Stagnari, Fabio; Perpetuini, Giorgia; Tofalo, Rosanna; Campanelli, Gabriele; Leteo, Fabrizio; Della Vella, Umberto; Schirone, Maria; Suzzi, Giovanna; Pisante, Michele
2014-01-01
In the present study, long-term organic and conventional managements were compared at the experimental field of Monsampolo del Tronto (Marche region, Italy) with the aim of investigating soil chemical fertility and microbial community structure. A polyphasic approach, combining soil fertility indicators with microbiological analyses (plate counts, PCR-denaturing gradient gel electrophoresis [DGGE] and phospholipid fatty acid analysis [PLFA]) was applied. Organic matter, N as well as some important macro and micronutrients (K, P, Mg, Mn, Cu, and Zn) for crop growth, were more available under organic management. Bacterial counts were higher in organic management. A significant influence of management system and management x crop interaction was observed for total mesophilic bacteria, nitrogen fixing bacteria and actinobacteria. Interestingly, cultivable fungi were not detected in all analyzed samples. PLFA biomass was higher in the organic and Gram positive bacteria dominated the microbial community in both systems. Even if fungal biomass was higher in organic management, fungal PCR-DGGE fingerprinting revealed that the two systems were very similar in terms of fungal species suggesting that 10 years were not enough to establish a new dynamic equilibrium among ecosystem components. A better knowledge of soil biota and in particular of fungal community structure will be useful for the development of sustainable management strategies.
Institute of Scientific and Technical Information of China (English)
XUE Dong; YAO Huai-Ying; GE De-Yong; HUANG Chang-Yong
2008-01-01
Biolog,16S rRNA gene denaturing gradient gel electrophoresis (DGGE),and phospholipid fatty acid (PLFA) analyses were used to assess soil microbial community characteristics in a chronosequence of tea garden systems (8-,50-,and 90year-old tea gardens),an adjacent wasteland,and a 90-year-old forest.Biolog analysis showed that the average well color development (AWCD) of all carbon sources and the functional diversity based on the Shannon index decreased (P<0.05)in the following order:wasteland>forest>tea garden.For the DGGE analysis,the genetic diversity based on the Shannon index was significantly lower in the tea garden soils than in the wasteland.However,compared to the 90-year-old forest,the tea garden soils showed significantly higher genetic diversity.PLFA analysis showed that the ratio of Gram positive bacteria to Gram negative bacteria was significantly higher in the tea garden soils than in the wasteland,and the highest value was found in the 90-year-old forest.Both the fungal PLFA and the ratio of fungi to bacteria were significantly higher in the three tea garden soils than in the wasteland and forest,indicating that fungal PLFA was significantly affected by land-use change.Based on cluster analysis of the soil microbial community structure,all three analytical methods showed that land-use change had a greater effect on soil microbial community structure than tea garden age.
Gunina, Anna; Dippold, Michaela; Kuzyakov, Yakov
2014-05-01
Microbial metabolisation is the main transformation pathway of low molecular weight organic substances (LMWOS), but detailed knowledge concerning the fate of LMWOS in soils is strongly limited. Considering that various LMWOS classes enter biochemical cycles at different steps, we hypothesise that the percentage of their LMWOS-Carbon (C) used for microbial biomass (MB) production and consequently medium-term stabilisation in soil is different. We traced the three main groups of LMWOS: amino acids, sugars and carboxylic acids, by uniformly labelled 13C-alanine, -glutamate, -glucose, -ribose, -acetate and -palmitate. Incorporation of 13C from these LMWOS into MB (fumigation-extraction method) and into phospholipid fatty acids (PLFAs) (Bligh-Dyer extraction, purification and GC-C-IRMS measurement) was investigated under field conditions 3 d and 10 d after LMWOS application. The activity of microbial utilization of LMWOS for cell membrane construction was estimated by replacement of PLFA-C with 13C. Decomposition of LMWOS-C comprised 20-65% of the total label, whereas incorporation of 13C into MB amounted to 20-50% of initially applied 13C on day three and was reduced to 5-30% on day 10. Incorporation of 13C-labelled LMWOS into MB followed the trend sugars > carboxylic acids > amino acids. Differences in microbial utilisation between LMWOS were observed mainly at day 10. Thus, instead of initial rapid uptake, further metabolism within microbial cells accounts for the individual fate of C from different LMWOS in soils. Incorporation of 13C from each LMWOS into each PLFA occurred, which reflects the ubiquitous ability of all functional microbial groups for LMWOS utilization. The preferential incorporation of palmitate can be attributed to its role as a direct precursor for many fatty acids (FAs) and PLFA formation. Higher incorporation of alanine and glucose compared to glutamate, ribose and acetate reflect the preferential use of glycolysis-derived substances in the FAs
Microbial population changes during bioremediation of an experimental oil spill
International Nuclear Information System (INIS)
MacNaughton, S.J.; Stephen, J.R.; Chang, Y.J.; Davis, G.A.; White, D.C.; Oak Ridge National Lab., TN
1999-01-01
Three crude oil bioremediation techniques were applied in a randomized block field experiment simulating a coastal oil spill. Four treatments (no oil control, oil alone, oil plus nutrients, and oil plus nutrients plus an indigenous inoculum) were applied. In situ microbial community structures were monitored by phospholipid fatty acid (PLFA) analysis and 16S rDNA PCR-denaturing gradient gel electrophoresis (DGGE) to (i) identify the bacterial community members responsible for the decontamination of the site and (ii) define an end point for the removal of the hydrocarbon substrate. The results of PLFA analysis demonstrated a community shift in all plots from primarily eukaryotic biomass to gram-negative bacterial biomass with time. PLFA profiles from the oiled plots suggested increased gram-negative biomass and adaptation to metabolic stress compared to unoiled controls. DGGE analysis of untreated control plots revealed a simple, dynamic dominant population structure throughout the experiment. This banding pattern disappeared in all oiled plots, indicating that the structure and diversity of the dominant bacterial community changed substantially. No consistent differences were detected between nutrient-amended and indigenous inoculum-treated plots, but both differed from the oil-only plots. Prominent bands were excised for sequence analysis and indicated that oil treatment encouraged the growth of gram-negative microorganisms within the α-proteobacteria and Flexibacter-Cytophaga-Bacteroides phylum. α-Proteobacteria were never detected in unoiled controls. PLFA analysis indicated that by week 14 the microbial community structures of the oiled plots were becoming similar to those of the unoiled controls from the same time point, but DGGE analysis suggested that major differences in the bacterial communities remained
Waters, Sinéad M; Murphy, Richard A; Power, Ronan F G
2006-08-01
Undefined Nurmi-type cultures (NTCs) have been used successfully to prevent salmonella colonisation in poultry for decades. Such cultures are derived from the caecal contents of specific-pathogen-free birds and are administered via drinking water or spray application onto eggs in the hatchery. These cultures consist of many non-culturable and obligately anaerobic bacteria. Due to their undefined nature it is difficult to obtain approval from regulatory agencies to use these preparations as direct fed microbials for poultry. In this study, 10 batches of prototype NTCs were produced using an identical protocol over a period of 2 years. Traditional microbiological techniques and a molecular culture-independent methodology, polymerase chain reaction combined with denaturing gradient gel electrophoresis (PCR-DGGE), were applied to characterise these cultures and also to examine if the constituents of the NTCs were identical. Culture-dependent analysis of these cultures included plating on a variety of selective and semi-selective agars, examination of colony morphology, Gram-staining and a series of biochemical tests (API, BioMerieux, France). Two sets of PCR-DGGE studies were performed. These involved the amplification of universal and subsequently lactic acid bacteria (LAB)-specific hypervariable regions of a 16S rRNA gene by PCR. Resultant amplicons were subjected to DGGE. Sequence analysis was performed on subsequent bands present in resultant DGGE profiles using the Basic Local Alignment Search Tool (BLAST). Microbiological culturing techniques tended to isolate common probiotic bacterial species from the genera Lactobacillus, Lactococcus, Bifidobacterium, Enterococcus, Clostridium, Escherichia, Pediococcus and Enterobacterium as well as members of the genera, Actinomyces, Bacteroides, Propionibacterium, Capnocytophaga, Proteus, and Klebsiella. Bacteroides, Enterococcus, Escherichia, Brevibacterium, Klebsiella, Lactobacillus, Clostridium, Bacillus, Eubacterium
Thornhill, D. J.; Kemp, D. W.; Sampayo, E. M.; Schmidt, G. W.
2010-03-01
Denaturing gradient gel electrophoresis (DGGE) is commonly utilized to identify and quantify microbial diversity, but the conditions required for different electrophoretic systems to yield equivalent results and optimal resolution have not been assessed. Herein, the influence of different DGGE system configuration parameters on microbial diversity estimates was tested using Symbiodinium, a group of marine eukaryotic microbes that are important constituents of coral reef ecosystems. To accomplish this, bacterial clone libraries were constructed and sequenced from cultured isolates of Symbiodinium for the ribosomal DNA internal transcribed spacer 2 (ITS2) region. From these, 15 clones were subjected to PCR with a GC clamped primer set for DGGE analyses. Migration behaviors of the resulting amplicons were analyzed using a range of conditions, including variation in the composition of the denaturing gradient, electrophoresis time, and applied voltage. All tests were conducted in parallel on two commercial DGGE systems, a C.B.S. Scientific DGGE-2001, and the Bio-Rad DCode system. In this context, identical nucleotide fragments exhibited differing migration behaviors depending on the model of apparatus utilized, with fragments denaturing at a lower gradient concentration and applied voltage on the Bio-Rad DCode system than on the C.B.S. Scientific DGGE-2001 system. Although equivalent PCR-DGGE profiles could be achieved with both brands of DGGE system, the composition of the denaturing gradient and application of electrophoresis time × voltage must be appropriately optimized to achieve congruent results across platforms.
Microbial community analysis of shallow subsurface samples with PCR-DGGE
Energy Technology Data Exchange (ETDEWEB)
Itaevaara, M.; Suihko, M. -L.; Kapanen, A.; Piskonen, R.; Juvonen, R. [VTT Biotechnology, Espoo (Finland)
2005-11-15
This work is part of the site investigations for the disposal of spent nuclear fuel in Olkiluoto bedrock. The purpose of the research was to study the suitability of PCR-DGGE (polymerase chain reaction - denaturing gradient gel electrophoresis) method for monitoring of hydrogeomicrobiology of Olkiluoto repository site. PCR-DGGE method has been applied for monitoring microbial processes in several applications. The benefit of the method is that microorganisms are not cultivated but the presence of microbial communities can be monitored by direct DNA extractions from the environmental samples. Partial 16SrDNA gene sequence is specifically amplified by PCR (polymerase chain reaction) which detect bacteria as a group. The gene sequences are separated in DGGE, and the nucleotide bands are then cut out, extracted, sequenced and identified by the genelibraries by e.g. Blast program. PCR-DGGE method can be used to detect microorganisms which are present abundantly in the microbial communities because small quantities of genes cannot be separated reliably. However, generally the microorganisms involved in several environmental processes are naturally enriched and present as major population. This makes it possible to utilize PCRDGGE as a monitoring method. In this study, we studied the structure of microbial communities in ten ground water samples originating from Olkiluoto. Two universal bacterial primer sets were compared which amplified two different regions of the 16SrDNA gene. The longer sequence amplified resulted in fewer bands in DGGE, in addition there were problems with purification of the sequences after DGGE. The shorter sequence gave more bands in DGGE and more clear results without any amplification problems. Comparison of the sequences from the gene-libraries resulted in the detection of the same species by both primer sets, in addition some different species were detected. Several species were anaerobic bacteria, such as acetogenic and sulphate reducing
Microbial community analysis of shallow subsurface samples with PCR-DGGE
International Nuclear Information System (INIS)
Itaevaara, M.; Suihko, M.-L.; Kapanen, A.; Piskonen, R.; Juvonen, R.
2005-11-01
This work is part of the site investigations for the disposal of spent nuclear fuel in Olkiluoto bedrock. The purpose of the research was to study the suitability of PCR-DGGE (polymerase chain reaction - denaturing gradient gel electrophoresis) method for monitoring of hydrogeomicrobiology of Olkiluoto repository site. PCR-DGGE method has been applied for monitoring microbial processes in several applications. The benefit of the method is that microorganisms are not cultivated but the presence of microbial communities can be monitored by direct DNA extractions from the environmental samples. Partial 16SrDNA gene sequence is specifically amplified by PCR (polymerase chain reaction) which detect bacteria as a group. The gene sequences are separated in DGGE, and the nucleotide bands are then cut out, extracted, sequenced and identified by the genelibraries by e.g. Blast program. PCR-DGGE method can be used to detect microorganisms which are present abundantly in the microbial communities because small quantities of genes cannot be separated reliably. However, generally the microorganisms involved in several environmental processes are naturally enriched and present as major population. This makes it possible to utilize PCRDGGE as a monitoring method. In this study, we studied the structure of microbial communities in ten ground water samples originating from Olkiluoto. Two universal bacterial primer sets were compared which amplified two different regions of the 16SrDNA gene. The longer sequence amplified resulted in fewer bands in DGGE, in addition there were problems with purification of the sequences after DGGE. The shorter sequence gave more bands in DGGE and more clear results without any amplification problems. Comparison of the sequences from the gene-libraries resulted in the detection of the same species by both primer sets, in addition some different species were detected. Several species were anaerobic bacteria, such as acetogenic and sulphate reducing
Directory of Open Access Journals (Sweden)
Jie Zhao
Full Text Available Ecological interactions between aboveground and belowground biodiversity have received many attentions in the recent decades. Although soil biodiversity declined with the decrease of plant diversity, many previous studies found plant species identities were more important than plant diversity in controlling soil biodiversity. This study focused on the responses of soil biodiversity to the altering of plant functional groups, namely overstory and understory vegetations, rather than plant diversity gradient. We conducted an experiment by removing overstory and/or understory vegetation to compare their effects on soil microbial phospholipid fatty acid (PLFA and nematode diversities in eucalyptus monocultures. Our results indicated that both overstory and understory vegetations could affect soil microbial PLFA and nematode diversities, which manifested as the decrease in Shannon-Wiener diversity index (H' and Pielou evenness index (J and the increase in Simpson dominance index (λ after vegetation removal. Soil microclimate change explained part of variance of soil biodiversity indices. Both overstory and understory vegetations positively correlated with soil microbial PLFA and nematode diversities. In addition, the alteration of soil biodiversity might be due to a mixing effect of bottom-up control and soil microclimate change after vegetation removal in the studied plantations. Given the studied ecosystem is common in humid subtropical and tropical region of the world, our findings might have great potential to extrapolate to large scales and could be conducive to ecosystem management and service.
Approach to determine the diversity of Legionella species by nested PCR-DGGE in aquatic environments
Huang, Wen-Chien; Tsai, Hsin-Chi; Tao, Chi-Wei; Chen, Jung-Sheng; Shih, Yi-Jia; Kao, Po-Min; Huang, Tung-Yi; Hsu, Bing-Mu
2017-01-01
In this study, we describe a nested PCR-DGGE strategy to detect Legionella communities from river water samples. The nearly full-length 16S rRNA gene was amplified using bacterial primer in the first step. After, the amplicons were employed as DNA templates in the second PCR using Legionella specific primer. The third round of gene amplification was conducted to gain PCR fragments apposite for DGGE analysis. Then the total numbers of amplified genes were observed in DGGE bands of products gained with primers specific for the diversity of Legionella species. The DGGE patterns are thus potential for a high-throughput preliminary determination of aquatic environmental Legionella species before sequencing. Comparative DNA sequence analysis of excised DGGE unique band patterns showed the identity of the Legionella community members, including a reference profile with two pathogenic species of Legionella strains. In addition, only members of Legionella pneumophila and uncultured Legionella sp. were detected. Development of three step nested PCR-DGGE tactic is seen as a useful method for studying the diversity of Legionella community. The method is rapid and provided sequence information for phylogenetic analysis. PMID:28166249
Herschbach, Jennifer; Apostel, Carolin; Spielvogel, Sandra; Kuzyakov, Yakov; Dippold, Michaela
2016-04-01
Microbial utilization is a key transformation process of soil organic matter (SOM). Sorption of low molecular weight organic substances (LMWOS) to soil mineral surfaces blocks or delays microbial uptake and therefore mineralization of LMWOS to CO2, as well as all other biochemical transformations. We used position-specific labeling, a tool of isotope applications novel to soil science, combined with 13C-phospholipid fatty acid (PLFA) analysis, to assess microbial utilization of sorbed and non-sorbed Alanine in soil. Alanine has various functional groups enabling different sorption mechanisms via its positive charge (e.g. to clay minerals by cation exchange), as well as via its negative charge (e.g. to iron oxides by ligand exchange). To assess changes in the transformation pathways caused by sorption, we added uniformly and position-specifically 13C and 14C labeled Alanine to the Ap of a loamy Luvisol in a short-term (10 days) incubation experiment. To allow for sorption of the tracer solution to an aliquot of this soil, microbial activity was minimized in this subsample by sterilizing the soil by γ-radiation. After shaking, the remaining solutions were filtered and the non-sorbed Alanine was removed with Millipore water and then added to non-sterilized soil. For the free Alanine treatment, solutions with Alanine of similar amount and isotopic composition were prepared, added to the soil and incubated as well. The respired CO2 was trapped in NaOH and its 14C-activity was determined at increasing times intervals. Microbial utilization of Alanine's individual C positions was evaluated in distinct microbial groups classified by 13C-PLFA analysis. Sorption to soil minerals delayed respiration to CO2 and reduced initial respiration rate by 80%. Irrespective of sorption, the highest amount was respired from the carboxylic position (C-1), whereas the amino-bound (C-2) and the methylic position (C-3) were preferentially incorporated into PLFA of microorganisms due to the
PCR-DGGE fingerprints of microbial successional changes during ...
African Journals Online (AJOL)
PCR-DGGE fingerprints of microbial successional changes during fermentation of cereal-legume weaning foods. ... African Journal of Biotechnology ... Phenotypic identification and monitoring of the dynamics of naturally occurring microbial community responsible for the spontaneous fermentation of different cereal-legume ...
PCR-DGGE Analysis of Bacterial Population Attached to the Bovine Rumen Wall
Lukáš, F. (Filip); Šimůnek, J. (Jiří); Mrázek, J. (Jakub); Kopečný, J. (Jan)
2010-01-01
We isolated and amplified by PCR 16S rDNA from bacteria attached to the bovine rumen wall and analyzed it by denaturing gradient gel electrophoresis (DGGE) with subsequent sequence analysis. The attached bacterial community differed from the bacteria of rumen content; however, no differences were observed among the five epithelial sampling sites taken from each animal. The DGGE profile of the bacterial population attached to the rumen wall represented a high inter-animal variation.
Delgado, Susana; Arroyo, Rebeca; Martín, Rocío; Rodríguez, Juan M
2008-04-18
Infectious mastitis is a common condition during lactation and in fact, represents one of the main causes leading to a precocious weaning. The number of studies dealing with lactational mastitis is low and, up to now, the etiological diagnosis is frequently made on the basis of unspecific clinical signs. The aim of this study was to investigate the microbial diversity of breast milk in 20 women with lactational mastitis employing culture-dependent and culture-independent (PCR-DGGE) approaches. Breast milk samples were cultured in different media to investigate the presence of bacteria and/or yeasts, and a total of 149 representative isolates were identified to the species level by 16S rRNA gene PCR sequencing. The microorganisms recovered were compared with those found by PCR-DGGE analysis. To identify the DGGE profiles two reference markers of different microbial species were constructed. Sequence analysis of unknown bands was also performed. Staphylococci were the dominant bacterial group and Staphylococcus epidermidis was the dominant species. In a lower number of samples, other bacteria (mainly streptococci and a few gram-negative species) were also identified. Globally, PCR-DGGE results showed a good correlation with those obtained by culture-based methods. However, although DNA bands corresponding to different lactic acid bacteria were detected, such bacteria could not be isolated from the milk samples. Staphylococci seem to be the main etiological agents of human lactational mastitis. The combined use of culture and molecular techniques allowed a better characterization of the bacterial diversity in milk from women suffering from infectious mastitis. Our results suggest that this condition could be the result of a disbiotic process where some of the bacterial species usually present in human milk outgrow (staphylococci) while others disappear (lactobacilli or lactococci).
Safety evaluation and bacterial community of kung-som using PCR-DGGE technique
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Sutanate Saelao
2016-08-01
Full Text Available This study evaluates the safety of kung-som which was distributed in local markets and using PCR-DGGE technique to identify microflora in kung-som. Lactic acid bacteria (LAB were found at counts of more than 7 log CFU g-1 in all samples and the total viable counts were about 5-8 log CFU g-1 . Bacillus cereus and yeasts were detected at around 2 log CFU g-1 and 5-6log CFU g-1, respectively. For DGGE analysis, LAB and coagulase negative staphylococci (CNS bacteria dominated over other microorganisms. The sequencing of the DNA bands from DGGE gels corresponding to kung-som samples showed the presence of LAB as the major microflora in the products, namely: Lactobacillus farciminis, Lactobacillus plantarum, Lactococcus garvieae, Tetragenococcus halophilus and Weissella thailandensis. In addition, Staphylococcus carnosus was detected in kung-som as minor microflora. These dominant strains would allow the development of defined starter cultures for improving the quality of kung-som.
Evaluation of denaturing gradient gel electrophoresis (DGGE) used ...
African Journals Online (AJOL)
Denaturing gradient gel electrophoresis (DGGE) is a powerful method used to study structure of bacterial communities, without cultivation, based on the diversity of the genes coding for ribosomal RNA. However, the results are strongly dependent on the respective target region of the used primer systems. Therefore, three ...
Chahorm, Kanchana; Prakitchaiwattana, Cheunjit
2018-01-02
The aim of this research was to evaluate the feasibility of PCR-DGGE and Reverse Transcriptase-PCR-DGGE techniques for rapid detection of Vibrio species in foods. Primers GC567F and 680R were initially evaluated for amplifying DNA and cDNA of ten references Vibrio species by PCR method. The GC-clamp PCR amplicons were separated according to their sequences by the DGGE using 10% (w/v) polyacrylamide gel containing 45-70% urea and formamide denaturants. Two pair of Vibrio species, which could not be differentiated on the gel, was Vibrio fluvialis - Vibrio furnissii and Vibrio parahaemolyticus - Vibrio harveyi. To determine the detection limit, in the community of 10 reference strains containing the same viable population, distinct DNA bands of 3 species; Vibrio cholerae, Vibrio mimicus and Vibrio alginolyticus were consistently observed by PCR-DGGE technique. In fact, 5 species; Vibrio cholerae, Vibrio mimicus, Vibrio alginolyticus, Vibrio parahaemolyticus and Vibrio fluvialis consistently observed by Reverse Transcriptase-PCR-DGGE. In the community containing different viable population increasing from 10 2 to 10 5 CFU/mL, PCR-DGGE analysis only detected the two most prevalent species, while RT-PCR-DGGE detected the five most prevalent species. Therefore, Reverse Transcriptase-PCR-DGGE was also selected for detection of various Vibrio cell conditions, including viable cell (VC), injured cells from frozen cultures (IVC) and injured cells from frozen cultures with pre-enrichment (PIVC). It was found that cDNA band of all cell conditions gave the same migratory patterns, except that multiple cDNA bands of Plesiomonas shigelloides under IVC and PIVC conditions were found. When Reverse Transcriptase-PCR-DGGE was used for detecting Vibrio parahaemolyticus in the pathogen-spiked food samples, Vibrio parahaemolyticus could be detected in the spiked samples containing at least 10 2 CFU/g of this pathogen. The results obtained also corresponded to standard method (USFDA, 2004
Wang, Lin; Mao, Jiugeng; Zhao, Hejuan; Li, Min; Wei, Qishun; Zhou, Ying; Shao, Heping
2016-09-01
Rice straw (RS) is an important raw material for the preparation of Agaricus bisporus compost in China. In this study, the characterization of composting process from RS and wheat straw (WS) was compared for mushroom production. The results showed that the temperature in RS compost increased rapidly compared with WS compost, and the carbon (C)/nitrogen (N) ratio decreased quickly. The microbial changes during the Phase I and Phase II composting process were monitored using denaturing gradient gel electrophoresis (DGGE) and phospholipid fatty acid (PLFA) analysis. Bacteria were the dominant species during the process of composting and the bacterial community structure dramatically changed during heap composting according to the DGGE results. The bacterial community diversity of RS compost was abundant compared with WS compost at stages 4-5, but no distinct difference was observed after the controlled tunnel Phase II process. The total amount of PLFAs of RS compost, as an indicator of microbial biomass, was higher than that of WS. Clustering by DGGE and principal component analysis of the PLFA compositions revealed that there were differences in both the microbial population and community structure between RS- and WS-based composts. Our data indicated that composting of RS resulted in improved degradation and assimilation of breakdown products by A. bisporus, and suggested that the RS compost was effective for sustaining A. bisporus mushroom growth as well as conventional WS compost.
Webster, Gordon; Watt, Lynsey C; Rinna, Joachim; Fry, John C; Evershed, Richard P; Parkes, R John; Weightman, Andrew J
2006-09-01
Marine sediment slurries enriched for anaerobic, sulfate-reducing prokaryotic communities utilizing glucose and acetate were used to provide the first comparison between stable-isotope probing (SIP) of phospholipid fatty acids (PLFA) and DNA (16S rRNA and dsrA genes) biomarkers. Different 13C-labelled substrates (glucose, acetate and pyruvate) at low concentrations (100 microM) were used over a 7-day incubation to follow and identify carbon flow into different members of the community. Limited changes in total PLFA and bacterial 16S rRNA gene DGGE profiles over 7 days suggested the presence of a stable bacterial community. A broad range of PLFA were rapidly labelled (within 12 h) in the 13C-glucose slurry but this changed with time, suggesting the presence of an active glucose-utilizing population and later development of another population able to utilize glucose metabolites. The identity of the major glucose-utilizers was unclear as 13C-enriched PLFA were common (16:0, 16:1, 18:1omega7, highest incorporation) and there was little difference between 12C- and 13C-DNA 16S rRNA gene denaturing gradient gel electrophoresis (DGGE) profiles. Seemingly glucose, a readily utilizable substrate, resulted in widespread incorporation consistent with the higher extent of 13C-incorporation (approximately 10 times) into PLFA compared with 13C-acetate or 13C-pyruvate. 13C-PLFA in the 13C-acetate and 13C-pyruvate slurries were similar to each other and to those that developed in the 13C-glucose slurry after 4 days. These were more diagnostic, with branched odd-chain fatty acids (i15:0, a15:0 and 15:1omega6) possibly indicating the presence of Desulfococcus or Desulfosarcina sulfate-reducing bacteria (SRB) and sequences related to these SRB were in the 13C-acetate-DNA dsrA gene library. The 13C-acetate-DNA 16S rRNA gene library also contained sequences closely related to SRB, but these were the acetate-utilizing Desulfobacter sp., as well as a broad range of uncultured Bacteria. In
Directory of Open Access Journals (Sweden)
Lingyu Yu
Full Text Available Microeukaryotic plankton are important components of aquatic environments and play key roles in marine microbial food webs; however, little is known about their genetic diversity in subtropical offshore areas. Here we examined the community composition and genetic diversity of the microeukaryotic plankton in Xiamen offshore water by PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis, clone-based sequencing and Illumina based sequencing. The Illumina MiSeq sequencing revealed a much (approximately two orders of magnitude higher species richness of the microeukaryotic community than DGGE, but there were no significant difference in species richness and diversity among the northern, eastern, southern or western stations based on both methods. In this study, Copepoda, Ciliophora, Chlorophyta, Dinophyceae, Cryptophyta and Bacillariophyta (diatoms were the dominant groups even though diatoms were not detected by DGGE. Our Illumina based results indicated that two northern communities (sites N2 and N3 were significantly different from others in having more protozoa and fewer diatoms. Redundancy analysis (RDA showed that both temperature and salinity were the significant environmental factors influencing dominant species communities, whereas the full microeukaryotic community appeared to be affected by a complex of environmental factors. Our results suggested that extensive sampling combined with more deep sequencing are needed to obtain the complete diversity of the microeukaryotic community, and different diversity patterns for both abundant and rare taxa may be important in evaluating the marine ecosystem health.
Analysis of phospholipid fatty acids (PLFA) to characterize microbial communities in aquifers
Green, Christopher T.; Scow, Kate M.
This paper reviews published applications of lipid-based biochemical techniques for characterizing microbial communities in aquifers and other deep subsurface habitats. These techniques, such as phospholipid fatty acid (PLFA) analysis, can provide information on a variety of microbial characteristics, such as biomass, physiology, taxonomic and functional identity, and overall community composition. In addition, multivariate statistical analysis of lipid data can relate spatial or temporal changes in microbial communities to environmental factors. The use of lipid-based techniques in the study of groundwater microbiology is advantageous because they do not require culturing and can provide quantitative data on entire communities. However, combined effects of physiological and phylogenetic changes on the lipid composition of a community can confound interpretation of the data, and many questions remain about the validity of various lipid techniques. Despite these caveats, lipid-based research has begun to show trends in community composition in contaminated and pristine aquifers that contribute to our understanding of groundwater microbial ecology and have potential for use in optimization of bioremediation of groundwater pollutants. Résumé Ce papier passe en revue les applications des techniques biochimiques basées sur les lipides pour caractériser les communautés microbiennes présentes dans les aquifères et dans les autres habitats souterrains profonds. Ces techniques, telles que l'analyse des acides gras phospholipidiques (PLFA), peuvent fournir des informations sur un ensemble de caractères microbiens, tels que la biomasse, la physiologie, l'identité taxonomique et fonctionnelle, et surtout la composition de la communauté. En outre, l'analyse statistique multivariée des données sur les lipides peut établir les liens entre des changements spatiaux ou temporels dans la communauté microbienne et des facteurs environnementaux. L'utilisation des
Garbeva, P.; Overbeek, van L.S.; Vuurde, van J.W.L.; Elsas, van J.D.
2001-01-01
The diversity of endophytic bacterial populations of potato (Solanum tuberosum cv Desiree) was assessed using a combination of dilution plating of plant macerates followed by isolation and characterization of isolates, and direct PCR-DGGE on the basis of DNA extracted from plants. The culturable
Luna Ramos, Lourdes; Pastorelli, Roberta; Miralles Mellado, Isabel; Fabiani, Arturo; Bastida López, Felipe; Hernández Fernández, María Teresa; García Izquierdo, Carlos; Solé Benet, Albert
2015-04-01
respect to that of reference soil. Fungal communities could be divided into main groups according to the organic amendment. Within each group, GM amendment generated fungal community structures with lower similarities with respect to the other mulch treatments. In contrast to PLFA results, DGGE fingerprints revealed significant influence of the combination of organic amendments and mulches on diversity and composition of soil microbial communities.
Characterization of spoilage bacteria in pork sausage by PCR-DGGE analysis
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Francesca Silva Dias
2013-09-01
Full Text Available To investigate microbial diversity and identify spoilage bacteria in fresh pork sausages during storage, twelve industrial pork sausages of different trademarks were stored at 4 ºC for 0, 14, 28 and 42 days, 80% relative humidity and packaged in sterile plastic bags. Microbiological analysis was performed. The pH and water activity (a w were measured. The culture-independent method performed was the Polymerase Chain Reaction - Denaturing Gradient Gel Electrophoresis (PCR-DGGE. The culture-dependent method showed that the populations of mesophilic bacteria and Lactic Acid Bacteria (LAB increased linearly over storage time. At the end of the storage time, the average population of microorganisms was detected, in general, at the level of 5 log cfu g-1. A significant (P < 0.005 increase was observed in pH and a w values at the end of the storage time. The PCR-DGGE allowed a rapid identification of dominant communities present in sausages. PCR-DGGE discriminated 15 species and seven genera of bacteria that frequently constitute the microbiota in sausage products. The most frequent spoilage bacteria identified in the sausages were Lactobacillus sakei and Brochothrix thermosphacta. The identification of dominant communities present in fresh pork sausages can help in the choice of the most effective preservation method for extending the product shelf-life.
Milanović, Vesna; Osimani, Andrea; Taccari, Manuela; Garofalo, Cristiana; Butta, Alessandro; Clementi, Francesca; Aquilanti, Lucia
2017-07-01
The bacterial diversity in fermenting dye vats with woad (Isatis tinctoria L.) prepared and maintained in a functional state for approximately 12 months was examined using a combination of culture-dependent and -independent PCR-DGGE analyses and next-generation sequencing of 16S rRNA amplicons. An extremely complex ecosystem including taxa potentially contributing to both indigo reduction and formation, as well as indigo degradation was found. PCR-DGGE analyses revealed the presence of Paenibacillus lactis, Sporosarcina koreensis, Bacillus licheniformis, and Bacillus thermoamylovorans, while Bacillus thermolactis, Bacillus pumilus and Bacillus megaterium were also identified but with sequence identities lower than 97%. Dominant operational taxonomic units (OTUs) identified by pyrosequencing included Clostridium ultunense, Tissierella spp., Alcaligenes faecalis, Erysipelothrix spp., Enterococcus spp., Virgibacillus spp. and Virgibacillus panthothenicus, while sub-dominant OTUs included clostridia, alkaliphiles, halophiles, bacilli, moderately thermophilic bacteria, lactic acid bacteria, Enterobacteriaceae, aerobes, and even photosynthetic bacteria. Based on the current knowledge of indigo-reducing bacteria, it is considered that indigo-reducing bacteria constituted only a small fraction in the unique microcosm detected in the natural indigo dye vats.
Lovell, Charles R; Decker, Peter V; Bagwell, Christopher E; Thompson, Shelly; Matsui, George Y
2008-05-01
Methods to assess the diversity of the diazotroph assemblage in the rhizosphere of the salt marsh cordgrass, Spartina alterniflora were examined. The effectiveness of nifH PCR-denaturing gradient gel electrophoresis (DGGE) was compared to that of nifH clone library analysis. Seventeen DGGE gel bands were sequenced and yielded 58 nonidentical nifH sequences from a total of 67 sequences determined. A clone library constructed using the GC-clamp nifH primers that were employed in the PCR-DGGE (designated the GC-Library) yielded 83 nonidentical sequences from a total of 257 nifH sequences. A second library constructed using an alternate set of nifH primers (N-Library) yielded 83 nonidentical sequences from a total of 138 nifH sequences. Rarefaction curves for the libraries did not reach saturation, although the GC-Library curve was substantially dampened and appeared to be closer to saturation than the N-Library curve. Phylogenetic analyses showed that DGGE gel band sequencing recovered nifH sequences that were frequently sampled in the GC-Library, as well as sequences that were infrequently sampled, and provided a species composition assessment that was robust, efficient, and relatively inexpensive to obtain. Further, the DGGE method permits a large number of samples to be examined for differences in banding patterns, after which bands of interest can be sampled for sequence determination.
