spectral flux and emission characteristics approaching that required for pumping organic dye lasers. Analytical studies were performed to investigate (1) methods of pulsing the light source to obtain higher radiant intensity and (2) methods of integrating the source with a reflective cavity for pumping a dye cell. (TFD)

Low temperature anaerobic bacterial diagenesis of ferrous monosulfide to pyrite

Science.gov (United States)

Donald, Ravin; Southam, Gordon

1999-07-01

In vitro enrichment cultures of dissimilatory sulfate-reducing bacteria precipitated FeS and catalyzed its transformation into FeS 2 at ambient temperature and pressure under anaerobic conditions. When compared to purely abiotic processes, the bacterially mediated transformation was shown to be more efficient in transforming FeS into FeS 2. This occurred due to the large, reactive surface area available for bacterially catalyzed diagenesis, where the biogenic FeS precursor was immobilized as a thin film (˜25 nm thick) on the μm-scale bacteria. The bacteria also contained the source(s) of sulfur for diagenesis to occur. Using a radiolabeled organic-sulfur tracer study, sulfur was released during cell autolysis and was immobilized at the bacterial cell surface forming FeS 2. The formation of FeS 2 occurred on both the inner and outer surfaces of the cell envelope and represented the first step of bacterial mineral diagenesis. Pyrite crystals, having linear dimensions of ˜1 μm, grew outward from the bacterial cell surfaces. These minerals were several orders of magnitude larger in volume than those originating abiotically.

Bacterial Diversity in Submarine Groundwater along the Coasts of the Yellow Sea.

Science.gov (United States)

Ye, Qi; Liu, Jianan; Du, Jinzhou; Zhang, Jing

2015-01-01

Submarine groundwater (SGD) is one of the most significant pathways for the exchange of groundwater and/or source of nutrients, metals and carbon to the ocean, subsequently cause deleterious impacts on the coastal ecosystems. Microorganisms have been recognized as the important participators in the biogeochemical processes in the SGD. In this study, by utilizing 16S rRNA-based Illumina Miseq sequencing technology, we investigated bacterial diversity and distribution in both fresh well water and brackish recirculated porewater along the coasts in the Yellow Sea. The results showed that Actinobacteria and Betaproteobacteria, especially Comamonas spp. and Limnohabitans spp. were dominated in fresh well samples. Distinct patterns of bacterial communities were found among the porewater samples due to different locations, for examples, Cyanbacteria was the most abundant in the porewater samples far from the algal bloomed areas. The analysis of correlation between representative bacterial taxonomic groups and the contexture environmental parameters showed that fresh well water and brackish porewater might provide different nutrients to the coastal waters. Potential key bacterial groups such as Comamonas spp. may be excellent candidates for the bioremediation of the natural pollutants in the SGD. Our comprehensive understanding of bacterial diversity in the SGD along the coasts of the Yellow Sea will create a basis for designing the effective clean-up approach in-situ, and provide valuable information for the coastal management.

Bacterial Diversity in Submarine Groundwater along the Coasts of the Yellow Sea

Directory of Open Access Journals (Sweden)

Qi eYe

2016-01-01

Full Text Available Submarine groundwater (SGD is one of the most significant pathways for the exchange of groundwater and/or source of nutrients, metals and carbon to the ocean, subsequently cause deleterious impacts on the coastal ecosystems. Microorganisms have been recognized as the important participators in the biogeochemical processes in the SGD. In this study, by utilizing 16S rRNA-based Illumina Miseq sequencing technology, we investigated bacterial diversity and distribution in both fresh well water and brackish recirculated porewater along the coasts in the Yellow Sea. The results showed that Actinobacteria and Betaproteobacteria, especially Comamonas spp. and Limnohabitans spp. were dominated in fresh well samples. Distinct patterns of bacterial communities were found among the porewater samples due to different locations, for examples, Cyanbacteria was the most abundant in the porewater samples far from the algal bloomed areas. The analysis of correlation between representative bacterial taxonomic groups and the contexture environmental parameters showed that fresh well water and brackish porewater might provide different nutrients to the coastal waters. Potential key bacterial groups such as Comamonas spp. may be excellent candidates for the bioremediation of the natural pollutants in the SGD. Our comprehensive understanding of bacterial diversity in the SGD along the coasts of the Yellow Sea will create a basis for designing the effective clean-up approach in-situ, and provide valuable information for the coastal management.

Investigation of critical inter-related factors affecting the efficacy of pulsed light for inactivating clinically relevant bacterial pathogens.

Science.gov (United States)

Farrell, H P; Garvey, M; Cormican, M; Laffey, J G; Rowan, N J

2010-05-01

To investigate critical electrical and biological factors governing the efficacy of pulsed light (PL) for the in vitro inactivation of bacteria isolated from the clinical environment. Development of this alternative PL decontamination approach is timely, as the incidence of health care-related infections remains unacceptably high. Predetermined cell numbers of clinically relevant Gram-positive and Gram-negative bacteria were inoculated separately on agar plates and were flashed with lamp discharge energy (range 3.2-20 J per pulse), the amount of pulsing applied (range 0-60 pulses) and the distance between light source and treatment surface (range 8-20 cm) used. Greater decontamination levels were achieved using a combination of higher lamp discharge energies, increased number of pulses and shorter distances between treatment surface and the xenon light source. Levels of microbial sensitivity also varied depending on the population type, size and age of cultures treated. Production of pigment pyocynanin and alginate slime in mucoid strains of Pseudomonas aeruginosa afforded some protection against lethal action of PL; however, this was evident only by using a combination of reduced amount of pulsing at the lower lamp discharge energies tested. A clear pattern was observed where Gram-positive bacterial pathogens were more resistant to cidal effects of PL compared to Gram negatives. While negligible photoreactivation of PL-treated bacterial strains occurred after full pulsing regimes at the different lamp discharge energies tested, some repair was evident when using a combination of reduced pulsing at the lower lamp discharge energies. Strains harbouring genes for multiple resistances to antibiotics were not significantly more resistant to PL treatments. Slight temperature rises (lamp discharge energies. Presence of organic matter on treatment surface did not significantly affect PL decontamination efficacy, nor did growth of PL-treated bacteria on selective agar

Investigation of gas discharge ion sources for on-line mass separation

International Nuclear Information System (INIS)

Kirchner, R.

1976-03-01

The development of efficient gas discharge ion sources with axial beam extraction for on-line mass separation is described. The aim of the investigation was to increase the ion source temperature, the lifetime and the ionisation yield in comparison to present low-pressure are discharge ion sources and to reduce the ion current density from usually 1 to 100 mA/cm 3 . In all ion sources the pressure range below the minimal ignition pressure of the arc discharge was investigated. As a result an ion source was developed which works at small changes in geometry and in electric device of a Nielsen source with high ionization yield (up to 50% for xenon) stabil and without ignition difficulties up to 10 -5 Torr. At a typical pressure of 3 x 10 -5 Torr ion current and ion current density are about 1 μA and 0.1 mA/cm 3 respectively besides high yield and a great emission aperture (diameter 1.2 mm). (orig.) [de

Evaluation of hyaluronan from different sources: Streptococcus zooepidemicus, rooster comb, bovine vitreous, and human umbilical cord.

Science.gov (United States)

Shiedlin, Aviva; Bigelow, Russell; Christopher, William; Arbabi, Saman; Yang, Laura; Maier, Ronald V; Wainwright, Norman; Childs, Alice; Miller, Robert J

2004-01-01

Sodium hyaluronate (HA) is widely distributed in extracellular matrixes and can play a role in orchestrating cell function. Consequently, many investigators have looked at the effect of exogenous HA on cell behavior in vitro. HA can be isolated from several sources (e.g., bacterial, rooster comb, umbilical cord) and therefore can possess diverse impurities. This current study compares the measured impurities and the differences in biological activity between HA preparations from these sources. It was demonstrated that nucleic acid and protein content was highest in human umbilical cord and bovine vitreous HA and was low in bacterial and rooster comb HA. Macrophages exposed to human umbilical cord HA produced significantly higher amounts of TNF-alpha relative to control or bacterial-derived HA. These results indicate that the source of HA should be considered due to differences in the amounts and types of contaminants that could lead to widely different behaviors in vitro and in vivo.

International seminar on structural investigations on pulsed neutron sources. Proceedings

International Nuclear Information System (INIS)

Aksenov, V.L.; Balagurov, A.M.; Taran, Yu.V.

1993-01-01

The proceedings of the International seminar on structural investigations using pulsed neutron sources are presented. The seminar is dedicated to the memory of Dr. Yu.M. Ostanevich, a world acknowledged physicist. The problems of structural analysis using pulsed neutron source at the IBR-2 reactor are discussed

Bacterial Cellulose Production from Industrial Waste and by-Product Streams

Directory of Open Access Journals (Sweden)

Erminda Tsouko

2015-07-01

Full Text Available The utilization of fermentation media derived from waste and by-product streams from biodiesel and confectionery industries could lead to highly efficient production of bacterial cellulose. Batch fermentations with the bacterial strain Komagataeibacter sucrofermentans DSM (Deutsche Sammlung von Mikroorganismen 15973 were initially carried out in synthetic media using commercial sugars and crude glycerol. The highest bacterial cellulose concentration was achieved when crude glycerol (3.2 g/L and commercial sucrose (4.9 g/L were used. The combination of crude glycerol and sunflower meal hydrolysates as the sole fermentation media resulted in bacterial cellulose production of 13.3 g/L. Similar results (13 g/L were obtained when flour-rich hydrolysates produced from confectionery industry waste streams were used. The properties of bacterial celluloses developed when different fermentation media were used showed water holding capacities of 102–138 g·water/g·dry bacterial cellulose, viscosities of 4.7–9.3 dL/g, degree of polymerization of 1889.1–2672.8, stress at break of 72.3–139.5 MPa and Young’s modulus of 0.97–1.64 GPa. This study demonstrated that by-product streams from the biodiesel industry and waste streams from confectionery industries could be used as the sole sources of nutrients for the production of bacterial cellulose with similar properties as those produced with commercial sources of nutrients.

Bacterial source tracking guides management of boat head waste in a coastal resort area.

Science.gov (United States)

Mallin, Michael A; Haltom, Mary I; Song, Bongkeun; Tavares, Mary E; Dellies, Stephen P

2010-12-01

Fecal contamination of water bodies causes a public health problem and economic loss. To control such contamination management actions need to be guided by sound science. From 2007-2009 a study was undertaken to determine the sources of fecal bacteria contamination to the marine waters adjoining the Town of Wrightsville Beach, North Carolina, USA. The research effort included sampling for fecal coliform and Enterococcus bacteria, sampling for optical brighteners, dye studies, and use of molecular bacterial source tracking techniques including polymerase chain reaction (PCR) and terminal restriction fragment polymorphism (T-RFLP) fingerprinting of the Bacteroides-Prevotella group. Of the 96 samples collected from nine locations during the study, the water contact standard for Enterococcus was exceeded on 13 occasions. The T-RFLP fingerprint analyses demonstrated that the most widespread source of fecal contamination was human, occurring in 38% of the samples, with secondary ruminant and avian sources also detected. Optical brightener concentrations were low, reflecting a lack of sewage line leakage or spills. A lack of sewer leaks and lack of septic systems in the town pointed toward discharge from boat heads into the marine waters as the major cause of fecal contamination; this was supported by dye studies. Based on these data, the Town initiated action to have the U.S. Environmental Protection Agency declare the coastal waters (out to 3 nautical miles), the nearby Atlantic Intracoastal Waterway and its tributaries a no-discharge zone (NDZ) to alleviate the human fecal pollution. The Town garnered supporting resolutions from other local communities who jointly petitioned the North Carolina Department of Environmental and Natural Resources. This State regulatory agency supported the local government resolutions and sent an application for an NDZ to the EPA in April 2009. The EPA concurred, and in February 2010 the coastal waters of New Hanover County, NC, became the

Thermal Performance and Efficiency Investigation of Conventional Boost, Z-source and Y-source Converters

DEFF Research Database (Denmark)

Gadalla, Brwene Salah Abdelkarim; Schaltz, Erik; Siwakoti, Yam Prasad

2016-01-01

Boost converters are needed in many applications that require the output voltage to be higher than the input voltage. Recently, boost type converters have been attracted by the industrial applications, and hence it has become an extremely hot topic of research. Recently, many researchers proposed...... the impedance source converters with their unique advantages as having a high voltage gain in a small range of duty cycle ratio. However, the thermal behaviour of the semiconductor devices and passive elements in the impedance source converter is an important issue from a reliability point of view and has...... not been investigated yet. Therefore this paper presents a comparison between the conventional boost, the Z-source, and the Y-source converters based on the thermal evaluation of semiconductors. In addition, the three topologies are also compared with respect to their efficiency. The operational principle...

Investigation of bacterial diversity in the feces of cattle fed different diets.

Science.gov (United States)

Kim, M; Kim, J; Kuehn, L A; Bono, J L; Berry, E D; Kalchayanand, N; Freetly, H C; Benson, A K; Wells, J E

2014-02-01

The objective of this study is to investigate individual animal variation of bovine fecal microbiota including as affected by diets. Fecal samples were collected from 426 cattle fed 1 of 3 diets typically fed to feedlot cattle: 1) 143 steers fed finishing diet (83% dry-rolled corn, 13% corn silage, and 4% supplement), 2) 147 steers fed late growing diet (66% dry-rolled corn, 26% corn silage, and 8% supplement), and 3) 136 heifers fed early growing diet (70% corn silage and 30% alfalfa haylage). Bacterial 16S rRNA gene amplicons were determined from individual fecal samples using next-generation pyrosequencing technology. A total of 2,149,008 16S rRNA gene sequences from 333 cattle with at least 2,000 sequences were analyzed. Firmicutes and Bacteroidetes were dominant phyla in all fecal samples. At the genus level, Oscillibacter, Turicibacter, Roseburia, Fecalibacterium, Coprococcus, Clostridium, Prevotella, and Succinivibrio were represented by more than 1% of total sequences. However, numerous sequences could not be assigned to a known genus. Dominant unclassified groups were unclassified Ruminococcaceae and unclassified Lachnospiraceae that could be classified to a family but not to a genus. These dominant genera and unclassified groups differed (P < 0.001) with diets. A total of 176,692 operational taxonomic units (OTU) were identified in combination across all the 333 cattle. Only 2,359 OTU were shared across 3 diet groups. UniFrac analysis showed that bacterial communities in cattle feces were greatly affected by dietary differences. This study indicates that the community structure of fecal microbiota in cattle is greatly affected by diet, particularly between forage- and concentrate-based diets.

Nitrate source apportionment using a combined dual isotope, chemical and bacterial property, and Bayesian model approach in river systems

Science.gov (United States)

Xia, Yongqiu; Li, Yuefei; Zhang, Xinyu; Yan, Xiaoyuan

2017-01-01

Nitrate (NO3-) pollution is a serious problem worldwide, particularly in countries with intensive agricultural and population activities. Previous studies have used δ15N-NO3- and δ18O-NO3- to determine the NO3- sources in rivers. However, this approach is subject to substantial uncertainties and limitations because of the numerous NO3- sources, the wide isotopic ranges, and the existing isotopic fractionations. In this study, we outline a combined procedure for improving the determination of NO3- sources in a paddy agriculture-urban gradient watershed in eastern China. First, the main sources of NO3- in the Qinhuai River were examined by the dual-isotope biplot approach, in which we narrowed the isotope ranges using site-specific isotopic results. Next, the bacterial groups and chemical properties of the river water were analyzed to verify these sources. Finally, we introduced a Bayesian model to apportion the spatiotemporal variations of the NO3- sources. Denitrification was first incorporated into the Bayesian model because denitrification plays an important role in the nitrogen pathway. The results showed that fertilizer contributed large amounts of NO3- to the surface water in traditional agricultural regions, whereas manure effluents were the dominant NO3- source in intensified agricultural regions, especially during the wet seasons. Sewage effluents were important in all three land uses and exhibited great differences between the dry season and the wet season. This combined analysis quantitatively delineates the proportion of NO3- sources from paddy agriculture to urban river water for both dry and wet seasons and incorporates isotopic fractionation and uncertainties in the source compositions.

Changes in Soil Bacterial Communities and Diversity in ...

Science.gov (United States)

Silver-induced selective pressure is becoming increasingly important due to the growing use of silver (Ag) as an antimicrobial agent in biomedical and commercial products. With demonstrated links between environmental resistomes and clinical pathogens, it is important to identify microbial profiles related to silver tolerance/resistance. We investigated the effects of ionic Ag stress on soil bacterial communities and identified resistant/persistant bacterial populations. Silver treatments of 50 - 400 mg Ag kg-1 soil were established in five soils. Chemical lability measurements using diffusive gradients in thin-film devices confirmed that significant (albeit decreasing) labile Ag concentrations were present throughout the 9-month incubation period. Synchrotron X-ray absorption near edge structure spectroscopy demonstrate that this decreasing lability was due to changes in Ag speciation to less soluble forms such as Ag0 and Ag2S. Real-time PCR and Illumina MiSeq screening of 16S rRNA bacterial genes showed β-diversity in response to Ag pressure, and immediate and significant reductions in 16S rRNA gene counts with varying degrees of recovery. These effects were more strongly influenced by exposure time than by Ag dose at these rates. Ag-selected dominant OTUs principally resided in known persister taxa (mainly Gram positive), including metal-tolerant bacteria and slow-growing Mycobacteria. Soil microbial communities have been implicated as sources of an

Using a Molecular-Genetic Approach to Investigate Bacterial Physiology in a Continuous, Research-Based, Semester-Long Laboratory for Undergraduates

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Jeremiah Foster Ault

2011-09-01

Full Text Available Designing investigative laboratory exercises that encourage critical thinking, problem solving, and independent thought for upper-division biology courses is a difficult but worthwhile task. In an effort to do so, we developed a semester-long, continuous, research-based investigative laboratory that integrates numerous genetic and molecular biology methods into the investigation of a bacterial physiological process. In this lab, students use random Tn5 transposon mutagenesis to create prodigiosin pigment mutants in the bacterium, Serratia marcescens. This is followed by phenotypic characterization, cloning, and sequencing the Tn insertion site to identify genes involved in pigment biosynthesis. During this lab, students gain ample experience performing basic lab techniques while learning about — and applying — methods for elucidating gene function. The approach to the laboratory and the outcomes are intimately integrated into the teaching of many fundamental physiological processes underlying prodigiosin production in bacteria. The result is a cohesive course that integrates the theory and application of molecular genetic techniques with the study of bacterial physiology. Assessments of student learning objectives demonstrated that students greatly improved their understanding of both physiological processes and the genetic techniques used to investigate them. In addition, students felt that this semester-long exercise provided the necessary laboratory experience they needed and desired in preparation for careers in molecular biology, microbiology, and biochemistry.

Physical therapy clinic therapeutic ultrasound equipment as a source for bacterial contamination.

Science.gov (United States)

Spratt, Henry G; Levine, David; Tillman, Larry

2014-10-01

A procedure commonly used in physical therapy (PT) clinics is therapeutic ultrasound (US). This equipment and associated gel comes in contact with patient skin, potentially serving as a reservoir for bacteria. In this study, we sampled US heads, gel bottle tips and gel from nine outpatient PT clinics in Southeastern Tennessee. Samples were collected using sterile swabs. At the microbiology laboratory, these swabs were used to inoculate mannitol salt agar and CHROM-MRSA agar (for Staphylococcal species) and tryptic soy broth to determine non-specific bacterial contamination. US heads, gel bottle tips and gel had variable levels of contamination. Tips of gel bottles had the highest contamination, with 52.7% positive for non-specific bacterial contamination and 3.6% positive for methicillin-resistant Staphylococcus aureus (MRSA). Contamination of gel by non-specific bacteria was found in 14.5% of bottles sampled. US heads (35.5% of those sampled) had non-specific bacterial contamination, with no MRSA detected. Disinfecting US heads after initial swabbing resulted in removal of 90.9% of non-specific contamination. Gel storage at temperatures below 40 °C was found to encourage the growth of mesophilic bacteria. This study demonstrates the need for better cleaning and storage protocols for US heads and gel bottles in PT clinics.

Next-generation sequencing identification of pathogenic bacterial genes and their relationship with fecal indicator bacteria in different water sources in the Kathmandu Valley, Nepal.

Science.gov (United States)

Ghaju Shrestha, Rajani; Tanaka, Yasuhiro; Malla, Bikash; Bhandari, Dinesh; Tandukar, Sarmila; Inoue, Daisuke; Sei, Kazunari; Sherchand, Jeevan B; Haramoto, Eiji

2017-12-01

Bacteriological analysis of drinking water leads to detection of only conventional fecal indicator bacteria. This study aimed to explore and characterize bacterial diversity, to understand the extent of pathogenic bacterial contamination, and to examine the relationship between pathogenic bacteria and fecal indicator bacteria in different water sources in the Kathmandu Valley, Nepal. Sixteen water samples were collected from shallow dug wells (n=12), a deep tube well (n=1), a spring (n=1), and rivers (n=2) in September 2014 for 16S rRNA gene next-generation sequencing. A total of 525 genera were identified, of which 81 genera were classified as possible pathogenic bacteria. Acinetobacter, Arcobacter, and Clostridium were detected with a relatively higher abundance (>0.1% of total bacterial genes) in 16, 13, and 5 of the 16 samples, respectively, and the highest abundance ratio of Acinetobacter (85.14%) was obtained in the deep tube well sample. Furthermore, the bla OXA23-like genes of Acinetobacter were detected using SYBR Green-based quantitative PCR in 13 (35%) of 37 water samples, including the 16 samples that were analyzed for next-generation sequencing, with concentrations ranging 5.3-7.5logcopies/100mL. There was no sufficient correlation found between fecal indicator bacteria, such as Escherichia coli and total coliforms, and potential pathogenic bacteria, as well as the bla OXA23-like gene of Acinetobacter. These results suggest the limitation of using conventional fecal indicator bacteria in evaluating the pathogenic bacteria contamination of different water sources in the Kathmandu Valley. Copyright © 2017 Elsevier B.V. All rights reserved.

Investigation of bacterial adherence to a non-precious alloy with radiolabeling method

International Nuclear Information System (INIS)

Sonugelen, M.; Iyiyapici Destan, U.; Oeztuerk, B.; Yurt Lambrecht, F.

2006-01-01

The objective of this study was to investigate the bacterial adherence to a non-precious alloy with radiolabeling method. S. mutans, E. coliand C. albicanswere labeled with 99m Tc by using stannous chloride and their radiolabeling yields were calculated. After the labeling procedure, metal disks (3 mm x 10 mm) were treated with microorganisms. The amount of labeled microorganisms adhered on metal surfaces was determined by activity measurements. The labeling yields for S. mutans, E. coliand C. albicanswere 69.95 ± 7.58%, 78.84 ± 0.44% and 79.71 ± 10.17%, respectively. The mean values for adherence for S. mutans, E. coliand C. albicans on metal samples were 7.02 ± 2.18%, 0.96 ± 0.49% and 8.80 ± 8.24%, respectively. The radiolabeling method could be considered as safe and precise for determining the adherence of microorganisms. (author)

UV radiation and organic matter composition shape bacterial functional diversity in sediments

Directory of Open Access Journals (Sweden)

Ellard Roy Hunting

2013-10-01

Full Text Available AbstractUV radiation and organic matter (OM composition are known to influence the speciescomposition of bacterioplankton communities. Potential effects of UV radiation onbacterial communities residing in sediments remain completely unexplored to date.However, it has been demonstrated that UV radiation can reach the bottom of shallowwaters and wetlands and alter the OM composition of the sediment, suggesting thatUV radiation may be more important for sediment bacteria than previously anticipated.It is hypothesized here that exposure of shallow OMcontaining sediments to UVradiation induces OMsource dependant shifts in the functional composition ofsediment bacterial communities. This study therefore investigated the combinedinfluence of both UV radiation and OM composition on bacterial functional diversity inlaboratory sediments. Two different organic matter sources, labile and recalcitrantorganic matter (OM, were used and metabolic diversity was measured with BiologGN. Radiation exerted strong negative effects on the metabolic diversity in thetreatments containing recalcitrant OM, more than in treatments containing labile OM.The functional composition of the bacterial community also differed significantlybetween the treatments. Our findings demonstrate that a combined effect of UVradiation and OM composition shapes the functional composition of microbialcommunities developing in sediments, hinting that UV radiation may act as animportant sorting mechanism for bacterial communities and driver for bacterialfunctioning in shallow lakes and wetlands.

Bacterial and fungal endophthalmitis in upper Egypt: related species and risk factors.

Science.gov (United States)

Gharamah, A A; Moharram, A M; Ismail, M A; Al-Hussaini, A K

2012-08-01

To study risk factors, contributing factors of bacterial and fungal endophthalmitis in Upper Egypt, test the isolated species sensitive to some therapeutic agents, and to investigate the air-borne bacteria and fungi in opthalmology operating rooms. Thirty one cases of endophthalmitis were clinically diagnosed and microbiologically studied. Indoor air-borne bacteria and fungi inside four air-conditioned operating rooms in the Ophthalmology Department at Assiut University Hospitals were also investigated. The isolated microbes from endophthalmitis cases were tested for their ability to produce some extracellular enzymes including protease, lipase, urease, phosphatase and catalase. Also the ability of 5 fungal isolates from endophthalmitis origin to produce mycotoxins and their sensitivity to some therapeutic agents were studied. Results showed that bacteria and fungi were responsihle for infection in 10 and 6 cases of endophthalmitis, respectively and only 2 cases produced a mixture of bacteria and fungi. Trauma was the most prevalent risk factor of endophthalmitis where 58.1% of the 31 cases were due to trauma. In ophthalmology operating rooms, different bacterial and fungal species were isolated. 8 bacterial and 5 fungal isolates showed their ability to produce enzymes while only 3 fungal isolates were able to produce mycotoxins. Terbinafine showed the highest effect against most isolates in vitro. The ability of bacterial and fungal isolates to produce extracellular enzymes and mycotoxins may be aid in the invasion and destruction of eye tissues. Microbial contamination of operating rooms with air-borne bacteria and fungi in the present work may be a source of postoperative endophthalmitis.

Investigating scintillometer source areas

Science.gov (United States)

Perelet, A. O.; Ward, H. C.; Pardyjak, E.

2017-12-01

Scintillometry is an indirect ground-based method for measuring line-averaged surface heat and moisture fluxes on length scales of 0.5 - 10 km. These length scales are relevant to urban and other complex areas where setting up traditional instrumentation like eddy covariance is logistically difficult. In order to take full advantage of scintillometry, a better understanding of the flux source area is needed. The source area for a scintillometer is typically calculated as a convolution of point sources along the path. A weighting function is then applied along the path to compensate for a total signal contribution that is biased towards the center of the beam path, and decreasing near the beam ends. While this method of calculating the source area provides an estimate of the contribution of the total flux along the beam, there are still questions regarding the physical meaning of the weighted source area. These questions are addressed using data from an idealized experiment near the Salt Lake City International Airport in northern Utah, U.S.A. The site is a flat agricultural area consisting of two different land uses. This simple heterogeneity in the land use facilitates hypothesis testing related to source areas. Measurements were made with a two wavelength scintillometer system spanning 740 m along with three standard open-path infrared gas analyzer-based eddy-covariance stations along the beam path. This configuration allows for direct observations of fluxes along the beam and comparisons to the scintillometer average. The scintillometer system employed measures the refractive index structure parameter of air for two wavelengths of electromagnetic radiation, 880 μm and 1.86 cm to simultaneously estimate path-averaged heat and moisture fluxes, respectively. Meteorological structure parameters (CT2, Cq2, and CTq) as well as surface fluxes are compared for various amounts of source area overlap between eddy covariance and scintillometry. Additionally, surface

Organic carbon source and salinity shape sediment bacterial composition in two China marginal seas and their major tributaries.

Science.gov (United States)

Wang, Kai; Zou, Li; Lu, Xinxin; Mou, Xiaozhen

2018-08-15

Marginal sea sediments receive organic substrates of different origins, but whether and to what extent sediment microbial communities are reflective of the different sources of organic substrates remain unclear. To address these questions, sediment samples were collected in two connected China marginal seas, i.e., Bohai Sea and Yellow Sea, and their two major tributaries (Yellow River and Liao River). Sediment bacterial community composition (BCC) was examined using 16S rRNA gene pyrosequencing. In addition, physicochemical variables that describe environmental conditions and sediment features were measured. Our results revealed that BCCs changed with salinity and organic carbon (OC) content. Members of Gaiellaceae and Comamonadaceae showed a rapid decrease as salinity and phytoplankton-derived OC increased, while Piscirickettsiaceae and Desulfobulbaceae exhibited an opposite distribution pattern. Differences of riverine vs. marginal sea sediment BCCs could be mostly explained by salinity. However, within the marginal seas, sediment BCC variations were mainly explained by OC-related variables, including terrestrial-derived fatty acids (Terr_FA), phytoplankton-derived polyunsaturated fatty acids (Phyto_PUFA), stable carbon isotopes (δ 13 C), and carbon to nitrogen ratio (C/N). In addition to environmental variables, network analysis suggested that interactions among individual bacterial taxa might be important in shaping sediment BCCs in the studied areas. Copyright © 2018 Elsevier B.V. All rights reserved.

Investigating source confusion in PMN J1603-4904

Science.gov (United States)

Krauß, F.; Kreter, M.; Müller, C.; Markowitz, A.; Böck, M.; Burnett, T.; Dauser, T.; Kadler, M.; Kreikenbohm, A.; Ojha, R.; Wilms, J.

2018-02-01

PMN J1603-4904 is a likely member of the rare class of γ-ray emitting young radio galaxies. Only one other source, PKS 1718-649, has been confirmed so far. These objects, which may transition into larger radio galaxies, are a stepping stone to understanding AGN evolution. It is not completely clear how these young galaxies, seen edge-on, can produce high-energy γ rays. PMN J1603-4904 has been detected by TANAMI Very Long Baseline Interferometry (VLBI) observations and has been followed-up with multiwavelength observations. A Fermi Gamma-ray Space Telescope Large Area Telescope (Fermi-LAT) γ-ray source has been associated with this young galaxy in the LAT catalogs. We have obtained Chandra observations of the source to consider the possibility of source confusion due to the relatively large positional uncertainty of Fermi-LAT. The goal was to investigate the possibility of other X-ray bright sources in the vicinity of PMN J1603-4904 that could be counterparts to the γ-ray emission. With Chandra/ACIS, we find no other sources in the uncertainty ellipse of Fermi-LAT data, which includes an improved localization analysis of eight years of data. We further study the X-ray fluxes and spectra. We conclude that PMN J1603-4904 is indeed the second confirmed γ-ray bright young radio galaxy.

Profiles of antibiotic susceptibilities of bacterial isolates and physico ...

African Journals Online (AJOL)

The Venda region of South Africa is predominantly rural and residents rely on untreated water sources for daily water needs. The physico-chemical quality of these water sources including antibiotic susceptibilities of enteric bacterial isolates which would guide clinicians in the empiric management of diarrhoea have ...

Exploiting rRNA operon copy number to investigate bacterial reproductive strategies.

Science.gov (United States)

Roller, Benjamin R K; Stoddard, Steven F; Schmidt, Thomas M

2016-09-12

The potential for rapid reproduction is a hallmark of microbial life, but microbes in nature must also survive and compete when growth is constrained by resource availability. Successful reproduction requires different strategies when resources are scarce and when they are abundant 1,2 , but a systematic framework for predicting these reproductive strategies in bacteria has not been available. Here, we show that the number of ribosomal RNA operons (rrn) in bacterial genomes predicts two important components of reproduction-growth rate and growth efficiency-which are favoured under contrasting regimes of resource availability 3,4 . We find that the maximum reproductive rate of bacteria doubles with a doubling of rrn copy number, and the efficiency of carbon use is inversely related to maximal growth rate and rrn copy number. We also identify a feasible explanation for these patterns: the rate and yield of protein synthesis mirror the overall pattern in maximum growth rate and growth efficiency. Furthermore, comparative analysis of genomes from 1,167 bacterial species reveals that rrn copy number predicts traits associated with resource availability, including chemotaxis and genome streamlining. Genome-wide patterns of orthologous gene content covary with rrn copy number, suggesting convergent evolution in response to resource availability. Our findings imply that basic cellular processes adapt in contrasting ways to long-term differences in resource availability. They also establish a basis for predicting changes in bacterial community composition in response to resource perturbations using rrn copy number measurements 5 or inferences 6,7 .

Hormone-dependent bacterial growth, persistence and biofilm formation--a pilot study investigating human follicular fluid collected during IVF cycles.

Directory of Open Access Journals (Sweden)

Elise S Pelzer

Full Text Available Human follicular fluid, considered sterile, is aspirated as part of an in vitro fertilization (IVF cycle. However, it is easily contaminated by the trans-vaginal collection route and little information exists in its potential to support the growth of microorganisms. The objectives of this study were to determine whether human follicular fluid can support bacterial growth over time, whether the steroid hormones estradiol and progesterone (present at high levels within follicular fluid contribute to the in vitro growth of bacterial species, and whether species isolated from follicular fluid form biofilms. We found that bacteria in follicular fluid could persist for at least 28 weeks in vitro and that the steroid hormones stimulated the growth of some bacterial species, specifically Lactobacillus spp., Bifidobacterium spp. Streptococcus spp. and E. coli. Several species, Lactobacillus spp., Propionibacterium spp., and Streptococcus spp., formed biofilms when incubated in native follicular fluids in vitro (18/24, 75%. We conclude that bacteria aspirated along with follicular fluid during IVF cycles demonstrate a persistent pattern of growth. This discovery is important since it can offer a new avenue for investigation in infertile couples.

Characterization of coastal urban watershed bacterial communities leads to alternative community-based indicators

Energy Technology Data Exchange (ETDEWEB)

Wu, C.H.; Sercu, B.; Van De Werhorst, L.C.; Wong, J.; DeSantis, T.Z.; Brodie, E.L.; Hazen, T.C.; Holden, P.A.; Andersen, G.L.

2010-03-01

Microbial communities in aquatic environments are spatially and temporally dynamic due to environmental fluctuations and varied external input sources. A large percentage of the urban watersheds in the United States are affected by fecal pollution, including human pathogens, thus warranting comprehensive monitoring. Using a high-density microarray (PhyloChip), we examined water column bacterial community DNA extracted from two connecting urban watersheds, elucidating variable and stable bacterial subpopulations over a 3-day period and community composition profiles that were distinct to fecal and non-fecal sources. Two approaches were used for indication of fecal influence. The first approach utilized similarity of 503 operational taxonomic units (OTUs) common to all fecal samples analyzed in this study with the watershed samples as an index of fecal pollution. A majority of the 503 OTUs were found in the phyla Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. The second approach incorporated relative richness of 4 bacterial classes (Bacilli, Bacteroidetes, Clostridia and a-proteobacteria) found to have the highest variance in fecal and non-fecal samples. The ratio of these 4 classes (BBC:A) from the watershed samples demonstrated a trend where bacterial communities from gut and sewage sources had higher ratios than from sources not impacted by fecal material. This trend was also observed in the 124 bacterial communities from previously published and unpublished sequencing or PhyloChip- analyzed studies. This study provided a detailed characterization of bacterial community variability during dry weather across a 3-day period in two urban watersheds. The comparative analysis of watershed community composition resulted in alternative community-based indicators that could be useful for assessing ecosystem health.

Bacterial desorption from food container and food processing surfaces.

Science.gov (United States)

McEldowney, S; Fletcher, M

1988-03-01

The desorption ofStaphylococcus aureus, Acinetobacter calcoaceticus, and a coryneform from the surfaces of materials used for manufacturing food containers (glass, tin plate, and polypropylene) or postprocess canning factory conveyor belts (stainless steel and nylon) was investigated. The effect of time, pH, temperature, and adsorbed organic layers on desorption was studied.S. aureus did not detach from the substrata at any pH investigated (between pH 5 and 9).A. calcoaceticus and the coryneform in some cases detached, depending upon pH and substratum composition. The degree of bacterial detachment from the substrata was not related to bacterial respiration at experimental pH values. Bacterial desorption was not affected by temperature (4-30°C) nor by an adsorbed layer of peptone and yeast extract on the substrata. The results indicate that bacterial desorption, hence bacterial removal during cleaning or their transfer via liquids flowing over colonized surfaces, is likely to vary with the surface composition and the bacterial species colonizing the surfaces.

Selection of potent bacterial strain for over-production of PHB by using low cost carbon source for eco-friendly bioplastics

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Rahat Abdul Rehman

2015-11-01

Full Text Available Background: The microbial PHB production is a promising tool for the plastic industry for the synthesis of environmental friendly, biodegradable plastic in contrast to the conventional petro-chemical based non-degradable plastics. The selection of potent bacterial strains, inexpensive carbon source, efficient fermentation and recovery processes are important aspects that were taken into account during this study. Methods: Different bacterial strains i.e. Bacillus Spp, P. putida and P. fluorescens were screened for maximum PHB production. Under media optimization, various carbon and nitrogen sources (alone or in combination were used to achieve the maximum PHB production. Finally the degradation tests of the PHB sheet were also performed to test its biodegradability potential. Results: Shake flask studies have shown the PHB concentrations upto 7.02, 4.50 and 34.4 mg/g of dry cell mass of P. putida, P. fluorescens and Bacillus Spp. respectively. Almost same results were observed at laboratory scale production of PHB in 10 L fermenter i.e. 6.28, 6.23 and 39.5 mg/g of dry cell mass by P. putida, P. fluorescens and Bacillus Spp. respectively. On the basis of these observations, Bacillus Spp. was chosen for laboratory scale PHB production. Corn steep liquor (4% was chosen as the best medium to achieve the highest PHB contents. Isolated PHB has shown biodegradation in soil up to 86.7% at 37oC. Conclusion: The Bacillus Spp. Proved to be the best strain for PHB production on only 4% CSL which is cheapest and easily available.

Cultivable Bacterial Microbiota of Northern Bobwhite (Colinus virginianus): A New Reservoir of Antimicrobial Resistance?

Science.gov (United States)

Su, Hongwen; McKelvey, Jessica; Rollins, Dale; Zhang, Michael; Brightsmith, Donald J.; Derr, James; Zhang, Shuping

2014-01-01

The northern bobwhite (Colinus virginianus) is an ecologically and economically important avian species. At the present time, little is known about the microbial communities associated with these birds. As the first step to create a quail microbiology knowledge base, the current study conducted an inventory of cultivable quail tracheal, crop, cecal, and cloacal microbiota and associated antimicrobial resistance using a combined bacteriology and DNA sequencing approach. A total of 414 morphologically unique bacterial colonies were selected from nonselective aerobic and anaerobic cultures, as well as selective and enrichment cultures. Analysis of the first 500-bp 16S rRNA gene sequences in conjunction with biochemical identifications revealed 190 non-redundant species-level taxonomic units, representing 160 known bacterial species and 30 novel species. The bacterial species were classified into 4 phyla, 14 orders, 37 families, and 59 or more genera. Firmicutes was the most commonly encountered phylum (57%) followed by Actinobacteria (24%), Proteobacteria (17%) and Bacteroidetes (0.02%). Extensive diversity in the species composition of quail microbiota was observed among individual birds and anatomical locations. Quail microbiota harbored several opportunistic pathogens, such as E. coli and Ps. aeruginosa, as well as human commensal organisms, including Neisseria species. Phenotypic characterization of selected bacterial species demonstrated a high prevalence of resistance to the following classes of antimicrobials: phenicol, macrolide, lincosamide, quinolone, and sulphate. Data from the current investigation warrant further investigation on the source, transmission, pathology, and control of antimicrobial resistance in wild quail populations. PMID:24937705

Cultivable bacterial microbiota of northern bobwhite (Colinus virginianus: a new reservoir of antimicrobial resistance?

Directory of Open Access Journals (Sweden)

Hongwen Su

Full Text Available The northern bobwhite (Colinus virginianus is an ecologically and economically important avian species. At the present time, little is known about the microbial communities associated with these birds. As the first step to create a quail microbiology knowledge base, the current study conducted an inventory of cultivable quail tracheal, crop, cecal, and cloacal microbiota and associated antimicrobial resistance using a combined bacteriology and DNA sequencing approach. A total of 414 morphologically unique bacterial colonies were selected from nonselective aerobic and anaerobic cultures, as well as selective and enrichment cultures. Analysis of the first 500-bp 16S rRNA gene sequences in conjunction with biochemical identifications revealed 190 non-redundant species-level taxonomic units, representing 160 known bacterial species and 30 novel species. The bacterial species were classified into 4 phyla, 14 orders, 37 families, and 59 or more genera. Firmicutes was the most commonly encountered phylum (57% followed by Actinobacteria (24%, Proteobacteria (17% and Bacteroidetes (0.02%. Extensive diversity in the species composition of quail microbiota was observed among individual birds and anatomical locations. Quail microbiota harbored several opportunistic pathogens, such as E. coli and Ps. aeruginosa, as well as human commensal organisms, including Neisseria species. Phenotypic characterization of selected bacterial species demonstrated a high prevalence of resistance to the following classes of antimicrobials: phenicol, macrolide, lincosamide, quinolone, and sulphate. Data from the current investigation warrant further investigation on the source, transmission, pathology, and control of antimicrobial resistance in wild quail populations.

Host-Derived Sialic Acids Are an Important Nutrient Source Required for Optimal Bacterial Fitness In Vivo

Directory of Open Access Journals (Sweden)

Nathan D. McDonald

2016-04-01

Full Text Available A major challenge facing bacterial intestinal pathogens is competition for nutrient sources with the host microbiota. Vibrio cholerae is an intestinal pathogen that causes cholera, which affects millions each year; however, our knowledge of its nutritional requirements in the intestinal milieu is limited. In this study, we demonstrated that V. cholerae can grow efficiently on intestinal mucus and its component sialic acids and that a tripartite ATP-independent periplasmic SiaPQM strain, transporter-deficient mutant NC1777, was attenuated for colonization using a streptomycin-pretreated adult mouse model. In in vivo competition assays, NC1777 was significantly outcompeted for up to 3 days postinfection. NC1777 was also significantly outcompeted in in vitro competition assays in M9 minimal medium supplemented with intestinal mucus, indicating that sialic acid uptake is essential for fitness. Phylogenetic analyses demonstrated that the ability to utilize sialic acid was distributed among 452 bacterial species from eight phyla. The majority of species belonged to four phyla, Actinobacteria (members of Actinobacillus, Corynebacterium, Mycoplasma, and Streptomyces, Bacteroidetes (mainly Bacteroides, Capnocytophaga, and Prevotella, Firmicutes (members of Streptococcus, Staphylococcus, Clostridium, and Lactobacillus, and Proteobacteria (including Escherichia, Shigella, Salmonella, Citrobacter, Haemophilus, Klebsiella, Pasteurella, Photobacterium, Vibrio, and Yersinia species, mostly commensals and/or pathogens. Overall, our data demonstrate that the ability to take up host-derived sugars and sialic acid specifically allows V. cholerae a competitive advantage in intestinal colonization and that this is a trait that is sporadic in its occurrence and phylogenetic distribution and ancestral in some genera but horizontally acquired in others.

Childhood asthma after bacterial colonization of the airway in neonates

DEFF Research Database (Denmark)

Bisgaard, Hans; Hermansen, Mette Northman; Buchvald, Frederik

2007-01-01

Pathological features of the airway in young children with severe recurrent wheeze suggest an association between bacterial colonization and the initiating events of early asthma. We conducted a study to investigate a possible association between bacterial colonization of the hypopharynx in asymp......Pathological features of the airway in young children with severe recurrent wheeze suggest an association between bacterial colonization and the initiating events of early asthma. We conducted a study to investigate a possible association between bacterial colonization of the hypopharynx...... in asymptomatic neonates and later development of recurrent wheeze, asthma, and allergy during the first 5 years of life....

Heme Synthesis and Acquisition in Bacterial Pathogens.

Science.gov (United States)

Choby, Jacob E; Skaar, Eric P

2016-08-28

Bacterial pathogens require the iron-containing cofactor heme to cause disease. Heme is essential to the function of hemoproteins, which are involved in energy generation by the electron transport chain, detoxification of host immune effectors, and other processes. During infection, bacterial pathogens must synthesize heme or acquire heme from the host; however, host heme is sequestered in high-affinity hemoproteins. Pathogens have evolved elaborate strategies to acquire heme from host sources, particularly hemoglobin, and both heme acquisition and synthesis are important for pathogenesis. Paradoxically, excess heme is toxic to bacteria and pathogens must rely on heme detoxification strategies. Heme is a key nutrient in the struggle for survival between host and pathogen, and its study has offered significant insight into the molecular mechanisms of bacterial pathogenesis. Copyright © 2016 Elsevier Ltd. All rights reserved.

Combining Inverse and Transport Modeling to Estimate Bacterial Loading and Transport in a Tidal Embayment

Directory of Open Access Journals (Sweden)

Mac Sisson

2016-11-01

Full Text Available Poquoson River is a tidal coastal embayment located along the Western Shore of the Chesapeake Bay about 4 km south of the York River mouth in the City of Poquoson and in York County, Virginia. Its drainage area has diversified land uses, including high densities of residence, agricultural, salt marsh land uses, as well as a National Wildlife Refuge. This embayment experiences elevated bacterial concentration due to excess bacterial inputs from storm water runoff, nonpoint sources, and wash off from marshes due to tide and wind-induced set-up and set-down. Bacteria can also grow in the marsh and small tributaries. It is difficult to use a traditional watershed model to simulate bacterial loading, especially in this low-lying marsh area with abundant wildlife, while runoff is not solely driven by precipitation. An inverse approach is introduced to estimate loading from unknown sources based on observations in the embayment. The estimated loadings were combined with loadings estimated from different sources (human, wildlife, agriculture, pets, etc. and input to the watershed model. The watershed model simulated long-term flow and bacterial loading and discharged to a three-dimensional transport model driven by tide, wind, and freshwater discharge. The transport model efficiently simulates the transport and fate of the bacterial concentration in the embayment and is capable of determining the loading reduction needed to improve the water quality condition of the embayment. Combining inverse, watershed, and transport models is a sound approach for simulating bacterial transport correctly in the coastal embayment with complex unknown bacterial sources, which are not solely driven by precipitation.

A quasi-monochromatic X-rays source for art painting pigments investigation

Energy Technology Data Exchange (ETDEWEB)

Albertin, F.; Franconieri, A.; Gambaccini, M.; Petrucci, F.; Chiozzi, S. [University of Ferrara, Department of Physics and INFN, Ferrara (Italy); Moro, D. [University of Padova, Department of Physics, Padova (Italy); LNL - INFN, Legnaro, Padova (Italy)

2009-08-15

Monochromatic X-ray sources can be used for several applications, like in medicine or in studying our cultural heritage. We are investigating imaging systems based on a tuneable energy band X-ray source, to obtain an element mapping of painting layers using the K-edge technique. The narrow energy band beams are obtained with conventional X-ray source via Bragg diffraction on a mosaic crystal; such an analysis has been performed at different diffraction angles, tuning the energy to investigate spectra of interest from the artistic point of view, like zinc and copper. In this paper the characteristics of the system in terms of fluence rate are reported, and first results of this technique on canvas samples and painting are presented. (orig.)

Response of Archaeal and Bacterial Soil Communities to Changes Associated with Outdoor Cattle Overwintering

OpenAIRE

Chro??kov?, Alica; Schloter-Hai, Brigitte; Radl, Viviane; Endesfelder, David; Quince, Christopher; Elhottov?, Dana; ?imek, Miloslav; Schloter, Michael

2015-01-01

Archaea and bacteria are important drivers for nutrient transformations in soils and catalyse the production and consumption of important greenhouse gases. In this study, we investigate changes in archaeal and bacterial communities of four Czech grassland soils affected by outdoor cattle husbandry. Two show short-term (3 years; STI) and long-term impact (17 years; LTI), one is regenerating from cattle impact (REG) and a control is unaffected by cattle (CON). Cattle manure (CMN), the source of...

Non-invasive shallow seismic source comparison for hazardous waste site investigations

International Nuclear Information System (INIS)

Doll, W.E.

1994-01-01

Many commonly used shallow seismic sources are unacceptable for hazardous waste site investigations because they risk exhumation of contaminants in the soil, they add contaminants (e.g. lead) which are not allowed by regulations, or they add new migration paths for contaminants. Furthermore, recently developed high frequency vibrators for shallow investigations could be more effective at some sites than non-invasive impulsive sources because of their ability to tailor the source spectrum and reduce interference. The authors show preliminary results of a comparison test of eight non-invasive impulsive and swept sources in preparation for seismic reflection profiling on the Oak Ridge Reservation, Tennessee. Well log data are used to determine geologic contacts and to generate synthetic seismograms for the site. Common midpoint (CMP) seismic data for each source were collected at 95 geophone groups from 125 shot points along a 400m test line. Hydrophone data were obtained at 1.5m spacing between 61m and 133m depth in a hole near the center of the CMP line. As of March, 1994, brute stacks have been completed for three of the eight sources. Depth penetration is demonstrated in brute stacks and shot gathers, which show a 200ms reflector for all of the sources tested along portions of the line. Source effectiveness will also be evaluated by comparing images of several shallower reflectors (40--150ms) which are apparent in many of the records. Imaging of these reflectors appears to depend upon the ability of the source to generate sufficient high frequency energy (>100 Hz)

Bacterial vaginosis in pregnant adolescents: proinflammatory cytokine and bacterial sialidase profile. Cross-sectional study

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Carolina Sanitá Tafner Ferreira

Full Text Available ABSTRACT CONTEXT AND OBJECTIVE: Bacterial vaginosis occurs frequently in pregnancy and increases susceptibility to sexually transmitted infections (STI. Considering that adolescents are disproportionally affected by STI, the aim of this study was to evaluate the cervicovaginal levels of interleukin (IL-1 beta, IL-6, IL-8 and bacterial sialidase in pregnant adolescents with bacterial vaginosis. DESIGN AND SETTING: Cross-sectional study at mother and child referral units in Belém, Pará, Brazil. METHODS: Vaginal samples from 168 pregnant adolescents enrolled were tested for trichomoniasis and candidiasis. Their vaginal microbiota was classified according to the Nugent criteria (1991 as normal, intermediate or bacterial vaginosis. Cervical infection due to Chlamydia trachomatisand Neisseria gonorrhoeae was also assessed. Cytokine and sialidase levels were measured, respectively, using enzyme-linked immunosorbent assays and MUAN conversion in cervicovaginal lavages. Forty-eight adolescents (28.6% were excluded because they tested positive for some of the infections investigated. The remaining 120 adolescents were grouped according to vaginal flora type: normal (n = 68 or bacterial vaginosis (n = 52. Their cytokine and sialidase levels were compared between the groups using the Mann-Whitney test (P < 0.05. RESULTS: The pregnant adolescents with bacterial vaginosis had higher levels of IL-1 beta, IL-6 and IL-8 (P < 0.05. Sialidase was solely detected in 35 adolescents (67.2% with bacterial vaginosis. CONCLUSIONS: Not only IL-1 beta and sialidase levels, but also IL-6 and IL-8 levels are higher in pregnant adolescents with bacterial vaginosis, thus indicating that this condition elicits a more pronounced inflammatory response in this population, which potentially increases vulnerability to STI acquisition.

Investigating Salmonella Eko from Various Sources in Nigeria by Whole Genome Sequencing to Identify the Source of Human Infections.

Directory of Open Access Journals (Sweden)

Pimlapas Leekitcharoenphon

Full Text Available Twenty-six Salmonella enterica serovar Eko isolated from various sources in Nigeria were investigated by whole genome sequencing to identify the source of human infections. Diversity among the isolates was observed and camel and cattle were identified as the primary reservoirs and the most likely source of the human infections.

Effect of electron beam irradiation on bacterial cellulose membranes used as transdermal drug delivery systems

Energy Technology Data Exchange (ETDEWEB)

Stoica-Guzun, Anicuta [Department of Chemical Engineering, ' Politehnica' University Bucharest, 313 Splaiul Independentei, 060042 Bucharest (Romania)], E-mail: astoica@mt.pub.ro; Stroescu, Marta; Tache, Florin [Department of Chemical Engineering, ' Politehnica' University Bucharest, 313 Splaiul Independentei, 060042 Bucharest (Romania); Zaharescu, Traian [Advanced Research Institute for Electrical Engineering, 313 Splaiul Unirii, 030138 Bucharest (Romania)], E-mail: zaharescut@icpe-ca.ro; Grosu, Elena [Department of Chemical Engineering, ' Politehnica' University Bucharest, 313 Splaiul Independentei, 060042 Bucharest (Romania)

2007-12-15

Ionizing radiation is an effective energetic source for polymer surfaces modification in order to obtain transdermal systems with different controlled release properties. In this work, gamma rays have been applied to induce changes in bacterial cellulose membranes. Permeation of drug (tetracycline) was theoretically and experimentally investigated starting from the effect of {gamma}-irradiation on membranes permeability. Release and permeation of drug from irradiated and non-irradiated membranes have been performed using a diffusion cell.

Effect of electron beam irradiation on bacterial cellulose membranes used as transdermal drug delivery systems

International Nuclear Information System (INIS)

Stoica-Guzun, Anicuta; Stroescu, Marta; Tache, Florin; Zaharescu, Traian; Grosu, Elena

2007-01-01

Ionizing radiation is an effective energetic source for polymer surfaces modification in order to obtain transdermal systems with different controlled release properties. In this work, gamma rays have been applied to induce changes in bacterial cellulose membranes. Permeation of drug (tetracycline) was theoretically and experimentally investigated starting from the effect of γ-irradiation on membranes permeability. Release and permeation of drug from irradiated and non-irradiated membranes have been performed using a diffusion cell

Effect of electron beam irradiation on bacterial cellulose membranes used as transdermal drug delivery systems

Science.gov (United States)

Stoica-Guzun, Anicuta; Stroescu, Marta; Tache, Florin; Zaharescu, Traian; Grosu, Elena

2007-12-01

Ionizing radiation is an effective energetic source for polymer surfaces modification in order to obtain transdermal systems with different controlled release properties. In this work, gamma rays have been applied to induce changes in bacterial cellulose membranes. Permeation of drug (tetracycline) was theoretically and experimentally investigated starting from the effect of γ-irradiation on membranes permeability. Release and permeation of drug from irradiated and non-irradiated membranes have been performed using a diffusion cell.

Medicinal plants - a potent antibacterial source against bacterial leaf blight (BLB) of rice

International Nuclear Information System (INIS)

Jabeen, R.

2011-01-01

The antibacterial potential of indigenous medicinal plants as alternative chemical pesticides for controlling bacterial leaf blight (BLB) of rice was investigated. Twenty-five different species of medicinal plants were collected from various sites in Pakistan. Decoctions of all medicinal plant species were screened by the disc plate diffusion method for testing the susceptibility of an aggressive isolate of Xanthomonas oryzae pv. oryzae (Xoo 105). Out of twenty five medicinal plants, Thuja orientalis (cone + leaves), Azadirachta indica (seeds + fruits), Amomum subulatum (fruits), Terminalia chebula (fruits), Terminalia bellirica (fruits), Anethum graveolens (fruits) and Ferula assa-foetida (fruits) decoctions showed significant activity. The efficacy of decoctions from six promising plants were further tested through detached leaf, glasshouse and field assays. A decoction of Terminalia chebula demonstrated the highest effectiveness in terms of regulating BLB in the plants both under laboratory and field conditions. Bioactive fractions of Terminalia chebula were purified, characterized and tentatively identified as allegic acid. (author)

Bacterial degradation of monocyclic aromatic amines

Directory of Open Access Journals (Sweden)

Pankaj Kumar Arora

2015-08-01

Full Text Available Aromatic amines are an important group of industrial chemicals, which are widely used for manufacturing of dyes, pesticides, drugs, pigments, and other industrial products. These compounds have been considered highly toxic to human beings due to their carcinogenic nature. Three groups of aromatic amines have been recognized: monocyclic, polycyclic and heterocyclic aromatic amines. Bacterial degradation of several monocyclic aromatic compounds has been studied in a variety of bacteria, which utilizes monocyclic aromatic amines as their sole source of carbon and energy. Several degradation pathways have been proposed and the related enzymes and genes have also been characterized. Many reviews have been reviewed toxicity of monocyclic aromatic amines; however, there is lack of review on biodegradation of monocyclic aromatic amines. The aim of this review is to summarize bacterial degradation of monocyclic aromatic amines. This review will increase our current understanding of biochemical and molecular basis of bacterial degradation of monocyclic aromatic amines.