Silva, da K.R.A.; Salles, J.F.; Seldin, L.; Elsas, van J.D.
2003-01-01
In this study, a Paenibacillus-specific PCR system, based on the specific primer PAEN515F in combination with bacterial primer R1401, was tested and used to amplify specific fragments of the 16S rRNA gene from rhizosphere DNA. The amplicons were used in a second (semi-nested) PCR for DGGE, in which
da Silva, Katia Regina Araujo; Falcao Salles, Joana; Seldin, Lucy; van Elsas, Jan
In this study, a Paenibacillus-specific PCR system, based on the specific primer PAEN515F in combination with bacterial primer R1401, was tested and used to amplify specific fragments of the 16S rRNA gene from rhizosphere DNA. The amplicons were used in a second (semi-nested) PCR for DGGE, in which
Using DGGE and 16S rRNA gene sequence analysis to evaluate changes in oral bacterial composition.
Chen, Zhou; Trivedi, Harsh M; Chhun, Nok; Barnes, Virginia M; Saxena, Deepak; Xu, Tao; Li, Yihong
2011-01-01
To investigate whether a standard dental prophylaxis followed by tooth brushing with an antibacterial dentifrice will affect the oral bacterial community, as determined by denaturing gradient gel electrophoresis (DGGE) combined with 16S rRNA gene sequence analysis. Twenty-four healthy adults were instructed to brush their teeth using commercial dentifrice for 1 week during a washout period. An initial set of pooled supragingival plaque samples was collected from each participant at baseline (0 h) before prophylaxis treatment. The subjects were given a clinical examination and dental prophylaxis and asked to brush for 1 min with a dentifrice containing 0.3% triclosan, 2.0% PVM/MA copolymer and 0.243% sodium fluoride (Colgate Total). On the following day, a second set of pooled supragingival plaque samples (24 h) was collected. Total bacterial genomic DNA was isolated from the samples. Differences in the microbial composition before and after the prophylactic procedure and tooth brushing were assessed by comparing the DGGE profiles and 16S rRNA gene segments sequence analysis. Two distinct clusters of DGGE profiles were found, suggesting that a shift in the microbial composition had occurred 24 h after the prophylaxis and brushing. A detailed sequencing analysis of 16S rRNA gene segments further identified 6 phyla and 29 genera, including known and unknown bacterial species. Importantly, an increase in bacterial diversity was observed after 24 h, including members of the Streptococcaceae family, Prevotella, Corynebacterium, TM7 and other commensal bacteria. The results suggest that the use of a standard prophylaxis followed by the use of the dentifrice containing 0.3% triclosan, 2.0% PVM/MA copolymer and 0.243% sodium fluoride may promote a healthier composition within the oral bacterial community.
Liang, Huipeng; Li, Wenfang; Luo, Qingchun; Liu, Chaolan; Wu, Zhengyun; Zhang, Wenxue
2015-10-01
The community structure of bacteria in aged and aging pit mud, which was judged according to their sensory and physicochemical characteristics, was analysed using polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) and quantitative real-time PCR (qPCR). The phyla Firmicutes, Actinobacteria, Proteobacteria, Synergistetes and Unclassified Bacteria were detected and the fermentative Firmicutes was predominant in both types of pit mud in the PCR-DGGE analysis. Among Firmicutes, Clostridiales was dominant in aged pit mud while Bacillales and Lactobacillales were dominant in aging pit mud. The diversity of bacterial communities in aged pit mud was higher than that in aging pit mud. In the qPCR analysis the abundance of Clostridium IV in aged pit mud was higher than that in aging pit mud and there were significant differences in the quantity of Clostridium IV between aged and aging pit mud of the same cellar (P mud. The differences in the quantity of Clostridium IV might be involved in the distinction that the aged pit mud has a strong aroma while the aging pit mud does not. © 2014 Society of Chemical Industry.
Directory of Open Access Journals (Sweden)
Paulo Teixeira Lacava
2006-04-01
Full Text Available O objetivo deste trabalho foi caracterizar a comunidade bacteriana endofítica de plantas assintomáticas (escapes e afetadas pela clorose variegada dos citros (CVC por meio de isolamento em meio de cultura, técnica de gradiente desnaturante em gel de eletroforese (DGGE e detecção de Methylobacterium mesophilicum e Xyllela fastidiosa por meio de PCR específico, para estudar esta comunidade e sua relação com a ocorrência da CVC. A análise da comunidade bacteriana via DGGE permitiu a detecção de X. fastidiosa, bem como Klebsiella sp. e Acinetobacter sp. como endófitos de citros. Foram observados também Curtobacterium sp., Pseudomonas sp., Enterobacter sp. e Bacillus spp. Utilizando primers específicos, Methylobacterium mesophilicum e X. fastidiosa também foram observadas, reforçando hipóteses de que estas bactérias podem estar interagindo no interior da planta hospedeira.The aim of this work was to characterize endophytic bacterial community of assintomatic (escape and Citrus Variegated Chlorosis (CVC-affected citrus plants using isolation in culture medium, denaturing gradient gel electrophoresis (DGGE technique and Methylobacterium mesophilicum as well as Xylella fastidiosa specific PCR, allowing to assess this community and its interactions with CVC. The study of bacterial community by DGGE analysis allowed the detection of X. fastidiosa, as well as Klebsiella sp. e Acinetobacter sp., which were not detected previously. Curtobacterium sp., Pseudomonas sp., Enterobacter sp. and Bacillus spp. were also observed as endophyte in citrus plants. Using specific primers Methylobacterium mesophilicum and X. fastidiosa were observed, reinforcing that these bacteria could interact inside the host plant.
Study of the dynamic of Bacillus species during of oil contaminated soil by PCR-DGGE
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Mahmoud Shavandi
2018-06-01
Discussion and conclusion: Comparison of the pattern of DGGE bands variation between the microcosms showed that by entry of the contaminant into the soil, the diversity of Bacillus species was increased, indicating that Bacillus species has a particular role in diesel degradation. Simultaneous with decline of the pollution and microbial count of the soil, diversity of DGGE bands was decreased. Out of these findings we may conclude that addition of diesel as a carbon source to the soil increases the Bacillus spp. diversity at the beginning of bioremediation and afterwards by elimination of the pollutant, the diversity decreases gradually and shifts back to its original structure.
Reeson, A F; Jankovic, T; Kasper, M L; Rogers, S; Austin, A D
2003-02-01
Invertebrates host numerous bacteria, with interactions ranging from pathogenesis to symbiosis. While certain symbiotic relationships have been well studied, little is known about the dynamics of these bacterial communities. Denaturing gradient gel electrophoresis (DGGE) was used to examine the bacterial microflora associated with the eusocial wasp Vespula germanica. DGGE profiles of larval guts revealed a variable microflora, suggesting that V. germanica is not dependent on a particular suite of mutualists. The variation in profiles was not related to season, nest size or macrohabitat. Sequences corresponding to Lactococcus, Lactobacillus, a novel Leuconostoc and two Rickettsiella grylli strains were obtained. DGGE proved to be a useful technique for characterizing the wasp microflora. Given the importance of microbial communities to invertebrates, there is much to be gained from the application of such techniques.
Ercolini, D; Mauriello, G; Blaiotta, G; Moschetti, G; Coppola, S
2004-01-01
To monitor the process and the starter effectiveness recording a series of fingerprints of the microbial diversity occurring at different steps of mozzarella cheese manufacture and to investigate the involvement of the natural starter to the achievement of the final product. Samples of raw milk, natural whey culture (NWC) used as starter, curd after ripening and final product were collected during a mozzarella cheese manufacture. Total microbial DNA was directly extracted from the dairy samples as well as bulk colonies collected from the plates of appropriate culture media generally used for viable counts of mesophilic and thermophilic lactic acid bacteria (LAB) and used in polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) experiments. The analysis of the DGGE profiles showed a strong influence of the microflora of the NWC on the whole process because after the starter addition, the profile of all the dairy samples was identical to the one shown by the NWC. Simple indexes were calculated for the DGGE profiles to have an objective estimation of biodiversity and of technological importance of specific groups of organisms. LAB grown on Man Rogosa Sharp (MRS) and Rogosa agar at 30 degrees C showed high viable counts and the highest diversity in species indicating their importance in the cheese making, which had not been considered so far. Moreover, the NWC profiles were shown to be the most similar to the curd profile suggesting to be effective in manufacture. The PCR-DGGE analysis showed that in premium quality manufacture the NWC used as starter had a strong influence on the microflora responsible for process development. The molecular approach appeared to be valid as a tool to control process development, starter effectiveness and product identity as well as to rank cheese quality.
Analysis of microbial diversity in Shenqu with different fermentation times by PCR-DGGE
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Tengfei Liu
Full Text Available Abstract Shenqu is a fermented product that is widely used in traditional Chinese medicine (TCM to treat indigestion; however, the microbial strains in the fermentation process are still unknown. The aim of this study was to investigate microbial diversity in Shenqu using different fermentation time periods. DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis profiles indicated that a strain of Pediococcus acidilactici (band 9 is the predominant bacteria during fermentation and that the predominant fungi were uncultured Rhizopus, Aspergillus oryzae, and Rhizopus oryzae. In addition, pathogenic bacteria, such as Enterobacter cloacae, Klebsiella oxytoca, Erwinia billingiae, and Pantoea vagan were detected in Shenqu. DGGE analysis showed that bacterial and fungal diversity declined over the course of fermentation. This determination of the predominant bacterial and fungal strains responsible for fermentation may contribute to further Shenqu research, such as optimization of the fermentation process.
DEFF Research Database (Denmark)
Petersen, Randi Føns; Harrington, C. S.; Kortegaard, H. E.
2007-01-01
Results: A semi-nested PCR was developed to allow sensitive detection of all Epsilobacteria, with species separation undertaken by DGGE. A database was constructed in BioNumerics using 145 strains covering 51 Campylobacter, Arcobacter and Helicobacter taxa; Nineteen distinct DGGE profile-groups were......Aims: To develop a PCR-denaturing gradient gel electrophoresis (PCR-DGGE) method for the detection and identification of Campylobacter, Helicobacter and Arcobacter species (Epsilobacteria) in clinical samples and evaluate its efficacy on saliva samples from humans and domestic pets. Methods ans...... distinguished. This approach detected Epsilobacteria in all saliva samples collected from humans, cats and dogs, and identified Campylobacter concisus and/or Campylobacter gracilis in the human samples. The pet animal samples were taken from individuals with oral/dental diseases; PCR-DGGE identified up to four...
Cowie, B. R.; Greenberg, B. M.; Slater, G. F.
2008-12-01
Optimizing remediation of petroleum-contaminated soils requires thorough understanding of the mechanisms and pathways involved in a proposed remediation system. In many engineered and natural attenuation systems, multiple degradation pathways may contribute to observed contaminant mass losses. In this study, biodegradation in the soil microbial community was identified as a major pathway for petroleum hydrocarbon removal in a Multi-Process Phytoremediation System (MPPS) using natural abundance 14C analysis of Phospholipid Fatty Acids (PLFA). In contaminated soils, PLFA were depleted in Δ14C to less than -800‰, directly demonstrating microbial uptake and utilization of petroleum derived carbon (Δ14C = -992‰) during bioremediation. Mass balance indicated that more than 80% of microbial carbon was derived from petroleum hydrocarbons and a maximum of 20% was produced from metabolism of modern carbon sources. In contrast, in a nearby uncontaminated control soil, the microbial community maintained a nearly modern 14C signature, suggesting preferential degradation of more labile, recent carbon. Mass balance using δ13C and Δ14C of soil CO2 demonstrated that mineralization of petroleum carbon contributed 60-65% of soil CO2 at the contaminated site. The remainder was derived from atmospheric (27-30%) and decomposition of non- petroleum natural organic carbon (5-10%). The clean control exhibited substantially lower CO2 concentrations that were derived from atmospheric (55%) and natural organic carbon (45%) sources. This study highlights the value of using multiple carbon isotopes to identify degradation pathways in petroleum- contaminated soils undergoing phytoremediation and the power of natural abundance 14C to detect petroleum metabolism in natural microbial communities.
Sun, Jing; Yu, Zhigang; Gao, Yahui; Zhou, Qianqian; Zhen, Yu; Chen, Hongtao; Zhao, Liyuan; Yao, Qingzhen; Mi, Tiezhu
2010-03-01
Relationships between phytoplankton community composition and environmental variables in the East China Sea (ECS) and Yellow Sea (YS) were investigated using geochemical and molecular microbiology methods. The diversity of phytoplankton was characterized using cultivation-independent PCR-based denaturing gradient gel electrophoresis (DGGE). Groups resulting from unweighted pair-group method with arithmetic averages clustering of the DGGE profiles showed good consistency with the eco-environmental characteristics of the sea area they belonged to. Additionally, the clustering results based on DGGE fingerprinting and those based on morphological compositions were practically identical. The relationship of phytoplankton diversity to environmental factors was statistically analyzed. Temperature, dissolved inorganic nitrogen (DIN), and silicate-Si were found significantly related to the phytoplankton community composition. Canonical correspondence analysis (CCA) was performed to reveal the relationship between community composition and these three environmental factors. Generally, values of the ECS are clearly separated from those of the YS in the CCA biplot, due to mainly the effect of temperature and DIN.
Ji, Zheng; Wang, Xiaochang C; Xu, Limei; Zhang, Chongmiao; Funamizu, Naoyuki; Okabe, Satoshi; Sano, Daisuke
2014-06-01
A polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) method was employed to estimate the contamination sources of human enteroviruses and understand how their dominant strains vary in a wastewater treatment and reclamation system consisting of sewage collection, wastewater treatment with membrane bioreactor and open lakes for reclaimed water storage and reuse. After PCR-DGGE using a selected primer set targeting enteroviruses, phylogenetic analysis of acquired enterovirus gene sequences was performed. Enteroviruses identified from the septic tank were much more diverse than those from grey water and kitchen wastewater. Several unique types of enterovirus different from those in wastewater samples were dominant in a biological wastewater treatment unit. Membrane filtration followed by chlorination was proved effective for physically eliminating enteroviruses; however, secondary contamination likely occurred as the reclaimed water was stored in artificial lakes. Enterovirus 71 (EV71), a hand-foot-and-mouth disease (HFMD) viral pathogen, was detected mainly from the artificial lakes, implying that wastewater effluent was not the contamination source of EV71 and that there were unidentified non-point sources of the contamination with the HFMD viral pathogen in the reclaimed water stored in the artificial lakes. The PCR-DGGE targeting enteroviruses provided robust evidence about viral contamination sources in the wastewater treatment and reclamation system.
Directory of Open Access Journals (Sweden)
Ed-Haun Chang
2017-10-01
Full Text Available Wildfire often causes tremendous changes in ecosystems, particularly in subalpine and alpine areas, which are vulnerable due to severe climate conditions such as cold temperature and strong wind. This study aimed to clarify the effect of tree re-planting on ecosystem services such as the soil microbial community after several decades. We compared the re-planted forest and grassland with the mature forest as a reference in terms of soil microbial biomass C and N (Cmic and Nmic, enzyme activities, phospholipid fatty acids (PLFA composition, and denaturing gradient gel electrophoresis (DGGE. The Cmic and Nmic did not differ among the grassland, re-planted forest and mature forest soil; however, ratios of Cmic/Corg and Nmic/Ntot decreased from the grassland to re-planted forest and mature forest soil. The total PLFAs and those attributed to bacteria and Gram-positive and Gram-negative bacteria did not differ between the re-planted forest and grassland soil. Principle component analysis of the PLFA content separated the grassland from re-planted forest and mature forest soil. Similarly, DGGE analysis revealed changes in both bacterial and fungal community structures with changes in vegetation. Our results suggest that the microbial community structure changes with the re-planting of trees after a fire event in this subalpine area. Recovery of the soil microbial community to the original state in a fire-damaged site in a subalpine area may require decades, even under a re-planted forest.
Saro, Cristina; Molina-Alcaide, Eduarda; Abecia, Leticia; Ranilla, María José; Carro, María Dolores
2018-04-01
The objective of this study was to compare the automated ribosomal intergenic spacer analysis (ARISA) and the denaturing gradient gel electrophoresis (DGGE) techniques for analysing the effects of diet on diversity in bacterial pellets isolated from the liquid (liquid-associated bacteria (LAB)) and solid (solid-associated bacteria (SAB)) phase of the rumen. The four experimental diets contained forage to concentrate ratios of 70:30 or 30:70 and had either alfalfa hay or grass hay as forage. Four rumen-fistulated animals (two sheep and two goats) received the diets in a Latin square design. Bacterial pellets (LAB and SAB) were isolated at 2 h post-feeding for DNA extraction and analysed by ARISA and DGGE. The number of peaks in individual samples ranged from 48 to 99 for LAB and from 41 to 95 for SAB with ARISA, and values of DGGE-bands ranged from 27 to 50 for LAB and from 18 to 45 for SAB. The LAB samples from high concentrate-fed animals tended (p forage-fed animals with ARISA, but no differences were identified with DGGE. The SAB samples from high concentrate-fed animals had lower (p forage diets with ARISA, but only a trend was noticed for these parameters with DGGE (p forage type on LAB diversity was detected by any technique. In this study, ARISA detected some changes in ruminal bacterial communities that were not detected by DGGE, and therefore ARISA was considered more appropriate for assessing bacterial diversity of ruminal bacterial pellets. The results highlight the impact of the fingerprinting technique used to draw conclusions on dietary factors affecting bacterial diversity in ruminal bacterial pellets.
DGGE and multivariate analysis of a yeast community in spontaneous cocoa fermentation process.
Ferreira, A C R; Marques, E L S; Dias, J C T; Rezende, R P
2015-12-28
Cocoa bean is the main raw material used in the production of chocolate. In southern Bahia, Brazil, cocoa farming and processing is an important economic activity. The fermentation of cocoa is the processing stage that yields important chocolate flavor precursors and complex microbial involvement is essential for this process. In this study, PCR-denaturing gradient gel electrophoreses (DGGE) was used to investigate the diversity of yeasts present during the spontaneous fermentation of cocoa in southern Bahia. The DGGE analysis revealed a richness of 8 to 13 distinct bands of varied intensities among the samples; and samples taken at 24, 36, and 48 h into the fermentation process were found to group with 70% similarity and showed the greatest diversity of bands. Hierarchical clustering showed that all samples had common operational taxonomic units (OTUs) and the highest number of OTUs was found in the 48 h sample. Variations in pH and temperature observed within the fermenting mass over time possibly had direct effects on the composition of the existing microbial community. The findings reported here indicate that a heterogeneous yeast community is involved in the complex cocoa fermentation process, which is known to involve a succession of specialized microorganisms.
Czech Academy of Sciences Publication Activity Database
Oravecz, O.; Elhottová, Dana; Krištůfek, Václav; Šustr, Vladimír; Frouz, Jan; Tříska, Jan; Márialigeti, K.
2004-01-01
Roč. 49, č. 1 (2004), s. 83-93 ISSN 0015-5632 R&D Projects: GA AV ČR IAB6066903; GA ČR GA526/99/P033 Institutional research plan: CEZ:AV0Z6066911 Keywords : ARDRA * PLFA analysis * bacterial community Subject RIV: EH - Ecology, Behaviour Impact factor: 1.034, year: 2004
Xiong, Xiaomao; Hu, Yuanliang; Yan, Nanfeng; Huang, Yingna; Peng, Nan; Liang, Yunxiang; Zhao, Shumiao
2014-08-01
A systematic investigation was performed on the bacterial, Bacillus, fungal, and yeast communities of the three types of Daqu (mechanically prepared, manually prepared, and mixed prepared) used in Baiyunbian Company by reconditioning PCR-denaturing gradient gel electrophoresis (PCR-DGGE). The DGGE results showed that the microbes in the three types of Daqu were mainly thermotolerant and thermophilic microbes, and the most dominant bacterial species were Bacillus and Virgibacillus, followed by Lactobacillus and Trichococcus. Furthermore, the dominant fungi were found to be molds, such as Rasamsonia, Penicillium, Aspergillus, and Monascus, and the dominant yeasts were Saccharomyces cerevisiae, Saccharomycopsis fibuligera, Pichia anomala, and Debaryomyces hansenii. In general, the three types of Daqu showed slight differences in microbial communities, and the Shannon indexes (H') of the manually prepared and mechanically prepared Daqu were similar. The results suggest that mechanically prepared Daqu can replace manually prepared Daqu in liquor production, and this research provides useful information for liquor production and process improvement.
Lv, Xu-Cong; Jiang, Ya-Jun; Liu, Jie; Guo, Wei-Ling; Liu, Zhi-Bin; Zhang, Wen; Rao, Ping-Fan; Ni, Li
2017-08-16
Denaturing gradient gel electrophoresis (DGGE) has become a widely used tool to examine microbial community structure. However, when DGGE is applied to evaluate the fungal community of traditional fermentation starters, the choice of hypervariable ribosomal RNA gene regions is still controversial. In the current study, several previously published fungal PCR primer sets were compared and evaluated using PCR-DGGE, with the purpose of screening a suitable primer set to study the fungal community of traditional fermentation starters for Hong Qu glutinous rice wine. Firstly, different primer sets were used to amplify different hypervariable regions from pure fungal cultures. Except NS1/FR1+ and ITS1fGC/ITS4, other primer sets (NL1+/LS2R, NL3A/NL4GC, FF390/FR1+, NS1/GCFung, NS3+/YM951r and ITS1fGC/ITS2r) amplified the target DNA sequences successfully. Secondly, the selected primer sets were further evaluated based on their resolution to distinguish different fungal cultures through DGGE fingerprints. Three primer sets (NL1+/LS2R, NS1/GCFung and ITS1fGC/ITS2r) were finally selected for investigating the fungal community structure of different traditional fermentation starters for Hong Qu glutinous rice wine. The internal transcribed spacer (ITS) region amplified by ITS1fGC/ITS2r, which is more hypervariable than the 18S rRNA gene and 26S rRNA gene, provides an excellent tool to separate amplification products of different fungal species. Results indicated that PCR-DGGE profile using ITS1fGC/ITS2r showed more abundant fungal species than that using NL1+/LS2R and NS1/GCFung. Therefore, ITS1fGC/ITS2r is the most suitable primer set for PCR-DGGE analysis of fungal community structure in traditional fermentation starters for Hong Qu glutinous rice wine. DGGE profiles based on ITS1fGC/ITS2r revealed the presence of twenty-four fungal species in traditional fermentation starter. A significant difference of fungal community can be observed directly from DGGE fingerprints and
de Oliveira, Valéria Maia; Manfio, Gilson Paulo; da Costa Coutinho, Heitor Luiz; Keijzer-Wolters, Anneke Christina; van Elsas, Jan Dirk
2006-03-01
A direct molecular method for assessing the diversity of specific populations of rhizobia in soil, based on nested PCR amplification of 16S-23S ribosomal RNA gene (rDNA) intergenic spacer (IGS) sequences, was developed. Initial generic amplification of bacterial rDNA IGS sequences from soil DNA was followed by specific amplification of (1) sequences affiliated with Rhizobium leguminosarum "sensu lato" and (2) R. tropici. Using analysis of the amplified sequences in clone libraries obtained on the basis of soil DNA, this two-sided method was shown to be very specific for rhizobial subpopulations in soil. It was then further validated as a direct fingerprinting tool of the target rhizobia based on denaturing gradient gel electrophoresis (DGGE). The PCR-DGGE approach was applied to soils from fields in Brazil cultivated with common bean (Phaseolus vulgaris) under conventional or no-tillage practices. The community fingerprints obtained allowed the direct analysis of the respective rhizobial community structures in soil samples from the two contrasting agricultural practices. Data obtained with both primer sets revealed clustering of the community structures of the target rhizobial types along treatment. Moreover, the DGGE profiles obtained with the R. tropici primer set indicated that the abundance and diversity of these organisms were favoured under NT practices. These results suggest that the R. leguminosarum-as well as R. tropici-targeted IGS-based nested PCR and DGGE are useful tools for monitoring the effect of agricultural practices on these and related rhizobial subpopulations in soils.
Institute of Scientific and Technical Information of China (English)
WANG Guang-Hua; JIN Jian; LIU Jun-Jie; CHEN Xue-Li; LIU Ju-Dong; LIU Xiao-Bing
2009-01-01
Soil microbial biomass and community structures are commonly used as indicators for soil quality and fertility.A investigation was performed to study the effects of long-term natural restoration,cropping,and bare fallow managements on the soil microbial biomass and bacterial community structures in depths of 0-10,20-30,and 40-50 cm in a black soil (Mollisol).Microbial biomass was estimated from chloroform fumigation-extraction,and bacterial community structures were determined by analysis of 16S rDNA using polymerase chain reaction-denaturing gradient gel electrophoresis (PCRDGGE).Experimental results showed that microbial biomass significantly declined with soil depth in the managements of restoration and cropping,but not in the bare fallow.DGGE profiles indicated that the band number in top 0-10 cm soils was less than that in depth of 20-30 or 40-50 cm.These suggested that the microbial population was high but the bacterial community structure was simple in the topsoil.Cluster and principle component analysis based on DGGE banding patterns showed that the bacterial community structure was affected by soil depth more primarily than by managements,and the succession of bacterial community as increase of soil depth has a similar tendency in the three managements.Fourteen predominating DGGE bands were excised and sequenced,in which 6 bands were identified as the taxa of Verrucomicrobia,2 bands as Actinobacteria,2 bands as α-Proteobacteria,and the other 4 bands as δ-Proteobacteria,Acidobacteria,Nitrospira,and unclassified bacteria.In addition,the sequences of 11 DGGE bands were closely related to uncultured bacteria.Thus,the bacterial community structure in black soil was stable,and the predominating bacterial groups were uncultured.
Analysis of oral microbiota in children with dental caries by PCR-DGGE and barcoded pyrosequencing.
Ling, Zongxin; Kong, Jianming; Jia, Peng; Wei, Chaochun; Wang, Yuezhu; Pan, Zhiwen; Huang, Wujing; Li, Lanjuan; Chen, Hui; Xiang, Charlie
2010-10-01
Oral microbiota plays a vital role in maintaining the homeostasis of oral cavity. Dental caries are among the most common oral diseases in children and pathogenic bacteria contribute to the development of the disease. However, the overall structure of bacterial communities in the oral cavity from children with dental caries has not been explored deeply heretofore. We used high-throughput barcoded pyrosequencing and PCR-denaturing gradient gel electrophoresis (DGGE) to examine bacterial diversity of oral microbiota in saliva and supragingival plaques from 60 children aged 3 to 6 years old with and without dental caries from China. The multiplex barcoded pyrosequencing was performed in a single run, with multiple samples tagged uniquely by multiplex identifiers. As PCR-DGGE analysis is a conventional molecular ecological approach, this analysis was also performed on the same samples and the results of both approaches were compared. A total of 186,787 high-quality sequences were obtained for evaluating bacterial diversity and 41,905 unique sequences represented all phylotypes. We found that the oral microbiota in children was far more diverse than previous studies reported, and more than 200 genera belonging to ten phyla were found in the oral cavity. The phylotypes in saliva and supragingival plaques were significantly different and could be divided into two distinct clusters (p oral microbiome analyzed by PCR-DGGE and barcoded pyrosequencing was employed to cross validate the data sets. The genera of Streptococcus, Veillonella, Actinomyces, Granulicatella, Leptotrichia, and Thiomonas in plaques were significantly associated with dental caries (p oral microbiota allowed for a better understanding of oral microecosystem, and these pathogenic populations in plaque provide new insights into the etiology of dental caries and suggest new targets for interventions of the disease.
Sułowicz, Sławomir; Cycoń, Mariusz; Piotrowska-Seget, Zofia
2016-08-01
Effect of the fungicide tetraconazole on microbial community in silt loam soils from orchard with long history of triazole application and from grassland with no known history of fungicide usage was investigated. Triazole tetraconazole that had never been used on these soils before was applied at the field rate and at tenfold the FR. Response of microbial communities to tetraconazole was investigated during 28-day laboratory experiment by determination of changes in their biomass and structure (phospholipid fatty acids method-PLFA), activity (fluorescein diacetate hydrolysis-FDA) as well as changes in genetic (DGGE) and functional (Biolog) diversity. Obtained results indicated that the response of soil microorganisms to tetraconazole depended on the management of the soils. DGGE patterns revealed that both dosages of fungicide affected the structure of bacterial community and the impact on genetic diversity and richness was more prominent in orchard soil. Values of stress indices-the saturated/monounsaturated PLFAs ratio and the cyclo/monounsaturated precursors ratio, were almost twice as high and the Gram-negative/Gram-positive ratio was significantly lower in the orchard soil compared with the grassland soil. Results of principal component analysis of PLFA and Biolog profiles revealed significant impact of tetraconazole in orchard soil on day 28, whereas changes in these profiles obtained for grassland soil were insignificant or transient. Obtained results indicated that orchards soil seems to be more vulnerable to tetraconazole application compared to grassland soil. History of pesticide application and agricultural management should be taken into account in assessing of environmental impact of studied pesticides.
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Atsuo Sugano
2005-01-01
Full Text Available The succession and phylogenetic profiles of methanogenic archaeal communities associated with rice straw decomposition in rice-field soil were studied by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE analysis followed by 16S rDNA sequencing. Nylon bags containing either leaf sheaths or blades were buried in the plowed layer of a Japanese rice field under drained conditions during the off-crop season and under flooded conditions after transplanting. In addition, rice straw samples that had been buried in the rice field under drained conditions during the off-crop season were temporarily removed during spring plowing and then re-buried in the same rice field under flooded conditions at transplanting. Populations of methanogenic archaea were examined by amplification of the 16S rRNA genes in the DNA extracted from the rice straw samples. No PCR product was produced for samples of leaf sheath or blade prior to burial or after burial under drained conditions, indicating that the methanogen population was very small during decomposition of rice straw under oxic conditions. Many common bands were observed in rice straw samples of leaf sheath and blade during decomposition of rice straw under flooded conditions. Cluster analysis based on DGGE patterns divided methanogenic archaeal communities into two groups before and after the mid-season drainage. Sequence analysis of DGGE bands that were commonly present were closely related to Methanomicrobiales and Rice cluster I. Methanomicrobiales, Rice cluster I and Methanosarcinales were major members before the mid-season drainage, whereas the DGGE bands that characterized methanogenic archaeal communities after the mid-season drainage were closely related to Methanomicrobiales. These results indicate that mid-season drainage affected the methanogenic archaeal communities irrespective of their location on rice straw (sheath and blade and the previous history of decomposition
Ferrocino, Ilario; Di Cagno, Raffaella; De Angelis, Maria; Turroni, Silvia; Vannini, Lucia; Bancalari, Elena; Rantsiou, Kalliopi; Cardinali, Gianluigi; Neviani, Erasmo; Cocolin, Luca
2015-01-01
In this study, the fecal microbiota of 153 healthy volunteers, recruited from four different locations in Italy, has been studied by coupling viable counts, on different microbiological media, with ribosomal RNA Denaturing Gradient Gel Electrophoresis (rRNA-DGGE). The volunteers followed three different diets, namely omnivore, ovo-lacto-vegetarian and vegan. The results obtained from culture-dependent and -independent methods have underlined a high level of similarity of the viable fecal microbiota for the three investigated diets. The rRNA DGGE profiles were very complex and comprised a total number of bands that varied from 67 to 64 for the V3 and V9 regions of the 16S rRNA gene, respectively. Only a few bands were specific in/of all three diets, and the presence of common taxa associated with the dietary habits was found. As far as the viable counts are concerned, the high similarity of the fecal microbiota was once again confirmed, with only a few of the investigated groups showing significant differences. Interestingly, the samples grouped differently, according to the recruitment site, thus highlighting a higher impact of the food consumed by the volunteers in the specific geographical locations than that of the type of diet. Lastly, it should be mentioned that the fecal microbiota DGGE profiles obtained from the DNA were clearly separated from those produced using RNA, thus underlining a difference between the total and viable populations in the fecal samples.
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Ilario Ferrocino
Full Text Available In this study, the fecal microbiota of 153 healthy volunteers, recruited from four different locations in Italy, has been studied by coupling viable counts, on different microbiological media, with ribosomal RNA Denaturing Gradient Gel Electrophoresis (rRNA-DGGE. The volunteers followed three different diets, namely omnivore, ovo-lacto-vegetarian and vegan. The results obtained from culture-dependent and -independent methods have underlined a high level of similarity of the viable fecal microbiota for the three investigated diets. The rRNA DGGE profiles were very complex and comprised a total number of bands that varied from 67 to 64 for the V3 and V9 regions of the 16S rRNA gene, respectively. Only a few bands were specific in/of all three diets, and the presence of common taxa associated with the dietary habits was found. As far as the viable counts are concerned, the high similarity of the fecal microbiota was once again confirmed, with only a few of the investigated groups showing significant differences. Interestingly, the samples grouped differently, according to the recruitment site, thus highlighting a higher impact of the food consumed by the volunteers in the specific geographical locations than that of the type of diet. Lastly, it should be mentioned that the fecal microbiota DGGE profiles obtained from the DNA were clearly separated from those produced using RNA, thus underlining a difference between the total and viable populations in the fecal samples.
Ferrocino, Ilario; Di Cagno, Raffaella; De Angelis, Maria; Turroni, Silvia; Vannini, Lucia; Bancalari, Elena; Rantsiou, Kalliopi; Cardinali, Gianluigi; Neviani, Erasmo; Cocolin, Luca
2015-01-01
In this study, the fecal microbiota of 153 healthy volunteers, recruited from four different locations in Italy, has been studied by coupling viable counts, on different microbiological media, with ribosomal RNA Denaturing Gradient Gel Electrophoresis (rRNA-DGGE). The volunteers followed three different diets, namely omnivore, ovo-lacto-vegetarian and vegan. The results obtained from culture-dependent and -independent methods have underlined a high level of similarity of the viable fecal microbiota for the three investigated diets. The rRNA DGGE profiles were very complex and comprised a total number of bands that varied from 67 to 64 for the V3 and V9 regions of the 16S rRNA gene, respectively. Only a few bands were specific in/of all three diets, and the presence of common taxa associated with the dietary habits was found. As far as the viable counts are concerned, the high similarity of the fecal microbiota was once again confirmed, with only a few of the investigated groups showing significant differences. Interestingly, the samples grouped differently, according to the recruitment site, thus highlighting a higher impact of the food consumed by the volunteers in the specific geographical locations than that of the type of diet. Lastly, it should be mentioned that the fecal microbiota DGGE profiles obtained from the DNA were clearly separated from those produced using RNA, thus underlining a difference between the total and viable populations in the fecal samples. PMID:26035837
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Ogino, A.; Nakahara, T.