Bacterial amplification and in-place carpet drying: implications for category 1 water intrusion restoration.

Science.gov (United States)

Holland, Jim; Banta, John; Passmore, Boni; Ayers, Mark; Abbott, Sean P; Cole, Eugene C

2012-05-01

The study described in this article investigated whether in-place carpet drying processes resulted in bacterial amplification following water intrusion from a clean water source (category 1) in a residential indoor environment. Bacterial amplification was examined after wetting a 10-year-old carpet and pad that had no history of water intrusion. Three test areas were extracted and dried using industry-recommended procedures for in-place drying and compared to a control area that was not extracted or dried. Results from carpet, pad, and subsurface dust demonstrated that bacterial amplification occurred in all test areas. CFUs of bacteria per gram of carpet surface dust and subsurface dust prior to water intrusion were lower than levels in subsurface dust after in-place drying. The authors' study contributes to information regarding the restoration of water-based carpet damage by professional water damage restoration companies, building maintenance personnel, and housekeeping managers. Results suggest that the appropriate response time for carpet pad salvage is considerably shorter than the current industry recommendation of 72 hours.

Investigation of bacterial transport in the large-block test, a thermally perturbed block of Topopah Spring tuff

Energy Technology Data Exchange (ETDEWEB)

Chen, C.I.; Meike, A.; Chuu, Y.J.; Sawvel, A.; Lin, W.

1999-07-01

Transport of bacteria is investigated as part of the Large-Block Test (LBT), a thermally perturbed block of Topopah Spring tuff. Two bacterial species, Bacillus subtilis and Arthrobacter oxydans, were isolated from the Yucca Mountain Tuff. Natural mutants that can grow under the simultaneous presence of the two antibiotics, streptomycin and rifampicin, were selected from these species by laboratory procedures, cultured, and injected into the five heater boreholes of the large block hours before heating was initiated. The temperature, as measured 5 cm above one of the heater boreholes, rose slowly over a matter of months to a maximum of 142 C and to 60 C at the top and bottom of the block. Samples were collected from boreholes located approximately 5 ft below the injection points. Double-drug-resistant microbes also appeared in the heater boreholes where the temperature had been sustainably high throughout the test. The number of double-drug-resistant bacteria that were identified in the collection boreholes increased with time until the heater was deactivated. Negative indications in the collection holes after the heater was deactivated support the supposition that these bacteria were the species that were injected. An apparent homogeneous distribution among the collection boreholes suggests no pattern to the migration of bacteria through the block. The relationship between bacterial migration and the movement of water is not yet understood. These observations indicate the possibility of rapid bacterial transport in a thermally perturbed geologic setting. The implications for colloid transport need to be reviewed.

Investigation of bacterial transport in the large-block test, a thermally perturbed block of Topopah Spring tuff

International Nuclear Information System (INIS)

Chen, C.I.; Meike, A.; Chuu, Y.J.; Sawvel, A.; Lin, W.

1999-01-01

Transport of bacteria is investigated as part of the Large-Block Test (LBT), a thermally perturbed block of Topopah Spring tuff. Two bacterial species, Bacillus subtilis and Arthrobacter oxydans, were isolated from the Yucca Mountain Tuff. Natural mutants that can grow under the simultaneous presence of the two antibiotics, streptomycin and rifampicin, were selected from these species by laboratory procedures, cultured, and injected into the five heater boreholes of the large block hours before heating was initiated. The temperature, as measured 5 cm above one of the heater boreholes, rose slowly over a matter of months to a maximum of 142 C and to 60 C at the top and bottom of the block. Samples were collected from boreholes located approximately 5 ft below the injection points. Double-drug-resistant microbes also appeared in the heater boreholes where the temperature had been sustainably high throughout the test. The number of double-drug-resistant bacteria that were identified in the collection boreholes increased with time until the heater was deactivated. Negative indications in the collection holes after the heater was deactivated support the supposition that these bacteria were the species that were injected. An apparent homogeneous distribution among the collection boreholes suggests no pattern to the migration of bacteria through the block. The relationship between bacterial migration and the movement of water is not yet understood. These observations indicate the possibility of rapid bacterial transport in a thermally perturbed geologic setting. The implications for colloid transport need to be reviewed

Counterimmunoelectrophoresis in the diagnosis of bacterial meningitis

DEFF Research Database (Denmark)

Colding, H; Lind, I

1977-01-01

The aim of the present study was to investigate whether counterimmunoelectrophoresis (CIE) would facilitate the rapid, etiological diagnosis of bacterial meningitis when used in parallel with other routine methods in a medical bacteriological laboratory. Of 3,674 consecutive specimens of cerebros......The aim of the present study was to investigate whether counterimmunoelectrophoresis (CIE) would facilitate the rapid, etiological diagnosis of bacterial meningitis when used in parallel with other routine methods in a medical bacteriological laboratory. Of 3,674 consecutive specimens....../139) of the culture-negative specimens. CSF specimens from 21 patients with bacterial meningitis caused by other species were all negative in CIE, except four, three of which contained Escherichia coli antigen reacting with antiserum to N. meningitidis group B and one E. coli antigen reacting with antiserum to H...

Linkage of the Nit1C gene cluster to bacterial cyanide assimilation as a nitrogen source.

Science.gov (United States)

Jones, Lauren B; Ghosh, Pallab; Lee, Jung-Hyun; Chou, Chia-Ni; Kunz, Daniel A

2018-05-21

A genetic linkage between a conserved gene cluster (Nit1C) and the ability of bacteria to utilize cyanide as the sole nitrogen source was demonstrated for nine different bacterial species. These included three strains whose cyanide nutritional ability has formerly been documented (Pseudomonas fluorescens Pf11764, Pseudomonas putida BCN3 and Klebsiella pneumoniae BCN33), and six not previously known to have this ability [Burkholderia (Paraburkholderia) xenovorans LB400, Paraburkholderia phymatum STM815, Paraburkholderia phytofirmans PsJN, Cupriavidus (Ralstonia) eutropha H16, Gluconoacetobacter diazotrophicus PA1 5 and Methylobacterium extorquens AM1]. For all bacteria, growth on or exposure to cyanide led to the induction of the canonical nitrilase (NitC) linked to the gene cluster, and in the case of Pf11764 in particular, transcript levels of cluster genes (nitBCDEFGH) were raised, and a nitC knock-out mutant failed to grow. Further studies demonstrated that the highly conserved nitB gene product was also significantly elevated. Collectively, these findings provide strong evidence for a genetic linkage between Nit1C and bacterial growth on cyanide, supporting use of the term cyanotrophy in describing what may represent a new nutritional paradigm in microbiology. A broader search of Nit1C genes in presently available genomes revealed its presence in 270 different bacteria, all contained within the domain Bacteria, including Gram-positive Firmicutes and Actinobacteria, and Gram-negative Proteobacteria and Cyanobacteria. Absence of the cluster in the Archaea is congruent with events that may have led to the inception of Nit1C occurring coincidentally with the first appearance of cyanogenic species on Earth, dating back 400-500 million years.

Bacterial carbon utilization in vertical subsurface flow constructed wetlands.

Science.gov (United States)

Tietz, Alexandra; Langergraber, Günter; Watzinger, Andrea; Haberl, Raimund; Kirschner, Alexander K T

2008-03-01

Subsurface vertical flow constructed wetlands with intermittent loading are considered as state of the art and can comply with stringent effluent requirements. It is usually assumed that microbial activity in the filter body of constructed wetlands, responsible for the removal of carbon and nitrogen, relies mainly on bacterially mediated transformations. However, little quantitative information is available on the distribution of bacterial biomass and production in the "black-box" constructed wetland. The spatial distribution of bacterial carbon utilization, based on bacterial (14)C-leucine incorporation measurements, was investigated for the filter body of planted and unplanted indoor pilot-scale constructed wetlands, as well as for a planted outdoor constructed wetland. A simple mass-balance approach was applied to explain the bacterially catalysed organic matter degradation in this system by comparing estimated bacterial carbon utilization rates with simultaneously measured carbon reduction values. The pilot-scale constructed wetlands proved to be a suitable model system for investigating microbial carbon utilization in constructed wetlands. Under an ideal operating mode, the bulk of bacterial productivity occurred within the first 10cm of the filter body. Plants seemed to have no significant influence on productivity and biomass of bacteria, as well as on wastewater total organic carbon removal.

Assessing Genetic Heterogeneity within Bacterial Species Isolated from Gastrointestinal and Environmental Samples: How Many Isolates Does It Take?▿

OpenAIRE

Döpfer, D.; Buist, W.; Soyer, Y.; Munoz, M. A.; Zadoks, R. N.; Geue, L.; Engel, B.

2008-01-01

Strain typing of bacterial isolates is increasingly used to identify sources of infection or product contamination and to elucidate routes of transmission of pathogens or spoilage organisms. Usually, the number of bacterial isolates belonging to the same species that is analyzed per sample is determined by convention, convenience, laboratory capacity, or financial resources. Statistical considerations and knowledge of the heterogeneity of bacterial populations in various sources can be used t...

Architectural design drives the biogeography of indoor bacterial communities.

Science.gov (United States)

Kembel, Steven W; Meadow, James F; O'Connor, Timothy K; Mhuireach, Gwynne; Northcutt, Dale; Kline, Jeff; Moriyama, Maxwell; Brown, G Z; Bohannan, Brendan J M; Green, Jessica L

2014-01-01

Architectural design has the potential to influence the microbiology of the built environment, with implications for human health and well-being, but the impact of design on the microbial biogeography of buildings remains poorly understood. In this study we combined microbiological data with information on the function, form, and organization of spaces from a classroom and office building to understand how design choices influence the biogeography of the built environment microbiome. Sequencing of the bacterial 16S gene from dust samples revealed that indoor bacterial communities were extremely diverse, containing more than 32,750 OTUs (operational taxonomic units, 97% sequence similarity cutoff), but most communities were dominated by Proteobacteria, Firmicutes, and Deinococci. Architectural design characteristics related to space type, building arrangement, human use and movement, and ventilation source had a large influence on the structure of bacterial communities. Restrooms contained bacterial communities that were highly distinct from all other rooms, and spaces with high human occupant diversity and a high degree of connectedness to other spaces via ventilation or human movement contained a distinct set of bacterial taxa when compared to spaces with low occupant diversity and low connectedness. Within offices, the source of ventilation air had the greatest effect on bacterial community structure. Our study indicates that humans have a guiding impact on the microbial biodiversity in buildings, both indirectly through the effects of architectural design on microbial community structure, and more directly through the effects of human occupancy and use patterns on the microbes found in different spaces and space types. The impact of design decisions in structuring the indoor microbiome offers the possibility to use ecological knowledge to shape our buildings in a way that will select for an indoor microbiome that promotes our health and well-being.

Investigating source processes of isotropic events

Science.gov (United States)

Chiang, Andrea

explosion. In contrast, recovering the announced explosive yield using seismic moment estimates from moment tensor inversion remains challenging but we can begin to put error bounds on our moment estimates using the NSS technique. The estimation of seismic source parameters is dependent upon having a well-calibrated velocity model to compute the Green's functions for the inverse problem. Ideally, seismic velocity models are calibrated through broadband waveform modeling, however in regions of low seismicity velocity models derived from body or surface wave tomography may be employed. Whether a velocity model is 1D or 3D, or based on broadband seismic waveform modeling or the various tomographic techniques, the uncertainty in the velocity model can be the greatest source of error in moment tensor inversion. These errors have not been fully investigated for the nuclear discrimination problem. To study the effects of unmodeled structures on the moment tensor inversion, we set up a synthetic experiment where we produce synthetic seismograms for a 3D model (Moschetti et al., 2010) and invert these data using Green's functions computed with a 1D velocity mode (Song et al., 1996) to evaluate the recoverability of input solutions, paying particular attention to biases in the isotropic component. The synthetic experiment results indicate that the 1D model assumption is valid for moment tensor inversions at periods as short as 10 seconds for the 1D western U.S. model (Song et al., 1996). The correct earthquake mechanisms and source depth are recovered with statistically insignificant isotropic components as determined by the F-test. Shallow explosions are biased by the theoretical ISO-CLVD tradeoff but the tectonic release component remains low, and the tradeoff can be eliminated with constraints from P wave first motion. Path-calibration to the 1D model can reduce non-double-couple components in earthquakes, non-isotropic components in explosions and composite sources and improve

Arsenic uptake in bacterial calcite

Science.gov (United States)

Catelani, Tiziano; Perito, Brunella; Bellucci, Francesco; Lee, Sang Soo; Fenter, Paul; Newville, Matthew; Rimondi, Valentina; Pratesi, Giovanni; Costagliola, Pilario

2018-02-01

Bio-mediated processes for arsenic (As) uptake in calcite were investigated by means of X-ray Diffraction (XRD) and X-ray Absorption Spectroscopy (XAS) coupled with X-ray Fluorescence measurements. The environmental bacterial strain Bacillus licheniformis BD5, sampled at the Bullicame Hot Springs (Viterbo, Central Italy), was used to synthesize calcite from As-enriched growth media. Both liquid and solid cultures were applied to simulate planktonic and biofilm community environments, respectively. Bacterial calcite samples cultured in liquid media had an As enrichment factor (Kd) 50 times higher than that from solid media. The XRD analysis revealed an elongation of the crystal lattice along the c axis (by 0.03 Å) for biogenic calcite, which likely resulted from the substitution of larger arsenate for carbonate in the crystal. The XAS data also showed a clear difference in the oxidation state of sorbed As between bacterial and abiotic calcite. Abiotic chemical processes yielded predominantly As(V) uptake whereas bacterial precipitation processes led to the uptake of both As(III) and As(V). The presence of As(III) in bacterial calcite is proposed to result from subsequent reduction of arsenate to arsenite by bacterial activities. To the best of our knowledge, this is the first experimental observation of the incorporation of As(III) in the calcite crystal lattice, revealing a critical role of biochemical processes for the As cycling in nature.

Arsenic uptake in bacterial calcite

Energy Technology Data Exchange (ETDEWEB)

Catelani, Tiziano; Perito, Brunella; Bellucci, Francesco; Lee, Sang Soo; Fenter, Paul; Newville, Matthew G.; Rimondi, Valentina; Pratesi, Giovanni; Costagliola, Pilario

2018-02-01

Bio-mediated processes for arsenic (As) uptake in calcite were investigated by means of X-ray Diffraction (XRD) and Xray Absorption Spectroscopy (XAS) coupled with X-ray Fluorescence measurements. The environmental bacterial strain Bacillus licheniformis BD5, sampled at the Bullicame Hot Springs (Viterbo, Central Italy), was used to synthesize calcite from As-enriched growth media. Both liquid and solid cultures were applied to simulate planktonic and biofilm community environments, respectively. Bacterial calcite samples cultured in liquid media had an As enrichment factor (Kd) 50 times higher than that from solid media. The XRD analysis revealed an elongation of the crystal lattice along the c axis (by 0.03Å) for biogenic calcite, which likely resulted from the substitution of larger arsenate for carbonate in the crystal. The XAS data also showed a clear difference in the oxidation state of sorbed As between bacterial and abiotic calcite. Abiotic chemical processes yielded predominantly As(V) uptake whereas bacterial precipitation processes led to the uptake of both As(III) and As(V). The presence of As(III) in bacterial calcite is proposed to result from subsequent reduction of arsenate to arsenite by bacterial activities. To the best of our knowledge, this is the first experimental observation of the incorporation of As(III) in the calcite crystal lattice, revealing a critical role of biochemical processes for the As cycling in nature.

Bacterial brown leaf spot of citrus, a new disease caused by Burkholderia andropogonis

Science.gov (United States)

A new bacterial disease of citrus was recently identified in Florida and named as bacterial brown leaf spot (BBLS) of citrus. BBLS-infected citrus displayed flat, circular and brownish lesions with water-soaked margins surrounded by a chlorotic halo on leaves. Based on Biolog carbon source metabolic...

Investigation of Biogenic and Non-biogenic Methane Sources in Texas

Science.gov (United States)

Yang, S.; Talbot, R. W.; Liu, L.; Lan, X.

2016-12-01

Methane (CH4) is a potent greenhouse gas with its mixing ratio increasing in the global atmosphere. Texas is one of the significant areas where underestimation of CH4 emissions by the U.S. inventories are pronounced. This study focused on two areas of Texas: Houston, the energy capital of the world, and the Barnett Shale area which is one of the largest onshore natural gas fields in the United States. The investigation of background CH4 and the fingerprints of CH4 emissions are critical to understanding potential impacts of extensive nature gas operations in these two areas. One-year of stationary CH4 measurements were studied to deduce the regional background CH4 characteristics and to identify the principle CH4 sources in Houston. Key information concerning CH4 sources can be obtained through the stable carbon isotope δ13CH4 during two field campaigns using a state-of-the-art mobile laboratory. CH4 mixing ratio and δ13C in CH4 were sampled by two cavity ring-down spectrometers (CRDS), one of which is coupled to a custom air core 13C sampling device which can supply more than 600 measurements for each plume analysis. Here, we report results of the overall δ13CH4 values and CH4 emission signatures derived from thirty-three sources in the two studied areas, ranging from oil production and processing, waste managements and landfills, to livestock. δ13CH4 signatures of these sources vary from -76‰ to -23‰. Several repeated measurements were sampled to investigate the variability of source signatures. We investigated a case of unexpected massive CH4 leaking detected near the San Jacinto River Fleet site. At the regional scale, the comparison of background δ13CH4 signatures were conducted to obtain the difference of dominate CH4 sources in two study areas. At the local scale, the combination of tower and mobile lab measurements were used to estimate and characterize CH4 emissions in Houston. The results and findings can supply valuable references for the local

Statistical modeling of dental unit water bacterial test kit performance.

Science.gov (United States)

Cohen, Mark E; Harte, Jennifer A; Stone, Mark E; O'Connor, Karen H; Coen, Michael L; Cullum, Malford E

2007-01-01

While it is important to monitor dental water quality, it is unclear whether in-office test kits provide bacterial counts comparable to the gold standard method (R2A). Studies were conducted on specimens with known bacterial concentrations, and from dental units, to evaluate test kit accuracy across a range of bacterial types and loads. Colony forming units (CFU) were counted for samples from each source, using R2A and two types of test kits, and conformity to Poisson distribution expectations was evaluated. Poisson regression was used to test for effects of source and device, and to estimate rate ratios for kits relative to R2A. For all devices, distributions were Poisson for low CFU/mL when only beige-pigmented bacteria were considered. For higher counts, R2A remained Poisson, but kits exhibited over-dispersion. Both kits undercounted relative to R2A, but the degree of undercounting was reasonably stable. Kits did not grow pink-pigmented bacteria from dental-unit water identified as Methylobacterium rhodesianum. Only one of the test kits provided results with adequate reliability at higher bacterial concentrations. Undercount bias could be estimated for this device and used to adjust test kit results. Insensitivity to methylobacteria spp. is problematic.

Investigation of Pseudo-Active State in Z-Source Inverter

DEFF Research Database (Denmark)

Schaltz, Erik; Oprea, Octavian; Larsen, Lasse

2005-01-01

This paper introduces a new operating state of the Z-source inverter denoted the pseudo-active state. The pseudoactive state is a state that may boost the output voltage of the Zsource inverter to a level higher than expected. The influence of the pseudo-active state is investigated and an equation...

Changes in bacterial composition of biofilm in a metropolitan drinking water distribution system.

Science.gov (United States)

Revetta, R P; Gomez-Alvarez, V; Gerke, T L; Santo Domingo, J W; Ashbolt, N J

2016-07-01

This study examined the development of bacterial biofilms within a metropolitan distribution system. The distribution system is fed with different source water (i.e. groundwater, GW and surface water, SW) and undergoes different treatment processes in separate facilities. The biofilm community was characterized using 16S rRNA gene clone libraries and functional potential analysis, generated from total DNA extracted from coupons in biofilm annular reactors fed with onsite drinking water for up to 18 months. Differences in the bacterial community structure were observed between GW and SW. Representatives that explained the dissimilarity were associated with the classes Betaproteobacteria, Alphaproteobacteria, Actinobacteria, Gammaproteobacteria and Firmicutes. After 9 months the biofilm bacterial community from both GW and SW were dominated by Mycobacterium species. The distribution of the dominant operational taxonomic unit (OTU) (Mycobacterium) positively correlated with the drinking water distribution system (DWDS) temperature. In this study, the biofilm community structure observed between GW and SW were dissimilar, while communities from different locations receiving SW did not show significant differences. The results suggest that source water and/or the water quality shaped by their respective treatment processes may play an important role in shaping the bacterial communities in the distribution system. In addition, several bacterial groups were present in all samples, suggesting that they are an integral part of the core microbiota of this DWDS. These results provide an ecological insight into biofilm bacterial structure in chlorine-treated drinking water influenced by different water sources and their respective treatment processes. Published 2016. This article is a U.S. Government work and is in the public domain in the USA.

Liver is the major source of elevated serum lipocalin-2 levels after bacterial infection or partial hepatectomy

DEFF Research Database (Denmark)

Xu, Ming-Jiang; Feng, Dechun; Wu, Hailong

2015-01-01

cell type responsible for LCN2 production after bacterial infection or PHx, and this response is dependent on IL-6 activation of the STAT3 signaling pathway. Thus, hepatocyte-derived LCN2 plays an important role in inhibiting bacterial infection and promoting liver regeneration....... or E. coli. These mice also had increased enteric bacterial translocation from the gut to the mesenteric lymph nodes and exhibited reduced liver regeneration after PHx. Treatment with interleukin (IL)-6 stimulated hepatocytes to produce LCN2 in vitro and in vivo. Hepatocyte-specific ablation of the IL...

Bacterial colonization of psoriasis plaques. Is it relevant?

Directory of Open Access Journals (Sweden)

Eva Marcus

2011-08-01

Full Text Available Bacterial colonization was investigated retrospectively in patients with plaque psoriasis (n=98 inpatient treatments, n=73 patients. At least one pathogen was found in 46% of all cases. Staphylococcus aureus was the most frequent bacterium. Bacterial colonization of psoriasis plaques could be relevant in individual cases.

Investigation of Endophytic Bacterial Community in Supposedly Axenic Cultures of Pineapple and Orchids with Evidence on Abundant Intracellular Bacteria.

Science.gov (United States)

Esposito-Polesi, Natalia Pimentel; de Abreu-Tarazi, Monita Fiori; de Almeida, Cristina Vieira; Tsai, Siu Mui; de Almeida, Marcílio

2017-01-01

Asepsis, defined as the absence of microbial contamination, is one of the most important requirements of plant micropropagation. In long-term micropropagated cultures, there may occasionally occur scattered microorganism growth in the culture medium. These microorganisms are common plant components and are known as latent endophytes. Thus, the aim of this research was to investigate the presence of endophytic bacteria in asymptomatic pineapple and orchid microplants, which were cultivated in three laboratories for 1 year. Isolation and characterization of bacterial isolates, PCR-DGGE from total genomic DNA of microplants and ultrastructural analysis of leaves were performed. In the culture-dependent technique, it was only possible to obtain bacterial isolates from pineapple microplants. In this case, the bacteria genera identified in the isolation technique were Bacillus, Acinetobacter, and Methylobacterium. The scanning electron microscopy and transmission electron microscopy (SEM and TEM) analyses revealed the presence of endophytic bacteria in intracellular spaces in the leaves of pineapple and orchid microplants, independent of the laboratory or cultivation protocol. Our results strongly indicate that there are endophytic bacterial communities inhabiting the microplants before initiation of the in vitro culture and that some of these endophytes persist in their latent form and can also grow in the culture medium even after long-term micropropagation, thus discarding the concept of "truly axenic plants."

Heterologous Expression of Secreted Bacterial BPP and HAP Phytases in Plants Stimulates Arabidopsis thaliana Growth on Phytate

Directory of Open Access Journals (Sweden)

Lia R. Valeeva

2018-02-01

Full Text Available Phytases are specialized phosphatases capable of releasing inorganic phosphate from myo-inositol hexakisphosphate (phytate, which is highly abundant in many soils. As inorganic phosphorus reserves decrease over time in many agricultural soils, genetic manipulation of plants to enable secretion of potent phytases into the rhizosphere has been proposed as a promising approach to improve plant phosphorus nutrition. Several families of biotechnologically important phytases have been discovered and characterized, but little data are available on which phytase families can offer the most benefits toward improving plant phosphorus intake. We have developed transgenic Arabidopsis thaliana plants expressing bacterial phytases PaPhyC (HAP family of phytases and 168phyA (BPP family under the control of root-specific inducible promoter Pht1;2. The effects of each phytase expression on growth, morphology and inorganic phosphorus accumulation in plants grown on phytate hydroponically or in perlite as the only source of phosphorus were investigated. The most enzymatic activity for both phytases was detected in cell wall-bound fractions of roots, indicating that these enzymes were efficiently secreted. Expression of both bacterial phytases in roots improved plant growth on phytate and resulted in larger rosette leaf area and diameter, higher phosphorus content and increased shoot dry weight, implying that these plants were indeed capable of utilizing phytate as the source of phosphorus for growth and development. When grown on phytate the HAP-type phytase outperformed its BPP-type counterpart for plant biomass production, though this effect was only observed in hydroponic conditions and not in perlite. Furthermore, we found no evidence of adverse side effects of microbial phytase expression in A. thaliana on plant physiology and seed germination. Our data highlight important functional differences between these members of bacterial phytase families and indicate

Heterologous Expression of Secreted Bacterial BPP and HAP Phytases in Plants Stimulates Arabidopsis thaliana Growth on Phytate.

Science.gov (United States)

Valeeva, Lia R; Nyamsuren, Chuluuntsetseg; Sharipova, Margarita R; Shakirov, Eugene V

2018-01-01

Phytases are specialized phosphatases capable of releasing inorganic phosphate from myo -inositol hexakisphosphate (phytate), which is highly abundant in many soils. As inorganic phosphorus reserves decrease over time in many agricultural soils, genetic manipulation of plants to enable secretion of potent phytases into the rhizosphere has been proposed as a promising approach to improve plant phosphorus nutrition. Several families of biotechnologically important phytases have been discovered and characterized, but little data are available on which phytase families can offer the most benefits toward improving plant phosphorus intake. We have developed transgenic Arabidopsis thaliana plants expressing bacterial phytases PaPhyC (HAP family of phytases) and 168phyA (BPP family) under the control of root-specific inducible promoter Pht1;2 . The effects of each phytase expression on growth, morphology and inorganic phosphorus accumulation in plants grown on phytate hydroponically or in perlite as the only source of phosphorus were investigated. The most enzymatic activity for both phytases was detected in cell wall-bound fractions of roots, indicating that these enzymes were efficiently secreted. Expression of both bacterial phytases in roots improved plant growth on phytate and resulted in larger rosette leaf area and diameter, higher phosphorus content and increased shoot dry weight, implying that these plants were indeed capable of utilizing phytate as the source of phosphorus for growth and development. When grown on phytate the HAP-type phytase outperformed its BPP-type counterpart for plant biomass production, though this effect was only observed in hydroponic conditions and not in perlite. Furthermore, we found no evidence of adverse side effects of microbial phytase expression in A. thaliana on plant physiology and seed germination. Our data highlight important functional differences between these members of bacterial phytase families and indicate that future

Heterologous Expression of Secreted Bacterial BPP and HAP Phytases in Plants Stimulates Arabidopsis thaliana Growth on Phytate

Science.gov (United States)

Valeeva, Lia R.; Nyamsuren, Chuluuntsetseg; Sharipova, Margarita R.; Shakirov, Eugene V.

2018-01-01

Phytases are specialized phosphatases capable of releasing inorganic phosphate from myo-inositol hexakisphosphate (phytate), which is highly abundant in many soils. As inorganic phosphorus reserves decrease over time in many agricultural soils, genetic manipulation of plants to enable secretion of potent phytases into the rhizosphere has been proposed as a promising approach to improve plant phosphorus nutrition. Several families of biotechnologically important phytases have been discovered and characterized, but little data are available on which phytase families can offer the most benefits toward improving plant phosphorus intake. We have developed transgenic Arabidopsis thaliana plants expressing bacterial phytases PaPhyC (HAP family of phytases) and 168phyA (BPP family) under the control of root-specific inducible promoter Pht1;2. The effects of each phytase expression on growth, morphology and inorganic phosphorus accumulation in plants grown on phytate hydroponically or in perlite as the only source of phosphorus were investigated. The most enzymatic activity for both phytases was detected in cell wall-bound fractions of roots, indicating that these enzymes were efficiently secreted. Expression of both bacterial phytases in roots improved plant growth on phytate and resulted in larger rosette leaf area and diameter, higher phosphorus content and increased shoot dry weight, implying that these plants were indeed capable of utilizing phytate as the source of phosphorus for growth and development. When grown on phytate the HAP-type phytase outperformed its BPP-type counterpart for plant biomass production, though this effect was only observed in hydroponic conditions and not in perlite. Furthermore, we found no evidence of adverse side effects of microbial phytase expression in A. thaliana on plant physiology and seed germination. Our data highlight important functional differences between these members of bacterial phytase families and indicate that future crop

Investigating Salmonella Eko from Various Sources in Nigeria by Whole Genome Sequencing to Identify the Source of Human Infections

DEFF Research Database (Denmark)

Leekitcharoenphon, Pimlapas; Raufu, Ibrahim; Thorup Nielsen, Mette

2016-01-01

Twenty-six Salmonella enterica serovar Eko isolated from various sources in Nigeria were investigated by whole genome sequencing to identify the source of human infections. Diversity among the isolates was observed and camel and cattle were identified as the primary reservoirs and the most likely...

Effects of alternative energy sources on bacterial cellulose characteristics produced by Komagataeibacter medellinensis.

Science.gov (United States)

Molina-Ramírez, Carlos; Enciso, Carla; Torres-Taborda, Mabel; Zuluaga, Robin; Gañán, Piedad; Rojas, Orlando J; Castro, Cristina

2018-05-27

Bacterial cellulose (BC) was produced by Komagataeibacter medellinensis using Hestrin and Schramm modified medium in the presence of alternative energy sources (AES), such as ethanol and acetic acid, to explore the effect of AES on the characteristics and properties of the resulting BC. In this study, the physicochemical and structural characteristics of the obtained BC were determined using Fourier-transform infrared spectroscopy, X-ray diffraction spectrometry, thermogravimetric analysis, and mechanical testing analysis. Ethanol and acetic acid (at 0.1 wt%) were proven to improve the BC yield by K. medellinensis by 279% and 222%, respectively. However, the crystallinity index (%), the degree of polymerization, and maximum rate of degradation temperatures decreased by 9.2%, 36%, and 4.96%, respectively, by the addition of ethanol and by 7.2%, 27%, and 4.21%, respectively, by the addition of acetic acid. The significance of this work, lies on the fact that there is not any report about how BC properties change when substances like ethanol or acetic acid are added to culture medium, and which is the mechanism that provokes those changes, that in our case we could demonstrate the relationship of a higher BC production rate (provoked by ethanol and acetic acid adding) and changes in BC properties. Copyright © 2018 Elsevier B.V. All rights reserved.

Algal-bacterial interactions in metal contaminated floodplain sediments

International Nuclear Information System (INIS)

Boivin, M.E.Y.; Greve, G.D.; Garcia-Meza, J.V.; Massieux, B.; Sprenger, W.; Kraak, M.H.S.; Breure, A.M.; Rutgers, M.; Admiraal, W.

2007-01-01

The aim of the present study was to investigate algal-bacterial interactions in a gradient of metal contaminated natural sediments. By means of multivariate techniques, we related the genetic structure (denaturing gradient gel electrophoresis, DGGE) and the physiological structure (community-level physiological profiling, CLPP) of the bacterial communities to the species composition of the algal communities and to the abiotic environmental variables, including metal contamination. The results revealed that genetic and physiological structure of the bacterial communities correlated with the species composition of the algal community, but hardly to the level of metal pollution. This must be interpreted as an indication for a strong and species-specific linkage of algal and bacterial species in floodplain sediments. Metals were, however, not proven to affect either the algal or the bacterial communities of the Dutch river floodplains. - Algal and bacterial communities in floodplain sediments are interlinked, but are not affected by metal pollution

Investigations into the Optimization of Multi-Source Strength Brachytherapy Treatment Procedures

CERN Document Server

Henderson, D L; Yoo, S

2002-01-01

The goal of this project is to investigate the use of multi-strength and multi-specie radioactive sources in permanent prostate implant brachytherapy. In order to fulfill the requirement for an optimal dose distribution, the prescribed dose should be delivered to the target in a nearly uniform dose distribution while simultaneously sparing sensitive structures. The treatment plan should use a small number of needles and sources while satisfying the treatment requirements. The hypothesis for the use of multi-strength and/or multi-specie sources is that a better treatment plan using fewer sources and needles could be obtained than by treatment plans using single-strength sources could reduce the overall number of sources used for treatment. We employ a recently developed greedy algorithm based on the adjoint concept as the optimization search engine. The algorithm utilizes and ''adjoint ratio'', which provides a means of ranking source positions, as the pseudo-objective function. It ha s been shown that the gre...

Investigations of Orchestra Auralizations Using the Multi-Channel Multi-Source Auralization Technique

DEFF Research Database (Denmark)

Vigeant, Michelle; Wang, Lily M.; Rindel, Jens Holger

2008-01-01

a multi-channel multi-source auralization technique, involving individual five-channel anechoic recordings of each instrumental part of two symphonies. In the first study, these auralizations were subjectively compared to orchestra auralizations made using (a) a single omni-directional source, (b......) a surface source, and (c) single-channel multi-source method. Results show that the multi-source auralizations were rated to be more realistic than the surface source ones and to have larger source width than the single omni-directional source auralizations. No significant differences were found between......Room acoustics computer modeling is a tool for generating impulse responses and auralizations from modeled spaces. The auralizations are commonly made from a single-channel anechoic recording of solo instruments. For this investigation, auralizations of an entire orchestra were created using...

Investigating the Antimicrobial Bioactivity of Cyano bacterial Extracts on Some Plant and Human Pathogens

International Nuclear Information System (INIS)

El-Semary, N.A.; Osman, M.E.; Ahmed, A.S.; Botros, H.W.; Farag, A.T.

2014-01-01

The search for broad spectrum antimicrobial agents against microbial pathogens, as the available bioactive compounds, has decreasing efficacy and the multidrug resistance trait is spreading among pathogens. Accordingly, the study was carried out to investigate the antimicrobial bioactivity of extracts derived from a cyano bacterial strain from Egypt. The solvents used were diethyl ether, chloroform and methanol. The antimicrobial bioassay of the lipophilic fraction dissolved in diethyl ether of Synechococcus spp. (isolated from Wadi El-Natroun, Egypt) showed the highest broad spectrum bioactivity as it inhibited the growth of both plant and human pathogens. The extract was also effective on the filamentous plant pathogenic fungi Aspergillus flavus and Aspergillus niger. The effects of incubation periods, growth media and pH values on both growth and antimicrobial activity of Synechococcus spp. were investigated. Chu medium was the medium that gave the highest growth followed by BG11 medium then Oscillatoria medium and all these three media showed antibacterial activities but only BG11 showed both antibacterial and antifungal activities after 18 days of incubation. The pH value 10 proved to be the best for growth and antimicrobial activities of Synechococcus spp. in BG11 medium

PRODUCTIVITY OF GROWING PONDS WHEN APPLYING THE BACTERIAL FERTILIZER «PHOSPHOBAKTERIN»

Directory of Open Access Journals (Sweden)

Т. Hryhorenko

2017-09-01

Full Text Available Purpose. To investigate the effect of the bacterial fertilizer "Phosphobacterin" on the formation of the hydrochemical regime, development of the natural food supply and fish productivity in the growing ponds. Methodology. The work was conducted according to generally accepted hydrochemical,, microbiological, hydrobiological and fish farming methods. Findings The article presents the results of a study of the productivity of growing ponds with different methods of the application of the bacterial fertilizer "Phosphobacterin". It was found that the hydrochemical regime of the experimental ponds was formed under the effect of the source of water supply and measures aimed at intensifying the development of the natural food supply and was favorable for the development of feed organisms and the cultivation of fish seeds. Application of the bacterial fertilizer at the beginning of the growing season along the water pond surface proved to be little effective for increasing the productivity of the pond ecosystem as a whole. A more effective method of increasing biological productivity, including fish productivity of growing ponds, was the application of "Phosphobacterin" during the growing season both on the bed and on the water surface in combination with the organic fertilizer - cattle humus. In the experimental pond under complex fertilization, the average phytoplankton biomass during the growing season was 1.5 times, bacterioplankton 1.1 times, zoobenthos 2.6 times higher, and the obtained total fish productivity was 1.2 times higher than in the control pond (when applying only cattle humus. Originality. The peculiarities of formation of hydrochemical and hydrobiological (phyto-, bacterio-, zooplankton, zoobenthos regimes of growing ponds and the fishery indices are studied, both for bacterial fertilizer "Phosphobacterin" independently and together with the traditional organic fertilizer - cattle humus. Practical value. Based on the obtained results

Non-homogeneous flow profiles in sheared bacterial suspensions

Science.gov (United States)

Samanta, Devranjan; Cheng, Xiang

Bacterial suspensions under shear exhibit interesting rheological behaviors including the remarkable ``superfluidic'' state with vanishing viscosity at low shear rates. Theoretical studies have shown that such ``superfluidic'' state is linked with non-homogeneous shear flows, which are induced by coupling between nematic order of active fluids and hydrodynamics of shear flows. However, although bulk rheology of bacterial suspensions has been experimentally studied, shear profiles within bacterial suspensions have not been explored so far. Here, we experimentally investigate the flow behaviors of E. coli suspensions under planar oscillatory shear. Using confocal microscopy and PIV, we measure velocity profiles across gap between two shear plates. We find that with increasing shear rates, high-concentration bacterial suspensions exhibit an array of non-homogeneous flow behaviors like yield-stress flows and shear banding. We show that these non-homogeneous flows are due to collective motion of bacterial suspensions. The phase diagram of sheared bacterial suspensions is systematically mapped as functions of shear rates an bacterial concentrations. Our experiments provide new insights into rheology of bacterial suspensions and shed light on shear induced dynamics of active fluids. Chemical Engineering and Material Science department.

Tank bromeliad water: similar or distinct environments for research of bacterial bioactives?

Science.gov (United States)

Carmo, F L; Santos, H F; Peixoto, R S; Rosado, A S; Araujo, F V

2014-01-01

The Atlantic Rainforest does not have a uniform physiognomy, its relief determines different environmental conditions that define the composition of its flora and fauna. Within this ecosystem, bromeliads that form tanks with their leaves hold water reservoirs throughout the year, maintaining complex food chains, based mainly on autotrophic and heterotrophic bacteria. Some works concluded that the water held by tank bromeliads concentrate the microbial diversity of their ecosystem. To investigate the bacterial diversity and the potential biotechnology of these ecosystems, tank bromeliads of the Neoregelia cruenta species from the Atlantic Rainforest in Brazil were used as models for this research. Bacteria isolated from these models were tested for production of bioactive compounds. DGGE of the water held by tank bromeliads was performed in different seasons, locations and sun exposure to verify whether these environmental factors affect bacterial communities. The DGGE bands profile showed no grouping of bacterial community by the environmental factors tested. Most of the isolates demonstrated promising activities in the tests performed. Collectively, these results suggest that tank bromeliads of the N. cruenta species provide important habitats for a diverse microbial community, suggesting that each tank forms a distinct micro-habitat. These tanks can be considered excellent sources for the search for new enzymes and/or new bioactive composites of microbial origin.

Data set from a comprehensive phosphoproteomic analysis of rice variety IRBB5 in response to bacterial blight

Directory of Open Access Journals (Sweden)

Yuxuan Hou

2016-03-01

Full Text Available Bacterial blight (BB caused by Xanthomonas oryzae pv. oryzae (Xoo has become one of the most devastating diseases for rice, a major food source for over half of the world populations. To investigate the roles of protein phosphorylation in rice bacterial blight resistance, a quantitative phosphoproteomic study was conducted in rice variety IRBB5 at 0 h and 24 h after Xoo infection. 2367 and 2223 phosphosites on 1334 and 1297 representative proteins were identified in 0 h and 24 h after Xoo infection, respectively, out of which 762 proteins were found to be differentially phosphorylated. In associated with the published article “A comprehensive quantitative phosphoproteome analysis of rice in response to bacterial blight” in BMC Plant Biology (Hou et al., 2015 [1], this dataset article provided the detailed information of experimental designing, methods, features as well as the raw data of mass spectrometry (MS identification. The MS proteomics data could be fully accessed from the ProteomeXchange Consortium with the dataset identifier http://www.ebi.ac.uk/pride/archive/projects/PXD002222. Keywords: Rice (Oryza sativa L., Bacterial blight, Phosphoproteome

Spatial and temporal changes in sulphate-reducing groundwater bacterial community structure in response to Managed Aquifer Recharge.

Science.gov (United States)

Reed, D A; Toze, S; Chang, B

2008-01-01

The population dynamics of bacterial able to be cultured under sulphate reducing condition was studied in conjunction with changes in aquifer geochemistry using multivariate statistics for two contrasting Managed Aquifer Recharge (MAR) techniques at two different geographical locations (Perth, Western Australia and Adelaide, South Australia). Principal component analysis (PCA) was used to investigate spatial and temporal changes in the overall chemical signature of the aquifers using an array of chemical analytes which demonstrated a migrating geochemical plume. Denaturing Gradient Gel Electrophoresis (DGGE) using DNA from sulphate-reducing bacteria cultures was used to detect spatial and temporal changes in population dynamics. Bacterial and geochemical evidence suggested that groundwater at greatest distance from the nutrient source was least affected by treated effluent recharge. The results suggested that bacterial populations that were able to be cultured in sulphate reducing media responded to the migrating chemical gradient and to the changes in aquifer geochemistry. Most noticeably, sulphate-reducing bacterial populations associated with the infiltration galleries were stable in community structure over time. Additionally, the biodiversity of these culturable bacteria was restored when aquifer geochemistry returned to ambient conditions during the recovery phase at the Adelaide Aquifer Storage and Recovery site. Copyright CSIRO 2008.

Upstream Freshwater and Terrestrial Sources Are Differentially Reflected in the Bacterial Community Structure along a Small Arctic River and Its Estuary

DEFF Research Database (Denmark)

Hauptmann, Aviaja Zenia Edna Lyberth; Markussen, Thor N; Stibal, Marek

2016-01-01

of different water sources on the microbial communities in Arctic rivers and estuaries remains unknown. In this study we used 16S rRNA gene amplicon sequencing to assess a small river and its estuary on the Disko Island, West Greenland (69°N). Samples were taken in August when there is maximum precipitation...... and temperatures are high in the Disko Bay area. We describe the bacterial community through a river into the estuary, including communities originating in a glacier and a proglacial lake. Our results show that water from the glacier and lake transports distinct communities into the river in terms of diversity...

Significant relationship between soil bacterial community structure and incidence of bacterial wilt disease under continuous cropping system.

Science.gov (United States)

She, Siyuan; Niu, Jiaojiao; Zhang, Chao; Xiao, Yunhua; Chen, Wu; Dai, Linjian; Liu, Xueduan; Yin, Huaqun

2017-03-01

Soil bacteria are very important in biogeochemical cycles and play significant role in soil-borne disease suppression. Although continuous cropping is responsible for soil-borne disease enrichment, its effect on tobacco plant health and how soil bacterial communities change are yet to be elucidated. In this study, soil bacterial communities across tobacco continuous cropping time-series fields were investigated through high-throughput sequencing of 16S ribosomal RNA genes. The results showed that long-term continuous cropping could significantly alter soil microbial communities. Bacterial diversity indices and evenness indices decreased over the monoculture span and obvious variations for community structures across the three time-scale tobacco fields were detected. Compared with the first year, the abundances of Arthrobacter and Lysobacter showed a significant decrease. Besides, the abundance of the pathogen Ralstonia spp. accumulated over the monoculture span and was significantly correlated with tobacco bacterial wilt disease rate. Moreover, Pearson's correlation demonstrated that the abundance of Arthrobacter and Lysobacter, which are considered to be beneficial bacteria had significant negative correlation with tobacco bacterial wilt disease. Therefore, after long-term continuous cropping, tobacco bacterial wilt disease could be ascribed to the alteration of the composition as well as the structure of the soil microbial community.

Investigation of specificity determinants in bacterial tRNA-guanine transglycosylase reveals queuine, the substrate of its eucaryotic counterpart, as inhibitor.

Directory of Open Access Journals (Sweden)

Inna Biela

Full Text Available Bacterial tRNA-guanine transglycosylase (Tgt catalyses the exchange of the genetically encoded guanine at the wobble position of tRNAs(His,Tyr,Asp,Asn by the premodified base preQ1, which is further converted to queuine at the tRNA level. As eucaryotes are not able to synthesise queuine de novo but acquire it through their diet, eucaryotic Tgt directly inserts the hypermodified base into the wobble position of the tRNAs mentioned above. Bacterial Tgt is required for the efficient pathogenicity of Shigella sp, the causative agent of bacillary dysentery and, hence, it constitutes a putative target for the rational design of anti-Shigellosis compounds. Since mammalian Tgt is known to be indirectly essential to the conversion of phenylalanine to tyrosine, it is necessary to create substances which only inhibit bacterial but not eucaryotic Tgt. Therefore, it seems of utmost importance to study selectivity-determining features within both types of proteins. Homology models of Caenorhabditis elegans Tgt and human Tgt suggest that the replacement of Cys158 and Val233 in bacterial Tgt (Zymomonas mobilis Tgt numbering by valine and accordingly glycine in eucaryotic Tgt largely accounts for the different substrate specificities. In the present study we have created mutated variants of Z. mobilis Tgt in order to investigate the impact of a Cys158Val and a Val233Gly exchange on catalytic activity and substrate specificity. Using enzyme kinetics and X-ray crystallography, we gained evidence that the Cys158Val mutation reduces the affinity to preQ1 while leaving the affinity to guanine unaffected. The Val233Gly exchange leads to an enlarged substrate binding pocket, that is necessary to accommodate queuine in a conformation compatible with the intermediately covalently bound tRNA molecule. Contrary to our expectations, we found that a priori queuine is recognised by the binding pocket of bacterial Tgt without, however, being used as a substrate.

An international point source outbreak of typhoid fever: a European collaborative investigation*

Science.gov (United States)

Stanwell-Smith, R. E.; Ward, L. R.

1986-01-01

A point source outbreak of Salmonella typhi, degraded Vi-strain 22, affecting 32 British visitors to Kos, Greece, in 1983 was attributed by a case—control study to the consumption of a salad at one hotel. This represents the first major outbreak of typhoid fever in which a salad has been identified as the vehicle. The source of the infection was probably a carrier in the hotel staff. The investigation demonstrates the importance of national surveillance, international cooperation, and epidemiological methods in the investigation and control of major outbreaks of infection. PMID:3488842

Chronic bacterial prostatitis in men with spinal cord injury.

Science.gov (United States)

Krebs, Jörg; Bartel, Peter; Pannek, Jürgen

2014-12-01

Recurrent urinary tract infections (UTI) are a major problem affecting spinal cord injury (SCI) patients and may stem from chronic bacterial prostatitis. We have therefore investigated the presence of chronic bacterial prostatitis and its role in the development of recurrent symptomatic UTI in SCI men. This study is a prospective cross-sectional investigation of bacterial prostatitis in SCI men in a single SCI rehabilitation center. In 50 men with chronic SCI presenting for a routine urologic examination, urine samples before and after prostate massage were taken for microbiologic investigation and white blood cell counting. Furthermore, patient characteristics, bladder diary details, and the annual rate of symptomatic UTI were collected retrospectively. No participant reported current symptoms of UTI or prostatitis. In most men (39/50, 78 %), the microbiologic analysis of the post-massage urine sample revealed growth of pathogenic bacteria. The majority of these men (32/39, 82 %) also presented with mostly (27/39, 69 %) the same pathogenic bacteria in the pre-massage sample. There was no significant (p = 0.48) difference in the number of symptomatic UTI in men with a positive post-massage culture compared with those with a negative culture. No significant (p = 0.67) difference in the frequency distribution of positive versus negative post-massage cultures was detected between men with recurrent and sporadic UTI. Most SCI men are affected by asymptomatic bacterial prostatitis; however, bacterial prostatitis does not play a major role in the development of recurrent UTI. The indication for antibiotic treatment of chronic bacterial prostatitis in asymptomatic SCI men with recurrent UTI is questionable.

Characterisation of the gill mucosal bacterial communities of four butterflyfish species: a reservoir of bacterial diversity in coral reef ecosystems.

Science.gov (United States)

Reverter, Miriam; Sasal, Pierre; Tapissier-Bontemps, N; Lecchini, D; Suzuki, M

2017-06-01

While recent studies have suggested that fish mucus microbiota play an important role in homeostasis and prevention of infections, very few studies have investigated the bacterial communities of gill mucus. We characterised the gill mucus bacterial communities of four butterflyfish species and although the bacterial diversity of gill mucus varied significantly between species, Shannon diversities were high (H = 3.7-5.7) in all species. Microbiota composition differed between butterflyfishes, with Chaetodon lunulatus and C. ornatissimus having the most similar bacterial communities, which differed significantly from C. vagabundus and C. reticulatus. The core bacterial community of all species consisted of mainly Proteobacteria followed by Actinobacteria and Firmicutes. Chaetodonlunulatus and C. ornatissimus bacterial communities were mostly dominated by Gammaproteobacteria with Vibrio as the most abundant genus. Chaetodonvagabundus and C. reticulatus presented similar abundances of Gammaproteobacteria and Alphaproteobacteria, which were well represented by Acinetobacter and Paracoccus, respectively. In conclusion, our results indicate that different fish species present specific bacterial assemblages. Finally, as mucus layers are nutrient hotspots for heterotrophic bacteria living in oligotrophic environments, such as coral reef waters, the high bacterial diversity found in butterflyfish gill mucus might indicate external fish mucus surfaces act as a reservoir of coral reef bacterial diversity. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Investigating the influence of DNAPL spill characteristics on source zone architecture and mass removal in pool-dominated source zones

Science.gov (United States)

Wallace, K. A.; Abriola, L.; Chen, M.; Ramsburg, A.; Pennell, K. D.; Christ, J.

2009-12-01

Multiphase, compositional simulators were employed to investigate the spill characteristics and subsurface properties that lead to pool-dominated, dense non-aqueous phase liquid (DNAPL) source zone architectures. DNAPL pools commonly form at textural interfaces where low permeability lenses restrict the vertical migration of DNAPL, allowing for DNAPL to accumulate, reaching high saturation. Significant pooling has been observed in bench-scale experiments and field settings. However, commonly employed numerical simulations rarely predict the pooling suspected in the field. Given the importance of pooling on the efficacy of mass recovery and the down-gradient contaminant signal, it is important to understand the predominant factors affecting the creation of pool-dominated source zones and their subsequent mass discharge. In this work, contaminant properties, spill characteristics and subsurface permeability were varied to investigate the factors contributing to the development of a pool-dominated source zone. DNAPL infiltration and entrapment simulations were conducted in two- and three-dimensional domains using the University of Texas Chemical Compositional (UTCHEM) simulator. A modified version of MT3DMS was then used to simulate DNAPL dissolution and mass discharge. Numerical mesh size was varied to investigate the importance of numerical model parameters on simulations results. The temporal evolution of commonly employed source zone architecture metrics, such as the maximum DNAPL saturation, first and second spatial moments, and fraction of DNAPL mass located in pools, was monitored to determine how the source zone architecture evolved with time. Mass discharge was monitored to identify the link between source zone architecture and down-gradient contaminant flux. Contaminant characteristics and the presence of extensive low permeability lenses appeared to have the most influence on the development of a pool-dominated source zone. The link between DNAPL mass

Do Honeybees Shape the Bacterial Community Composition in Floral Nectar?

Science.gov (United States)

Aizenberg-Gershtein, Yana; Izhaki, Ido; Halpern, Malka

2013-01-01

Floral nectar is considered the most important reward animal-pollinated plants offer to attract pollinators. Here we explore whether honeybees, which act as pollinators, affect the composition of bacterial communities in the nectar. Nectar and honeybees were sampled from two plant species: Amygdalus communis and Citrus paradisi. To prevent the contact of nectar with pollinators, C. paradisi flowers were covered with net bags before blooming (covered flowers). Comparative analysis of bacterial communities in the nectar and on the honeybees was performed by the 454-pyrosequencing technique. No significant differences were found among bacterial communities in honeybees captured on the two different plant species. This resemblance may be due to the presence of dominant bacterial OTUs, closely related to the Arsenophonus genus. The bacterial communities of the nectar from the covered and uncovered C. paradisi flowers differed significantly; the bacterial communities on the honeybees differed significantly from those in the covered flowers’ nectar, but not from those in the uncovered flowers’ nectar. We conclude that the honeybees may introduce bacteria into the nectar and/or may be contaminated by bacteria introduced into the nectar by other sources such as other pollinators and nectar thieves. PMID:23844027

Effects of different nitrogen sources on the biogas production - a lab-scale investigation.

Science.gov (United States)

Wagner, Andreas Otto; Hohlbrugger, Peter; Lins, Philipp; Illmer, Paul

2012-12-20

For anaerobic digestion processes nitrogen sources are poorly investigated although they are known as possible process limiting factors (in the hydrolysis phase) but also as a source for fermentations for subsequent methane production by methanogenic archaea. In the present study different complex and defined nitrogen sources were investigated in a lab-scale experiment in order to study their potential to build up methane. The outcome of the study can be summarised as follows: from complex nitrogen sources yeast extract and casamino acids showed the highest methane production with approximately 600 ml methane per mole of nitrogen, whereas by the use of skim milk no methane production could be observed. From defined nitrogen sources L-arginine showed the highest methane production with almost 1400 ml methane per mole of nitrogen. Moreover it could be demonstrated that the carbon content and therefore C/N-ratio has only minor influence for the methane production from the used substrates. Copyright © 2011 Elsevier GmbH. All rights reserved.

Characterization of soil bacterial, archaeal and fungal communities inhabiting archaeological human-impacted layers at Monte Iato settlement (Sicily, Italy).

Science.gov (United States)

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

2018-01-30

Microbial communities in human-impacted soils of ancient settlements have been proposed to be used as ecofacts (bioindicators) of different ancient anthropogenic activities. In this study, bacterial, archaeal and fungal communities inhabiting soil of three archaic layers, excavated at the archaeological site on Monte Iato (Sicily, Italy) and believed to have been created in a chronological order in archaic times in the context of periodic cultic feasts, were investigated in terms of (i) abundance (phospholipid fatty acid (PLFA) analysis and quantitative PCR)), (ii) carbon(C)-source consumption patterns (Biolog-Ecoplates) and (iii) diversity and community composition (Illumina amplicon sequencing). PLFA analyses demonstrated the existence of living bacteria and fungi in the soil samples of all three layers. The upper layer showed increased levels of organic C, which were not concomitant with an increment in the microbial abundance. In taxonomic terms, the results indicated that bacterial, archaeal and fungal communities were highly diverse, although differences in richness or diversity among the three layers were not detected for any of the communities. However, significantly different microbial C-source utilization patterns and structures of bacterial, archaeal and fungal communities in the three layers confirmed that changing features of soil microbial communities reflect different past human activities.

Disinfection byproduct formation from chlorination of pure bacterial cells and pipeline biofilms.