2001-01-01
Aims: The objective of this study was to investigate the changes in the indigenous bacterial community structure for assessing the impact of biostimulation on spilled oil. Methods and Results: Changes in the bacterial community structure were monitored by denaturing gradient gel electrophoresis (DGGE) and clone library methods based on 16S rRNA gene (rDNA) sequences. The results of DGGE, coupled with the use of the Shannon index and principal component analysis (PCA) and clone library analyses, were consistent. In the treated (fertilized) area, one operational taxonomic unit (OTU) became dominant during the fertilization period, and it was most closely related to Pseudomonas putida. Conclusions: The bacterial community structure in the treated area was markedly different from that in the control (non-fertilized) area during the fertilization period, but in the two areas it became similar at 14 weeks after the end of fertilization. Significance and Impact of the Study: The results suggest that the bacterial community structure was disrupted by the biostimulation treatment, but that it recovered immediately after the end of fertilization. (Author)
Application of PCR-DGGE method for identification of nematode communities in pepper growing soil
Nguyen, Thi Phuong; Ha, Duy Ngo; Nguyen, Huu Hung; Duong, Duc Hieu
2017-01-01
Soil nematodes play an important role in indication for assessing soil environments and ecosystems. Previous studies of nematode community analyses based on molecular identification have shown to be useful for assessing soil environments. Here we applied PCR-DGGE method for molecular analysis of five soil nematode communities (designed as S1 to S5) collected from four provinces in Southeastern Vietnam (Binh Duong, Ba Ria Vung Tau, Binh Phuoc and Dong Nai) based on SSU gene. By sequencing DNA ...
Lin, Xiao-Li; Pan, Qin-Jian; Tian, Hong-Gang; Douglas, Angela E; Liu, Tong-Xian
2015-03-01
Microbial abundance and diversity of different life stages (fourth instar larvae, pupae and adults) of the diamondback moth, Plutella xylostella L., collected from field and reared in laboratory, were investigated using bacteria culture-dependent method and PCR-DGGE analysis based on the sequence of bacteria 16S rRNA V3 region gene. A large quantity of bacteria was found in all life stages of P. xylostella. Field population had higher quantity of bacteria than laboratory population, and larval gut had higher quantity than pupae and adults. Culturable bacteria differed in different life stages of P. xylostella. Twenty-five different bacterial strains were identified in total, among them 20 strains were presented in larval gut, only 8 strains in pupae and 14 strains in adults were detected. Firmicutes bacteria, Bacillus sp., were the most dominant species in every life stage. 15 distinct bands were obtained from DGGE electrophoresis gel. The sequences blasted in GenBank database showed these bacteria belonged to six different genera. Phylogenetic analysis showed the sequences of the bacteria belonged to the Actinobacteri, Proteobacteria and Firmicutes. Serratia sp. in Proteobacteria was the most abundant species in larval gut. In pupae, unculturable bacteria were the most dominant species, and unculturable bacteria and Serratia sp. were the most dominant species in adults. Our study suggested that a combination of molecular and traditional culturing methods can be effectively used to analyze and to determine the diversity of gut microflora. These known bacteria may play important roles in development of P. xylostella. © 2013 Institute of Zoology, Chinese Academy of Sciences.
Wang, Hai-Feng; Zhu, Wei-Yun; Yao, Wen; Liu, Jian-Xin
2007-01-01
The effect of feeding whole crop rice (WCR) to growing-finishing pigs at three levels 0 (Control), 10% and 20% on bacterial communities in colon content and feces was analyzed using 16S rDNA-based techniques. Amplicons of the V6-V8 variable regions of bacterial 16S rDNA were analyzed by denaturing gradient gel electrophoresis (DGGE), cloning and sequencing. The total number of DGGE bands and Shannon index of diversity for feces samples were higher in the pigs fed WCR-containing diets compared with the control, while a decrease trend was observed in these two parameters for colon content samples with the inclusion of WCR in the diets, although statistical differences were not significant. In general, the intestinal bacterial communities were prone to form the cluster for pig fed the same diet. Feeding of WCR induced the presence of special DGGE band with the sequence showing 99% similarity to that of Lactobacillus reuteri (DSM 20016T). The sequences of seven amplicons in total nine clones showed less than 97% similarity with those of previously identified or unidentified bacteria, suggesting that most bacteria in gastrointestinal tracts have not been cultured or identified. The results suggest that the diet containing WCR did not affect the major groups of bacteria, but stimulated the growth of L. reuteri-like species.
Kreuzinger, N; Farnleitner, A; Wandl, G; Hornek, R; Mach, R
2003-01-01
Incomplete nitrification at an activated sludge plant for biological pre-treatment of rendering plant effluents led to a detailed investigation on the origin and solution of this problem. Preliminary studies revealed that an inhibition of ammonia oxidising microorganisms (AOM) by process waters of the rendering plant was responsible for the situation. We were able to show a correlation between the existence of specific AOM and nitrification capacity expressed as oxygen uptake rate for maximal nitrification (OURNmax). Only Nitrosospira sp. was found in the activated sludge of the rendering plant and another industrial wastewater treatment plant with problems in nitrification, while reference plants without nitrification problems showed Nitrosomonas spp. as the predominant ammonia oxidising bacteria. By accompanying engineering investigations and experiments (cross-feeding experiments, operation of a two-stage laboratory plant) with molecular biological methods (DGGE--Denaturing Gradient Gel Electrophoresis) we were able to elaborate an applicable solution for the rendering plant. Laboratory experiments with a two-stage process layout finally provided complete nitrification overcoming the inhibiting nature of process waters from the rendering plant. DGGE analysis of the second stage activated sludge from the laboratory plant showed a shift in population structure from Nitrosospira sp. towards Nitrosomonas spp. simultaneous to the increase of nitrification capacity. Nitrification capacities comparable to full-scale municipal wastewater treatment plants could be maintained for more than two months. As the design of wastewater treatment plants for nitrification is linked to the growth characteristics of Nitrosomonas spp., established criteria can be applied for the redesign of the full-scale plant.
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Ai-dong Ruan
2015-10-01
Full Text Available Solid or liquid waste containing a high concentration of nicotine can pollute sediment in rivers and lakes, and may destroy the ecological balance if it is directly discharged into the environment without any treatment. In this study, the polymerase chain reaction (PCR and denaturing gradient gel electrophoresis (DGGE method was used to analyze the variation of the microbial community structure in the control and nicotine-contaminated sediment samples with nicotine concentration and time of exposure. The results demonstrated that the growth of some bacterial species in the nicotine-contaminated sediment samples was inhibited during the exposure. Some bacteria decreased in species diversity and in quantity with the increase of nicotine concentration or time of exposure, while other bacteria were enriched under the effect of nicotine, and their DGGE bands changed from undertones to deep colors. The microbial community structure, however, showed a wide variation in the nicotine-contaminated sediment samples, especially in the sediment samples treated with high-concentration nicotine. The Jaccard index was only 35.1% between the initial sediment sample and the sediment sample with a nicotine concentration of 0.030 μg/g after 28 d of exposure. Diversity indices showed that the contaminated groups had a similar trend over time. The diversity indices of contaminated groups all decreased in the first 7 d after exposure, then increased until day 42. It has been found that nicotine decreased the diversity of the microbial community in the sediment.
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Ai-dong Ruan
2015-10-01
Full Text Available Solid or liquid waste containing a high concentration of nicotine can pollute sediment in rivers and lakes, and may destroy the ecological balance if it is directly discharged into the environment without any treatment. In this study, the polymerase chain reaction (PCR and denaturing gradient gel electrophoresis (DGGE method was used to analyze the variation of the microbial community structure in the control and nicotine-contaminated sediment samples with nicotine concentration and time of exposure. The results demonstrated that the growth of some bacterial species in the nicotine-contaminated sediment samples was inhibited during the exposure. Some bacteria decreased in species diversity and in quantity with the increase of nicotine concentration or time of exposure, while other bacteria were enriched under the effect of nicotine, and their DGGE bands changed from undertones to deep colors. The microbial community structure, however, showed a wide variation in the nicotine-contaminated sediment samples, especially in the sediment samples treated with high-concentration nicotine. The Jaccard index was only 35.1% between the initial sediment sample and the sediment sample with a nicotine concentration of 0.030 μg/g after 28 d of exposure. Diversity indices showed that the contaminated groups had a similar trend over time. The diversity indices of contaminated groups all decreased in the first 7 d after exposure, then increased until day 42. It has been found that nicotine decreased the diversity of the microbial community in the sediment.
Bao, Zhihua; Ikunaga, Yoko; Matsushita, Yuko; Morimoto, Sho; Takada-Hoshino, Yuko; Okada, Hiroaki; Oba, Hirosuke; Takemoto, Shuhei; Niwa, Shigeru; Ohigashi, Kentaro; Suzuki, Chika; Nagaoka, Kazunari; Takenaka, Makoto; Urashima, Yasufumi; Sekiguchi, Hiroyuki; Kushida, Atsuhiko; Toyota, Koki; Saito, Masanori; Tsushima, Seiya
2012-01-01
We simultaneously examined the bacteria, fungi and nematode communities in Andosols from four agro-geographical sites in Japan using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and statistical analyses to test the effects of environmental factors including soil properties on these communities depending on geographical sites. Statistical analyses such as Principal component analysis (PCA) and Redundancy analysis (RDA) revealed that the compositions of the three soil biota communities were strongly affected by geographical sites, which were in turn strongly associated with soil characteristics such as total C (TC), total N (TN), C/N ratio and annual mean soil temperature (ST). In particular, the TC, TN and C/N ratio had stronger effects on bacterial and fungal communities than on the nematode community. Additionally, two-way cluster analysis using the combined DGGE profile also indicated that all soil samples were classified into four clusters corresponding to the four sites, showing high site specificity of soil samples, and all DNA bands were classified into four clusters, showing the coexistence of specific DGGE bands of bacteria, fungi and nematodes in Andosol fields. The results of this study suggest that geography relative to soil properties has a simultaneous impact on soil microbial and nematode community compositions. This is the first combined profile analysis of bacteria, fungi and nematodes at different sites with agricultural Andosols.
Delgado, Susana; Rachid, Caio T C C; Fernández, Elena; Rychlik, Tomasz; Alegría, Angel; Peixoto, Raquel S; Mayo, Baltasar
2013-10-01
Thermophilic lactic acid bacteria (LAB) species, such as Streptococcus thermophilus, Lactobacillus delbrueckii and Lactobacillus helveticus, enjoy worldwide economic importance as dairy starters. To assess the diversity of thermophilic bacteria in milk, milk samples were enriched in thermophilic organisms through a stepwise procedure which included pasteurization of milk at 63 °C for 30 min (PM samples) and pasteurization followed by incubation at 42 °C for 24 h (IPM samples). The microbial composition of these samples was analyzed by culture-dependent (at 42 °C) and culture-independent (PCR-DGGE and pyrosequencing of 16S rRNA gene amplicons) microbial techniques. The results were then compared to those obtained for their corresponding starting raw milk counterparts (RM samples). Twenty different species were scored by culturing among 352 isolates purified from the counting plates and identified by molecular methods. Mesophilic LAB species (Lactococcus lactis, Lactococcus garvieae) were dominant (87% of the isolates) among the RM samples. However, S. thermophilus and Lb. delbrueckii were found to be the dominant recoverable organisms in both PM and IPM samples. The DGGE profiles of RM and PM samples were found to be very similar; the most prominent bands belonging to Lactococcus, Leuconostoc and Streptococcus species. In contrast, just three DGGE bands were obtained for IPM samples, two of which were assigned to S. thermophilus. The pyrosequencing results scored 95 operational taxonomic units (OTUs) at 3% sequence divergence in an RM sample, while only 13 were encountered in two IPM samples. This technique identified Leuconostoc citreum as the dominant microorganism in the RM sample, while S. thermophilus constituted more than 98% of the reads in the IPM samples. The procedure followed in this study allowed to estimate the bacterial diversity in milk and afford a suitable strategy for the isolation of new thermophilic LAB strains, among which adequate
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Mathew, G.M.
2011-01-01
Full Text Available Aims: Termites thrive in terrestrial ecosystems and play an important role in the bio-recycling of lignocellulose. The objective of this study is to isolate and detect bacteria from the termite gut of Coptotermes formosanus and to screen their various enzyme activities by qualitative methods. In addition, this study was aimed to isolate lignin and furfural tolerant strains for various industrial bioprocesses.Methodology and Results: In this study, 50 worker termites of Coptotermes formosanus were collected from dead trees, from a forest in Taichung, Taiwan in June 2008 and the composition of the microbial flora from the termite guts was analyzed by DGGE analysis. The results proved that anaerobic and facultatively anaerobic bacteria consisting of Acinetobacter, Bacteroides thetaiotaomicron, Escherichia coli, and Caulobacter readily existed in the guts of termites. Although the majority of these gut symbionts have not yet been cultivated or identified, some related bacteria were isolated. Two isolates 1-8 and 2-2 of Genus Bacillus, exhibited endocellulase, protease, lipase, amylase, peroxidase and lignin peroxidase activity. Under aerobic conditions, the growth density of isolate 1-8 cultured in 1000 ppm lignin containing MSM medium was two-folds higher than cultured in MSM medium without lignin. Furthermore, the isolate 1-8 was tolerant to 20 mM furfural supplemented in the MSM medium. HPLC analysis confirmed Bacillus isolate 1-8 could degrade up to 15 mM furfural.Conclusion, significance and impact of study: Hind gut bacteria from C. formosanus were detected by culture independent DGGE method. Also, Bacillus isolates 1-8 and 2-2 obtained by culture dependent methods could withstand higher concentration of furfural and as well as lignin. These isolates may be co-cultured with ethanologenic bacteria and be used as an industrial biocatalyst for biofuel production.
Li, Hong; Guan, Rui; Sun, Jinghua; Hou, Benxiang
2014-10-01
The entire microbial population and predominant microflora of root canals (RCs) and adjacent periodontal pockets (PPs) from teeth with combined periodontal-endodontic lesions were determined and compared. Pooled RC and PP samples were collected from the molars of 20 patients diagnosed with combined periodontal-endodontic lesions. DNA was extracted for polymerase chain reaction-based denaturing gradient gel electrophoresis (PCR-DGGE), cloning, and sequence analysis. A coefficient of similarity (Cs) was used to determine the similarity of the bacterial profiles from RCs and PPs. Significantly fewer bands were produced by PCR-DGGE from RCs (5.9 ± 1.7) than from PPs (8.0 ± 1.8) (P bacteria in both the RC and PP samples were (in descending order) Filifactor alocis, Parvimonas micra, Porphyromonas gingivalis, and Tannerella forsythia. The high similarity in the sets of organisms present in both RC and PP samples in this study suggests that the pocket could be a source of RC infection. The data also demonstrate that combined periodontal-endodontic lesions consist of a diverse and complex microbial community.
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David A. Potts
2013-04-01
Full Text Available Soil-based wastewater treatment systems, or leachfields, rely on microbial processes for improving the quality of wastewater before it reaches the groundwater. These processes are affected by physicochemical system properties, such as O2 availability, and disturbances, such as the presence of antimicrobial compounds in wastewater. We examined the microbial community structure of leachfield mesocosms containing native soil and receiving domestic wastewater under intermittently-aerated (AIR and unaerated (LEACH conditions before and after dosing with tetracycline (TET. Community structure was assessed using phospholipid fatty acid analysis (PLFA, analysis of dominant phylotypes using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR–DGGE, and cloning and sequencing of 16S rRNA genes. Prior to dosing, the same PLFA biomarkers were found in soil from AIR and LEACH treatments, although AIR soil had a larger active microbial population and higher concentrations for nine of 32 PLFA markers found. AIR soil also had a larger number of dominant phylotypes, most of them unique to this treatment. Dosing of mesocosms with TET had a more marked effect on AIR than LEACH soil, reducing the size of the microbial population and the number and concentration of PLFA markers. Dominant phylotypes decreased by ~15% in response to TET in both treatments, although the AIR treatment retained a higher number of phylotypes than the LEACH treatment. Fewer than 10% of clones were common to both OPEN ACCESS Water 2013, 5 506 AIR and LEACH soil, and fewer than 25% of the clones from either treatment were homologous with isolates of known genus and species. These included human pathogens, as well as bacteria involved in biogeochemical transformations of C, N, S and metals, and biodegradation of various organic contaminants. Our results show that intermittent aeration has a marked effect on the size and structure of the microbial community that develops in
Jousset, Alexandre; Lara, Enrique; Nikolausz, Marcell; Harms, Hauke; Chatzinotas, Antonis
2010-02-01
Ciliates (or Ciliophora) are ubiquitous organisms which can be widely used as bioindicators in ecosystems exposed to anthropogenic and industrial influences. The evaluation of the environmental impact on soil ciliate communities with methods relying on morphology-based identification may be hampered by the large number of samples usually required for a statistically supported, reliable conclusion. Cultivation-independent molecular-biological diagnostic tools are a promising alternative to greatly simplify and accelerate such studies. In this present work a ciliate-specific fingerprint method based on the amplification of a phylogenetic marker gene (i.e. the 18S ribosomal RNA gene) with subsequent analysis by denaturing gradient gel electrophoresis (DGGE) was developed and used to monitor community shifts in a polycyclic aromatic hydrocarbon (PAH) polluted soil. The semi-nested approach generated ciliate-specific amplification products from all soil samples and allowed to distinguish community profiles from a PAH-polluted and a non-polluted control soil. Subsequent sequence analysis of excised bands provided evidence that polluted soil samples are dominated by organisms belonging to the class Colpodea. The general DGGE approach presented in this study might thus in principle serve as a fast and reproducible diagnostic tool, complementing and facilitating future ecological and ecotoxicological monitoring of ciliates in polluted habitats. Copyright 2009 Elsevier B.V. All rights reserved.
Xia, Minghui; Qi, Qingguo
2013-01-01
We used denaturing gradient gel electrophoresis (DGGE) to compare bacterial profiles in periodontium and root canals of teeth with combined periodontal-endodontic lesions. Samples of dental plaque and necrotic pulp were collected from thirteen extracted teeth with advanced periodontitis. Genomic DNA was extracted for polymerase chain reaction (PCR) analysis using universal bacterial primers. The PCR products were then loaded onto DGGE gels to obtain fractionated bands. Characteristic DGGE bands were excised and DNA was cloned and sequenced. The number of bands, which indicates the number of bacterial species, was compared between dental plaques and necrotic pulp tissues from the same tooth. Although the difference was statistically significant (P bacteria species were present in both the periodontal pockets and root canals of the same tooth; however, periodontal bacteria did not always invade the root canals, and some bacteria in root canals were not present in periodontal pockets of the same tooth. In some teeth, unique bacteria in root canals had not passed from periodontal pockets. A basic local alignment search tool (BLAST) sequence search in Genbank indicated that new bacteria species were present in periodontal pockets and root canals. Their characteristics must thus be further analyzed.
Urashima, Yasufumi; Sonoda, Takahiro; Fujita, Yuko; Uragami, Atsuko
2012-01-01
Growth inhibition due to continuous cropping of asparagus is a major problem; the yield of asparagus in replanted fields is low compared to that in new fields, and missing plants occur among young seedlings. Although soil-borne disease and allelochemicals are considered to be involved in this effect, this is still controversial. We aimed to develop a technique for the biological field diagnosis of growth inhibition due to continuous cropping. Therefore, in this study, fungal community structure and Fusarium community structure in continuously cropped fields of asparagus were analyzed by polymerase chain reaction/denaturing-gradient gel electrophoresis (PCR-DGGE). Soil samples were collected from the Aizu region of Fukushima Prefecture, Japan. Soil samples were taken from both continuously cropped fields of asparagus with growth inhibition and healthy neighboring fields of asparagus. The soil samples were collected from the fields of 5 sets in 2008 and 4 sets in 2009. We were able to distinguish between pathogenic and non-pathogenic Fusarium by using Alfie1 and Alfie2GC as the second PCR primers and PCR-DGGE. Fungal community structure was not greatly involved in the growth inhibition of asparagus due to continuous cropping. By contrast, the band ratios of Fusarium oxysporum f. sp. asparagi in growth-inhibited fields were higher than those in neighboring healthy fields. In addition, there was a positive correlation between the band ratios of Fusarium oxysporum f. sp. asparagi and the ratios of missing asparagus plants. We showed the potential of biological field diagnosis of growth inhibition due to continuous cropping of asparagus using PCR-DGGE.
Cocolin, L; Manzano, M; Aggio, D; Cantoni, C; Comi, G
2001-05-01
A new molecular method consisting of polymerase chain reaction (PCR) amplification and denaturing gradient gel electrophoresis (DGGE) of a small fragment from the 16S rRNA gene identified the Micrococcaceae strains isolated from natural fermented Italian sausages. Lactic acid bacteria, total aerobic mesophilic flora, Enterobacteriaceae and faecal enterococci were also monitored. Micrococcaceaea control strains from international collections were used to optimise the method and 90 strains, isolated from fermented sausages, were identified by biochemical tests and PCR-DGGE. No differences were observed between the methods used. The results reported in this paper prove that Staphylococcus xylosus is the main bacterium involved in fermented sausage production, representing, from the tenth day of ripening, the only Micrococcaceaea species isolated.
Osimani, Andrea; Milanović, Vesna; Garofalo, Cristiana; Cardinali, Federica; Roncolini, Andrea; Sabbatini, Riccardo; De Filippis, Francesca; Ercolini, Danilo; Gabucci, Claudia; Petruzzelli, Annalisa; Tonucci, Franco; Clementi, Francesca; Aquilanti, Lucia
2018-07-02
The present study aimed to identify the microbiota present in six species of processed edible insects produced in Thailand and marketed worldwide via the internet, namely, giant water bugs (Belostoma lutarium), black ants (Polyrhachis), winged termites (alates, Termitoidae), rhino beetles (Hyboschema contractum), mole crickets (Gryllotalpidae), and silkworm pupae (Bombyx mori). For each species, two samples of boiled, dried and salted insects were purchased. The microbial DNA was extracted from the insect samples and subjected to polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), high-throughput sequencing and qualitative real-time PCR assays. The microbiota of the analyzed samples were widely characterized by the presence of spore-forming bacteria mainly represented by the genera Bacillus and Clostridium. Moreover, the genera Anaerobacillus, Paenibacillus, Geobacillus, Pseudomonas, Stenotrophomonas, Massilia, Delftia, Lactobacillus, Staphylococcus, Streptococcus, Vagococcus, and Vibrio were also detected. Real-time PCR allowed for ascertainment of the absence of Coxiella burnetii, Shiga toxin-producing E. coli (STEC), and Pseudomonas aeruginosa in all samples. The results of this study confirm the importance of combining different molecular techniques to characterize the biodiversity of complex ecosystems such as edible insects. The presence of potential human pathogens suggests the need for a careful application of good manufacturing practices during insect processing. This study provides further data that will be useful in risk analyses of edible insects as a novel food source. Copyright © 2018 Elsevier B.V. All rights reserved.
Li, Meiju; Zhou, Mi; Adamowicz, Elizabeth; Basarab, John A; Guan, Le Luo
2012-02-24
Currently, knowledge regarding the ecology and function of bacteria attached to the epithelial tissue of the rumen wall is limited. In this study, the diversity of the bacterial community attached to the rumen epithelial tissue was compared to the rumen content bacterial community using 16S rRNA gene sequencing, PCR-DGGE, and qRT-PCR analysis. Sequence analysis of 2785 randomly selected clones from six 16S rDNA (∼1.4kb) libraries showed that the community structures of three rumen content libraries clustered together and were separated from the rumen tissue libraries. The diversity index of each library revealed that ruminal content bacterial communities (4.12/4.42/4.88) were higher than ruminal tissue communities (2.90/2.73/3.23), based on 97% similarity. The phylum Firmicutes was predominant in the ruminal tissue communities, while the phylum Bacteroidetes was predominant in the ruminal content communities. The phyla Fibrobacteres, Planctomycetes, and Verrucomicrobia were only detected in the ruminal content communities. PCR-DGGE analysis of the bacterial profiles of the rumen content and ruminal epithelial tissue samples from 22 steers further confirmed that there is a distinct bacterial community that inhibits the rumen epithelium. The distinctive epimural bacterial communities suggest that Firmicutes, together with other epithelial-specific species, may have additional functions other than food digestion. Copyright © 2011 Elsevier B.V. All rights reserved.
Han, Pei-pei; Shen, Shi-gang; Jia, Shi-ru; Wang, Hui-yan; Zhong, Cheng; Tan, Zhi-lei; Lv, He-xin
2015-07-01
Filamentous Nostoc flagelliforme form colloidal complex, with beaded cells interacting with other bacteria embedded in the complex multilayer sheath. However, the species of bacteria in the sheath and the interaction between N. flagelliforme and associated bacteria remain unclear. In this study, PCR-denaturing gradient gel electrophoresis (DGGE) was used to investigate the bacterial communities of N. flagelliforme from three regions of China. DGGE patterns showed variations in all samples, exhibiting 25 discrete bands with various intensities. The diversity index analysis of bands profiles suggested the high similarity of bacterial communities to each other but also the dependence of microbial composition on each location. Phylogenetic affiliation indicated that the majority of the sequences obtained were affiliated with Actinobacteria, Cyanobacteria, Proteobacteria, Acidobacteria, Bacteroidetes, of which Cyanobacteria was dominant, followed the Proteobacteria. Members of the genus Nostoc were the most abundant in all samples. Rhizobiales and Actinobacteria were identified, whereas, Craurococcus, Caulobacter, Pseudomonas, Terriglobus and Mucilaginibacter were also identified at low levels. Through comparing the bacterial composition of N. flagelliforme from different regions, it was revealed that N. flagelliforme could facilitate the growth of other microorganisms including both autotrophic bacteria and heterotrophic ones and positively contributed to their harsh ecosystems. The results indicated N. flagelliforme played an important role in diversifying the microbial community composition and had potential application in soil desertification.
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Jutta Zwielehner
Full Text Available BACKGROUND: We investigated whether chemotherapy with the presence or absence of antibiotics against different kinds of cancer changed the gastrointestinal microbiota. METHODOLOGY/PRINCIPAL FINDINGS: Feces of 17 ambulant patients receiving chemotherapy with or without concomitant antibiotics were analyzed before and after the chemotherapy cycle at four time points in comparison to 17 gender-, age- and lifestyle-matched healthy controls. We targeted 16S rRNA genes of all bacteria, Bacteroides, bifidobacteria, Clostridium cluster IV and XIVa as well as C. difficile with TaqMan qPCR, denaturing gradient gel electrophoresis (DGGE fingerprinting and high-throughput sequencing. After a significant drop in the abundance of microbiota (p = 0.037 following a single treatment the microbiota recovered within a few days. The chemotherapeutical treatment marginally affected the Bacteroides while the Clostridium cluster IV and XIVa were significantly more sensitive to chemotherapy and antibiotic treatment. DGGE fingerprinting showed decreased diversity of Clostridium cluster IV and XIVa in response to chemotherapy with cluster IV diversity being particularly affected by antibiotics. The occurrence of C. difficile in three out of seventeen subjects was accompanied by a decrease in the genera Bifidobacterium, Lactobacillus, Veillonella and Faecalibacterium prausnitzii. Enterococcus faecium increased following chemotherapy. CONCLUSIONS/SIGNIFICANCE: Despite high individual variations, these results suggest that the observed changes in the human gut microbiota may favor colonization with C. difficile and Enterococcus faecium. Perturbed microbiota may be a target for specific mitigation with safe pre- and probiotics.
Directory of Open Access Journals (Sweden)
Meldrum Cliff J
2003-12-01
Full Text Available Abstract Denaturing high performance liquid chromatography is a relatively new method by which heteroduplex structures formed during the PCR amplification of heterozygote samples can be rapidly identified. The use of this technology for mutation detection in hereditary non-polyposis colorectal cancer (HNPCC has the potential to appreciably shorten the time it takes to analyze genes associated with this disorder. Prior to acceptance of this method for screening genes associated with HNPCC, assessment of the reliability of this method should be performed. In this report we have compared mutation and polymorphism detection by denaturing gradient gel electrophoresis (DGGE with denaturing high performance liquid chromatography (DHPLC in a set of 130 families. All mutations/polymorphisms representing base substitutions, deletions, insertions and a 23 base pair inversion were detected by DHPLC whereas DGGE failed to identify four single base substitutions and a single base pair deletion. In addition, we show that DHPLC has been used for the identification of 5 different mutations in exon 7 of hMSH2 that could not be detected by DGGE. From this study we conclude that DHPLC is a more effective and rapid alternative to the detection of mutations in hMSH2 and hMLH1 with the same or better accuracy than DGGE. Furthermore, this technique offers opportunities for automation, which have not been realised for the majority of other methods of gene analysis.
Ling, Juan; Zhang, Yan-Ying; Dong, Jun-De; Wang, You-Shao; Feng, Jing-Bing; Zhou, Wei-Hua
2015-10-01
Bacteria play important roles in the structure and function of marine food webs by utilizing nutrients and degrading the pollutants, and their distribution are determined by surrounding water chemistry to a certain extent. It is vital to investigate the bacterial community's structure and identifying the significant factors by controlling the bacterial distribution in the paper. Flow cytometry showed that the total bacterial abundance ranged from 5.27 × 10(5) to 3.77 × 10(6) cells/mL. Molecular fingerprinting technique, denaturing gradient gel electrophoresis (DGGE) followed by DNA sequencing has been employed to investigate the bacterial community composition. The results were then interpreted through multivariate statistical analysis and tended to explain its relationship to the environmental factors. A total of 270 bands at 83 different positions were detected in DGGE profiles and 29 distinct DGGE bands were sequenced. The predominant bacteria were related to Phyla Protebacteria species (31 %, nine sequences), Cyanobacteria (37.9 %, eleven sequences) and Actinobacteria (17.2 %, five sequences). Other phylogenetic groups identified including Firmicutes (6.9 %, two sequences), Bacteroidetes (3.5 %, one sequences) and Verrucomicrobia (3.5 %, one sequences). Conical correspondence analysis was used to elucidate the relationships between the bacterial community compositions and environmental factors. The results showed that the spatial variations in the bacterial community composition was significantly related to phosphate (P = 0.002, P < 0.01), dissolved organic carbon (P = 0.004, P < 0.01), chemical oxygen demand (P = 0.010, P < 0.05) and nitrite (P = 0.016, P < 0.05). This study revealed the spatial variations of bacterial community and significant environmental factors driving the bacterial composition shift. These results may be valuable for further investigation on the functional microbial structure and expression quantitatively under the polluted
Monitoring Biological Activity at Geothermal Power Plants
Energy Technology Data Exchange (ETDEWEB)
Peter Pryfogle
2005-09-01
The economic impact of microbial growth in geothermal power plants has been estimated to be as high as $500,000 annually for a 100 MWe plant. Many methods are available to monitor biological activity at these facilities; however, very few plants have any on-line monitoring program in place. Metal coupon, selective culturing (MPN), total organic carbon (TOC), adenosine triphosphate (ATP), respirometry, phospholipid fatty acid (PLFA), and denaturing gradient gel electrophoresis (DGGE) characterizations have been conducted using water samples collected from geothermal plants located in California and Utah. In addition, the on-line performance of a commercial electrochemical monitor, the BIoGEORGE?, has been evaluated during extended deployments at geothermal facilities. This report provides a review of these techniques, presents data on their application from laboratory and field studies, and discusses their value in characterizing and monitoring biological activities at geothermal power plants.
Assessment of the bacterial community of soils contaminated with used lubricating oil by PCR-DGGE
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Naruemon Meeboon
2016-12-01
Full Text Available The diversity of indigenous bacteria in three soils contaminated with used lubricating oil (ULO was determined and compared using molecular analysis of bacteria cultured during the enrichment process. Sequencing analyses demonstrated that the majority of the DGGE bands in enrichment cultures were affiliated with four phyla of the domain, Bacteria: α, β, γ- Proteobacteria, Bacteroidetes, Firmicutes and Actinobacteria. Soil C had a higher ULO contamination level than soil A and B, which may explain why enrichment culture C had the greatest diversity of bacteria, but further studies would be needed to determine whether ULO concentration results in higher diversity of ULO-degraders in soils. The diversity of ULO-degraders detected in these three different soils suggests that biostimulation methods for increasing the activity of indigenous microorganisms may be a viable approach to bioremediation, and that future studies to determine how to increase their activity in situ are warranted.
Aydin, Sevcan
2016-07-01
While anaerobic treatment is capable of treating pharmaceutical wastewater and removing antibiotics in liquid phases, solid phases may still contain significant amounts of antibiotics following this treatment. The main goal of this study was to evaluate the use of white-rot fungi to remove erythromycin, sulfamethoxazole, and tetracycline combinations from biosolids. The degradation potential of Trametes versicolor and Bjerkandera adusta was evaluated via the sequential treatment of anaerobic sludge. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analyses were used to identify competition between the autochthonous microbial communities and white-rot fungi. Solid-phase treatment using white-rot fungi substantially reduced antibiotic concentrations and toxicity in sludge. According to PCR-DGGE results, there is an association between species of fungus and antibiotic type as a result of the different transformation pathways of fungal strains. Fungal post-treatment of sludge represents a promising method of removing antibiotic combinations, therefore holding a significant promise as an environmentally friendly means of degrading the antibiotics present in sludge.