Science.gov (United States)

Wang, Jun-Jian; Liu, Xin; Ng, Tsz Wai; Xiao, Jie-Wen; Chow, Alex T; Wong, Po Keung

2013-05-15

Disinfection byproduct (DBP) formation is commonly attributed to the reaction between natural organic matters and disinfectants, yet few have considered the contribution from disinfecting bacterial materials - the essential process of water disinfection. Here, we explored the DBP formation from chlorination and chloramination of Escherichia coli and found that most selected DBPs were detectable, including trihalomethanes, haloacetonitriles, chloral hydrate, chloropicrin, and 1,1,1-trichloro-2-propanone. A positive correlation (P = 0.08-0.09) between DBP formation and the log reduction of E. coli implied that breaking down of bacterial cells released precursors for DBP formation. As Pseudomonas aeruginosa is a dominant bacterial species in pipeline biofilms, the DBP formation potentials (DBPFPs) from its planktonic cells and biofilms were characterized. Planktonic cells formed 7-11 times greater trihalomethanes per carbon of those from biofilms but significantly lower (P biofilms on polyvinyl chloride compared to that on galvanized zinc. This study revealed both the in situ disinfection of bacterial planktonic cells in source water and ex situ reaction between biofilms and residual chlorine in pipeline networks as hitherto unknown DBP sources in drinking water. Copyright © 2013 Elsevier Ltd. All rights reserved.

Generation of mutation hotspots in ageing bacterial colonies

DEFF Research Database (Denmark)

Sekowska, Agnieszka; Wendel, Sofie; Nørholm, Morten

How do ageing bacterial colonies generate adaptive mutants? Over a period of two months, we isolated on ageing colonies outgrowing mutants able to use a new carbon source, and sequenced their genomes. This allowed us to uncover exquisite details on the molecular mechanism behind their adaptation:...

Conventional and nonconventional strategies for controlling bacterial contamination in fuel ethanol fermentations.

Science.gov (United States)

Ceccato-Antonini, Sandra Regina

2018-05-25

Ethanol bio-production in Brazil has some unique characteristics that inevitably lead to bacterial contamination, which results in the production of organic acids and biofilms and flocculation that impair the fermentation yield by affecting yeast viability and diverting sugars to metabolites other than ethanol. The ethanol-producing units commonly give an acid treatment to the cells after each fermentative cycle to decrease the bacterial number, which is not always effective. An alternative strategy must be employed to avoid bacterial multiplication but must be compatible with economic, health and environmental aspects. This review analyzes the issue of bacterial contamination in sugarcane-based fuel ethanol fermentation, and the potential strategies that may be utilized to control bacterial growth besides acid treatment and antibiotics. We have emphasized the efficiency and suitability of chemical products other than acids and those derived from natural sources in industrial conditions. In addition, we have also presented bacteriocins, bacteriophages, and beneficial bacteria as non-conventional antimicrobial agents to mitigate bacterial contamination in the bioethanol industry.

Viral-bacterial associations in acute apical abscesses.

Science.gov (United States)

Ferreira, Dennis C; Rôças, Isabela N; Paiva, Simone S M; Carmo, Flávia L; Cavalcante, Fernanda S; Rosado, Alexandre S; Santos, Kátia R N; Siqueira, José F

2011-08-01

Viral-bacterial and bacterial synergism have been suggested to contribute to the pathogenesis of several human diseases. This study sought to investigate the possible associations between 9 candidate endodontic bacterial pathogens and 9 human viruses in samples from acute apical abscesses. DNA extracts from purulent exudate aspirates of 33 cases of acute apical abscess were surveyed for the presence of 9 selected bacterial species using a 16S ribosomal RNA gene-based nested polymerase chain reaction (PCR) approach. Single or nested PCR assays were used for detection of the human papillomavirus (HPV) and herpesviruses types 1 to 8. Two-thirds of the abscess samples were positive for at least one of the target viruses. Specifically, the most frequently detected viruses were HHV-8 (54.5%); HPV (9%); and varicella zoster virus (VZV), Epstein-Barr virus (EBV), and HHV-6 (6%). Bacterial DNA was present in all cases and the most prevalent bacterial species were Treponema denticola (70%), Tannerella forsythia (67%), Porphyromonas endodontalis (67%), Dialister invisus (61%), and Dialister pneumosintes (57.5%). HHV-8 was positively associated with 7 of the target bacterial species and HPV with 4, but all these associations were weak. Several bacterial pairs showed a moderate positive association. Viral coinfection was found in 6 abscess cases, but no significant viral association could be determined. Findings demonstrated that bacterial and viral DNA occurred concomitantly in two-thirds of the samples from endodontic abscesses. Although this may suggest a role for viruses in the etiology of apical abscesses, the possibility also exists that the presence of viruses in abscess samples is merely a consequence of the bacterially induced disease process. Further studies are necessary to clarify the role of these viral-bacterial interactions, if any, in the pathogenesis of acute apical abscesses. Copyright © 2011 Mosby, Inc. All rights reserved.

Bacterial prostatitis.

Science.gov (United States)

Gill, Bradley C; Shoskes, Daniel A

2016-02-01

The review provides the infectious disease community with a urologic perspective on bacterial prostatitis. Specifically, the article briefly reviews the categorization of prostatitis by type and provides a distillation of new findings published on bacterial prostatitis over the past year. It also highlights key points from the established literature. Cross-sectional prostate imaging is becoming more common and may lead to more incidental diagnoses of acute bacterial prostatitis. As drug resistance remains problematic in this condition, the reemergence of older antibiotics such as fosfomycin, has proven beneficial. With regard to chronic bacterial prostatitis, no clear clinical risk factors emerged in a large epidemiological study. However, bacterial biofilm formation has been associated with more severe cases. Surgery has a limited role in bacterial prostatitis and should be reserved for draining of a prostatic abscess or the removal of infected prostatic stones. Prostatitis remains a common and bothersome clinical condition. Antibiotic therapy remains the basis of treatment for both acute and chronic bacterial prostatitis. Further research into improving prostatitis treatment is indicated.

Analysis of bacterial communities and bacterial pathogens in a biogas plant by the combination of ethidium monoazide, PCR and Ion Torrent sequencing

DEFF Research Database (Denmark)

Luo, Gang; Angelidaki, Irini

2014-01-01

with time were also observed. This could be attributed to varying composition of the influent. Batch experiments showed that the methane recovery from the digested residues (obtained from biogas reactor) was mainly related with post-digestion temperature. However, post-digestion time rather than temperature......The present study investigated the changes of bacterial community composition including bacterial pathogens along a biogas plant, i.e. from the influent, to the biogas reactor and to the post-digester. The effects of post-digestion temperature and time on the changes of bacterial community...... showed that the bacterial community composition in the influent was changed after anaerobic digestion. Firmicutes were dominant in all the samples, while Proteobacteria decreased in the biogas reactor compared with the influent. Variations of bacterial community composition in the biogas reactor...

Impact of bacterial and fungal processes on 14C-hexadecane mineralisation in weathered hydrocarbon contaminated soil

International Nuclear Information System (INIS)

Adetutu, Eric M.; Ball, Andy S.; Weber, John; Aleer, Samuel; Dandie, Catherine E.; Juhasz, Albert L.

2012-01-01

In this study, the impact of bacterial and fungal processes on 14 C-hexadecane mineralisation was investigated in weathered hydrocarbon contaminated soil. The extent of 14 C-hexadecane mineralisation varied depending on the bioremediation strategy employed. Under enhanced natural attenuation conditions, 14 C-hexadecane mineralisation after 98 days was 8.5 ± 3.7% compared to 14 C-hexadecane mineralisation was further enhanced through Tween 80 amendments (28.9 ± 2.4%) which also promoted the growth of a Phanerochaete chyrsosporium fungal mat. Although fungal growth in weathered hydrocarbon contaminated soil could be promoted through supplementing additional carbon sources (Tween 80, sawdust, compost, pea straw), fungal 14 C-hexadecane mineralisation was negligible when sodium azide was added to soil microcosms to inhibit bacterial activity. In contrast, when fungal activity was inhibited through nystatin additions, 14 C-hexadecane mineralisation ranged from 6.5 ± 0.2 to 35.8 ± 3.8% after 98 days depending on the supplied amendment. Bacteria inhibition with sodium azide resulted in a reduction in bacterial diversity (33–37%) compared to microcosms supplemented with nystatin or microcosms without inhibitory supplements. However, alkB bacterial groups were undetected in sodium azide supplemented microcosms, highlighting the important role of this bacterial group in 14 C-hexadecane mineralisation. - Highlights: ► The roles of different microbial groups in hydrocarbon mineralisation was assessed. ► Inhibiting fungal growth did not affect 14 C-hexadecane mineralisation. ► Inhibiting bacterial growth resulted in negligible 14 C-hexadecane mineralisation. ► alkB bacterial groups were undetected in sodium azide supplemented microcosms. ► The importance of alkB groups in 14 C-hexadecane mineralisation was highlighted.

Application of Multi-Source Remote Sensing Image in Yunnan Province Grassland Resources Investigation

Science.gov (United States)

Li, J.; Wen, G.; Li, D.

2018-04-01

Trough mastering background information of Yunnan province grassland resources utilization and ecological conditions to improves grassland elaborating management capacity, it carried out grassland resource investigation work by Yunnan province agriculture department in 2017. The traditional grassland resource investigation method is ground based investigation, which is time-consuming and inefficient, especially not suitable for large scale and hard-to-reach areas. While remote sensing is low cost, wide range and efficient, which can reflect grassland resources present situation objectively. It has become indispensable grassland monitoring technology and data sources and it has got more and more recognition and application in grassland resources monitoring research. This paper researches application of multi-source remote sensing image in Yunnan province grassland resources investigation. First of all, it extracts grassland resources thematic information and conducts field investigation through BJ-2 high space resolution image segmentation. Secondly, it classifies grassland types and evaluates grassland degradation degree through high resolution characteristics of Landsat 8 image. Thirdly, it obtained grass yield model and quality classification through high resolution and wide scanning width characteristics of MODIS images and sample investigate data. Finally, it performs grassland field qualitative analysis through UAV remote sensing image. According to project area implementation, it proves that multi-source remote sensing data can be applied to the grassland resources investigation in Yunnan province and it is indispensable method.

Degradation and mineralization of high-molecular-weight polycyclic aromatic hydrocarbons by defined fungal-bacterial cocultures

International Nuclear Information System (INIS)

Boonchan, S.; Britz, M.L.; Stanley, G.A.

2000-01-01

This study investigated the biodegradation of high-molecular-weight polycyclic aromatic hydrocarbons (PAHs) in liquid media and soil by bacteria (Stenotrophomonas maltophilia VUN 10,010 and bacterial consortium VUN 10,009) and a fungus (Penicillium janthinellum VUO 10,201) that were isolated from separate creosote- and manufactured-gas plant-contaminated soils. The bacteria could use pyrene as their sole carbon and energy source in a basal salts medium (BSM) and mineralized significant amounts of benzo[a]pyrene cometabolically when pyrene was also present in BSM. P. janthinellum VUO 10,201 could not utilize any high-molecular-weight PAH as sole carbon and energy source but could partially degrade these if cultured in a nutrient broth. Although small amounts of chrysene, benz[a]pyrene, and dibenz[a,h]anthracene were degraded by axenic cultures of these isolates in BSM containing a single PAH, such conditions did not support significant microbial growth or PAH mineralization. However, significant degradation of, and microbial growth on, pyrene, chrysene, benz[a]anthracene, benzo[a]pyrene, and dibenz[a,h]anthracene, each as a single PAH in BSM, occurred when P. janthinellum VUO 10,201 and either bacterial consortium VUN 10,009 or S. maltophilia VUN 10,010 were combined in the one culture, i.e., fungal-bacterial cocultures: 25% of the benzo[a]pyrene was mineralized to CO 2 by these cocultures over 49 days, accompanied by transient accumulation and disappearance of intermediates detected by high-pressure liquid chromatography. Inoculation of fungal-bacterial cocultures into PAH-contaminated soil resulted in significantly improved degradation of high-molecular-weight PAHs, benzo[a]pyrene mineralization, and reduction in the mutagenicity of organic soil extracts, compared with the indigenous microbes and soil amended with only axenic inocula

Emission sources and quantities

International Nuclear Information System (INIS)

Heinen, B.

1991-01-01

The paper examines emission sources and quantities for SO 2 and NO x . Natural SO 2 is released from volcanic sources and to a much lower extent from marsh gases. In nature NO x is mainly produced in the course of the chemical and bacterial denitrification processes going on in the soil. Manmade pollutants are produced in combustion processes. The paper concentrates on manmade pollution. Aspects discussed include: mechanism of pollution development; manmade emission sources (e.g. industry, traffic, power plants and domestic sources); and emission quantities and forecasts. 11 refs., 2 figs., 5 tabs

Evaluation of various pesticides-degrading pure bacterial cultures ...

African Journals Online (AJOL)

Due to the intensive use of pesticides within the greenhouse-rose production, remediation of polluted soils has become a hot topic for researchers in recent decades. Several bacterial strains having the ability to utilize various pesticides as a sole source of carbon and energy were isolated from pesticidecontaminated soils ...

Effect of Weak Magnetic Field on Bacterial Growth

Science.gov (United States)

Masood, Samina

Effects of weak magnetic fields are observed on the growth of various bacterial strains. Different sources of a constant magnetic field are used to demonstrate that ion transport in the nutrient broth and bacterial cellular dynamics is perturbed in the presence of weak magnetic field which affects the mobility and absorption of nutrients in cells and hence their doubling rate. The change is obvious after a few hours of exposure and keeps on increasing with time for all the observed species. The growth rate depends on the field strength and the nature of the magnetic field. The field effect varies with the shape and the structure of the bacterial cell wall as well as the concentration of nutrient broth. We closely study the growth of three species Escherichia coli, Pseudomonas aeruginosa and Staphylococcus epidermidis with the same initial concentrations at the same temperature in the same laboratory environment. Our results indicate that the weak static field of a few gauss after a few hours gives a measurable change in the growth rates of all bacterial species. This shows that the same magnetic field has different effects on different species in the same environment.

Utilization of Glyphosate as Phosphate Source: Biochemistry and Genetics of Bacterial Carbon-Phosphorus Lyase

Science.gov (United States)

Zechel, David L.; Jochimsen, Bjarne

2014-01-01

SUMMARY After several decades of use of glyphosate, the active ingredient in weed killers such as Roundup, in fields, forests, and gardens, the biochemical pathway of transformation of glyphosate phosphorus to a useful phosphorus source for microorganisms has been disclosed. Glyphosate is a member of a large group of chemicals, phosphonic acids or phosphonates, which are characterized by a carbon-phosphorus bond. This is in contrast to the general phosphorus compounds utilized and metabolized by microorganisms. Here phosphorus is found as phosphoric acid or phosphate ion, phosphoric acid esters, or phosphoric acid anhydrides. The latter compounds contain phosphorus that is bound only to oxygen. Hydrolytic, oxidative, and radical-based mechanisms for carbon-phosphorus bond cleavage have been described. This review deals with the radical-based mechanism employed by the carbon-phosphorus lyase of the carbon-phosphorus lyase pathway, which involves reactions for activation of phosphonate, carbon-phosphorus bond cleavage, and further chemical transformation before a useful phosphate ion is generated in a series of seven or eight enzyme-catalyzed reactions. The phn genes, encoding the enzymes for this pathway, are widespread among bacterial species. The processes are described with emphasis on glyphosate as a substrate. Additionally, the catabolism of glyphosate is intimately connected with that of aminomethylphosphonate, which is also treated in this review. Results of physiological and genetic analyses are combined with those of bioinformatics analyses. PMID:24600043

Bacterial Adhesion & Blocking Bacterial Adhesion

DEFF Research Database (Denmark)

Vejborg, Rebecca Munk

2008-01-01

, which influence the transition from a planktonic lifestyle to a sessile lifestyle, have been studied. Protein conditioning film formation was found to influence bacterial adhesion and subsequent biofilm formation considerable, and an aqueous extract of fish muscle tissue was shown to significantly...... tract to the microbial flocs in waste water treatment facilities. Microbial biofilms may however also cause a wide range of industrial and medical problems, and have been implicated in a wide range of persistent infectious diseases, including implantassociated microbial infections. Bacterial adhesion...... is the first committing step in biofilm formation, and has therefore been intensely scrutinized. Much however, still remains elusive. Bacterial adhesion is a highly complex process, which is influenced by a variety of factors. In this thesis, a range of physico-chemical, molecular and environmental parameters...

The Self-Taught Career Musician: Investigating Learning Sources and Experiences

Science.gov (United States)

Watson, Leah

2016-01-01

This article reports early findings from a qualitative study of 10 full-time musicians who are self-taught, to investigate their learning biographies. The aim is to identify, define and explore learning sources and experiences across the musician's learning biography. Conducted in Melbourne, Australia, the musicians were recruited through snowball…

Advances in high-order harmonic generation sources for time-resolved investigations

Energy Technology Data Exchange (ETDEWEB)

Reduzzi, Maurizio [Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano (Italy); Institute of Photonics and Nanotechnologies, CNR-IFN, Piazza Leonardo da Vinci 32, 20133 Milano (Italy); Carpeggiani, Paolo [Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano (Italy); Kühn, Sergei [ELI-ALPS, ELI-Hu Kft., Dugonics ter 13, H-6720 Szeged (Hungary); Calegari, Francesca [Institute of Photonics and Nanotechnologies, CNR-IFN, Piazza Leonardo da Vinci 32, 20133 Milano (Italy); Nisoli, Mauro; Stagira, Salvatore [Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano (Italy); Institute of Photonics and Nanotechnologies, CNR-IFN, Piazza Leonardo da Vinci 32, 20133 Milano (Italy); Vozzi, Caterina [Institute of Photonics and Nanotechnologies, CNR-IFN, Piazza Leonardo da Vinci 32, 20133 Milano (Italy); Dombi, Peter [ELI-ALPS, ELI-Hu Kft., Dugonics ter 13, H-6720 Szeged (Hungary); Wigner Research Center for Physics, 1121 Budapest (Hungary); Kahaly, Subhendu [ELI-ALPS, ELI-Hu Kft., Dugonics ter 13, H-6720 Szeged (Hungary); Tzallas, Paris; Charalambidis, Dimitris [ELI-ALPS, ELI-Hu Kft., Dugonics ter 13, H-6720 Szeged (Hungary); Foundation for Research and Technology – Hellas, Institute of Electronic Structure and Lasers, P.O. Box 1527, GR-711 10 Heraklion, Crete (Greece); Varju, Katalin [ELI-ALPS, ELI-Hu Kft., Dugonics ter 13, H-6720 Szeged (Hungary); Department of Optics and Quantum Electronics, University of Szeged, Dóm tér 9, 6720 Szeged (Hungary); Osvay, Karoly [ELI-ALPS, ELI-Hu Kft., Dugonics ter 13, H-6720 Szeged (Hungary); and others

2015-10-15

We review the main research directions ongoing in the development of extreme ultraviolet sources based on high-harmonic generation for the synthesization and application of trains and isolated attosecond pulses to time-resolved spectroscopy. A few experimental and theoretical works will be discussed in connection to well-established attosecond techniques. In this context, we present the unique possibilities offered for time-resolved investigations on the attosecond timescale by the new Extreme Light Infrastructure Attosecond Light Pulse Source, which is currently under construction.

Advances in high-order harmonic generation sources for time-resolved investigations

International Nuclear Information System (INIS)

Reduzzi, Maurizio; Carpeggiani, Paolo; Kühn, Sergei; Calegari, Francesca; Nisoli, Mauro; Stagira, Salvatore; Vozzi, Caterina; Dombi, Peter; Kahaly, Subhendu; Tzallas, Paris; Charalambidis, Dimitris; Varju, Katalin; Osvay, Karoly

2015-01-01

We review the main research directions ongoing in the development of extreme ultraviolet sources based on high-harmonic generation for the synthesization and application of trains and isolated attosecond pulses to time-resolved spectroscopy. A few experimental and theoretical works will be discussed in connection to well-established attosecond techniques. In this context, we present the unique possibilities offered for time-resolved investigations on the attosecond timescale by the new Extreme Light Infrastructure Attosecond Light Pulse Source, which is currently under construction.

Investigation of Grid-connected Voltage Source Converter Performance under Unbalanced Faults

DEFF Research Database (Denmark)

Jia, Jundi; Yang, Guangya; Nielsen, Arne Hejde

2016-01-01

Renewable energy sources (RES) and HVDC links are typically interfaced with the grid by power converters, whose performance during grid faults is significantly different from that of traditional synchronous generators. This paper investigates the performance of grid-connected voltage source...... that the performance of VSCs varies with their control strategies. Negative-sequence current control is necessary to restrict converter current in each phase under unbalanced faults. Among presented control strategies, the balanced current control strategy complies with the present voltage support requirement best...

Cadmium Bio sorption by Some Bacterial Isolates and Their Mutants Induced by gamma Radiation

International Nuclear Information System (INIS)

Tawfik, Z.S.; Elsonbaty, S.M.; Abdalla, N.M.

1999-01-01

Cadmium bio sorption by bacterial cells is recognized as a potential alternative to existing recovery technologies. Bacterial strains under investigation were isolated from air surrounding gamma industrial facility Co 60 source of the NCRRT, Cairo. The effect of different concentrations of cadmium on the growth was determined for the spore forming bacteria B.coagulans, B.megaterium, B.pumilus, B.pantothenticus, and also for Staphylo coccus aureus, the reference standard strain used in these study for comparison was B.subtilis MERK 10646. The results indicated that, B.pantothenticus was the most tolerant isolate, and it can resist up to 400 ppm. Cadmium capacity for B.subtilis parent strain was increased through the influence of different doses of gamma radiation, selected mutant of B.subtilis show enhanced level of cadmium accumulation. The effect of environmental parameters as ph, temperature and also the effect of biomass factor on cadmium uptake by B.pantothenticus and B.subtilis (m) was traced

Irrigation water quality in southern Mexico City based on bacterial and heavy metal analyses

International Nuclear Information System (INIS)

Solis, C.; Sandoval, J.; Perez-Vega, H.; Mazari-Hiriart, M.

2006-01-01

Xochimilco is located in southern Mexico City and represents the reminiscence of the pre-Columbian farming system, the 'chinampa' agriculture. 'Chinampas' are island plots surrounded by a canal network. At present the area is densely urbanized and populated, with various contaminant sources contributing to the water quality degradation. The canal system is recharged by a combination of treated-untreated wastewater, and precipitation during the rainy season. Over 40 agricultural species, including vegetables, cereals and flowers, are produced in the 'chinampas'. In order to characterize the quality of Xochimilcos' water used for irrigation, spatial and temporal contaminant indicators such as microorganisms and heavy metals were investigated. Bacterial indicators (fecal coliforms, fecal enterococcus) were analyzed by standard analytical procedures, and heavy metals (such as Fe, Cu, Zn and Pb) were analyzed by particle induced X-ray emission (PIXE). The more contaminated sites coincide with the heavily populated areas. Seasonal variation of contaminants was observed, with the higher bacterial counts and heavy metal concentrations reported during the rainy season

Irrigation water quality in southern Mexico City based on bacterial and heavy metal analyses

Science.gov (United States)

Solís, C.; Sandoval, J.; Pérez-Vega, H.; Mazari-Hiriart, M.

2006-08-01

Xochimilco is located in southern Mexico City and represents the reminiscence of the pre-Columbian farming system, the "chinampa" agriculture. "Chinampas" are island plots surrounded by a canal network. At present the area is densely urbanized and populated, with various contaminant sources contributing to the water quality degradation. The canal system is recharged by a combination of treated-untreated wastewater, and precipitation during the rainy season. Over 40 agricultural species, including vegetables, cereals and flowers, are produced in the "chinampas". In order to characterize the quality of Xochimilcos' water used for irrigation, spatial and temporal contaminant indicators such as microorganisms and heavy metals were investigated. Bacterial indicators (fecal coliforms, fecal enterococcus) were analyzed by standard analytical procedures, and heavy metals (such as Fe, Cu, Zn and Pb) were analyzed by particle induced X-ray emission (PIXE). The more contaminated sites coincide with the heavily populated areas. Seasonal variation of contaminants was observed, with the higher bacterial counts and heavy metal concentrations reported during the rainy season.

Evaluation of gastrointestinal bacterial population for the production of holocellulose enzymes for biomass deconstruction.

Science.gov (United States)

Asem, Dhaneshwaree; Leo, Vincent Vineeth; Passari, Ajit Kumar; Tonsing, Mary Vanlalhruaii; Joshi, J Beslin; Uthandi, Sivakumar; Hashem, Abeer; Abd Allah, Elsayed Fathi; Singh, Bhim Pratap

2017-01-01

The gastrointestinal (GI) habitat of ruminant and non-ruminant animals sustains a vast ensemble of microbes that are capable of utilizing lignocellulosic plant biomass. In this study, an indigenous swine (Zovawk) and a domesticated goat (Black Bengal) were investigated to isolate bacteria having plant biomass degrading enzymes. After screening and enzymatic quantification of eighty-one obtained bacterial isolates, Serratia rubidaea strain DBT4 and Aneurinibacillus aneurinilyticus strain DBT87 were revealed as the most potent strains, showing both cellulase and xylanase production. A biomass utilization study showed that submerged fermentation (SmF) of D2 (alkaline pretreated pulpy biomass) using strain DBT4 resulted in the most efficient biomass deconstruction with maximum xylanase (11.98 U/mL) and FPase (0.5 U/mL) activities (55°C, pH 8). The present study demonstrated that bacterial strains residing in the gastrointestinal region of non-ruminant swine are a promising source for lignocellulose degrading microorganisms that could be used for biomass conversion.

Evaluation of gastrointestinal bacterial population for the production of holocellulose enzymes for biomass deconstruction.

Directory of Open Access Journals (Sweden)

Dhaneshwaree Asem

Full Text Available The gastrointestinal (GI habitat of ruminant and non-ruminant animals sustains a vast ensemble of microbes that are capable of utilizing lignocellulosic plant biomass. In this study, an indigenous swine (Zovawk and a domesticated goat (Black Bengal were investigated to isolate bacteria having plant biomass degrading enzymes. After screening and enzymatic quantification of eighty-one obtained bacterial isolates, Serratia rubidaea strain DBT4 and Aneurinibacillus aneurinilyticus strain DBT87 were revealed as the most potent strains, showing both cellulase and xylanase production. A biomass utilization study showed that submerged fermentation (SmF of D2 (alkaline pretreated pulpy biomass using strain DBT4 resulted in the most efficient biomass deconstruction with maximum xylanase (11.98 U/mL and FPase (0.5 U/mL activities (55°C, pH 8. The present study demonstrated that bacterial strains residing in the gastrointestinal region of non-ruminant swine are a promising source for lignocellulose degrading microorganisms that could be used for biomass conversion.

Bacterial adherence to polymethylmethacrylate posterior chamber IOLs

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Tyagi Shalini

2001-01-01

Full Text Available Purpose: Bacterial adherence to intraocular lenses (IOLs has been incriminated in the pathogenesis of postoperative endophthalmitis. Staphylococcus epidermidis is the most common organism isolated. We studied the in-vitro adhesion of Staphylococcus epidermidis to Polymethylmethacrylate (PMMA IOLs and the effect of duration of exposure to adherence. Methods: Two groups of 10 IOLs each were incubated in Staphylococcus epidermidis suspension for 2 minutes and 20 minutes respectively. Adhesion of bacterial cells was determined by counting the number of viable bacteria attached to IOLs. Results: The mean bacterial adherence with 2 minutes incubation was 12,889 ± 7,150 bacteria / IOL and with 20 minutes incubation was 84,226 ± 35,024 bacteria/IOL (P< 0.01. Conclusion: Our results show that Staphylococcus epidermidis adheres to PMMA IOLs in vitro and the degree of adherence is less for shorter duration of exposure. We conclude that viable bacteria irreversibly adherent to IOLs may play a role in the pathogenesis of postoperative endophthalmitis. Shorter duration of operative manipulation and exposure to contaminating sources may decrease the chances of postoperative endophthalmitis.

A Straightforward Approach for 3D Bacterial Printing.

Science.gov (United States)

Lehner, Benjamin A E; Schmieden, Dominik T; Meyer, Anne S

2017-07-21

Sustainable and personally tailored materials production is an emerging challenge to society. Living organisms can produce and pattern an extraordinarily wide range of different molecules in a sustainable way. These natural systems offer an abundant source of inspiration for the development of new environmentally friendly materials production techniques. In this paper, we describe the first steps toward the 3-dimensional printing of bacterial cultures for materials production and patterning. This methodology combines the capability of bacteria to form new materials with the reproducibility and tailored approach of 3D printing systems. For this purpose, a commercial 3D printer was modified for bacterial systems, and new alginate-based bioink chemistry was developed. Printing temperature, printhead speed, and bioink extrusion rate were all adapted and customized to maximize bacterial health and spatial resolution of printed structures. Our combination of 3D printing technology with biological systems enables a sustainable approach for the production of numerous new materials.

The Bacterial Sequential Markov Coalescent.

Science.gov (United States)

De Maio, Nicola; Wilson, Daniel J

2017-05-01

Bacteria can exchange and acquire new genetic material from other organisms directly and via the environment. This process, known as bacterial recombination, has a strong impact on the evolution of bacteria, for example, leading to the spread of antibiotic resistance across clades and species, and to the avoidance of clonal interference. Recombination hinders phylogenetic and transmission inference because it creates patterns of substitutions (homoplasies) inconsistent with the hypothesis of a single evolutionary tree. Bacterial recombination is typically modeled as statistically akin to gene conversion in eukaryotes, i.e. , using the coalescent with gene conversion (CGC). However, this model can be very computationally demanding as it needs to account for the correlations of evolutionary histories of even distant loci. So, with the increasing popularity of whole genome sequencing, the need has emerged for a faster approach to model and simulate bacterial genome evolution. We present a new model that approximates the coalescent with gene conversion: the bacterial sequential Markov coalescent (BSMC). Our approach is based on a similar idea to the sequential Markov coalescent (SMC)-an approximation of the coalescent with crossover recombination. However, bacterial recombination poses hurdles to a sequential Markov approximation, as it leads to strong correlations and linkage disequilibrium across very distant sites in the genome. Our BSMC overcomes these difficulties, and shows a considerable reduction in computational demand compared to the exact CGC, and very similar patterns in simulated data. We implemented our BSMC model within new simulation software FastSimBac. In addition to the decreased computational demand compared to previous bacterial genome evolution simulators, FastSimBac provides more general options for evolutionary scenarios, allowing population structure with migration, speciation, population size changes, and recombination hotspots. FastSimBac is

Bioinformatic analysis reveals high diversity of bacterial genes for laccase-like enzymes.

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Luka Ausec

Full Text Available Fungal laccases have been used in various fields ranging from processes in wood and paper industries to environmental applications. Although a few bacterial laccases have been characterized in recent years, prokaryotes have largely been neglected as a source of novel enzymes, in part due to the lack of knowledge about the diversity and distribution of laccases within Bacteria. In this work genes for laccase-like enzymes were searched for in over 2,200 complete and draft bacterial genomes and four metagenomic datasets, using the custom profile Hidden Markov Models for two- and three-domain laccases. More than 1,200 putative genes for laccase-like enzymes were retrieved from chromosomes and plasmids of diverse bacteria. In 76% of the genes, signal peptides were predicted, indicating that these bacterial laccases may be exported from the cytoplasm, which contrasts with the current belief. Moreover, several examples of putatively horizontally transferred bacterial laccase genes were described. Many metagenomic sequences encoding fragments of laccase-like enzymes could not be phylogenetically assigned, indicating considerable novelty. Laccase-like genes were also found in anaerobic bacteria, autotrophs and alkaliphiles, thus opening new hypotheses regarding their ecological functions. Bacteria identified as carrying laccase genes represent potential sources for future biotechnological applications.

A kinetic Monte Carlo approach to investigate antibiotic translocation through bacterial porins

International Nuclear Information System (INIS)

Ceccarelli, Matteo; Ruggerone, Paolo; Vargiu, Attilio V

2012-01-01

Many relevant biological processes take place on time scales not reachable by standard all-atom computer simulations. The translocation of antibiotics through non-specific bacterial porins is an example. Microscopic effects compete to determine penetration routes and, consequently, free energy barriers to be overcome. Since bacteria can develop resistance to treatment also by reducing their antibiotic permeability, to understand the microscopic aspects of antibiotic translocation is an important step to rationalize drug design. Here, to investigate the translocation we propose a complete numerical model that combines the diffusion-controlled rate theory and a kinetic Monte Carlo scheme based on both experimental data and microscopically well-founded all-atom simulations. Within our model, an antibiotic translocating through an hour-glass-shaped channel can be described as a molecule moving on a potential of mean force featuring several affinity sites and a high central barrier. The implications of our results for the characterization of antibiotic translocation at in vivo concentrations are discussed. The presence of an affinity site close to the mouth of the channel seems to favor the translocation of antibiotics, the affinity site acting as a particle reservoir. Possible connections between results and the appearance of mutations in clinical strains are also outlined. (paper)

Perforation and bacterial contamination of microscope covers in lumbar spinal decompressive surgery.

Science.gov (United States)

Osterhoff, Georg; Spirig, José; Klasen, Jürgen; Kuster, Stefan P; Zinkernagel, Annelies S; Sax, Hugo; Min, Kan

2014-01-01

To determine the integrity of microscope covers and bacterial contamination at the end of lumbar spinal decompressive surgery. A prospective study of 25 consecutive lumbar spinal decompressions with the use of a surgical microscope was performed. For detection of perforations, the microscope covers were filled with water at the end of surgery and the presence of water leakage in 3 zones (objective, ocular and control panel) was examined. For detection of bacterial contamination, swabs were taken from the covers at the same locations before and after surgery. Among the 25 covers, 1 (4%) perforation was observed and no association between perforation and bacterial contamination was seen; 3 (4%) of 75 smears from the 25 covers showed post-operative bacterial contamination, i.e. 2 in the ocular zone and 1 in the optical zone, without a cover perforation. The incidence of microscope cover perforation was very low and was not shown to be associated with bacterial contamination. External sources of bacterial contamination seem to outweigh the problem of contamination due to failure of cover integrity. © 2014 S. Karger AG, Basel.

Bleeding Sap and Old Wood Are the Two Main Sources of Contamination of Merging Organs of Vine Plants by Xylophilus ampelinus, the Causal Agent of Bacterial Necrosis

OpenAIRE

Grall, S.; Roulland, C.; Guillaumès, J.; Manceau, C.

2005-01-01

The spatial distribution of vine plants contaminated by Xylophilus ampelinus, the agent responsible for bacterial necrosis, was studied over a 5-year period within two vineyards in the Cognac area. Both vineyards were planted with Vitis vinifera cv. Ugni blanc but were different in age and agronomic location. The emission of X. ampelinus in contaminated bleeding sap was observed during vine sprouting. Contaminated bleeding sap is an important source of inoculum for external contamination due ...

Molecular methods for bacterial genotyping and analyzed gene regions

Directory of Open Access Journals (Sweden)

İbrahim Halil Yıldırım1, Seval Cing Yıldırım2, Nadir Koçak3

2011-06-01

Full Text Available Bacterial strain typing is an important process for diagnosis, treatment and epidemiological investigations. Current bacterial strain typing methods may be classified into two main categories: phenotyping and genotyping. Phenotypic characters are the reflection of genetic contents. Genotyping, which refers discrimination of bacterial strains based on their genetic content, has recently become widely used for bacterial strain typing. The methods already used in genotypingof bacteria are quite different from each other. In this review we tried to summarize the basic principles of DNA-based methods used in genotyping of bacteria and describe some important DNA regions that are used in genotyping of bacteria. J Microbiol Infect Dis 2011;1(1:42-46.

Bacterial diversity in permanently cold and alkaline ikaite columns from Greenland.

Science.gov (United States)

Schmidt, Mariane; Priemé, Anders; Stougaard, Peter

2006-12-01

Bacterial diversity in alkaline (pH 10.4) and permanently cold (4 degrees C) ikaite tufa columns from the Ikka Fjord, SW Greenland, was investigated using growth characterization of cultured bacterial isolates with Terminal-restriction fragment length polymorphism (T-RFLP) and sequence analysis of bacterial 16S rRNA gene fragments. More than 200 bacterial isolates were characterized with respect to pH and temperature tolerance, and it was shown that the majority were cold-active alkaliphiles. T-RFLP analysis revealed distinct bacterial communities in different fractions of three ikaite columns, and, along with sequence analysis, it showed the presence of rich and diverse bacterial communities. Rarefaction analysis showed that the 109 sequenced clones in the 16S rRNA gene library represented between 25 and 65% of the predicted species richness in the three ikaite columns investigated. Phylogenetic analysis of the 16S rRNA gene sequences revealed many sequences with similarity to alkaliphilic or psychrophilic bacteria, and showed that 33% of the cloned sequences and 33% of the cultured bacteria showed less than 97% sequence identity to known sequences in databases, and may therefore represent yet unknown species.

Lake Bacterial Assemblage Composition Is Sensitive to Biological Disturbance Caused by an Invasive Filter Feeder.

Science.gov (United States)

Denef, Vincent J; Carrick, Hunter J; Cavaletto, Joann; Chiang, Edna; Johengen, Thomas H; Vanderploeg, Henry A

2017-01-01

One approach to improve forecasts of how global change will affect ecosystem processes is to better understand how anthropogenic disturbances alter bacterial assemblages that drive biogeochemical cycles. Species invasions are important contributors to global change, but their impacts on bacterial community ecology are rarely investigated. Here, we studied direct impacts of invasive dreissenid mussels (IDMs), one of many invasive filter feeders, on freshwater lake bacterioplankton. We demonstrated that direct effects of IDMs reduced bacterial abundance and altered assemblage composition by preferentially removing larger and particle-associated bacteria. While this increased the relative abundances of many free-living bacterial taxa, some were susceptible to filter feeding, in line with efficient removal of phytoplankton cells of <2 μm. This selective removal of particle-associated and larger bacteria by IDMs altered inferred bacterial functional group representation, defined by carbon and energy source utilization. Specifically, we inferred an increased relative abundance of chemoorganoheterotrophs predicted to be capable of rhodopsin-dependent energy generation. In contrast to the few previous studies that have focused on the longer-term combined direct and indirect effects of IDMs on bacterioplankton, our study showed that IDMs act directly as a biological disturbance to which freshwater bacterial assemblages are sensitive. The negative impacts on particle-associated bacteria, which have been shown to be more active than free-living bacteria, and the inferred shifts in functional group representation raise the possibility that IDMs may directly alter bacterially mediated ecosystem functions. IMPORTANCE Freshwater bacteria play fundamental roles in global elemental cycling and are an intrinsic part of local food webs. Human activities are altering freshwater environments, and much has been learned regarding the sensitivity of bacterial assemblages to a variety of

Glyphosate Shapes a Dinoflagellate-Associated Bacterial Community While Supporting Algal Growth as Sole Phosphorus Source

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Cong Wang

2017-12-01

Full Text Available Glyphosate is a widely used herbicide that can potentially be a phosphorus (P source for phytoplankton and microbes when discharged into the coastal ocean. In contrast to bacteria, few eukaryotic phytoplankton species appear capable of directly utilizing glyphosate. In this study, we observed, after a long delay (>60 days, Prorocentrum donghaiense, a dinoflagellate known to cause major harmful algal blooms in the East China Sea, could grow in a medium with glyphosate as the sole P source; suggesting that P. donghaiense growth was through bacterial mediation. To understand how the bacteria community might respond to glyphosate, we analyzed the 16S rRNA genes of the microbial community present in P. donghaiense cultures when grown under lower (36 μM and higher (360 μM glyphosate concentrations. Based on both Sanger and Illumina high throughput sequencing, we obtained more than 55,323 good-quality sequences, which were classified into six phyla. As the concentration of glyphosate rose, our results showed a significant increase in the phyla Proteobacteria and Firmicutes and a decrease in the phylum Bacteroidetes. Further qPCR (Quantitative PCR analysis showed higher abundances of two specific phylotypes in the higher-glyphosate P. donghaiense cultures when compared to the lower-glyphosate and no-glyphosate cultures. Correspondingly, qPCR displayed the same trend for the abundance of a gammaproteobacterial type of phnJ, a gene encoding Alpha-D-ribose 1-methylphosphonate 5-phosphate C-P lyase, which is responsible for phosphonate degradation. In addition, Tax4Fun analysis based on our 16S rRNA gene sequences results in higher predicted abundances of phosphonate metabolizing genes in glyphosate-treated cultures. This study demonstrates that glyphosate could selectively promote the growth of particular groups of bacteria within an algal culture and in glyphosate enriched coastal waters, this interaction may potentially further facilitate the growth of

PMAnalyzer: a new web interface for bacterial growth curve analysis.

Science.gov (United States)

Cuevas, Daniel A; Edwards, Robert A

2017-06-15

Bacterial growth curves are essential representations for characterizing bacteria metabolism within a variety of media compositions. Using high-throughput, spectrophotometers capable of processing tens of 96-well plates, quantitative phenotypic information can be easily integrated into the current data structures that describe a bacterial organism. The PMAnalyzer pipeline performs a growth curve analysis to parameterize the unique features occurring within microtiter wells containing specific growth media sources. We have expanded the pipeline capabilities and provide a user-friendly, online implementation of this automated pipeline. PMAnalyzer version 2.0 provides fast automatic growth curve parameter analysis, growth identification and high resolution figures of sample-replicate growth curves and several statistical analyses. PMAnalyzer v2.0 can be found at https://edwards.sdsu.edu/pmanalyzer/ . Source code for the pipeline can be found on GitHub at https://github.com/dacuevas/PMAnalyzer . Source code for the online implementation can be found on GitHub at https://github.com/dacuevas/PMAnalyzerWeb . dcuevas08@gmail.com. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

Investigations of the structure and function of bacterial communities associated with Sphagnum mosses.

Science.gov (United States)

Opelt, Katja; Chobot, Vladimir; Hadacek, Franz; Schönmann, Susan; Eberl, Leo; Berg, Gabriele

2007-11-01

High acidity, low temperature and extremely low concentration of nutrients form Sphagnum bogs into extreme habitats for organisms. Little is known about the bacteria associated with living Sphagnum plantlets, especially about their function for the host. Therefore, we analysed the endo- and ectophytic bacterial populations associated with two widely distributed Sphagnum species, Sphagnum magellanicum and Sphagnum fallax, by a multiphasic approach. The screening of 1222 isolates for antagonistic activity resulted in 326 active isolates. The bacterial communities harboured a high proportion of antifungal (26%) but a low proportion of antibacterial isolates (0.4%). Members of the genus Burkholderia (38%) were found to be the most dominant group of antagonistic bacteria. The finding that a large proportion (89%) of the antagonistic bacteria produced antifungal compounds may provide an explanation for the well-known antimicrobial activity of certain Sphagnum species. The secondary metabolites of the Sphagnum species themselves were analysed by HPLC-PDA. The different spectra of detected compounds may not only explain the antifungal activity but also the species specificity of the microbial communities. The latter was analysed using cultivation-independent single-stranded conformation polymorphism (SSCP) analysis. Using Burkholderia-specific primers we found a high diversity of Burkholderia isolates in the endophytic and ectophytic habitats of Sphagnum. Furthermore, a high diversity of nitrogen-fixing bacteria was detected by using nifH-specific primers, especially inside Sphagnum mosses. In conclusion, this study provides evidence that both Sphagnum species were colonized by characteristic bacterial populations, which appear to be important for pathogen defence and nitrogen fixation.

Biochemical fingerprinting of water coliform bacteria, a new method for measuring phenotypic diversity and for comparing different bacterial populations.

Science.gov (United States)

Kühn, I; Allestam, G; Stenström, T A; Möllby, R

1991-01-01

A simple, automated microplate system for biochemical characterization of water isolates can be used to obtain fingerprints of the bacterial flora from various water samples. Mathematical models for calculating the diversities and similarities between bacterial populations are described for such fingerprints. The diversity may give information on whether an indigenous or allochthonous flora is present, and the similarities between bacterial populations, as calculated by using a population similarity coefficient (Sp), may indicate contaminations between different water samples. The system was demonstrated on coliform bacterial populations from various water samples, with or without suspected intercontamination. For unrelated water samples, the Sps were close to 0, whereas repeated samples of the same source showed Sps of 0.64 to 0.74. The Sp values from several water samples were also clustered to form a dendrogram, thus indicating the relative similarities between the bacterial populations to confirm suspected common sources of pollution. PMID:1781680

Factors shaping bacterial phylogenetic and functional diversity in coastal waters of the NW Mediterranean Sea

Science.gov (United States)

Boras, Julia A.; Vaqué, Dolors; Maynou, Francesc; Sà, Elisabet L.; Weinbauer, Markus G.; Sala, Maria Montserrat

2015-03-01

To evaluate the main factors shaping bacterioplankton phylogenetic and functional diversity in marine coastal waters, we carried out a two-year study based on a monthly sampling in Blanes Bay (NW Mediterranean). We expected the key factors driving bacterial diversity to be (1) temperature and nutrient concentration, together with chlorophyll a concentration as an indicator of phytoplankton biomass and, hence, a carbon source for bacteria (here called bottom-up factors), and (2) top-down pressure (virus- and protist-mediated mortality of bacteria). Phylogenetic diversity was analyzed by denaturing gradient gel electrophoresis (DGGE) of 16S rRNA. Functional diversity was assessed by using monomeric carbon sources in Biolog EcoPlates and by determining the activity of six extracellular enzymes. Our results indicate that the bacterial phylogenetic and functional diversity in this coastal system is shaped mainly by bottom-up factors. A dendrogram analysis of the DGGE banding patterns revealed three main sample clusters. Two clusters differed significantly in temperature, nitrate and chlorophyll a concentration, and the third was characterized by the highest losses of bacterial production due to viral lysis detected over the whole study period. Protistan grazing had no effect on bacterial functional diversity, since there were no correlations between protist-mediated mortality (PMM) and extracellular enzyme activities, and utilization of only two out of the 31 carbon sources (N-acetyl-D-glucosamine and α-cyclodextrin) was correlated with PMM. In contrast, virus-mediated mortality correlated with changes in the percentage of use of four carbon sources, and also with specific leu-aminopeptidase and β-glucosidase activity. This suggests that viral lysate provides a pool of labile carbon sources, presumably including amino acids and glucose, which may inhibit proteolytic and glucosidic activity. Our results indicate that bottom-up factors play a more important role than

Analysis of bacterial communities and bacterial pathogens in a biogas plant by the combination of ethidium monoazide, PCR and Ion Torrent sequencing.

Science.gov (United States)

Luo, Gang; Angelidaki, Irini

2014-09-01

The present study investigated the changes of bacterial community composition including bacterial pathogens along a biogas plant, i.e. from the influent, to the biogas reactor and to the post-digester. The effects of post-digestion temperature and time on the changes of bacterial community composition and bacterial pathogens were also studied. Microbial analysis was made by Ion Torrent sequencing of the PCR amplicons from ethidium monoazide treated samples, and ethidium monoazide was used to cleave DNA from dead cells and exclude it from PCR amplification. Both similarity and taxonomic analysis showed that the bacterial community composition in the influent was changed after anaerobic digestion. Firmicutes were dominant in all the samples, while Proteobacteria decreased in the biogas reactor compared with the influent. Variations of bacterial community composition in the biogas reactor with time were also observed. This could be attributed to varying composition of the influent. Batch experiments showed that the methane recovery from the digested residues (obtained from biogas reactor) was mainly related with post-digestion temperature. However, post-digestion time rather than temperature had a significant effect on the changes of bacterial community composition. The changes of bacterial community composition were also reflected in the changes of relative abundance of bacterial pathogens. The richness and relative abundance of bacterial pathogens were reduced after anaerobic digestion in the biogas reactor. It was found in batch experiments that bacterial pathogens showed the highest relative abundance and richness after 30 days' post-digestion. Streptococcus bovis was found in all the samples. Our results showed that special attention should be paid to the post-digestion since the increase in relative abundance of bacterial pathogens after post-digestion might reflect regrowth of bacterial pathogens and limit biosolids disposal vectors. Copyright © 2014 Elsevier

Investigation of the source of residual phthalate in sundried salt.

Science.gov (United States)

Kim, Jin Hyo; Lee, Jin Hwan; Kim, So-Young

2014-03-01

Phthalate contamination in sundried salt has recently garnered interest in Korea. Phthalate concentrations were investigated in Korean sundried salts, source waters, and aqueous extracts from polyvinyl chloride materials used in salt ponds. Preliminary screening results for phthalates in Korean sundried salts revealed that only di(2-ethylhexyl)phthalate (DEHP) was over the limit of detection, with an 8.6% detection rate, and the concentration ranged from below the limit of detection to 0.189 mg/kg. The tolerable daily intake contribution ratio of the salt was calculated to be only 0.001%. Residual phthalates were below 0.026 mg/liter in source water, and the aqueous extracted di-n-butylphthalate, benzylbutylphthalate, and DEHP, which are considered endocrine disruptors, were below 0.029 mg/kg as derived from the polyvinyl chloride materials in salt ponds. The transfer ratios of the six phthalates from seawater to sundried salts were investigated; transfer ratio was correlated with vapor pressure (r(2) = 0.9875). Thus, di-n-butylphthalate, benzylbutylphthalate, DEHP, and di-n-octylphthalate can be considered highly likely residual pollutants in some consumer salts.

Death and cannibalism in a seasonal environment facilitate bacterial coexistence

NARCIS (Netherlands)

Rozen, D.E.; Philippe, N.; Visser, de J.A.G.M.; Lenski, R.E.; Schneider, D.

2009-01-01

Bacterial populations can evolve and adapt to become diverse niche specialists, even in seemingly homogeneous environments. One source of this diversity arises from newly 'constructed' niches that result from the activities of the bacteria themselves. Ecotypes specialized to exploit these distinct

Bacterial Cellulose Production from Beet Molasses | Keshk | African ...

African Journals Online (AJOL)

The yield of the bacterial cellulose (BC) produced from beet molasses was higher than that using glucose as a sole carbon source. The structure of BC produced in presence of beet molasses was studied using IR spectroscopy and X-ray diffractometry. IR spectra show the relative absorbance of CO- C ether linkage (at 1120 ...

Mitigation of methane emission from Holstein dairy cows: Effects of dietary manipulation on bacterial and methanogen communities

DEFF Research Database (Denmark)

Poulsen, Morten

2012-01-01

). Future demands for meat and milk are expected to increase, with concomitant increase in CH4 emissions to the atmosphere. Thus, reducing CH4 emission from ruminant production constitutes a massive challenge. Using in vitro rumen fluid fermentations and in vivo animal trials we investigated 1) effects...... of carbohydrate fermentation and pH on CH4 production and on bacterial community composition, and 2) effects of dietary manipulation (primarily through fat supplementation aiming at reducing enteric CH4 production) on community composition and activity of the rumen microbiota, with particular focus...... on methanogenic archaea. In vitro fermentations revealed that pH and carbohydrate source had only minor effects on the rumen bacterial community composition, but significantly affected volatile fatty acid production patterns. pH significantly affected CH4 emission from rumen fluid, with optimum CH4 production...

Phytoplankton-bacterial interactions mediate micronutrient colimitation at the coastal Antarctic sea ice edge.

Science.gov (United States)

Bertrand, Erin M; McCrow, John P; Moustafa, Ahmed; Zheng, Hong; McQuaid, Jeffrey B; Delmont, Tom O; Post, Anton F; Sipler, Rachel E; Spackeen, Jenna L; Xu, Kai; Bronk, Deborah A; Hutchins, David A; Allen, Andrew E

2015-08-11

Southern Ocean primary productivity plays a key role in global ocean biogeochemistry and climate. At the Southern Ocean sea ice edge in coastal McMurdo Sound, we observed simultaneous cobalamin and iron limitation of surface water phytoplankton communities in late Austral summer. Cobalamin is produced only by bacteria and archaea, suggesting phytoplankton-bacterial interactions must play a role in this limitation. To characterize these interactions and investigate the molecular basis of multiple nutrient limitation, we examined transitions in global gene expression over short time scales, induced by shifts in micronutrient availability. Diatoms, the dominant primary producers, exhibited transcriptional patterns indicative of co-occurring iron and cobalamin deprivation. The major contributor to cobalamin biosynthesis gene expression was a gammaproteobacterial population, Oceanospirillaceae ASP10-02a. This group also contributed significantly to metagenomic cobalamin biosynthesis gene abundance throughout Southern Ocean surface waters. Oceanospirillaceae ASP10-02a displayed elevated expression of organic matter acquisition and cell surface attachment-related genes, consistent with a mutualistic relationship in which they are dependent on phytoplankton growth to fuel cobalamin production. Separate bacterial groups, including Methylophaga, appeared to rely on phytoplankton for carbon and energy sources, but displayed gene expression patterns consistent with iron and cobalamin deprivation. This suggests they also compete with phytoplankton and are important cobalamin consumers. Expression patterns of siderophore- related genes offer evidence for bacterial influences on iron availability as well. The nature and degree of this episodic colimitation appear to be mediated by a series of phytoplankton-bacterial interactions in both positive and negative feedback loops.

Molecular Epidemiologic Typing Systems of Bacterial Pathogens: Current Issues and Perpectives

Directory of Open Access Journals (Sweden)

Struelens Marc J

1998-01-01

Full Text Available The epidemiologic typing of bacterial pathogens can be applied to answer a number of different questions: in case of outbreak, what is the extent and mode of transmission of epidemic clone(s ? In case of long-term surveillance, what is the prevalence over time and the geographic spread of epidemic and endemic clones in the population? A number of molecular typing methods can be used to classify bacteria based on genomic diversity into groups of closely-related isolates (presumed to arise from a common ancestor in the same chain of transmission and divergent, epidemiologically-unrelated isolates (arising from independent sources of infection. Ribotyping, IS-RFLP fingerprinting, macrorestriction analysis of chromosomal DNA and PCR-fingerprinting using arbitrary sequence or repeat element primers are useful methods for outbreak investigations and regional surveillance. Library typing systems based on multilocus sequence-based analysis and strain-specific probe hybridization schemes are in development for the international surveillance of major pathogens like Mycobacterium tuberculosis. Accurate epidemiological interpretation of data obtained with molecular typing systems still requires additional research on the evolution rate of polymorphic loci in bacterial pathogens.

A dynamic regression analysis tool for quantitative assessment of bacterial growth written in Python.

Science.gov (United States)

Hoeflinger, Jennifer L; Hoeflinger, Daniel E; Miller, Michael J

2017-01-01

Herein, an open-source method to generate quantitative bacterial growth data from high-throughput microplate assays is described. The bacterial lag time, maximum specific growth rate, doubling time and delta OD are reported. Our method was validated by carbohydrate utilization of lactobacilli, and visual inspection revealed 94% of regressions were deemed excellent. Copyright © 2016 Elsevier B.V. All rights reserved.

Assessment of self-organizing maps to analyze sole-carbon source utilization profiles.

Science.gov (United States)

Leflaive, Joséphine; Céréghino, Régis; Danger, Michaël; Lacroix, Gérard; Ten-Hage, Loïc

2005-07-01

The use of community-level physiological profiles obtained with Biolog microplates is widely employed to consider the functional diversity of bacterial communities. Biolog produces a great amount of data which analysis has been the subject of many studies. In most cases, after some transformations, these data were investigated with classical multivariate analyses. Here we provided an alternative to this method, that is the use of an artificial intelligence technique, the Self-Organizing Maps (SOM, unsupervised neural network). We used data from a microcosm study of algae-associated bacterial communities placed in various nutritive conditions. Analyses were carried out on the net absorbances at two incubation times for each substrates and on the chemical guild categorization of the total bacterial activity. Compared to Principal Components Analysis and cluster analysis, SOM appeared as a valuable tool for community classification, and to establish clear relationships between clusters of bacterial communities and sole-carbon sources utilization. Specifically, SOM offered a clear bidimensional projection of a relatively large volume of data and were easier to interpret than plots commonly obtained with multivariate analyses. They would be recommended to pattern the temporal evolution of communities' functional diversity.