Chen, Yin; Dumont, Marc G; McNamara, Niall P; Chamberlain, Paul M; Bodrossy, Levente; Stralis-Pavese, Nancy; Murrell, J Colin
2008-02-01
The active methanotroph community was investigated for the first time in heather (Calluna)-covered moorlands and Sphagnum/Eriophorum-covered UK peatlands. Direct extraction of mRNA from these soils facilitated detection of expression of methane monooxygenase genes, which revealed that particulate methane monooxygenase and not soluble methane monooxygenase was probably responsible for CH(4) oxidation in situ, because only pmoA transcripts (encoding a subunit of particulate methane monooxygenase) were readily detectable. Differences in methanotroph community structures were observed between the Calluna-covered moorland and Sphagnum/Eriophorum-covered gully habitats. As with many other Sphagnum-covered peatlands, the Sphagnum/Eriophorum-covered gullies were dominated by Methylocystis. Methylocella and Methylocapsa-related species were also present. Methylobacter-related species were found as demonstrated by the use of a pmoA-based diagnostic microarray. In Calluna-covered moorlands, in addition to Methylocella and Methylocystis, a unique group of peat-associated type I methanotrophs (Gammaproteobacteria) and a group of uncultivated type II methanotrophs (Alphaproteobacteria) were also found. The pmoA sequences of the latter were only distantly related to Methylocapsa and also to the RA-14 group of methanotrophs, which are believed to be involved in oxidation of atmospheric concentrations of CH(4). Soil samples were also labelled with (13)CH(4), and subsequent analysis of the (13)C-labelled phospholipid fatty acids (PLFAs) showed that 16:1 omega 7, 18:1 omega 7 and 18:1 omega 9 were the major labelled PLFAs. The presence of (13)C-labelled 18:1 omega 9, which was not a major PLFA of any extant methanotrophs, indicated the presence of novel methanotrophs in this peatland.
Lan, Mu-ling; Gao, Ming
2015-11-01
Based on rice, wheat, corn straw and rape, broad bean green stalk as the research object, using phospholipid fatty acid (PLFA) method, combining principal component analysis method to study the soil microbial quantity, distribution of flora, community structure characteristics under dry and water farming as two different cultivated land use types. The PLFA analysis results showed that: under dry farming, total PLFA quantity ranged 8.35-25.15 nmol x g(-1), showed rape > broad bean > corn > rice > wheat, rape and broad bean significantly increased total PLFA quantity by 1.18 and 1.08 times compared to the treatment without straw; PLFA quantity of bacterial flora in treatments with straws was higher than that without straw, and fungal biomass was significantly increased, so was the species richness of microbial community. Under water faming, the treatments of different straws returning with landfill have improved the PLFA quantity of total soil microbial and flora comparing with the treatment without straw, fungi significantly increased, and species richness of microbial communities value also increased significantly. Total PLFA quantity ranged 4.04-22.19 nmol x g(-1), showed rice > corn > wheat > broad bean > rape, which in rape and broad bean treatments were lower than the treatment without straw; fungal PLFA amount in 5 kinds of straw except broad bean treatment was significantly higher than that of the treatment without straw, bacteria and total PLFA quantity in broad bean processing were significantly lower than those of other treatments, actinomycetes, G+, G- had no significant difference between all treatments; rice, wheat, corn, rape could significantly increase the soil microbial species richness index and dominance index under water faming. The results of principal component analysis showed that broad bean green stalk had the greatest impact on the microbial community structure in the dry soil, rape green stalk and wheat straw had the biggest influence on
Transfer of bacteria between stainless steel and chicken meat: A CLSM and DGGE study of biofilms
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Christine C. Gaylarde
2016-08-01
Full Text Available This study aimed to assess the interaction between bacteria and food processing surfaces using novel methods. Microbial cross contamination between stainless steel, a common food processing material, and raw chicken was studied using microbiological culture, specialized microscope and molecular techniques. Confocal laser scanning microscopy (CLSM allowed the visualization of biofilms containing single or dual species of Escherichia coli O157:H7, Salmonella typhimurium, Bacillus cereus, Staphylococcus aureus and Pseudomonas aeruginosa, formed after 6 days’ incubation on stainless steel or 4h on raw chicken. The results provided information on intra-biofilm location and stratification of species within dual species biofilms. Top-to-bottom Z-stack images revealed that, on both materials, S. typhimurium and E. coli attached concurrently, the former in greater numbers. E. coli and B. cereus segregated on steel, E. coli more frequent near the metal surface, B. cereus almost the only species in outer layers. Few cells of S. aureus, found at all depths, were seen in the 2.9 µm thick biofilm on steel with E. coli. Greatest attachment was shown by P. aeruginosa, followed by S. typhimurium, E. coli and finally Gram positive species. Large amounts of EPS in P. aeruginosa biofilms made visualization difficult on both materials, but especially on chicken meat, a limitation of this technique. Nevertheless, CLSM was useful for determining time sequence of adhesion and species makeup of thin biofilms. The technique showed that five min contact between bacterially-contaminated chicken and sterile steel resulted in greatest transfer of P. aeruginosa, followed by S. typhimurium. This was confirmed using DGGE. Gram positive bacteria transferred poorly. A biofilm containing 2.3 × 105 cfu·cm−2 B. cereus on steel transferred an undetectable number of cells to chicken after 5 min contact. This species was unable to form biofilm on chicken when incubated for 4 h
Zhang, Hong; Jiang, Yong-jun; Zhang, Yuan-zhu; Duan, Yi-fan; Lü, Xian-fu; He, Qiu-fang
2016-05-15
Microbial contamination in karst groundwater continually increases and tracing the source researches has become a hot topic for international researchers. In this study, Laolongdong underground river at Nanshan, Chongqing was chosen as an example to adopt filter membrane methods to monitor the fecal microbial contaminations including the total bacterial concentration (TB), the total E. coli concentration (TE), the total fecal coliform (FC) and the total fecal Streptocoocci (FS). Bacteriodes was used as an indicator and PCR-DGGE analysis was used to trace fecal contamination sources in karst groundwater. The results suggested that groundwater in this area was seriously polluted by microbes from feces. The concentrations of microbial parameters exceeded limited levels greatly and the total bacterial amounts ranged 10-2.9 x 10⁷ CFU · mL⁻¹, the concentrations of E. coli were between 4.3-4.0 x 10⁵ CFU · mL⁻¹, the max concentration of FC was 1.1 x 10⁶ CFU · (100 mL)⁻¹ and the max concentration of FS was 1.1 x 10⁵ CFU · (100 mL)⁻¹. The FC/FS ratios were mostly over 2 which suggested that the main fecal source in groundwater was human feces. In addition, PCR-DGGE contrastive analysis of Bacteroides communities showed that the similarities between groundwater samples and human feces were in range of 7. 1% -69. 1% , and the similarity of the groundwater sample from Laolongdong underground river outlet was 69.1% . Bacteroides community similarities between groundwater samples and swine feces were in range of 1.1%-53.4%, and the similarity of Laolongdong underground river outlet was merely 1.5%. The similarity data implied that groundwater contamination resulted mainly from human feces, swine feces contamination composed part of animals' fecal contamination, and other animals' feces participated too. Furthermore, sequencing results of PCR-DGGE products revealed that most Bacteroides in groundwater originated from human intestinal tract and human feces.
Differential Utilization of Carbon Substrates by Bacteria and Fungi in Tundra Soil
DEFF Research Database (Denmark)
Rinnan, Riikka; Bååth, Erland
2009-01-01
Little is known about the contribution of bacteria and fungi to decomposition of different carbon compounds in arctic soils, which are an important carbon store and possibly vulnerable to climate warming. Soil samples from a subarctic tundra heath were incubated with 13C-labeled glucose, acetic...... at concentrations low enough not to affect the total amount of PLFA. The label of glucose and acetic acid was rapidly incorporated into the PLFA in a pattern largely corresponding to the fatty acid concentration profile, while glycine and especially starch were mainly taken up by bacteria and not fungi, showing......, the allocation decreased over time, indicating use of the storage products, whereas for vanillin incorporation into fungal NLFA increased during the incubation. In addition to providing information on functioning of the microbial communities in an arctic soil, our study showed that the combination of PLFA...
Domingues, Patrícia M; Louvado, António; Oliveira, Vanessa; Coelho, Francisco J C R; Almeida, Adelaide; Gomes, Newton C M; Cunha, Angela
2013-01-01
The potential of estuarine microniches as reservoirs of biosurfactant-producing bacteria was evaluated by testing different combinations of inocula and hydrophobic carbon sources. Selective cultures using diesel, petroleum, or paraffin as hydrophobic carbon sources were prepared and inoculated with water from the surface microlayer, bulk sediments, and sediment of the rhizosphere of Halimione portulacoides. These inocula were compared regarding the frequency of biosurfactant-producing strains among selected isolates. The community structure of the selective cultures was profiled using denaturing gradient gel electrophoresis (DGGE) of the 16S rRNA gene fragments at the end of the incubation. The DGGE profiles corresponding to the communities established in selective cultures at the end of the incubation revealed that communities were different in terms of structural diversity. The highest diversity was observed in the selective cultures containing paraffin (H (') = 2.5). Isolates were obtained from the selective cultures (66) and tested for biosurfactant production by the atomized oil assay. Biosurfactant production was detected in 17 isolates identified as Microbacterium, Pseudomonas, Rhodococcus, and Serratia. The combination of estuarine surface microlayer (SML) water as inoculum and diesel as carbon source seems promising for the isolation of surfactant-producing bacteria. Supplemental materials are available for this article. Go to the publisher's online edition of Preparative Biochemistry and Biotechnology to view the supplemental file.
Xu, Zhenqiang; Yao, Maosheng
2013-05-01
Increasing evidences show that inhalation of indoor bioaerosols has caused numerous adverse health effects and diseases. However, the bioaerosol size distribution, composition, and concentration level, representing different inhalation risks, could vary with different living environments. The six-stage Andersen sampler is designed to simulate the sampling of different human lung regions. Here, the sampler was used in investigating the bioaerosol exposure in six different environments (student dorm, hospital, laboratory, hotel room, dining hall, and outdoor environment) in Beijing. During the sampling, the Andersen sampler was operated for 30 min for each sample, and three independent experiments were performed for each of the environments. The air samples collected onto each of the six stages of the sampler were incubated on agar plates directly at 26 °C, and the colony forming units (CFU) were manually counted and statistically corrected. In addition, the developed CFUs were washed off the agar plates and subjected to polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) for diversity analysis. Results revealed that for most environments investigated, the culturable bacterial aerosol concentrations were higher than those of culturable fungal aerosols. The culturable bacterial and fungal aerosol fractions, concentration, size distribution, and diversity were shown to vary significantly with the sampling environments. PCR-DGGE analysis indicated that different environments had different culturable bacterial aerosol compositions as revealed by distinct gel band patterns. For most environments tested, larger (>3 μm) culturable bacterial aerosols with a skewed size distribution were shown to prevail, accounting for more than 60 %, while for culturable fungal aerosols with a normal size distribution, those 2.1-4.7 μm dominated, accounting for 20-40 %. Alternaria, Cladosporium, Chaetomium, and Aspergillus were found abundant in most
Response of the soil microbial community to imazethapyr application in a soybean field.
Xu, Jun; Guo, Liqun; Dong, Fengshou; Liu, Xingang; Wu, Xiaohu; Sheng, Yu; Zhang, Ying; Zheng, Yongquan
2013-01-01
The objective of this study was to determine the effects of imazethapyr on soil microbial communities combined with its effect on soybean growth. A short-term field experiment was conducted, and imazethapyr was applied to the soil at three different doses [1-fold, 10-fold, and 50-fold of the recommended field rate (H1, H10, H50)] during the soybean seedling period (with two leaves). Soil sampling was performed after 1, 7, 30, 60, 90, and 120 days of application to determine the imazethapyr concentration and microbial community structure by investigating phospholipid fatty acids (PLFA) and microbial biomass carbon (MBC). The half-lives of the imazethapyr in the field soil varied from 30.1 to 43.3 days. Imazethapyr at H1 was innocuous to soybean plants, but imazethapyr at H10 and H50 led to a significant inhibition in soybean plant height and leaf number. The soil MBC, total PLFA, and bacterial PLFA were decreased by the application of imazethapyr during the initial period and could recover by the end of the experiment. The ratio of Gram-negative/Gram-positive (GN/GP) bacteria during the three treatments went through increases and decreases, and then recovered at the end of the experiment. The fungal PLFA of all three treatments increased during the initial period and then declined, and only the fungal PLFA at H50 recovered by the end of the treatment. A principal component analysis (PCA) of the PLFA clearly separated the treatments and sampling times, and the results demonstrate that imazethapyr alters the microbial community structure. This is the first systemic study reporting the effects of imazethapyr on the soil microbial community structure under soybean field conditions.
Directory of Open Access Journals (Sweden)
Marisela Carmona
Full Text Available Infectious Salmon Anemia is a devastating disease critically affecting world-wide salmon production. Chile has been particularly stricken by this disease which in all cases has been directly related with its causative agent, a novel orthomyxovirus which presents specific and distinctive infective features. Among these, two molecular markers have been directly associated with pathogenicity in two of the eight RNA sub genomic coding units of the virus: an insertion hot spot region present in viral segment 5 and a Highly Polymorphic Region (HPR located in viral segment 6. Here we report the successful adaptation of a PCR-dependent denaturing gel electrophoresis technique (DGGE, which enables differentiation of selected reported HPR epizootic variants detected in Chile. At the same time, the technique allows us to distinguish one nucleotide differences in sequences associated with the intriguing, and still not well-understood, insertion events which tend to occur on RNA Segment 5. Thus, the versatility of the technique opens new opportunities for improved understanding of the complex biology of all ISA variants as well as possible applications to other highly variable pathogens.
Xiao, Yong; Yang, Zhao-hui; Zeng, Guang-ming; Ma, Yan-he; Liu, You-sheng; Wang, Rong-juan; Xu, Zheng-yong
2007-05-01
For studying the bacterial diversity and the mechanism of denitrification in sequencing bath biofilm reactor (SBBR) treating landfill leachate to provide microbial evidence for technique improvements, total microbial DNA was extracted from samples which were collected from natural landfill leachate and biofilm of a SBBR that could efficiently remove NH4+ -N and COD of high concentration. 16S rDNA fragments were amplified from the total DNA successfully using a pair of universal bacterial 16S rDNA primer, GC341F and 907R, and then were used for denaturing gradient gel electrophoresis (DGGE) analysis. The bands in the gel were analyzed by statistical methods and excided from the gel for sequencing, and the sequences were used for homology analysis and then two phylogenetic trees were constructed using DNAStar software. Results indicated that the bacterial diversity of the biofilm in SBBR and the landfill leachate was abundant, and no obvious change of community structure happened during running in the biofilm, in which most bacteria came from the landfill leachate. There may be three different modes of denitrification in the reactor because several different nitrifying bacteria, denitrifying bacteria and anaerobic ammonia oxidation bacteria coexisted in it. The results provided some valuable references for studying microbiological mechanism of denitrification in SBBR.
Long, Xi-En; Yao, Huaiying; Wang, Juan; Huang, Ying; Singh, Brajesh K; Zhu, Yong-Guan
2015-06-16
Previous studies suggested that microbial photosynthesis plays a potential role in paddy fields, but little is known about chemoautotrophic carbon fixers in drained paddy soils. We conducted a microcosm study using soil samples from five paddy fields to determine the environmental factors and quantify key functional microbial taxa involved in chemoautotrophic carbon fixation. We used stable isotope probing in combination with phospholipid fatty acid (PLFA) and molecular approaches. The amount of microbial (13)CO2 fixation was determined by quantification of (13)C-enriched fatty acid methyl esters and ranged from 21.28 to 72.48 ng of (13)C (g of dry soil)(-1), and the corresponding ratio (labeled PLFA-C:total PLFA-C) ranged from 0.06 to 0.49%. The amount of incorporationof (13)CO2 into PLFAs significantly increased with soil pH except at pH 7.8. PLFA and high-throughput sequencing results indicated a dominant role of Gram-negative bacteria or proteobacteria in (13)CO2 fixation. Correlation analysis indicated a significant association between microbial community structure and carbon fixation. We provide direct evidence of chemoautotrophic C fixation in soils with statistical evidence of microbial community structure regulation of inorganic carbon fixation in the paddy soil ecosystem.
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Gbenga Adedeji Adewumi
2013-01-01
Full Text Available In this study, bacterial composition of iru produced by natural, uncontrolled fermentation of Parkia biglobosa seeds was assessed using culture-independent method in combination with culture-based genotypic typing techniques. PCR-denaturing gradient gel electrophoresis (DGGE revealed similarity in DNA fragments with the two DNA extraction methods used and confirmed bacterial diversity in the sixteen iru samples from different production regions. DNA sequencing of the highly variable V3 region of the 16S rRNA genes obtained from PCR-DGGE identified species related to Bacillus subtilis as consistent bacterial species in the fermented samples, while other major bands were identified as close relatives of Staphylococcus vitulinus, Morganella morganii, B. thuringiensis, Staphylococcus saprophyticus, Tetragenococcus halophilus, Ureibacillus thermosphaericus, Brevibacillus parabrevis, Salinicoccus jeotgali, Brevibacterium sp. and Uncultured bacteria clones. Bacillus species were cultured as potential starter cultures and clonal relationship of different isolates determined using amplified ribosomal DNA restriction analysis (ARDRA combined with 16S-23S rRNA gene internal transcribed spacer (ITS PCR amplification, restriction analysis (ITS-PCR-RFLP and randomly amplified polymorphic DNA (RAPD-PCR. This further discriminated Bacillus subtilis and its variants from food-borne pathogens such as Bacillus cereus and suggested the need for development of controlled fermentation processes and good manufacturing practices (GMP for iru production to achieve product consistency, safety quality and improved shelf life.
International Nuclear Information System (INIS)
Peng Fangfang; Luo Xuegang
2014-01-01
Using the modified gradient gel electrophoresis (DGGE) analysis method, the structure diversity of the soil microbial in the tested soils was investigated after the remediation of Broken rice sedges, Broussonetia papyrifera, and Abutilon for the simulated uranium tailings contaminated soils. The results showed that 52.2% of all the sequences information belong to proteobacteria. Additionally, compared with the contrast, the decrease in Shannon-Wiener Index (H) was observed ranging from 14.7 to 31.3% in the Broussonetia papyrifera group while the decrease ranging from 38.8 to 56.9% in the abutilon group. However, the Broken rice sedge group was different from the other two groups. The dominant microorganisms that have a strong tolerance to uranium belong to Acidobacteria and the microbial groups that was difficult to determine its classification. This study provided a basic information for the development and the application of microorganism resources resistant to stress. (authors)
Jin, Zhengzhong; Lei, Jiaqiang; Li, Shengyu; Xu, Xinwen
2013-10-01
Soil microbes in forest land are crucial to soil development in extreme areas. In this study, methods of conventional culture, PLFA and PCR-DGGE were utilized to analyze soil microbial quantity, fatty acids and microbial DNA segments of soils subjected to different site conditions in the Tarim Desert Highway forest land. The main results were as follows: the soil microbial amount, diversity indexes of fatty acid and DNA segment differed significantly among sites with different conditions (F 84%), followed by actinomycetes and then fungi (<0.05%). Vertical differences in the soil microbial diversity were insignificant at 0-35 cm. Correlation analysis indicated that the forest trees grew better as the soil microbial diversity index increased. Therefore, construction of the Tarim Desert Highway shelter-forest promoted soil biological development; however, for enhancing sand control efficiency and promoting sand development, we should consider the effects of site condition in the construction and regeneration of shelter-forest ecological projects. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Motato, Karina Edith; Milani, Christian; Ventura, Marco; Valencia, Francia Elena; Ruas-Madiedo, Patricia; Delgado, Susana
2017-12-01
"Suero Costeño" (SC) is a traditional soured cream elaborated from raw milk in the Northern-Caribbean coast of Colombia. The natural microbiota that characterizes this popular Colombian fermented milk is unknown, although several culturing studies have previously been attempted. In this work, the microbiota associated with SC from three manufacturers in two regions, "Planeta Rica" (Córdoba) and "Caucasia" (Antioquia), was analysed by means of culturing methods in combination with high-throughput sequencing and DGGE analysis of 16S rRNA gene amplicons. The bacterial ecosystem of SC samples was revealed to be composed of lactic acid bacteria belonging to the Streptococcaceae and Lactobacillaceae families; the proportions and genera varying among manufacturers and region of elaboration. Members of the Lactobacillus acidophilus group, Lactocococcus lactis, Streptococcus infantarius and Streptococcus salivarius characterized this artisanal product. In comparison with culturing, the use of molecular in deep culture-independent techniques provides a more realistic picture of the overall bacterial communities residing in SC. Besides the descriptive purpose, these approaches will facilitate a rational strategy to follow (culture media and growing conditions) for the isolation of indigenous strains that allow standardization in the manufacture of SC. Copyright © 2017 Elsevier Ltd. All rights reserved.
Diversity of diazotrophic gut inhabitants of pikas (Ochotonidae) revealed by PCR-DGGE analysis.
Kizilova, A K; Kravchenko, I K
2014-01-01
Diazotrophic gut symbionts are considered to act as nitrogen providers for their hosts, as was shown for various termite species. Although the diet of lagomorphs, like pikas or rabbits, is very poor in nitrogen and energy, their fecal matter contains 30-40% of protein. Since our hypothesis was that pikas maintained a diazotrophic consortium in their gastrointestinal tract, we conducted the first investigation of microbial diversity in pika guts. We obtained gut samples from animals of several Ochotona species, O. hyperborea (Northern pika), O. mantchurica (Manchurian pika), and O. dauurica (Daurian pika), in order to retrieve and compare the nitrogen-fixing communities of different pika species. The age and gender of the animals were taken into consideration. We amplified 320-bp long fragments of the nifH gene using the DNA extracted directly from the colon and cecum samples of pika's gut, resolved them by DGGE, and performed phylogenetic reconstruction of 51 sequences obtained from excised bands. No significant difference was detected between the nitrogen-fixing gut inhabitants of different pika species. NifH sequences fell into two clusters. The first cluster contained the sequences affiliated with NifH Cluster I (Zehr et al., 2003) with similarity to Sphingomonas sp., Bradyrhizobium sp., and various uncultured bacteria from soil and rhizosphere. Sequences from the second group were related to Treponema sp., Fibrobacter succinogenes, and uncultured clones from the guts of various termites and belonged to NifH Cluster III. We suggest that diazotrophic organisms from the second cluster are genuine endosymbionts of pikas and provide nitrogen for further synthesis processes thus allowing these animals not to be short of protein.
Microbial sulfate reduction and metal attenuation in pH 4 acid mine water
Directory of Open Access Journals (Sweden)
Alpers Charles N
2007-10-01
Full Text Available Abstract Sediments recovered from the flooded mine workings of the Penn Mine, a Cu-Zn mine abandoned since the early 1960s, were cultured for anaerobic bacteria over a range of pH (4.0 to 7.5. The molecular biology of sediments and cultures was studied to determine whether sulfate-reducing bacteria (SRB were active in moderately acidic conditions present in the underground mine workings. Here we document multiple, independent analyses and show evidence that sulfate reduction and associated metal attenuation are occurring in the pH-4 mine environment. Water-chemistry analyses of the mine water reveal: (1 preferential complexation and precipitation by H2S of Cu and Cd, relative to Zn; (2 stable isotope ratios of 34S/32S and 18O/16O in dissolved SO4 that are 2–3 ‰ heavier in the mine water, relative to those in surface waters; (3 reduction/oxidation conditions and dissolved gas concentrations consistent with conditions to support anaerobic processes such as sulfate reduction. Scanning electron microscope (SEM analyses of sediment show 1.5-micrometer, spherical ZnS precipitates. Phospholipid fatty acid (PLFA and denaturing gradient gel electrophoresis (DGGE analyses of Penn Mine sediment show a high biomass level with a moderately diverse community structure composed primarily of iron- and sulfate-reducing bacteria. Cultures of sediment from the mine produced dissolved sulfide at pH values near 7 and near 4, forming precipitates of either iron sulfide or elemental sulfur. DGGE coupled with sequence and phylogenetic analysis of 16S rDNA gene segments showed populations of Desulfosporosinus and Desulfitobacterium in Penn Mine sediment and laboratory cultures.
Microbial sulfate reduction and metal attenuation in pH 4 acid mine water
Church, C.D.; Wilkin, R.T.; Alpers, Charles N.; Rye, R.O.; Blaine, R.B.
2007-01-01
Sediments recovered from the flooded mine workings of the Penn Mine, a Cu-Zn mine abandoned since the early 1960s, were cultured for anaerobic bacteria over a range of pH (4.0 to 7.5). The molecular biology of sediments and cultures was studied to determine whether sulfate-reducing bacteria (SRB) were active in moderately acidic conditions present in the underground mine workings. Here we document multiple, independent analyses and show evidence that sulfate reduction and associated metal attenuation are occurring in the pH-4 mine environment. Water-chemistry analyses of the mine water reveal: (1) preferential complexation and precipitation by H2S of Cu and Cd, relative to Zn; (2) stable isotope ratios of 34S/32S and 18O/16O in dissolved SO4 that are 2-3 ??? heavier in the mine water, relative to those in surface waters; (3) reduction/oxidation conditions and dissolved gas concentrations consistent with conditions to support anaerobic processes such as sulfate reduction. Scanning electron microscope (SEM) analyses of sediment show 1.5-micrometer, spherical ZnS precipitates. Phospholipid fatty acid (PLFA) and denaturing gradient gel electrophoresis (DGGE) analyses of Penn Mine sediment show a high biomass level with a moderately diverse community structure composed primarily of iron- and sulfate-reducing bacteria. Cultures of sediment from the mine produced dissolved sulfide at pH values near 7 and near 4, forming precipitates of either iron sulfide or elemental sulfur. DGGE coupled with sequence and phylogenetic analysis of 16S rDNA gene segments showed populations of Desulfosporosinus and Desulfitobacterium in Penn Mine sediment and laboratory cultures. ?? 2007 Church et al; licensee BioMed Central Ltd.
Dijkman, N.A.; Kromkamp, J.C.
2006-01-01
Phospholipid-derived fatty acids (PLFA) are widely used as chemotaxonomic markers in microbial ecology. In this paper we explore the use of PLFA as chemotaxonomic markers for phytoplankton species. The PLFA composition was determined for 23 species relevant to estuarine phytoplankton. The taxonomic
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Slater, G.F.; Nelson, R.K.; Kile, B.M.; Reddy, C.M.
2006-01-01
Natural abundance, molecular-level C 14 analysis was combined with comprehensive gas chromatography (GC x GC) to investigate, in situ, the role of intrinsic biodegradation in the loss of petroleum hydrocarbons from the rocky, inter-tidal zone impacted by the Bouchard 120 oil spill. GC x GC analysis indicated accelerated losses of n-alkane components of the residual petroleum hydrocarbons between day 40 and day 50 after the spill. 14 C analysis of bacterial phospholipid fatty acids (PLFA) from the impacted zone on day 44 showed that the polyunsaturated fatty acids attributed to the photoautotrophic component of the microbial community had the same ( 14 C as the local dissolved inorganic carbon (DIG), indicating that this DIG was their carbon source. In contrast there was significant (C depletion in the saturated and mono-unsaturated PLFA indicating incorporation of petroleum carbon. This correlation between the observed accelerated n-alkane losses and microbial incorporation of (C-depleted carbon directly demonstrated, in situ, that intrinsic biodegradation was affecting the petroleum. Since the majority of organic contaminants originate from petroleum feed-stocks, in situ molecular-level 14 C analysis of microbial PLFA can provide insights into the occurrence and pathways of biodegradation of a wide range of organic contaminants. (Author)
Wang, Liang; Liu, Jinli; Zhao, Quanyu; Wei, Wei; Sun, Yuhan
2016-07-01
Algal-bacterial synergistic cultivation could be an optional wastewater treatment technology in temperate areas. In this study, a locally screened vigorous Chlorella strain was characterized and then it was used in a comparative study of wastewater treatment and nutrient recycle assessment via activated sludge (AS), microalgae and their combination systems. Chlorella sp. cultured with AS in light showed the best performance, in which case the removal efficiencies of COD, NH3-N and TP were 87.3%, 99.2% and 83.9%, respectively, within a short period of 1day. Algal-bacterial combination in light had the best settleability. Chlorella sp. contained biomass, could be processed to feed, fertilizer or fuel due to the improved quality (higher C/H/N) compared with sludge. PCR-DGGE analysis shows that two types of rhizobacteria, namely, Pseudomonas putida and Flavobacterium hauense were enriched in sludge when cultured with algae in light, serving as the basics for artificial consortium construction for improved wastewater treatment. Copyright © 2016 Elsevier Ltd. All rights reserved.
Fernández, D A; Roldán, A; Azcón, R; Caravaca, F; Bååth, E
2012-05-01
Our aim was to examine the effect of water stress on plant growth and development of two native plant species (Tetraclinis articulata and Crithmum maritimum) and on microbial community composition and activity in the rhizosphere soil, following the addition of an organic amendment, namely sugar beet residue (SBR), and/or the inoculation with an arbuscular mycorrhizal (AM) fungus, namely Glomus mosseae, in a non-sterile heavy metal-polluted soil. The AM inoculation did not have any significant effect on plant growth of both species. In T. articulata, SBR increased shoot growth, foliar P, total phospholipid fatty acids (PLFA), fungi-related PLFA, AM fungi-related neutral lipid fatty acid, bacterial gram-positive/gram-negative PLFA ratio and the β-glucosidase and dehydrogenase activities. SBR and AM inoculation increased phosphatase activity in T. articulata plants grown under drought conditions. In both plants, there was a synergistic effect between AM inoculation and SBR on mycorrhizal colonisation under drought conditions. In C. maritimum, the increase produced by the SBR on total amounts of PLFA, bacterial gram-positive-related PLFA and bacterial gram-negative-related PLFA was considerably higher under drought conditions. Our results suggest that the effectiveness of the amendment with regard to stimulating microbial communities and plant growth was largely limited by drought, particularly for plant species with a low degree of mycorrhizal colonisation.
Directory of Open Access Journals (Sweden)
Puntipar Sonthiphand
Full Text Available Anaerobic ammonia oxidizing (anammox bacteria play an important role in transforming ammonium to nitrogen gas and contribute to fixed nitrogen losses in freshwater environments. Understanding the diversity and abundance of anammox bacteria requires reliable molecular tools, and these are not yet well established for these important Planctomycetes. To help validate PCR primers for the detection of anammox bacteria within freshwater ecosystems, we analyzed representative positive controls and selected samples from Grand River and groundwater sites, both from Ontario, Canada. The objectives of this study were to identify a suitable anammox denaturing gradient gel electrophoresis (DGGE fingerprint method by using GC-clamp modifications to existing primers, and to verify the specificity of anammox-specific primers used for DGGE, cloning and qPCR methods. Six primer combinations were tested from four published primer sets (i.e. A438f/A684r, Amx368f/Amx820r, An7f/An1388r, and Pla46/1392r for both direct and nested PCR amplifications. All PCR products were run subsequently on DGGE gels to compare the resulting patterns. Two anammox-specific primer combinations were also used to generate clone libraries and quantify anammox bacterial 16S rRNA genes with qPCR. The primer set A438f/A684r was highly specific to anammox bacteria, provided reliable DGGE fingerprints and generated a high proportion of anammox-related clones. A second primer set (Amx368f/Amx820r was anammox specific, based on clone library analysis, but PCR products from different candidate species of anammox bacteria resolved poorly using DGGE analysis. Both DGGE and cloning results revealed that Ca. Brocadia and an uncharacterized anammox bacterial cluster represented the majority of anammox bacteria found in Grand River sediment and groundwater samples, respectively. Together, our results demonstrate that although Amx368f/Amx820r was useful for anammox-specific qPCR and clone library
Pennanen; Fritze; Vanhala; Kiikkila; Neuvonen; Baath
1998-06-01
Humus samples were collected 12 growing seasons after the start of a simulated acid rain experiment situated in the subarctic environment. The acid rain was simulated with H2SO4, a combination of H2SO4 and HNO3, and HNO3 at two levels of moderate acidic loads close to the natural anthropogenic pollution levels of southern Scandinavia. The higher levels of acid applications resulted in acidification, as defined by humus chemistry. The concentrations of base cations decreased, while the concentrations of exchangeable H+, Al, and Fe increased. Humus pH decreased from 3.83 to 3.65. Basal respiration decreased with decreasing humus pH, and total microbial biomass, measured by substrate-induced respiration and total amount of phospholipid fatty acids (PLFA), decreased slightly. An altered PLFA pattern indicated a change in the microbial community structure at the higher levels of acid applications. In general, branched fatty acids, typical of gram-positive bacteria, increased in the acid plots. PLFA analysis performed on the bacterial community growing on agar plates also showed that the relative amount of PLFA specific for gram-positive bacteria increased due to the acidification. The changed bacterial community was adapted to the more acidic environment in the acid-treated plots, even though bacterial growth rates, estimated by thymidine and leucine incorporation, decreased with pH. Fungal activity (measured as acetate incorporation into ergosterol) was not affected. This result indicates that bacteria were more affected than fungi by the acidification. The capacity of the bacterial community to utilize 95 different carbon sources was variable and only showed weak correlations to pH. Differences in the toxicities of H2SO4 and HNO3 for the microbial community were not found.
Margesin, Rosa; Hämmerle, Marion; Tscherko, Dagmar
2007-02-01
We investigated the influence of three factors-diesel oil concentration [2500, 5000, 10,000, 20,000 mg total petroleum hydrocarbons (TPH) kg(-1) soil], biostimulation (unfertilized, inorganic fertilization with NPK nutrients, or oleophilic fertilization with Inipol EAP22), and incubation time-on hydrocarbon removal, enzyme activity (lipase), and microbial community structure [phospholipid fatty acids (PLFA)] in a laboratory soil bioremediation treatment. Fertilization enhanced TPH removal and lipase activity significantly (P 0.05). Microbial communities, as assessed by PLFA patterns, were primarily influenced by the TPH content, followed by fertilization, and the interaction of these two factors, whereas incubation time was of minor importance. This was demonstrated by three-factorial analysis of variance and multidimensional scaling analysis. Low TPH content had no significant effect on soil microbial community, independent of the treatment. High TPH content generally resulted in increased PLFA concentrations, whereby a significant increase in microbial biomass with time was only observed with inorganic fertilization, whereas oleophilic fertilization (Inipol EAP22) tended to inhibit microbial activity and to reduce PLFA contents with time. Among bacteria, PLFA indicative of the Gram-negative population were significantly (P diesel oil and fertilized with NPK after 21-38 days of incubation at 20 degrees C. The Gram-positive population was not significantly influenced by TPH content or biostimulation treatment.
Costa, Rodrigo; Gomes, Newton C. M.; Kroegerrecklenfort, Ellen; Opelt, Katja; Berg, Gabriele; Smalla, Kornelia
The Pseudomonas community structure and antagonistic potential in the rhizospheres of strawberry and oilseed rape (host plants of the fungal phytopathogen Verticillium dahliae) were assessed. The use of a new PCR-DGGE system, designed to target Pseudomonas-specific gacA gene fragments in
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Schryver, Jack C.; Brandt, Craig C.; Pfiffner, Susan M.; Palumbo, A V.; Peacock, Aaron D.; White, David C.; McKinley, James P.; Long, Philip E.