Pyroprinting: a rapid and flexible genotypic fingerprinting method for typing bacterial strains.

Science.gov (United States)

Black, Michael W; VanderKelen, Jennifer; Montana, Aldrin; Dekhtyar, Alexander; Neal, Emily; Goodman, Anya; Kitts, Christopher L

2014-10-01

Bacterial strain typing is commonly employed in studies involving epidemiology, population ecology, and microbial source tracking to identify sources of fecal contamination. Methods for differentiating strains generally use either a collection of phenotypic traits or rely on some interrogation of the bacterial genotype. This report introduces pyroprinting, a novel genotypic strain typing method that is rapid, inexpensive, and discriminating compared to the most sensitive methods already in use. Pyroprinting relies on the simultaneous pyrosequencing of polymorphic multicopy loci, such as the intergenic transcribed spacer regions of rRNA operons in bacterial genomes. Data generated by sequencing combinations of variable templates are reproducible and intrinsically digitized. The theory and development of pyroprinting in Escherichia coli, including the selection of similarity thresholds to define matches between isolates, are presented. The pyroprint-based strain differentiation limits and phylogenetic relevance compared to other typing methods are also explored. Pyroprinting is unique in its simplicity and, paradoxically, in its intrinsic complexity. This new approach serves as an excellent alternative to more cumbersome or less phylogenetically relevant strain typing methods. Copyright © 2014 Elsevier B.V. All rights reserved.

Distinct Habitats Select Particular Bacterial Communities in Mangrove Sediments

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Lidianne L. Rocha

2016-01-01

Full Text Available We investigated the relationship among environmental variables, composition, and structure of bacterial communities in different habitats in a mangrove located nearby to an oil exploitation area, aiming to retrieve the natural pattern of bacterial communities in this ecosystem. The T-RFLP analysis showed a high diversity of bacterial populations and an increase in the bacterial richness from habitats closer to the sea and without vegetation (S1 to habitats covered by Avicennia schaueriana (S2 and Rhizophora mangle (S3. Environmental variables in S1 and S2 were more similar than in S3; however, when comparing the bacterial compositions, S2 and S3 shared more OTUs between them, suggesting that the presence of vegetation is an important factor in shaping these bacterial communities. In silico analyses of the fragments revealed a high diversity of the class Gammaproteobacteria in the 3 sites, although in general they presented quite different bacterial composition, which is probably shaped by the specificities of each habitat. This study shows that microhabitats inside of a mangrove ecosystem harbor diverse and distinct microbiota, reinforcing the need to conserve these ecosystems as a whole.

Distinct Habitats Select Particular Bacterial Communities in Mangrove Sediments

Science.gov (United States)

Rocha, Lidianne L.; Colares, Geórgia B.; Nogueira, Vanessa L. R.; Paes, Fernanda A.; Melo, Vânia M. M.

2016-01-01

We investigated the relationship among environmental variables, composition, and structure of bacterial communities in different habitats in a mangrove located nearby to an oil exploitation area, aiming to retrieve the natural pattern of bacterial communities in this ecosystem. The T-RFLP analysis showed a high diversity of bacterial populations and an increase in the bacterial richness from habitats closer to the sea and without vegetation (S1) to habitats covered by Avicennia schaueriana (S2) and Rhizophora mangle (S3). Environmental variables in S1 and S2 were more similar than in S3; however, when comparing the bacterial compositions, S2 and S3 shared more OTUs between them, suggesting that the presence of vegetation is an important factor in shaping these bacterial communities. In silico analyses of the fragments revealed a high diversity of the class Gammaproteobacteria in the 3 sites, although in general they presented quite different bacterial composition, which is probably shaped by the specificities of each habitat. This study shows that microhabitats inside of a mangrove ecosystem harbor diverse and distinct microbiota, reinforcing the need to conserve these ecosystems as a whole. PMID:26989418

Decolorization of azo dyes (Direct Blue 151 and Direct Red 31 by moderately alkaliphilic bacterial consortium

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Sylvine Lalnunhlimi

2016-03-01

Full Text Available Abstract Removal of synthetic dyes is one of the main challenges before releasing the wastes discharged by textile industries. Biodegradation of azo dyes by alkaliphilic bacterial consortium is one of the environmental-friendly methods used for the removal of dyes from textile effluents. Hence, this study presents isolation of a bacterial consortium from soil samples of saline environment and its use for the decolorization of azo dyes, Direct Blue 151 (DB 151 and Direct Red 31 (DR 31. The decolorization of azo dyes was studied at various concentrations (100–300 mg/L. The bacterial consortium, when subjected to an application of 200 mg/L of the dyes, decolorized DB 151 and DR 31 by 97.57% and 95.25% respectively, within 5 days. The growth of the bacterial consortium was optimized with pH, temperature, and carbon and nitrogen sources; and decolorization of azo dyes was analyzed. In this study, the decolorization efficiency of mixed dyes was improved with yeast extract and sucrose, which were used as nitrogen and carbon sources, respectively. Such an alkaliphilic bacterial consortium can be used in the removal of azo dyes from contaminated saline environment.

Could public restrooms be an environment for bacterial resistomes?

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Hermine V Mkrtchyan

Full Text Available Antibiotic resistance in bacteria remains a major problem and environments that help to maintain such resistance, represent a significant problem to infection control in the community. Restrooms have always been regarded as potential sources of infectious diseases and we suggest they have the potential to sustain bacterial "resistomes". Recent studies have demonstrated the wide range of different bacterial phyla that can be found in non-healthcare restrooms. In our study we focused on the Staphylococci. These species are often skin contaminants on man and have been reported as common restroom isolates in recent molecular studies. We collected samples from 18 toilets sited in 4 different public buildings. Using MALDI-TOF-MS and other techniques, we identified a wide range of antibiotic resistant Staphylococci and other bacteria from our samples. We identified 19 different Staphylococcal species within our isolates and 37.8% of the isolates were drug resistant. We also identified different Staphylococcal species with the same antibiograms inhabiting the same restrooms. Bacterial "resistomes" are communities of bacteria often localised in specific areas and within these environments drug resistance determinants may be freely transferred. Our study shows that non-healthcare restrooms are a source of antibiotic resistant bacteria where a collection of antibiotic resistance genes in pathogenic and non-pathogenic bacteria could form a resistome containing a "nexus of genetic diversity"

Studies on bacterial flora and biological control agent of Cydia ...

African Journals Online (AJOL)

In the present study, in order to find a more effective and safe biological control agent against Cydia pomonella, we investigated the bacterial flora and tested them for insecticidal effects on this insect. According to morphological, physiological and biochemical tests, bacterial flora were identified as Proteus rettgeri (Cp1), ...

Effect of selected essential oil plants on bacterial wilt disease ...

African Journals Online (AJOL)

Objective: Bacterial wilt disease caused by Ralstonia solanacearum is a major constrain to production of potatoes (Solanum tuberosum). Control of bacterial wilt is very difficult as there are no effective curative chemicals. This study was aimed at investigating the potential roles of essential oil plants in control of the disease.

Impact of bacterial and fungal processes on {sup 14}C-hexadecane mineralisation in weathered hydrocarbon contaminated soil

Energy Technology Data Exchange (ETDEWEB)

Adetutu, Eric M.; Ball, Andy S. [School of Biological Sciences, Flinders University, Adelaide, South Australia, 5001 (Australia); Weber, John; Aleer, Samuel; Dandie, Catherine E. [Centre for Environmental Risk Assessment and Remediation (CERAR), University of South Australia, Mawson Lakes Campus, Adelaide, South Australia, 5095 (Australia); Cooperative Research Centre for Contamination Assessment and Remediation of the Environment (CRC CARE), Mawson Lakes, Adelaide, South Australia, 5095 (Australia); Juhasz, Albert L., E-mail: Albert.Juhasz@unisa.edu.au [Centre for Environmental Risk Assessment and Remediation (CERAR), University of South Australia, Mawson Lakes Campus, Adelaide, South Australia, 5095 (Australia); Cooperative Research Centre for Contamination Assessment and Remediation of the Environment (CRC CARE), Mawson Lakes, Adelaide, South Australia, 5095 (Australia)

2012-01-01

In this study, the impact of bacterial and fungal processes on {sup 14}C-hexadecane mineralisation was investigated in weathered hydrocarbon contaminated soil. The extent of {sup 14}C-hexadecane mineralisation varied depending on the bioremediation strategy employed. Under enhanced natural attenuation conditions, {sup 14}C-hexadecane mineralisation after 98 days was 8.5 {+-} 3.7% compared to < 1.2% without nitrogen and phosphorus additions. {sup 14}C-hexadecane mineralisation was further enhanced through Tween 80 amendments (28.9 {+-} 2.4%) which also promoted the growth of a Phanerochaete chyrsosporium fungal mat. Although fungal growth in weathered hydrocarbon contaminated soil could be promoted through supplementing additional carbon sources (Tween 80, sawdust, compost, pea straw), fungal {sup 14}C-hexadecane mineralisation was negligible when sodium azide was added to soil microcosms to inhibit bacterial activity. In contrast, when fungal activity was inhibited through nystatin additions, {sup 14}C-hexadecane mineralisation ranged from 6.5 {+-} 0.2 to 35.8 {+-} 3.8% after 98 days depending on the supplied amendment. Bacteria inhibition with sodium azide resulted in a reduction in bacterial diversity (33-37%) compared to microcosms supplemented with nystatin or microcosms without inhibitory supplements. However, alkB bacterial groups were undetected in sodium azide supplemented microcosms, highlighting the important role of this bacterial group in {sup 14}C-hexadecane mineralisation. - Highlights: Black-Right-Pointing-Pointer The roles of different microbial groups in hydrocarbon mineralisation was assessed. Black-Right-Pointing-Pointer Inhibiting fungal growth did not affect {sup 14}C-hexadecane mineralisation. Black-Right-Pointing-Pointer Inhibiting bacterial growth resulted in negligible {sup 14}C-hexadecane mineralisation. Black-Right-Pointing-Pointer alkB bacterial groups were undetected in sodium azide supplemented microcosms. Black

Influence of the Biliary System on Biliary Bacteria Revealed by Bacterial Communities of the Human Biliary and Upper Digestive Tracts.

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Fuqiang Ye

Full Text Available Biliary bacteria have been implicated in gallstone pathogenesis, though a clear understanding of their composition and source is lacking. Moreover, the effects of the biliary environment, which is known to be generally hostile to most bacteria, on biliary bacteria are unclear. Here, we investigated the bacterial communities of the biliary tract, duodenum, stomach, and oral cavity from six gallstone patients by using 16S rRNA amplicon sequencing. We found that all observed biliary bacteria were detectable in the upper digestive tract. The biliary microbiota had a comparatively higher similarity with the duodenal microbiota, versus those of the other regions, but with a reduced diversity. Although the majority of identified bacteria were greatly diminished in bile samples, three Enterobacteriaceae genera (Escherichia, Klebsiella, and an unclassified genus and Pyramidobacter were abundant in bile. Predictive functional analysis indicated enhanced abilities of environmental information processing and cell motility of biliary bacteria. Our study provides evidence for the potential source of biliary bacteria, and illustrates the influence of the biliary system on biliary bacterial communities.

An investigation of the closure problem applied to reactor accident source terms

International Nuclear Information System (INIS)

Brearley, I.R.; Nixon, W.; Hayns, M.R.

1987-01-01

The closure problem, as considered here, focuses attention on the question of when in current research programmes enough has been learned about the source terms for reactor accident releases. Noting that current research is tending to reduce the estimated magnitude of the aerosol component of atmospheric, accidental releases, several possible criteria for closure are suggested. Moreover, using the reactor accident consequence model CRACUK, the effect of gradually reducing the aerosol release fractions of a pressurized water reactor (PWR2) source term (as defined in the WASH-1400 study) is investigated and the implications of applying the suggested criteria to current source term research discussed. (author)

Molecular Analysis of Bacterial Microbiota on Brazilian Currency Note Surfaces

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Tairacan Augusto Pereira da Fonseca

2015-10-01

Full Text Available Currency notes have been implicated as a vehicle for transmitting community-acquired bacterial infections. However, the overall diversity of the bacterial population residing on banknotes is still unknown in Brazil. In this study, we aimed to investigate the overall bacterial population from 150 different Brazilian Rial (R$ notes in circulation using a culture-independent Illumina massively parallel sequencing approach of the 16S rRNA genes. Samples were randomly collected from three different street markets or “feiras” in the metropolitan region of São Paulo. Taxonomical composition revealed the abundance of Proteobacteria phyla, followed by Firmicutes and Streptophyta, with a total of 1193 bacterial families and 3310 bacterial genera. Most of these bacterial genera are of human, animal, and environmental origins. Also, our analysis revealed the presence of some potential pathogenic bacterial genera including Salmonella, Staphylococcus, and Klebsiella. The results demonstrate that there is a tremendous diversity of bacterial contamination on currency notes, including organisms known to be opportunistic pathogens. One of the factors that may contribute to the richness of bacterial diversity in currency notes is personal hygiene. Thus, our results underscore the need to increase public awareness of the importance of personal hygiene of money handlers who also handle food.

Molecular Analysis of Bacterial Microbiota on Brazilian Currency Note Surfaces.

Science.gov (United States)

Pereira da Fonseca, Tairacan Augusto; Pessôa, Rodrigo; Sanabani, Sabri Saeed

2015-10-22

Currency notes have been implicated as a vehicle for transmitting community-acquired bacterial infections. However, the overall diversity of the bacterial population residing on banknotes is still unknown in Brazil. In this study, we aimed to investigate the overall bacterial population from 150 different Brazilian Rial (R$) notes in circulation using a culture-independent Illumina massively parallel sequencing approach of the 16S rRNA genes. Samples were randomly collected from three different street markets or "feiras" in the metropolitan region of São Paulo. Taxonomical composition revealed the abundance of Proteobacteria phyla, followed by Firmicutes and Streptophyta, with a total of 1193 bacterial families and 3310 bacterial genera. Most of these bacterial genera are of human, animal, and environmental origins. Also, our analysis revealed the presence of some potential pathogenic bacterial genera including Salmonella, Staphylococcus, and Klebsiella. The results demonstrate that there is a tremendous diversity of bacterial contamination on currency notes, including organisms known to be opportunistic pathogens. One of the factors that may contribute to the richness of bacterial diversity in currency notes is personal hygiene. Thus, our results underscore the need to increase public awareness of the importance of personal hygiene of money handlers who also handle food.

Towards Spectral Library-free MALDI-TOF MS Bacterial Identification.

Science.gov (United States)

Cheng, Ding; Qiao, Liang; Horvatovich, Péter

2018-05-11

Bacterial identification is of great importance in clinical diagnosis, environmental monitoring and food safety control. Among various strategies, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has drawn significant interests, and has been clinically used. Nevertheless, current bioinformatics solutions use spectral libraries for the identification of bacterial strains. Spectral library generation requires acquisition of MALDI-TOF spectra from monoculture bacterial colonies, which is time-consuming and not possible for many species and strains. We propose a strategy for bacterial typing by MALDI-TOF using protein sequences from public database, i.e. UniProt. Ten genes were identified to encode proteins most often observed by MALD-TOF from bacteria through 500 times repeated a 10-fold double cross-validation procedure, using 403 MALDI-TOF spectra corresponding to 14 genera, 81 species and 403 strains, and the protein sequences of 1276 species in UniProt. The 10 genes were then used to annotate peaks on MALDI-TOF spectra of bacteria for bacterial identification. With the approach, bacteria can be identified at the genus level by searching against a database containing the protein sequences of 42 genera of bacteria from UniProt. Our approach identified 84.1% of the 403 spectra correctly at the genus level. Source code of the algorithm is available at https://github.com/dipcarbon/BacteriaMSLF.

Structural transformations of heat-treated bacterial iron oxide

Energy Technology Data Exchange (ETDEWEB)

Hashimoto, Hideki, E-mail: hideki-h@cc.okayama-u.ac.jp [Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530 (Japan); JST, CREST, Okayama 700-8530 (Japan); Fujii, Tatsuo [Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530 (Japan); Kohara, Shinji [Japan Synchrotron Radiation Research Institute, Sayo, Hyogo 679-5198 (Japan); Nakanishi, Koji [Office of Society-Academia Collaboration for Innovation, Kyoto University, Uji 611-0011 (Japan); Yogi, Chihiro [SR Center, Ritsumeikan University, Kusatsu, Shiga 525-8577 (Japan); Peterlik, Herwig [Faculty of Physics, University of Vienna, A-1090 Vienna (Austria); Nakanishi, Makoto [Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530 (Japan); Takada, Jun [Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530 (Japan); JST, CREST, Okayama 700-8530 (Japan)

2015-04-01

A bacterial siliceous iron oxide microtubule (diameter: ca. 1 μm, 15Fe{sub 2}O{sub 3}·8SiO{sub 2}·P{sub 2}O{sub 5}·30H{sub 2}O) produced by Leptothrix ochracea was heat treated in air and its structural transformation was investigated in detail by microscopy, diffractometry, and spectroscopy. Although the heat-treated bacterial iron oxide retained its original microtubular structure, its nanoscopic, middle-range, and local structures changed drastically. Upon heat treatment, nanosized pores were formed and their size changed depending on temperature. The Fe–O–Si linkages were gradually cleaved with increasing temperature, causing the progressive separation of Fe and Si ions into iron oxide and amorphous silicate phases, respectively. Concomitantly, global connectivity and local structure of FeO{sub 6} octahedra in the iron oxide nanoparticles systematically changed depending on temperature. These comprehensive investigations clearly revealed various structural changes of the bacterial iron oxide which is an important guideline for the future exploration of novel bio-inspired materials. - Highlights: • Structural transformation of a bacterial iron oxide microtubule was investigated. • Si–O–Fe was cleaved with increasing temperature to form α-Fe{sub 2}O{sub 3}/silicate composite. • Crystallization to 2Fh started at 500 °C to give α-Fe{sub 2}O{sub 3} >700 °C. • FeO{sub 6} octahedra were highly distorted <500 °C. • Formation of face-sharing FeO{sub 6} was promoted >500 °C, releasing the local strain of FeO{sub 6}.

Dispersal networks for enhancing bacterial degradation in heterogeneous environments

International Nuclear Information System (INIS)

Banitz, Thomas; Wick, Lukas Y.; Fetzer, Ingo; Frank, Karin; Harms, Hauke; Johst, Karin

2011-01-01

Successful biodegradation of organic soil pollutants depends on their bioavailability to catabolically active microorganisms. In particular, environmental heterogeneities often limit bacterial access to pollutants. Experimental and modelling studies revealed that fungal networks can facilitate bacterial dispersal and may thereby improve pollutant bioavailability. Here, we investigate the influence of such bacterial dispersal networks on biodegradation performance under spatially heterogeneous abiotic conditions using a process-based simulation model. To match typical situations in polluted soils, two types of abiotic conditions are studied: heterogeneous bacterial dispersal conditions and heterogeneous initial resource distributions. The model predicts that networks facilitating bacterial dispersal can enhance biodegradation performance for a wide range of these conditions. Additionally, the time horizon over which this performance is assessed and the network's spatial configuration are key factors determining the degree of biodegradation improvement. Our results support the idea of stimulating the establishment of fungal mycelia for enhanced bioremediation of polluted soils. - Highlights: → Bacterial dispersal networks can considerably improve biodegradation performance. → They facilitate bacterial access to dispersal-limited areas and remote resources. → Abiotic conditions, time horizon and network structure govern the improvements. → Stimulating the establishment of fungal mycelia promises enhanced soil remediation. - Simulation modelling demonstrates that fungus-mediated bacterial dispersal can considerably improve the bioavailability of organic pollutants under spatially heterogeneous abiotic conditions typical for water-unsaturated soils.

Dispersal networks for enhancing bacterial degradation in heterogeneous environments

Energy Technology Data Exchange (ETDEWEB)

Banitz, Thomas, E-mail: thomas.banitz@ufz.de [Department of Ecological Modelling, UFZ - Helmholtz Centre for Environmental Research, Permoserstr. 15, 04318 Leipzig (Germany); Wick, Lukas Y.; Fetzer, Ingo [Department of Environmental Microbiology, UFZ - Helmholtz Centre for Environmental Research, Permoserstr. 15, 04318 Leipzig (Germany); Frank, Karin [Department of Ecological Modelling, UFZ - Helmholtz Centre for Environmental Research, Permoserstr. 15, 04318 Leipzig (Germany); Harms, Hauke [Department of Environmental Microbiology, UFZ - Helmholtz Centre for Environmental Research, Permoserstr. 15, 04318 Leipzig (Germany); Johst, Karin [Department of Ecological Modelling, UFZ - Helmholtz Centre for Environmental Research, Permoserstr. 15, 04318 Leipzig (Germany)

2011-10-15

Successful biodegradation of organic soil pollutants depends on their bioavailability to catabolically active microorganisms. In particular, environmental heterogeneities often limit bacterial access to pollutants. Experimental and modelling studies revealed that fungal networks can facilitate bacterial dispersal and may thereby improve pollutant bioavailability. Here, we investigate the influence of such bacterial dispersal networks on biodegradation performance under spatially heterogeneous abiotic conditions using a process-based simulation model. To match typical situations in polluted soils, two types of abiotic conditions are studied: heterogeneous bacterial dispersal conditions and heterogeneous initial resource distributions. The model predicts that networks facilitating bacterial dispersal can enhance biodegradation performance for a wide range of these conditions. Additionally, the time horizon over which this performance is assessed and the network's spatial configuration are key factors determining the degree of biodegradation improvement. Our results support the idea of stimulating the establishment of fungal mycelia for enhanced bioremediation of polluted soils. - Highlights: > Bacterial dispersal networks can considerably improve biodegradation performance. > They facilitate bacterial access to dispersal-limited areas and remote resources. > Abiotic conditions, time horizon and network structure govern the improvements. > Stimulating the establishment of fungal mycelia promises enhanced soil remediation. - Simulation modelling demonstrates that fungus-mediated bacterial dispersal can considerably improve the bioavailability of organic pollutants under spatially heterogeneous abiotic conditions typical for water-unsaturated soils.

[Studies on the repair of damaged DNA in bacteriophage, bacterial and mammalian systems]: Final report

International Nuclear Information System (INIS)

Friedberg, E.C.

1987-08-01

This study sought to exploit the use of uv radiation as a source of genomic damage. We explored the molecular mechanism of the repair of DNA damage at a number of different levels of biological organization, by investigating bacteriophage, bacterial, yeast and mammalian cells. Not only have observations obtained in one biological system suggested specific experimental approaches in others, but we have also learned that some biochemical pathways for DNA repair are unique to specific organisms. Our studies are summarized in terms of 4 major areas of research activity that span the past 16 years. 86 refs

Production of bacterial protein from sugar cane bagasse pith

Energy Technology Data Exchange (ETDEWEB)

Molina, O E; Callieri, D A.S.; Perotti de Galvez, N

1980-01-01

Bacterial protein was produced during the fermentation of sugar cane bagasse pith (BP) by a mixture of cellulolytic bacteria, one of them being a species of Cellulomonas. If the BP were treated with 1% NaOH prior to fermentation, the liquor could be used twice more without affecting the yield of bacterial protein. After that, the liquor became too dark and impaired the subsequent washing of BP. If the concentration of N (as NaN0/sub 3/) in the fermentation medium were raised, the conversion factor to protein was lowered, but the amount of protein formed per L per h and the ratio of protein to BP became higher. The evolution of pH, the dry matter content, cellulolytic activity, and protein yield were all affected by the type of N source used. The yield of bacterial protein can probably be increased by automatically controlling the pH and dissolved O levels of the culture.

Investigations into the Optimization of Multi-Source Strength Brachytherapy Treatment Procedures

International Nuclear Information System (INIS)

Henderson, D. L.; Yoo, S.; Thomadsen, B.R.

2002-01-01

The goal of this project is to investigate the use of multi-strength and multi-specie radioactive sources in permanent prostate implant brachytherapy. In order to fulfill the requirement for an optimal dose distribution, the prescribed dose should be delivered to the target in a nearly uniform dose distribution while simultaneously sparing sensitive structures. The treatment plan should use a small number of needles and sources while satisfying the treatment requirements. The hypothesis for the use of multi-strength and/or multi-specie sources is that a better treatment plan using fewer sources and needles could be obtained than by treatment plans using single-strength sources could reduce the overall number of sources used for treatment. We employ a recently developed greedy algorithm based on the adjoint concept as the optimization search engine. The algorithm utilizes and ''adjoint ratio'', which provides a means of ranking source positions, as the pseudo-objective function. It ha s been shown that the greedy algorithm can solve the optimization problem efficiently and arrives at a clinically acceptable solution in less than 10 seconds. Our study was inclusive, that is there was no combination of sources that clearly stood out from the others and could therefore be considered the preferred set of sources for treatment planning. Source strengths of 0.2 mCi (low), 0.4 mCi (medium), and 0.6 mCi (high) of 125 I in four different combinations were used for the multi-strength source study. The combination of high- and medium-strength sources achieved a more uniform target dose distribution due to few source implants whereas the combination of low-and medium-strength sources achieved better sparing of sensitive tissues including that of the single-strength 0.4 mCi base case. 125 I at 0.4 mCi and 192 Ir at 0.12 mCi and 0.25 mCi source strengths were used for the multi-specie source study. This study also proved inconclusive , Treatment plans using a combination of two 0

Description of a novel approach to engineer cartilage with porous bacterial nanocellulose for reconstruction of a human auricle.

Science.gov (United States)

Feldmann, Eva-Maria; Sundberg, J F; Bobbili, B; Schwarz, S; Gatenholm, P; Rotter, N

2013-11-01

In this study, we investigated the effects of human primary chondrocytes, derived from routine septorhino- and otoplasties on a novel nondegradable biomaterial. This biomaterial, porous bacterial nanocellulose, is produced by Gluconacetobacter xylinus. Porosity is generated by paraffin beads embedded during the fermentation process. Human primary chondrocytes were able to adhere to bacterial nanocellulose and produce cartilaginous matrix proteins such as aggrecan (after 14 days) and collagen type II (after 21 days) in the presence of differentiation medium. Cells were located within the pores and in a dense cell layer covering the surface of the biomaterial. Cells were able to re-differentiate, as cell shape and extra cellular matrix gene expression showed a chondrogenic phenotype in three-dimensional bacterial nanocellulose culture. Collagen type I and versican expression decreased during three-dimensional culture. Variations in pore sizes of 150-300 µm and 300-500 µm did not influence cartilaginous extra cellular matrix synthesis. Varying seeding densities from 9.95 × 10(2) to 1.99 × 10(3) cells/mm(2) and 3.98 × 10(3) cells/mm(2) did not result in differences in quality of extra cellular matrix neo-synthesis. Our results demonstrated that both nasal and auricular chondrocytes are equally suitable to synthesize new extra cellular matrix on bacterial nanocellulose. Therefore, we propose both cell sources in combination with bacterial nanocellulose as promising candidates for the special needs of auricular reconstruction.

Molecular mechanisms of action of bacterial exotoxins.

Science.gov (United States)

Balfanz, J; Rautenberg, P; Ullmann, U

1996-07-01

Toxins are one of the inventive strategies that bacteria have developed in order to survive. As virulence factors, they play a major role in the pathogenesis of infectious diseases. Recent discoveries have once more highlighted the effectiveness of these precisely adjusted bacterial weapons. Furthermore, toxins have become an invaluable tool in the investigation of fundamental cell processes, including regulation of cellular functions by various G proteins, cytoskeletal dynamics and neural transmission. In this review, the bacterial toxins are presented in a rational classification based on the molecular mechanisms of action.

Occurrence of Antibiotic Resistance Genes and Bacterial Markers in a Tropical River Receiving Hospital and Urban Wastewaters.

Directory of Open Access Journals (Sweden)

Naresh Devarajan

Full Text Available The occurrence of emerging biological contaminants including antibiotic resistance genes (ARGs and Faecal Indicator Bacteria (FIB is still little investigated in developing countries under tropical conditions. In this study, the total bacterial load, the abundance of FIB (E. coli and Enterococcus spp. (ENT, Pseudomonas spp. and ARGs (blaTEM, blaCTX-M, blaSHV, blaNDM and aadA were quantified using quantitative PCR in the total DNA extracted from the sediments recovered from hospital outlet pipes (HOP and the Cauvery River Basin (CRB, Tiruchirappalli, Tamil Nadu, India. The abundance of bacterial marker genes were 120, 104 and 89 fold higher for the E. coli, Enterococcus spp. and Pseudomonas spp., respectively at HOP when compared with CRB. The ARGs aadA and blaTEM were most frequently detected in higher concentration than other ARGs at all the sampling sites. The ARGs blaSHV and blaNDM were identified in CRB sediments contaminated by hospital and urban wastewaters. The ARGs abundance strongly correlated (r ≥ 0.36, p < 0.05, n = 45 with total bacterial load and E. coli in the sediments, indicating a common origin and extant source of contamination. Tropical aquatic ecosystems receiving wastewaters can act as reservoir of ARGs, which could potentially be transferred to susceptible bacterial pathogens at these sites.

Investigation of bacterial diversity of hot springs of Odisha, India

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Rajesh Kumar Sahoo

2015-12-01

Full Text Available 16S rRNA deep sequencing analysis, targeting V3 region was performed using Illumina bar coded sequencing. Sediment samples from two hot springs (Atri and Taptapani were collected. Atri and Taptapani metagenomes were classified into 50 and 51 bacterial phyla. Proteobacteria (45.17% dominated the Taptapani sample metagenome followed by Bacteriodetes (23.43% and Cyanobacteria (10.48% while in the Atri sample, Chloroflexi (52.39%, Nitrospirae (10.93% and Proteobacteria (9.98% dominated. A large number of sequences remained taxonomically unresolved in both hot springs, indicating the presence of potentially novel microbes in these two unique habitats thus unraveling the importance of the current study. Metagenome sequence information is now available at NCBI, SRA database accession no. SRP057428.

Bacterial levels in the Nyl River system, Limpopo province, South ...

African Journals Online (AJOL)

Heterotrophic plate counts, faecal coliform counts and total coliform counts indicated that the system was stressed. The Modimolle sewage treatment works and local agricultural activities were found to be the point and diffuse sources of bacterial contamination, respectively. African Journal of Aquatic Science 2010, 35(1): ...

Bacterial polyhydroxyalkanoates: Still fabulous?

Science.gov (United States)

Możejko-Ciesielska, Justyna; Kiewisz, Robert

2016-11-01

Bacterial polyhydroxyalkanoates (PHA) are polyesters accumulated as carbon and energy storage materials under limited growth conditions in the presence of excess carbon sources. They have been developed as biomaterials with unique properties for the past many years being considered as a potential substitute for conventional non-degradable plastics. Due to the increasing concern towards global climate change, depleting petroleum resource and problems with an utilization of a growing number of synthetic plastics, PHAs have gained much more attention from industry and research. These environmentally friendly microbial polymers have great potential in biomedical, agricultural, and industrial applications. However, their production on a large scale is still limited. This paper describes the backgrounds of PHAs and discussed the current state of knowledge on the polyhydroxyalkanoates. Ability of bacteria to convert different carbon sources to PHAs, the opportunities and challenges of their introduction to global market as valuable renewable products have been also discussed. Copyright © 2016 Elsevier GmbH. All rights reserved.

Isolation, Characterization and Application of Bacterial Population From Agricultural Soil at Sohag Province, Egypt

Directory of Open Access Journals (Sweden)

Bahig, A. E.

2008-01-01

Full Text Available Forty soil samples of agriculture soil were collected from two different sites in Sohag province, Egypt, during hot and cold seasons. Twenty samples were from soil irrigated with canal water (site A and twenty samples were from soil irrigated with wastewater (site B. This study aimed to compare the incidence of plasmids in bacteria isolated from soil and to investigate the occurrence of metal and antibiotic resistance bacteria, and consequently to select the potential application of these bacteria in bioremediation. The total bacterial count (CFU/gm in site (B was higher than that in site (A. Moreover, the CFU values in summer were higher than those values in winter at both sites. A total of 771 bacterial isolates were characterized as Bacillus, Micrococcus, Staphylococcus, Pseudomonas, Eschershia, Shigella, Xanthomonas, Acetobacter, Citrobacter, Enterobacter, Moraxella and Methylococcus. Minimum inhibitory concentrations (MICs of Pb+2, Cu+2, Zn+2, Hg+2, Co+2, Cd+2, Cr+3, Te+2, As+2 and Ni+2 for plasmid-possessed bacteria were determined and the highest MICs were 1200 µg/mL for lead, 800 µg/mL for both Cobalt and Arsenate, 1200 µg/mL for Nickel, 1000 µg/ml for Copper and less than 600 µg/mL for other metals. Bacterial isolates from both sites A and B showed multiple heavy metal resistance. A total of 337 bacterial isolates contained plasmids and the incidence of plasmids was approximately 25-50% higher in bacteria isolated from site (B than that from site (A. These isolates were resistance to different antibiotics. Approximately, 61% of the bacterial isolates were able to assimilate insecticide, carbaryl, as a sole source of carbon and energy. However, the Citrobacter AA101 showed the best growth on carbaryl.

Procoagulant and fibrinolytic activity in cerebrospinal fluid from adults with bacterial meningitis

NARCIS (Netherlands)

Weisfelt, Martijn; Determann, Rogier M.; de Gans, Jan; van der Ende, Arie; Levi, Marcel; van de Beek, Diederik; Schultz, Marcus J.

2007-01-01

OBJECTIVES: This study investigated levels of coagulation and fibrinolysis factors in cerebrospinal fluid (CSF) from adults with bacterial meningitis in relation to development of brain infarction. METHODS: CSF was collected from 92 adults with community-acquired bacterial meningitis, who

Assessing genetic heterogeneity within bacterial species isolated from gastrointestinal and environmental samples: How many isolates does it take?

NARCIS (Netherlands)

Dopfer, D.; Buist, W.; Soyer, Y.; Munoz, M.A.; Zadoks, R.N.; Geue, L.; Engel, B.

2008-01-01

Strain typing of bacterial isolates is increasingly used to identify sources of infection or product contamination and to elucidate routes of transmission of pathogens or spoilage organisms. Usually, the number of bacterial isolates belonging to the same species that is analyzed per sample is

Bacterial growth on ion exchange resin - investigations with a strong cationic exchanger. Pt. 3. Disinfection with peracetic acid

Energy Technology Data Exchange (ETDEWEB)

Flemming, H.C.

1984-12-01

The suitability of peracetic acid (PAA) for the disinfection of ion exchangers was investigated. 0.02% PAA is suitable for satisfactory disinfection. In this way corrosive effects are strongly reduced. Ca/sup 2+/-ions seem to protect the bacteria, therefore the disinfection should be done with the Na/sup +/-form. The disinfection has no remanent effect and therefore is not suitable for preventing bacterial aftergrowth during off-periods. A combination of silver and disinfectant can accomplish this, until a new, silver-tolerant microflora has evolved. In this case the use of 0.02% PAA is imperative, because higher concentrations will dissolve the silver. As a principle the effectiveness of disinfection procedure should be monitored bacteriologically.

Antibiotic resistance profile of bacterial isolates from food sold on a ...

African Journals Online (AJOL)

The antibiotic resistance profile of bacterial isolates from cooked food samples sold in different eateries on the campus of the University of Ado-Ekiti was investigated. A total of seventy-eight bacterial isolates belonging to six genera were encountered in the following proportion: Escherichia coli (29.5%), Klebsiella spp.

Mur Ligase Inhibitors as Anti-bacterials: A Comprehensive Review.

Science.gov (United States)

Sangshetti, Jaiprakash N; Joshi, Suyog S; Patil, Rajendra H; Moloney, Mark G; Shinde, Devanand B

2017-01-01

Exploring a new target for antibacterial drug discovery has gained much attention because of the emergence of Multidrug Resistance (MDR) strains of bacteria. To overcome this problem the development of novel antibacterial was considered as highest priority task and was one of the biggest challenge since multiple factors were involved. The bacterial peptidoglycan biosynthetic pathway has been well documented in the last few years and has been found to be imperative source for the development of novel antibacterial agents with high target specificity as they are essential for bacterial survival and have no homologs in humans. We have therefore reviewed the process of peptidoglycan biosynthesis which involves various steps like formation of UDP-Nacetylglucosamine (GlcNAc), UDP-N-acetylmuramic acid (MurNAc) and lipid intermediates (Lipid I and Lipid II) which are controlled by various enzymes like GlmS, GlmM, GlmU enzyme, followed by Mur Ligases (MurAMurF) and finally by MraY and MurG respectively. These four amide ligases MurC-MurF can be used as the source for the development of novel multi-target antibacterial agents as they shared and conserved amino acid regions, catalytic mechanisms and structural features. This review begins with the need for novel antibacterial agents and challenges in their development even after the development of bacterial genomic studies. An overview of the peptidoglycan monomer formation, as a source of disparity in this process is presented, followed by detailed discussion of structural and functional aspects of all Mur enzymes and different chemical classes of their inhibitors along with their SAR studies and inhibitory potential. This review finally emphasizes on different patents and novel Mur inhibitors in the development phase. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Functional recovery of biofilm bacterial communities after copper exposure

International Nuclear Information System (INIS)

Boivin, Marie-Elene Y.; Massieux, Boris; Breure, Anton M.; Greve, Gerdit D.; Rutgers, Michiel; Admiraal, Wim

2006-01-01

Potential of bacterial communities in biofilms to recover after copper exposure was investigated. Biofilms grown outdoor in shallow water on glass dishes were exposed in the laboratory to 0.6, 2.1, 6.8 μmol/l copper amended surface water and a reference and subsequently to un-amended surface water. Transitions of bacterial communities were characterised with denaturing gradient gel electrophoresis (DGGE) and community-level physiological profiles (CLPP). Exposure to 6.8 μmol/l copper provoked distinct changes in DGGE profiles of bacterial consortia, which did not reverse upon copper depuration. Exposure to 2.1 and 6.8 μmol/l copper was found to induce marked changes in CLPP of bacterial communities that proved to be reversible during copper depuration. Furthermore, copper exposure induced the development of copper-tolerance, which was partially lost during depuration. It is concluded that bacterial communities exposed to copper contaminated water for a period of 26 days are capable to restore their metabolic attributes after introduction of unpolluted water in aquaria for 28 days. - Genetically different bacterial communities can have similar functions and tolerance to copper

A pilot study of bacterial regrowth in water pipelines.

Science.gov (United States)

Mancini, Laura; Marcheggiani, Stefania; Grasso, Cinzia; Romanelli, Cristina; Mistretta, Antonio; Marranzano, Marina

2016-01-01

Bacterial regrowth in water distribution systems results in deterioration of bacteriological quality of drinking water, as well as accelerated corrosion of the pipelines. The aim of the present study was to analyze the phenomena of colonization and bacterial regrowth in source water and in the water distribution systems of three distribution networks in the province of Catania (Sicily, Italy). The BART™ (Biological Activity Reaction Test) method was used, which is also capable of determining the potential aggressiveness of microbial species in water. We searched for sulfate reducing bacteria, iron-related bacteria, nitrifying and denitrifying bacteria, heterotrophic bacteria, slime-forming bacteria and fluorescent Pseudomonads. A high concentration of heterotrophic bacteria was found in almost every water sample analyzed. Sulfate reducing bacteria and iron-related bacteria were found in all three distribution networks, while non-fluorescing Pseudomonas were detected in source water of only one of the distribution networks. The BART™ method was found to be a practical and easy to use tool to detect the different bacteria groups involved in regrowth phenomena.

Bacterial mycophagy: definition and diagnosis of a unique bacterial-fungal interaction

NARCIS (Netherlands)

Leveau, J.H.J.; Preston, G.M.

2008-01-01

This review analyses the phenomenon of bacterial mycophagy, which we define as a set of phenotypic behaviours that enable bacteria to obtain nutrients from living fungi and thus allow the conversion of fungal into bacterial biomass. We recognize three types of bacterial strategies to derive

Irrigation water quality in southern Mexico City based on bacterial and heavy metal analyses

Energy Technology Data Exchange (ETDEWEB)

Solis, C. [Instituto de Fisica, Universidad Nacional Autonoma de Mexico, Apdo Postal 20-364, 01000 Mexico, DF (Mexico)]. E-mail: corina@fisica.unam.mx; Sandoval, J. [Instituto de Ecologia, Universidad Nacional Autonoma de Mexico, Apdo Postal 70-275, 04510 Mexico, DF (Mexico); Perez-Vega, H. [Ciencias Agropecuarias, Universidad Juarez Autonoma de Tabasco, Ave. Universidad S/N. Zona de la Cultura, 86040 Villa Hermosa, Tabasco (Mexico); Mazari-Hiriart, M. [Instituto de Ecologia, Universidad Nacional Autonoma de Mexico, Apdo Postal 70-275, 04510 Mexico, DF (Mexico)

2006-08-15

Xochimilco is located in southern Mexico City and represents the reminiscence of the pre-Columbian farming system, the 'chinampa' agriculture. 'Chinampas' are island plots surrounded by a canal network. At present the area is densely urbanized and populated, with various contaminant sources contributing to the water quality degradation. The canal system is recharged by a combination of treated-untreated wastewater, and precipitation during the rainy season. Over 40 agricultural species, including vegetables, cereals and flowers, are produced in the 'chinampas'. In order to characterize the quality of Xochimilcos' water used for irrigation, spatial and temporal contaminant indicators such as microorganisms and heavy metals were investigated. Bacterial indicators (fecal coliforms, fecal enterococcus) were analyzed by standard analytical procedures, and heavy metals (such as Fe, Cu, Zn and Pb) were analyzed by particle induced X-ray emission (PIXE). The more contaminated sites coincide with the heavily populated areas. Seasonal variation of contaminants was observed, with the higher bacterial counts and heavy metal concentrations reported during the rainy season.

Starting material radiation source for Moessbauer investigations of tellurium compounds

International Nuclear Information System (INIS)

Alexandrov, A.J.; Grushko, J.S.; Makarov, E.F.; Mishin, K.Y.; Baltrunas, D.A.J.

1977-01-01

A method is described of preparing a radiation source for Mossbauer investigations of tellurium compounds manufactured on the basis of 5 MgO . Te 124 O 3 . 5 MgO . Te 124 O 3 is irradiated in a reactor by means of thermal neutrons, followed by annealing at a temperature ranging from 600 0 to 1,100 0 C for a period of from 5 to 10 hours

Bacterial leaching of pyritic gold ores

International Nuclear Information System (INIS)

Gagliardi, F.M.; Cashion, J.D.; Brown, J.; Jay, W.H.

1998-01-01

Full text: Pyritic ores (pyrite and arsenopyrite) containing gold concentrations in excess of 50g Au/t can be processed to recover the gold by the removal of the sulphur from the ore. This may be achieved by roasting (producing sulphur dioxide emissions), pressure oxidation (expensive and suitable for large high grade deposits), pressure leaching (still currently being developed) or bacterial oxidation. The bacterial oxidation process is a well known process in nature but has only recently come under investigation as a economically viable and relatively clean method of gold recovery from deep low grade sulphidic ores. Samples were obtained from the Wiluna Gold Mine in Western Australia consisting of the original ore, six successive bacterial reactors and the final products. Moessbauer experiments have been performed at room temperature, liquid nitrogen and liquid helium temperatures, and in applied magnetic fields. The main components of the iron phases which were present during the bacterial treatment were pyrite and arsenopyrite which were readily oxidised by the bacteria. Ferric sulfates and ferric arsenates were identified as by-products of the process with a small amount of the oxyhydroxide goethite. These results are in contrast to the similar study of the Fairview Mine in South Africa where principally Fe(II) species were observed

Bacterial leaching of pyritic gold ores

Energy Technology Data Exchange (ETDEWEB)

Gagliardi, F.M.; Cashion, J.D.; Brown, L.J. [Monash Univ., Clayton, VIC (Australia). Dept. of Physics; Jay, W.H. [Monash Univ., Clayton, VIC (Australia). Chemical Engineering Department

1996-12-31

The bacterial oxidation process is well known in nature but has only recently come under investigation as a viable and relatively clean method of gold recovery from ores. However there is currently little information about the process at an atomic scale. It is known that the bacterial attack progresses preferentially along grain boundaries which is precisely where the gold has been deposited from aqueous infiltration. Samples have been obtained from the Wiluna mine in Western Australia consisting of the original ore, 2 pre-treatments, and from six successive bacterial reactors. {sup 57}Fe Moessbauer spectra taken at room temperature show only two quadrupole split doublets which can be ascribed to pyrite, FeS{sub 2}, and arsenopyrite, FeAsS. However, the presence of any superparamagnetic oxide or oxyhydroxide species would be expected to give a spectrum very similar to that of pyrite and would be undetectable in small quantities. At a temperature of 5K, a broad magnetically split sextet is observable with a mean hyperfine field of approximately 50T. This field is characteristic of magnetically ordered ferric iron surrounded by an octahedron of oxygens. The intensity and characteristics of this subspectrum alters through the series and interpretations will be given on the oxidation products of the bacterial leaching

Bacterial leaching of pyritic gold ores

International Nuclear Information System (INIS)

Gagliardi, F.M.; Cashion, J.D.; Brown, L.J.; Jay, W.H.

1996-01-01

The bacterial oxidation process is well known in nature but has only recently come under investigation as a viable and relatively clean method of gold recovery from ores. However there is currently little information about the process at an atomic scale. It is known that the bacterial attack progresses preferentially along grain boundaries which is precisely where the gold has been deposited from aqueous infiltration. Samples have been obtained from the Wiluna mine in Western Australia consisting of the original ore, 2 pre-treatments, and from six successive bacterial reactors. 57 Fe Moessbauer spectra taken at room temperature show only two quadrupole split doublets which can be ascribed to pyrite, FeS 2 , and arsenopyrite, FeAsS. However, the presence of any superparamagnetic oxide or oxyhydroxide species would be expected to give a spectrum very similar to that of pyrite and would be undetectable in small quantities. At a temperature of 5K, a broad magnetically split sextet is observable with a mean hyperfine field of approximately 50T. This field is characteristic of magnetically ordered ferric iron surrounded by an octahedron of oxygens. The intensity and characteristics of this subspectrum alters through the series and interpretations will be given on the oxidation products of the bacterial leaching

Bacterial Succession on Rat Carcasses and Applications for PMI Estimation.

Science.gov (United States)

Zhang, Lin; Guo, Juan-juan; Telet-Siyit; Peng, Yu-long; Xie, Dan; Guo, Ya-dong; Yan, Jie; Zha, Lagabaiyila; Cai, Ji-feng

2016-02-01

Abstract: To investigate the bacterial succession on rat carcasses and to evaluate the use of bacterial succession for postmortem interval (PMI) estimation. Adult female SD rat remains were placed in carton boxes. The bacterial colonization of circumocular skin, mouth and vagina was collected to be identified using culture-dependent biochemical methods. The changes in community composition were regularly documented. The bacterial succession in three habitats showed that Staphylococcus and Neisseria were predominated in early PMI, especially Staphylococcus aureus and Neisseria lactamica in 6 hours after death. Lactobacillus casei developed on the 3-4 days regularly, and kept stable at a certain level in late PMI. The involvement of normal and putrefactive bacteria in three body habitats of rat remains can be used for PMI estimation.

Bacterial invasion of the uterus and oviducts in bovine pyometra

DEFF Research Database (Denmark)

Karstrup, C. C.; Pedersen, H. G.; Jensen, Tim Kåre

2017-01-01

of bacterial pathogenicity and development of lesions, have not been investigated. Bacterial invasion of the uterus and oviducts was studied in 21 cows diagnosed with pyometra at the time of slaughter by applying fluorescence in situ hybridization using probes targeting 16S ribosomal RNA of Fusobacterium...... necrophorum, Porphyromonas levii, Trueperella pyogenes and the overall bacterial domain Bacteria. Fusobacterium necrophorum and P. levii were found to invade the endometrium, especially if the endometrium was ulcerated, and penetrated deep into the lamina propria. These species co-localized within the tissue...... thus indicating a synergism. Trueperella pyogenes did not invade the uterine tissue. In addition to endometrial lesions, most cows with pyometra also had salpingitis but without significant bacterial invasion of the oviductal wall....

Production of Bacterial Cellulose by Gluconacetobacter hansenii Using Corn Steep Liquor As Nutrient Sources

Directory of Open Access Journals (Sweden)

Andrea F. S. Costa

2017-10-01

Full Text Available Cellulose is mainly produced by plants, although many bacteria, especially those belonging to the genus Gluconacetobacter, produce a very peculiar form of cellulose with mechanical and structural properties that can be exploited in numerous applications. However, the production cost of bacterial cellulose (BC is very high to the use of expensive culture media, poor yields, downstream processing, and operating costs. Thus, the purpose of this work was to evaluate the use of industrial residues as nutrients for the production of BC by Gluconacetobacter hansenii UCP1619. BC pellicles were synthesized using the Hestrin–Schramm (HS medium and alternative media formulated with different carbon (sugarcane molasses and acetylated glucose and nitrogen sources [yeast extract, peptone, and corn steep liquor (CSL]. A jeans laundry was also tested. None of the tested sources (beside CSL worked as carbon and nutrient substitute. The alternative medium formulated with 1.5% glucose and 2.5% CSL led to the highest yield in terms of dry and hydrated mass. The BC mass produced in the alternative culture medium corresponded to 73% of that achieved with the HS culture medium. The BC pellicles demonstrated a high concentration of microfibrils and nanofibrils forming a homogenous, compact, and three-dimensional structure. The biopolymer produced in the alternative medium had greater thermal stability, as degradation began at 240°C, while degradation of the biopolymer produced in the HS medium began at 195°C. Both biopolymers exhibited high crystallinity. The mechanical tensile test revealed the maximum breaking strength and the elongation of the break of hydrated and dry pellicles. The dry BC film supported up to 48 MPa of the breaking strength and exhibited greater than 96.98% stiffness in comparison with the hydrated film. The dry film supported up to 48 MPa of the breaking strength and exhibited greater than 96.98% stiffness in comparison with the hydrated film

Estimation of decay rates for fecal indicator bacteria and bacterial pathogens in agricultural field-applied manure

Science.gov (United States)

Field-applied manure is an important source of pathogenic exposure in surface water bodies for humans and ecological receptors. We analyzed the persistence and decay of fecal indicator bacteria and bacterial pathogens from three sources (cattle, poultry, swine) for agricultural f...

BSim: an agent-based tool for modeling bacterial populations in systems and synthetic biology.

Directory of Open Access Journals (Sweden)

Thomas E Gorochowski

Full Text Available Large-scale collective behaviors such as synchronization and coordination spontaneously arise in many bacterial populations. With systems biology attempting to understand these phenomena, and synthetic biology opening up the possibility of engineering them for our own benefit, there is growing interest in how bacterial populations are best modeled. Here we introduce BSim, a highly flexible agent-based computational tool for analyzing the relationships between single-cell dynamics and population level features. BSim includes reference implementations of many bacterial traits to enable the quick development of new models partially built from existing ones. Unlike existing modeling tools, BSim fully considers spatial aspects of a model allowing for the description of intricate micro-scale structures, enabling the modeling of bacterial behavior in more realistic three-dimensional, complex environments. The new opportunities that BSim opens are illustrated through several diverse examples covering: spatial multicellular computing, modeling complex environments, population dynamics of the lac operon, and the synchronization of genetic oscillators. BSim is open source software that is freely available from http://bsim-bccs.sf.net and distributed under the Open Source Initiative (OSI recognized MIT license. Developer documentation and a wide range of example simulations are also available from the website. BSim requires Java version 1.6 or higher.

Childhood asthma after bacterial colonization of the airway in neonates

DEFF Research Database (Denmark)

Bisgaard, H.; Hermansen, M.N.; Buchvald, F.

2007-01-01

Pathological features of the airway in young children with severe recurrent wheeze suggest an association between bacterial colonization and the initiating events of early asthma. We conducted a study to investigate a possible association between bacterial colonization of the hypopharynx in asymp...... in asymptomatic neonates and later development of recurrent wheeze, asthma, and allergy during the first 5 years of life....

Bacterial flora of spices and its control by gamma irradiation

International Nuclear Information System (INIS)

El-Zawahry, Y.A.; Youssef, Y.A.; Awny, N.M.; Hussein, H.A.

1985-01-01

The bacterial contamination was tested in 26 samples of spices. Chili, allspice and paprika were the most contaminated spices by bacteria. Five bacterial genera were isolated, namely bacillus, staphylococcus, streptococcus, micrococcus, and coccobacillus, all being gram-positive. Most isolates have been related to the genus bacillus. The bacterial isolates were identified as B. alvei, B. circulans, B. megaterium, B. pasteurii, B. pumilus, B. thuringiensis, B. sphaericus, B. incertaesedis, Micrococcus luteus, staphylococcus aureus, streptococcus sp. and coccobacillus sp. Irradiation of spices led to a significant decrease in the bacterial count of all samples. The dose required to inhibit completely the natural bacterial flora was 25 KGY. The most radioresistant isolates were staphylococcus aureus and micrococcus luteus which were subjected to sublethal doses of 15 and 20 KGY respectively. The dose response curves of the 2 most radioresistant isolates showed simple exponential relationship. The D 10-value of S. aureus and M. luteus were 0.9 and 1.1 KGY, respectively. The effect of storage period on the bacterial load of, as well as, the antibacterial activity of the tested spices were investigated. (author)

Bacterial flora of spices and its control by gamma irradiation

Energy Technology Data Exchange (ETDEWEB)

El-Zawahry, Y A; Youssef, Y A; Awny, N M; Hussein, H A

1985-01-01

The bacterial contamination was tested in 26 samples of spices. Chili, allspice and paprika were the most contaminated spices by bacteria. Five bacterial genera were isolated, namely bacillus, staphylococcus, streptococcus, micrococcus, and coccobacillus, all being gram-positive. Most isolates have been related to the genus bacillus. The bacterial isolates were identified as B. alvei, B. circulans, B. megaterium, B. pasteurii, B. pumilus, B. thuringiensis, B. sphaericus, B. incertaesedis, Micrococcus luteus, staphylococcus aureus, streptococcus sp. and coccobacillus sp. Irradiation of spices led to a significant decrease in the bacterial count of all samples. The dose required to inhibit completely the natural bacterial flora was 25 KGY. The most radioresistant isolates were staphylococcus aureus and micrococcus luteus which were subjected to sublethal doses of 15 and 20 KGY respectively. The dose response curves of the 2 most radioresistant isolates showed simple exponential relationship. The D 10-value of S. aureus and M. luteus were 0.9 and 1.1 KGY, respectively. The effect of storage period on the bacterial load of, as well as, the antibacterial activity of the tested spices were investigated.

Analytical investigation of low temperature lift energy conversion systems with renewable energy source

International Nuclear Information System (INIS)

Lee, Hoseong; Hwang, Yunho; Radermacher, Reinhard

2014-01-01

The efficiency of the renewable energy powered energy conversion system is typically low due to its moderate heat source temperature. Therefore, improving its energy efficiency is essential. In this study, the performance of the energy conversion system with renewable energy source was theoretically investigated in order to explore its design aspect. For this purpose, a computer model of n-stage low temperature lift energy conversion (LTLEC) system was developed. The results showed that under given operating conditions such as temperatures and mass flow rates of heat source and heat sink fluids the unit power generation of the system increased with the number of stage, and it became saturated when the number of staging reached four. Investigation of several possible working fluids for the optimum stage LTLEC system revealed that ethanol could be an alternative to ammonia. The heat exchanger effectiveness is a critical factor on the system performance. The power generation was increased by 7.83% for the evaporator and 9.94% for the condenser with 10% increase of heat exchanger effectiveness. When these low temperature source fluids are applied to the LTLEC system, the heat exchanger performance would be very critical and it has to be designed accordingly. - Highlights: •Energy conversion system with renewable energy is analytically investigated. •A model of multi-stage low temperature lift energy conversion systems was developed. •The system performance increases as the stage number is increased. •The unit power generation is increased with increase of HX effectiveness. •Ethanol is found to be a good alternative to ammonia

Survey of bacterial pathogens on leaves and seeds of red mangrove ...

African Journals Online (AJOL)

Bacterial pathogens of red mangrove (Rhizophora mangle) were investigated. 50 samples each of leaves and seeds (healthy and diseased) were randomly collected and used for the analysis. Mean bacterial counts obtained were: healthy and diseased leaves; 8.26 x 103 and 5.9 l x l03 cfu/ml respectively; healthy seeds ...

Bacterial meningitis

NARCIS (Netherlands)

Roos, Karen L.; van de Beek, Diederik

2010-01-01

Bacterial meningitis is a neurological emergency. Empiric antimicrobial and adjunctive therapy should be initiated as soon as a single set of blood cultures has been obtained. Clinical signs suggestive of bacterial meningitis include fever, headache, meningismus, vomiting, photophobia, and an

Bacterial Diversity and Bioremediation Potential of the Highly Contaminated Marine Sediments at El-Max District (Egypt, Mediterranean Sea)

KAUST Repository

Amer, Ranya A.

2015-02-01

Coastal environments worldwide are threatened by the effects of pollution, a risk particularly high in semienclosed basins like the Mediterranean Sea that is poorly studied from bioremediation potential perspective especially in the Southern coast. Here, we investigated the physical, chemical, and microbiological features of hydrocarbon and heavy metals contaminated sediments collected at El-Max bay (Egypt). Molecular and statistical approaches assessing the structure of the sediment-dwelling bacterial communities showed correlations between the composition of bacterial assemblages and the associated environmental parameters. Fifty strains were isolated on mineral media supplemented by 1% crude oil and identified as a diverse range of hydrocarbon-degrading bacteria involved in different successional stages of biodegradation. We screened the collection for biotechnological potential studying biosurfactant production, biofilm formation, and the capability to utilize different hydrocarbons. Some strains were able to grow on multiple hydrocarbons as unique carbon source and presented biosurfactant-like activities and/or capacity to form biofilm and owned genes involved in different detoxification/degradation processes. El-Max sediments represent a promising reservoir of novel bacterial strains adapted to high hydrocarbon contamination loads. The potential of the strains for exploitation for in situ intervention to combat pollution in coastal areas is discussed.

Source evaluation report phase 2 investigation: Limited field investigation. Final report: United States Air Force Environmental Restoration Program, Eielson Air Force Base, Alaska

Energy Technology Data Exchange (ETDEWEB)

1994-10-01

This report describes the limited field investigation work done to address issues and answer unresolved questions regarding a collection of potential contaminant sources at Eielson Air Force Base (AFB), near Fairbanks, Alaska. These sources were listed in the Eielson AFB Federal Facility Agreement supporting the Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) cleanup of the base. The limited field investigation began in 1993 to resolve all remaining technical issues and provide the data and analysis required to evaluate the environmental hazard associated with these sites. The objective of the limited field investigation was to allow the remedial project managers to sort each site into one of three categories: requiring remedial investigation/feasibility study, requiring interim removal action, or requiring no further remedial action.

Antibiotics promote aggregation within aquatic bacterial communities

Directory of Open Access Journals (Sweden)

Gianluca eCorno

2014-07-01

Full Text Available The release of antibiotics (AB into the environment poses several threats for human health due to potential development of ABresistant natural bacteria. Even though the use of low-dose antibiotics has been promoted in health care and farming, significant amounts of AB are observed in aquatic environments. Knowledge on the impact of AB on natural bacterial communities is missing both in terms of spread and evolution of resistance mechanisms, and of modifications of community composition and productivity. New approaches are required to study the response of microbial communities rather than individual resistance genes. In this study a chemostat-based experiment with 4 coexisting bacterial strains has been performed to mimicking the response of a freshwater bacterial community to the presence of antibiotics in low and high doses. Bacterial abundance rapidly decreased by 75% in the presence of AB, independently of their concentration, and remained constant until the end of the experiment. The bacterial community was mainly dominated by Aeromonas hydrophila and Brevundimonas intermedia while the other two strains, Micrococcus luteus and Rhodococcus sp. never exceed 10%. Interestingly, the bacterial strains, which were isolated at the end of the experiment, were not AB-resistant, while reassembled communities composed of the 4 strains, isolated from treatments under AB stress, significantly raised their performance (growth rate, abundance in the presence of AB compared to the communities reassembled with strains isolated from the treatment without AB. By investigating the phenotypic adaptations of the communities subjected to the different treatments, we found that the presence of AB significantly increased co-aggregation by 5-6 fold.These results represent the first observation of co-aggregation as a successful strategy of AB resistance based on phenotype in aquatic bacterial communities, and can represent a fundamental step in the understanding of

Upstream Freshwater and Terrestrial Sources Are Differentially Reflected in the Bacterial Community Structure along a Small Arctic River and Its Estuary

DEFF Research Database (Denmark)

Hauptmann, Aviaja Zenia Edna Lyberth; Markussen, Thor N; Stibal, Marek

2016-01-01

of different water sources on the microbial communities in Arctic rivers and estuaries remains unknown. In this study we used 16S rRNA gene amplicon sequencing to assess a small river and its estuary on the Disko Island, West Greenland (69°N). Samples were taken in August when there is maximum precipitation......Glacier melting and altered precipitation patterns influence Arctic freshwater and coastal ecosystems. Arctic rivers are central to Arctic water ecosystems by linking glacier meltwaters and precipitation with the ocean through transport of particulate matter and microorganisms. However, the impact...... and temperatures are high in the Disko Bay area. We describe the bacterial community through a river into the estuary, including communities originating in a glacier and a proglacial lake. Our results show that water from the glacier and lake transports distinct communities into the river in terms of diversity...

Marine organisms as source of extracts to disrupt bacterial communication: bioguided isolation and identification of quorum sensing inhibitors from Ircinia felix

Directory of Open Access Journals (Sweden)

Jairo Quintana

Full Text Available AbstractIn this study, 39 extracts from marine organisms were evaluated as quorum sensing inhibitors, collected in the Colombian Caribbean Sea and the Brazilian Coast including 26 sponges, seven soft corals, five algae and one zooanthid. The results showed that crude extracts from the soft coral Eunicea laciniata, and the sponges Svenzea tubulosa, Ircinia felix and Neopetrosia carbonaria were the most promising source of quorum sensing inhibitors compounds without affecting bacterial growth, unlike the raw extracts of Agelas citrina, Agelas tubulata, Iotrochota arenosa, Topsentia ophiraphidites, Niphates caycedoi, Cliona tenuis, Ptilocaulis walpersi, Petrosia pellasarca, and the algae Laurencia catarinensis and Laurencia obtusa, which displayed potent antibacterial activity against the biosensors employed. The crude extract from the sponge I. felix was fractionated, obtaining furanosesterterpenes which were identified and evaluated as quorum sensing inhibitors, showing a moderate activity without affecting the biosensor's growth.

Tuning bacterial hydrodynamics with magnetic fields

Science.gov (United States)

Pierce, C. J.; Mumper, E.; Brown, E. E.; Brangham, J. T.; Lower, B. H.; Lower, S. K.; Yang, F. Y.; Sooryakumar, R.

2017-06-01

Magnetotactic bacteria are a group of motile prokaryotes that synthesize chains of lipid-bound, magnetic nanoparticles called magnetosomes. This study exploits their innate magnetism to investigate previously unexplored facets of bacterial hydrodynamics at surfaces. Through use of weak, uniform, external magnetic fields and local, micromagnetic surface patterns, the relative strength of hydrodynamic, magnetic, and flagellar force components is tuned through magnetic control of the bacteria's orientation. The resulting swimming behaviors provide a means to experimentally determine hydrodynamic parameters and offer a high degree of control over large numbers of living microscopic entities. The implications of this controlled motion for studies of bacterial motility near surfaces and for micro- and nanotechnology are discussed.

Investigation of the process of vacuum freeze drying of bacterial concentrates for the meat industry with cryogenic freezing

Directory of Open Access Journals (Sweden)

V. V. Poymanov

2016-01-01

Full Text Available The research results of the nutritional value of the products manufactured are presented in the article. The main directions of bacterial concentrates application in the meat industry were determined. The analysis of starter cultures was given. The range of products manu-factured with bacterial concentrates was analyzed. It was shown that the introduction of innovative technologies will enable dynamic development of both large and small enterprises, which will create prerequisites for the growth of the Russian market of meat products. Economic efficiency of the studied substances treatment methods was proved. The relevance of the development of technology of pro-duction of dry bacterial concentrates with cryogenic freezing was proved. An integrated approach to the development of competitive domestic technologies and equipment for cryofreezing and sublimation dehydration by the use of granulation for the intensification of the internal heat and mass transfer, reducing specific energy consumption through the use of a combined cold supply system was pro-posed. Results of the study of the kinetics of the freezing process with the traditional method and cryofreezing are given in the paper. Rational parameters of the cryofreezing process were proposed. The optimum composition of cryoprotective medium was recommended. The research of the process of bacterial concentrate vacuum sublimation dehydration in the layer and granular form were conducted. The research confirmed that the use of the cryofreezing and granulation can increase the number of viable microorganisms in the bacterial concentrate and reduce the drying time. Rational vacuum sublimation dehydration modes were proposed. Methods of reduc-ing the defects of the processed products and improvement of the efficiency of production facilities were specified. Quality indicators of dried bacterial concentrates were given. The results obtained allow to carry out engineering calculations

A Brief Review of Viral and Bacterial Sexually Transmitted Diseases in Colorectal Practice

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Nabi

2015-12-01

Full Text Available Context Sexually transmitted diseases (STDs are a common source of presentation to colorectal surgeons. Clinicians need to remain mindful of the possibility of STDs when faced with atypical clinical presentations. This article aims to provide surgeons with a synopsis of common pathogens, their clinical presentations, diagnostic investigations and treatment regimens. Evidence Acquisition The most common bacterial pathogens include Chlamydia trachomatis and Neisseria gonorrhea with synchronous infections at presentation occurring frequently. Patients often present with proctitis. Gonorrhea patients can also experience bloody purulent perianal discharge. Less common bacterial pathogens include syphilis, chancroid and donovanosis. The commonest STD worldwide remains human papillomavirus. Given its vast array of subtypes its manifestations include benign hyperproliferative lesions like perianal warts and extend to anal intraepithelial neoplasia and squamous cell carcinoma. Other important viral infections of the anorectum include human immunodeficiency virus and subsequent acquired immune deficiency disease as well as herpes simplex virus and molluscum contangiosum. Results Debate exists whether the increasing incidence of STDs affecting the anorectum reported in western literature represents a real increase or a reflection of greater patient and clinician recognition and reporting. Conclusions Regardless, a broad understanding of common bacterial and viral pathogens remains important part of modern colorectal practice. Remaining mindful of the manifestations of these common pathogens, options for diagnosis and management are important in disease control to limit the impact of these pathogens across the wider community.

Bacterial Community Dynamics in Dichloromethane-Contaminated Groundwater Undergoing Natural Attenuation

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Justin Wright

2017-11-01

Full Text Available The uncontrolled release of the industrial solvent methylene chloride, also known as dichloromethane (DCM, has resulted in widespread groundwater contamination in the United States. Here we investigate the role of groundwater bacterial communities in the natural attenuation of DCM at an undisclosed manufacturing site in New Jersey. This study investigates the bacterial community structure of groundwater samples differentially contaminated with DCM to better understand the biodegradation potential of these autochthonous bacterial communities. Bacterial community analysis was completed using high-throughput sequencing of the 16S rRNA gene of groundwater samples (n = 26 with DCM contamination ranging from 0.89 to 9,800,000 μg/L. Significant DCM concentration-driven shifts in overall bacterial community structure were identified between samples, including an increase in the abundance of Firmicutes within the most contaminated samples. Across all samples, a total of 6,134 unique operational taxonomic units (OTUs were identified, with 16 taxa having strong correlations with increased DCM concentration. Putative DCM degraders such as Pseudomonas, Dehalobacterium and Desulfovibrio were present within groundwater across all levels of DCM contamination. Interestingly, each of these taxa dominated specific DCM contamination ranges respectively. Potential DCM degrading lineages yet to be cited specifically as a DCM degrading organisms, such as the Desulfosporosinus, thrived within the most heavily contaminated groundwater samples. Co-occurrence network analysis revealed aerobic and anaerobic bacterial taxa with DCM-degrading potential were present at the study site. Our 16S rRNA gene survey serves as the first in situ bacterial community assessment of contaminated groundwater harboring DCM concentrations ranging over seven orders of magnitude. Diversity analyses revealed known as well as potentially novel DCM degrading taxa within defined DCM concentration

BACTERIAL POPULATION DYNAMICS IN WASTE OILY EMULSIONS FROM THE METAL-PROCESSING INDUSTRY

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Paweł Kaszycki

2014-07-01

Full Text Available Oil-containing wastewaters are regarded as main industrial pollutants of soil and water environments. They can occur as free-floating oil, unstable or stable oil-in-water (O/W emulsions, and in the case of extreme organic load, as water-in-oil (W/O emulsions. In this study two types of oily effluents, a typical O/W emulsion marked as E1 and a W/O emulsion E2, both discharged by local metal processing plants were examined to test their toxicity to microbial communities and the ability to serve as nutrient sources for bacterial growth. The organic contaminant load of the samples was evaluated on the basis of chemical oxygen demand (COD parameter values and was equal to 48 200 mg O2·dm-3 and >300 000 mg O2·dm-3 for E1 and E2, respectively.Both emulsions proved to be non toxic to bacterial communities and were shown to contain biodiverse autochthonous microflora consisting of several bacterial strains adapted to the presence of xenobiotics (the total of 1.36 · 106 CFU·cm-3 and 1.72 · 105 CFU·cm-3 was determined for E1 and E2, respectively. These indigenous bacteria as well as exogenously inoculated specialized allochthonous microorganisms were biostimulated so as to proliferate within the wastewater environment whose organic content served as the only source of carbon. The most favorable cultivation conditions were determined as fully aerobic growth at the temperature of 25 ºC. In 9 to 18 day-tests, autochthonous as well as bioaugmented allochthonous bacterial population dynamics were monitored. For both emulsions tested there was a dramatic increase (up to three orders of magnitude in bacterial frequency, as compared to the respective initial values. The resultant high biomass densities suggest that the effluents are susceptible to bioremediation. A preliminary xenobiotic biodegradation test confirmed that mixed auto- and allochthonous bacterial consortia obtained upon inoculation of the samples with microbiocenoses preselected for efficient

An assessment of air as a source of DNA contamination encountered when performing PCR.

Science.gov (United States)

Witt, Nina; Rodger, Gillian; Vandesompele, Jo; Benes, Vladimir; Zumla, Alimuddin; Rook, Graham A; Huggett, Jim F

2009-12-01

Sensitive molecular methods, such as the PCR, can detect low-level contamination, and careful technique is required to reduce the impact of contaminants. Yet, some assays that are designed to detect high copy-number target sequences appear to be impossible to perform without contamination, and frequently, personnel or laboratory environment are held responsible as the source. This complicates diagnostic and research analysis when using molecular methods. To investigate the air specifically as a source of contamination, which might occur during PCR setup, we exposed tubes of water to the air of a laboratory and clean hood for up to 24 h. To increase the chances of contamination, we also investigated a busy open-plan office in the same way. All of the experiments showed the presence of human and rodent DNA contamination. However, there was no accumulation of the contamination in any of the environments investigated, suggesting that the air was not the source of contamination. Even the air from a busy open-plan office was a poor source of contamination for all of the DNA sequences investigated (human, bacterial, fungal, and rodent). This demonstrates that the personnel and immediate laboratory environment are not necessarily to blame for the observed contamination.

Brain ventricular dimensions and relationship to outcome in adult patients with bacterial meningitis

DEFF Research Database (Denmark)

Sporrborn, Janni L; Knudsen, Gertrud B; Sølling, Mette

2015-01-01

BACKGROUND: Experimental studies suggest that changes in brain ventricle size are key events in bacterial meningitis. This study investigated the relationship between ventricle size, clinical condition and risk of poor outcome in patients with bacterial meningitis. METHODS: Adult patients diagnos...

Source-case investigation of Mycobacterium wolinskyi cardiac surgical site infection.

Science.gov (United States)

Dupont, C; Terru, D; Aguilhon, S; Frapier, J-M; Paquis, M-P; Morquin, D; Lamy, B; Godreuil, S; Parer, S; Lotthé, A; Jumas-Bilak, E; Romano-Bertrand, S

2016-07-01

The non-tuberculous mycobacteria (NTM) Mycobacterium wolinskyi caused bacteraemia and massive colonization of an aortic prosthesis in a patient 16 days after cardiac surgery, necessitating repeat surgery and targeted antimicrobial chemotherapy. The infection control team investigated the source and conditions of infection. Peri-operative management of the patient complied with recommendations. The environmental investigation showed that although M. wolinskyi was not recovered, diverse NTM species were present in water from point-of-use taps and heater-cooler units for extracorporeal circulation. This case and increasing evidence of emerging NTM infections in cardiac surgery led to the implementation of infection control procedures in cardiac surgery wards. Copyright © 2016 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.

Fertilization Shapes Bacterial Community Structure by Alteration of Soil pH

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Yuting Zhang

2017-07-01

Full Text Available Application of chemical fertilizer or manure can affect soil microorganisms directly by supplying nutrients and indirectly by altering soil pH. However, it remains uncertain which effect mostly shapes microbial community structure. We determined soil bacterial diversity and community structure by 454 pyrosequencing the V1-V3 regions of 16S rRNA genes after 7-years (2007–2014 of applying chemical nitrogen, phosphorus and potassium (NPK fertilizers, composted manure or their combination to acidic (pH 5.8, near-neutral (pH 6.8 or alkaline (pH 8.4 Eutric Regosol soil in a maize-vegetable rotation in southwest China. In alkaline soil, nutrient sources did not affect bacterial Operational Taxonomic Unit (OTU richness or Shannon diversity index, despite higher available N, P, K, and soil organic carbon in fertilized than in unfertilized soil. In contrast, bacterial OTU richness and Shannon diversity index were significantly lower in acidic and near-neutral soils under NPK than under manure or their combination, which corresponded with changes in soil pH. Permutational multivariate analysis of variance showed that bacterial community structure was significantly affected across these three soils, but the PCoA ordination patterns indicated the effect was less distinct among nutrient sources in alkaline than in acidic and near-neural soils. Distance-based redundancy analysis showed that bacterial community structures were significantly altered by soil pH in acidic and near-neutral soils, but not by any soil chemical properties in alkaline soil. The relative abundance (% of most bacterial phyla was higher in near-neutral than in acidic or alkaline soils. The most dominant phyla were Proteobacteria (24.6%, Actinobacteria (19.7%, Chloroflexi (15.3% and Acidobacteria (12.6%; the medium dominant phyla were Bacterioidetes (5.3%, Planctomycetes (4.8%, Gemmatimonadetes (4.5%, Firmicutes (3.4%, Cyanobacteria (2.1%, Nitrospirae (1.8%, and candidate division TM7 (1

Fertilization Shapes Bacterial Community Structure by Alteration of Soil pH.

Science.gov (United States)

Zhang, Yuting; Shen, Hong; He, Xinhua; Thomas, Ben W; Lupwayi, Newton Z; Hao, Xiying; Thomas, Matthew C; Shi, Xiaojun

2017-01-01

Application of chemical fertilizer or manure can affect soil microorganisms directly by supplying nutrients and indirectly by altering soil pH. However, it remains uncertain which effect mostly shapes microbial community structure. We determined soil bacterial diversity and community structure by 454 pyrosequencing the V1-V3 regions of 16S rRNA genes after 7-years (2007-2014) of applying chemical nitrogen, phosphorus and potassium (NPK) fertilizers, composted manure or their combination to acidic (pH 5.8), near-neutral (pH 6.8) or alkaline (pH 8.4) Eutric Regosol soil in a maize-vegetable rotation in southwest China. In alkaline soil, nutrient sources did not affect bacterial Operational Taxonomic Unit (OTU) richness or Shannon diversity index, despite higher available N, P, K, and soil organic carbon in fertilized than in unfertilized soil. In contrast, bacterial OTU richness and Shannon diversity index were significantly lower in acidic and near-neutral soils under NPK than under manure or their combination, which corresponded with changes in soil pH. Permutational multivariate analysis of variance showed that bacterial community structure was significantly affected across these three soils, but the PCoA ordination patterns indicated the effect was less distinct among nutrient sources in alkaline than in acidic and near-neural soils. Distance-based redundancy analysis showed that bacterial community structures were significantly altered by soil pH in acidic and near-neutral soils, but not by any soil chemical properties in alkaline soil. The relative abundance (%) of most bacterial phyla was higher in near-neutral than in acidic or alkaline soils. The most dominant phyla were Proteobacteria (24.6%), Actinobacteria (19.7%), Chloroflexi (15.3%) and Acidobacteria (12.6%); the medium dominant phyla were Bacterioidetes (5.3%), Planctomycetes (4.8%), Gemmatimonadetes (4.5%), Firmicutes (3.4%), Cyanobacteria (2.1%), Nitrospirae (1.8%), and candidate division TM7 (1

Effects of food on bacterial community composition associated with the copepod Acartia tonsa Dana

OpenAIRE

Tang, Kam; Dziallas, Claudia; Hutalle-Schmelzer, Kristine; Grossart, Hans-Peter

2009-01-01

The estuarine copepod Acartia tonsa naturally carried diverse strains of bacteria on its body. The bacterial community composition (BCC) remained very conservative even when the copepod was fed different axenic algal species, indicating that the food per se did not much affect BCC associated with the copepod. In xenic algal treatments, however, copepod-associated BCC differed with each alga fed, even though the same bacterial source was used to inoculate the algae. In addition, starved copepo...

Provision of micro-nano bacterial cellulose as bio plastic filler by sonication method

Science.gov (United States)

Maryam; Rahmad, D.; Yunizurwan; Kasim, A.; Novelina; Emriadi

2017-07-01

Research and development of bioplastic has increased recently as a solution for substitution of conventional plastic which have many negative impacts to environment. However, physical properties and mechanical properties of its still lower than conventional plastic. An alternative solution for that problem is by using fillers that can increase the strength. Bacterial cellulose is considered as potential source for filler, but still need to be explored more. The privileges of bacterial cellulose are easy to get and does not have lignin, pectin, and hemicelluloses which are impurities in other celluloses. This research focused on gaining bacterial cellulose in micro-nano particle form and its impact on increasing the strength of bio plastic. Ultrasonication has been used as method to form micro-nano particle from bacterial cellulose. The result showed this method may form the particle size of bacterial cellulose approximately ± 3μm. Next step, after getting ± 3μm particle of bacterial cellulose, is making bio plastic with casting method by adding 1% of bacterial cellulose, from the total material in making bio plastic. Physical characteristic of the bio plastic which are tensile strength 11.85 MPa, modulus young 3.13 MPa, elongation 4.11% and density 0.42 g/cm3. The numbers of physical properties showwthat, by adding 1% of bacterial cellulose, the strength of bio plastic was significantly increase, even value of tensile strength has complied the international standard for bio plastic.

Bacterial strain changes during chronic otitis media surgery.

Science.gov (United States)

Kim, G J; Yoo, S; Han, S; Bu, J; Hong, Y; Kim, D-K

2017-09-01

Cultures obtained from pre-operative middle-ear swabs from patients with chronic otitis media have traditionally been used to guide antibiotic selection. This study investigated changes in the bacterial strains of the middle ear during chronic otitis media surgery. Pre-operative bacterial cultures of otorrhoea, and peri-operative cultures of the granulation tissue in either the middle ear or mastoid cavity, were obtained. Post-operative cultures were selectively obtained when otorrhoea developed after surgery. Bacterial growth was observed in 45.5 per cent of pre-operative cultures, 13.5 per cent of peri-operative cultures and 4.5 per cent of post-operative cultures. Methicillin-resistant Staphylococcus aureus was identified as the most common bacteria in all pre-operative (32.4 per cent), peri-operative (52.4 per cent) and post-operative (71.4 per cent) tests, and the percentage of Methicillin-resistant S aureus increased from the pre- to the post-operative period. The bacterial culture results for post-operative otorrhoea showed low agreement with those for pre-operative or peri-operative culture, and strain re-identification was required.

Bacteriophages for detection of bacterial pathogens

International Nuclear Information System (INIS)

Kutateladze, M.

2009-01-01

The G. Eliava Institute of Bacteriophages, Microbiology and Virology (Tbilisi, Georgia) is one of the most famous institutions focused on bacteriophage research for the elaboration of appropriate phage methodologies for human and animal protection. The main direction of the institute is the study and production of bacteriophages against intestinal disorders (dysentery, typhoid, intesti) and purulent-septic infections (staphylococcus, streptococcus, pyophage, etc.). These preparations were successfully introduced during the Soviet era, and for decades were used throughout the former Soviet Union and in other Socialist countries for the treatment, prophylaxis, and diagnosis of various infectious diseases, including those caused by antibiotic-resistant bacterial strains. Bacteriophages were widely used for identifying and detecting infections caused by the most dangerous pathogens and causative agents of epidemiological outbreaks. The specific topic of this presentation is the phage typing of bacterial species, which can be an important method for epidemiological diagnostics. Together with different genetic methodologies - such as PCR-based methods, PFGE, plasmid fingerprinting, and ribosomal typing - phage typing is one method for identifying bacterial pathogens. The method has a high percentage of determination of phage types, high specificity of reaction, and is easy for interpretation and use by health workers. Phage typing was applied for inter-species differentiation of different species of Salmonella, S. typhi, Brucella spp, Staphylococcus aureus, E. col,i Clostridium deficile, Vibrio cholerae, Yersinia pestis, Yersinia enterocolitica, Lysteria monocytogenes, Clostridium perfringens, Clostridium tetani, plant pathogens, and other bacterial pathogens. In addition to addressing the utility and efficacy of phage typing, the paper will discuss the isolation and selection of diagnostic typing phages for interspecies differentiation of pathogens that is necessary

Upstream freshwater and terrestrial sources are differentially reflected in the bacterial community structure along a small Arctic river and its estuary

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Aviaja Lyberth Hauptmann

2016-09-01

Full Text Available Glacier melting and altered precipitation patterns influence Arctic freshwater and coastal ecosystems. Arctic rivers are central to Arctic water ecosystems by linking glacier meltwaters and precipitation with the ocean through transport of particulate matter and microorganisms. However, the impact of different water sources on the microbial communities in Arctic rivers and estuaries remains unknown. In this study we used 16S rRNA gene amplicon sequencing to assess a small river and its estuary on the Disko Island, West Greenland (69°N. Samples were taken in August when there is maximum precipitation and temperatures are high in the Disko Bay area. We describe the bacterial community through a river into the estuary, including communities originating in a glacier and a proglacial lake. Our results show that water from the glacier and lake transports distinct communities into the river in terms of diversity and community composition. Bacteria of terrestrial origin were among the dominating OTUs in the main river, while the glacier and lake supplied the river with water containing fewer terrestrial organisms. Also, more psychrophilic taxa were found in the community supplied by the lake. At the river mouth, the presence of dominant bacterial taxa from the lake and glacier was unnoticeable, but these taxa increased their abundances again further into the estuary. On average 23% of the estuary community consisted of indicator OTUs from different sites along the river. Environmental variables showed only weak correlations with community composition, suggesting that hydrology largely influences the observed patterns.

Upstream Freshwater and Terrestrial Sources Are Differentially Reflected in the Bacterial Community Structure along a Small Arctic River and Its Estuary

Science.gov (United States)

Hauptmann, Aviaja L.; Markussen, Thor N.; Stibal, Marek; Olsen, Nikoline S.; Elberling, Bo; Bælum, Jacob; Sicheritz-Pontén, Thomas; Jacobsen, Carsten S.

2016-01-01

Glacier melting and altered precipitation patterns influence Arctic freshwater and coastal ecosystems. Arctic rivers are central to Arctic water ecosystems by linking glacier meltwaters and precipitation with the ocean through transport of particulate matter and microorganisms. However, the impact of different water sources on the microbial communities in Arctic rivers and estuaries remains unknown. In this study we used 16S rRNA gene amplicon sequencing to assess a small river and its estuary on the Disko Island, West Greenland (69°N). Samples were taken in August when there is maximum precipitation and temperatures are high in the Disko Bay area. We describe the bacterial community through a river into the estuary, including communities originating in a glacier and a proglacial lake. Our results show that water from the glacier and lake transports distinct communities into the river in terms of diversity and community composition. Bacteria of terrestrial origin were among the dominating OTUs in the main river, while the glacier and lake supplied the river with water containing fewer terrestrial organisms. Also, more psychrophilic taxa were found in the community supplied by the lake. At the river mouth, the presence of dominant bacterial taxa from the lake and glacier was unnoticeable, but these taxa increased their abundances again further into the estuary. On average 23% of the estuary community consisted of indicator OTUs from different sites along the river. Environmental variables showed only weak correlations with community composition, suggesting that hydrology largely influences the observed patterns. PMID:27708629

High bacterial biodiversity increases degradation performance of hydrocarbons during bioremediation of contaminated harbor marine sediments

International Nuclear Information System (INIS)

Dell'Anno, Antonio; Beolchini, Francesca; Rocchetti, Laura; Luna, Gian Marco; Danovaro, Roberto

2012-01-01

We investigated changes of bacterial abundance and biodiversity during bioremediation experiments carried out on oxic and anoxic marine harbor sediments contaminated with hydrocarbons. Oxic sediments, supplied with inorganic nutrients, were incubated in aerobic conditions at 20 °C and 35 °C for 30 days, whereas anoxic sediments, amended with organic substrates, were incubated in anaerobic conditions at the same temperatures for 60 days. Results reported here indicate that temperature exerted the main effect on bacterial abundance, diversity and assemblage composition. At higher temperature bacterial diversity and evenness increased significantly in aerobic conditions, whilst decreased in anaerobic conditions. In both aerobic and anaerobic conditions, biodegradation efficiencies of hydrocarbons were significantly and positively related with bacterial richness and evenness. Overall results presented here suggest that bioremediation strategies, which can sustain high levels of bacterial diversity rather than the selection of specific taxa, may significantly increase the efficiency of hydrocarbon degradation in contaminated marine sediments. - Highlights: ► Bioremediation performance was investigated on hydrocarbon contaminated sediments. ► Major changes in bacterial diversity and assemblage composition were observed. ► Temperature exerted the major effect on bacterial assemblages. ► High bacterial diversity increased significantly biodegradation performance. ► This should be considered for sediment remediation by bio-treatments. - Bioremediation strategies which can sustain high levels of bacterial diversity may significantly increase the biodegradation of hydrocarbons in contaminated marine sediments.

Influence of the nano-micro structure of the surface on bacterial adhesion

Directory of Open Access Journals (Sweden)

Carolina Díaz

2007-03-01

Full Text Available Biomaterials failures are frequently associated to the formation of bacterial biofilms on the surface. The aim of this work is to study the adhesion of non motile bacteria streptococci consortium and motile Pseudomonas fluorescens. Substrates with micro and nanopatterned topography were used. The influence of surface characteristics on bacterial adhesion was investigated using optical and epifluorescence microscopy, scanning electron microscopy (SEM and atomic force microscopy (AFM. Results showed an important influence of the substratum nature. On microrough surfaces, initial bacterial adhesion was less significant than on smooth surfaces. In contrast, nanopatterned samples showed more bacterial attachment than the smooth control. It was also noted a remarkable difference in morphology, orientation and distribution of bacteria between the smooth and the nanostructured substrate. The results show the important effect of substratum nature and topography on bacterial adhesion which depended on the relation between roughness characteristics dimensions and bacterial size.

Synthesis of arborane triterpenols by a bacterial oxidosqualene cyclase

Science.gov (United States)

Banta, Amy B.; Wei, Jeremy H.; Gill, Clare C. C.; Giner, José-Luis; Welander, Paula V.

2017-01-01

Cyclic triterpenoids are a broad class of polycyclic lipids produced by bacteria and eukaryotes. They are biologically relevant for their roles in cellular physiology, including membrane structure and function, and biochemically relevant for their exquisite enzymatic cyclization mechanism. Cyclic triterpenoids are also geobiologically significant as they are readily preserved in sediments and are used as biomarkers for ancient life throughout Earth's history. Isoarborinol is one such triterpenoid whose only known biological sources are certain angiosperms and whose diagenetic derivatives (arboranes) are often used as indicators of terrestrial input into aquatic environments. However, the occurrence of arborane biomarkers in Permian and Triassic sediments, which predates the accepted origin of angiosperms, suggests that microbial sources of these lipids may also exist. In this study, we identify two isoarborinol-like lipids, eudoraenol and adriaticol, produced by the aerobic marine heterotrophic bacterium Eudoraea adriatica. Phylogenetic analysis demonstrates that the E. adriatica eudoraenol synthase is an oxidosqualene cyclase homologous to bacterial lanosterol synthases and distinct from plant triterpenoid synthases. Using an Escherichia coli heterologous sterol expression system, we demonstrate that substitution of four amino acid residues in a bacterial lanosterol synthase enabled synthesis of pentacyclic arborinols in addition to tetracyclic sterols. This variant provides valuable mechanistic insight into triterpenoid synthesis and reveals diagnostic amino acid residues to differentiate between sterol and arborinol synthases in genomic and metagenomic datasets. Our data suggest that there may be additional bacterial arborinol producers in marine and freshwater environments that could expand our understanding of these geologically informative lipids.

Bacterial contamination of platelet components not detected by BacT/ALERT®.

Science.gov (United States)

Abela, M A; Fenning, S; Maguire, K A; Morris, K G

2018-02-01

To investigate the possible causes for false negative results in BacT/ALERT ® 3D Signature System despite bacterial contamination of platelet units. The Northern Ireland Blood Transfusion Service (NIBTS) routinely extends platelet component shelf life to 7 days. Components are sampled and screened for bacterial contamination using an automated microbial detection system, the BacT/ALERT ® 3D Signature System. We report on three platelet components with confirmed bacterial contamination, which represent false negative BacT/ALERT ® results and near-miss serious adverse events. NIBTS protocols for risk reduction of bacterial contamination of platelet components are described. The methodology for bacterial detection using BacT/ALERT ® is outlined. Laboratory tests, relevant patient details and relevant follow-up information are analysed. In all three cases, Staphylococcus aureus was isolated from the platelet residue and confirmed on terminal sub-culture using BacT/ALERT ® . In two cases, S. aureus with similar genetic makeup was isolated from the donors. Risk reduction measures for bacterial contamination of platelet components are not always effective. Automated bacterial culture detection does not eliminate the risk of bacterial contamination. Visual inspection of platelet components prior to release, issue and administration remains an important last line of defence. © 2017 British Blood Transfusion Society.

Bacterial Communities in Women with Bacterial Vaginosis: High Resolution Phylogenetic Analyses Reveal Relationships of Microbiota to Clinical Criteria

Science.gov (United States)

Srinivasan, Sujatha; Hoffman, Noah G.; Morgan, Martin T.; Matsen, Frederick A.; Fiedler, Tina L.; Hall, Robert W.; Ross, Frederick J.; McCoy, Connor O.; Bumgarner, Roger; Marrazzo, Jeanne M.; Fredricks, David N.

2012-01-01

Background Bacterial vaginosis (BV) is a common condition that is associated with numerous adverse health outcomes and is characterized by poorly understood changes in the vaginal microbiota. We sought to describe the composition and diversity of the vaginal bacterial biota in women with BV using deep sequencing of the 16S rRNA gene coupled with species-level taxonomic identification. We investigated the associations between the presence of individual bacterial species and clinical diagnostic characteristics of BV. Methodology/Principal Findings Broad-range 16S rRNA gene PCR and pyrosequencing were performed on vaginal swabs from 220 women with and without BV. BV was assessed by Amsel’s clinical criteria and confirmed by Gram stain. Taxonomic classification was performed using phylogenetic placement tools that assigned 99% of query sequence reads to the species level. Women with BV had heterogeneous vaginal bacterial communities that were usually not dominated by a single taxon. In the absence of BV, vaginal bacterial communities were dominated by either Lactobacillus crispatus or Lactobacillus iners. Leptotrichia amnionii and Eggerthella sp. were the only two BV-associated bacteria (BVABs) significantly associated with each of the four Amsel’s criteria. Co-occurrence analysis revealed the presence of several sub-groups of BVABs suggesting metabolic co-dependencies. Greater abundance of several BVABs was observed in Black women without BV. Conclusions/Significance The human vaginal bacterial biota is heterogeneous and marked by greater species richness and diversity in women with BV; no species is universally present. Different bacterial species have different associations with the four clinical criteria, which may account for discrepancies often observed between Amsel and Nugent (Gram stain) diagnostic criteria. Several BVABs exhibited race-dependent prevalence when analyzed in separate groups by BV status which may contribute to increased incidence of BV in

Bacterial and archaeal diversity in two hot spring microbial mats from the geothermal region of Tengchong, China.

Science.gov (United States)

Pagaling, Eulyn; Grant, William D; Cowan, Don A; Jones, Brian E; Ma, Yanhe; Ventosa, Antonio; Heaphy, Shaun

2012-07-01

We investigated the bacterial and archaeal diversity in two hot spring microbial mats from the geothermal region of Tengchong in the Yunnan Province, China, using direct molecular analyses. The Langpu (LP) laminated mat was found by the side of a boiling pool with temperature of 60-65 °C and a pH of 8.5, while the Tengchong (TC) streamer mat consisted of white streamers in a slightly acidic (pH 6.5) hot pool outflow with a temperature of 72 °C. Four 16S rRNA gene clone libraries were constructed and restriction enzyme analysis of the inserts was used to identify unique sequences and clone frequencies. From almost 200 clones screened, 55 unique sequences were retrieved. Phylogenetic analysis showed that the LP mat consisted of a diverse bacterial population [Cyanobacteria, Chloroflexi, Chlorobia, Nitrospirae, 'Deinococcus-Thermus', Proteobacteria (alpha, beta and delta subdivisions), Firmicutes, Bacteroidetes and Actinobacteria], while the archaeal population was dominated by methanogenic Euryarchaeota and Crenarchaeota. In contrast, the TC streamer mat consisted of a bacterial population dominated by Aquificae, while the archaeal population also contained Korarchaeota as well as Crenarchaeota and methanogenic Euryarchaeota. These mats harboured clone sequences affiliated to unidentified lineages, suggesting that they are a potential source for discovering novel bacteria and archaea.

Bacterial lung abscess

International Nuclear Information System (INIS)

Groskin, S.A.; Panicek, D.M.; Ewing, D.K.; Rivera, F.; Math, K.; Teixeira, J.; Heitzman, E.R.

1987-01-01

A retrospective review of patients with bacterial lung abscess was carried out. Demographic, clinical, and radiographical features of this patient group are compared with similar data from patients with empyema and/or cavitated lung carcinoma; differential diagnostic points are stressed. The entity of radiographically occult lung abscess is discussed. Complications associated with bacterial lung abscess are discussed. Current therapeutic options and treatment philosophy for patients with bacterial lung abscess are noted

Bacterial growth on macrophyte leachate and fate of bacterial production

International Nuclear Information System (INIS)

Findlay, S.; Carlough, L.; Crocker, M.T.; Gill, H.K.; Meyer, J.L.; Smith, P.J.

1986-01-01

The role bacteria play in transferring organic carbon to other trophic levels in aquatic ecosystems depends on the efficiency with which they convert dissolved organic [ 14 C]-labelled carbon into bacterial biomass and on the ability of consumers to graze bacteria. The authors have measured the conversion efficiency for bacteria growing on macrophyte-derived dissolved organic carbon and estimated the amount of bacterial production removed by grazing. Bacteria converted this DOC into new tissue with an efficiency of 53%, substantially higher than the apparent conversion efficiency of macrophyte-derived particulate organic carbon or other types of DOC. Two estimates of grazing indicate that the decline in bacterial numbers after the bloom was probably due to grazing by flagellates. These results show the significance of the bacterial link between DOC and other trophic levels

The effect of dietary bacterial organic selenium on growth performance, antioxidant capacity, and Selenoproteins gene expression in broiler chickens.

Science.gov (United States)

Dalia, A M; Loh, T C; Sazili, A Q; Jahromi, M F; Samsudin, A A

2017-08-18

Selenium (Se) is an essential trace mineral in broilers, which has several important roles in biological processes. Organic forms of Se are more efficient than inorganic forms and can be produced biologically via Se microbial reduction. Hence, the possibility of using Se-enriched bacteria as feed supplement may provide an interesting source of organic Se, and benefit broiler antioxidant system and other biological processes. The objective of this study was to examine the impacts of inorganic Se and different bacterial organic Se sources on the performance, serum and tissues Se status, antioxidant capacity, and liver mRNA expression of selenoproteins in broilers. Results indicated that different Se sources did not significantly (P ≤ 0.05) affect broiler growth performance. However, bacterial organic Se of T5 (basal diet +0.3 mg /kg feed ADS18 Se), T4 (basal diet +0.3 mg /kg feed ADS2 Se), and T3 (basal diet +0.3 mg /kg feed ADS1 Se) exhibited significantly (P ≤ 0.05) highest Se concentration in serum, liver, and kidney respectively. Dietary inorganic Se and bacterial organic Se were observed to significantly affect broiler serum ALT, AST, LDH activities and serum creatinine level. ADS18 supplemented Se of (Stenotrophomonas maltophilia) bacterial strain showed the highest GSH-Px activity with the lowest MDA content in serum, and the highest GSH-Px and catalase activity in the kidney, while bacterial Se of ADS2 (Klebsiella pneumoniae) resulted in a higher level of GSH-Px1 and catalase in liver. Moreover, our study showed that in comparison with sodium selenite, only ADS18 bacterial Se showed a significantly higher mRNA level in GSH-Px1, GSH-Px4, DIO1, and TXNDR1, while both ADS18 and ADS2 showed high level of mRNA of DIO2 compared to sodium selenite. The supplementation of bacterial organic Se in broiler chicken, improved tissue Se deposition, antioxidant status, and selenoproteins gene expression, and can be considered as an effective alternative source of

Is low-energy-ion bombardment generated X-ray emission a secondary mutational source to ion-beam-induced genetic mutation?

Energy Technology Data Exchange (ETDEWEB)

Thongkumkoon, P. [Plasma and Beam Physics Research Facility, Department of Physics and Materials Science, Faculty of Science, Chiang Mai University, Chiang Mai 50200 (Thailand); Thailand Center of Excellence in Physics, Commission on Higher Education, 328 Si Ayutthaya Road, Bangkok 10400 (Thailand); Prakrajang, K. [Plasma and Beam Physics Research Facility, Department of Physics and Materials Science, Faculty of Science, Chiang Mai University, Chiang Mai 50200 (Thailand); Faculty of Science, Maejo University, Chiang Mai 50290 (Thailand); Thopan, P.; Yaopromsiri, C. [Plasma and Beam Physics Research Facility, Department of Physics and Materials Science, Faculty of Science, Chiang Mai University, Chiang Mai 50200 (Thailand); Suwannakachorn, D. [Plasma and Beam Physics Research Facility, Department of Physics and Materials Science, Faculty of Science, Chiang Mai University, Chiang Mai 50200 (Thailand); Thailand Center of Excellence in Physics, Commission on Higher Education, 328 Si Ayutthaya Road, Bangkok 10400 (Thailand); Yu, L.D., E-mail: yuld@fnrf.science.cmu.ac.th [Plasma and Beam Physics Research Facility, Department of Physics and Materials Science, Faculty of Science, Chiang Mai University, Chiang Mai 50200 (Thailand); Thailand Center of Excellence in Physics, Commission on Higher Education, 328 Si Ayutthaya Road, Bangkok 10400 (Thailand)

2013-07-15

Highlights: ► Detected X-ray emission from metal, plastic and biological samples. ► Characteristic X-ray emission was detected from metal but not from non-metals. ► Low-energy ion bombarded bacteria held in different sample holders. ► Bacteria held in metal holder had higher mutation rate than in plastic holder. ► Ion-beam-induced X-ray from biological sample is not a basic mutation source. -- Abstract: Low-energy ion beam biotechnology has achieved tremendous successes in inducing crop mutation and gene transfer. However, mechanisms involved in the related processes are not yet well understood. In ion-beam-induced mutation, ion-bombardment-produced X-ray has been proposed to be one of the secondary mutation sources, but the speculation has not yet been experimentally tested. We carried out this investigation to test whether the low-energy ion-beam-produced X-ray was a source of ion-beam-induced mutation. In the investigation, X-ray emission from 29-keV nitrogen- or argon- ion beam bombarded bacterial Escherichia coli (E. coli) cells held in a metal or plastic sample holder was in situ detected using a highly sensitive X-ray detector. The ion beam bombarded bacterial cells held in different material holders were observed for mutation induction. The results led to a conclusion that secondary X-ray emitted from ion-beam-bombarded biological living materials themselves was not a, or at least a negligible, mutational source, but the ion-beam-induced X-ray emission from the metal that made the sample holder could be a source of mutation.

Is low-energy-ion bombardment generated X-ray emission a secondary mutational source to ion-beam-induced genetic mutation?

International Nuclear Information System (INIS)

Thongkumkoon, P.; Prakrajang, K.; Thopan, P.; Yaopromsiri, C.; Suwannakachorn, D.; Yu, L.D.

2013-01-01

Highlights: ► Detected X-ray emission from metal, plastic and biological samples. ► Characteristic X-ray emission was detected from metal but not from non-metals. ► Low-energy ion bombarded bacteria held in different sample holders. ► Bacteria held in metal holder had higher mutation rate than in plastic holder. ► Ion-beam-induced X-ray from biological sample is not a basic mutation source. -- Abstract: Low-energy ion beam biotechnology has achieved tremendous successes in inducing crop mutation and gene transfer. However, mechanisms involved in the related processes are not yet well understood. In ion-beam-induced mutation, ion-bombardment-produced X-ray has been proposed to be one of the secondary mutation sources, but the speculation has not yet been experimentally tested. We carried out this investigation to test whether the low-energy ion-beam-produced X-ray was a source of ion-beam-induced mutation. In the investigation, X-ray emission from 29-keV nitrogen- or argon- ion beam bombarded bacterial Escherichia coli (E. coli) cells held in a metal or plastic sample holder was in situ detected using a highly sensitive X-ray detector. The ion beam bombarded bacterial cells held in different material holders were observed for mutation induction. The results led to a conclusion that secondary X-ray emitted from ion-beam-bombarded biological living materials themselves was not a, or at least a negligible, mutational source, but the ion-beam-induced X-ray emission from the metal that made the sample holder could be a source of mutation

Estimation of Throughfall and Stemflow Bacterial Flux in a Subtropical Oak-Cedar Forest

Science.gov (United States)

Bittar, Thais B.; Pound, Preston; Whitetree, Ansley; Moore, L. Dean; Van Stan, John T.

2018-02-01

Transport pathways of microbes between ecosystem spheres (atmosphere, phyllosphere, and pedosphere) represent major fluxes in nutrient cycles and have the potential to affect microbially mediated biogeochemical processes. Novel data on bacterial fluxes from the phyllosphere to the pedosphere during rainfall via throughfall (rain dripping from/through the canopy) and stemflow (rain funneled down tree stems) are reported. Bacterial concentrations were quantified using flow cytometry and validated with quantitative polymerase chain reaction assays in rainfall samples from an oak-cedar forest in coastal Georgia (southeastern U.S.). Bacteria concentrations (cells mL-1) and storm-normalized fluxes (cells m-2 h-1, cells m-2 mm-1) were greater for cedar versus oak. Total bacterial flux was 1.5 × 1016 cells ha-1 yr-1. These previously unexamined bacterial fluxes are interpreted in the context of major elemental pools and fluxes in forests and could represent inoculum-level sources of bacteria (if alive), and organic matter and inorganic solute inputs (if lysed) to soils.

System automation for a bacterial colony detection and identification instrument via forward scattering

International Nuclear Information System (INIS)

Bae, Euiwon; Hirleman, E Daniel; Aroonnual, Amornrat; Bhunia, Arun K; Robinson, J Paul

2009-01-01

A system design and automation of a microbiological instrument that locates bacterial colonies and captures the forward-scattering signatures are presented. The proposed instrument integrates three major components: a colony locator, a forward scatterometer and a motion controller. The colony locator utilizes an off-axis light source to illuminate a Petri dish and an IEEE1394 camera to capture the diffusively scattered light to provide the number of bacterial colonies and two-dimensional coordinate information of the bacterial colonies with the help of a segmentation algorithm with region-growing. Then the Petri dish is automatically aligned with the respective centroid coordinate with a trajectory optimization method, such as the Traveling Salesman Algorithm. The forward scatterometer automatically computes the scattered laser beam from a monochromatic image sensor via quadrant intensity balancing and quantitatively determines the centeredness of the forward-scattering pattern. The final scattering signatures are stored to be analyzed to provide rapid identification and classification of the bacterial samples

Sources of the Geomagnetic Field and the Modern Data That Enable Their Investigation

DEFF Research Database (Denmark)

Olsen, Nils; Hulot, Gauthier; Sabaka, Terence J.

2014-01-01

has a large and complicated magnetic field, a major part of which is produced by a self-sustaining dynamo operating in the fluid outer core. What is measured at or near the surface of the Earth, however, is the superposition of the core field and of additional fields caused by magnetized rocks......The geomagnetic field one can measure at the Earth’s surface or on board satellites is the sum of contributions from many different sources. These sources have different physical origins and can be found both below (in the form of electrical currents and magnetized material) and above (only...... in the form of electrical currents) the Earth’s surface. Each source happens to produce a contribution with rather specific spatio-temporal properties. This fortunate situation is what makes the identification and investigation of the contribution of each source possible, provided appropriate observational...

Bacterial growth in solar heating prepared and traditional tanks

International Nuclear Information System (INIS)

Bagh, L.K.

2000-01-01

In Denmark it has been put forward that the introduction of solar heating prepared tanks into the building regulation can cause increased nuisance with respect to bacterial growth in hot water for domestic use. The reason is that solar heating prepared tanks have a larger volume and another form of operation than traditional tanks. In this investigation the difference between bacterial growth in solar heating prepared and traditional tanks was measured by heterotrophic plate counts as a general parameter for microbiological growth. There was no significant difference between the bacterial number in the solar heating prepared tanks and in the traditional tanks, either for bacteria determined at 37 deg. C, 44 deg. C, 55 deg. C or at 65 deg. C. The hot water for domestic use from the solar heating prepared tanks and the traditional tanks had in most cases a bacterial number below 1.000 CFU/ml, and all tests had a bacterial number below 10.000 CFU/ml. The number of bacteria must be considered low seen in relation to the other measurements of bacteria in hot water for domestic use, particularly in larger block of flats. (au)

Impact of disinfection on drinking water biofilm bacterial community.

Science.gov (United States)

Mi, Zilong; Dai, Yu; Xie, Shuguang; Chen, Chao; Zhang, Xiaojian

2015-11-01

Disinfectants are commonly applied to control the growth of microorganisms in drinking water distribution systems. However, the effect of disinfection on drinking water microbial community remains poorly understood. The present study investigated the impacts of different disinfectants (chlorine and chloramine) and dosages on biofilm bacterial community in bench-scale pipe section reactors. Illumina MiSeq sequencing illustrated that disinfection strategy could affect both bacterial diversity and community structure of drinking water biofilm. Proteobacteria tended to predominate in chloraminated drinking water biofilms, while Firmicutes in chlorinated and unchlorinated biofilms. The major proteobacterial groups were influenced by both disinfectant type and dosage. In addition, chloramination had a more profound impact on bacterial community than chlorination. Copyright © 2015. Published by Elsevier B.V.

Bioelectrogenesis with microbial fuel cells (MFCs using the microalga Chlorella vulgaris and bacterial communities

Directory of Open Access Journals (Sweden)

Ronald Huarachi-Olivera

2018-01-01

Conclusions: These findings suggest that MFCs with C. vulgaris and bacterial community have a simultaneous efficiency in the production of bioelectricity and bioremediation processes, becoming an important source of bioenergy in the future.

Chemical synthesis of perfectly isotactic and high melting bacterial poly(3-hydroxybutyrate) from bio-sourced racemic cyclic diolide.

Science.gov (United States)

Tang, Xiaoyan; Chen, Eugene Y-X

2018-06-11

Bacterial poly(3-hydroxybutyrate) (P3HB) is a perfectly isotactic, crystalline material possessing properties suitable for substituting petroleum plastics, but high costs and low volumes of its production are impractical for commodity applications. The chemical synthesis of P3HB via ring-opening polymerization (ROP) of racemic β-butyrolactone has attracted intensive efforts since the 1960s, but not yet produced P3HB with high isotacticity and molecular weight. Here, we report a route utilizing racemic cyclic diolide (rac-DL) derived from bio-sourced succinate. With stereoselective racemic catalysts, the ROP of rac-DL under ambient conditions produces rapidly P3HB with perfect isotacticity ([mm] > 99%), high melting temperature (T m  = 171 °C), and high molecular weight (M n  = 1.54 × 10 5  g mol -1 , Đ = 1.01). With enantiomeric catalysts, kinetic resolution polymerizations of rac-DL automatically stops at 50% conversion and yields enantiopure (R,R)-DL and (S,S)-DL with >99% e.e. and the corresponding poly[(S)-3HB] and poly[(R)-3HB] with high T m  = 175 °C.

The Sponge-associated Bacterium Bacillus licheniformis SAB1: A Source of Antimicrobial Compounds

Directory of Open Access Journals (Sweden)

Prabha Devi

2010-04-01

Full Text Available Several bacterial cultures were isolated from sponge Halichondria sp., collected from the Gujarat coast of the Indo Pacific region. These bacterial cultures were fermented in the laboratory (100 mL and the culture filtrate was assayed for antibiotic activity against 16 strains of clinical pathogens. Bacillus sp. (SAB1, the most potent of them and antagonistic to several clinically pathogenic Gram-positive, Gram-negative bacteria and the fungus Aspergillus fumigatus was chosen for further investigation. Analysis of the nucleotide sequence of the 16S rDNA gene of Bacillus sp. SAB1 showed a strong similarity (100% with the 16S rDNA gene of Bacillus licheniformis HNL09. The bioactive compounds produced by Bacillus licheniformis SAB1 (GenBank accession number: DQ071568 were identified as indole (1, 3-phenylpropionic acid (2 and a dimer 4,4′-oxybis[3-phenylpropionic acid] (3 on the basis of their Fourier Transform Infrared (FTIR, Nuclear Magnetic Resonance (NMR and Electrospray Ionization Mass Spectrometer (ESI-MS data. There is a single reference on the natural occurrence of compound 3 from the leaves of a terrestrial herb Aptenia cordifolia in the literature, so to the best of our knowledge, this is a first report of its natural occurrence from a marine source. The recovery of bacterial strains with antimicrobial activity suggests that marine-invertebrates remain a rich source for the isolation of culturable isolates capable of producing novel bioactive secondary metabolites.

Haematoxylin and eosin staining identifies medium to large bacterial aggregates with a reliable specificity: A comparative analysis of follicular bacterial aggregates in axillary biopsies using peptide nucleic acid-fluorescence in situ hybridization and haematoxylin and eosin staining.