2006-01-01
The relationship between groundwater geochemistry and microbial community structure can be complex and difficult to assess. We applied nonlinear and generalized linear data analysis methods to relate microbial biomarkers (phospholipids fatty acids, PLFA) to groundwater geochemical characteristics at the Shiprock uranium mill tailings disposal site that is primarily contaminated by uranium, sulfate, and nitrate. First, predictive models were constructed using feedforward artificial neural networks (NN) to predict PLFA classes from geochemistry. To reduce the danger of overfitting, parsimonious NN architectures were selected based on pruning of hidden nodes and elimination of redundant predictor (geochemical) variables. The resulting NN models greatly outperformed the generalized linear models. Sensitivity analysis indicated that tritium, which was indicative of riverine influences, and uranium were important in predicting the distributions of the PLFA classes. In contrast, nitrate concentration and inorganic carbon were least important, and total ionic strength was of intermediate importance. Second, nonlinear principal components (NPC) were extracted from the PLFA data using a variant of the feedforward NN. The NPC grouped the samples according to similar geochemistry. PLFA indicators of Gram-negative bacteria and eukaryotes were associated with the groups of wells with lower levels of contamination. The more contaminated samples contained microbial communities that were predominated by terminally branched saturates and branched monounsaturates that are indicative of metal reducers, actinomycetes, and Gram-positive bacteria. These results indicate that the microbial community at the site is coupled to the geochemistry and knowledge of the geochemistry allows prediction of the community composition
Llivisaca, Susana Alexandra; Burgos, Felix Adolfo; Vargas, Jeffrey David
2011-01-01
El proyecto sobre el cual tratamos, se refiere el uso de la técnica molecular PCR-DGGE, para la caracterización de bacterias, y su potencial existencia en las aguas del río Gala de la parroquia Tenguel. La selección del sitio se basó al alto grado de contaminación con metales pesados en la que este se encuentra este rio. La probabilidad sobre la presencia de microorganismos con capacidad metalofijadora, es alta dada sus características biológicas y bioquímicas con las que cuenta esta bacteria...
Bekaert, Karen; Devriese, Lisa; Maes, Sara; Robbens, Johan
2015-04-01
The aim of this study was to investigate the microbial quality of whole Norway lobster (Nephrops norvegicus) and Norway lobster tails to optimize handling conditions. This was done by assessing the total viable count (TVC) and characterizing the dominant microbiota. The cultivable microorganisms were quantified via classical microbiological plating methods. To characterize as many bacterial species present as possible, we performed advanced molecular identification techniques (PCR-DGGE). The initial TVC of fresh Norway lobster meat was high (3.0 log cfu/g) as compared to fish. No significant difference between whole Norway lobster and Norway lobster tails could be found during the storage period. From day 6 of storage, a significant difference between Plate Count Agar (PCA) and Marine Agar (MA) was observed. The microbiota of Norway lobster was dominated by members of the Gram-negative genera such as Psychrobacter spp., Pseudoalteromonas spp., Pseudomonas spp., Luteimonas spp., and Aliivibrio spp. From these bacteria, mainly Psychrobacter spp. and Pseudomonas spp. remained present until the end of the storage period. These are known spoilage organisms in fishery products. Other known spoilage organisms of crustaceans such as Photobacterium spp. could not be identified. Copyright © 2014 Elsevier Ltd. All rights reserved.
Bellinger, Brent J; Hagerthey, Scot E; Newman, Susan; Cook, Mark I
2012-11-01
Alterations in microbial community composition, biomass, and function in the Florida Everglades impacted by cultural eutrophication reflect a new physicochemical environment associated with monotypic stands of Typha domingensis. Phospholipid fatty acid (PLFA) biomarkers were used to quantify microbial responses in detritus and surface soils in an active management experiment in the eutrophic Everglades. Creation of open plots through removal of Typha altered the physical and chemical characteristics of the region. Mass of PLFA biomarkers increased in open plots, but magnitude of changes differed among microbial groups. Biomarkers indicative of Gram-negative bacteria and fungi were significantly greater in open plots, reflective of the improved oxic environment. Reduction in the proportion of cyclopropyl lipids and the ratio of Gram-positive to Gram-negative bacteria in open plots further suggested an altered oxygen environment and conditions for the rapid growth of Gram-negative bacteria. Changes in the PLFA composition were greater in floc relative to soils, reflective of rapid inputs of new organic matter and direct interaction with the new physicochemical environment. Created open plot microbial mass and composition were significantly different from the oligotrophic Everglades due to differences in phosphorus availability, plant community structure, and a shift to organic peat from marl-peat soils. PLFA analysis also captured the dynamic inter-annual hydrologic variability, notably in PLFA concentrations, but to a lesser degree content. Recently, use of concentration has been advocated over content in studies of soil biogeochemistry, and our results highlight the differential response of these two quantitative measures to similar pressures.
Tzeneva, V.A.; Li, Y.; Felske, A.; Vos, de W.M.; Akkermans, A.D.L.; Vaughan, E.E.; Smidt, H.
2004-01-01
The worldwide presence of a hitherto-nondescribed group of predominant soil microorganisms related to Bacillus benzoevorans was analyzed after development of two sets of selective primers targeting 16S rRNA genes in combination with denaturing gradient gel electrophoresis (DGGE). The high abundance
Molecular Characterization of Microbial Communities in a JP-4 Fuel Contaminated Soil
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Barcelona, M.J.; Chang, Y.-J.; Gan, Y.D.; Macnaughton, S.J.; Peacock, A.; Stephen, J.R.; White, D.C.
1999-01-01
In this study, lipid biomarker characterization of the bacterial and eukaryotic communities was combined with PCR-DGGE analysis of the eubacterial community to evaluate correlation between JP-4 fuel concentration and community structure shifts. Vadose, capillary fringe and saturated-soils were taken from cores within, up- and down-gradient of the contaminant plume. Significant differences in biomass and proportion of Gram negative bacteria were found inside and outside the plume. Sequence analysis of DGGE bands from within the spill site suggested dominance by a limited number of phylogenetically diverse bacteria. Used in tandem with pollutant quantification, these molecular techniques should facilitate significant improvements over current assessment procedures for determination of remediation end points
Zhang, L; Zhou, R; Niu, M; Zheng, J; Wu, C
2015-11-01
Artificial pit muds (APMs) is produced by peats, aged pit muds, yellow and black clays etc. and is one of essential factors for Luzhou-flavour liquor production. The microbial community of APMs significantly influence the quality of Luzhou-flavour liquor. The aim of this study was to investigate the differences in bacterial, archaeal and fungal community of APMs, starters and materials. Multiphase culture-independent technology were employed in this study, including nested PCR-denaturing gradient gel electrophoresis (nested PCR-DGGE), phospholipid fatty acid (PLFA), phospholipid ether lipids (PLEL) and fluorescence in situ hybridization (FISH) analysis. Results suggested that the microbial diversity significantly changed under environmental stress and different culture patterns during APMs cultivation. The dominant bacteria in APMs mainly fell into Clostridiales, Lactobacillales, Bacteroidales and Rhizobiales, Archaea affiliated with Methanomicrobiales and Methanosarcinales, and fungi belonged to Saccharomycetales and Eurotiales. Furthermore, the microbial community structures of APMs cultured by ground pile pattern were more similar with that of aged pit muds, meanwhile, the relative bands intensities of microbes, which are the main contributors for liquor brewing, increased with the culture times. Not only the niche selection and biogeochemical properties of APMs, but also the mutual collaboration and constraint between different microbes may result in enriching different liquor-brewing microbes into APMs. APM cultivation technology was necessary to promote enriching functional liquor-brewing microbes into APMs. These results may facilitate understanding the microbial succession during APMs manufacture. © 2015 The Society for Applied Microbiology.
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Ed-Haun Chang
2016-10-01
Full Text Available The effects of long-term reforestation on soil microbial communities and biomass are poorly understood. This study was conducted on two coniferous plantations: Cunninghamia konishii Hayata, planted 40 years ago (CONIF-40, and Calocedrus formosana (Florin Florin, planted 80 years ago (CONIF-80. An adjacent natural broadleaf forest (BROAD-Nat was used as a control. We determined microbial biomass C and N contents, enzyme activities, and community composition (via phospholipid fatty acid [PLFA] assessment. Both microbial biomass and PLFA content were higher in the summer than in the winter and differed among the forests in summer only. Total PLFA, total bacterial, gram-positive bacterial, gram-negative bacterial, and vesicular arbuscular mycorrhizal fungal contents followed the same pattern. Total fungal content and the ratios of fungi to bacteria and of gram-positive to gram-negative bacteria were highest in CONIF-40, with no difference between the other forests. Principal component analysis of PLFA contents revealed that CONIF-40 communities were distinct from those of CONIF-80 and BROAD-Nat. Our results suggest that vegetation replacement during reforestation exerts a prolonged impact on the soil microbial community. The understory broadleaf shrubs and trees established after coniferous plantation reforestation may balance out the effects of coniferous litter, contributing to bacterial recovery.
Fernández-Suárez, Rocío; Ramírez-Villatoro, Guadalupe; Díaz-Ruiz, Gloria; Eslava, Carlos; Calderón, Montserrat; Navarro-Ocaña, Arturo; Trejo-Márquez, Andrea; Wacher, Carmen
2013-01-01
Since Mexico is the second largest exporter of mangoes, its safety assurance is essential. Research in microbial ecology and knowledge of complex interactions among microbes must be better understood to achieve maximal control of pathogens. Therefore, we investigated the effect of UV-C treatments on bacterial diversity of the Ataulfo mangoes surface using PCR-DGGE analysis of variable region V3 of 16S rRNA genes, and the survival of E. coli, by plate counting. The UV-C irradiation reduced the microbial load on the surface of mangoes immediately after treatment and the structure of bacterial communities was modified during storage. We identified the key members of the bacterial communities on the surface of fruits, predominating Enterobacter genus. Genera as Lactococcus and Pantoea were only detected on the surface of non-treated (control) mangoes. This could indicate that these genera were affected by the UV-C treatment. On the other hand, the treatment did not have a significant effect on survival of E. coli. However, genera that have been recognized as antagonists against foodborne pathogens were identified in the bands patterns. Also, phenolic compounds were determined by HPLC and antimicrobial activity was assayed according to the agar diffusion method. The main phenolic compounds were chlorogenic, gallic, and caffeic acids. Mango peel methanol extracts (UV-C treated and control mangoes) showed antimicrobial activity against strains previously isolated from mango, detecting significant differences (P < 0.05) among treated and control mangoes after 4 and 12 days of storage. Ps. fluorescens and Ps. stutszeri were the most sensitive. PMID:23761788
García-Orenes, Fuensanta; Morugan, Alicia; Mataix-Solera, Jorge; Scow, Kate
2013-04-01
Agriculture has been practiced in semi-arid Mediterranean regions for 10.000 years and in many cases these practices have been unsuitable causing land degradation for millennium and an important loss of soil quality. The land management can provide solutions to find the best agricultural practices in order to maintain the soil quality and get a sustainable agriculture model. Microbiological properties are the most sensitive and rapid indicators of soil perturbations and land use managements. The study of microbial community and diversity has an important interest as indicators of changes in soil quality. The main objective of this work was to asses the effect of different agricultural management practices in soil microbial community (evaluated as abundance of phospholipid fatty acids, PLFA). Four different treatments were selected, based on the most commonly practices applied by farmers in the study area, "El Teularet Experimental Station", located at the Enguera Range in the southern part of the Valencia province (eastern Spain). These treatments were: a) ploughing, b) herbicides c) mulch, using the types applied by organic farmers to develop a sustainable agriculture, such as oat straw and d) control that was established as plot where the treatment was abandonment after farming. An adjacent area with the same type of soil, but with natural vegetation was used as a standard or reference high quality soil. Soil samples were taken to evaluate the changes in microbial soil structure, analysing the abundance of PLFA. The results showed a major content of total PLFA in soils treated with oats straw, being these results similar to the content of PLFA in the soil with natural vegetation, also these soils were similar in the distribution of abundance of different PLFA studied. However, the herbicide and tillage treatments showed great differences regarding the soil used as reference (soil under natural vegetation).
Estimating Cyanobacteria Community Dynamics and its Relationship with Environmental Factors
Luo, Wenhuai; Chen, Huirong; Lei, Anping; Lu, Jun; Hu, Zhangli
2014-01-01
The cyanobacteria community dynamics in two eutrophic freshwater bodies (Tiegang Reservoir and Shiyan Reservoir) was studied with both a traditional microscopic counting method and a PCR-DGGE genotyping method. Results showed that cyanobacterium Phormidium tenue was the predominant species; twenty-six cyanobacteria species were identified in water samples collected from the two reservoirs, among which fourteen were identified with the morphological method and sixteen with the PCR-DGGE method. The cyanobacteria community composition analysis showed a seasonal fluctuation from July to December. The cyanobacteria population peaked in August in both reservoirs, with cell abundances of 3.78 × 108 cells L-1 and 1.92 × 108 cells L-1 in the Tiegang and Shiyan reservoirs, respectively. Canonical Correspondence Analysis (CCA) was applied to further investigate the correlation between cyanobacteria community dynamics and environmental factors. The result indicated that the cyanobacteria community dynamics was mostly correlated with pH, temperature and total nitrogen. This study demonstrated that data obtained from PCR-DGGE combined with a traditional morphological method could reflect cyanobacteria community dynamics and its correlation with environmental factors in eutrophic freshwater bodies. PMID:24448632
Qu, Juanjuan; Ren, Guangming; Chen, Bao; Fan, Jinghua; E, Yong
2011-11-01
In the process of mining activity, many kinds of heavy metals enter into soils with dust, causing serious contamination to the environment. In this study, six soils were sampled from cropland at different distances from a lead/zinc mine in Heilongjiang Province, China. The total contents of lead and zinc in the vicinal cropland exceeded the third level of environmental quality standard for soil in China, which indicated that soils in this area were moderately contaminated. Bacterial community diversity and population were greatly decreased when the concentrations of lead and zinc were beyond 1,500 and 995 mg kg(-1), respectively, as analyzed by plate counting and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). The bands of DGGE patterns varied with the degree of contamination. The activities of soil urease, phosphatase, and dehydrogenase were negatively correlated with the concentrations of lead and zinc. The highest inhibitory effect of heavy metals on soil enzyme activities was observed in urease. It was noted that PCR-DGGE patterns combined with soil enzyme activity analysis can be indices for the soil quality assessment by heavy metal contamination.
Hoefel, Daniel; Monis, Paul T.; Grooby, Warwick L.; Andrews, Stuart; Saint, Christopher P.
2005-01-01
Chloramination is often the disinfection regimen of choice for extended drinking water systems. However, this process is prone to instability due to the growth of nitrifying bacteria. This is the first study to use alternative approaches for rapid investigation of chloraminated drinking water system instability in which flow cytometric cell sorting of bacteria with intact membranes (membrane-intact fraction) (BacLight kit) or with active esterases (esterase-active fraction) (carboxyfluorescein diacetate) was combined with 16S rRNA gene-directed PCR and denaturing gradient gel electrophoresis (DGGE). No active bacteria were detected when water left the water treatment plant (WTP), but 12 km downstream the chloramine residual had diminished and the level of active bacteria in the bulk water had increased to more than 1 × 105 bacteria ml−1. The bacterial diversity in the system was represented by six major DGGE bands for the membrane-intact fraction and 10 major DGGE bands for the esterase-active fraction. PCR targeting of the 16S rRNA gene of chemolithotrophic ammonia-oxidizing bacteria (AOB) and subsequent DGGE and DNA sequence analysis revealed the presence of an active Nitrosospira-related species and Nitrosomonas cryotolerans in the system, but no AOB were detected in the associated WTP. The abundance of active AOB was then determined by quantitative real-time PCR (qPCR) targeting the amoA gene; 3.43 × 103 active AOB ml−1 were detected in the membrane-intact fraction, and 1.40 × 104 active AOB ml−1 were detected in the esterase-active fraction. These values were several orders of magnitude greater than the 2.5 AOB ml−1 detected using a routine liquid most-probable-number assay. Culture-independent techniques described here, in combination with existing chemical indicators, should allow the water industry to obtain more comprehensive data with which to make informed decisions regarding remedial action that may be required either prior to or during an
Vanhoutte, Tom; De Preter, Vicky; De Brandt, Evie; Verbeke, Kristin; Swings, Jean; Huys, Geert
2006-01-01
Diet is a major factor in maintaining a healthy human gastrointestinal tract, and this has triggered the development of functional foods containing a probiotic and/or prebiotic component intended to improve the host's health via modulation of the intestinal microbiota. In this study, a long-term placebo-controlled crossover feeding study in which each subject received several treatments was performed to monitor the effect of a prebiotic substrate (i.e., lactulose), a probiotic organism (i.e., Saccharomyces boulardii), and their synbiotic combination on the fecal microbiota of three groups of 10 healthy human subjects differing in prebiotic dose and/or intake of placebo versus synbiotic. For this purpose, denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA gene amplicons was used to detect possible changes in the overall bacterial composition using the universal V3 primer and to detect possible changes at the subpopulation level using group-specific primers targeting the Bacteroides fragilis subgroup, the genus Bifidobacterium, the Clostridium lituseburense group (cluster XI), and the Clostridium coccoides-Eubacterium rectale group (cluster XIVa). Although these populations remained fairly stable based on DGGE profiling, one pronounced change was observed in the universal fingerprint profiles after lactulose ingestion. Band position analysis and band sequencing revealed that a band appearing or intensifying following lactulose administration could be assigned to the species Bifidobacterium adolescentis. Subsequent analysis with real-time PCR (RT-PCR) indicated a statistically significant increase (P < 0.05) in total bifidobacteria in one of the three subject groups after lactulose administration, whereas a similar but nonsignificant trend was observed in the other two groups. Combined RT-PCR results from two subject groups indicated a borderline significant increase (P = 0.074) of B. adolescentis following lactulose intake. The probiotic yeast S
Bacterial diversity characterization in petroleum samples from Brazilian reservoirs
de Oliveira, Valéria Maia; Sette, Lara Durães; Simioni, Karen Christina Marques; dos Santos Neto, Eugênio Vaz
2008-01-01
This study aimed at evaluating potential differences among the bacterial communities from formation water and oil samples originated from biodegraded and non-biodegraded Brazilian petroleum reservoirs by using a PCR-DGGE based approach. Environmental DNA was isolated and used in PCR reactions with bacterial primers, followed by separation of 16S rDNA fragments in the DGGE. PCR products were also cloned and sequenced, aiming at the taxonomic affiliation of the community members. The fingerprints obtained allowed the direct comparison among the bacterial communities from oil samples presenting distinct degrees of biodegradation, as well as between the communities of formation water and oil sample from the non-biodegraded reservoir. Very similar DGGE band profiles were observed for all samples, and the diversity of the predominant bacterial phylotypes was shown to be low. Cloning and sequencing results revealed major differences between formation water and oil samples from the non-biodegraded reservoir. Bacillus sp. and Halanaerobium sp. were shown to be the predominant components of the bacterial community from the formation water sample, whereas the oil sample also included Alicyclobacillus acidoterrestris, Rhodococcus sp., Streptomyces sp. and Acidithiobacillus ferrooxidans. The PCR-DGGE technique, combined with cloning and sequencing of PCR products, revealed the presence of taxonomic groups not found previously in these samples when using cultivation-based methods and 16S rRNA gene library assembly, confirming the need of a polyphasic study in order to improve the knowledge of the extent of microbial diversity in such extreme environments. PMID:24031244
Chapter 11. Community analysis-based methods
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Cao, Y.; Wu, C.H.; Andersen, G.L.; Holden, P.A.
2010-05-01
Microbial communities are each a composite of populations whose presence and relative abundance in water or other environmental samples are a direct manifestation of environmental conditions, including the introduction of microbe-rich fecal material and factors promoting persistence of the microbes therein. As shown by culture-independent methods, different animal-host fecal microbial communities appear distinctive, suggesting that their community profiles can be used to differentiate fecal samples and to potentially reveal the presence of host fecal material in environmental waters. Cross-comparisons of microbial communities from different hosts also reveal relative abundances of genetic groups that can be used to distinguish sources. In increasing order of their information richness, several community analysis methods hold promise for MST applications: phospholipid fatty acid (PLFA) analysis, denaturing gradient gel electrophoresis (DGGE), terminal restriction fragment length polymorphism (TRFLP), cloning/sequencing, and PhyloChip. Specific case studies involving TRFLP and PhyloChip approaches demonstrate the ability of community-based analyses of contaminated waters to confirm a diagnosis of water quality based on host-specific marker(s). The success of community-based MST for comprehensively confirming fecal sources relies extensively upon using appropriate multivariate statistical approaches. While community-based MST is still under evaluation and development as a primary diagnostic tool, results presented herein demonstrate its promise. Coupled with its inherently comprehensive ability to capture an unprecedented amount of microbiological data that is relevant to water quality, the tools for microbial community analysis are increasingly accessible, and community-based approaches have unparalleled potential for translation into rapid, perhaps real-time, monitoring platforms.
DEFF Research Database (Denmark)
Ferrari, Alejandro E.; Ravnskov, Sabine; Larsen, John
2015-01-01
practices while NLFA 20:0 appears to be a good marker of HRsoils despite season or location. The PLFA-based taxonomic biomarkers for total bacteria, Gramnegativebacteria and arbuscular mycorrhiza showed a significant trend NE>HR>LR in the wintersampling. HR management was also characterized by high levels......Analysis of phospholipids (PLFA) and neutral lipids fatty acids (NLFA) was used to characterizeno-till productive agricultural soils associated with different crop rotation levels, replicated across a400 km transect in the Argentinean pampas, during two sampling seasons, summer and winter...
How bioavailable is highly weathered Deepwater Horizon oil?
Bostic, J.; Ziolkowski, L. A.; Reddy, C. M.; Aeppli, C.; Swarthout, B.
2016-02-01
Oiled sand patties continue to be deposited on northern Gulf of Mexico beaches five years after the Deepwater Horizon (DwH) oil spill. It is known that during the first 18 months post-spill, sand patties from DwH were chemically transformed, both biotically and abiotically, from wellhead release to beach deposition. However, the chemically transformed oil, which appears to become more polar over time, is not well understood in regards to its biodegradation potential. Biodegradation exerts a large control on the fate of spilled oil, representing a major conduit for its removal from the environment. To assess the bioavailability of this weathered oil, sand patties were collected from intertidal and supratidal zones of beaches in Florida, Alabama, and Mississippi in July 2015. Microbial biomarkers of the viable community, phospholipid fatty acids (PLFA), were detected on all samples collected. The PLFA distributions (mostly saturated and branched structures) and abundances (2 - 9 x 1013 cells/g sand patty) were similar across sampling locations. The positive correlation between PLFA abundance and surface area to volume ratios of sand patties indicates that microbes are preferentially inhabiting outside surfaces of the patties. We will present data on the radiocarbon (14C) content of PLFA to assess carbon (C) sources assimilated by microbes. 14C of PLFA is a powerful tool for assessing C sources assimilated in this setting. Oil has no 14C (Δ14C= -1000‰) while modern organic matter has relatively abundant 14C (Δ14C= 0‰). Fingerprinting analysis of biomarker ratios using comprehensive two-dimensional gas chromatography will be presented to ascertain if oil originated from DwH. The extent of the chemical transformation of the oil into more polar compounds will also be measured using thin layer chromatography. Results of this investigation aim to determine the bioavailability and ultimate fate of oiled sand patties that continue to wash ashore on Gulf of Mexico
Chen, Hsi-Chia; Wang, Sheng-Yao; Chen, Ming-Ju
2008-05-01
Lactic acid bacteria (LAB) in different original kefir grains were first assessed using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) by a culture-dependent way, and were further confirmed by DNA sequencing techniques. Results indicated that a combined method of cultivation with PCR-DGGE and subsequent DNA sequencing could successfully identify four LAB strains from three kefir grains from Taiwan (named Hsinchu, Mongolia and Ilan). Lactobacillus kefiri accounted, in the three kefir grains, for at least half of the isolated colonies while Lb. kefiranofaciens was the second most frequently isolated species. Leuconostoc mesenteroides was less frequently found but still in the three kefir grains conversely to Lactococcus lactis which based on culture-dependent isolation was only found in two of the kefir grains. It was interesting to find that all three kefir grains contain similar LAB species. Furthermore, the DGGE as a culture-independent method was also applied to detect the LAB strains. Results indicated that Lb. kefiranofaciens was found in all three kefir grains, whereas Lb. kefiri was only observed in Hsinchu kefir grain and Lc. lactis was found in both Mongolia and Ilan samples. Two additional strains, Pseudomonas spp. and E. coli, were also detected in kefir grains.
Directory of Open Access Journals (Sweden)
Mauritz Vestberg
2012-03-01
Full Text Available The impact of host mycotrophy on arbuscular mycorrhizal fungal (AMF markers was studied in a temperate agricultural soil cropped with mycorrhizal barley, flax, reed canary-grass, timothy, caraway and quinoa and non-mycorrhizal buckwheat, dyer's woad, nettle and false flax. The percentage of AMF root colonization, the numbers of infective propagules by the Most Probable Number (MPN method, and the amounts of signature Phospholipid Fatty Acid (PLFA 16:1ω5 and Neutral Lipid Fatty Acid (NLFA 16:1ω5 were measured as AMF markers. Crop had a significant impact on MPN levels of AMF, on NLFA 16:1ω5 levels in bulk and rhizosphere soil and on PLFA 16:1ω5 levels in rhizosphere soil. Reed canary-grass induced the highest levels of AMF markers. Mycorrhizal markers were at low levels in all non-mycorrhizal crops. NLFA 16:1ω5 and the ratio of NLFA to PLFA 16:1ω5 from bulk soil are adequate methods as indicators of AMF biomass in soil.
Phospholipid fatty acid analysis as part of the Yucca Mountain Project. Final report
International Nuclear Information System (INIS)
Ringelberg, D.B.; White, D.C.
1996-01-01
In support of the Yucca Mountain subsurface microbial characterization project phospholipid fatty acid (PLFA) analyses for viable microbial biomass, community composition and nutritional status were performed. Results showed a positive correlation between a decrease in viable biomass and increase in depth with the lowest biomass values being obtained from the Topopah Spring geologic horizon. A plot of the ratio of non-viable (diglyceride fatty acids) to viable (PLFA) cells also showed the lowest values to derive from the Topopah Spring horizon. Estimations of microbial community composition, made from the patterns of PLFA recovered from the sediment samples, revealed similarities between samples collected within the same geologic horizons: Tiva Canyon, Pre-Pah Canyon and Topopah Spring. Results indicated the presence of mixed communities composed of gram positive, gram negative, actinomycete and obligate anaerobic bacteria. Culturable organisms, recovered from similar sediments, were representative of the same bacterial classifications although gram positive bacterial isolates typically outnumbered gram negative isolates. Within the gram negative bacterial community, corroborative indicators of physiological stress were apparent in the Topopah Spring horizon
DEFF Research Database (Denmark)
Bendtsen, Katja Maria Bangsgaard; Krych, Lukasz; Sørensen, Dorte Bratbo
2012-01-01
to grid floor. Stressing the mice clearly changed the cecal microbiota as determined by both DGGE and pyrosequencing. Odoribacter, Alistipes and an unclassified genus from the Coriobacteriaceae family increased significantly in the grid floor housed mice. Compared to baseline, the mice exposed to grid......Stress has profound influence on the gastro-intestinal tract, the immune system and the behavior of the animal. In this study, the correlation between gut microbiota composition determined by Denaturing Grade Gel Electrophoresis (DGGE) and tag-encoded 16S rRNA gene amplicon pyrosequencing (454/FLX......) and behavior in the Tripletest (Elevated Plus Maze, Light/Dark Box, and Open Field combined), the Tail Suspension Test, and Burrowing in 28 female BALB/c mice exposed to two weeks of grid floor induced stress was investigated. Cytokine and glucose levels were measured at baseline, during and after exposure...
Energy Technology Data Exchange (ETDEWEB)
Crossman, Z.M.; Evershed, R.P. [Bristol Univ., Organic Geochemistry Unit, Biogeochemistry Research Centre, Bristol (United Kingdom); Ineson, P. [York Univ., Dept. of Biology, York (United Kingdom)
2005-05-15
The occurrence of methane-oxidising bacteria in soils has received increasing attention because of their role as a sink for atmospheric methane. However, such bacteria are not amenable to modern culturing techniques and hence the widespread interest in the development of methods of cultivation-independent analysis. In the following investigation, a combination of stable isotope labelling with phospholipid fatty acid (PLFA) and bacteriohopanoid analysis was employed in an effort to characterise this functional group of bacteria. Results suggest a novel population of methane-oxidising bacteria related to type II culturable methanotrophs, in particular, the Methylocapsa and Methylocella genera of bacteria. (Author)
Randazzo, Cinzia L; Torriani, Sandra; Akkermans, Antoon D L; de Vos, Willem M; Vaughan, Elaine E
2002-04-01
The diversity and dynamics of the microbial communities during the manufacturing of Ragusano cheese, an artisanal cheese produced in Sicily (Italy), were investigated by a combination of classical and culture-independent approaches. The latter included PCR, reverse transcriptase-PCR (RT-PCR), and denaturing gradient gel electrophoresis (DGGE) of 16S rRNA genes (rDNA). Bacterial and Lactobacillus group-specific primers were used to amplify the V6 to V8 and V1 to V3 regions of the 16S rRNA gene, respectively. DGGE profiles from samples taken during cheese production indicated dramatic shifts in the microbial community structure. Cloning and sequencing of rDNA amplicons revealed that mesophilic lactic acid bacteria (LAB), including species of Leuconostoc, Lactococcus lactis, and Macrococcus caseolyticus were dominant in the raw milk, while Streptococcus thermophilus prevailed during lactic fermentation. Other thermophilic LAB, especially Lactobacillus delbrueckii and Lactobacillus fermentum, also flourished during ripening. Comparison of the rRNA-derived patterns obtained by RT-PCR to the rDNA DGGE patterns indicated a substantially different degree of metabolic activity for the microbial groups detected. Identification of cultivated LAB isolates by phenotypic characterization and 16S rDNA analysis indicated a variety of species, reflecting to a large extent the results obtained from the 16S rDNA clone libraries, with the significant exception of the Lactobacillus delbrueckii species, which dominated in the ripening cheese but was not detected by cultivation. The present molecular approaches combined with culture can effectively describe the complex ecosystem of natural fermented dairy products, giving useful information for starter culture design and preservation of artisanal fermented food technology.
Lee, O. O.
2009-04-10
This study attempted to assess whether conspecific or congeneric sponges around San Juan Island, Washington, harbor specific bacterial communities. We used a combination of culture-independent DNA fingerprinting techniques (terminal restriction fragment length polymorphism and denaturing gradient gel electrophoresis [DGGE]) and culture-dependent approaches. The results indicated that the bacterial communities in the water column consisted of more diverse bacterial ribotypes than and were drastically different from those associated with the sponges. High levels of similarity in sponge-associated bacterial communities were found only in Myxilla incrustans and Haliclona rufescens, while the bacterial communities in Halichondria panicea varied substantially among sites. Certain terminal restriction fragments or DGGE bands were consistently obtained for different individuals of M. incrustans and H. rufescens collected from different sites, suggesting that there are stable or even specific associations of certain bacteria in these two sponges. However, no specific bacterial associations were found for H. panicea or for any one sponge genus. Sequencing of nine DGGE bands resulted in recovery of seven sequences that best matched the sequences of uncultured Proteobacteria. Three of these sequences fell into the sponge-specific sequence clusters previously suggested. An uncultured alphaproteobacterium and a culturable Bacillus sp. were found exclusively in all M. incrustans sponges, while an uncultured gammaproteobacterium was unique to H. rufescens. In contrast, the cultivation approach indicated that sponges contained a large proportion of Firmicutes, especially Bacillus, and revealed large variations in the culturable bacterial communities associated with congeneric and conspecific sponges. This study revealed sponge species-specific but not genus- or site-specific associations between sponges and bacterial communities and emphasized the importance of using a combination
Jin, V. L.; Schaeffer, S. M.; Ziegler, S. E.; Evans, R. D.
2011-06-01
Changes in the rates of nitrogen (N) cycling, microbial carbon (C) substrate use, and extracellular enzyme activities in a Mojave Desert ecosystem exposed to elevated atmospheric CO2 suggest shifts in the size and/or functional characteristics of microbial assemblages in two dominant soil microsites: plant interspaces and under the dominant shrub Larrea tridentata. We used ester-linked phospholipid fatty acid (PLFA) biomarkers as a proxy for microbial biomass to quantify spatial and temporal differences in soil microbial communities from February 2003 to May 2005. Further, we used the 13C signature of the fossil CO2 source for elevated CO2 plots to trace recent plant C inputs into soil organic matter (SOM) and broad microbial groups using δ13C (‰). Differences between individual δ13CPLFA and δ13CSOM for fungal biomarkers indicated active metabolism of newer C in elevated CO2 soils. Total PLFA-C was greater in shrub microsites compared to plant interspaces, and CO2 treatment differences within microsites increased under higher soil water availability. Total, fungal, and bacterial PLFA-C increased with decreasing soil volumetric water content (VWC) in both microsites, suggesting general adaptations to xeric desert conditions. Increases in fungal-to-bacterial PLFA-C ratio with decreasing VWC reflected functional group-specific responses to changing soil water availability. While temporal and spatial extremes in resource availability in desert ecosystems contribute to the difficulty in identifying common trends or mechanisms driving microbial responses in less extreme environments, we found that soil water availability and soil microsite interacted with elevated CO2 to shift fungal and bacterial biomarker abundances in Mojave Desert soils.
International Nuclear Information System (INIS)
Vetter, Alexandra; Mangelsdorf, Kai; Wolfgramm, Markus; Rauppach, Kerstin; Schettler, Georg; Vieth-Hillebrand, Andrea
2012-01-01
In order to monitor the operating mode of the cold storage of the German Parliament (North German Basin) the fluid chemistry and the phospholipid fatty acid (PLFA) composition of the indigenous microbial community have been monitored from August 2006 to August 2009. During this time two periods of reduced injection (clogging events) characterized by Fe precipitates and microbial biofilms in filters occurred in the injection wells impairing the operating state of the investigated cold storage. The fluid monitoring revealed the presence of sufficient amounts of potential C and energy sources (e.g. DOC and SO 4 2- ) in the process water to sustain microbial life in the cold storage. In times of reduced injection the PLFA inventory of the microbial community differs significantly from times of normal operating phases indicating compositional changes in the indigenous microbial ecosystem. The most affected fatty acids (FAs) are 16:1ω7c (increase), 16:1ω7t (decrease) and 18:1ω7c (increase), interpreted to originate mainly from Fe and S oxidizers, as well as branched FA with 15, 16 and 17 C atoms (decrease) most likely representing sulfate-reducing bacteria (SRB). Based on this variability, PLFA ratios have been created to reflect the increasing dominance of biofilm forming S and Fe oxidizers during the disturbance periods. These ratios are potential diagnostic tools to assess the microbiological contribution to the clogging events and to find appropriate counteractive measures (e.g. mechanical cleaning vs disinfection). The correlation between changes in the PLFA composition and the operational state suggests that microbially mediated processes play a significant role in the observed clogging events in the investigated cold storage.