Science.gov (United States)

Ring, Hans Christian; Theut Riis, Peter; Bay, Lene; Kallenbach, Klaus; Bjarnsholt, Thomas; Jemec, Gregor B E

2017-10-01

Although peptide nucleic acid (PNA), fluorescence in situ hybridization (FISH) and confocal laser scanning microscopy (CLSM) are the reference tools in the study of bacterial aggregates/biofilms, it may also be rather time-consuming. This study aimed to investigate the sensitivity and specificity between bacterial aggregates identified by haematoxylin and eosin (HE) staining vs bacterial aggregates in corresponding PNA-FISH samples. Axillary biopsies were obtained in 24 healthy controls. HE-stained and PNA-FISH samples were investigated using traditional light microscopy and CLSM, respectively. The data demonstrate that HE staining identifies large bacterial aggregates (>10 μm) with a sensitivity of 0.43 and specificity of 1. The methods, however, are not equivalent as demonstrated by a McNemar's test (P=.04). Where bacterial aggregates >10 μm in diameter, HE staining may offer a rapid and practical low-cost tool to evaluate bacterial aggregates. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Respiratory bacterial infections in cystic fibrosis

DEFF Research Database (Denmark)

Ciofu, Oana; Hansen, Christine R; Høiby, Niels

2013-01-01

PURPOSE OF REVIEW: Bacterial respiratory infections are the main cause of morbidity and mortality in patients with cystic fibrosis (CF). Pseudomonas aeruginosa remains the main pathogen in adults, but other Gram-negative bacteria such as Achromobacter xylosoxidans and Stenotrophomonas maltophilia...... respiratory tract (nasal sampling) should be investigated and both infection sites should be treated....

Isolation of hydrocarbon utilizing bacteria from different ecological sources

International Nuclear Information System (INIS)

Iqbal, M.J.; Choudri, S.F.; Hameed, A.

1991-01-01

Among the various samples from different ecological sources oil contaminated soil samples and waste from sugar processing industry were found to have bacterial populations with ability of utilizing oil. In addition to oil, molasses base medium was also used to study the utilizing ability. Selection was made on the basis on the high gas production, decrease in pH, percentage of oil consumed and bacterial counts. Fermented scum and oil contaminated soil from Sehala (Islamabad) were found to contain microbes having maximum oil degrading ability. The bacterial isolates belong to the genera of Bacillus, Pseudomonas, Enterobacter and Escherichia. (author)

S1PR3 Signaling Drives Bacterial Killing and Is Required for Survival in Bacterial Sepsis.

Science.gov (United States)

Hou, JinChao; Chen, QiXing; Wu, XiaoLiang; Zhao, DongYan; Reuveni, Hadas; Licht, Tamar; Xu, MengLong; Hu, Hu; Hoeft, Andreas; Ben-Sasson, Shmuel A; Shu, Qiang; Fang, XiangMing

2017-12-15

Efficient elimination of pathogenic bacteria is a critical determinant in the outcome of sepsis. Sphingosine-1-phosphate receptor 3 (S1PR3) mediates multiple aspects of the inflammatory response during sepsis, but whether S1PR3 signaling is necessary for eliminating the invading pathogens remains unknown. To investigate the role of S1PR3 in antibacterial immunity during sepsis. Loss- and gain-of-function experiments were performed using cell and murine models. S1PR3 levels were determined in patients with sepsis and healthy volunteers. S1PR3 protein levels were up-regulated in macrophages upon bacterial stimulation. S1pr3 -/- mice showed increased mortality and increased bacterial burden in multiple models of sepsis. The transfer of wild-type bone marrow-derived macrophages rescued S1pr3 -/- mice from lethal sepsis. S1PR3-overexpressing macrophages further ameliorated the mortality rate of sepsis. Loss of S1PR3 led to markedly decreased bacterial killing in macrophages. Enhancing endogenous S1PR3 activity using a peptide agonist potentiated the macrophage bactericidal function and improved survival rates in multiple models of sepsis. Mechanically, the reactive oxygen species levels were decreased and phagosome maturation was delayed in S1pr3 -/- macrophages due to impaired recruitment of vacuolar protein-sorting 34 to the phagosomes. In addition, S1RP3 expression levels were elevated in monocytes from patients with sepsis. Higher levels of monocytic S1PR3 were associated with efficient intracellular bactericidal activity, better immune status, and preferable outcomes. S1PR3 signaling drives bacterial killing and is essential for survival in bacterial sepsis. Interventions targeting S1PR3 signaling could have translational implications for manipulating the innate immune response to combat pathogens.

The oral cavity is not a primary source for implantable pacemaker or cardioverter defibrillator infections

Science.gov (United States)

2013-01-01

Background To test the hypothesis that the oral cavity is a potential source for implantable pacemaker and cardioverter defibrillators infections, the bacterial diversity on explanted rhythm heart management devices was investigated and compared to the oral microbiome. Methods A metagenomic approach was used to analyze the bacterial diversity on the surfaces of non-infected and infected pacemakers. The DNA from surfaces swaps of 24 non-infected and 23 infected pacemaker were isolated and subjected to bacterial-specific DNA amplification, single strand conformation polymorphism- (SSCP) and sequencing analysis. Species-specific primer sets were used to analyze for any correlation between bacterial diversity on pacemakers and in the oral cavity. Results DNA of bacterial origin was detected in 21 cases on infected pacemakers and assigned to the bacterial phylotypes Staphylococcus epidermidis, Propionibacterium acnes, Staphylococcus aureus, Staphylococcus schleiferi and Stapyhlococcus. In 17 cases bacterial DNA was found on pacemakers with no clinical signs of infections. On the basis of the obtained sequence data, the phylotypes Propionibacterium acnes, Staphylococcus and an uncultured bacterium were identified. Propionibacterium acnes and Staphylococcus epidermidis were the only bacteria detected in pacemeaker (n = 25) and oral samples (n = 11). Conclusions The frequency of the coincidental detection of bacteria on infected devices and in the oral cavity is low and the detected bacteria are highly abundant colonizers of non-oral human niches. The transmission of oral bacteria to the lead or device of implantable pacemaker or cardioverter defibrillators is unlikely relevant for the pathogenesis of pacemaker or cardioverter defibrillators infections. PMID:23575037

BACTERIAL CONSORTIUM

Directory of Open Access Journals (Sweden)

Payel Sarkar

2013-01-01

Full Text Available Petroleum aromatic hydrocarbons like benzen e, toluene, ethyl benzene and xylene, together known as BTEX, has almost the same chemical structure. These aromatic hydrocarbons are released as pollutants in th e environment. This work was taken up to develop a solvent tolerant bacterial cons ortium that could degrade BTEX compounds as they all share a common chemical structure. We have isolated almost 60 different types of bacterial strains from different petroleum contaminated sites. Of these 60 bacterial strains almost 20 microorganisms were screene d on the basis of capability to tolerate high concentration of BTEX. Ten differe nt consortia were prepared and the compatibility of the bacterial strains within the consortia was checked by gram staining and BTEX tolerance level. Four successful mi crobial consortia were selected in which all the bacterial strains concomitantly grew in presence of high concentration of BTEX (10% of toluene, 10% of benzene 5% ethyl benzene and 1% xylene. Consortium #2 showed the highest growth rate in pr esence of BTEX. Degradation of BTEX by consortium #2 was monitored for 5 days by gradual decrease in the volume of the solvents. The maximum reduction observed wa s 85% in 5 days. Gas chromatography results also reveal that could completely degrade benzene and ethyl benzene within 48 hours. Almost 90% degradation of toluene and xylene in 48 hours was exhibited by consortium #2. It could also tolerate and degrade many industrial solvents such as chloroform, DMSO, acetonitrile having a wide range of log P values (0.03–3.1. Degradation of aromatic hydrocarbon like BTEX by a solvent tolerant bacterial consortium is greatly significant as it could degrade high concentration of pollutants compared to a bacterium and also reduces the time span of degradation.

Fabrication and investigation of a biocompatible microfilament with high mechanical performance based on regenerated bacterial cellulose and bacterial cellulose.

Science.gov (United States)

Wu, Huan-Ling; Bremner, David H; Wang, Hai-Jun; Wu, Jun-Zi; Li, He-Yu; Wu, Jian-Rong; Niu, Shi-Wei; Zhu, Li-Min

2017-10-01

A high-strength regenerated bacterial cellulose (RBC)/bacterial cellulose (BC) microfilament of potential use as a biomaterial was successfully prepared via a wet spinning process. The BC not only consists of a 3-D network composed of nanofibers with a diameter of several hundred nanometers but also has a secondary structure consisting of highly oriented nanofibrils with a diameter ranging from a few nanometers to tens of nanometers which explains the reason for the high mechanical strength of BC. Furthermore, a strategy of partially dissolving BC was used and this greatly enhanced the mechanical performance of spun filament and a method called post-treatment was utilized to remove residual solvents from the RBC/BC filaments. A comparison of structure, properties, as well as cytocompatibility between BC nanofibers and RBC/BC microfilaments was achieved using morphology, mechanical properties, X-ray Diffraction (XRD) and an enzymatic hydrolysis assay. The RBC/BC microfilament has a uniform groove structure with a diameter of 50-60μm and XRD indicated that the crystal form was transformed from cellulose Iα to cellulose III I and the degree of crystallinity of RBC/BC (33.22%) was much lower than the original BC (60.29%). The enzymatic hydrolysis assay proved that the RBC/BC material was more easily degraded than BC. ICP detection indicated that the residual amount of lithium was 0.07mg/g (w/w) and GC-MS analysis showed the residual amount of DMAc to be 8.51μg/g (w/w) demonstrating that the post-treatment process is necessary and effective for removal of residual materials from the RBC/BC microfilaments. Also, a cell viability assay demonstrated that after post-treatment the RBC/BC filaments had good cytocompatibility. Copyright © 2017 Elsevier B.V. All rights reserved.

Bacterial communities associated with white shrimp (Litopenaeus vannamei larvae at early developmental stages

Directory of Open Access Journals (Sweden)

ANTONIUS SUWANTO

2010-04-01

Full Text Available Bacterial communities associated with white shrimp (Litopenaeus vannamei larvae at early developmental stages. Biodiversitas 11 (2: 65-68.Terminal Restriction Fragment Length Polymorphism (T-RFLP was used to monitor the dynamics of the bacterial communities associated with early developmental stages of white shrimp (Litopenaeus vannamei larvae. Samples for analysis were egg, hatching nauplii, 24 hours old nauplii, and 48 hours old nauplii which were collected from one cycle of production at commercial hatchery. T-RFLP results indicated that the bacterial community associated with early stages of shrimp development might be transferred vertically from broodstock via egg. There was no significant difference between bacterial communities investigated, except the bacterial community of 48 hours old nauplii. Diversity analyses showed that the bacterial community of egg had the highest diversity and evenness, meanwhile the bacterial community of 48 hours old nauplii had the lowest diversity. Nine phylotypes were found at all stages with high abundance. Those TRFs were identified as γ- proteobacteria, α-proteobacteria, and bacteroidetes group.

Investigating sources and pathways of perfluoroalkyl acids (PFAAs) in aquifers in Tokyo using multiple tracers

International Nuclear Information System (INIS)

Kuroda, Keisuke; Murakami, Michio; Oguma, Kumiko; Takada, Hideshige; Takizawa, Satoshi

2014-01-01

We employed a multi-tracer approach to investigate sources and pathways of perfluoroalkyl acids (PFAAs) in urban groundwater, based on 53 groundwater samples taken from confined aquifers and unconfined aquifers in Tokyo. While the median concentrations of groundwater PFAAs were several ng/L, the maximum concentrations of perfluorooctane sulfonate (PFOS, 990 ng/L), perfluorooctanoate (PFOA, 1800 ng/L) and perfluorononanoate (PFNA, 620 ng/L) in groundwater were several times higher than those of wastewater and street runoff reported in the literature. PFAAs were more frequently detected than sewage tracers (carbamazepine and crotamiton), presumably owing to the higher persistence of PFAAs, the multiple sources of PFAAs beyond sewage (e.g., surface runoff, point sources) and the formation of PFAAs from their precursors. Use of multiple methods of source apportionment including principal component analysis–multiple linear regression (PCA–MLR) and perfluoroalkyl carboxylic acid ratio analysis highlighted sewage and point sources as the primary sources of PFAAs in the most severely polluted groundwater samples, with street runoff being a minor source (44.6% sewage, 45.7% point sources and 9.7% street runoff, by PCA–MLR). Tritium analysis indicated that, while young groundwater (recharged during or after the 1970s, when PFAAs were already in commercial use) in shallow aquifers (< 50 m depth) was naturally highly vulnerable to PFAA pollution, PFAAs were also found in old groundwater (recharged before the 1950s, when PFAAs were not in use) in deep aquifers (50–500 m depth). This study demonstrated the utility of multiple uses of tracers (pharmaceuticals and personal care products; PPCPs, tritium) and source apportionment methods in investigating sources and pathways of PFAAs in multiple aquifer systems. - Highlights: • Aquifers in Tokyo had high levels of perfluoroalkyl acids (up to 1800 ng/L). • PFAAs were more frequently detected than sewage

Investigating sources and pathways of perfluoroalkyl acids (PFAAs) in aquifers in Tokyo using multiple tracers

Energy Technology Data Exchange (ETDEWEB)

Kuroda, Keisuke, E-mail: keisukekr@gmail.com [Department of Urban Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-8656 (Japan); Murakami, Michio [Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8505 (Japan); Oguma, Kumiko [Department of Urban Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-8656 (Japan); Takada, Hideshige [Laboratory of Organic Geochemistry (LOG), Institute of Symbiotic Science and Technology, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509 (Japan); Takizawa, Satoshi [Department of Urban Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-8656 (Japan)

2014-08-01

We employed a multi-tracer approach to investigate sources and pathways of perfluoroalkyl acids (PFAAs) in urban groundwater, based on 53 groundwater samples taken from confined aquifers and unconfined aquifers in Tokyo. While the median concentrations of groundwater PFAAs were several ng/L, the maximum concentrations of perfluorooctane sulfonate (PFOS, 990 ng/L), perfluorooctanoate (PFOA, 1800 ng/L) and perfluorononanoate (PFNA, 620 ng/L) in groundwater were several times higher than those of wastewater and street runoff reported in the literature. PFAAs were more frequently detected than sewage tracers (carbamazepine and crotamiton), presumably owing to the higher persistence of PFAAs, the multiple sources of PFAAs beyond sewage (e.g., surface runoff, point sources) and the formation of PFAAs from their precursors. Use of multiple methods of source apportionment including principal component analysis–multiple linear regression (PCA–MLR) and perfluoroalkyl carboxylic acid ratio analysis highlighted sewage and point sources as the primary sources of PFAAs in the most severely polluted groundwater samples, with street runoff being a minor source (44.6% sewage, 45.7% point sources and 9.7% street runoff, by PCA–MLR). Tritium analysis indicated that, while young groundwater (recharged during or after the 1970s, when PFAAs were already in commercial use) in shallow aquifers (< 50 m depth) was naturally highly vulnerable to PFAA pollution, PFAAs were also found in old groundwater (recharged before the 1950s, when PFAAs were not in use) in deep aquifers (50–500 m depth). This study demonstrated the utility of multiple uses of tracers (pharmaceuticals and personal care products; PPCPs, tritium) and source apportionment methods in investigating sources and pathways of PFAAs in multiple aquifer systems. - Highlights: • Aquifers in Tokyo had high levels of perfluoroalkyl acids (up to 1800 ng/L). • PFAAs were more frequently detected than sewage

Bacterial surface adaptation

Science.gov (United States)

Utada, Andrew

2014-03-01

Biofilms are structured multi-cellular communities that are fundamental to the biology and ecology of bacteria. Parasitic bacterial biofilms can cause lethal infections and biofouling, but commensal bacterial biofilms, such as those found in the gut, can break down otherwise indigestible plant polysaccharides and allow us to enjoy vegetables. The first step in biofilm formation, adaptation to life on a surface, requires a working knowledge of low Reynolds number fluid physics, and the coordination of biochemical signaling, polysaccharide production, and molecular motility motors. These crucial early stages of biofilm formation are at present poorly understood. By adapting methods from soft matter physics, we dissect bacterial social behavior at the single cell level for several prototypical bacterial species, including Pseudomonas aeruginosa and Vibrio cholerae.

Bacterial infections and hepatic encephalopathy in liver cirrhosis-prophylaxis and treatment.

Science.gov (United States)

Piotrowski, Damian; Boroń-Kaczmarska, Anna

2017-09-01

Infections are common among patients with liver cirrhosis. They occur more often in cirrhotic patient groups than in the general population and result in higher mortality. One reason for this phenomenon is bacterial translocation from the intestinal lumen that occurs as a consequence of intestinal bacterial overgrowth, increased permeability and decreased motility. The most common infections in cirrhotic patients are spontaneous bacterial peritonitis and urinary tract infections, followed by pneumonia, skin and soft tissue infections. Intestinal bacterial overgrowth is also responsible for hyperammonemia, which leads to hepatic encephalopathy. All of these complications make this group of patients at high risk for mortality. The role of antibiotics in liver cirrhosis is to treat and in some cases to prevent the development of infectious complications. Based on our current knowledge, antibiotic prophylaxis should be administered to patients with gastrointestinal hemorrhage, low ascitic fluid protein concentration combined with liver or renal failure, and spontaneous bacterial peritonitis as a secondary prophylaxis, as well as after hepatic encephalopathy episodes (also as a secondary prophylaxis). In some cases, the use of non-antibiotic prophylaxis can also be considered. Current knowledge of the treatment of infections allows the choice of a preferred antibiotic for empiric therapy depending on the infection location and whether the source of the disease is nosocomial or community-acquired. Copyright © 2017 Medical University of Bialystok. Published by Elsevier B.V. All rights reserved.

Sugar Lego: gene composition of bacterial carbohydrate metabolism genomic loci.

Science.gov (United States)

Kaznadzey, Anna; Shelyakin, Pavel; Gelfand, Mikhail S

2017-11-25

Bacterial carbohydrate metabolism is extremely diverse, since carbohydrates serve as a major energy source and are involved in a variety of cellular processes. Bacterial genes belonging to same metabolic pathway are often co-localized in the chromosome, but it is not a strict rule. Gene co-localization in linked to co-evolution and co-regulation. This study focuses on a large-scale analysis of bacterial genomic loci related to the carbohydrate metabolism. We demonstrate that only 53% of 148,000 studied genes from over six hundred bacterial genomes are co-localized in bacterial genomes with other carbohydrate metabolism genes, which points to a significant role of singleton genes. Co-localized genes form cassettes, ranging in size from two to fifteen genes. Two major factors influencing the cassette-forming tendency are gene function and bacterial phylogeny. We have obtained a comprehensive picture of co-localization preferences of genes for nineteen major carbohydrate metabolism functional classes, over two hundred gene orthologous clusters, and thirty bacterial classes, and characterized the cassette variety in size and content among different species, highlighting a significant role of short cassettes. The preference towards co-localization of carbohydrate metabolism genes varies between 40 and 76% for bacterial taxa. Analysis of frequently co-localized genes yielded forty-five significant pairwise links between genes belonging to different functional classes. The number of such links per class range from zero to eight, demonstrating varying preferences of respective genes towards a specific chromosomal neighborhood. Genes from eleven functional classes tend to co-localize with genes from the same class, indicating an important role of clustering of genes with similar functions. At that, in most cases such co-localization does not originate from local duplication events. Overall, we describe a complex web formed by evolutionary relationships of bacterial

New insights into valve-related intramural and intracellular bacterial diversity in infective endocarditis.

Science.gov (United States)

Oberbach, Andreas; Schlichting, Nadine; Feder, Stefan; Lehmann, Stefanie; Kullnick, Yvonne; Buschmann, Tilo; Blumert, Conny; Horn, Friedemann; Neuhaus, Jochen; Neujahr, Ralph; Bagaev, Erik; Hagl, Christian; Pichlmaier, Maximilian; Rodloff, Arne Christian; Gräber, Sandra; Kirsch, Katharina; Sandri, Marcus; Kumbhari, Vivek; Behzadi, Armirhossein; Behzadi, Amirali; Correia, Joao Carlos; Mohr, Friedrich Wilhelm; Friedrich, Maik

2017-01-01

In infective endocarditis (IE), a severe inflammatory disease of the endocardium with an unchanged incidence and mortality rate over the past decades, only 1% of the cases have been described as polymicrobial infections based on microbiological approaches. The aim of this study was to identify potential biodiversity of bacterial species from infected native and prosthetic valves. Furthermore, we compared the ultrastructural micro-environments to detect the localization and distribution patterns of pathogens in IE. Using next-generation sequencing (NGS) of 16S rDNA, which allows analysis of the entire bacterial community within a single sample, we investigated the biodiversity of infectious bacterial species from resected native and prosthetic valves in a clinical cohort of 8 IE patients. Furthermore, we investigated the ultrastructural infected valve micro-environment by focused ion beam scanning electron microscopy (FIB-SEM). Biodiversity was detected in 7 of 8 resected heart valves. This comprised 13 bacterial genera and 16 species. In addition to 11 pathogens already described as being IE related, 5 bacterial species were identified as having a novel association. In contrast, valve and blood culture-based diagnosis revealed only 4 species from 3 bacterial genera and did not show any relevant antibiotic resistance. The antibiotics chosen on this basis for treatment, however, did not cover the bacterial spectra identified by our amplicon sequencing analysis in 4 of 8 cases. In addition to intramural distribution patterns of infective bacteria, intracellular localization with evidence of bacterial immune escape mechanisms was identified. The high frequency of polymicrobial infections, pathogen diversity, and intracellular persistence of common IE-causing bacteria may provide clues to help explain the persistent and devastating mortality rate observed for IE. Improved bacterial diagnosis by 16S rDNA NGS that increases the ability to tailor antibiotic therapy may

Characterization of bacterial diversity associated with deep sea ferromanganese nodules from the South China Sea.

Science.gov (United States)

Zhang, De-Chao; Liu, Yan-Xia; Li, Xin-Zheng

2015-09-01

Deep sea ferromanganese (FeMn) nodules contain metallic mineral resources and have great economic potential. In this study, a combination of culture-dependent and culture-independent (16S rRNA genes clone library and pyrosequencing) methods was used to investigate the bacterial diversity in FeMn nodules from Jiaolong Seamount, the South China Sea. Eleven bacterial strains including some moderate thermophiles were isolated. The majority of strains belonged to the phylum Proteobacteria; one isolate belonged to the phylum Firmicutes. A total of 259 near full-length bacterial 16S rRNA gene sequences in a clone library and 67,079 valid reads obtained using pyrosequencing indicated that members of the Gammaproteobacteria dominated, with the most abundant bacterial genera being Pseudomonas and Alteromonas. Sequence analysis indicated the presence of many organisms whose closest relatives are known manganese oxidizers, iron reducers, hydrogen-oxidizing bacteria and methylotrophs. This is the first reported investigation of bacterial diversity associated with deep sea FeMn nodules from the South China Sea.

Bacterial Communities Associated with the Lichen Symbiosis▿ †

Science.gov (United States)

Bates, Scott T.; Cropsey, Garrett W. G.; Caporaso, J. Gregory; Knight, Rob; Fierer, Noah

2011-01-01

Lichens are commonly described as a mutualistic symbiosis between fungi and “algae” (Chlorophyta or Cyanobacteria); however, they also have internal bacterial communities. Recent research suggests that lichen-associated microbes are an integral component of lichen thalli and that the classical view of this symbiotic relationship should be expanded to include bacteria. However, we still have a limited understanding of the phylogenetic structure of these communities and their variability across lichen species. To address these knowledge gaps, we used bar-coded pyrosequencing to survey the bacterial communities associated with lichens. Bacterial sequences obtained from four lichen species at multiple locations on rock outcrops suggested that each lichen species harbored a distinct community and that all communities were dominated by Alphaproteobacteria. Across all samples, we recovered numerous bacterial phylotypes that were closely related to sequences isolated from lichens in prior investigations, including those from a lichen-associated Rhizobiales lineage (LAR1; putative N2 fixers). LAR1-related phylotypes were relatively abundant and were found in all four lichen species, and many sequences closely related to other known N2 fixers (e.g., Azospirillum, Bradyrhizobium, and Frankia) were recovered. Our findings confirm the presence of highly structured bacterial communities within lichens and provide additional evidence that these bacteria may serve distinct functional roles within lichen symbioses. PMID:21169444

CHANGES IN BACTERIAL COMPOSITION OF BIOFILM IN A METROPOLITAN DRINKING WATER DISTRIBUTION SYSTEM

Science.gov (United States)

This study examined the development of bacterial biofilms within a metropolitan distribution system. The distribution system is fed with different source water (i.e., groundwater, GW and surface water, SW) and undergoes different treatment processes in separate facilities. The b...

Effect of Vibration on Bacterial Growth and Antibiotic Resistance

Science.gov (United States)

Juergensmeyer, Elizabeth A.; Juergensmeyer, Margaret A.

2004-01-01

The purpose of this research grant was to provide a fundamental, systematic investigation of the effects of oscillatory acceleration on bacterial proliferation and their responses to antibiotics in a liquid medium.

Distribution of bacterial contamination in non-sterile pharmaceutical materials and assessment of its risk to the health of the final consumers quantitatively

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Mostafa Essam Eissa

2016-09-01

Full Text Available Bacterial contamination control in pharmaceutical products is a critical aspect in the field of drug manufacturing industry due to the encountered risk to the patients' health and possibly their life. The application of commercial bacterial identification system is crucial to identify the type of contamination and its source to anticipate the impact of bioburden on the products and setting corrective and preventive actions. During the period of one year, random samples from raw materials and final products were tested according to United States Pharmacopeia, and those that showed suspect results for specified microorganisms and/or out-of-specification limits or showed out-of-trend results were subjected to further identification by using miniaturized biochemical identification system after performing Gram stain. From the total bacterial isolates of the investigated products, more than 60% were primarily belonging to Micrococcaceae 16.98% (empty hard gelatin capsules, Enterobacteriaceae 18.86% (vaginal cream applicator, plastic caps for bottles, Sorbitol solution, finished hard gelatin capsule product, topical cream and oral suspension and Bacillaceae 24.53% (Talc powder, liquid oral preparation and finished hard gelatin capsule product. Gram Positive and Negative samples were 56.60% and 41.51% respectively from the total investigated sample products and materials. Finished pharmaceutical products constituted 53.33% and 68.18% from Gram-positive and Gram-negative microorganisms respectively. An approach to quantitative risk assessment for pharmaceutical products was conducted on selected medicinal items and showed that Enterobacteriaceae followed by Burkholderiaceae contributed by more than 80% to the major hazard that could be delivered to patients through drugs. The applied risk can be used as a milestone for setting goals by pharmaceutical companies to improve the safety of medicinal products microbiologically and to identify the major sources

Interaction of multiple biomimetic antimicrobial polymers with model bacterial membranes

Energy Technology Data Exchange (ETDEWEB)

Baul, Upayan, E-mail: upayanb@imsc.res.in; Vemparala, Satyavani, E-mail: vani@imsc.res.in [The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113 (India); Kuroda, Kenichi, E-mail: kkuroda@umich.edu [Department of Biologic and Materials Sciences, University of Michigan School of Dentistry, Ann Arbor, Michigan 48109 (United States)

2014-08-28

Using atomistic molecular dynamics simulations, interaction of multiple synthetic random copolymers based on methacrylates on prototypical bacterial membranes is investigated. The simulations show that the cationic polymers form a micellar aggregate in water phase and the aggregate, when interacting with the bacterial membrane, induces clustering of oppositely charged anionic lipid molecules to form clusters and enhances ordering of lipid chains. The model bacterial membrane, consequently, develops lateral inhomogeneity in membrane thickness profile compared to polymer-free system. The individual polymers in the aggregate are released into the bacterial membrane in a phased manner and the simulations suggest that the most probable location of the partitioned polymers is near the 1-palmitoyl-2-oleoyl-phosphatidylglycerol (POPG) clusters. The partitioned polymers preferentially adopt facially amphiphilic conformations at lipid-water interface, despite lacking intrinsic secondary structures such as α-helix or β-sheet found in naturally occurring antimicrobial peptides.

StrainSeeker: fast identification of bacterial strains from raw sequencing reads using user-provided guide trees.

Science.gov (United States)

Roosaare, Märt; Vaher, Mihkel; Kaplinski, Lauris; Möls, Märt; Andreson, Reidar; Lepamets, Maarja; Kõressaar, Triinu; Naaber, Paul; Kõljalg, Siiri; Remm, Maido

2017-01-01

Fast, accurate and high-throughput identification of bacterial isolates is in great demand. The present work was conducted to investigate the possibility of identifying isolates from unassembled next-generation sequencing reads using custom-made guide trees. A tool named StrainSeeker was developed that constructs a list of specific k -mers for each node of any given Newick-format tree and enables the identification of bacterial isolates in 1-2 min. It uses a novel algorithm, which analyses the observed and expected fractions of node-specific k -mers to test the presence of each node in the sample. This allows StrainSeeker to determine where the isolate branches off the guide tree and assign it to a clade whereas other tools assign each read to a reference genome. Using a dataset of 100 Escherichia coli isolates, we demonstrate that StrainSeeker can predict the clades of E. coli with 92% accuracy and correct tree branch assignment with 98% accuracy. Twenty-five thousand Illumina HiSeq reads are sufficient for identification of the strain. StrainSeeker is a software program that identifies bacterial isolates by assigning them to nodes or leaves of a custom-made guide tree. StrainSeeker's web interface and pre-computed guide trees are available at http://bioinfo.ut.ee/strainseeker. Source code is stored at GitHub: https://github.com/bioinfo-ut/StrainSeeker.

Bacterial Protein-Tyrosine Kinases

DEFF Research Database (Denmark)

Shi, Lei; Kobir, Ahasanul; Jers, Carsten

2010-01-01

in exopolysaccharide production, virulence, DNA metabolism, stress response and other key functions of the bacterial cell. BY-kinases act through autophosphorylation (mainly in exopolysaccharide production) and phosphorylation of other proteins, which have in most cases been shown to be activated by tyrosine......Bacteria and Eukarya share essentially the same family of protein-serine/threonine kinases, also known as the Hanks-type kinases. However, when it comes to protein-tyrosine phosphorylation, bacteria seem to have gone their own way. Bacterial protein-tyrosine kinases (BY-kinases) are bacterial...... and highlighted their importance in bacterial physiology. Having no orthologues in Eukarya, BY-kinases are receiving a growing attention from the biomedical field, since they represent a particularly promising target for anti-bacterial drug design....

Bacterial Diversity and Bioremediation Potential of the Highly Contaminated Marine Sediments at El-Max District (Egypt, Mediterranean Sea

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Ranya A. Amer

2015-01-01

Full Text Available Coastal environments worldwide are threatened by the effects of pollution, a risk particularly high in semienclosed basins like the Mediterranean Sea that is poorly studied from bioremediation potential perspective especially in the Southern coast. Here, we investigated the physical, chemical, and microbiological features of hydrocarbon and heavy metals contaminated sediments collected at El-Max bay (Egypt. Molecular and statistical approaches assessing the structure of the sediment-dwelling bacterial communities showed correlations between the composition of bacterial assemblages and the associated environmental parameters. Fifty strains were isolated on mineral media supplemented by 1% crude oil and identified as a diverse range of hydrocarbon-degrading bacteria involved in different successional stages of biodegradation. We screened the collection for biotechnological potential studying biosurfactant production, biofilm formation, and the capability to utilize different hydrocarbons. Some strains were able to grow on multiple hydrocarbons as unique carbon source and presented biosurfactant-like activities and/or capacity to form biofilm and owned genes involved in different detoxification/degradation processes. El-Max sediments represent a promising reservoir of novel bacterial strains adapted to high hydrocarbon contamination loads. The potential of the strains for exploitation for in situ intervention to combat pollution in coastal areas is discussed.

Bacterial Diversity and Bioremediation Potential of the Highly Contaminated Marine Sediments at El-Max District (Egypt, Mediterranean Sea)

Science.gov (United States)

Amer, Ranya A.; El Gendi, Hamada M.; Goda, Doaa A.; Corsini, Anna; Cavalca, Lucia; Fusi, Marco; Daffonchio, Daniele; Abdel-Fattah, Yasser R.

2015-01-01

Coastal environments worldwide are threatened by the effects of pollution, a risk particularly high in semienclosed basins like the Mediterranean Sea that is poorly studied from bioremediation potential perspective especially in the Southern coast. Here, we investigated the physical, chemical, and microbiological features of hydrocarbon and heavy metals contaminated sediments collected at El-Max bay (Egypt). Molecular and statistical approaches assessing the structure of the sediment-dwelling bacterial communities showed correlations between the composition of bacterial assemblages and the associated environmental parameters. Fifty strains were isolated on mineral media supplemented by 1% crude oil and identified as a diverse range of hydrocarbon-degrading bacteria involved in different successional stages of biodegradation. We screened the collection for biotechnological potential studying biosurfactant production, biofilm formation, and the capability to utilize different hydrocarbons. Some strains were able to grow on multiple hydrocarbons as unique carbon source and presented biosurfactant-like activities and/or capacity to form biofilm and owned genes involved in different detoxification/degradation processes. El-Max sediments represent a promising reservoir of novel bacterial strains adapted to high hydrocarbon contamination loads. The potential of the strains for exploitation for in situ intervention to combat pollution in coastal areas is discussed. PMID:26273661

The function of advanced treatment process in a drinking water treatment plant with organic matter-polluted source water.

Science.gov (United States)

Lin, Huirong; Zhang, Shuting; Zhang, Shenghua; Lin, Wenfang; Yu, Xin

2017-04-01

To understand the relationship between chemical and microbial treatment at each treatment step, as well as the relationship between microbial community structure in biofilms in biofilters and their ecological functions, a drinking water plant with severe organic matter-polluted source water was investigated. The bacterial community dynamics of two drinking water supply systems (traditional and advanced treatment processes) in this plant were studied from the source to the product water. Analysis by 454 pyrosequencing was conducted to characterize the bacterial diversity in each step of the treatment processes. The bacterial communities in these two treatment processes were highly diverse. Proteobacteria, which mainly consisted of beta-proteobacteria, was the dominant phylum. The two treatment processes used in the plant could effectively remove organic pollutants and microbial polution, especially the advanced treatment process. Significant differences in the detection of the major groups were observed in the product water samples in the treatment processes. The treatment processes, particularly the biological pretreatment and O 3 -biological activated carbon in the advanced treatment process, highly influenced the microbial community composition and the water quality. Some opportunistic pathogens were found in the water. Nitrogen-relative microorganisms found in the biofilm of filters may perform an important function on the microbial community composition and water quality improvement.

Sealed source and device design safety testing. Volume 4: Technical report on the findings of Task 4, Investigation of sealed source for paper mill digester

International Nuclear Information System (INIS)

Benac, D.J.; Iddings, F.A.

1995-10-01

This report covers the Task 4 activities for the Sealed Source and Device Safety testing program. SwRI was contracted to investigate a suspected leaking radioactive source that was installed in a gauge that was on a paper mill digester. The actual source that was leaking was not available, therefore, SwRI examined another source. SwRI concluded that the encapsulated source examined by SwRI was not leaking. However, the presence of Cs-137 on the interior and exterior of the outer encapsulation and hending tube suggests that contamination probably occurred when the source was first manufactured, then installed in the handling tube

Molecular Mechanisms of Enhanced Bacterial Growth on Hexadecane with Red Clay.

Science.gov (United States)

Jung, Jaejoon; Jang, In-Ae; Ahn, Sungeun; Shin, Bora; Kim, Jisun; Park, Chulwoo; Jee, Seung Cheol; Sung, Jung-Suk; Park, Woojun

2015-11-01

Red clay was previously used to enhance bioremediation of diesel-contaminated soil. It was speculated that the enhanced degradation of diesel was due to increased bacterial growth. In this study, we selected Acinetobacter oleivorans DR1, a soil-borne degrader of diesel and alkanes, as a model bacterium and performed transcriptional analysis using RNA sequencing to investigate the cellular response during hexadecane utilization and the mechanism by which red clay promotes hexadecane degradation. We confirmed that red clay promotes the growth of A. oleivorans DR1 on hexadecane, a major component of diesel, as a sole carbon source. Addition of red clay to hexadecane-utilizing DR1 cells highly upregulated β-oxidation, while genes related to alkane oxidation were highly expressed with and without red clay. Red clay also upregulated genes related to oxidative stress defense, such as superoxide dismutase, catalase, and glutaredoxin genes, suggesting that red clay supports the response of DR1 cells to oxidative stress generated during hexadecane utilization. Increased membrane fluidity in the presence of red clay was confirmed by fatty acid methyl ester analysis at different growth phases, suggesting that enhanced growth on hexadecane could be due to increased uptake of hexadecane coupled with upregulation of downstream metabolism and oxidative stress defense. The monitoring of the bacterial community in soil with red clay for a year revealed that red clay stabilized the community structure.

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

Science.gov (United States)

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

2017-01-01

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

Biodegradation of petroleum oil by certain bacterial strains

International Nuclear Information System (INIS)

Zakaria, A.E.M.

1998-01-01

Balaeam base oil was chosen as a model oil in the present study through which some abiotic treatments were implemented aiming at attenuating its naphthenic and aromatic contents; such as the adsorptive technique and the gamma-irradiation technique . In an attempt to apply the biodegrading bacteria as oil pollutant bio indicators upon coastal water samples, a correlation between hydrocarbon concentration and the relative enumeration of the bacterial oil degraders was detected for some litter locations along the mediterranean Sea shore west and east Delta, Suez canal. and suez gulf. 24 petroleum utilizing bacterial isolates were isolated from El-Zayteia port (suez) and identified by morphological, physiological and environmental examination . the biodegradation capacity of the isolates towards the chosen model oil and its separate components was studied in comparison with the standard isolate pseudomonas aeruginosa. Further, the role of the bacterial plasmids taking part in the biodegradation process was investigated as well

Bacterial community profiles in low microbial abundance sponges

KAUST Repository

Giles, Emily

2012-09-04

It has long been recognized that sponges differ in the abundance of associated microorganisms, and they are therefore termed either \\'low microbial abundance\\' (LMA) or \\'high microbial abundance\\' (HMA) sponges. Many previous studies concentrated on the dense microbial communities in HMA sponges, whereas little is known about microorganisms in LMA sponges. Here, two LMA sponges from the Red Sea, two from the Caribbean and one from the South Pacific were investigated. With up to only five bacterial phyla per sponge, all LMA sponges showed lower phylum-level diversity than typical HMA sponges. Interestingly, each LMA sponge was dominated by a large clade within either Cyanobacteria or different classes of Proteobacteria. The overall similarity of bacterial communities among LMA sponges determined by operational taxonomic unit and UniFrac analysis was low. Also the number of sponge-specific clusters, which indicate bacteria specifically associated with sponges and which are numerous in HMA sponges, was low. A biogeographical or host-dependent distribution pattern was not observed. In conclusion, bacterial community profiles of LMA sponges are clearly different from profiles of HMA sponges and, remarkably, each LMA sponge seems to harbour its own unique bacterial community. © 2012 Federation of European Microbiological Societies.

Role of overexpressed CFA/I fimbriae in bacterial swimming.

Science.gov (United States)

Cao, Ling; Suo, Zhiyong; Lim, Timothy; Jun, Sangmu; Deliorman, Muhammedin; Riccardi, Carol; Kellerman, Laura; Avci, Recep; Yang, Xinghong

2012-06-01

Enterotoxigenic Escherichia coli CFA/I is a protective antigen and has been overexpressed in bacterial vectors, such as Salmonella Typhimurium H683, to generate vaccines. Effects that overexpressed CFA/I may engender on the bacterial host remain largely unexplored. To investigate, we constructed a high CFA/I expression strain, H683-pC2, and compared it to a low CFA/I expression strain, H683-pC, and to a non-CFA/I expression strain, H683-pY. The results showed that H683-pC2 was less able to migrate into semisolid agar (0.35%) than either H683-pC or H683-pY. Bacteria that migrated showed motility halo sizes of H683-pC2 CFA/I fimbriae on bacterial swimming motility.

Multipoint investigation of the source region of storm-time chorus

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O. Santolík

2004-07-01

Full Text Available In this case study we investigate the source region of whistler-mode chorus located close to the geomagnetic equator at a radial distance of 4.4 Earth radii. We use measurements from the four Cluster spacecraft at separations of less than a few hundreds of km, recorded during the geomagnetic storm of 18 April 2002. The waveforms of the electric field fluctuations were obtained by the WBD instruments in the frequency range 50Hz-9.5kHz. Using these data, we calculate linear and rank correlation coefficients of the frequency averaged power-spectral density measured by the different spacecraft. Those coefficients have been recently shown to decrease with spacecraft separation distance perpendicular to the static magnetic field cchor03 with a characteristic scale length of 100km. We find this characteristic scale varying between 60 and 200km for different data intervals inside the source region. We examine possible explanations for the observed large scatter of the correlation coefficients, and we suggest a simultaneously acting effect of random positions of locations at which the individual chorus wave packets are generated. The statistical properties of the observations are approximately reproduced by a simple 2-D model of the source region, assuming a perpendicular half-width of 35km (approximately one wavelength of the whistler-mode waves for the distribution of power radiated from individual active areas.

Bacterial diversity in two Neonatal Intensive Care Units (NICUs.

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Krissi M Hewitt

Full Text Available Infants in Neonatal Intensive Care Units (NICUs are particularly susceptible to opportunistic infection. Infected infants have high mortality rates, and survivors often suffer life-long neurological disorders. The causes of many NICU infections go undiagnosed, and there is debate as to the importance of inanimate hospital environments (IHEs in the spread of infections. We used culture-independent next-generation sequencing to survey bacterial diversity in two San Diego NICUs and to track the sources of microbes in these environments. Thirty IHE samples were collected from two Level-Three NICU facilities. We extracted DNA from these samples and amplified the bacterial small subunit (16S ribosomal RNA gene sequence using 'universal' barcoded primers. The purified PCR products were pooled into a single reaction for pyrosequencing, and the data were analyzed using QIIME. On average, we detected 93+/-39 (mean +/- standard deviation bacterial genera per sample in NICU IHEs. Many of the bacterial genera included known opportunistic pathogens, and many were skin-associated (e.g., Propionibacterium. In one NICU, we also detected fecal coliform bacteria (Enterobacteriales in a high proportion of the surface samples. Comparison of these NICU-derived sequences to previously published high-throughput 16S rRNA amplicon studies of other indoor environments (offices, restrooms and healthcare facilities, as well as human- and soil-associated environments, found the majority of the NICU samples to be similar to typical building surface and air samples, with the notable exception of the IHEs which were dominated by Enterobacteriaceae. Our findings provide evidence that NICU IHEs harbor a high diversity of human-associated bacteria and demonstrate the potential utility of molecular methods for identifying and tracking bacterial diversity in NICUs.

Differentiation of bacterial and non-bacterial community-acquired pneumonia by thin-section computed tomography

Energy Technology Data Exchange (ETDEWEB)

Ito, Isao [Department of Respiratory Medicine, Kurashiki Central Hospital, 1-1-1 Miwa, Kurashiki 710-8602 (Japan); Department of Respiratory Medicine, Kyoto University, 54 Shogoin-kawaharacho, Sakyo-ku, Kyoto 606-8507 (Japan)], E-mail: isaoito@kuhp.kyoto-u.ac.jp; Ishida, Tadashi [Department of Respiratory Medicine, Kurashiki Central Hospital, 1-1-1 Miwa, Kurashiki 710-8602 (Japan)], E-mail: ishidat@kchnet.or.jp; Togashi, Kaori [Department of Diagnostic Imaging and Nuclear Medicine, Kyoto University, 54 Shogoin-kawaharacho, Sakyo-ku, Kyoto 606-8507 (Japan)], E-mail: ktogashi@kuhp.kyoto-u.ac.jp; Niimi, Akio [Department of Respiratory Medicine, Kyoto University, 54 Shogoin-kawaharacho, Sakyo-ku, Kyoto 606-8507 (Japan)], E-mail: niimi@kuhp.kyoto-u.ac.jp; Koyama, Hiroshi [General Internal Medicine, National Hospital Organization Kyoto Medical Center, 1-1 Fukakusa-Mukohatacho, Fushimi-ku, Kyoto 612-8555 (Japan)], E-mail: hkoyama-kyt@umin.ac.jp; Ishimori, Takayoshi [Department of Radiology, Kurashiki Central Hospital, 1-1-1 Miwa, Kurashiki 710-8602 (Japan)], E-mail: ti10794@kchnet.or.jp; Kobayashi, Hisataka [Department of Diagnostic Imaging and Nuclear Medicine, Kyoto University, 54 Shogoin-kawaharacho, Sakyo-ku, Kyoto 606-8507 (Japan); Molecular Imaging Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Building 10, Room 1B40, MSC1088, 10 Center Drive, Bethesda, MD 20892-1088 (United States)], E-mail: kobayash@mail.nih.gov; Mishima, Michiaki [Department of Respiratory Medicine, Kyoto University, 54 Shogoin-kawaharacho, Sakyo-ku, Kyoto 606-8507 (Japan)], E-mail: mishima@kuhp.kyoto-u.ac.jp

2009-12-15

Background and objective: The management of community-acquired pneumonia (CAP) depends, in part, on the identification of the causative agents. The objective of this study was to determine the potential of thin-section computed tomography (CT) in differentiating bacterial and non-bacterial pneumonia. Patients and methods: Thin-section CT studies were prospectively examined in hospitalized CAP patients within 2 days of admission, followed by retrospective assessment by two pulmonary radiologists. Thin-section CT findings on the pneumonias caused by each pathogen were examined, and two types of pneumonias were compared. Using multivariate logistic regression analyses, receiver operating characteristic (ROC) curves were produced. Results: Among 183 CAP episodes (181 patients, 125 men and 56 women, mean age {+-} S.D.: 61.1 {+-} 19.7) examined by thin-section CT, the etiologies of 125 were confirmed (94 bacterial pneumonia and 31 non-bacterial pneumonia). Centrilobular nodules were specific for non-bacterial pneumonia and airspace nodules were specific for bacterial pneumonia (specificities of 89% and 94%, respectively) when located in the outer lung areas. When centrilobular nodules were the principal finding, they were specific but lacked sensitivity for non-bacterial pneumonia (specificity 98% and sensitivity 23%). To distinguish the two types of pneumonias, centrilobular nodules, airspace nodules and lobular shadows were found to be important by multivariate analyses. ROC curve analysis discriminated bacterial pneumonia from non-bacterial pneumonia among patients without underlying lung diseases, yielding an optimal point with sensitivity and specificity of 86% and 79%, respectively, but was less effective when all patients were analyzed together (70% and 84%, respectively). Conclusion: Thin-section CT examination was applied for the differentiation of bacterial and non-bacterial pneumonias. Though showing some potential, this examination at the present time would

Differentiation of bacterial and non-bacterial community-acquired pneumonia by thin-section computed tomography

International Nuclear Information System (INIS)

Ito, Isao; Ishida, Tadashi; Togashi, Kaori; Niimi, Akio; Koyama, Hiroshi; Ishimori, Takayoshi; Kobayashi, Hisataka; Mishima, Michiaki

2009-01-01

Background and objective: The management of community-acquired pneumonia (CAP) depends, in part, on the identification of the causative agents. The objective of this study was to determine the potential of thin-section computed tomography (CT) in differentiating bacterial and non-bacterial pneumonia. Patients and methods: Thin-section CT studies were prospectively examined in hospitalized CAP patients within 2 days of admission, followed by retrospective assessment by two pulmonary radiologists. Thin-section CT findings on the pneumonias caused by each pathogen were examined, and two types of pneumonias were compared. Using multivariate logistic regression analyses, receiver operating characteristic (ROC) curves were produced. Results: Among 183 CAP episodes (181 patients, 125 men and 56 women, mean age ± S.D.: 61.1 ± 19.7) examined by thin-section CT, the etiologies of 125 were confirmed (94 bacterial pneumonia and 31 non-bacterial pneumonia). Centrilobular nodules were specific for non-bacterial pneumonia and airspace nodules were specific for bacterial pneumonia (specificities of 89% and 94%, respectively) when located in the outer lung areas. When centrilobular nodules were the principal finding, they were specific but lacked sensitivity for non-bacterial pneumonia (specificity 98% and sensitivity 23%). To distinguish the two types of pneumonias, centrilobular nodules, airspace nodules and lobular shadows were found to be important by multivariate analyses. ROC curve analysis discriminated bacterial pneumonia from non-bacterial pneumonia among patients without underlying lung diseases, yielding an optimal point with sensitivity and specificity of 86% and 79%, respectively, but was less effective when all patients were analyzed together (70% and 84%, respectively). Conclusion: Thin-section CT examination was applied for the differentiation of bacterial and non-bacterial pneumonias. Though showing some potential, this examination at the present time would not

Temperature adaptation of bacterial communities in experimentally warmed forest soils.

Science.gov (United States)

Rousk, Johannes; Frey, Serita D; Bååth, Erland

2012-10-01

A detailed understanding of the influence of temperature on soil microbial activity is critical to predict future atmospheric CO 2 concentrations and feedbacks to anthropogenic warming. We investigated soils exposed to 3-4 years of continuous 5 °C-warming in a field experiment in a temperate forest. We found that an index for the temperature adaptation of the microbial community, T min for bacterial growth, increased by 0.19 °C per 1 °C rise in temperature, showing a community shift towards one adapted to higher temperature with a higher temperature sensitivity (Q 10(5-15 °C) increased by 0.08 units per 1 °C). Using continuously measured temperature data from the field experiment we modelled in situ bacterial growth. Assuming that warming did not affect resource availability, bacterial growth was modelled to become 60% higher in warmed compared to the control plots, with the effect of temperature adaptation of the community only having a small effect on overall bacterial growth (bacterial growth, most likely due to substrate depletion because of the initially higher growth in warmed plots. When this was factored in, the result was similar rates of modelled in situ bacterial growth in warmed and control plots after 3 years, despite the temperature difference. We conclude that although temperature adaptation for bacterial growth to higher temperatures was detectable, its influence on annual bacterial growth was minor, and overshadowed by the direct temperature effect on growth rates. © 2012 Blackwell Publishing Ltd.

Risk Assessment and effect of Penicillin-G on bacterial diversity in drinking water

Science.gov (United States)

Wu, Qing; Zhao, Xiaofei; Peng, Sen; Wang, Lei; Zhao, Xinhua

2018-02-01

Penicillin-G was detected in drinking water by LC-MS/MS and the bacterial diversity was investigated by PCR and high-throughput sequencing. The results showed that bacteria community structure in drinking water has undergone major changes when added different concentrations of penicillin-G. The diversity index of each sample was calculated. The results showed that the total number and abundance of bacterial community species in drinking water samples decreased significantly after the addition of penicillin-G. However, the number and abundance of community structure did not change with the concentration. Penicillin-G inhibits the activity of bacterial community in drinking water and can reduce the bacterial diversity in drinking water.

Pigments Characterization and Molecular Identification of Bacterial Symbionts of Brown Algae Padinasp. Collected from Karimunjawa Island

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Damar Bayu Murti

2016-06-01

Full Text Available The search for carotenoids in nature has been extensively studied because of their applications in foods. One treasure of the biopigment source is symbiotic-microorganisms with marine biota. The advantages of symbiont bacteria are easy to culture and sensitize pigments. The use of symbiont bacteria helps to conserve fish, coral reefs, seagrass, and seaweed. Therefore, the bacteria keeps their existence in their ecosystems. In this study, bacterial symbionts were successfully isolated from brown algae Padina sp. The bacterial symbionts had yellow pigment associated with carotenoids. The pigments were characterized using High Performance Liquid Chromatography (HPLC with a Photo Diode Array (PDA detector. The carotenoid pigments in the bacterial symbionts were identified as dinoxanthin, lutein and neoxanthin. Molecular identification by using a 16S rRNA gene sequence method, reveals that the bacterial symbionts were closely related to Bacillus marisflavi with a homology of 99%. Keywords :carotenoid pigments, brown algae, Padina, bacterial symbionts, 16S rRNA

Airway fungal colonization compromises the immune system allowing bacterial pneumonia to prevail.

Science.gov (United States)

Roux, Damien; Gaudry, Stéphane; Khoy-Ear, Linda; Aloulou, Meryem; Phillips-Houlbracq, Mathilde; Bex, Julie; Skurnik, David; Denamur, Erick; Monteiro, Renato C; Dreyfuss, Didier; Ricard, Jean-Damien

2013-09-01

To study the correlation between fungal colonization and bacterial pneumonia and to test the effect of antifungal treatments on the development of bacterial pneumonia in colonized rats. Experimental animal investigation. University research laboratory. Pathogen-free male Wistar rats weighing 250-275 g. Rats were colonized by intratracheal instillation of Candida albicans. Fungal clearance from the lungs and immune response were measured. Both colonized and noncolonized animals were secondarily instilled with different bacterial species (Pseudomonas aeruginosa, Escherichia coli, or Staphylococcus aureus). Bacterial phagocytosis by alveolar macrophages was evaluated in the presence of interferon-gamma, the main cytokine produced during fungal colonization. The effect of antifungal treatments on fungal colonization and its immune response were assessed. The prevalence of P. aeruginosa pneumonia was compared in antifungal treated and control colonized rats. C. albicans was slowly cleared and induced a Th1-Th17 immune response with very high interferon-gamma concentrations. Airway fungal colonization favored the development of bacterial pneumonia. Interferon-gamma was able to inhibit the phagocytosis of unopsonized bacteria by alveolar macrophages. Antifungal treatment decreased airway fungal colonization, lung interferon-gamma levels and, consequently, the prevalence of subsequent bacterial pneumonia. C. albicans airway colonization elicited a Th1-Th17 immune response that favored the development of bacterial pneumonia via the inhibition of bacterial phagocytosis by alveolar macrophages. Antifungal treatment decreased the risk of bacterial pneumonia in colonized rats.

The bacterial contamination rate of glucose meter test strips in the hospital setting

Science.gov (United States)

Al-Rubeaan, Khalid A.; Saeb, Amr T. M.; AlNaqeb, Dhekra M.; AlQumaidi, Hamed M.; AlMogbel, Turki A.

2016-01-01

Objectives: To assess the rate of bacterial contamination of the multi-use vial and single-use packed glucose meter strips, and to identify the type and frequency of various bacterial contamination in different hospital wards. Methods: This prospective observational study was conducted by a team from the Strategic Center for Diabetes Research in 7 general hospitals in the Central region of Saudi Arabia during the period from August to September 2014 to assess the bacterial contamination rate of the unused strips. A total of 10,447 strips were cultured using proper agar media and incubated both aerobically and anaerobically. Results: The total bacterial contamination rate for the multi-use vials glucose strips was 31.7%, while single-use packed strips were not contaminated at all. Ministry of Health hospitals had the highest contamination rates compared with other hospitals. Critical, obstetric, and surgical wards had the highest bacterial isolates number, where most were in the risk group 3 according to the National Institute of Health guidelines. Staphylococcus species were the most common bacteria found. Conclusion: Glucose meter strips should be recognized as a source of bacterial contamination that could be behind serious hospital acquired infections. The hospital infection control team should adopt proper measures to implement protocols for glucose meter cleaning and glucose strips handling. PMID:27570855

Humidity-dependent bacterial cells functional morphometry investigations using atomic force microscope.

Science.gov (United States)

Nikiyan, Hike; Vasilchenko, Alexey; Deryabin, Dmitry

2010-01-01

The effect of a relative humidity (RH) in a range of 93-65% on morphological and elastic properties of Bacillus cereus and Escherichia coli cells was evaluated using atomic force microscopy. It is shown that gradual dehumidification of bacteria environment has no significant effect on cell dimensional features and considerably decreases them only at 65% RH. The increasing of the bacteria cell wall roughness and elasticity occurs at the same time. Observed changes indicate that morphological properties of B. cereus are rather stable in wide range of relative humidity, whereas E. coli are more sensitive to drying, significantly increasing roughness and stiffness parameters at RH bacterial cells.

Humidity-Dependent Bacterial Cells Functional Morphometry Investigations Using Atomic Force Microscope

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Hike Nikiyan

2010-01-01

Full Text Available The effect of a relative humidity (RH in a range of 93–65% on morphological and elastic properties of Bacillus cereus and Escherichia coli cells was evaluated using atomic force microscopy. It is shown that gradual dehumidification of bacteria environment has no significant effect on cell dimensional features and considerably decreases them only at 65% RH. The increasing of the bacteria cell wall roughness and elasticity occurs at the same time. Observed changes indicate that morphological properties of B. cereus are rather stable in wide range of relative humidity, whereas E. coli are more sensitive to drying, significantly increasing roughness and stiffness parameters at RH ≤ 84% RH. It is discussed the dependence of the response features on differences in cell wall structure of gram-positive and gram-negative bacterial cells.

Investigation of bacterial transport in the large-block test, a thermally perturbed block of Topopah Spring Tuff

International Nuclear Information System (INIS)

Chen, C. I.; Chuu, Y. J.; Lin, W.; Meike, A.; Sawvel, A.

1998-01-01

This study investigates the transport of bacteria in a large, thermally perturbed block of Topopah Spring tuff. The study was part of the Large-Block Test (LBT), thermochemical and physical studies conducted on a 10 ft x 10 ft x 14 ft block of volcanic tuff excavated on 5 of 6 sides out of Fran Ridge, Nevada. Two bacterial species, Bacillus subtilis and Arthrobacter oxydans, were isolated from the Yucca Mountain tuff. Natural mutants that can grow under the simultaneous presence of the two antibiotics, streptomycin and rifampicin, were selected from these species by laboratory procedures. The double-drug-resistant mutants, which could be thus distinguished from the indigenous species, were injected into the five heater boreholes of the large block hours before heating was initiated. The temperature, as measured 5 cm above one of the heater boreholes, rose slowly and steadily over a matter of months to a maximum of 142 C. Samples (cotton cloths inserted the length of the hole, glass fiber swabs, and filter papers) were collected from the boreholes that were approximately 5 ft below the injection points. Double-drug-resistant bacteria were found in the collection boreholes nine months after injection. Surprisingly, they also appeared in the heater boreholes where the temperature had been sustainably high throughout the test. These bacteria appear to be the species that were injected. The number of double-drug-resistant bacteria that were identified in the collection boreholes increased with time. An apparent homogeneous distribution among the observation boreholes and heater boreholes suggests that a random motion could be the pattern that the bacteria migrated in the block. These observations indicated the possibility of rapid bacterial transport in a thermally perturbed geologic setting

Probing living bacterial adhesion by single cell force spectroscopy using atomic force microscopy

DEFF Research Database (Denmark)

Zeng, Guanghong; Ogaki, Ryosuke; Regina, Viduthalai R.

be considered. We have therefore developed a simple and versatile method to make single-cell bacterial probes for measuring single cell adhesion with atomic force microscopy (AFM).[1] A single-cell probe was readily made by picking up a bacterial cell from a glass surface using a tipless AFM cantilever coated...... random immobilization is obtained by submerging the cantilever in a bacterial suspension. The reported method provides a general platform for investigating single cell interactions of bacteria with different surfaces and other cells by AFM force spectroscopy, thus improving our understanding....... The strain-dependent susceptibility to bacterial colonization on conventional PLL-g-PEG illustrates how bacterial diversity challenges development of “universal” antifouling coatings, and AFM single-cell force spectroscopy was proven to be a powerful tool to provide insights into the molecular mechanisms...

Baby bottle steam sterilizers disinfect home nebulizers inoculated with bacterial respiratory pathogens.

Science.gov (United States)

Towle, Dana; Callan, Deborah A; Farrel, Patricia A; Egan, Marie E; Murray, Thomas S

2013-09-01

Contaminated nebulizers are a potential source of bacterial infection but no single method is universally accepted for disinfection. We hypothesized that baby-bottle steam sterilizers effectively disinfect home nebulizers. Home nebulizers were inoculated with the common CF respiratory pathogens methicillin resistant Staphylococcus aureus, Burkholderia cepacia, Haemophilus influenzae, mucoid and non mucoid Pseudomonas aeruginosa, and Stenotrophomonas maltophilia. The nebulizers were swabbed for bacterial growth, treated with either the AVENT (Philips), the NUK Quick & Ready (Gerber) or DRY-POD (Camera Baby) baby bottle steam sterilizer and reswabbed for bacterial growth. All steam sterilizers were effective at disinfecting all home nebulizers. Viable bacteria were not recovered from any inoculated site after steam treatment, under any conditions tested. Steam treatment is an effective disinfection method. Additional studies are needed to confirm whether these results are applicable to the clinical setting. Copyright © 2012 European Cystic Fibrosis Society. Published by Elsevier B.V. All rights reserved.

Transfer of intestinal bacterial components to mammary secretions in the cow

Directory of Open Access Journals (Sweden)

Wayne Young

2015-04-01

Full Text Available Results from large multicentre epidemiological studies suggest an association between the consumption of raw milk and a reduced incidence of allergy and asthma in children. Although the underlying mechanisms for this association are yet to be confirmed, researchers have investigated whether bacteria or bacterial components that naturally occur in cow’s milk are responsible for modulating the immune system to reduce the risk of allergic diseases. Previous research in human and mice suggests that bacterial components derived from the maternal intestine are transported to breast milk through the bloodstream. The aim of our study was to assess whether a similar mechanism of bacterial trafficking could occur in the cow. Through the application of culture-independent methodology, we investigated the microbial composition and diversity of milk, blood and feces of healthy lactating cows. We found that a small number of bacterial OTUs belonging to the genera Ruminococcus and Bifidobacterium, and the Peptostreptococcaceae family were present in all three samples from the same individual animals. Although these results do not confirm the hypothesis that trafficking of intestinal bacteria into mammary secretions does occur in the cow, they support the existence of an endogenous entero-mammary pathway for some bacterial components during lactation in the cow. Further research is required to define the specific mechanisms by which gut bacteria are transported into the mammary gland of the cow, and the health implications of such bacteria being present in milk.

Isolasi, Seleksi Dan Opttmasi Produksi Protease Daribeberapaisolat Bakteri*(isolation, Selection and Optimalization of Protease Production of Some Bacterial Isolates)

OpenAIRE

Naiola, Elidar; Widhyastuti, Nunuk

2002-01-01

Thirty-seven out of sixty-one bacterial isolates from various sources of samples were screened for protease production. The isolate of ISO PL3 could produce the highest enzyme activity, and it was used as a standard bacterial strain in this observation. For any reason,we implemented ISO PL2 to study the optimum condition for producing bacterial protease. Result shows that the maximum protease activity was obtained in a medium containing 100 gram of rice brand in a liter tofu liquid waste. The...

Field Efficiency Trial of 72% Streptomycin against Konjac Bacterial Soft Rot

Institute of Scientific and Technical Information of China (English)

Huang; Yongsheng; Li; Xiaojun; Zhu; Shijin; Ma; Yongsheng; Wang; Li

2014-01-01

72% Streptomycin soluble powder was used to control konjac bacterial soft rot in the study. The control efficiency and yield of different treatments were investigated,and the benefit was analyzed. The control scheme against konjac bacterial soft rot was as follows: spraying 72% atreptomycinon twice on rotation fields after all the seedlings were strong and uniform,or irrigating roots with 72% atreptomycinon once and spraying twice on continuous cropping fields.

Molecular Approaches to Understanding Transmission and Source Attribution in Nontyphoidal Salmonella and Their Application in Africa.

Science.gov (United States)

Mather, Alison E; Vaughan, Timothy G; French, Nigel P

2015-11-01

Nontyphoidal Salmonella (NTS) is a frequent cause of diarrhea around the world, yet in many African countries it is more commonly associated with invasive bacterial disease. Various source attribution models have been developed that utilize microbial subtyping data to assign cases of human NTS infection to different animal populations and foods of animal origin. Advances in molecular microbial subtyping approaches, in particular whole-genome sequencing, provide higher resolution data with which to investigate these sources. In this review, we provide updates on the source attribution models developed for Salmonella, and examine the application of whole-genome sequencing data combined with evolutionary modeling to investigate the putative sources and transmission pathways of NTS, with a focus on the epidemiology of NTS in Africa. This is essential information to decide where, what, and how control strategies might be applied most effectively. © The Author 2015. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Obstructive jaundice promotes bacterial translocation in humans.

Science.gov (United States)

Kuzu, M A; Kale, I T; Cöl, C; Tekeli, A; Tanik, A; Köksoy, C

1999-01-01

Significant bacterial translocation was demonstrated following experimental biliary obstruction, however very little is known about the importance and the prevalence of gut-origin sepsis in obstructive jaundice patients. Therefore, the aim of this study was to investigate the concept of gut-origin sepsis in obstructive jaundiced patients and its clinical importance. Twenty-one patients requiring laparotomy for obstructive jaundice (group I) and thirty patients operated on electively mainly for chronic cholecystitis (group II) were studied. Peritoneal swab, mesenteric lymph node, portal venous blood, liver wedge biopsy and bile were sampled for culture immediately after opening the peritoneum. Additionally, peripheral blood samples were taken pre- and post-operatively from all patients. Post-operatively, patients were monitored for infectious complications. The mean serum bilirubin concentration, gamma glutamyl transferase and alkaline phosphatase levels in jaundiced patients before therapeutic intervention were significantly higher than in control patients. Five patients demonstrated bacterial translocation in group I (24%), whereas only one did so in group II (3.5%, p jaundice significantly promotes bacterial translocation in humans, however, its clinical importance has yet to be defined.

Bacterial biofilm and associated infections

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Muhsin Jamal

2018-01-01

Full Text Available Microscopic entities, microorganisms that drastically affect human health need to be thoroughly investigated. A biofilm is an architectural colony of microorganisms, within a matrix of extracellular polymeric substance that they produce. Biofilm contains microbial cells adherent to one-another and to a static surface (living or non-living. Bacterial biofilms are usually pathogenic in nature and can cause nosocomial infections. The National Institutes of Health (NIH revealed that among all microbial and chronic infections, 65% and 80%, respectively, are associated with biofilm formation. The process of biofilm formation consists of many steps, starting with attachment to a living or non-living surface that will lead to formation of micro-colony, giving rise to three-dimensional structures and ending up, after maturation, with detachment. During formation of biofilm several species of bacteria communicate with one another, employing quorum sensing. In general, bacterial biofilms show resistance against human immune system, as well as against antibiotics. Health related concerns speak loud due to the biofilm potential to cause diseases, utilizing both device-related and non-device-related infections. In summary, the understanding of bacterial biofilm is important to manage and/or to eradicate biofilm-related diseases. The current review is, therefore, an effort to encompass the current concepts in biofilm formation and its implications in human health and disease.

Host species and environmental effects on bacterial communities associated with Drosophila in the laboratory and in the natural environment.

Directory of Open Access Journals (Sweden)

Fabian Staubach

Full Text Available The fruit fly Drosophila is a classic model organism to study adaptation as well as the relationship between genetic variation and phenotypes. Although associated bacterial communities might be important for many aspects of Drosophila biology, knowledge about their diversity, composition, and factors shaping them is limited. We used 454-based sequencing of a variable region of the bacterial 16S ribosomal RNA gene to characterize the bacterial communities associated with wild and laboratory Drosophila isolates. In order to specifically investigate effects of food source and host species on bacterial communities, we analyzed samples from wild Drosophila melanogaster and D. simulans collected from a variety of natural substrates, as well as from adults and larvae of nine laboratory-reared Drosophila species. We find no evidence for host species effects in lab-reared flies; instead, lab of origin and stochastic effects, which could influence studies of Drosophila phenotypes, are pronounced. In contrast, the natural Drosophila-associated microbiota appears to be predominantly shaped by food substrate with an additional but smaller effect of host species identity. We identify a core member of this natural microbiota that belongs to the genus Gluconobacter and is common to all wild-caught flies in this study, but absent from the laboratory. This makes it a strong candidate for being part of what could be a natural D. melanogaster and D. simulans core microbiome. Furthermore, we were able to identify candidate pathogens in natural fly isolates.

Bacterial Reduction Of Barium Sulphate By Sulphate-Reducing Bacteria

Directory of Open Access Journals (Sweden)

Luptáková Alena

2015-12-01

Full Text Available Acid mine drainage (AMD is a worldwide problem leading to contamination of water sources. AMD are characterized by low pH and high content of heavy metals and sulphates. The barium salts application presents one of the methods for the sulphates removing from AMD. Barium chloride, barium hydroxide and barium sulphide are used for the sulphates precipitation in the form of barium sulphate. Because of high investment costs of barium salts, barium sulphide is recycled from barium sulphate precipitates. It can be recycled by thermic or bacterial reduction of barium sulphate. The aim of our study was to verify experimentally the possibility of the bacterial transformation of BaSO4 to BaS by sulphate-reducing bacteria. Applied BaSO4 came from experiments of sulphates removal from Smolnik AMD using BaCl2.

Reproducibility of subgingival bacterial samples from patients with peri-implant mucositis

DEFF Research Database (Denmark)

Hallström, Hadar; Persson, G Rutger; Strömberg, Ulf

2015-01-01

collected with paper points and analyzed using the checkerboard DNA-DNA hybridization technique. Whole genomic probes of 74 preselected bacterial species were used. Based on the bacterial scores, Cohen's kappa coefficient was used to calculate the inter-annotator agreement for categorical data......OBJECTIVE: The aim of the present study was to investigate the reproducibility of bacterial enumeration from subsequent subgingival samples collected from patients with peri-implant mucositis. MATERIAL AND METHODS: Duplicate microbial samples from 222 unique implant sites in 45 adult subjects were....... The percentage agreement was considered as "good" when the two samples showed the same score or differed by 1 to the power of 10. RESULTS: Moderate to fair kappa values were displayed for all bacterial species in the test panel (range 0.21-0.58). There were no significant differences between Gram...

Recent advances in synthesis of bacterial rare sugar building blocks and their applications.

Science.gov (United States)

Emmadi, Madhu; Kulkarni, Suvarn S

2014-07-01

Covering: 1964 to 2013. Bacteria have unusual glycans on their surfaces which distinguish them from the host cells. These unique structures offer avenues for targeting bacteria with specific therapeutics and vaccine. However, these rare sugars are not accessible in acceptable purity and amounts by isolation from natural sources. Thus, procurement of orthogonally protected rare sugar building blocks through efficient chemical synthesis is regarded as a crucial step towards the development of glycoconjugate vaccines. This Highlight focuses on recent advances in the synthesis of the bacterial deoxy amino hexopyranoside building blocks and their application in constructing various biologically important bacterial O-glycans.

Glycerol as a Cheaper Carbon Source in Bacterial Cellulose (BC) Production by Gluconacetobacter Xylinus DSM46604 in Batch Fermentation System

International Nuclear Information System (INIS)

Azila Adnan; Nair, G.R.; Roslan Umar; Roslan Umar

2015-01-01

Bacterial cellulose (BC) is a polymer of glucose monomers, which has unique properties including high crystallinity and high strength. It has potential to be used in biomedical applications such as making artificial blood vessel, wound dressings, and in the paper making industry. Extensive study on BC aimed to improve BC production such as by using glycerol as a cheaper carbon source. BC was produced in shake flask culture using five different concentrations of glycerol (10, 20, 30, 40 and 50 g/ L). Using concentration of glycerol above 20 g/ L inhibited culture growth and BC production. Further experiments were performed in batch culture (3-L bioreactor) using 20 g/ L glycerol. It produced yield and productivity of 0.15 g/ g and 0.29 g/ L/ day BC, respectively. This is compared with the control medium, 50 g/ L glucose, which only gave yield and productivity of 0.05 g/ g and 0.23 g/ L/ day, respectively. Twenty g/ L of glycerol enhanced BC production by Gluconacetobacter xylinus DSM46604 in batch fermentation system. (author)

Changes of Bacterial Diversity Depend on the Spoilage of Fresh Vegetables

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Dong Hwan Lee

2011-04-01

Full Text Available Almost 10~30% of vegetables were discarded by the spoilage from farms to tables. After harvest, vegetables are often spoiled by a wide variety of microorganisms including many bacterial and fungal species. This investigation was conducted to extent the knowledge of relationship the spoilage of vegetables and the diversity of microbes. The total aerobic bacterial numbers in fresh lettuce, perilla leaf, and chicory were 2.6~2.7×106, 4.6×105, 1.2×106 CFU/g of fresh weight, respectively. The most common bacterial species were Pseudomonas spp., Alysiella spp., and Burkholderia spp., and other 18 more genera were involved in. After one week of incubation of those vegetables at 28℃, the microbial diversity had been changed. The total aerobic bacterial numbers increased to 1.1~4.6×108, 4.9×107, and 7.6×108 CFU/g of fresh weight for lettuce, perilla leaf, and chicory that is about 102 times increased bacterial numbers than that before spoilage. However, the diversity of microbes isolated had been simplified and fewer bacterial species had been isolated. The most bacterial population (~48% was taken up by Pseudomonas spp., and followed by Arthrobacter spp. and Bacillus spp. The spoilage activity of individual bacterial isolates had been tested using axenic lettuce plants. Among tested isolates, Pseudomonas fluorescence and Pantoea agglomerans caused severe spoilage on lettuce.

Investigations of incorporating source directivity into room acoustics computer models to improve auralizations

Science.gov (United States)

Vigeant, Michelle C.

Room acoustics computer modeling and auralizations are useful tools when designing or modifying acoustically sensitive spaces. In this dissertation, the input parameter of source directivity has been studied in great detail to determine first its effect in room acoustics computer models and secondly how to better incorporate the directional source characteristics into these models to improve auralizations. To increase the accuracy of room acoustics computer models, the source directivity of real sources, such as musical instruments, must be included in the models. The traditional method for incorporating source directivity into room acoustics computer models involves inputting the measured static directivity data taken every 10° in a sphere-shaped pattern around the source. This data can be entered into the room acoustics software to create a directivity balloon, which is used in the ray tracing algorithm to simulate the room impulse response. The first study in this dissertation shows that using directional sources over an omni-directional source in room acoustics computer models produces significant differences both in terms of calculated room acoustics parameters and auralizations. The room acoustics computer model was also validated in terms of accurately incorporating the input source directivity. A recently proposed technique for creating auralizations using a multi-channel source representation has been investigated with numerous subjective studies, applied to both solo instruments and an orchestra. The method of multi-channel auralizations involves obtaining multi-channel anechoic recordings of short melodies from various instruments and creating individual channel auralizations. These auralizations are then combined to create a total multi-channel auralization. Through many subjective studies, this process was shown to be effective in terms of improving the realism and source width of the auralizations in a number of cases, and also modeling different

Incidence and sources of native and prosthetic joint infection: a community based prospective survey

NARCIS (Netherlands)

Kaandorp, C. J.; Dinant, H. J.; van de Laar, M. A.; Moens, H. J.; Prins, A. P.; Dijkmans, B. A.

1997-01-01

To determine the incidence and sources of bacterial arthritis in the Amsterdam health district and the maximum percentage of cases that theoretically would be preventable. Patients with bacterial arthritis diagnosed between 1 October 1990 and 1 October 1993 were prospectively reported to the study

Lessons learned from bacterial transport research at the South Oyster Site

Energy Technology Data Exchange (ETDEWEB)

Scheibe, T.; Hubbard, S.S.; Onstott, T.C.; DeFlaun, M.F.

2011-04-01

This paper provides a review of bacterial transport experiments conducted by a multi-investigator, multi-institution, multi-disciplinary team of researchers under the auspices of the U. S. Department of Energy (DOE). The experiments were conducted during the time period 1999-2001 at a field site near the town of Oyster, Virginia known as the South Oyster Site, and included four major experimental campaigns aimed at understanding and quantifying bacterial transport in the subsurface environment. Several key elements of the research are discussed here: (1) quantification of bacterial transport in physically, chemically and biologically heterogeneous aquifers, (2) evaluation of the efficacy of conventional colloid filtration theory, (3) scale effects in bacterial transport, (4) development of new methods for microbial enumeration and screening for low adhesion strains, (5) application of novel hydrogeophysical techniques for aquifer characterization, and (6) experiences regarding management of a large field research effort. Lessons learned are summarized in each of these areas. The body of literature resulting from South Oyster Site research has been widely cited and continues to influence research into the controls exerted by aquifer heterogeneity on reactive transport (including microbial transport). It also served as a model (and provided valuable experience) for subsequent and ongoing highly-instrumented field research efforts conducted by DOE-sponsored investigators.

CRISPR/Cas systems: new players in gene regulation and bacterial physiology

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David eWeiss

2014-04-01

Full Text Available CRISPR-Cas systems are bacterial defenses against foreign nucleic acids derived from bacteriophages, plasmids or other sources. These systems are targeted in an RNA-dependent, sequence-specific manner, and are also adaptive, providing protection against previously encountered foreign elements. In addition to their canonical function in defense against foreign nucleic acid, their roles in various aspects of bacterial physiology are now being uncovered. We recently revealed a role for a Cas9-based Type II CRISPR-Cas system in the control of endogenous gene expression, a novel form of prokaryotic gene regulation. Cas9 functions in association with two small RNAs to target and alter the stability of an endogenous transcript encoding a bacterial lipoprotein (BLP. Since BLPs are recognized by the host innate immune protein Toll-like Receptor 2 (TLR2, CRISPR-Cas-mediated repression of BLP expression facilitates evasion of TLR2 by the intracellular bacterial pathogen Francisella novicida, and is essential for its virulence. Here we describe the Cas9 regulatory system in detail, as well as data on its role in controlling virulence traits of Neisseria meningitidis and Campylobacter jejuni. We also discuss potential roles of CRISPR-Cas systems in the response to envelope stress and other aspects of bacterial physiology. Since ~45% of bacteria and ~83% of Archaea encode these machineries, the newly appreciated regulatory functions of CRISPR-Cas systems are likely to play broad roles in controlling the pathogenesis and physiology of diverse prokaryotes.

Bacterial cell wall preservation during organic matter diagenesis in sediments off Peru

DEFF Research Database (Denmark)

Lomstein, Bente Aagaard; Niggemann, Jutta; Jørgensen, Bo Barker

BACTERIAL CELL WALL PRESERVATION DURING ORGANIC MATTER DIAGENESIS IN SEDIMENTS OFF PERU The spatial distribution of total hydrolysable amino acids, total hydrolysable amino sugars and amino acid enantiomers (D- and L-forms) were investigated in surface sediments at 20 stations in the Peru margin: 9......°45 S - 13º32 S. The objective of this study was to assess the preservation of bacterial cell walls during diagenesis of organic matter. Bacterial cell walls were traced by analysis of biomarkers uniquely produced by bacteria (D-amino acids and muramic acid). The diagenetic status of the sediments......:00 Presentation is given by student: No...

Cost-effective production of bacterial cellulose using acidic food industry by-products.

Science.gov (United States)

Revin, Victor; Liyaskina, Elena; Nazarkina, Maria; Bogatyreva, Alena; Shchankin, Mikhail

2018-03-13

To reduce the cost of obtaining bacterial cellulose, acidic by-products of the alcohol and dairy industries were used without any pretreatment or addition of other nitrogen sources. Studies have shown that the greatest accumulation of bacterial cellulose (6.19g/L) occurs on wheat thin stillage for 3 days of cultivation under dynamic conditions, which is almost 3 times higher than on standard Hestrin and Schramm medium (2.14g/L). The use of whey as a nutrient medium makes it possible to obtain 5.45g/L bacterial cellulose under similar conditions of cultivation. It is established that the pH of the medium during the growth of Gluconacetobacter sucrofermentans B-11267 depends on the feedstock used and its initial value. By culturing the bacterium on thin stillage and whey, there is a decrease in the acidity of the waste. It is shown that the infrared spectra of bacterial cellulose obtained in a variety of environments have a similar character, but we found differences in the micromorphology and crystallinity of the resulting biopolymer. Copyright © 2018 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

Isolation and identification of biocellulose-producing bacterial strains from Malaysian acidic fruits.

Science.gov (United States)

Voon, W W Y; Rukayadi, Y; Meor Hussin, A S

2016-05-01

Biocellulose (BC) is pure extracellular cellulose produced by several species of micro-organisms that has numerous applications in the food, biomedical and paper industries. However, the existing biocellulose-producing bacterial strain with high yield was limited. The aim of this study was to isolate and identify the potential biocellulose-producing bacterial isolates from Malaysian acidic fruits. One hundred and ninety-three bacterial isolates were obtained from 19 local acidic fruits collected in Malaysia and screened for their ability to produce BC. A total of 15 potential bacterial isolates were then cultured in standard Hestrin-Schramm (HS) medium statically at 30°C for 2 weeks to determine the BC production. The most potent bacterial isolates were identified using 16S rRNA gene sequence analysis, morphological and biochemical characteristics. Three new and potent biocellulose-producing bacterial strains were isolated from soursop fruit and identified as Stenotrophomonas maltophilia WAUPM42, Pantoea vagans WAUPM45 and Beijerinckia fluminensis WAUPM53. Stenotrophomonas maltophilia WAUPM42 was the most potent biocellulose-producing bacterial strain that produced the highest amount of BC 0·58 g l(-1) in standard HS medium. Whereas, the isolates P. vagans WAUPM45 and B. fluminensis WAUPM53 showed 0·50 and 0·52 g l(-1) of BC production, respectively. Biocellulose (BC) is pure extracellular cellulose that is formed by many micro-organisms in the presence of carbon source and acidic condition. It can replace plant-based cellulose in multifarious applications due to its unique characteristics. In this study, three potential biocellulose-producing bacterial strains were obtained from Malaysian acidic fruits and identified as Stenotrophomonas maltophilia WAUPM42, Pantoea vagans WAUPM45 and Beijerinckia fluminensis WAUPM53. This study reports for the first time the new biocellulose-producing bacterial strains isolated from Malaysian acidic fruits. © 2016 The

Multiple approaches to microbial source tracking in tropical northern Australia

KAUST Repository

Neave, Matthew

2014-09-16

Microbial source tracking is an area of research in which multiple approaches are used to identify the sources of elevated bacterial concentrations in recreational lakes and beaches. At our study location in Darwin, northern Australia, water quality in the harbor is generally good, however dry-season beach closures due to elevated Escherichia coli and enterococci counts are a cause for concern. The sources of these high bacteria counts are currently unknown. To address this, we sampled sewage outfalls, other potential inputs, such as urban rivers and drains, and surrounding beaches, and used genetic fingerprints from E. coli and enterococci communities, fecal markers and 454 pyrosequencing to track contamination sources. A sewage effluent outfall (Larrakeyah discharge) was a source of bacteria, including fecal bacteria that impacted nearby beaches. Two other treated effluent discharges did not appear to influence sites other than those directly adjacent. Several beaches contained fecal indicator bacteria that likely originated from urban rivers and creeks within the catchment. Generally, connectivity between the sites was observed within distinct geographical locations and it appeared that most of the bacterial contamination on Darwin beaches was confined to local sources.

The Sit-and-Wait Hypothesis in Bacterial Pathogens: A Theoretical Study of Durability and Virulence

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Liang Wang

2017-11-01

Full Text Available The intriguing sit-and-wait hypothesis predicts that bacterial durability in the external environment is positively correlated with their virulence. Since its first proposal in 1987, the hypothesis has been spurring debates in terms of its validity in the field of bacterial virulence. As a special case of the vector-borne transmission versus virulence tradeoff, where vector is now replaced by environmental longevity, there are only sporadic studies over the last three decades showing that environmental durability is possibly linked with virulence. However, no systematic study of these works is currently available and epidemiological analysis has not been updated for the sit-and-wait hypothesis since the publication of Walther and Ewald’s (2004 review. In this article, we put experimental evidence, epidemiological data and theoretical analysis together to support the sit-and-wait hypothesis. According to the epidemiological data in terms of gain and loss of virulence (+/- and durability (+/- phenotypes, we classify bacteria into four groups, which are: sit-and-wait pathogens (++, vector-borne pathogens (+-, obligate-intracellular bacteria (--, and free-living bacteria (-+. After that, we dive into the abundant bacterial proteomic data with the assistance of bioinformatics techniques in order to investigate the two factors at molecular level thanks to the fast development of high-throughput sequencing technology. Sequences of durability-related genes sourced from Gene Ontology and UniProt databases and virulence factors collected from Virulence Factor Database are used to search 20 corresponding bacterial proteomes in batch mode for homologous sequences via the HMMER software package. Statistical analysis only identified a modest, and not statistically significant correlation between mortality and survival time for eight non-vector-borne bacteria with sit-and-wait potentials. Meanwhile, through between-group comparisons, bacteria with higher

A maize resistance gene functions against bacterial streak disease in rice.

Science.gov (United States)

Zhao, Bingyu; Lin, Xinghua; Poland, Jesse; Trick, Harold; Leach, Jan; Hulbert, Scot

2005-10-25

Although cereal crops all belong to the grass family (Poacea), most of their diseases are specific to a particular species. Thus, a given cereal species is typically resistant to diseases of other grasses, and this nonhost resistance is generally stable. To determine the feasibility of transferring nonhost resistance genes (R genes) between distantly related grasses to control specific diseases, we identified a maize R gene that recognizes a rice pathogen, Xanthomonas oryzae pv. oryzicola, which causes bacterial streak disease. Bacterial streak is an important disease of rice in Asia, and no simply inherited sources of resistance have been identified in rice. Although X. o. pv. oryzicola does not cause disease on maize, we identified a maize gene, Rxo1, that conditions a resistance reaction to a diverse collection of pathogen strains. Surprisingly, Rxo1 also controls resistance to the unrelated pathogen Burkholderia andropogonis, which causes bacterial stripe of sorghum and maize. The same gene thus controls resistance reactions to both pathogens and nonpathogens of maize. Rxo1 has a nucleotide-binding site-leucine-rich repeat structure, similar to many previously identified R genes. Most importantly, Rxo1 functions after transfer as a transgene to rice, demonstrating the feasibility of nonhost R gene transfer between cereals and providing a valuable tool for controlling bacterial streak disease.

Some quantitative data on bacterial attachment to pyrite

NARCIS (Netherlands)

Florian, B.; Noël, N.; Thyssen, C.; Felschau, I.; Sand, W.

2011-01-01

Bacterial attachment and biofilm formation are important for microbial bioleaching of metal sulfides, however, many details of the role played by bacteria are still unknown. Attachment as the first step in biofilm formation is critical. Our investigations are focused on these processes to control

Physio-chemical characteristics and bacterial diversity in copper ...

African Journals Online (AJOL)

The effects of seasonal change in temperature on the chemical compositions of water and bacterial diversity in copper mining wastewater reservoir (CMWR) located in Jiangxi province, China, was investigated. Wastewater samples were collected collected in December 2008 and May 2009 from different points of CMWR ...

Phylogenetic Analysis of Bacterial Communities in Different Regions of the Gastrointestinal Tract of Agkistrodon piscivorus, the Cottonmouth Snake.

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Timothy J Colston

Full Text Available Vertebrates are metagenomic organisms in that they are composed not only of their own genes but also those of their associated microbial cells. The majority of these associated microorganisms are found in the gastrointestinal tract (GIT and presumably assist in processes such as energy and nutrient acquisition. Few studies have investigated the associated gut bacterial communities of non-mammalian vertebrates, and most rely on captive animals and/or fecal samples only. Here we investigate the gut bacterial community composition of a squamate reptile, the cottonmouth snake, Agkistrodon piscivorus through pyrosequencing of the bacterial 16S rRNA gene. We characterize the bacterial communities present in the small intestine, large intestine and cloaca. Many bacterial lineages present have been reported by other vertebrate gut community studies, but we also recovered unexpected bacteria that may be unique to squamate gut communities. Bacterial communities were not phylogenetically clustered according to GIT region, but there were statistically significant differences in community composition between regions. Additionally we demonstrate the utility of using cloacal swabs as a method for sampling snake gut bacterial communities.

Haematoxylin and eosin staining identifies medium to large bacterial aggregates with a reliable specificity: A comparative analysis of follicular bacterial aggregates in axillary biopsies using peptide nucleic acid-fluorescence in situ hybridization and haematoxylin and eosin staining

DEFF Research Database (Denmark)

Ring, Hans Christian; Riis, Peter Theut; Bay, Lene

2017-01-01

between bacterial aggregates identified by haematoxylin and eosin (HE) staining vs bacterial aggregates in corresponding PNA-FISH samples. Axillary biopsies were obtained in 24 healthy controls. HE-stained and PNA-FISH samples were investigated using traditional light microscopy and CLSM, respectively....... The data demonstrate that HE staining identifies large bacterial aggregates (>10 μm) with a sensitivity of 0.43 and specificity of 1. The methods, however, are not equivalent as demonstrated by a McNemar's test (P=.04). Where bacterial aggregates >10 μm in diameter, HE staining may offer a rapid...... and practical low-cost tool to evaluate bacterial aggregates....

Investigation Of The Origin Of Various Water Sources In The Vicinity Of Ngancar Dam, Wonogiri Using Natural Isotopes

International Nuclear Information System (INIS)

Sidauruk, Paston; Indrojoyo; Wibagoyo; Pratikno, Bungkus; Evarista Ristin, P.I.

2000-01-01

The investigation of the origin of various water sources in the vicinity of Ngancar Dam, Wonogiri, using natural isotopes technique has been conducted. The study includes collecting and analyzing water samples from various sources in the vicinity of the dam such as reservoir water, water discharges, springs, local water well, rain water, water from piezometer and observation wells. For this investigation, natural isotopes composition and hydro chemical ions of the samples have been analyzed and interpreted. From the data interpretation, it is concluded that most of the water in various sources originated from water reservoir

Brood size modifications affect plumage bacterial assemblages of European starlings.

Science.gov (United States)

Lucas, Françoise S; Moureau, Benoit; Jourdie, Violaine; Heeb, Philipp

2005-02-01

During reproduction, birds face trade-offs between time and energy devoted to parental effort and traits associated with self-maintenance. We manipulated brood sizes to investigate the effects of such trade-offs on feather bacterial densities and the structure of bacterial assemblages on feathers in adult European starlings, Sturnus vulgaris, and in vitro feather degradation. As predicted by a trade-off between parental effort and self-maintenance, we found that birds with enlarged broods had more free-living bacteria on their feathers than birds with reduced broods. Furthermore, we found a significant interaction between brood manipulation and original brood size on free-living bacterial densities suggesting that the trade-off is mediated by the adults' initial reproductive investment. In contrast, brood size manipulations had no significant effect on densities of attached bacteria. Using ribosomal intergenic spacer analysis (RISA), we demonstrated that brood manipulations significantly modified the structure (band pattern) of feather-degrading bacterial assemblages, but had no significant effect on their richness (number of bands) or the in vitro feather degradation. In vitro feather degradation varied in relation to the premanipulation brood size and positively with the richness of the feather degrading bacterial community. Besides brood manipulation effect, we found that ecological factors and individual traits, such as the age, the nest location or the capture date, shaped bacterial assemblages and feather degradation capacities.

Coupling Bacterial Activity Measurements with Cell Sorting by Flow Cytometry.

Science.gov (United States)

Servais; Courties; Lebaron; Troussellier

1999-08-01

> Abstract A new procedure to investigate the relationship between bacterial cell size and activity at the cellular level has been developed; it is based on the coupling of radioactive labeling of bacterial cells and cell sorting by flow cytometry after SYTO 13 staining. Before sorting, bacterial cells were incubated in the presence of tritiated leucine using a procedure similar to that used for measuring bacterial production by leucine incorporation and then stained with SYTO 13. Subpopulations of bacterial cells were sorted according to their average right-angle light scatter (RALS) and fluorescence. Average RALS was shown to be significantly related to the average biovolume. Experiments were performed on samples collected at different times in a Mediterranean seawater mesocosm enriched with nitrogen and phosphorus. At four sampling times, bacteria were sorted in two subpopulations (cells smaller and larger than 0.25 µm(3)). The results indicate that, at each sampling time, the growth rate of larger cells was higher than that of smaller cells. In order to confirm this tendency, cell sorting was performed on six subpopulations differing in average biovolume during the mesocosm follow-up. A clear increase of the bacterial growth rates was observed with increasing cell size for the conditions met in this enriched mesocosm.http://link.springer-ny.com/link/service/journals/00248/bibs/38n2p180.html

Bacterial Cell Mechanics.

Science.gov (United States)

Auer, George K; Weibel, Douglas B

2017-07-25

Cellular mechanical properties play an integral role in bacterial survival and adaptation. Historically, the bacterial cell wall and, in particular, the layer of polymeric material called the peptidoglycan were the elements to which cell mechanics could be primarily attributed. Disrupting the biochemical machinery that assembles the peptidoglycan (e.g., using the β-lactam family of antibiotics) alters the structure of this material, leads to mechanical defects, and results in cell lysis. Decades after the discovery of peptidoglycan-synthesizing enzymes, the mechanisms that underlie their positioning and regulation are still not entirely understood. In addition, recent evidence suggests a diverse group of other biochemical elements influence bacterial cell mechanics, may be regulated by new cellular mechanisms, and may be triggered in different environmental contexts to enable cell adaptation and survival. This review summarizes the contributions that different biomolecular components of the cell wall (e.g., lipopolysaccharides, wall and lipoteichoic acids, lipid bilayers, peptidoglycan, and proteins) make to Gram-negative and Gram-positive bacterial cell mechanics. We discuss the contribution of individual proteins and macromolecular complexes in cell mechanics and the tools that make it possible to quantitatively decipher the biochemical machinery that contributes to bacterial cell mechanics. Advances in this area may provide insight into new biology and influence the development of antibacterial chemotherapies.

The Lag-Luminosity Relation in the GRB Source Frame: An Investigation with Swift BAT Bursts

Science.gov (United States)

Ukwatta, T. N.; Dhuga, K. S.; Stamatikos, M.; Dermer, C. D.; Sakamoto, T.; Sonbas, E.; Parke, W. C.; Maximon, L. C.; Linnemann, J. T.; Bhat, P. N.;

A Rules-Based Simulation of Bacterial Turbulence

Science.gov (United States)

Mikel-Stites, Maxwell; Staples, Anne

2015-11-01

In sufficiently dense bacterial populations (>40% bacteria by volume), unusual collective swimming behaviors have been consistently observed, resembling von Karman vortex streets. The source of these collective swimming behavior has yet to be fully determined, and as of yet, no research has been conducted that would define whether or not this behavior is derived predominantly from the properties of the surrounding media, or if it is an emergent behavior as a result of the ``rules'' governing the behavior of individual bacteria. The goal of this research is to ascertain whether or not it is possible to design a simulation that can replicate the qualitative behavior of the densely packed bacterial populations using only behavioral rules to govern the actions of each bacteria, with the physical properties of the media being neglected. The results of the simulation will address whether or not it is possible for the system's overall behavior to be driven exclusively by these rule-based dynamics. In order to examine this, the behavioral simulation was written in MATLAB on a fixed grid, and updated sequentially with the bacterial behavior, including randomized tumbling, gathering and perceptual sub-functions. If the simulation is successful, it will serve as confirmation that it is possible to generate these qualitatively vortex-like behaviors without specific physical media (that the phenomena arises in emergent fashion from behavioral rules), or as evidence that the observed behavior requires some specific set of physical parameters.

Response of Archaeal and Bacterial Soil Communities to Changes Associated with Outdoor Cattle Overwintering.

Science.gov (United States)

Chroňáková, Alica; Schloter-Hai, Brigitte; Radl, Viviane; Endesfelder, David; Quince, Christopher; Elhottová, Dana; Šimek, Miloslav; Schloter, Michael

2015-01-01

Archaea and bacteria are important drivers for nutrient transformations in soils and catalyse the production and consumption of important greenhouse gases. In this study, we investigate changes in archaeal and bacterial communities of four Czech grassland soils affected by outdoor cattle husbandry. Two show short-term (3 years; STI) and long-term impact (17 years; LTI), one is regenerating from cattle impact (REG) and a control is unaffected by cattle (CON). Cattle manure (CMN), the source of allochthonous microbes, was collected from the same area. We used pyrosequencing of 16S rRNA genes to assess the composition of archaeal and bacterial communities in each soil type and CMN. Both short- and long- term cattle impact negatively altered archaeal and bacterial diversity, leading to increase of homogenization of microbial communities in overwintering soils over time. Moreover, strong shifts in the prokaryotic communities were observed in response to cattle overwintering, with the greatest impact on archaea. Oligotrophic and acidophilic microorganisms (e.g. Thaumarchaeota, Acidobacteria, and α-Proteobacteria) dominated in CON and expressed strong negative response to increased pH, total C and N. Whereas copiotrophic and alkalophilic microbes (e.g. methanogenic Euryarchaeota, Firmicutes, Chloroflexi, Actinobacteria, and Bacteroidetes) were common in LTI showing opposite trends. Crenarchaeota were also found in LTI, though their trophic interactions remain cryptic. Firmicutes, Bacteroidetes, Methanobacteriaceae, and Methanomicrobiaceae indicated the introduction and establishment of faecal microbes into the impacted soils, while Chloroflexi and Methanosarcinaceae suggested increased abundance of soil-borne microbes under altered environmental conditions. The observed changes in prokaryotic community composition may have driven corresponding changes in soil functioning.

Bacteriophage-encoded shiga toxin gene in atypical bacterial host

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Casas Veronica

2011-07-01

Full Text Available Abstract Background Contamination from fecal bacteria in recreational waters is a major health concern since bacteria capable of causing human disease can be found in animal feces. The Dog Beach area of Ocean Beach in San Diego, California is a beach prone to closures due to high levels of fecal indicator bacteria (FIB. A potential source of these FIB could be the canine feces left behind by owners who do not clean up after their pets. We tested this hypothesis by screening the DNA isolated from canine feces for the bacteriophage-encoded stx gene normally found in the virulent strains of the fecal bacterium Escherichia coli. Results Twenty canine fecal samples were collected, processed for total and bacterial fraction DNA, and screened by PCR for the stx gene. The stx gene was detected in the total and bacterial fraction DNA of one fecal sample. Bacterial isolates were then cultivated from the stx-positive fecal sample. Eighty nine of these canine fecal bacterial isolates were screened by PCR for the stx gene. The stx gene was detected in five of these isolates. Sequencing and phylogenetic analyses of 16S rRNA gene PCR products from the canine fecal bacterial isolates indicated that they were Enterococcus and not E. coli. Conclusions The bacteriophage-encoded stx gene was found in multiple species of bacteria cultivated from canine fecal samples gathered at the shoreline of the Dog Beach area of Ocean Beach in San Diego, California. The canine fecal bacteria carrying the stx gene were not the typical E. coli host and were instead identified through phylogenetic analyses as Enterococcus. This suggests a large degree of horizontal gene transfer of exotoxin genes in recreational waters.

Chemical mediation of bacterial surface colonisation by secondary metabolites from the red alga Delisea pulchra

DEFF Research Database (Denmark)

Maximilien, Ria; de Nys, Rocky; Holmström, Carola

1998-01-01

-occurring algal species, all of which lack furanones. There was also a strong inverse correlation between bacterial abundance and furanone content (previously determined) for different sections of the thallus of D. pulchra, consistent with inhibition of bacteria by furanones. Based on these observations we....... pulchra the most. As inhibition of growth did not provide an adequate explanation for the inverse relationship between levels of furanones and bacteria abundance on D. pulchra, we proceeded to investigate the effects of these metabolites on other bacterial characteristics relevant to colonisation...... of different bacterial isolates or phenotypes by furanones, as well as affecting overall bacterial abundance on the alga, should have strong effects on the species composition of the bacterial community on the alga's surface. The effects of furanones on specific bacterial colonisation traits are discussed...

Host-Derived Sialic Acids Are an Important Nutrient Source Required for Optimal Bacterial Fitness In Vivo.

Science.gov (United States)

McDonald, Nathan D; Lubin, Jean-Bernard; Chowdhury, Nityananda; Boyd, E Fidelma

2016-04-12

A major challenge facing bacterial intestinal pathogens is competition for nutrient sources with the host microbiota.Vibrio cholerae is an intestinal pathogen that causes cholera, which affects millions each year; however, our knowledge of its nutritional requirements in the intestinal milieu is limited. In this study, we demonstrated that V. cholerae can grow efficiently on intestinal mucus and its component sialic acids and that a tripartite ATP-independent periplasmic SiaPQM strain, transporter-deficient mutant NC1777, was attenuated for colonization using a streptomycin-pretreated adult mouse model. In in vivo competition assays, NC1777 was significantly outcompeted for up to 3 days postinfection. NC1777 was also significantly outcompeted in in vitro competition assays in M9 minimal medium supplemented with intestinal mucus, indicating that sialic acid uptake is essential for fitness. Phylogenetic analyses demonstrated that the ability to utilize sialic acid was distributed among 452 bacterial species from eight phyla. The majority of species belonged to four phyla, Actinobacteria (members of Actinobacillus, Corynebacterium, Mycoplasma, and Streptomyces), Bacteroidetes (mainly Bacteroides, Capnocytophaga, and Prevotella), Firmicutes (members of Streptococcus, Staphylococcus, Clostridium, and Lactobacillus), and Proteobacteria (including Escherichia, Shigella, Salmonella, Citrobacter, Haemophilus, Klebsiella, Pasteurella, Photobacterium, Vibrio, and Yersinia species), mostly commensals and/or pathogens. Overall, our data demonstrate that the ability to take up host-derived sugars and sialic acid specifically allows V. cholerae a competitive advantage in intestinal colonization and that this is a trait that is sporadic in its occurrence and phylogenetic distribution and ancestral in some genera but horizontally acquired in others. Sialic acids are nine carbon amino sugars that are abundant on all mucous surfaces. The deadly human pathogen Vibrio cholerae contains

Amorphous structure of iron oxide of bacterial origin

Energy Technology Data Exchange (ETDEWEB)

Hashimoto, Hideki; Fujii, Tatsuo [Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530 (Japan); Kohara, Shinji [Japan Synchrotron Radiation Research Institute, Sayo, Hyogo 679-5198 (Japan); Asaoka, Hiroshi [Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530 (Japan); Kusano, Yoshihiro [Department of Fine and Applied Arts, Kurashiki University of Science and the Arts, Kurashiki, Okayama 712-8505 (Japan); Ikeda, Yasunori [Research Institute for Production Development, Sakyo-ku, Kyoto 606-0805 (Japan); Nakanishi, Makoto [Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530 (Japan); Benino, Yasuhiko; Nanba, Tokuro [Graduate School of Environmental Science, Okayama University, Okayama 700-8530 (Japan); Takada, Jun, E-mail: jtakada@cc.okayama-u.ac.jp [Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530 (Japan); JST, CREST, Okayama 700-8530 (Japan)

2012-12-14

In nature, there are various iron oxides produced by the water-habitant bacterial group called 'iron-oxidizing bacteria'. These iron oxides have been studied mainly from biological and geochemical perspectives. Today, attempts are made to use such iron oxides as novel functional materials in several applications. However, their quantitative structural characteristics are still unclear. We studied the structure of iron oxide of microtubular form consisting of amorphous nanoparticles formed by an iron-oxidizing bacterium, Leptothrix ochracea, using a combination of high-energy X-ray diffraction and reverse Monte Carlo simulation. We found that its structure consists of a framework of corner- and edge-sharing distorted FeO{sub 6} octahedral units, while SiO{sub 4} tetrahedral units are isolated in the framework. The results reveal the atomic arrangement of iron oxide of bacterial origin, which is essential for investigating its potential as a functional material. -- Highlights: Black-Right-Pointing-Pointer The amorphous structure of bacterial iron oxide was investigated. Black-Right-Pointing-Pointer The structure was simulated by high-energy X-ray diffraction and reverse Monte Carlo simulation. Black-Right-Pointing-Pointer The structure was constructed of a framework of corner- and edge-sharing distorted FeO{sub 6} octahedral units. Black-Right-Pointing-Pointer SiO{sub 4} tetrahedral units were distributed isolatedly in the framework of FeO{sub 6} octahedral units.

Nitrate and ammonia as nitrogen sources for deep subsurface microorganisms

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Heini eKutvonen

2015-10-01

Full Text Available We investigated the N-utilizing bacterial community in anoxic brackish groundwater of the low and intermediate level nuclear waste repository cave in Olkiluoto, Finland, at 100 m depth using 15N-based stable isotope probing (SIP and enrichment with 14/15N-ammonium or 14/15N-nitrate complemented with methane. 28 days of incubation at 12°C increased the concentration of bacterial 16S rRNA and nitrate reductase (narG gene copies in the substrate amended microcosms simultaneously with a radical drop in the overall bacterial diversity and OTU richness. Hydrogenophaga/Malikia were enriched in all substrate amended microcosms and Methylobacter in the ammonium and ammonium+methane supplemented microcosms. Sulfuricurvum was especially abundant in the nitrate+methane treatment and the unamended incubation control. Membrane-bound nitrate reductase genes (narG from Polarimonas sp. were detected in the original groundwater, while Burkholderia, Methylibium and Pseudomonas narG genes were enriched due to substrate supplements. Identified amoA genes belonged to Nitrosomonas sp. 15N-SIP revealed that Burkholderiales and Rhizobiales clades belonging to the minority groups in the original groundwater used 15N from ammonium and nitrate as N source indicating an important ecological function of these bacteria, despite their low number, in the groundwater N cycle in Olkiluoto bedrock system.

Housefly Larva Vermicomposting Efficiently Attenuates Antibiotic Resistance Genes in Swine Manure, with Concomitant Bacterial Population Changes.

Science.gov (United States)

Wang, Hang; Li, Hongyi; Gilbert, Jack A; Li, Haibo; Wu, Longhua; Liu, Meng; Wang, Liling; Zhou, Qiansheng; Yuan, Junxiang; Zhang, Zhijian

2015-11-01

Manure from swine treated with antimicrobials as feed additives is a major source for the expansion of the antibiotic resistance gene (ARG) reservoir in the environment. Vermicomposting via housefly larvae (Musca domestica) can be efficiently used to treat manure and regenerate biofertilizer, but few studies have investigated its effect on ARG attenuation. Here, we tracked the abundances of 9 ARGs and the composition and structure of the bacterial communities in manure samples across 6 days of full-scale manure vermicomposting. On day 6, the abundances of genes encoding tetracycline resistance [tet(M), tet(O), tet(Q), and tet(W)] were reduced (P biofertilizer in agroecosystems. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

The bacterial diversity associated with bacterial diseases on Mud Crab (Scylla serrata Fab.) from Pemalang Coast, Indonesia

Science.gov (United States)

Sarjito; Desrina; Haditomo, AHC; Budi Prayitno, S.

2018-05-01

Bacterial disease is a problem in mud crab culture in Pemalang, Indonesia. The purpose of this study was to find out the bacteria associated with bacterial diseases on mud crab based on the molecular approach. Exploratory methods were conducted in this reserach. Twenty two bacteria (SJP 01 – SJP 22) were isolated from carapace and gills and hepathopancreas of moribound mud crab with TCBS and TSA medium. Based on rep PCR, five isolates (SJP 01, SJP 02, SJP 04, SJP 10 and SJP 11) were choosen for further investigation. Result from 16S rDNA sequence analysis, SJP 01, SJP 02, SJP 04, SJP 10 and SJP 11 were closely related to Exiguobacterium sp. ZJ2505 (99%), V. harveyi strain NCIMB1280 (98%), V. alginolyticus strain ATCC 17749(98%.), B. marisflavi strain TF-11 (97%) and E. aestuarii strain TF-16 (99%) respectively.

Mineralization of linear alkylbenzene sulfonate by a four-member aerobic bacterial consortium

International Nuclear Information System (INIS)

Jimenez, L.; Breen, A.; Thomas, N.; Sayler, G.S.; Federle, T.W.

1991-01-01

A bacterial consortium capable of linear alkylbenzene sulfonate (LAS) mineralization under aerobic conditions was isolated from a chemostat inoculated with activated sludge. The consortium, designated KJB, consisted of four members, all of which were gram-negative, rod-shaped bacteria that grew in pairs and short chains. Three isolates had biochemical properties characteristic of Pseudomonas spp.; the fourth showed characteristics of the Aeromonas spp. Cell suspensions were grown together in minimal medium with [ 14 C]LAS as the only carbon source. After 13 days of incubation, more than 25% of the [ 14 C]LAS was mineralized to 14 CO 2 by the consortium. Pure bacterial cultures and combinations lacking any one member of the KJB bacterial consortium did not mineralize LAS. Three isolates carried out primary biodegradation of the surfactant, and one did not. This study shows that the four bacteria complemented each other and synergistically mineralized LAS, indicating catabolic cooperation among the four consortium members

Bacterial vaginosis diagnosed by analysis of first-void-urine specimens

DEFF Research Database (Denmark)

Datcu, Raluca; Gesink, Dionne; Mulvad, Gert

2014-01-01

Bacterial vaginosis (BV) is traditionally diagnosed using vaginal samples. The aim of this study was to investigate whether BV can be diagnosed from first-void urine (FVU). Self-collected vaginal smears, vaginal swabs, and FVU were obtained from 176 women. BV was diagnosed by Nugent's criteria....... The FVU and vaginal swabs were analyzed by quantitative PCRs (qPCRs) for selected vaginal bacteria (Atopobium vaginae, Prevotella spp., Gardnerella vaginalis, bacterial vaginosis-associated bacterium 2, Eggerthella-like bacterium, "Leptotrichia amnionii," Megasphaera type 1), and all had an area under...

Investigation of spore forming bacterial flooding for enhanced oil recovery in a North Sea chalk Reservoir

DEFF Research Database (Denmark)

Halim, Amalia Yunita; Nielsen, Sidsel Marie; Eliasson Lantz, Anna

2015-01-01

Little has been done to study microbial enhanced oil recovery (MEOR) in chalk reservoirs. The present study focuses on core flooding experiments designed to see microbial plugging and its effect on oil recovery. A pressure tapped core holder was used for this purpose. A spore forming bacteria...... Bacillus licheniformis 421 was used as it was shown to be a good candidate in a previous study. Bacterial spore can penetrate deeper into the chalk rock, squeezing through the pore throats. Our results showed that injection of B. licheniformis 421 as a tertiary oil recovery method, in the residual oil...... saturation state, was able to produce additionally 1.0-2.3% original oil in place (OOIP) in homogeneous cores and 6.9-8.8% OOIP in heterogeneous cores. In addition, the pressure gradient was much higher in the heterogeneous cores, which confirms that bacterial selective plugging plays an important role...

Bacterial community survey of sediments at Naracoorte Caves, Australia

Directory of Open Access Journals (Sweden)

Ball Andrew S.

2012-07-01

Full Text Available Bacterial diversity in sediments at UNESCO World Heritage listed Naracoorte Caves was surveyed as part of an investigation carried out in a larger study on assessing microbial communities in caves. Cave selection was based on tourist accessibility; Stick Tomato and Alexandra Cave (> 15000 annual visits and Strawhaven Cave was used as control (no tourist access. Microbial analysis showed that Bacillus was the most commonly detected microbial genus by culture dependent and independent survey of tourist accessible and inaccessible areas of show (tourist accessible and control caves. Other detected sediment bacterial groups were assigned to the Firmicutes, Actinobacteria and Proteobacteria. The survey also showed differences in bacterial diversity in caves with human access compared to the control cave with the control cave having unique microbial sequences (Acinetobacter, Agromyces, Micrococcus and Streptomyces. The show caves had higher bacterial counts, different 16S rDNA based DGGE cluster patterns and principal component groupings compared to Strawhaven. Different factors such as human access, cave use and configurations could have been responsible for the differences observed in the bacterial community cluster patterns (tourist accessible and inaccessible areas of these caves. Cave sediments can therefore act as reservoirs of microorganisms. This might have some implications on cave conservation activities especially if these sediments harbor rock art degrading microorganisms in caves with rock art.