Membrane Lipids as Indicators for Viable Bacterial Communities Inhabiting Petroleum Systems.
Gruner, Andrea; Mangelsdorf, Kai; Vieth-Hillebrand, Andrea; Horsfield, Brian; van der Kraan, Geert M; Köhler, Thomas; Janka, Christoph; Morris, Brandon E L; Wilkes, Heinz
2017-08-01
Microbial activity in petroleum reservoirs has been implicated in a suite of detrimental effects including deterioration of petroleum quality, increases in oil sulfur content, biofouling of steel pipelines and other infrastructures, and well plugging. Here, we present a biogeochemical approach, using phospholipid fatty acids (PLFAs), for detecting viable bacteria in petroleum systems. Variations within the bacterial community along water flow paths (producing well, topside facilities, and injection well) can be elucidated in the field using the same technique, as shown here within oil production plants in the Molasse Basin of Upper Austria. The abundance of PLFAs is compared to total cellular numbers, as detected by qPCR of the 16S rDNA gene, to give an overall comparison between the resolutions of both methods in a true field setting. Additionally, the influence of biocide applications on lipid- and DNA-based quantification was investigated. The first oil field, Trattnach, showed significant PLFA abundances and cell numbers within the reservoir and topside facilities. In contrast, the second field (Engenfeld) showed very low PLFA levels overall, likely due to continuous treatment of the topside facilities with a glutaraldehyde-based antimicrobial. In comparison, Trattnach is dosed once per week in a batch fashion. Changes within PLFA compositions across the flow path, throughout the petroleum production plants, point to cellular adaptation within the system and may be linked to shifts in the dominance of certain bacterial types in oil reservoirs versus topside facilities. Overall, PLFA-based monitoring provides a useful tool to assess the abundance and high-level taxonomic diversity of viable microbial populations in oil production wells, topside infrastructure, pipelines, and other related facilities.
Hume, Michael; Sohail, Muhammad Umar
2018-04-01
Enteropathogen colonization and product contamination are major poultry industry problems. The emergence of antibiotic resistance, and associated risks to human health, is limiting the use of antibiotics as first-line defense against enteropathogens in poultry. The chitin derivative, chitosan, has drawn substantial attention for its bactericidal properties. Different molecular weight (MW) chitosans can have varied effects against different bacteria in monoculture. In the current study, cecal contents from each of three market-age broilers and Salmonella Typhimurium, as indicator enteropathogen, were exposed to in vitro anaerobic culture to three chitosan preparations (0.08%, wt/vol), low (LMW), medium (MMW), and coarse (CMW). Effects of chitosan and the carrier solvent acetic acid, on cecal bacteria and Salmonella, were examined by denaturing gradient gel electrophoresis (DGGE) and Salmonella enumeration. Bacterial profiles for the three cecal contents were shown by DGGE to be very different. Each of the three cecal contents grown in the presence of 0.08% acetic acid was very different from the same contents grown without the chitosan solvent. Culturing cecal contents in the presence of chitosan altered the bacterial DGGE profiles from the control and acetic acid-only cultures. The DGGE chitosan-treated profiles for all three cecal sources were identical to each other regardless of the MW chitosan in the culture medium. Compared with Salmonella in monoculture, Salmonella decreased (p < 0.05) by about 1.5 log CFU/mL when grown in mixed culture with cecal contents. Salmonella monocultures in the presence of 0.08% of the chitosan solvent acetic acid decreased (p < 0.05) counts by almost 3.5 log CFU/mL. Combining acetic acid and cecal contents reduced (p < 0.05) Salmonella by 7 log CFU/mL. Adding the chitosan preparations to the mixtures reduced (p < 0.05) Salmonella by 8 log CFU/mL.
Mangrove succession enriches the sediment microbial community in South China.
Chen, Quan; Zhao, Qian; Li, Jing; Jian, Shuguang; Ren, Hai
2016-06-06
Sediment microorganisms help create and maintain mangrove ecosystems. Although the changes in vegetation during mangrove forest succession have been well studied, the changes in the sediment microbial community during mangrove succession are poorly understood. To investigate the changes in the sediment microbial community during succession of mangroves at Zhanjiang, South China, we used phospholipid fatty acid (PLFA) analysis and the following chronosequence from primary to climax community: unvegetated shoal; Avicennia marina community; Aegiceras corniculatum community; and Bruguiera gymnorrhiza + Rhizophora stylosa community. The PLFA concentrations of all sediment microbial groups (total microorganisms, fungi, gram-positive bacteria, gram-negative bacteria, and actinomycetes) increased significantly with each stage of mangrove succession. Microbial PLFA concentrations in the sediment were significantly lower in the wet season than in the dry season. Regression and ordination analyses indicated that the changes in the microbial community with mangrove succession were mainly associated with properties of the aboveground vegetation (mainly plant height) and the sediment (mainly sediment organic matter and total nitrogen). The changes in the sediment microbial community can probably be explained by increases in nutrients and microhabitat heterogeneity during mangrove succession.
Directory of Open Access Journals (Sweden)
Koichi Fujie
2012-03-01
Full Text Available Supercritical fluid extraction (SFE was used in the analysis of bacterial respiratory quinone (RQ, bacterial phospholipid fatty acid (PLFA, and archaeal phospholipid ether lipid (PLEL from anaerobically digested sludge. Bacterial RQ were determined using ultra performance liquid chromatography (UPLC. Determination of bacterial PLFA and archaeal PLEL was simultaneously performed using gas chromatography-mass spectrometry (GC-MS. The effects of pressure, temperature, and modifier concentration on the total amounts of RQ, PLFA, and PLEL were investigated by 23 experiments with five settings chosen for each variable. The optimal extraction conditions that were obtained through a multiple-response optimization included a pressure of 23.6 MPa, temperature of 77.6 °C, and 10.6% (v/v of methanol as the modifier. Thirty nine components of microbial lipid biomarkers were identified in the anaerobically digested sludge. Overall, the SFE method proved to be more effective, rapid, and quantitative for simultaneously extracting bacterial and archaeal lipid biomarkers, compared to conventional organic solvent extraction. This work shows the potential application of SFE as a routine method for the comprehensive analysis of microbial community structures in environmental assessments using the lipid biomarkers profile.
Cullings, Ken; Raleigh, Christopher; New, Michael H.; Henson, Joan
2005-01-01
Loss of photosynthetic area can affect soil microbial communities by altering the availability of fixed carbon. We used denaturing gradient gel electrophoresis (DGGE) and Biolog filamentous-fungus plates to determine the effects of artificial defoliation of pines in a mixed pine-spruce forest on the composition of the fungal community in a forest soil. As measured by DGGE, two fungal species were affected significantly by the defoliation of pines (P soil fungus increased. The decrease in the amount of Cenococcum organisms may have occurred because of the formation of extensive hyphal networks by species of this genus, which require more of the carbon fixed by their host, or because this fungus is dependent upon quantitative differences in spruce root exudates. The defoliation of pines did not affect the overall composition of the soil fungal community or fungal-species richness (number of species per core). Biolog filamentous-fungus plate assays indicated a significant increase (P soil fungi and the rate at which these substrates were used, which could indicate an increase in fungal-species richness. Thus, either small changes in the soil fungal community give rise to significant increases in physiological capabilities or PCR bias limits the reliability of the DGGE results. These data indicate that combined genetic and physiological assessments of the soil fungal community are needed to accurately assess the effect of disturbance on indigenous microbial systems.
DEFF Research Database (Denmark)
Nielsen, Dennis Sandris; Snitkjær, Pia; van der Berg, Franciscus Winfried J
2008-01-01
demonstrating the microbial succession taking place during the fermentation. Subsequently the DGGE spectra were correlated to the NIR spectra using Partial Least Squares regression models (PLS2). Correlations of 0.87 (bacterial derived DGGE spectra) and 0.81 (yeast derived DGGE spectra) were obtained indicating......Raw cocoa has an astringent, unpleasant taste and flavour, and has to be fermented, dried and roasted in order to obtain the characteristic cocoa flavour and taste. During the fermentation microbial activity outside the cocoa beans induces biochemical and physical changes inside the beans...... of the beans and the chemical processes inside the beans have been carried out previously. Recently it has been shown that Denaturing Gradient Gel Electrophoresis (DGGE) offers an efficient tool for monitoring the microbiological changes taking place during the fermentation of cocoa. Near Infrared (NIR...
Rocke, Emma; Jing, Hongmei; Xia, Xiaomin; Liu, Hongbin
2016-07-01
Tolo Harbor, a subtropical semi-enclosed coastal water body, is surrounded by an expanding urban community, which contributes to large concentrations of nutrient runoff, leading to algal blooms and localized hypoxic episodes. Present knowledge of protist distributions in subtropical waters during hypoxic conditions is very limited. In this study, therefore, we combined parallel 454 pyrosequencing technology and denaturing gradient gel electrophoresis (DGGE) fingerprint analyses to reveal the protist community shifts before, during, and after a 2-week hypoxic episode during the summer of 2011. Hierarchical clustering for DGGE demonstrated similar grouping of hypoxic samples separately from oxic samples. Dissolved oxygen (DO) concentration and dissolved inorganic nitrogen:phosphate (DIN:PO4) concentrations significantly affected OTU distribution in 454 sequenced samples, and a shift toward a ciliate and marine alveolate clade II (MALV II) species composition occurred as waters shifted from oxic to hypoxic. These results suggest that protist community shifts toward heterotrophic and parasitic tendencies as well as decreased diversity and richness in response to hypoxic outbreaks.
Interactions between selected PAHs and the microbial community in rhizosphere of a paddy soil.
Su, Yu H; Yang, Xue Y
2009-01-15
This study investigated the interaction of three polycyclic aromatic hydrocarbons (PAHs), i.e., naphthalene (NAP), phenanthrene (PHN), and pyrene (PYR), with the microbial community in the rhizosphere of a paddy soil and the influence of the rice (Oryza sativa) rhizosphere on the microbial community structure. A range of initial NAP, PHN and PYR levels in soil (50-200, 18-72, and 6.6-26.6 mg kg(-1), respectively) were prepared and the soil samples were then aged for 4 months (to yield PAH concentrations at 1.02-1.42, 1.32-4.77, and 2.98-18.5 mg kg(-)(1), respectively) before the soil samples were planted with rice seedlings. The microbial phospholipid-fatty-acid (PLFA) patterns in PAH-contaminated soils were analyzed to elucidate the changes of the microbial biomass and community composition. Results indicated that at the applied concentrations the PAHs were not toxic to rice seedlings, as evidenced by no growth inhibition during the 8-week planting period. However, the microbial biomass, as revealed by PLFAs, decreased significantly with increasing PAH concentration in both rhizospheric and non-rhizospheric soils. The PAHs in soils were obviously toxic to microorganisms, and the toxicity of PHN was greater than PYR due likely to the higher PHN bioavailability. Total PLFAs in rhizospheric soils were profoundly higher than those in non-rhizospheric soils, suggesting that the inhibitive effect of PAHs on microbial activities was alleviated by the rice roots. The principal component analysis (PCA) of the PLFA signatures revealed pronounced changes in PLFA pattern in rhizospheric and non-rhizospheric soils with or without spiked PAHs. Using the PLFA patterns as a biomarker, it was found that Gram-positive bacteria were more sensitive to PAHs than Gram-negative bacteria, and the rhizosphere of rice roots stimulated the growth of aerobic bacteria.
Directory of Open Access Journals (Sweden)
Valéria Maia de Oliveira
2008-09-01
Full Text Available This study aimed at evaluating potential differences among the bacterial communities from formation water and oil samples originated from biodegraded and non-biodegraded Brazilian petroleum reservoirs by using a PCR-DGGE based approach. Environmental DNA was isolated and used in PCR reactions with bacterial primers, followed by separation of 16S rDNA fragments in the DGGE. PCR products were also cloned and sequenced, aiming at the taxonomic affiliation of the community members. The fingerprints obtained allowed the direct comparison among the bacterial communities from oil samples presenting distinct degrees of biodegradation, as well as between the communities of formation water and oil sample from the non-biodegraded reservoir. Very similar DGGE band profiles were observed for all samples, and the diversity of the predominant bacterial phylotypes was shown to be low. Cloning and sequencing results revealed major differences between formation water and oil samples from the non-biodegraded reservoir. Bacillus sp. and Halanaerobium sp. were shown to be the predominant components of the bacterial community from the formation water sample, whereas the oil sample also included Alicyclobacillus acidoterrestris, Rhodococcus sp., Streptomyces sp. and Acidithiobacillus ferrooxidans. The PCR-DGGE technique, combined with cloning and sequencing of PCR products, revealed the presence of taxonomic groups not found previously in these samples when using cultivation-based methods and 16S rRNA gene library assembly, confirming the need of a polyphasic study in order to improve the knowledge of the extent of microbial diversity in such extreme environments.Este estudo teve como objetivo comparar as comunidades bacterianas de amostras de água de formação e de óleo de reservatórios de petróleo brasileiros com diferentes graus de biodegradação usando a técnica de PCR-DGGE. O DNA ambiental foi isolado e empregado em reações de PCR com primers bacterianos
Zhang, Qian; Wu, Junjun; Yang, Fan; Lei, Yao; Zhang, Quanfa; Cheng, Xiaoli
2016-11-04
The effect of agricultural land use change on soil microbial community composition and biomass remains a widely debated topic. Here, we investigated soil microbial community composition and biomass [e.g., bacteria (B), fungi (F), Arbuscular mycorrhizal fungi (AMF) and Actinomycete (ACT)] using phospholipid fatty acids (PLFAs) analysis, and basal microbial respiration in afforested, cropland and adjacent uncultivated soils in central China. We also investigated soil organic carbon and nitrogen (SOC and SON), labile carbon and nitrogen (LC and LN), recalcitrant carbon and nitrogen (RC and RN), pH, moisture, and temperature. Afforestation averaged higher microbial PLFA biomass compared with cropland and uncultivated soils with higher values in top soils than deep soils. The microbial PLFA biomass was strongly correlated with SON and LC. Higher SOC, SON, LC, LN, moisture and lower pH in afforested soils could be explained approximately 87.3% of total variation of higher total PLFAs. Afforestation also enhanced the F: B ratios compared with cropland. The basal microbial respiration was higher while the basal microbial respiration on a per-unit-PLFA basis was lower in afforested land than adjacent cropland and uncultivated land, suggesting afforestation may increase soil C utilization efficiency and decrease respiration loss in afforested soils.
Bioremediation potential of toxics by manipulation of deep terrestrial subsurface ecosystems
International Nuclear Information System (INIS)
Phelps, T.J.
1990-01-01
Mixed physiological types of bacteria in consortia recovered from subsurface contaminated sediments degrade mixed organic wastes containing carbon-rich (benzene, xylene, toluene) and halogenated hydrocarbon substrates (chlorobenzene, trichloroethylene, dichloroethylenes, vinyl chloride) in column bioreactors when provided with oxygen and methane and/or propane substrates. In expanded bed bioreactors degradation proceeds to 99% completion for several organic and chlorocarbon contaminants (60% for tetrachloroethylene) to carbon dioxide on repeated cycles in 21 days with little loss of volatiles in the control bioreactor except for a 70% loss of vinyl chloride in the control. Biodegradation is most efficient when the microbial consortia is maintained in a suboptimal nutritional state which can be monitored by ratios of endogenous storage lipid (poly beta-hydroxy alkanoic acid, PHA) to total phospholipid ester-linked fatty acids (PLFA). Under the best conditions the efficiency of biodegradation was 50-65 moles substrate (propane or propane + methane)/mole of TEC degraded. The microbial communities showed a rich diversity of microbes based on PLFA biomarkers. The effects of adding methane and/or propane in inducing specific subsets of the microbial community can readily be detected in the PLFA biomarker. Despite the presence of carbon rich substrates (benzene, toluene, xylene) in the mixed wastes, no evidence of plugging of interstitial spaces by exopolysaccharide was detected
Fungi benefit from two decades of increased nutrient availability in tundra heath soil.
Rinnan, Riikka; Michelsen, Anders; Bååth, Erland
2013-01-01
If microbial degradation of carbon substrates in arctic soil is stimulated by climatic warming, this would be a significant positive feedback on global change. With data from a climate change experiment in Northern Sweden we show that warming and enhanced soil nutrient availability, which is a predicted long-term consequence of climatic warming and mimicked by fertilization, both increase soil microbial biomass. However, while fertilization increased the relative abundance of fungi, warming caused only a minimal shift in the microbial community composition based on the phospholipid fatty acid (PLFA) and neutral lipid fatty acid (NLFA) profiles. The function of the microbial community was also differently affected, as indicated by stable isotope probing of PLFA and NLFA. We demonstrate that two decades of fertilization have favored fungi relative to bacteria, and increased the turnover of complex organic compounds such as vanillin, while warming has had no such effects. Furthermore, the NLFA-to-PLFA ratio for (13)C-incorporation from acetate increased in warmed plots but not in fertilized ones. Thus, fertilization cannot be used as a proxy for effects on warming in arctic tundra soils. Furthermore, the different functional responses suggest that the biomass increase found in both fertilized and warmed plots was mediated via different mechanisms.
Oral administration of kefiran exerts a bifidogenic effect on BALB/c mice intestinal microbiota.
Hamet, M F; Medrano, M; Pérez, P F; Abraham, A G
2016-01-01
The activity of kefiran, the exopolysaccharide present in kefir grains, was evaluated on intestinal bacterial populations in BALB/c mice. Animals were orally administered with kefiran and Eubacteria, lactobacilli and bifidobacteria populations were monitored in faeces of mice at days 0, 2, 7, 14 and 21. Profiles obtained by Denaturing Gradient Gel Electrophoresis (DGGE) with primers for Eubacteria were compared by principal component analysis and clearly defined clusters, correlating with the time of kefiran consumption, were obtained. Furthermore, profile analysis of PCR products amplified with specific oligonucleotides for bifidobacteria showed an increment in the number of DGGE bands in the groups administered with kefiran. Fluorescent In Situ Hybridisation (FISH) with specific probes for bifidobacteria showed an increment of this population in faeces, in accordance to DGGE results. The bifidobacteria population was also studied on distal colon content after 0, 2 and 7 days of kefiran administration. Analysis of PCR products by DGGE with Eubacteria primers showed an increment in the number and intensity of bands with high GC content of mice administered with kefiran. Sequencing of DGGE bands confirmed that bifidobacteria were one of the bacterial populations modified by kefiran administration. DGGE profiles of PCR amplicons obtained by using Bifidobacterium or Lactobacillus specific primers confirmed that kefiran administration enhances bifidobacteria, however no changes were observed in Lactobacillus populations. The results of the analysis of bifidobacteria populations assessed on different sampling sites in a murine model support the use of this exopolysaccharide as a bifidogenic functional ingredient.
Different substrates and starter inocula govern microbial community structures in biogas reactors.
Satpathy, Preseela; Steinigeweg, Sven; Cypionka, Heribert; Engelen, Bert
2016-01-01
The influence of different starter inocula on the microbial communities in biogas batch reactors fed with fresh maize and maize silage as substrates was investigated. Molecular biological analysis by Denaturing Gradient Gel Electrophoresis (DGGE) of 16S rRNA gene fragments showed that each inoculum bore specific microbial communities with varying predominant phylotypes. Both, bacterial and archaeal DGGE profiles displayed three distinct communities that developed depending on the type of inoculum. Although maize and silage are similar substrates, different communities dominated the lactate-rich silage compared to lactate-free fresh maize. Cluster analysis of DGGE gels showed the communities of the same substrates to be stable with their respective inoculum. Bacteria-specific DGGE analysis revealed a rich diversity with Firmicutes being predominant. The other abundant phylotypes were Bacteroidetes and Synergistetes. Archaea-specific DGGE analysis displayed less diverse community structures, identifying members of the Methanosarcinales as the dominant methanogens present in all the three biogas digesters. In general, the source of inoculum played a significant role in shaping microbial communities. Adaptability of the inoculum to the substrates fed also influenced community compositions which further impacted the rates of biogas production.
Prescreening of microbial populations for the assessment of sequencing potential.
Hanning, Irene B; Ricke, Steven C
2011-01-01
Next-generation sequencing (NGS) is a powerful tool that can be utilized to profile and compare microbial populations. By amplifying a target gene present in all bacteria and subsequently sequencing amplicons, the bacteria genera present in the populations can be identified and compared. In some scenarios, little to no difference may exist among microbial populations being compared in which case a prescreening method would be practical to determine which microbial populations would be suitable for further analysis by NGS. Denaturing density-gradient electrophoresis (DGGE) is relatively cheaper than NGS and the data comparing microbial populations are ready to be viewed immediately after electrophoresis. DGGE follows essentially the same initial methodology as NGS by targeting and amplifying the 16S rRNA gene. However, as opposed to sequencing amplicons, DGGE amplicons are analyzed by electrophoresis. By prescreening microbial populations with DGGE, more efficient use of NGS methods can be accomplished. In this chapter, we outline the protocol for DGGE targeting the same gene (16S rRNA) that would be targeted for NGS to compare and determine differences in microbial populations from a wide range of ecosystems.
Zhang, Wei; Zhang, Meng; An, Shuai; Lin, Kuangfei; Li, Hui; Cui, Changzheng; Fu, Rongbing; Zhu, Jiang
2012-09-01
Waste electrical and electronic equipment (e-waste) is now the fastest growing waste stream in the world. It is reported that polybrominated diphenyl ethers (PBDEs) and heavy metals were main contaminants in e-waste recycling site. Among these contaminants BDE-209 and Cu were widespread, yet their combined effect on soil enzyme activities and microbial community structure are not well understood. In this study, the ecotoxicological effects of both combined and single pollution of BDE-209 and Cu at different concentration levels were studied under laboratory conditions. The activities of soil catalase, urease and saccharase were sensitive to BDE-209 and Cu pollution. Although the enzyme activities varied over time, the concentration effects were obvious. Statistical analyses revealed that, at the same incubation time, as the concentration of BDE-209 or Cu increased, the enzyme activities were decreased. Combined effects of both BDE-209 and Cu were different from that of BDE-209 or Cu alone. Enzyme activities data were essentially based on the multiple regression technique. The results showed that the action and interaction between BDE-209 and Cu were strongly dependent on the exposure time, as the combined effects of BDE-209 and Cu were either synergistic or antagonistic at different incubation times. Soil catalase and saccharase were more comfortable used as indicators of BDE-209 and Cu combined pollution, as the variation trends were similar to the single contaminant treatments, and the responses were quick and significant. Denaturing Gradient Gel Electrophoresis (DGGE) analysis of bacterial 16S rDNA gene showed that BDE-209 and Cu pollution altered the bacterial community structure by promoting changes in species composition and species richness. The existence of BDE-209 and Cu in soils reduced the microbial diversity, and the concentration effects were obvious. Overall, microbial diversity in the combined treatments were lower than the single ones, and when the
Ruminal microbe of biohydrogenation of trans-vaccenic acid to stearic acid in vitro
Directory of Open Access Journals (Sweden)
Li Dan
2012-02-01
Full Text Available Abstract Background Optimization of the unsaturated fatty acid composition of ruminant milk and meat is desirable. Alteration of the milk and fatty acid profile was previously attempted by the management of ruminal microbial biohydrogenation. The aim of this study was to identify the group of ruminal trans-vaccenic acid (trans-11 C18:1, t-VA hydrogenating bacteria by combining enrichment studies in vitro. Methods The enrichment culture growing on t-VA was obtained by successive transfers in medium containing t-VA. Fatty acids were detected by gas chromatograph and changes in the microbial composition during enrichment were analyzed by denaturing gradient gel electrophoresis (DGGE. Prominent DGGE bands of the enrichment cultures were identified by 16S rRNA gene sequencing. Results The growth of ruminal t-VA hydrogenating bacteria was monitored through the process of culture transfer according to the accumulation of stearic acid (C18:0, SA and ratio of the substrate (t-VA transformed to the product (SA. A significant part of the retrieved 16S rRNA gene sequences was most similar to those of uncultured bacteria. Bacteria corresponding to predominant DGGE bands in t-VA enrichment cultures clustered with t-VA biohydrogenated bacteria within Group B. Conclusions This study provides more insight into the pathway of biohydrogenation. It also may be important to control the production of t-VA, which has metabolic and physiological benefits, through management of ruminal biohydrogenation bacterium.
Directory of Open Access Journals (Sweden)
C. Zhang
2017-10-01
Full Text Available The nitrate to ammonium ratios in nitrogen (N compounds in wet atmospheric deposits have increased over the recent past, which is a cause for some concern as the individual effects of nitrate and ammonium deposition on the biomass of different soil microbial communities and enzyme activities are still poorly defined. We established a field experiment and applied ammonium (NH4Cl and nitrate (NaNO3 at monthly intervals over a period of 4 years. We collected soil samples from the ammonium and nitrate treatments and control plots in three different seasons, namely spring, summer, and fall, to evaluate the how the biomass of different soil microbial communities and enzyme activities responded to the ammonium (NH4Cl and nitrate (NaNO3 applications. Our results showed that the total contents of phospholipid fatty acids (PLFAs decreased by 24 and 11 % in the ammonium and nitrate treatments, respectively. The inhibitory effects of ammonium on Gram-positive bacteria (G+ and bacteria, fungi, actinomycetes, and arbuscular mycorrhizal fungi (AMF PLFA contents ranged from 14 to 40 % across the three seasons. We also observed that the absolute activities of C, N, and P hydrolyses and oxidases were inhibited by ammonium and nitrate, but that nitrate had stronger inhibitory effects on the activities of acid phosphatase (AP than ammonium. The activities of N-acquisition specific enzymes (enzyme activities normalized by total PLFA contents were about 21 and 43 % lower in the ammonium and nitrate treatments than in the control, respectively. However, the activities of P-acquisition specific enzymes were about 19 % higher in the ammonium treatment than in the control. Using redundancy analysis (RDA, we found that the measured C, N, and P hydrolysis and polyphenol oxidase (PPO activities were positively correlated with the soil pH and ammonium contents, but were negatively correlated with the nitrate contents. The PLFA biomarker contents were positively
Zhang, Chuang; Zhang, Xin-Yu; Zou, Hong-Tao; Kou, Liang; Yang, Yang; Wen, Xue-Fa; Li, Sheng-Gong; Wang, Hui-Min; Sun, Xiao-Min
2017-10-01
The nitrate to ammonium ratios in nitrogen (N) compounds in wet atmospheric deposits have increased over the recent past, which is a cause for some concern as the individual effects of nitrate and ammonium deposition on the biomass of different soil microbial communities and enzyme activities are still poorly defined. We established a field experiment and applied ammonium (NH4Cl) and nitrate (NaNO3) at monthly intervals over a period of 4 years. We collected soil samples from the ammonium and nitrate treatments and control plots in three different seasons, namely spring, summer, and fall, to evaluate the how the biomass of different soil microbial communities and enzyme activities responded to the ammonium (NH4Cl) and nitrate (NaNO3) applications. Our results showed that the total contents of phospholipid fatty acids (PLFAs) decreased by 24 and 11 % in the ammonium and nitrate treatments, respectively. The inhibitory effects of ammonium on Gram-positive bacteria (G+) and bacteria, fungi, actinomycetes, and arbuscular mycorrhizal fungi (AMF) PLFA contents ranged from 14 to 40 % across the three seasons. We also observed that the absolute activities of C, N, and P hydrolyses and oxidases were inhibited by ammonium and nitrate, but that nitrate had stronger inhibitory effects on the activities of acid phosphatase (AP) than ammonium. The activities of N-acquisition specific enzymes (enzyme activities normalized by total PLFA contents) were about 21 and 43 % lower in the ammonium and nitrate treatments than in the control, respectively. However, the activities of P-acquisition specific enzymes were about 19 % higher in the ammonium treatment than in the control. Using redundancy analysis (RDA), we found that the measured C, N, and P hydrolysis and polyphenol oxidase (PPO) activities were positively correlated with the soil pH and ammonium contents, but were negatively correlated with the nitrate contents. The PLFA biomarker contents were positively correlated with soil
Cabrol, Léa; Malhautier, Luc; Poly, Franck; Lepeuple, Anne-Sophie; Fanlo, Jean-Louis
2010-01-01
In this study, we explored methodological aspects of nucleic acid recovery from microbial communities involved in a gas biofilter filled with pine bark woodchips. DNA was recovered indirectly in two steps, comparing different methods: cell dispersion (crushing, shaking, and sonication) and DNA extraction (three commercial kits and a laboratory protocol). The objectives were (a) to optimize cell desorption from the packing material and (b) to compare the 12 combinations of desorption and extraction methods, according to three relevant criteria: DNA yield, DNA purity, and community structure representation by denaturing gradient gel electrophoresis (DGGE). Cell dispersion was not influenced by the operational parameters tested for shaking and blending, while it increased with time for sonication. DNA extraction by the laboratory protocol provided the highest DNA yields, whereas the best DNA purity was obtained by a commercial kit designed for DNA extraction from soil. After successful PCR amplification, the 12 methods did not generate the same bias in microbial community representation. Eight combinations led to high diversity estimation, independently of the experimental procedure. Among them, six provided highly similar DGGE profiles. Two protocols generated a significantly dissimilar community profile, with less diversity. This study highlighted the crucial importance of DNA recovery bias evaluation.
Genotyping isolates of the entomopathogenic fungus Beauveria ...
African Journals Online (AJOL)
Multi-locus denaturing gradient gel electrophoresis (DGGE) analysis was developed to investigate the genotypes of Beauveria bassiana sensu lato. ... These results demonstrated that multi-locus DGGE is a potentially useful molecular marker for genotyping, identifying and tracking the fates of experimentally released ...
Andreazza, Robson; Okeke, Benedict C; Pieniz, Simone; Bortolon, Leandro; Lambais, Márcio R; Camargo, Flávio A O
2012-04-01
Long-term copper application in vineyards and copper mining activities cause heavy metal pollution sites. Such sites need remediation to protect soil and water quality. Bioremediation of contaminated areas through bioleaching can help to remove copper ions from the contaminated soils. Thus, the aim of this work was to evaluate the effects of different treatments for copper bioleaching in two diverse copper-contaminated soils (a 40-year-old vineyard and a copper mining waste) and to evaluate the effect on microbial community by applying denaturing gradient gel electrophoresis (DGGE) of 16S ribosomal DNA amplicons and DNA sequence analysis. Several treatments with HCl, H(2)SO(4), and FeSO(4) were evaluated by stimulation of bioleaching of copper in the soils. Treatments and extractions using FeSO(4) and H(2)SO(4) mixture at 30°C displayed more copper leaching than extractions with deionized water at room temperature. Treatment with H(2)SO(4) supported bioleaching of as much as 120 mg kg(-1) of copper from vineyard soil after 115 days of incubation. DGGE analysis of the treatments revealed that some treatments caused greater diversity of microorganisms in the vineyard soil compared to the copper mining waste. Nucleotide Blast of PCR-amplified fragments of 16S rRNA gene bands from DGGE indicated the presence of Rhodobacter sp., Silicibacter sp., Bacillus sp., Paracoccus sp., Pediococcus sp., a Myxococcales, Clostridium sp., Thiomonas sp., a firmicute, Caulobacter vibrioides, Serratia sp., and an actinomycetales in vineyard soil. Contrarily, Sphingomonas was the predominant genus in copper mining waste in most treatments. Paracoccus sp. and Enterobacter sp. were also identified from DGGE bands of the copper mining waste. Paracoccus species is involved in the copper bioleaching by sulfur oxidation system, liberating the copper bounded in the soils and hence promoting copper bioremediation. Results indicate that stimulation of bioleaching with a combination of FeSO(4
Stsepetova, J.; Sepp, E.; Julge, K.; Vaughan, E.E.; Mikelsaar, M.; Vos, de W.M.
2007-01-01
The composition of intestinal microbiota and the Bifidobacterium group community in 20 allergic and 20 nonallergic 5-year-old children was visualized by PCR-denaturing gradient gel electrophoresis (DGGE). The number of dominant bands in the DGGE profiles was smaller in allergic children than in
Effects of specific carbohydrates on the intestinal microbiota
DEFF Research Database (Denmark)
Hemmingsen, Lene; Holck, Jesper; Meyer, Anne S.
that S2 produced a DGGE profile different from fermentations of S1 and the control substrate FOS in a Pearson correlation cluster analysis, indicating that the degree of polymerization (DP) was decisive for which bacteria were stimulated by the oligosaccharides. Additionally, DGGE results...
Bacterial population in traditional sourdough evaluated by molecular methods.
Randazzo, C L; Heilig, H; Restuccia, C; Giudici, P; Caggia, C
2005-01-01
To study the microbial communities in artisanal sourdoughs, manufactured by traditional procedure in different areas of Sicily, and to evaluate the lactic acid bacteria (LAB) population by classical and culture-independent approaches. Forty-five LAB isolates were identified both by phenotypic and molecular methods. The restriction fragment length polymorphism and 16S ribosomal DNA gene sequencing gave evidence of a variety of species with the dominance of Lactobacillus sanfranciscensis and Lactobacillus pentosus, in all sourdoughs tested. Culture-independent method, such as denaturing gradient gel electrophoresis (DGGE) of the V6-V8 regions of the 16S rDNA, was applied for microbial community fingerprint. The DGGE profiles revealed the dominance of L. sanfranciscensis species. In addition, Lactobacillus-specific primers were used to amplify the V1-V3 regions of the 16S rDNA. DGGE profiles flourished the dominance of L. sanfranciscensis and Lactobacillus fermentum in the traditional sourdoughs, and revealed that the closely related species Lactobacillus kimchii and Lactobacillus alimentarius were not discriminated. Lactobacillus-specific PCR-DGGE analysis is a rapid tool for rapid detection of Lactobacillus species in artisanal sourdough. This study reports a characterization of Lactobacillus isolates from artisanal sourdoughs and highlights the value of DGGE approach to detect uncultivable Lactobacillus species.