Organic carbon source and C/N ratio affect inorganic nitrogen profile in the biofloc-based culture media of Pacific white shrimp (Litopenaeus vannamei

Directory of Open Access Journals (Sweden)

Muhammad Hanif Azhar

2016-03-01

Full Text Available Organic carbon source and C/N ratio play an important role in aquaculture system with biofloc technology application. Nitrogen control by adding carbohydrates to the water to stimulate heterotrophic bacterial growth by converting nitrogen into bacterial biomass. The study investigated the effect molasses, tapioca, tapioca by product and rice bran as carbon sources in a biofloc media at three different C/N ratios i.e. 10, 15, and 20 on total ammonia reduction in biofloc media. Five liters of biofloc media in a conical tank was prepared for each replicate, which consisted of 500 mL of biofloc suspension collected from a shrimp culture unit with biofloc technology application and 4.5 L seawater. Pacific white shrimp culture was performed in 40L glass aquaria at a shrimp density of 30/aquarium. There was a significant interaction between carbon source and the C/N ratio applied (P<0.05. The use of molasses resulted in the highest reduction rate irrespective to the C/N ratio. Keywords: molasses, tapioca, tapioca by product, rice bran, biofloc, total ammonia nitrogen

Production and Rheological Properties of Welan Gum Produced by Sphingomonas sp. ATCC 31555 with Different Nitrogen Sources.

Science.gov (United States)

Xu, Xiaopeng; Nie, Zuoming; Zheng, Zhiyong; Zhu, Li; Zhan, Xiaobei

2017-01-01

This study aimed to investigate the effect of nitrogen sources on the production and rheological properties of welan gum produced by Sphingomonas sp. ATCC 31555. Six different nitrogen sources were used for ATCC 31555 fermentation, and 2 of these were further analyzed due to their more positive influence on welan gum production and bacterial biomass. Bacterial biomass, welan gum yield, welan viscosity, molecular weight, monosaccharide composition, acyl content, and welan structure were analyzed. Welan gum production and the biomass concentration of ATCC 31555 were higher in media containing NaNO3 and beef extract. Welan viscosity decreased at higher temperatures of 30-90°C, and it increased with a higher welan concentration. In the media containing NaNO3 (3 g·L-1), welan viscosity was higher at 30-70°C and a welan solution concentration of 6-10 g·L-1. With a reduced NaNO3 concentration, the molecular weight of welan gum and the molar ratio of mannose decreased, but the molar ratio of glucuronic acid increased. With different nitrogen sources, the acetyl content of welan gum differed but its structure was similar. NaNO3 and beef extract facilitated welan production. A reduced NaNO3 concentration promoted welan viscosity. © 2017 S. Karger AG, Basel.

Surveillance of bacterial pathogens of diarrhoea in two selected sub ...

African Journals Online (AJOL)

GAR) have witnessed several episodes of cholera outbreaks, with some deaths. Compared to previous epidemics, which usually followed heavy rains, recent outbreaks show no seasonality. Objectives: To investigate infective bacterial diseases ...

Effect of gamma rays on gram negative bacterial endotoxin

International Nuclear Information System (INIS)

Hilmy, N.; Dzulkarnain, B.

1977-01-01

Escherichia coli br and a Flavobacterium sp., isolated from Tjiptomangunkusumo Hospital in Jakarta, were used as bacterial endotoxin (pyrogen) source. Suspensoion of 10 7 , 10 6 , and 10 5 bacteria in sterile and pyrogen free Sodium Chloride Injection, that had been treated by heat at 80 deg C for 15 minutes or treated by irradiation with a dose of 2.5 x 10 6 rad, were injected each to nine rabbits. Maximum temperature rises were registered and compared. Data were interpreted according to the requirements of Indonesian Pharmacopea (1972) and British Pharmacopea (1973). The results showed that a dose of 2.5 x 10 6 rad did not reduce the pyrogenic activity. The rate of bacterial multiplications in the pharmaceutical preparations were tested by using sterile Dextrose (2.5%) and Sodium Chloride Injection as medium; storage time were 0; 6; and 24 hours. (author)

Detection of Bacterial Endospores in Soil by Terbium Fluorescence

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Andrea Brandes Ammann

2011-01-01

Full Text Available Spore formation is a survival mechanism of microorganisms when facing unfavorable environmental conditions resulting in “dormant” states. We investigated the occurrence of bacterial endospores in soils from various locations including grasslands (pasture, meadow, allotment gardens, and forests, as well as fluvial sediments. Bacterial spores are characterized by their high content of dipicolinic acid (DPA. In the presence of terbium, DPA forms a complex showing a distinctive photoluminescence spectrum. DPA was released from soil by microwaving or autoclaving. The addition of aluminium chloride reduced signal quenching by interfering compounds such as phosphate. The highest spore content (up to 109 spores per gram of dry soil was found in grassland soils. Spore content is related to soil type, to soil depth, and to soil carbon-to-nitrogen ratio. Our study might provide a basis for the detection of “hot spots” of bacterial spores in soil.

Characterisation of the bacterial community structures in the intestine of Lampetra morii.

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Li, Yingying; Xie, Wenfang; Li, Qingwei

2016-07-01

The metagenomic analysis and 16S rDNA sequencing method were used to investigate the bacterial community in the intestines of Lampetra morii. The bacterial community structure in L. morii intestine was relatively simple. Eight different operational taxonomic units were observed. Chitinophagaceae_unclassified (26.5 %) and Aeromonas spp. (69.6 %) were detected as dominant members at the genus level. The non-dominant genera were as follows: Acinetobacter spp. (1.4 %), Candidatus Bacilloplasma (2.5 %), Enterobacteria spp. (1.5 %), Shewanella spp. (0.04 %), Vibrio spp. (0.09 %), and Yersinia spp. (1.8 %). The Shannon-Wiener (H) and Simpson (1-D) indexes were 0.782339 and 0.5546, respectively. The rarefaction curve representing the bacterial community richness and Shannon-Wiener curve representing the bacterial community diversity reached asymptote, which indicated that the sequence depth were sufficient to represent the majority of species richness and bacterial community diversity. The number of Aeromonas in lamprey intestine was two times higher after stimulation by lipopolysaccharide than PBS. This study provides data for understanding the bacterial community harboured in lamprey intestines and exploring potential key intestinal symbiotic bacteria essential for the L. morii immune response.

Nematode grazing promotes bacterial community dynamics in soil at the aggregate level.

Science.gov (United States)

Jiang, Yuji; Liu, Manqiang; Zhang, Jiabao; Chen, Yan; Chen, Xiaoyun; Chen, Lijun; Li, Huixin; Zhang, Xue-Xian; Sun, Bo

2017-12-01

Nematode predation has important roles in determining bacterial community composition and dynamics, but the extent of the effects remains largely rudimentary, particularly in natural environment settings. Here, we investigated the complex microbial-microfaunal interactions in the rhizosphere of maize grown in red soils, which were derived from four long-term fertilization regimes. Root-free rhizosphere soil samples were separated into three aggregate fractions whereby the abundance and community composition were examined for nematode and total bacterial communities. A functional group of alkaline phosphomonoesterase (ALP) producing bacteria was included to test the hypothesis that nematode grazing may significantly affect specific bacteria-mediated ecological functions, that is, organic phosphate cycling in soil. Results of correlation analysis, structural equation modeling and interaction networks combined with laboratory microcosm experiments consistently indicated that bacterivorous nematodes enhanced bacterial diversity, and the abundance of bacterivores was positively correlated with bacterial biomass, including ALP-producing bacterial abundance. Significantly, such effects were more pronounced in large macroaggregates than in microaggregates. There was a positive correlation between the most dominant bacterivores Protorhabditis and the ALP-producing keystone 'species' Mesorhizobium. Taken together, these findings implicate important roles of nematodes in stimulating bacterial dynamics in a spatially dependent manner.

Bacterial flavin-containing monooxygenase is trimethylamine monooxygenase.

Science.gov (United States)

Chen, Yin; Patel, Nisha A; Crombie, Andrew; Scrivens, James H; Murrell, J Colin

2011-10-25

Flavin-containing monooxygenases (FMOs) are one of the most important monooxygenase systems in Eukaryotes and have many important physiological functions. FMOs have also been found in bacteria; however, their physiological function is not known. Here, we report the identification and characterization of trimethylamine (TMA) monooxygenase, termed Tmm, from Methylocella silvestris, using a combination of proteomic, biochemical, and genetic approaches. This bacterial FMO contains the FMO sequence motif (FXGXXXHXXXF/Y) and typical flavin adenine dinucleotide and nicotinamide adenine dinucleotide phosphate-binding domains. The enzyme was highly expressed in TMA-grown M. silvestris and absent during growth on methanol. The gene, tmm, was expressed in Escherichia coli, and the purified recombinant protein had high Tmm activity. Mutagenesis of this gene abolished the ability of M. silvestris to grow on TMA as a sole carbon and energy source. Close homologs of tmm occur in many Alphaproteobacteria, in particular Rhodobacteraceae (marine Roseobacter clade, MRC) and the marine SAR11 clade (Pelagibacter ubique). We show that the ability of MRC to use TMA as a sole carbon and/or nitrogen source is directly linked to the presence of tmm in the genomes, and purified Tmm of MRC and SAR11 from recombinant E. coli showed Tmm activities. The tmm gene is highly abundant in the metagenomes of the Global Ocean Sampling expedition, and we estimate that 20% of the bacteria in the surface ocean contain tmm. Taken together, our results suggest that Tmm, a bacterial FMO, plays an important yet overlooked role in the global carbon and nitrogen cycles.

Investigations on a hybrid positron source with a granular converter

Energy Technology Data Exchange (ETDEWEB)

Artru, X. [Institut de Physique Nucleaire de Lyon, Universite Lyon 1, CNRS/IN2P3, Villeurbanne (France); Chaikovska, I. [Laboratoire de l’Accelerateur Lineaire (LAL), Universite Paris-Sud, Bat. 200, 91898 Orsay (France); Chehab, R., E-mail: chehab@lal.in2p3.fr [Institut de Physique Nucleaire de Lyon, Universite Lyon 1, CNRS/IN2P3, Villeurbanne (France); Chevallier, M. [Institut de Physique Nucleaire de Lyon, Universite Lyon 1, CNRS/IN2P3, Villeurbanne (France); Dadoun, O. [Laboratoire de l’Accelerateur Lineaire (LAL), Universite Paris-Sud, Bat. 200, 91898 Orsay (France); Furukawa, K. [Accelerator Laboratory (KEK), Oho, Tsukuba, Ibaraki 305-0801 (Japan); Guler, H. [Laboratoire de l’Accelerateur Lineaire (LAL), Universite Paris-Sud, Bat. 200, 91898 Orsay (France); Kamitani, T.; Miyahara, F.; Satoh, M. [Accelerator Laboratory (KEK), Oho, Tsukuba, Ibaraki 305-0801 (Japan); Sievers, P. [CERN, Geneva (Switzerland); Suwada, T.; Umemori, K. [Accelerator Laboratory (KEK), Oho, Tsukuba, Ibaraki 305-0801 (Japan); Variola, A. [Laboratoire de l’Accelerateur Lineaire (LAL), Universite Paris-Sud, Bat. 200, 91898 Orsay (France)

2015-07-15

Promising results obtained with crystal targets for positron production led to the elaboration of a hybrid source made of an axially oriented tungsten crystal, as a radiator, and an amorphous tungsten converter. If the converter is granular, made of small spheres, the heat dissipation is greatly enhanced and the thermal shocks reduced, allowing the consideration of such device for the future linear colliders. A positron source of this kind is investigated. Previous simulations have shown very promising results for the yield as for the energy deposition and the PEDD (Peak Energy Deposition Density). Here, we present detailed simulations made in this granular converter with emphasis on the energy deposition density, which is a critical parameter as learned from the breakdown of the SLC target. A test on the KEKB linac is foreseen; it will allow a determination of the energy deposited and the PEDD in the converter through temperature measurements. Four granular converters, made of W spheres of mm radius have been built at LAL-Orsay; they will be installed at KEK and compared to compact converters. A description of the experimental layout at KEK is provided. Applications to future linear colliders as CLIC and ILC are considered.

Highly Heterogeneous Soil Bacterial Communities around Terra Nova Bay of Northern Victoria Land, Antarctica

Science.gov (United States)

Lim, Hyoun Soo; Hong, Soon Gyu; Kim, Ji Hee; Lee, Joohan; Choi, Taejin; Ahn, Tae Seok; Kim, Ok-Sun

2015-01-01

Given the diminished role of biotic interactions in soils of continental Antarctica, abiotic factors are believed to play a dominant role in structuring of microbial communities. However, many ice-free regions remain unexplored, and it is unclear which environmental gradients are primarily responsible for the variations among bacterial communities. In this study, we investigated the soil bacterial community around Terra Nova Bay of Victoria Land by pyrosequencing and determined which environmental variables govern the bacterial community structure at the local scale. Six bacterial phyla, Actinobacteria, Proteobacteria, Acidobacteria, Chloroflexi, Cyanobacteria, and Bacteroidetes, were dominant, but their relative abundance varied greatly across locations. Bacterial community structures were affected little by spatial distance, but structured more strongly by site, which was in accordance with the soil physicochemical compositions. At both the phylum and species levels, bacterial community structure was explained primarily by pH and water content, while certain earth elements and trace metals also played important roles in shaping community variation. The higher heterogeneity of the bacterial community structure found at this site indicates how soil bacterial communities have adapted to different compositions of edaphic variables under extreme environmental conditions. Taken together, these findings greatly advance our understanding of the adaption of soil bacterial populations to this harsh environment. PMID:25799273

Effects of Fe nanoparticles on bacterial growth and biosurfactant production

Science.gov (United States)

Liu, Jia; Vipulanandan, Cumaraswamy; Cooper, Tim F.; Vipulanandan, Geethanjali

2013-01-01

Environmental conditions can have a major impact on bacterial growth and production of secondary products. In this study, the effect of different concentrations of Fe nanoparticles on the growth of Serratia sp. and on its production of a specific biosurfactant was investigated. The Fe nanoparticles were produced using the foam method, and the needle-shaped nanoparticles were about 30 nm in diameter. It was found that Fe nanoparticles can have either a positive or a negative impact on the bacterial growth and biosurfactant production, depending on their concentration. At 1 mg/L of Fe nanoparticle concentration the bacterial growth increased by 57 % and biosurfactant production increased by 63 %. When the Fe nanoparticle concentration was increased to 1 g/L, the bacterial growth decreased by 77 % and biosurfactant activity was undetectable. The biosurfactant itself was not directly affected by Fe nanoparticles over the range of concentrations studied, indicating that the observed changes in biosurfactant activity resulted indirectly from the effect of nanoparticles on the bacteria. These negative effects with nanoparticle exposures were temporary, demonstrated by the restoration of biosurfactant activity when the bacteria initially exposed to Fe nanoparticles were allowed to regrow in the absence of nanoparticles. Finally, the kinetics of bacterial growth and biosurfactant production were modeled. The model's predictions agreed with the experimental results.

Role of lipids in bacterial radioresistance

International Nuclear Information System (INIS)

Abushady, M.R.; Fawkia, M.E.; Tawfik, Z.S.

1992-01-01

The radioresistance of three bacterial isolates was determined. S. aureus was the most sensitive one (D 1 0 value 0.14 KGy), B. coagulans was moderate resistant (D 1 0 value 3.3 KGy) and the most resistant one was B.megaterium (D 1 0 value 3.7 KGy). Total lipids and lipid patterns of these bacteria were determined and the role of lipids in radioresistance was investigated. Least amount of total lipids was detected in the most sensitive organism (S. aureus). The increase in the bacterial content of total lipids was concomitant with high degrees of radioresistance. The most resistant organism (B. megaterium was characterized by high content of methyl esters of fatty acids, phosphatidylcholine and phosphatidylethanolamine, followed by appreciable amounts in the moderate resistant (B. coagulans) and the least amounts were detected in the most sensitive organism (S.aureus).6 fig., 3 tab

Salt Marsh Bacterial Communities before and after the Deepwater Horizon Oil Spill.

Science.gov (United States)

Engel, Annette Summers; Liu, Chang; Paterson, Audrey T; Anderson, Laurie C; Turner, R Eugene; Overton, Edward B

2017-10-15

Coastal salt marshes along the northern Gulf of Mexico shoreline received varied types and amounts of weathered oil residues after the 2010 Deepwater Horizon oil spill. At the time, predicting how marsh bacterial communities would respond and/or recover to oiling and other environmental stressors was difficult because baseline information on community composition and dynamics was generally unavailable. Here, we evaluated marsh vegetation, physicochemistry, flooding frequency, hydrocarbon chemistry, and subtidal sediment bacterial communities from 16S rRNA gene surveys at 11 sites in southern Louisiana before the oil spill and resampled the same marshes three to four times over 38 months after the spill. Calculated hydrocarbon biomarker indices indicated that oil replaced native natural organic matter (NOM) originating from Spartina alterniflora and marine phytoplankton in the marshes between May 2010 and September 2010. At all the studied marshes, the major class- and order-level shifts among the phyla Proteobacteria , Firmicutes , Bacteroidetes , and Actinobacteria occurred within these first 4 months, but another community shift occurred at the time of peak oiling in 2011. Two years later, hydrocarbon levels decreased and bacterial communities became more diverse, being dominated by Alphaproteobacteria ( Rhizobiales ), Chloroflexi ( Dehalococcoidia ), and Planctomycetes Compositional changes through time could be explained by NOM source differences, perhaps due to vegetation changes, as well as marsh flooding and salinity excursions linked to freshwater diversions. These findings indicate that persistent hydrocarbon exposure alone did not explain long-term community shifts. IMPORTANCE Significant deterioration of coastal salt marshes in Louisiana has been linked to natural and anthropogenic stressors that can adversely affect how ecosystems function. Although microorganisms carry out and regulate most biogeochemical reactions, the diversity of bacterial

Factors limiting heterotrophic bacterial production in the southern Pacific Ocean

Directory of Open Access Journals (Sweden)

F. Van Wambeke

2008-05-01

Full Text Available The role of potential factors limiting bacterial growth was investigated along vertical and longitudinal gradients across the South Eastern Pacific Gyre. The effects of glucose, nitrate, ammonium and phosphate additions on heterotrophic bacterial production (using leucine technique were studied in parallel in unfiltered seawater samples incubated under natural daily irradiance. The enrichments realized on the subsurface showed three types of responses. From 141° W (Marquesas plateau to approx 125° W, bacteria were not bottom-up controlled, as confirmed by the huge potential of growth in non-enriched seawater (median of enhancement factor×39 in 24 h. Within the Gyre (125° W–95° W, nitrogen alone stimulated leucine incorporation rates (median×4.2, but rapidly labile carbon (glucose became a second limiting factor (median×37 when the two elements were added. Finally from the border of the gyre to the Chilean upwelling (95° W–73° W, labile carbon was the only factor stimulating heterotrophic bacterial production. Interaction between phytoplankton and heterotrophic bacterial communities and the direct versus indirect effect of iron and macronutrients on bacterial production were also investigated in four selected sites: two sites on the vicinity of the Marquesas plateau, the centre of the gyre and the Eastern border of the gyre. Both phytoplankton and heterotrophic bacteria were limited by availability of nitrogen within the gyre, but not by iron. Iron limited phytoplankton at Marquesas plateau and at the eastern border of the gyre. However 48 h enrichment experiments were not sufficient to show any clear limitation of heterotrophic bacteria within Marquesas plateau and showed a limitation of these organisms by labile carbon in the eastern border of the Gyre.

Anaerobic bacterial quantitation of Yucca Mountain, Nevada DOE site samples

International Nuclear Information System (INIS)

Clarkson, W.W.; Krumholz, L.R.; Suflita, J.M.

1996-01-01

Anaerobic bacteria were studied from samples of excavated rock material as one phase of the overall Yucca Mountain site characterization effort. An indication of the abundance of important groups of anaerobic bacteria would enable inferences to be made regarding the natural history of the site and allow for more complete risk evaluation of the site as a nuclear repository. Six bacterial groups were investigated including anaerobic heterotrophs, acetogens, methanogens, sulfate-, nitrate-, and iron-reducing bacteria. The purpose of this portion of the study was to detect and quantify the aforementioned bacterial groups

Bacterial Diversity and Community Structure in Korean Ginseng Field Soil Are Shifted by Cultivation Time.

Science.gov (United States)

Nguyen, Ngoc-Lan; Kim, Yeon-Ju; Hoang, Van-An; Subramaniyam, Sathiyamoorthy; Kang, Jong-Pyo; Kang, Chang Ho; Yang, Deok-Chun

2016-01-01

Traditional molecular methods have been used to examine bacterial communities in ginseng-cultivated soil samples in a time-dependent manner. Despite these efforts, our understanding of the bacterial community is still inadequate. Therefore, in this study, a high-throughput sequencing approach was employed to investigate bacterial diversity in various ginseng field soil samples over cultivation times of 2, 4, and 6 years in the first and second rounds of cultivation. We used non-cultivated soil samples to perform a comparative study. Moreover, this study assessed changes in the bacterial community associated with soil depth and the health state of the ginseng. Bacterial richness decreased through years of cultivation. This study detected differences in relative abundance of bacterial populations between the first and second rounds of cultivation, years of cultivation, and health states of ginseng. These bacterial populations were mainly distributed in the classes Acidobacteria, Alphaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, and Sphingobacteria. In addition, we found that pH, available phosphorus, and exchangeable Ca+ seemed to have high correlations with bacterial class in ginseng cultivated soil.

Factors affecting use of ballistics gelatin in laboratory studies of bacterial contamination in projectile wounds.

Science.gov (United States)

Evans, Jessica J; Bost, Aaron; Muci-Küchler, Karim H; DeVeaux, Linda C

2018-05-25

Ballistics gelatin is a common tissue surrogate used in bacterial contamination models for projectile wounds. Although these studies have demonstrated that bacteria are transferred from the surface of the gelatin to the wound track by a projectile, quantifiable results have been inconsistent and not repeatable in successive tests. In this study, five areas of a typical contamination model in which bacterial recovery or survival are affected were identified for optimization. The first was a contaminated "skin" surrogate, where the novel use of vacuum filtration of a bacterial culture and buffer onto filter paper was employed. The other possibly problematic areas of the bacterial distribution model included the determination of bacterial survival when the contamination model is dried, survival in solid and molten gelatin, and the effect of high-intensity lights used for recording high-speed video. Vacuum filtration of bacteria and buffer resulted in a consistent bacterial distribution and recovery. The use of phosphate buffer M9 (pH 7) aided in neutralizing the ballistics gelatin and improving bacterial survival in solid gelatin. Additionally, the use of high-intensity lights to record high-speed video and the use of a 42 ° C water bath to melt the gelatin were found to be bactericidal for gram-positive and gram-negative bacteria. Multiple areas of a typical contamination model in which bacterial survival may be impeded were identified, and methods were proposed to improve survival in each area. These methods may be used to optimize the results of bacterial contamination models for medical applications, such as understanding the progression of infection in penetrating wounds and to identify possible sources of contamination for forensic purposes.

Characteristics and crystal structure of bacterial inosine-5'-monophosphate dehydrogenase.

Energy Technology Data Exchange (ETDEWEB)

Zhang, R.; Evans, G.; Rotella, F. J.; Westbrook, E. M.; Beno, D.; Huberman, E.; Joachimiak, A.; Collart, F. R.

1999-01-01

IMP dehydrogenase (IMPDH) is an essential enzyme that catalyzes the first step unique to GTP synthesis. To provide a basis for the evaluation of IMPDH inhibitors as antimicrobial agents, we have expressed and characterized IMPDH from the pathogenic bacterium Streptococcus pyogenes. Our results show that the biochemical and kinetic characteristics of S. pyogenes IMPDH are similar to other bacterial IMPDH enzymes. However, the lack of sensitivity to mycophenolic acid and the K{sub m} for NAD (1180 {mu}M) exemplify some of the differences between the bacterial and mammalian IMPDH enzymes, making it an attractive target for antimicrobial agents. To evaluate the basis for these differences, we determined the crystal structure of the bacterial enzyme at 1.9 {angstrom} with substrate bound in the catalytic site. The structure was determined using selenomethionine-substituted protein and multiwavelength anomalous (MAD) analysis of data obtained with synchrotron radiation from the undulator beamline (19ID) of the Structural Biology Center at Argonne's Advanced Photon Source. S. pyogenes IMPDH is a tetramer with its four subunits related by a crystallographic 4-fold axis. The protein is composed of two domains: a TIM barrel domain that embodies the catalytic framework and a cystathione {beta}-synthase (CBS) dimer domain of so far unknown function. Using information provided by sequence alignments and the crystal structure, we prepared several site-specific mutants to examine the role of various active site regions in catalysis. These variants implicate the active site flap as an essential catalytic element and indicate there are significant differences in the catalytic environment of bacterial and mammalian IMPDH enzymes. Comparison of the structure of bacterial IMPDH with the known partial structures from eukaryotic organisms will provide an explanation of their distinct properties and contribute to the design of specific bacterial IMPDH inhibitors.

Use of DNA Markers for Investigating Sources of Bacteria in Contaminated Ground Water: Wooster Township, Wayne County, Ohio

Science.gov (United States)

Dumouchelle, Denise H.

2006-01-01

In 2004, a public-health nuisance was declared by the Wayne County Board of Health in the Scenic Heights Drive-Batdorf Road area of Wooster Township, Wayne County, Ohio, because of concerns about the safety of water from local wells. Repeated sampling had detected the presence of fecal-indicator bacteria and elevated nitrate concentrations. In June 2006, the U.S. Geological Survey (USGS), in cooperation with the Ohio Environmental Protection Agency (Ohio EPA), collected and analyzed samples from some of the affected wells to help investigate the possibility of human-origin bacterial contamination. Water samples from 12 wells and 5 home sewage-treatment systems (HSTS) were collected. Bromide concentrations were determined in samples from the 12 wells. Samples from 5 of the 12 wells were analyzed for wastewater compounds. Total coliform, enterococci and Escherichia coli (E. coli) bacteria concentrations were determined for samples from 8 of the 12 wells. In addition, two microbial source-tracking tools that employ DNA markers were used on samples from several wells and a composite sample of water from five septic tanks. The DNA markers from the Enterococcus faecium species and the order Bacteroidales are associated with specific sources, either human or ruminant sources. Bromide concentrations ranged from 0.04 to 0.18 milligrams per liter (mg/L). No wastewater compounds were detected at concentrations above the reporting limits. Samples from the 12 wells also were collected by Ohio EPA and analyzed for chloride and nitrate. Chloride concentrations ranged from 12.6 to 61.6 mg/L and nitrate concentrations ranged from 2.34 to 11.9 mg/L (as N). Total coliforms and enterococci were detected in samples from 8 wells, at concentrations from 2 to 200 colony-forming units per 100 milliliters (CFU/100 mL) and 0.5 to 17 CFU/100 mL, respectively. E. coli were detected in samples from three of the eight wells, at concentrations of 1 or 2 CFU/100 mL. Tests for the human

Characteristics of bacterial community in cloud water at Mt Tai: similarity and disparity under polluted and non-polluted cloud episodes

Science.gov (United States)

Wei, Min; Xu, Caihong; Chen, Jianmin; Zhu, Chao; Li, Jiarong; Lv, Ganglin

2017-04-01

Bacteria are widely distributed in atmospheric aerosols and are indispensable components of clouds, playing an important role in the atmospheric hydrological cycle. However, limited information is available about the bacterial community structure and function, especially for the increasing air pollution in the North China Plain. Here, we present a comprehensive characterization of bacterial community composition, function, variation, and environmental influence for cloud water collected at Mt Tai from 24 July to 23 August 2014. Using Miseq 16S rRNA gene sequencing, the highly diverse bacterial community in cloud water and the predominant phyla of Proteobacteria, Bacteroidetes, Cyanobacteria, and Firmicutes were investigated. Bacteria that survive at low temperature, radiation, and poor nutrient conditions were found in cloud water, suggesting adaption to an extreme environment. The bacterial gene functions predicted from the 16S rRNA gene using the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) suggested that the pathways related to metabolism and disease infections were significantly correlated with the predominant genera. The abundant genera Acinetobacter, Stenotrophomonas, Pseudomonas, and Empedobacter originated from a wide range of habitats including cloud condensation nuclei and ice nuclei active species, opportunistic pathogens, and functional species, demonstrating the importance of ecology and health in cloud water. Cluster analysis including hierarchical cluster (Hcluster) and principal coordinate analysis (PCoA) indicated a significant disparity between polluted and non-polluted samples. Linear discriminant analysis effect size (LEfSe) demonstrated that potential pathogens were enriched in the polluted cloud samples, whereas the diverse ecological function groups were significant in the non-polluted samples. Discrepant community structure determined by redundancy analysis (RDA) indicated that the major ions in

Bacterial Contribution in Chronicity of Wounds.

Science.gov (United States)

Rahim, Kashif; Saleha, Shamim; Zhu, Xudong; Huo, Liang; Basit, Abdul; Franco, Octavio Luiz

2017-04-01

A wound is damage of a tissue usually caused by laceration of a membrane, generally the skin. Wound healing is accomplished in three stages in healthy individuals, including inflammatory, proliferative, and remodeling stages. Healing of wounds normally starts from the inflammatory phase and ends up in the remodeling phase, but chronic wounds remain in an inflammatory stage and do not show progression due to some specific reasons. Chronic wounds are classified in different categories, such as diabetic foot ulcer (DFU), venous leg ulcers (VLU) and pressure ulcer (PU), surgical site infection (SSI), abscess, or trauma ulcers. Globally, the incidence rate of DFU is 1-4 % and prevalence rate is 5.3-10.5 %. However, colonization of pathogenic bacteria at the wound site is associated with wound chronicity. Most chronic wounds contain more than one bacterial species and produce a synergetic effect that results in previously non-virulent bacterial species becoming virulent and causing damage to the host. While investigating bacterial diversity in chronic wounds, Staphylococcus, Pseudomonas, Peptoniphilus, Enterobacter, Stenotrophomonas, Finegoldia, and Serratia were found most frequently in chronic wounds. Recently, it has been observed that bacteria in chronic wounds develop biofilms that contribute to a delay in healing. In a mature biofilm, bacteria grow slowly due to deficiency of nutrients that results in the resistance of bacteria to antibiotics. The present review reflects the reasons why acute wounds become chronic. Interesting findings include the bacterial load, which forms biofilms and shows high-level resistance toward antibiotics, which is a threat to human health in general and particularly to some patients who have acute wounds.

Bacterial Urease and its Role in Long-Lasting Human Diseases

Science.gov (United States)

Konieczna, Iwona; Żarnowiec, Paulina; Kwinkowski, Marek; Kolesińska, Beata; Frączyk, Justyna; Kamiński, Zbigniew; Kaca, Wiesław

2012-01-01

Urease is a virulence factor found in various pathogenic bacteria. It is essential in colonization of a host organism and in maintenance of bacterial cells in tissues. Due to its enzymatic activity, urease has a toxic effect on human cells. The presence of ureolytic activity is an important marker of a number of bacterial infections. Urease is also an immunogenic protein and is recognized by antibodies present in human sera. The presence of such antibodies is connected with progress of several long-lasting diseases, like rheumatoid arthritis, atherosclerosis or urinary tract infections. In bacterial ureases, motives with a sequence and/or structure similar to human proteins may occur. This phenomenon, known as molecular mimicry, leads to the appearance of autoantibodies, which take part in host molecules destruction. Detection of antibodies-binding motives (epitopes) in bacterial proteins is a complex process. However, organic chemistry tools, such as synthetic peptide libraries, are helpful in both, epitope mapping as well as in serologic investigations. In this review, we present a synthetic report on a molecular organization of bacterial ureases - genetic as well as structural. We characterize methods used in detecting urease and ureolytic activity, including techniques applied in disease diagnostic processes and in chemical synthesis of urease epitopes. The review also provides a summary of knowledge about a toxic effect of bacterial ureases on human body and about occurrence of anti-urease antibodies in long-lasting diseases. PMID:23305365

Bacterial acquisition in juveniles of several broadcast spawning coral species.

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Sharp, Koty H; Ritchie, Kim B; Schupp, Peter J; Ritson-Williams, Raphael; Paul, Valerie J

2010-05-28

Coral animals harbor diverse microorganisms in their tissues, including archaea, bacteria, viruses, and zooxanthellae. The extent to which coral-bacterial associations are specific and the mechanisms for their maintenance across generations in the environment are unknown. The high diversity of bacteria in adult coral colonies has made it challenging to identify species-specific patterns. Localization of bacteria in gametes and larvae of corals presents an opportunity for determining when bacterial-coral associations are initiated and whether they are dynamic throughout early development. This study focuses on the early onset of bacterial associations in the mass spawning corals Montastraea annularis, M. franksi, M. faveolata, Acropora palmata, A. cervicornis, Diploria strigosa, and A. humilis. The presence of bacteria and timing of bacterial colonization was evaluated in gametes, swimming planulae, and newly settled polyps by fluorescence in situ hybridization (FISH) using general eubacterial probes and laser-scanning confocal microscopy. The coral species investigated in this study do not appear to transmit bacteria via their gametes, and bacteria are not detectable in or on the corals until after settlement and metamorphosis. This study suggests that mass-spawning corals do not acquire, or are not colonized by, detectable numbers of bacteria until after larval settlement and development of the juvenile polyp. This timing lays the groundwork for developing and testing new hypotheses regarding general regulatory mechanisms that control bacterial colonization and infection of corals, and how interactions among bacteria and juvenile polyps influence the structure of bacterial assemblages in corals.

Role of the chronic bacterial infection in urinary bladder carcinogenesis

International Nuclear Information System (INIS)

Higgy, N.A.

1985-01-01

The purpose of this thesis was to determine whether or not bacterial infection of the urinary bladder had a role in urinary bladder carcinogenesis. To investigate this proposition, four separate studies were conducted. The first study developed an experimental animal model where bacterial infection of the urinary bladder could be introduced and maintained for a period in excess of one year. The method of infection, inoculation of bacteria (Escherichia coli type 04) subserosally into the vesical wall, successfully caused persistent infection in the majority of animals. In the second study the temporal effects of bacterial infection on the induction of urothelial ornithine decarboxylase (ODC) and 3 H-thymidine uptake and DNA synthesis were examined. Bacterial infection of the urinary bladder induced urothelial ODC with a peak in enzyme activity 6 hr after infection. 3 H-Thymidine uptake and DNA synthesis peaked 48 hr after infection and coincided with the urothelial hyperplasia that occurred in response to the infection. In the third study the specific bladder carcinogen N-butyl-N-(4-hydroxybutyl)nitrosamine (BBN) was given to rats concurrent with the urinary bacterial infection. In the fourth study rats were administered sodium nitrate and either dibutylamine or piperazine in the drinking water. The infected group developed bladder tumors while none were detected in the non-infected rats. From these studies it may be concluded that bacterial infection may have a significant role in the process of urinary bladder carcinogenesis

Procedures involving lipid media for detection of bacterial contamination in breweries.

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Van Vuuren, H J; Louw, H A; Loos, M A; Meisel, R

1977-02-01

The liquid equivalent of universal beer agar, designated universal beer liquid medium, and its beer-free equivalent, universal liquid medium (UL), were equally effective in demonstrating bacterial contamination in 120 of 200 samples from different stages of commercial brewing process. Growth of the contaminants after 3 days was consistently more luxuriant in the UL medium. A yeast-water substrate medium failed to reveal many contaminants detected with UL in 392 samples from three breweries and revealed only a few not detected with UL. The use of UL and a lactose-peptone medium, with microscope examination of the media for bacterial growth, permitted detection of 93% of the known contaminants compared to 87%, detected with UL alone; this combination or universal beer liquid medium plus lactose-peptone medium can therefore be recommended for the detection of bacterial contaminants in brewery samples. Bacterial contamination of pitching yeasts appeared to be a particular problem in the breweries investigated.

Inhibitory Effect of Lactobacillus reuteri on Some Pathogenic Bacteria Isolated From Women With Bacterial Vaginosis

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Eslami

2014-08-01

Full Text Available Background Considering the high prevalence of bacterial vaginosis and its association with urinary tract infection in women and treatment of gynecologic problems occur when a high recurrence of bacterial vaginosis is often treated with antibiotics. Objectives The purpose of this study was to investigate the inhibitory effect of Lactobacillus reuteri on pathogenic bacteria isolated from women with bacterial vaginosis. Materials and Methods Ninety-six samples were obtained from vaginal discharge of women with bacterial vaginosis by a gynecologist with a Dacron swab and put in sterile tubes containing TSB broth and Thioglycollate broth. Then were immediately sent to the laboratory in cold chain for further assessment. Afterward, culture was transferred on blood agar, EMB, Palcam and differential diagnosis environments. Then cultures were incubated for 24 hours at 37 °C. Lactobacillus reuteri strains were cultured in MRS environment and transferred to laboratory. After purification of pathogenic bacteria, Lactobacillus reuteri inhibitory effect on pathogenic bacteria was evaluated by minimum inhibitory concentration (MIC and antibiogram. Statistical analysis was performed using SPSS software v.16. Results The results of this study demonstrated the inhibitory effect of Lactobacillus reuteri on some pathogenic bacteria that cause bacterial, including Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcus saprophyticus, Streptococcus agalactiae, Enterococcus, Listeria monocytogenes and E. coli. Microscopic examination of stained smears of most Lactobacillus and pathogenic bacteria showed reduced. The prevalence of abnormal vaginal discharge, history of drug use, contraceptive methods and douching were 61%, 55%, 42% and 13%, respectively. Significant difference was observed between the use and non-use of IUD in women with bacterial. Conclusions Our findings indicated the inhibitory effect of Lactobacillus reuteri on pathogenic bacteria that

Investigations Concerning Possibilities of Diagnosis and Treatement in One Pesthole of Bacterial Haemorrhagic Septicemia in Carp (Cyprinus Carpio

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Octavian Negrea

2010-10-01

Full Text Available Investigations were done on 7 alive samples in agonic or death stage, taken from an extensive exploitation pond, innorth-east Transylvanian zone, with an water surface of 0,2 ha and a total fish quantity of about 200 kg, secondsummer carp of an average weight of 300 g/individual. As a result of clinical, bacterioscopy and bacteriology andalso necropsy laboratory exam it were put in evidence some aspects. So, clinical exam has revealed, by the presenceof integument hemorrhagic ulcerous lesions, also the presence of some crustacaee ectoparasites, Argulus foliaceusspecies, which have made easier the disease spreading in whole effective. Necropsy exam puts in evidence, anatomyclinic,the presence of integument hemorrhagic lesions under a point or diffuse form, but also ulcers and muscle –cutaneous necrosis. As a following of bacterioscopy exam of smears done from pathologic material taken incutaneous lesions and colored by Gram method it was ascertained the presence of a bacterial polymorph flora, ofbacillus and cocobacillus type, Gram negative. Bacteriologic exam (cultural, realized on ordinary culture mediums(sauce, water and selective mediums (agar with blood isolates in pure culture germs from Aeromonas kind, basis onmorphological and cultural characters, which are framed in Aeromonas genus patterns described by specialityliterature. As a following of biochemical characters exam, with the help of multitest API20E system it wasestablished that Aeromonas spp. strains isolated, belong to hydrophila group 1 species, species which is responsibleof bacterial hemorrhagic septicemia performing in carp. By testing the sensitiveness to antibodies and chemiotherapyin strains which have been found as diagnosis (diffusiometric method of antibiogram, it was ascertained that group 1Aeromonas hydrophila strains, isolated from disease pesthole, were in decreasing order sensitive to: Eurofloxocin,Florfenicol (Floron and Oxitetracycline and resistant to

Antibiotic susceptibility profile of bacteria isolated from natural sources of water from rural areas of East Sikkim

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Shubra Poonia

2014-01-01

Full Text Available Background: Contamination of water, food, and environment with antibiotic-resistant bacteria poses a serious public health issue. Objective: The objective was to study the bacterial pollution of the natural sources of water in east Sikkim and to determine the antimicrobial profile of the bacterial isolates. Materials and Methods: A total of 225 samples, 75 each during winter, summer, and monsoon season were collected from the same source in every season for bacteriological analysis by membrane filtration method. Antibiotic susceptibility test was performed using standard disc diffusion method. Results: A total of 19 bacterial species of the genera Escherichia, Klebsiella, Proteus, Salmonella, Shigella, Enterobacter, Citrobacter, Morganella, Pseudomonas, Acinetobacter, Flavobacterium, and Serratia were isolated and their antimicrobial sensitivity tested. Generally, most bacterial isolates except Salmonella and Shigella species were found resistant to commonly used antibiotics such as ampicillin (57.5%, trimethoprim/sulfamethoxaole (39.1%, amoxicillin/clavulanic acid (37.4%, cefixime (34.5%, tetracycline (29.1%, ceftazidime (26.3%, ofloxacin (25.9%, amikacin (8.7%, and gentamicin (2.7% but sensitive to imipenem and piperacillin/tazobactam. Conclusion: Natural sources of water in east Sikkim are grossly contaminated with bacteria including enteropathogens. The consumption of untreated water from these sources might pose health risk to consumers.

Statin Treatment and Mortality in Bacterial Infections – A Systematic Review and Meta-Analysis

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Björkhem-Bergman, Linda; Bergman, Peter; Andersson, Jan; Lindh, Jonatan D.

2010-01-01

Background Several studies have reported improved survival in severe bacterial infections among statin treated patients. In addition, statins have been ascribed beneficial anti-inflammatory effects. The aim of this study was to evaluate the effect of statin-treatment on mortality in patients with bacterial infections, by means of a systematic review and a meta-analysis. Methodology and Principal Findings Studies investigating the association between statin use and mortality in patients with bacterial disease were identified in a systematic literature review and a meta-analysis was performed to calculate the overall odds ratio of mortality in statin users. The literature search identified 947 citations from which 40 relevant studies were extracted. In all, 15 studies comprising 113 910 patients were included in the final analysis. Statin use was associated with a significantly (pstatin treatment was no longer significant, with an OR of 0.79 (95% CI 0.58–1.07). Conclusion/Significance According to the meta-analysis of observational studies presented here, patients on statin therapy seem to have a better outcome in bacterial infections. However, the association did not reach statistical significance after adjustment for apparent publication bias. Thus, there is a great need for randomised controlled trials investigating the possible beneficial effect of statins in bacterial infections. PMID:20502712

Liver abscess caused by periodontal bacterial infection with Fusobacterium necrophorum.

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Yoneda, Masato; Kato, Shingo; Mawatari, Hironori; Kirikoshi, Hiroyuki; Imajo, Kento; Fujita, Koji; Endo, Hiroki; Takahashi, Hirokazu; Inamori, Masahiko; Kobayashi, Noritoshi; Kubota, Kensuke; Saito, Satoru; Tohnai, Iwai; Watanuki, Kei; Wada, Koichiro; Maeda, Shin; Nakajima, Atsushi

2011-02-01

Liver abscess is recognized as a life-threatening disease. However, even in recent years, approximately 50% of liver abscess cases are considered to be cryptogenic. Here, we report a case of liver abscess associated with periodontal bacterial infection by Fusobacterium necrophorum, which is commonly found in the oropharyngeal flora. A 36-year-old man presented with fever and contrast-enhanced abdominal computed tomography revealed multiple liver abscesses. F.necrophorum was isolated from oral smears, liver aspirates and blood samples. Liver abscesses caused by periodontal bacterial infection are rare, however, the incidence is expected to increase in the future, as periodontitis is extremely common and is on the rise as one of the most common chronic infections in the world. A systemic survey including periodontitis may be required for the exact diagnosis of the source of infection. © 2011 The Japan Society of Hepatology.

Molecular bacterial diversity and bioburden of commercial airliner cabin air

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La Duc, M.T.; Stuecker, T.; Venkateswaran, K. [California Inst. of Technology, Pasadena, CA (United States). Jet Propulsion Laboratory, Biotechnology and Planetary Protection Group

2007-11-15

Microorganisms that exist in aircraft air systems are considered to be the primary source of microbial contamination that can lead to illness shortly after flying. More than 600 million passengers board commercial airline flights annually in the United States alone. In this study, culture-independent, biomarker-targeted bacterial enumeration and identification strategies were used to estimate total bacterial burden and diversity within the cabin air of commercial airliners. Air-impingement was used to collect samples of microorganisms from 4 flights on 2 commercial carriers. The total viable microbial population ranged from below detection limits to 4.1 x 10{sup 6} cells/m{sup 3} of air. Microbes were found to gradually accumulate from the time of passenger boarding through mid-flight. A sharp decline in bacterial abundance was then observed. Representatives of the {alpha}, {beta} and {gamma} Proteobacteria, as well as Gram-positive bacteria, were isolated in varying abundance. Airline A had large abundances of Neisseria meningitidis rRNA gene sequences and Streptococcus oralis/mitis sequences. Airline B was dominated by pseudomonas synxantha sequences as well as N. meningitidis and S. oralis/mitis. The cabin air samples housed low bacterial diversity and were typically dominated by a particular subset of bacteria, notably opportunistic pathogenic inhabitants of the human respiratory tract and oral cavity. The microbes were found largely around the ventilation ducts and gasper conduits that supply cabin air. 45 refs., 4 tabs., 3 figs.

The Lag-Luminosity Relation in the GRB Source-Frame: An Investigation with Swift BAT Bursts

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Ukwatta, T. N.; Dhuga, K. S.; Stamatikos, M.; Dermer, C. D.; Sakamoto, T.; Sonbas, E.; Parke, W. C.; Maximon, L. C.; Linnemann, J. T.; Bhat, P. N.;

The potential of endomycorrhizal fungi in controlling tomato bacterial ...

African Journals Online (AJOL)

The impact of colonization by three mycorrhizal fungi on tomato bacterial wilt caused by Ralstonia solanaceraum was investigated. Three species of arbuscular mycorrhizal fungal (AMF) were tested (Glomus mosseae, Scutellospora sp. and Gigaspora margarita). Siginificant differences in tomato growth based on plant ...

Putative bacterial interactions from metagenomic knowledge with an integrative systems ecology approach.

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Bordron, Philippe; Latorre, Mauricio; Cortés, Maria-Paz; González, Mauricio; Thiele, Sven; Siegel, Anne; Maass, Alejandro; Eveillard, Damien

2016-02-01

Following the trend of studies that investigate microbial ecosystems using different metagenomic techniques, we propose a new integrative systems ecology approach that aims to decipher functional roles within a consortium through the integration of genomic and metabolic knowledge at genome scale. For the sake of application, using public genomes of five bacterial strains involved in copper bioleaching: Acidiphilium cryptum, Acidithiobacillus ferrooxidans, Acidithiobacillus thiooxidans, Leptospirillum ferriphilum, and Sulfobacillus thermosulfidooxidans, we first reconstructed a global metabolic network. Next, using a parsimony assumption, we deciphered sets of genes, called Sets from Genome Segments (SGS), that (1) are close on their respective genomes, (2) take an active part in metabolic pathways and (3) whose associated metabolic reactions are also closely connected within metabolic networks. Overall, this SGS paradigm depicts genomic functional units that emphasize respective roles of bacterial strains to catalyze metabolic pathways and environmental processes. Our analysis suggested that only few functional metabolic genes are horizontally transferred within the consortium and that no single bacterial strain can accomplish by itself the whole copper bioleaching. The use of SGS pinpoints a functional compartmentalization among the investigated species and exhibits putative bacterial interactions necessary for promoting these pathways. © 2015 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Combined effect of zinc, chromium, and cadmium on bacterial biomass production

Energy Technology Data Exchange (ETDEWEB)

Korsak, M N; Nakani, D V; Chol' naya, G G

1976-01-01

The present work was carried out at the Rybinskoye storage-lake in 1974. Some tolerance limits of zinc, chromium and cadmium were chosen for the investigation. The bacterial production was estimated by /sup 14/C heterotrophic assimilation. Natural water included in polyethylene reservoirs was used. The bacterial production was determined in one to three days after the beginning of the experiment. In most off the experiments the negative influence of zinc and chromium on the bacterial biomass production was registered only after 3 days of exposure. The effect of cadmium during the entire period of observations proved to be unreliable. The effect of chromium was fairly constant in different seasons. The interaction of toxicants was not revealed in any the of experiments. 8 references.

Assessment of the bacterial contamination of hand air dryer in washrooms

OpenAIRE

Alharbi, Sulaiman Ali; Salmen, Saleh Hussein; Chinnathambi, Arunachalam; Alharbi, Naiyf S.; Zayed, M.E.; Al-Johny, Bassam O.; Wainwright, Milton

2016-01-01

The present study was carried out, using standard techniques, to identify and count the bacterial contamination of hand air dryers, used in washrooms. Bacteria were isolated from the air flow, outlet nozzle of warm air dryers in fifteen air dryers used in these washrooms. Bacteria were found to be relatively numerous in the air flows. Bacterially contaminated air was found to be emitted whenever a warm air dryer was running, even when not being used for hand drying. Our investigation shows th...

Age- and calorie-independent life span extension from dietary restriction by bacterial deprivation in Caenorhabditis elegans

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Sager Jennifer

2008-05-01

Full Text Available Abstract Background Dietary restriction (DR increases life span and delays age-associated disease in many organisms. The mechanism by which DR enhances longevity is not well understood. Results Using bacterial food deprivation as a means of DR in C. elegans, we show that transient DR confers long-term benefits including stress resistance and increased longevity. Consistent with studies in the fruit fly and in mice, we demonstrate that DR also enhances survival when initiated late in life. DR by bacterial food deprivation significantly increases life span in worms when initiated as late as 24 days of adulthood, an age at which greater than 50% of the cohort have died. These survival benefits are, at least partially, independent of food consumption, as control fed animals are no longer consuming bacterial food at this advanced age. Animals separated from the bacterial lawn by a barrier of solid agar have a life span intermediate between control fed and food restricted animals. Thus, we find that life span extension from bacterial deprivation can be partially suppressed by a diffusible component of the bacterial food source, suggesting a calorie-independent mechanism for life span extension by dietary restriction. Conclusion Based on these findings, we propose that dietary restriction by bacterial deprivation increases longevity in C. elegans by a combination of reduced food consumption and decreased food sensing.

Bacmeta: simulator for genomic evolution in bacterial metapopulations.

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Sipola, Aleksi; Marttinen, Pekka; Corander, Jukka

2018-02-20

The advent of genomic data from densely sampled bacterial populations has created a need for flexible simulators by which models and hypotheses can be efficiently investigated in the light of empirical observations. Bacmeta provides fast stochastic simulation of neutral evolution within a large collection of interconnected bacterial populations with completely adjustable connectivity network. Stochastic events of mutations, recombinations, insertions/deletions, migrations and microepidemics can be simulated in discrete non-overlapping generations with a Wright-Fisher model that operates on explicit sequence data of any desired genome length. Each model component, including locus, bacterial strain, population, and ultimately the whole metapopulation, is efficiently simulated using C ++ objects, and detailed metadata from each level can be acquired. The software can be executed in a cluster environment using simple textual input files, enabling, e.g., large-scale simulations and likelihood-free inference. Bacmeta is implemented with C ++ for Linux, Mac and Windows. It is available at https://bitbucket.org/aleksisipola/bacmeta under the BSD 3-clause license. aleksi.sipola@helsinki.fi, jukka.corander@medisin.uio.no. Supplementary data are available at Bioinformatics online.

Glycoside hydrolase activities of thermophilic bacterial consortia adapted to switchgrass.

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Gladden, John M; Allgaier, Martin; Miller, Christopher S; Hazen, Terry C; VanderGheynst, Jean S; Hugenholtz, Philip; Simmons, Blake A; Singer, Steven W

2011-08-15

Industrial-scale biofuel production requires robust enzymatic cocktails to produce fermentable sugars from lignocellulosic biomass. Thermophilic bacterial consortia are a potential source of cellulases and hemicellulases adapted to harsher reaction conditions than commercial fungal enzymes. Compost-derived microbial consortia were adapted to switchgrass at 60°C to develop thermophilic biomass-degrading consortia for detailed studies. Microbial community analysis using small-subunit rRNA gene amplicon pyrosequencing and short-read metagenomic sequencing demonstrated that thermophilic adaptation to switchgrass resulted in low-diversity bacterial consortia with a high abundance of bacteria related to thermophilic paenibacilli, Rhodothermus marinus, and Thermus thermophilus. At lower abundance, thermophilic Chloroflexi and an uncultivated lineage of the Gemmatimonadetes phylum were observed. Supernatants isolated from these consortia had high levels of xylanase and endoglucanase activities. Compared to commercial enzyme preparations, the endoglucanase enzymes had a higher thermotolerance and were more stable in the presence of 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]), an ionic liquid used for biomass pretreatment. The supernatants were used to saccharify [C2mim][OAc]-pretreated switchgrass at elevated temperatures (up to 80°C), demonstrating that these consortia are an excellent source of enzymes for the development of enzymatic cocktails tailored to more extreme reaction conditions.

BIGSdb: Scalable analysis of bacterial genome variation at the population level

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Maiden Martin CJ

2010-12-01

Full Text Available Abstract Background The opportunities for bacterial population genomics that are being realised by the application of parallel nucleotide sequencing require novel bioinformatics platforms. These must be capable of the storage, retrieval, and analysis of linked phenotypic and genotypic information in an accessible, scalable and computationally efficient manner. Results The Bacterial Isolate Genome Sequence Database (BIGSDB is a scalable, open source, web-accessible database system that meets these needs, enabling phenotype and sequence data, which can range from a single sequence read to whole genome data, to be efficiently linked for a limitless number of bacterial specimens. The system builds on the widely used mlstdbNet software, developed for the storage and distribution of multilocus sequence typing (MLST data, and incorporates the capacity to define and identify any number of loci and genetic variants at those loci within the stored nucleotide sequences. These loci can be further organised into 'schemes' for isolate characterisation or for evolutionary or functional analyses. Isolates and loci can be indexed by multiple names and any number of alternative schemes can be accommodated, enabling cross-referencing of different studies and approaches. LIMS functionality of the software enables linkage to and organisation of laboratory samples. The data are easily linked to external databases and fine-grained authentication of access permits multiple users to participate in community annotation by setting up or contributing to different schemes within the database. Some of the applications of BIGSDB are illustrated with the genera Neisseria and Streptococcus. The BIGSDB source code and documentation are available at http://pubmlst.org/software/database/bigsdb/. Conclusions Genomic data can be used to characterise bacterial isolates in many different ways but it can also be efficiently exploited for evolutionary or functional studies. BIGSDB

Restructuring of the Aquatic Bacterial Community by Hydric Dynamics Associated with Superstorm Sandy.

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Ulrich, Nikea; Rosenberger, Abigail; Brislawn, Colin; Wright, Justin; Kessler, Collin; Toole, David; Solomon, Caroline; Strutt, Steven; McClure, Erin; Lamendella, Regina

2016-06-15

Bacterial community composition and longitudinal fluctuations were monitored in a riverine system during and after Superstorm Sandy to better characterize inter- and intracommunity responses associated with the disturbance associated with a 100-year storm event. High-throughput sequencing of the 16S rRNA gene was used to assess microbial community structure within water samples from Muddy Creek Run, a second-order stream in Huntingdon, PA, at 12 different time points during the storm event (29 October to 3 November 2012) and under seasonally matched baseline conditions. High-throughput sequencing of the 16S rRNA gene was used to track changes in bacterial community structure and divergence during and after Superstorm Sandy. Bacterial community dynamics were correlated to measured physicochemical parameters and fecal indicator bacteria (FIB) concentrations. Bioinformatics analyses of 2.1 million 16S rRNA gene sequences revealed a significant increase in bacterial diversity in samples taken during peak discharge of the storm. Beta-diversity analyses revealed longitudinal shifts in the bacterial community structure. Successional changes were observed, in which Betaproteobacteria and Gammaproteobacteria decreased in 16S rRNA gene relative abundance, while the relative abundance of members of the Firmicutes increased. Furthermore, 16S rRNA gene sequences matching pathogenic bacteria, including strains of Legionella, Campylobacter, Arcobacter, and Helicobacter, as well as bacteria of fecal origin (e.g., Bacteroides), exhibited an increase in abundance after peak discharge of the storm. This study revealed a significant restructuring of in-stream bacterial community structure associated with hydric dynamics of a storm event. In order to better understand the microbial risks associated with freshwater environments during a storm event, a more comprehensive understanding of the variations in aquatic bacterial diversity is warranted. This study investigated the bacterial

The effect of bacterial cellulose on the shape memory behavior of polyvinyl alcohol nanocomposite hydrogel