Electrochemical Energy Summit An International Summit in Support of Societal Energy Needs
2015-03-31
grouped by the unweighted pair-group method using arithmetic averages ( UPGMA ) and relying on the Bray-Curtis coefficient using the BioNumerics 4.61...illumination, the DGGE fingerprint gel was numerically analysed using the BioNumerics 4.61 software. The DGGE fingerprints were clustered using UPGMA
Comparison of bacterial communities of tilapia fish from Cameroon ...
African Journals Online (AJOL)
Comparison of bacterial communities of tilapia fish from Cameroon and Vietnam using PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis) ... The different PCR-DGGE 16S rDNA banding profiles obtained were analysed and results showed that there were specific bands for each geographical ...
Haruta, Shin; Ueno, Shintaro; Egawa, Isao; Hashiguchi, Kazunori; Fujii, Akira; Nagano, Masanobu; Ishii, Masaharu; Igarashi, Yasuo
2006-05-25
Denaturing gradient gel electrophoresis (DGGE) based on small subunit rRNA gene was applied to a traditional rice vinegar fermentation process in which the conversion of rice starch into acetic acid proceeded in a pot. The fungal DGGE profile indicated that the transition from Aspergillus oryzae to Saccharomyces sp. took place at the initial stage at which alcohol production was observed. The early stage was characterized by the coexistence of Saccharomyces sp. and lactic acid bacteria. Almost all of the bacterial DGGE bands related to lactic acid bacteria were replaced by bands derived from Lactobacillus acetotolerance and Acetobacter pasteurianus at the stage at which acetic acid started to accumulate. The microbial succession, tested in three different pots, was found to be essentially identical. Among the bacteria isolated at the early stage, some species differed from those detected by DGGE. This is the first report to reveal the microbial community succession that occurs during a unique vinegar fermentation process, as determined by a culture-independent method.
Successive changes in community structure of an ethylbenzene-degrading sulfate-reducing consortium.
Nakagawa, Tatsunori; Sato, Shinya; Yamamoto, Yoko; Fukui, Manabu
2002-06-01
The microbial community structure and successive changes in a mesophilic ethylbenzene-degrading sulfate-reducing consortium were for the first time clarified by the denaturing gradient gel electrophoresis (DGGE) analysis of the PCR amplified 16S rRNA gene fragments. At least ten bands on the DGGE gel were detected in the stationary phase. Phylogenetic analysis of the DGGE bands revealed that the consortium consisted of different eubacterial phyla including the delta subgroup of Proteobacteria, the order Sphingobacteriales, the order Spirochaetales, and the unknown bacterium. The most abundant band C was closely related to strain mXyS1, an m-xylene-degrading sulfate-reducing bacterium (SRB), and occurred as a sole band on DGGE gels in the logarithmic growth phase that 40% ethylbenzene was consumed accompanied by sulfide production. During further prolonged incubation, the dominancy of band C did not change. These results suggest that SRB corresponds to the most abundant band C and contributes mainly to the degradation of ethylbenzene coupled with sulfate reduction.
McAuliffe, Laura; Lawes, Joanna; Bell, Suzanna; Barlow, Alex; Ayling, Roger; Nicholas, Robin
2006-10-31
Although the role of Mycoplasma wenyonii in disease is still subject to some debate, infections have been reported to result in parasitaemia, anaemia, scrotal and hind limb oedema, tachycardia, pyrexia, infertility, swollen teats, prefemoral lymphadenopathy and decreased milk production. Previously, diagnosis of M. wenyonii has been based on blood smears but is not specific for M. wenyonii and can be difficult to interpret. We have previously described the use of PCR and denaturing gradient gel electrophoresis (DGGE) for the detection and differentiation of Mycoplasma species. DGGE enables the rapid and specific identification of Mycoplasma species and is ideally suited to detecting both mixed infections and new and unusual species. In this study, we have used DGGE with universal primers to detect M. wenyonii DNA from blood samples. DGGE can be used on blood samples as a rapid and specific test for M. wenyonii and can also be used as a screening test for other blood borne pathogens.
International Nuclear Information System (INIS)
Wang Ping; Wang Haizhen; Wu Laosheng; Di Hongjie; He Yan; Xu Jianming
2012-01-01
Biodegradation processes and changes in microbial community structure were investigated in black carbon (BC) amended soils in a laboratory experiment using two soils (black soil and red soil). We applied different percentages of charcoal as BC (0%, 0.5% and 1% by weight) with 100 mg kg −1 of phenanthrene. Soil samples were collected at different incubation times (0, 7, 15, 30, 60, 120 d). The amendment with BC caused a marked decrease in the dissipation (ascribed to mainly degradation and/or sequestration) of phenanthrene residues from soil. Extracted phenanthrene in black soil with 1% BC were higher, oppositely in red soil, 0.5% BC amendments were higher. There were significant changes in the PLFA pattern in phenanthrene-spiked soils with time but BC had little effect on the microbial community structure of phenanthrene-spiked soils, as indicated by principal component analysis (PCA) of the PLFA signatures. - Highlights: ► Extracted phenanthrene increased substantially as the BC amount increased. ► Extracted phenanthrene in black soil with 1% BC were higher, oppositely in red soil. ► BC caused a marked decrease in the dissipation of phenanthrene from soil. ► PLFA pattern in phenanthrene-spiked soils with time had significant changes. - BC amendments on phenanthrene extraction were different for two soils and time was a more effective factor in microbial community changes.
Xiao, Lie; Liu, Guo Bin; Li, Peng; Xue, Sha
2017-10-01
A water control pot experiment was conducted in climate controlled chambers to study soil carbon, nitrogen and microbial community structure and their rhizosphere effects in the rhizosphere and non rhizosphere soil of Bothriochloa ischaemum at elevated CO2 concentrations (800 μmol·mol -1 ) under three water regimes, i.e., well watered (75%-80% of field capacity, FC), moderate drought stress (55%-60% of FC), and severe drought stress (35%-40% of FC). The results showed that elevated CO2 concentration and drought stress did not have significant impacts on the content of soil organic carbon, total nitrogen or dissolved organic carbon (DOC) in the rhizosphere and bulk soils or their rhizosphere effects. Elevated CO2 concentration significantly decreased dissolved organic nitrogen (DON) content in the rhizosphere soil under moderate drought stress, increased DOC/DON, and significantly increased the negative rhizosphere effect of DON and positive rhizosphere effect of DOC/DON. Drought stress and elevated CO2 concentration did not have significant impacts on the rhizosphere effect of total and bacterial phospholipid fatty acids (PLFA). Drought stress under elevated CO2 concentration significantly increased the G + /G - PLFA in the rhizosphere soil and decreased the G + /G - PLFA in the bulk soil, so its rhizosphere effect significantly increased, indicating that the soil microbial community changed from chemoautotroph microbes to heterotrophic microbes.
Directory of Open Access Journals (Sweden)
Josef Trögl
2015-02-01
Full Text Available The phospholipid fatty acid (PLFA content was determined in samples of Paracoccus denitrificans encapsulated in silica hydrogel films prepared from prepolymerized tetramethoxysilane (TMOS. Immediately after encapsulation the total PLFA concentration was linearly proportional to the optical density (600 nm of the input microbial suspension (R2 = 0.99. After 7 days this relationship remained linear, but with significantly decreased slope, indicating a higher extinction of bacteria in suspensions of input concentration 108 cells/mL and higher. trans-Fatty acids, indicators of cytoplasmatic membrane disturbances, were below the detection limit. The cy/pre ratio (i.e., ratio of cyclopropylated fatty acids (cy17:0 + cy19:0 to their metabolic precursors (16:1ω7 + 18:1ω7, an indicator of the transition of the culture to a stationary growth-phase, decreased depending on co-immobilization of nutrients in the order phosphate buffer > mineral medium > Luria Broth rich medium. The ratio, too, was logarithmically proportional to cell concentration. These results confirm the applicability of total PLFA as an indicator for the determination of living biomass and cy/pre ratio for determination of nutrient limitation of microorganisms encapsulated in sol-gel matrices. This may be of interest for monitoring of sol-gel encapsulated bacteria proposed as optical recognition elements in biosensor construction, as well as other biotechnological applications.
Tissue-Specific Fatty Acids Response to Different Diets in Common Carp (Cyprinus carpio L.)
Böhm, Markus; Schultz, Sebastian; Koussoroplis, Apostolos-Manuel; Kainz, Martin J.
2014-01-01
Fish depend on dietary fatty acids (FA) to support their physiological condition and health. Exploring the FA distribution in common carp (Cyprinus carpio), one of the world's most consumed freshwater fish, is important to understand how and where FA of different sources are allocated. We investigated diet effects on the composition of polar and neutral lipid fatty acids (PLFA and NLFA, respectively) in eight different tissues (dorsal and ventral muscle, heart, kidney, intestine, eyes, liver and adipose tissue) of common carp. Two-year old carp were exposed to three diet sources (i.e., zooplankton, zooplankton plus supplementary feeds containing vegetable, VO, or fish oil, FO) with different FA composition. The PLFA and NLFA response was clearly tissue-specific after 210 days of feeding on different diets. PLFA were generally rich in omega-3 polyunsaturated FA and only marginally influenced by dietary FA, whereas the NLFA composition strongly reflected dietary FA profiles. However, the NLFA composition in carp tissues varied considerably at low NLFA mass ratios, suggesting that carp is able to regulate the NLFA composition and thus FA quality in its tissues when NLFA contents are low. Finally, this study shows that FO were 3X more retained than VO as NLFA particularly in muscle tissues, indicating that higher nutritional quality feeds are selectively allocated into tissues and thus available for human consumption. PMID:24733499
Tissue-specific fatty acids response to different diets in common carp (Cyprinus carpio L.).
Böhm, Markus; Schultz, Sebastian; Koussoroplis, Apostolos-Manuel; Kainz, Martin J
2014-01-01
Fish depend on dietary fatty acids (FA) to support their physiological condition and health. Exploring the FA distribution in common carp (Cyprinus carpio), one of the world's most consumed freshwater fish, is important to understand how and where FA of different sources are allocated. We investigated diet effects on the composition of polar and neutral lipid fatty acids (PLFA and NLFA, respectively) in eight different tissues (dorsal and ventral muscle, heart, kidney, intestine, eyes, liver and adipose tissue) of common carp. Two-year old carp were exposed to three diet sources (i.e., zooplankton, zooplankton plus supplementary feeds containing vegetable, VO, or fish oil, FO) with different FA composition. The PLFA and NLFA response was clearly tissue-specific after 210 days of feeding on different diets. PLFA were generally rich in omega-3 polyunsaturated FA and only marginally influenced by dietary FA, whereas the NLFA composition strongly reflected dietary FA profiles. However, the NLFA composition in carp tissues varied considerably at low NLFA mass ratios, suggesting that carp is able to regulate the NLFA composition and thus FA quality in its tissues when NLFA contents are low. Finally, this study shows that FO were 3X more retained than VO as NLFA particularly in muscle tissues, indicating that higher nutritional quality feeds are selectively allocated into tissues and thus available for human consumption.
Tissue-specific fatty acids response to different diets in common carp (Cyprinus carpio L..
Directory of Open Access Journals (Sweden)
Markus Böhm
Full Text Available Fish depend on dietary fatty acids (FA to support their physiological condition and health. Exploring the FA distribution in common carp (Cyprinus carpio, one of the world's most consumed freshwater fish, is important to understand how and where FA of different sources are allocated. We investigated diet effects on the composition of polar and neutral lipid fatty acids (PLFA and NLFA, respectively in eight different tissues (dorsal and ventral muscle, heart, kidney, intestine, eyes, liver and adipose tissue of common carp. Two-year old carp were exposed to three diet sources (i.e., zooplankton, zooplankton plus supplementary feeds containing vegetable, VO, or fish oil, FO with different FA composition. The PLFA and NLFA response was clearly tissue-specific after 210 days of feeding on different diets. PLFA were generally rich in omega-3 polyunsaturated FA and only marginally influenced by dietary FA, whereas the NLFA composition strongly reflected dietary FA profiles. However, the NLFA composition in carp tissues varied considerably at low NLFA mass ratios, suggesting that carp is able to regulate the NLFA composition and thus FA quality in its tissues when NLFA contents are low. Finally, this study shows that FO were 3X more retained than VO as NLFA particularly in muscle tissues, indicating that higher nutritional quality feeds are selectively allocated into tissues and thus available for human consumption.
Responses of soil microbial activity to cadmium pollution and elevated CO2.
Chen, Yi Ping; Liu, Qiang; Liu, Yong Jun; Jia, Feng An; He, Xin Hua
2014-03-06
To address the combined effects of cadmium (Cd) and elevated CO2 on soil microbial communities, DGGE (denaturing gradient gel electrophoresis) profiles, respiration, carbon (C) and nitrogen (N) concentrations, loessial soils were exposed to four levels of Cd, i.e., 0 (Cd0), 1.5 (Cd1.5), 3.0 (Cd3.0) and 6.0 (Cd6.0) mg Cd kg(-1) soil, and two levels of CO2, i.e., 360 (aCO2) and 480 (eCO2) ppm. Compared to Cd0, Cd1.5 increased fungal abundance but decreased bacterial abundance under both CO2 levels, whilst Cd3.0 and Cd6.0 decreased both fungal and bacterial abundance. Profiles of DGGE revealed alteration of soil microbial communities under eCO2. Soil respiration decreased with Cd concentrations and was greater under eCO2 than under aCO2. Soil total C and N were greater under higher Cd. These results suggest eCO2 could stimulate, while Cd pollution could restrain microbial reproduction and C decomposition with the restraint effect alleviated by eCO2.
Microbial community analysis of perchlorate-reducing cultures growing on zero-valent iron
International Nuclear Information System (INIS)
Son, Ahjeong; Schmidt, Carl J.; Shin, Hyejin; Cha, Daniel K.
2011-01-01
Anaerobic microbial mixed cultures demonstrated its ability to completely remove perchlorate in the presence of zero-valent iron. In order to understand the major microbial reaction in the iron-supported culture, community analysis comprising of microbial fatty acids and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) techniques was performed for perchlorate reducing cultures. Analysis of fatty acid methyl esters (FAMEs) and subsequent principal component analysis (PCA) showed clear distinctions not only between iron-supported perchlorate reducing culture and seed bacteria, but also among perchlorate-reducing cultures receiving different electron donors. The DGGE pattern targeting the chlorite dismutase (cld) gene showed that iron-supported perchlorate reducing culture is similar to hydrogen-fed cultures as compared to acetate-fed culture. The phylogenetic tree suggested that the dominant microbial reaction may be a combination of the autotrophic and heterotrophic reduction of perchlorate. Both molecular and chemotaxonomic experimental results support further understanding in the function of zero-valent iron as an adequate electron source for enhancing the microbial perchlorate reduction in natural and engineered systems.
Microbial community analysis of perchlorate-reducing cultures growing on zero-valent iron
Energy Technology Data Exchange (ETDEWEB)
Son, Ahjeong, E-mail: ason@auburn.edu [Department of Civil Engineering, Auburn University, Auburn, AL 36849 (United States); Schmidt, Carl J. [Department of Animal and Food Sciences, University of Delaware, Newark, DE 19716 (United States); Shin, Hyejin [Department of Mathematics and Statistics, Auburn University, Auburn, AL 36849 (United States); Cha, Daniel K. [Department of Civil and Environmental Engineering, University of Delaware, Newark, DE 19716 (United States)
2011-01-30
Anaerobic microbial mixed cultures demonstrated its ability to completely remove perchlorate in the presence of zero-valent iron. In order to understand the major microbial reaction in the iron-supported culture, community analysis comprising of microbial fatty acids and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) techniques was performed for perchlorate reducing cultures. Analysis of fatty acid methyl esters (FAMEs) and subsequent principal component analysis (PCA) showed clear distinctions not only between iron-supported perchlorate reducing culture and seed bacteria, but also among perchlorate-reducing cultures receiving different electron donors. The DGGE pattern targeting the chlorite dismutase (cld) gene showed that iron-supported perchlorate reducing culture is similar to hydrogen-fed cultures as compared to acetate-fed culture. The phylogenetic tree suggested that the dominant microbial reaction may be a combination of the autotrophic and heterotrophic reduction of perchlorate. Both molecular and chemotaxonomic experimental results support further understanding in the function of zero-valent iron as an adequate electron source for enhancing the microbial perchlorate reduction in natural and engineered systems.
[Effects and Biological Response on Bioremediation of Petroleum Contaminated Soil].
Yang, Qian; Wu, Man-li; Nie, Mai-qian; Wang, Ting-ting; Zhang, Ming-hui
2015-05-01
Bioaugmentation and biostimulation were used to remediate petroleum-contaminated soil which were collected from Zichang city in North of Shaanxi. The optimal bioremediation method was obtained by determining the total petroleum hydrocarbon(TPH) using the infrared spectroscopy. During the bioremediation, number of degrading strains, TPH catabolic genes, and soil microbial community diversity were determined by Most Probable Number (MPN), polymerase chain reaction (PCR) combined agarose electrophoresis, and PCR-denaturing gradient electrophoresis (DGGE). The results in different treatments showed different biodegradation effects towards total petroleum hydrocarbon (TPH). Biostimulation by adding N and P to soils achieved the best degradation effects towards TPH, and the bioaugmentation was achieved by inoculating strain SZ-1 to soils. Further analysis indicated the positive correlation between catabolic genes and TPH removal efficiency. During the bioremediation, the number of TPH and alkanes degrading strains was higher than the number of aromatic degrading strains. The results of PCR-DGGE showed microbial inoculums could enhance microbial community functional diversity. These results contribute to understand the ecologically microbial effects during the bioremediation of petroleum-polluted soil.
Cullings, Ken; Raleigh, Christopher; New, Michael H.; Henson, Joan
2005-01-01
Loss of photosynthetic area can affect soil microbial communities by altering the availability of fixed carbon. We used denaturing gradient gel electrophoresis (DGGE) and Biolog filamentous-fungus plates to determine the effects of artificial defoliation of pines in a mixed pine-spruce forest on the composition of the fungal community in a forest soil. As measured by DGGE, two fungal species were affected significantly by the defoliation of pines (P the frequency of members of the ectomycorrhizal fungus genus Cenococcum decreased significantly, while the frequency of organisms of an unidentified soil fungus increased. The decrease in the amount of Cenococcum organisms may have occurred because of the formation of extensive hyphal networks by species of this genus, which require more of the carbon fixed by their host, or because this fungus is dependent upon quantitative differences in spruce root exudates. The defoliation of pines did not affect the overall composition of the soil fungal community or fungal-species richness (number of species per core). Biolog filamentous-fungus plate assays indicated a significant increase (P the number of carbon substrates utilized by the soil fungi and the rate at which these substrates were used, which could indicate an increase in fungal-species richness. Thus, either small changes in the soil fungal community give rise to significant increases in physiological capabilities or PCR bias limits the reliability of the DGGE results. These data indicate that combined genetic and physiological assessments of the soil fungal community are needed to accurately assess the effect of disturbance on indigenous microbial systems.
Johansen, C H; Bjerrum, L; Finster, K; Pedersen, K
2006-04-01
The effect of a Campylobacter jejuni colonization on the development of the microflora of the cecum and the ileum of broiler chickens was studied using molecular methods. The infection did affect the development and complexity of the microbial communities of the ceca, but we found no permanent effect of a C. jejuni infection on the ileal microflora of the broilers. In addition, denaturant gradient gel electrophoresis (DGGE) profiles generated from cecal and ileal contents revealed several DGGE bands that were present in the control chickens, but not in the chickens colonized with C. jejuni. Some of these DGGE bands could be affiliated with Lactobacillus reuteri, Clostridium perfringens, and the genus Klebsiella.
Fungi benefit from two decades of increased nutrient availability in tundra heath soil
DEFF Research Database (Denmark)
Rinnan, Riikka; Michelsen, Anders; Bååth, Erland
2013-01-01
is a predicted long-term consequence of climatic warming and mimicked by fertilization, both increase soil microbial biomass. However, while fertilization increased the relative abundance of fungi, warming caused only a minimal shift in the microbial community composition based on the phospholipid fatty acid......If microbial degradation of carbon substrates in arctic soil is stimulated by climatic warming, this would be a significant positive feedback on global change. With data from a climate change experiment in Northern Sweden we show that warming and enhanced soil nutrient availability, which...... (PLFA) and neutral lipid fatty acid (NLFA) profiles. The function of the microbial community was also differently affected, as indicated by stable isotope probing of PLFA and NLFA. We demonstrate that two decades of fertilization have favored fungi relative to bacteria, and increased the turnover...
Directory of Open Access Journals (Sweden)
Cong Pei
2017-01-01
Full Text Available Culture-dependent and culture-independent methods were compared and evaluated in the study of the endophytic diversity of Dendrobium officinale. Culture-independent methods consisted of polymerase chain reaction–denaturing gradient gel electrophoresis (PCR-DGGE and metagenome methods. According to the results, differences were found between the three methods. Three phyla, namely Firmicutes, Proteobacteria, and Actinobacteria, were detected using the culture-dependent method, and two phyla, Firmicutes and Proteobacteria, were detected by the DGGE method. Using the metagenome method, four major phyla were determined, including Proteobacteria (76.54%, Actinobacteria (18.56%, Firmicutes (2.27%, and Bacteroidetes (1.56%. A distinct trend was obtained at the genus level in terms of the method and the corresponding number of genera determined. There were 449 genera and 16 genera obtained from the metagenome and DGGE methods, respectively, and only 7 genera were obtained through the culture-dependent method. By comparison, all the genera from the culture-dependent and DGGE methods were contained in the members determined using the metagenome method. Overall, culture-dependent methods are limited to ‘finding’ endophytic bacteria in plants. DGGE is an alternative to investigating primary diversity patterns; however, the metagenome method is still the best choice for determining the endophytic profile in plants. It is essential to use multiphasic approaches to study cultured and uncultured microbes.
Braem, G; De Vliegher, S; Verbist, B; Piessens, V; Van Coillie, E; De Vuyst, L; Leroy, F
2013-03-01
Swab samples (n=72) obtained from the teat apex of lactating dairy cows without visual signs of inflammation (n=18) were gathered on 2 well-managed Flemish dairy herds (herds 1 and 2) during the same month to assess the bacterial diversity of teat apices before milking. A combination of both culture-dependent [plating and (GTG)(5)-PCR fingerprinting of the colonies] and culture-independent [denaturing gradient gel electrophoresis (PCR-DGGE)] techniques indicated that the teat apices contain a wide diversity of bacterial genera. Despite a low bacterial load, 20 bacterial genera of 3 phyla (Actinobacteria, Firmicutes, and Proteobacteria) were present. The most prevalent bacteria were the coagulase-negative staphylococci (CNS), encompassing a total of 15 species, which were identified to the species level using a combination of (GTG)(5)-PCR fingerprinting, gene sequencing (16S ribosomal RNA and rpoB genes), and a novel PCR-DGGE technique based on the tuf-PCR amplicon. Overall bacterial diversity did not differ significantly between the herds or between noninfected and subclinically infected quarters in herd 1. In herd 1, borderline significant lower CNS species diversity was found on teat apices of noninfected quarters compared with subclinically infected quarters. The most prevalent CNS species were Staphylococcus haemolyticus and Staphylococcus equorum in both herds and Staphylococcus carnosus in herd 2. Copyright © 2013 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.
Czech Academy of Sciences Publication Activity Database
Ascher, J.; Ceccherini, M.T.; Chroňáková, Alica; Jirout, Jiří; Borgogni, F.; Elhottová, Dana; Šimek, Miloslav; Pietramellara, G.
2010-01-01
Roč. 26, č. 9 (2010), s. 1721-1726 ISSN 0959-3993 R&D Projects: GA MŠk LC06066; GA AV ČR IAA600660605 Institutional research plan: CEZ:AV0Z60660521 Keywords : cattle impact * DGGE * DGGE interfering factors Subject RIV: EH - Ecology, Behaviour Impact factor: 1.214, year: 2010
Effect of environmental conditions on the fatty acid fingerprint of microbial communities
Biryukov, Mikhail; Dippold, Michaela; Kuzyakov, Yakov
2014-05-01
Lipid biomarkers, especially phospholipids, are routinely used to characterize microbial community structure in environmental samples. Interpretations of these fingerprints mainly depend on rare results of pure cultures which were cultivated under standardized batch conditions. However, membrane lipids (e.g. phopholipid biomarker) build up the interface between microorganisms and their environment and consequently are prone to be adapted according to the environmental conditions. We cultivated several bacteria, isolated from soil (gram-positive and gram-negative) under various conditions e.g. C supply and temperature regimes. Effect of growth conditions on phospholipids fatty acid (PLFA) as well as neutral lipid fatty acids (NLFA) and glycolipid fatty acids (GLFA) was investigated by conventional method of extraction and derivatization, followed by assessments with gas chromatography mass spectrometry (GC-MS). In addition, phospholipids were measured as intact molecules by ultra high performance liquid chromatography - quadrupole - time of flight mass spectrometer (UHPLC-Q-ToF) to further assess the composition of headgroups with fatty acids residues and their response on changing environmental conditions. PLFA fingerprints revealed a strong effect of growth stage, C supply and temperature e.g. decrease of temperature increased the amount of branched and/or unsaturated fatty acids to maintain the membrane fluidity. This strongly changes the ratio of specific to unspecific fatty acids depending on environmental conditions. Therefore, amounts of specific fatty acids cannot be used to assess biomass of a functional microbial group in soil. Intracellular neutral lipids depended less on environmental conditions reflecting a more stable biomarker group but also showed less specific fatty acids then PLFA. Therefore, combination of several lipid classes is suggested as more powerful tool to assess amounts and functionality of environmental microbial communities. Further
Mutation screening of the TP53 gene by temporal temperature gradient gel electrophoresis.
Sørlie, Therese; Johnsen, Hilde; Vu, Phuong; Lind, Guro Elisabeth; Lothe, Ragnhild; Børresen-Dale, Anne-Lise
2005-01-01
A protocol for detection of mutations in the TP53 gene using temporal temperature gradient gel electrophoresis (TTGE) is described. TTGE is a mutation detection technique that separates DNA fragments differing by single base pairs according to their melting properties in a denaturing gel. It is based on constant denaturing conditions in the gel combined with a temperature gradient during the electrophoretic run. This method combines some of the advantages of the related techniques denaturing gradient gel electrophoresis (DGGE) and constant denaturant gel electrophoresis (CDGE) and eliminates some of the problems. The result is a rapid and sensitive screening technique that is robust and easily set up in smaller laboratory environments.
International Nuclear Information System (INIS)
Takahashi, Noria; Hiyama, Keiko; Kodaira, Mieko; Satoh, Chiyoko
1992-10-01
An analysis of the ATTTT repeat polymorphism located approximately 1,400 base pairs upstream from the β-globin structural gene was carried out by denaturing gradient gel electrophoresis (DGGE) of RNA:DNA duplexes. Genomic or cloned DNAs were digested with restriction enzymes and hybridized with 32 P-labeled RNA probes, and resulting RNA:DNA duplexes were examined by DGGE. A difference in the number of repeat units was recognized by differences in duplex mobility on the DGGE gel. In this study of 81 unrelated Japanese from Hiroshima, a sequence heteromorphism was observed at this site. Alleles with 5 and 6 repeats of the ATTTT unit, which had already been reported, were found in polymorphic proportions. In addition, two unreported alleles, one having 7 repeats and the other having an A-to-G nucleotide substitution in the 5th repeat, were detected. Family study data showed that the segregation of these four types of variants is consistent with an autosomal codominant mode of inheritance. This study also demonstrated that DGGE of RNA:DNA duplexes is a sensitive tool for detecting variations in DNA. (author)
Zhang, Juan; Wang, Renqing; Du, Xiaoming; Li, Fasheng; Dai, Jiulan
2012-01-01
To evaluate contamination caused by petroleum, surface soil samples were collected from both upland and paddy fields along the irrigation canals in the Hunpu wastewater irrigation region in northeast China. N-alkanes, terpanes, steranes, and phospholipid fatty acids (PLFA) in the surface soil samples were analyzed. The aliphatic hydrocarbon concentration was highest in the samples obtained from the upland field near an operational oil well; it was lowest at I-3P where wastewater irrigation promoted the downward movement of hydrocarbons. The Hunpu region was found contaminated by heavy petroleum from oxic lacustrine fresh water or marine deltaic source rocks. Geochemical parameters also indicated significantly heavier contamination and degradation in the upland fields compared with the paddy fields. Principal component analysis based on PLFA showed various microbial communities between petroleum contaminated upland and paddy fields. Gram-negative bacteria indicated by 15:0, 3OH 12:0, and 16:1(9) were significantly higher in the paddy fields, whereas Gram-positive bacteria indicated by i16:0 and 18:1(9)c were significantly higher in the upland fields (p petroleum contamination. Poly-unsaturated PLFA (18:2omega6, 9; indicative of hydrocarbon-degrading bacteria and fungi) was also significantly elevated in the upland fields. This paper recommends more sensitive indicators of contamination and degradation of petroleum in soil. The results also provide guidelines on soil pollution control and remediation in the Hunpu region and other similar regions.
Mills, Christopher T.; Slater, Gregory F.; Dias, Robert F.; Carr, Stephanie A.; Reddy, Christopher M.; Schmidt, Raleigh; Mandernack, Kevin W.
2013-01-01
Seepage of coal-bed methane (CBM) through soils is a potential source of atmospheric CH4 and also a likely source of ancient (i.e. 14C-dead) carbon to soil microbial communities. Natural abundance 13C and 14C compositions of bacterial membrane phospholipid fatty acids (PLFAs) and soil gas CO2 and CH4 were used to assess the incorporation of CBM-derived carbon into methanotrophs and other members of the soil microbial community. Concentrations of type I and type II methanotroph PLFA biomarkers (16:1ω8c and 18:1ω8c, respectively) were elevated in CBM-impacted soils compared with a control site. Comparison of PLFA and 16s rDNA data suggested type I and II methanotroph populations were well estimated and overestimated by their PLFA biomarkers, respectively. The δ13C values of PLFAs common in type I and II methanotrophs were as negative as −67‰ and consistent with the assimilation of CBM. PLFAs more indicative of nonmethanotrophic bacteria had δ13C values that were intermediate indicating assimilation of both plant- and CBM-derived carbon. Δ14C values of select PLFAs (−351 to −936‰) indicated similar patterns of CBM assimilation by methanotrophs and nonmethanotrophs and were used to estimate that 35–91% of carbon assimilated by nonmethanotrophs was derived from CBM depending on time of sampling and soil depth.
The prokarotic, endogenous storage polymer poly--hydroxybutyrate (PHB) accumulated in soil from a methane-enriched, halogenated hydrocarbon-degrading soil column. Based on phospholipid ester-linked fatty acid (PLFA) profiles, this mocrocosm has been previously reported to be sign...
Institute of Scientific and Technical Information of China (English)
Jiajia Ni; Yuhe Yu; Weisong Feng; Qingyun Yan; Gang pan; Bo Yang; Xiang Zhang; Xuemei Li
2010-01-01
It is important to assess the effect on zooplankton when perform the environmental protection or restoration technology,especially removing algal blooms,because algae were the major primary producer in algal lakes.The influence on zooplankton community after half a year of algal blooms removed by chitosan-modified soils in Taihu Lake was assessed and the rationality of carrying out the process semiannually was evaluated in the present study.Morphological composition and genetic diversity of zooplankton community were investigated by microscope checkup and polymerase chain reaction-denatured gradient gel electrophoresis (PCR-DGGE).A total of 44 zooplankton taxa (23 protozoa,17 rotifers,3 copepoda and 1 cladocera) were detected by microscope checkup,and a total of 91 bands (28 bands amplified by primers F1427-GC and R1616,63 bands amplified by primers Fung-G-C and NS1) were detected by PCR-DGGE.The results of cluster analysis or detrended correspondence analysis indicated that there was no considerable difference in morphological composition of zooplankton and DGGE profiles between experimental and control sites,and DGGE profiles could represent the biologic diversity.The study showed that zooplankton community could recover original condition after half year of algal blooms removed by chitosan-modified soils and it was acceptable to apply this process semiannually.In addition,the results revealed that PCR-DGGE could be applied to investigate the impacts of the environmental protection or restoration engineering on zooplankton community diversity.
Czech Academy of Sciences Publication Activity Database
Rejmánková, E.; Houdková, Kateřina
2006-01-01
Roč. 80, - (2006), s. 245-262 ISSN 0168-2563 Grant - others:National Science Foundation, USA 0089211 Keywords : Eleocharis cellulosa * Northern Belize * Litter bags * Cellulose * Nitrogen * Phosphorus * PLFA Subject RIV: EH - Ecology, Behaviour Impact factor: 2.536, year: 2006
Czech Academy of Sciences Publication Activity Database
Jílková, V.; Cajthaml, Tomáš; Frouz, Jan
2015-01-01
Roč. 86, JUL 2015 (2015), s. 50-57 ISSN 0038-0717 Institutional support: RVO:61388971 ; RVO:60077344 Keywords : CO2 * Microorganisms * PLFA Subject RIV: EE - Microbiology, Virology; DF - Soil Science (BC-A) Impact factor: 4.152, year: 2015
Energy Technology Data Exchange (ETDEWEB)
Lladó, S., E-mail: llado@biomed.cas.cz [Department of Microbiology, University of Barcelona, Diagonal 645, E-08028 Barcelona (Spain); Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídenská 1083, 142 20 Prague 4 (Czech Republic); Covino, S., E-mail: covino@biomed.cas.cz [Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídenská 1083, 142 20 Prague 4 (Czech Republic); Solanas, A.M., E-mail: asolanas@ub.edu [Department of Microbiology, University of Barcelona, Diagonal 645, E-08028 Barcelona (Spain); Petruccioli, M., E-mail: petrucci@unitus.it [Department for Innovation in Biological, Agro-Food and Forest Systems [DIBAF], University of Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo (Italy); D’annibale, A., E-mail: dannib@unitus.it [Department for Innovation in Biological, Agro-Food and Forest Systems [DIBAF], University of Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo (Italy); Viñas, M., E-mail: marc.vinas@irta.cat [GIRO Joint Research Unit IRTA-UPC, Institute of Research and Technology Food and Agriculture [IRTA], Torre Marimon, E-08140 Caldes de Montbui (Spain)
2015-02-11
Highlights: • Soil microbial community assessment through classical (MPN) and molecular tools (DGGE and pyrosequencing) is provided. • A failure of exogenous white rot fungi to colonize the polluted soil is shown by DGGE and pyrosequencing. • Surfactant Brij 30 hampers 4-ring PAHs degradation due to toxicity over Actinobacteria and Bacteroidetes populations. • A high prevalence of Fusarium and Scedosporium populations is revealed during soil bioremediation. • Cupriavidus, Mycobacterium and Chithinophagaceae are potential HMW–PAH degraders in the soil. - Abstract: Bacterial and fungal biodiversity throughout different biostimulation and bioaugmentation treatments applied to an industrial creosote-polluted soil were analyzed by means of polyphasic approach in order to gain insight into the microbial community structure and dynamics. Pyrosequencing data obtained from initial creosote polluted soil (after a biopiling step) revealed that Alpha and Gammaproteobacteria were the most abundant bacterial groups, whereas Fusarium and Scedosporium were the main fungal genera in the contaminated soil. At the end of 60-days laboratory scale bioremediation assays, pyrosequencing and DGGE data showed that (i) major bacterial community shifts were caused by the type of mobilizing agent added to the soil and, to a lesser extent, by the addition of lignocellulosic substrate; and (ii) the presence of the non-ionic surfactant (Brij 30) hampered the proliferation of Actinobacteria (Mycobacteriaceae) and Bacteroidetes (Chitinophagaceae) and, in the absence of lignocellulosic substrate, also impeded polycyclic aromatic hydrocarbons (PAHs) degradation. The results show the importance of implementing bioremediation experiments combined with microbiome assessment to gain insight on the effect of crucial parameters (e.g. use of additives) over the potential functions of complex microbial communities harbored in polluted soils, essential for bioremediation success.
International Nuclear Information System (INIS)
Lladó, S.; Covino, S.; Solanas, A.M.; Petruccioli, M.; D’annibale, A.; Viñas, M.
2015-01-01
Highlights: • Soil microbial community assessment through classical (MPN) and molecular tools (DGGE and pyrosequencing) is provided. • A failure of exogenous white rot fungi to colonize the polluted soil is shown by DGGE and pyrosequencing. • Surfactant Brij 30 hampers 4-ring PAHs degradation due to toxicity over Actinobacteria and Bacteroidetes populations. • A high prevalence of Fusarium and Scedosporium populations is revealed during soil bioremediation. • Cupriavidus, Mycobacterium and Chithinophagaceae are potential HMW–PAH degraders in the soil. - Abstract: Bacterial and fungal biodiversity throughout different biostimulation and bioaugmentation treatments applied to an industrial creosote-polluted soil were analyzed by means of polyphasic approach in order to gain insight into the microbial community structure and dynamics. Pyrosequencing data obtained from initial creosote polluted soil (after a biopiling step) revealed that Alpha and Gammaproteobacteria were the most abundant bacterial groups, whereas Fusarium and Scedosporium were the main fungal genera in the contaminated soil. At the end of 60-days laboratory scale bioremediation assays, pyrosequencing and DGGE data showed that (i) major bacterial community shifts were caused by the type of mobilizing agent added to the soil and, to a lesser extent, by the addition of lignocellulosic substrate; and (ii) the presence of the non-ionic surfactant (Brij 30) hampered the proliferation of Actinobacteria (Mycobacteriaceae) and Bacteroidetes (Chitinophagaceae) and, in the absence of lignocellulosic substrate, also impeded polycyclic aromatic hydrocarbons (PAHs) degradation. The results show the importance of implementing bioremediation experiments combined with microbiome assessment to gain insight on the effect of crucial parameters (e.g. use of additives) over the potential functions of complex microbial communities harbored in polluted soils, essential for bioremediation success
MICROBIAL DIVERSITY IN SURFACE SEDIMENTS: A COMPARISON OF TWO ESTUARINE CONTINUUMS
The microbial diversity in estuarine sediments of the Altamaha and Savannah Rivers in Georgia were compared temporally and spatially using phospholipid fatty acid (PLFA) analysis. Surface sediment samples collected along a salinity gradient were also analyzed for ATP, TOC, and C ...
Randazzo, Cinzia L.; Torriani, Sandra; Akkermans, Antoon D. L.; de Vos, Willem M.; Vaughan, Elaine E.
2002-01-01
The diversity and dynamics of the microbial communities during the manufacturing of Ragusano cheese, an artisanal cheese produced in Sicily (Italy), were investigated by a combination of classical and culture-independent approaches. The latter included PCR, reverse transcriptase-PCR (RT-PCR), and denaturing gradient gel electrophoresis (DGGE) of 16S rRNA genes (rDNA). Bacterial and Lactobacillus group-specific primers were used to amplify the V6 to V8 and V1 to V3 regions of the 16S rRNA gene...
Characterization of redox conditions in groundwater contaminant plumes
DEFF Research Database (Denmark)
Christensen, Thomas Højlund; Bjerg, Poul Løgstrup; Banwarth, Steven A.
2000-01-01
tools, such as MPN counts, PLFA biomarkers and redox bioassays. This paper reviews the principles behind the different approaches, summarizes methods used and evaluates the approaches based on the experience from the reported applications. C 2000 Elsevier Science B.V. All rights reserved....
32 CFR 1285.4 - Responsibilities.
2010-07-01
... Defense Other Regulations Relating to National Defense DEFENSE LOGISTICS AGENCY MISCELLANEOUS DEFENSE LOGISTICS AGENCY FREEDOM OF INFORMATION ACT PROGRAM § 1285.4 Responsibilities. (a) The Staff Director... program, providing guidance and instructions to PLFA's and PSE's. (2) Designates a FOIA manager to...
Czech Academy of Sciences Publication Activity Database
Frouz, Jan; Jílková, V.; Cajthaml, T.; Pižl, Václav; Tajovský, Karel; Háněl, Ladislav; Burešová, A.; Šimáčková, H.; Kolaříková, K.; Franklin, J.; Nawrot, J.; Groninger, J.W.; Stahl, P.D.
2013-01-01
Roč. 67, December (2013), s. 212-225 ISSN 0038-0717 R&D Projects: GA MŠk ME08019 Institutional support: RVO:60077344 Keywords : restoration * succession * ergosterol * macrofauna * microbial biomass * PLFA Subject RIV: EH - Ecology, Behaviour Impact factor: 4.410, year: 2013
Czech Academy of Sciences Publication Activity Database
Józefowska, A.; Pietrzykowski, M.; Woś, B.; Cajthaml, T.; Frouz, Jan
2017-01-01
Roč. 292, April (2017), s. 9-16 ISSN 0016-7061 Institutional support: RVO:60077344 Keywords : post mining soil * PLFA * bioturbation * C:N ratio * carbon stock * nitrogen stock Subject RIV: DF - Soil Science OBOR OECD: Soil science Impact factor: 4.036, year: 2016
The objective of this work was to evaluate the effects of fire regimes and vegetation cover on the structure and dynamics of soil microbial communities, through phospholipid fatty acid (PLFA) analysis. Comparisons were made between native areas with different woody covers ("cerra...
Bučková, Mária; Puškárová, Andrea; Ženišová, Katarína; Kraková, Lucia; Piknová, Ľubica; Kuchta, Tomáš; Pangallo, Domenico
2018-02-02
Culture-dependent and culture-independent strategies were applied to investigate the microbiota of autumn undamaged and damaged berries, winter berries and ice wine must samples of Grüner Veltliner (Veltlínske zelené) from Small Carpathian wine-producing region. One hundred twenty-six yeasts and 242 bacterial strains isolated from several microbiological media (YPD, PDA, R2A, GYC, MRS and MRS-T) were clustered by ITS-PCR and subsequent Qiaxcel electrophoresis. Representatives of each cluster were identified by sequencing. The extracellular hydrolytic properties and intracellular activities of esterase and β-glucosidase of isolates were assayed. The culture-independent approach permitted the analysis of extracted DNA and RNA coupling DGGE fingerprinting with construction of clone libraries (bacterial and fungal; DGGE-cloning). The combination of the two approaches provided comprehensive data that evidenced the presence of a complex microbiota in each analyzed sample. RNA and DNA analyses facilitated differentiation of living microorganisms from the entire microbiota. Diverse microbial communities colonized the autumn and winter berries. Generally, the combination of results obtained by the methods suggested that the must samples contained mainly Saccharomyces cerevisiae, Metschnikowia spp., Hanseniaspora uvarum, Lactococcus lactis and Leuconostoc spp. The strains exhibited interesting esterase and β-glucosidase properties, which are important for aroma formation in wine. Fermentation strategies utilising these microorganisms, could be attempted in the future in order to modulate the ice wine characteristics. Copyright © 2017 Elsevier B.V. All rights reserved.
Schäfer, Hendrik
2007-01-01
Dimethylsulfide (DMS)-degrading enrichment cultures were established from samples of coastal seawater, nonaxenic Emiliania huxleyi cultures, and mixed marine methyl halide-degrading enrichment cultures. Bacterial populations from a broad phylogenetic range were identified in the mixed DMS-degrading enrichment cultures by denaturing gradient gel electrophoresis (DGGE). Sequences of dominant DGGE bands were similar to those of members of the genera Methylophaga and Alcanivorax. Several closely ...
Lessons Learned on Bioaugmentation of DNAPL Source Zone Areas
2007-10-01
but rather have stringers, ganglia or blobs that can create an “effective pool length”. As the leading edge of these discontinuous DNAPL free-phases...terminal restriction fragment length polymorphism (T-RFLP), denaturing gradient gel electrophoresis (DGGE), and fluorescent in situ hybridization ( FISH ...question of interest (e.g. PCR, FISH , DGGE); (ii) sampling location(s); (iii) an appropriate sampling procedure; and (iv) an appropriate sample handling
DEFF Research Database (Denmark)
Albrechtsen, Hans-Jørgen; Heron, Gorm; Christensen, Thomas Højlund
1995-01-01
Aquifer sediment samples from two locations within the anaerobic leachate plume of a municipal landfill were compared with respect to microbiology (especially Fe(III)-reduction) and geochemistry. The samples close to the landfill were characterized by low contents of Fe(III), whereas samples from...... the more distant cluster were rich in Fe(III)-oxides. The active microbial population seemed to be less dense in samples more distant from the landfill (measured by ATP and phospholipid fatty acids (PLFA)), but the microbial communities were very similar in the two sample clusters according...... to the composition of PLFA. Very little, if any, Fe(III)-reduction was observed close to the landfill, but all the more distant samples showed evident microbially mediated Fe(III)-reduction. After amendment with both acetate and Fe(III), all the samples showed a potential for Fe(III)-reduction, and the in situ Fe...
DEFF Research Database (Denmark)
Reinsch, Sabine; Michelsen, Anders; Sárossy, Zsuzsa
2014-01-01
An in-situ13C pulse-labeling experiment was carried out in a temperate heath/grassland to study the impacts of elevated CO2 concentration (510ppm), prolonged summer droughts (annual exclusion of 7.6±0.8%) and increased temperature (~1°C) on belowground carbon (C) utilization. Recently assimilated C...... (13C from the pulse-label) was traced into roots, soil and microbial biomass 1, 2 and 8 days after pulse-labeling. The importance of the microbial community in C utilization was investigated using 13C enrichment patterns in different microbial functional groups on the basis of phospholipid fatty acid...... (PLFA) biomarker profiles. Climate treatments did not affect microbial abundance in soil or rhizosphere fractions in terms of total PLFA-C concentration. Elevated CO2 significantly reduced the abundance of gram-negative bacteria (17:0cy), but did not affect the abundance of decomposers (fungi...
Removal of dimethyl sulfide by the combination of non-thermal plasma and biological process.
Wei, Z S; Li, H Q; He, J C; Ye, Q H; Huang, Q R; Luo, Y W
2013-10-01
A bench scale system integrated with a non-thermal plasma (NTP) and a biotricking filtration (BTF) unit for the treatment of gases containing dimethyl sulfide (DMS) was investigated. DMS removal efficiency in the integrated system was up to 96%. Bacterial communities in the BTF were assessed by PCR-DGGE, which play the dominant role in the biological processes of metabolism, sulfur oxidation, sulfate-reducing and carbon oxidation. The addition of ozone from NTP made microbial community in BTF more complicated and active for DMS removal. The NTP oxidize DMS to simple compounds such as methanol and carbonyl sulfide; the intermediate organic products and DMS are further oxidized to sulfate, carbon dioxide, water vapors by biological degradation. These results show that NTP-BTF is achievable and open new possibilities for applying the integrated with NTP and BTF to odour gas treatment. Copyright © 2013 The Authors. Published by Elsevier Ltd.. All rights reserved.
Directory of Open Access Journals (Sweden)
L. Madueño
2009-06-01
Full Text Available Se estudió el efecto de la inoculación con la cepa Sphingomonas paucimobilis 20006FA sobre la composición bacteriana de un consorcio degradador de fenantreno en cultivos discontinuos (batch con 8 repiques sucesivos. El consorcio original se obtuvo a partir de un suelo prístino. A los fines del estudio, se obtuvieron y mantuvieron dos consorcios: uno inoculado (F200+I y otro sin inocular (F200. Se estudió la diversidad bacteriana de los consorcios mediante el análisis de microorganismos cultivables (por caracterización fenotípica y genotípica y totales (por PCR-DGGE. A lo largo de los repiques sucesivos pudo observarse en ambos consorcios una tendencia a la pérdida de la capacidad degradadora de fenantreno, acompañada por una disminución de la diversidad bacteriana. Si bien la inoculación no produjo cambios significativos en la capacidad degradadora de fenantreno de los consorcios (29,9% para F200 y 27,6% para F200+I hacia el tercer repique, sí produjo cambios en la composición bacteriana, ya que los perfiles de DGGE revelaron una dinámica estructural diferente en el consorcio inoculado. En ambos consorcios se pudo observar la presencia de una banda intensa posicionada a la misma altura que el ADN del inóculo en el gel de DGGE; sin embargo, los cultivos aislados de los consorcios que presentaban idéntica posición de banda en el perfil PCR-DGGE que la cepa S. paucimobilis 20006FA mostraron baja similitud con la cepa inoculada mediante la técnica de RAPD.The effect of the inoculant strain Sphingomonas paucimobilis 20006FA on the bacterial composition of a phenanthrene-degrading consortium obtained from a pristine soil in sequencing batch cultures was studied. Inoculated (F200+I and non-inoculated (F200 phenanthrene-degrading consortia, were obtained. Bacterial diversity of consortia was studied at cultivable (phenotype and genotype characterization and non-cultivable (PCR-DGGE levels. During the successive cultures, a loss in
Seasonal changes in and relationship between soil microbial and ...
African Journals Online (AJOL)
In April, June and October 2010, soil samples were taken from an estuary of the Yellow River. We measured microbiomass (using the soil chloroform fumigation extraction method), substrate induced respiration (SIR), and phospholipid fatty acids (PLFA). Microbe community structure and soil nematode species richness ...
Tian, Jing; Wang, Jingyuan; Dippold, Michaela; Gao, Yang; Blagodatskaya, Evgenia; Kuzyakov, Yakov
2016-06-15
The application of biochar (BC) in conjunction with mineral fertilizers is one of the most promising management practices recommended to improve soil quality. However, the interactive mechanisms of BC and mineral fertilizer addition affecting microbial communities and functions associated with soil organic matter (SOM) cycling are poorly understood. We investigated the SOM in physical and chemical fractions, microbial community structure (using phospholipid fatty acid analysis, PLFA) and functions (by analyzing enzymes involved in C and N cycling and Biolog) in a 6-year field experiment with BC and NPK amendment. BC application increased total soil C and particulate organic C for 47.4-50.4% and 63.7-74.6%, respectively. The effects of BC on the microbial community and C-cycling enzymes were dependent on fertilization. Addition of BC alone did not change the microbial community compared with the control, but altered the microbial community structure in conjunction with NPK fertilization. SOM fractions accounted for 55% of the variance in the PLFA-related microbial community structure. The particulate organic N explained the largest variation in the microbial community structure. Microbial metabolic activity strongly increased after BC addition, particularly the utilization of amino acids and amines due to an increase in the activity of proteolytic (l-leucine aminopeptidase) enzymes. These results indicate that microorganisms start to mine N from the SOM to compensate for high C:N ratios after BC application, which consequently accelerate cycling of stable N. Concluding, BC in combination with NPK fertilizer application strongly affected microbial community composition and functions, which consequently influenced SOM cycling. Copyright © 2016 Elsevier B.V. All rights reserved.
Energy Technology Data Exchange (ETDEWEB)
Touzet, N., E-mail: touzet.nicolas@itsligo.ie [Centre for Environmental Research, Innovation and Sustainability, School of Science, Department of Environmental Science, Institute of Technology Sligo, Sligo (Ireland); McCarthy, D.; Gill, A.; Fleming, G.T.A. [Microbiology, School of Natural Sciences, National University of Ireland, Galway, Galway (Ireland)
2016-05-15
The eutrophication of lakes is typically associated with high biomass proliferations of potentially toxic cyanobacteria. At a regional level, the sustainable management of water resources necessitates an approach that recognises the interconnectivity of multiple water systems within river catchments. This study examined the dynamics in summer diversity of planktonic cyanobacterial communities and microcystin toxin concentrations in two inter-connected lakes from the west of Ireland prone to nutrient enrichment. DGGE analysis of 16S rRNA gene amplicons of genotype-I cyanobacteria (typically spherical) showed changes in the communities of both Lough Corrib and Ballyquirke Lough throughout the summer, and identified cyanobacterial genotypes both unique and shared to both lakes. Microcystin concentrations, estimated via the protein phosphatase 2A inhibition assay, were greater in August than in July and June in both lakes. This was concomitant to the increased occurrence of Microcystis as evidenced by DGGE band excision and subsequent sequencing and BLAST analysis. RFLP analysis of PCR amplified mcy-A/E genes clustered together the August samples of both lakes, highlighting a potential change in microcystin producers across the two lakes. Finally, the multiple factor analysis of the combined environmental data set for the two lakes highlighted the expected pattern opposing greater water temperature and chlorophyll concentration against macronutrient concentrations, but also indicated a negative relationship between microcystin concentration and cyanobacterial diversity, possibly underlining allelopathic interactions. Despite some element of connectivity, the dissimilarity in the composition of the cyanobacterial assemblages and the timing of community change in the two lakes likely were a reflexion of niche differences determined by meteorologically-forced variation in physico-chemical parameters in the two water bodies. - Highlights: • DGGE highlighted
Directory of Open Access Journals (Sweden)
Jun Mei
Full Text Available The biochemical changes occurring during cheese ripening are directly and indirectly dependent on the microbial associations of starter cultures. Freeze-dried Tibetan kefir coculture was used as a starter culture in the Camembert-type cheese production for the first time. Therefore, it's necessary to elucidate the stability, organization and identification of the dominant microbiota presented in the cheese. Bacteria and yeasts were subjected to culture-dependent on selective media and culture-independent polymerase chain reaction (PCR-denaturing gradient gel electrophoresis (DGGE analysis and sequencing of dominant bands to assess the microbial structure and dynamics through ripening. In further studies, kefir grains were observed using scanning electron microscopy (SEM methods. A total of 147 bacteria and 129 yeasts were obtained from the cheese during ripening. Lactobacillus paracasei represents the most commonly identified lactic acid bacteria isolates, with 59 of a total of 147 isolates, followed by Lactococcus lactis (29 isolates. Meanwhile, Kazachstania servazzii (51 isolates represented the mainly identified yeast isolate, followed by Saccharomyces cerevisiae (40 isolates. However, some lactic acid bacteria detected by sequence analysis of DGGE bands were not recovered by plating. The yeast S. cerevisiae and K. servazzii are described for the first time with kefir starter culture. SEM showed that the microbiota were dominated by a variety of lactobacilli (long and curved cells growing in close association with a few yeasts in the inner portion of the grain and the short lactobacilli were observed along with yeast cells on the exterior portion. Results indicated that conventional culture method and PCR-DGGE should be combined to describe in maximal detail the microbiological composition in the cheese during ripening. The data could help in the selection of appropriate commercial starters for Camembert-type cheese.
Mei, Jun; Guo, Qizhen; Wu, Yan; Li, Yunfei
2014-01-01
The biochemical changes occurring during cheese ripening are directly and indirectly dependent on the microbial associations of starter cultures. Freeze-dried Tibetan kefir coculture was used as a starter culture in the Camembert-type cheese production for the first time. Therefore, it's necessary to elucidate the stability, organization and identification of the dominant microbiota presented in the cheese. Bacteria and yeasts were subjected to culture-dependent on selective media and culture-independent polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) analysis and sequencing of dominant bands to assess the microbial structure and dynamics through ripening. In further studies, kefir grains were observed using scanning electron microscopy (SEM) methods. A total of 147 bacteria and 129 yeasts were obtained from the cheese during ripening. Lactobacillus paracasei represents the most commonly identified lactic acid bacteria isolates, with 59 of a total of 147 isolates, followed by Lactococcus lactis (29 isolates). Meanwhile, Kazachstania servazzii (51 isolates) represented the mainly identified yeast isolate, followed by Saccharomyces cerevisiae (40 isolates). However, some lactic acid bacteria detected by sequence analysis of DGGE bands were not recovered by plating. The yeast S. cerevisiae and K. servazzii are described for the first time with kefir starter culture. SEM showed that the microbiota were dominated by a variety of lactobacilli (long and curved) cells growing in close association with a few yeasts in the inner portion of the grain and the short lactobacilli were observed along with yeast cells on the exterior portion. Results indicated that conventional culture method and PCR-DGGE should be combined to describe in maximal detail the microbiological composition in the cheese during ripening. The data could help in the selection of appropriate commercial starters for Camembert-type cheese. PMID:25360757
Hume, Michael E; Barbosa, Nei A; Dowd, Scot E; Sakomura, Nilva K; Nalian, Armen G; Martynova-Van Kley, Alexandra; Oviedo-Rondón, Edgar O
2011-11-01
A protective digestive microflora helps prevent and reduce broiler infection and colonization by enteropathogens. In the current experiment, broilers fed diets supplemented with probiotics and essential oil (EO) blends were infected with a standard mixed Eimeria spp. to determine effects of performance enhancers on ileal and cecal microbial communities (MCs). Eight treatment groups included four controls (uninfected-unmedicated [UU], unmedicated-infected, the antibiotic BMD plus the ionophore Coban as positive control, and the ionophore as negative control), and four treatments (probiotics BC-30 and Calsporin; and EO, Crina Poultry Plus, and Crina PoultryAF). Day-old broilers were raised to 14 days in floor pens on used litter and then were moved to Petersime batteries and inoculated at 15 days with mixed Eimeria spp. Ileal and cecal samples were collected at 14 days and 7 days postinfection. Digesta DNA was subjected to pyrosequencing for sequencing of individual cecal bacteria and denaturing gradient gel electrophoresis (DGGE) for determination of changes in ileal and cecal MC according to percentage similarity coefficient (%SC). Pyrosequencing is very sensitive detecting shifts in individual bacterial sequences, whereas DGGE is able to detect gross shifts in entire MC. These combined techniques offer versatility toward identifying feed additive and mild Eimeria infection modulation of broiler MC. Pyrosequencing detected 147 bacterial species sequences. Additionally, pyrosequencing revealed the presence of relatively low levels of the potential human enteropathogens Campylobacter sp. and four Shigella spp. as well as the potential poultry pathogen Clostridiun perfringens. Pre- and postinfection changes in ileal (56%SC) and cecal (78.5%SC) DGGE profiles resulted from the coccidia infection and with increased broiler age. Probiotics and EO changed MC from those seen in UU ilea and ceca. Results potentially reflect the performance enhancement above expectations in
Mei, Jun; Guo, Qizhen; Wu, Yan; Li, Yunfei
2014-01-01
The biochemical changes occurring during cheese ripening are directly and indirectly dependent on the microbial associations of starter cultures. Freeze-dried Tibetan kefir coculture was used as a starter culture in the Camembert-type cheese production for the first time. Therefore, it's necessary to elucidate the stability, organization and identification of the dominant microbiota presented in the cheese. Bacteria and yeasts were subjected to culture-dependent on selective media and culture-independent polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) analysis and sequencing of dominant bands to assess the microbial structure and dynamics through ripening. In further studies, kefir grains were observed using scanning electron microscopy (SEM) methods. A total of 147 bacteria and 129 yeasts were obtained from the cheese during ripening. Lactobacillus paracasei represents the most commonly identified lactic acid bacteria isolates, with 59 of a total of 147 isolates, followed by Lactococcus lactis (29 isolates). Meanwhile, Kazachstania servazzii (51 isolates) represented the mainly identified yeast isolate, followed by Saccharomyces cerevisiae (40 isolates). However, some lactic acid bacteria detected by sequence analysis of DGGE bands were not recovered by plating. The yeast S. cerevisiae and K. servazzii are described for the first time with kefir starter culture. SEM showed that the microbiota were dominated by a variety of lactobacilli (long and curved) cells growing in close association with a few yeasts in the inner portion of the grain and the short lactobacilli were observed along with yeast cells on the exterior portion. Results indicated that conventional culture method and PCR-DGGE should be combined to describe in maximal detail the microbiological composition in the cheese during ripening. The data could help in the selection of appropriate commercial starters for Camembert-type cheese.
International Nuclear Information System (INIS)
Touzet, N.; McCarthy, D.; Gill, A.; Fleming, G.T.A.
2016-01-01
The eutrophication of lakes is typically associated with high biomass proliferations of potentially toxic cyanobacteria. At a regional level, the sustainable management of water resources necessitates an approach that recognises the interconnectivity of multiple water systems within river catchments. This study examined the dynamics in summer diversity of planktonic cyanobacterial communities and microcystin toxin concentrations in two inter-connected lakes from the west of Ireland prone to nutrient enrichment. DGGE analysis of 16S rRNA gene amplicons of genotype-I cyanobacteria (typically spherical) showed changes in the communities of both Lough Corrib and Ballyquirke Lough throughout the summer, and identified cyanobacterial genotypes both unique and shared to both lakes. Microcystin concentrations, estimated via the protein phosphatase 2A inhibition assay, were greater in August than in July and June in both lakes. This was concomitant to the increased occurrence of Microcystis as evidenced by DGGE band excision and subsequent sequencing and BLAST analysis. RFLP analysis of PCR amplified mcy-A/E genes clustered together the August samples of both lakes, highlighting a potential change in microcystin producers across the two lakes. Finally, the multiple factor analysis of the combined environmental data set for the two lakes highlighted the expected pattern opposing greater water temperature and chlorophyll concentration against macronutrient concentrations, but also indicated a negative relationship between microcystin concentration and cyanobacterial diversity, possibly underlining allelopathic interactions. Despite some element of connectivity, the dissimilarity in the composition of the cyanobacterial assemblages and the timing of community change in the two lakes likely were a reflexion of niche differences determined by meteorologically-forced variation in physico-chemical parameters in the two water bodies. - Highlights: • DGGE highlighted
Li, Y; Saxena, D; Barnes, V M; Trivedi, H M; Ge, Y; Xu, T
2006-10-01
Clinical evaluation of oral microbial reduction after a standard prophylactic treatment has traditionally been based on bacterial cultivation methods. However, not all microbes in saliva or dental plaque can be cultivated. Polymerase chain reaction-based denaturing gradient gel electrophoresis (PCR-DGGE) is a cultivation-independent molecular fingerprinting technique that allows the assessment of the predominant bacterial species present in the oral cavity. This study sought to evaluate the oral microbial changes that occurred after a standard prophylactic treatment with a conventional oral care product using PCR-DGGE. Twelve healthy adults participated in the study. Pooled plaque samples were collected at baseline, 24 h after prophylaxis (T1), and 4 days after toothbrushing with fluoride toothpaste (T4). The total microbial genomic DNA of the plaque was isolated. PCR was performed with a set of universal bacterial 16S rDNA primers. The PCR-amplified 16S rDNA fragments were separated by DGGE. The effects of the treatment and of dental brushing were assessed by comparing the PCR-DGGE fingerprinting profiles. The mean numbers of detected PCR amplicons were 22.3 +/- 6.1 for the baseline group, 13.0 +/- 3.1 for the T1 group, and 13.5 +/- 4.3 for the T4 group; the differences among the three groups were statistically significant (P < 0.01). The study also found a significant difference in the mean similarities of microbial profiles between the baseline and the treatment groups (P < 0.001). PCR-based DGGE has been shown to be an excellent means of rapidly and accurately assessing oral microbial changes in this clinical study.
Czech Academy of Sciences Publication Activity Database
Bartuška, Martin; Pawlett, M.; Frouz, Jan
2015-01-01
Roč. 131, August (2015), s. 92-98 ISSN 0341-8162 Grant - others:GA ČR(CZ) GAP504/12/1288 Program:GA Institutional support: RVO:60077344 Keywords : soil organic matter * PLFA * chronosequence * succession * reclamation Subject RIV: DF - Soil Science Impact factor: 2.612, year: 2015
Gu, Likun; Bai, Zhihui; Jin, Bo; Hu, Qing; Wang, Huili; Zhuang, Guoqiang; Zhang, Hongxun
2010-01-01
Fungicides have been used extensively for controlling fungal pathogens of plants. However, little is known regarding the effects that fungicides upon the indigenous bacterial communities within the plant phyllosphere. The aims of this study were to assess the impact of fungicide enostroburin upon bacterial communities in wheat phyllosphere. Culture-independent methodologies of 16S rDNA clone library and 16S rDNA directed polymerase chain reaction with denaturing gradient gel electrophoresis (PCR-DGGE) were used for monitoring the change of bacterial community. The 16S rDNA clone library and PCR-DGGE analysis both confirmed the microbial community of wheat plant phyllosphere were predominantly of the gamma-Proteobacteria phyla. Results from PCR-DGGE analysis indicated a significant change in bacterial community structure within the phyllosphere following fungicide enostroburin application. Bands sequenced within control cultures were predominantly of Pseudomonas genus, but those bands sequenced in the treated samples were predominantly strains of Pantoea genus and Pseudomonas genus. Of interest was the appearance of two DGGE bands following fungicide treatment, one of which had sequence similarities (98%) to Pantoea sp. which might be a competitor of plant pathogens. This study revealed the wheat phyllosphere bacterial community composition and a shift in the bacterial community following fungicide enostroburin application.
Microbial Community Structure of Casing Soil During Mushroom Growth
Institute of Scientific and Technical Information of China (English)
CAI Wei-Ming; YAO Huai-Ying; FENG Wei-Lin; JIN Qun-Li; LIU Yue-Yan; LI Nan-Yi; ZHENG Zhong
2009-01-01
The culturable bacterial population and phospholipid fatty acid (PLFA)profile of casing soil were investigated at different mushroom (Agaricus bisporusI cropping stages.The change in soil bacterial PLFAs was always accompanied by a change in the soil culturable bacterial population in the first flush.Comparatively higher culturable bacterial population and bacterial PLFAs were found in the casing soil at the primordia formation stage of the first flush.There was a significant increase in the ratio of fungal to bacterial PLFAs during mushroom growth.Multivariate analysis of PLFA data demonstrated that the mushroom cropping stage could considerably affect the microbial community structure of the casing soil.The bacterial population increased significantly from casing soil application to the primordia formation stage of the first flush.Casing soil application resulted in an increase in the ratio of gram-negative bacterial PLFAs to gram-positive bacterial PLFAs,suggesting that some gram-negative bacteria might play an important role in mushroom sporophore initiation.
2010-07-01
... Other Regulations Relating to National Defense DEFENSE LOGISTICS AGENCY MISCELLANEOUS DEFENSE LOGISTICS... proper receipt of the referral by the PLFA FOIA manager to respond. (7) Accumulating fees. Requesters... reading room, the FOIA manager will arrange for a review of “(a)(2)” material at a suitable time and...
Czech Academy of Sciences Publication Activity Database
Voříšková, A.; Jansa, Jan; Püschel, David; Krüger, M.; Cajthaml, Tomáš; Vosátka, M.; Janoušková, M.
2017-01-01
Roč. 27, č. 6 (2017), s. 577-585 ISSN 0940-6360 R&D Projects: GA ČR GA15-05466S Institutional support: RVO:61388971 Keywords : Arbuscular mycorrhizal fung * Real-time PCR * PLFA Subject RIV: EE - Microbiology, Virology OBOR OECD: Microbiology Impact factor: 3.047, year: 2016
Yang, Wenhao; Zhang, Taoxiang; Lin, Sen; Ni, Wuzhong
2017-06-01
The recovery of microbial community and activities is crucial to the remediation of contaminated soils. Distance-dependent variations of microbial community composition and metabolic characteristics in the rhizospheric soil of hyperaccumulator during phytoextraction are poorly understood. A 12-month phytoextraction experiment with Sedum alfredii in a Cd-contaminated soil was conducted. A pre-stratified rhizobox was used for separating sub-layer rhizospheric (0-2, 2-4, 4-6, 6-8, 8-10 mm from the root mat)/bulk soils. Soil microbial structure and function were analyzed by phospholipid fatty acid (PLFA) and MicroResp™ methods. The concentrations of total and specified PLFA biomarkers and the utilization rates for the 14 substrates (organic carbon) in the 0-2-mm sub-layer rhizospheric soil were significantly increased, as well as decreased with the increase in the distance from the root mat. Microbial structure measured by the ratios of different groups of PLFAs such as fungal/bacterial, monounsaturated/saturated, ratios of Gram-positive to Gram-negative (GP/GN) bacterial, and cyclopropyl/monoenoic precursors and 19:0 cyclo/18:1ω7c were significantly changed in the 0-2-mm soil. The PLFA contents and substrate utilization rates were negatively correlated with pH and total, acid-soluble, and reducible fractions of Cd, while positively correlated with labile carbon. The dynamics of microbial community were likely due to root exudates and Cd uptake by S. alfredii. This study revealed the stimulations and gradient changes of rhizosphere microbial community through phytoextraction, as reduced Cd concentration, pH, and increased labile carbons are due to the microbial community responses.
International Nuclear Information System (INIS)
Chang, Yun-Juan; Peacock, A D.; Long, Philip E.; Stephen, John R.; McKinley, James P.; Mcnaughton, Sarah J.; Hussain, A K M A.; Saxton, A M.; White, D C.
2000-01-01
Microbially mediated reduction and immobilization of U(VI) to U(TV) plays a role in both natural attenuation and accelerated bioremediation of uranium contaminated sites. To realize bioremediation potential and accurately predict natural attenuation, it is important to first understand the microbial diversity of such sites. In this paper, the distribution of sulfate-reducing bacteria (SRB) in contaminated groundwater associated with a uranium mill tailings disposal site at Shiprock, N.Mex,, was investigated. Two culture-independent analyses were employed: sequencing of clone libraries of PCR-amplified dissimilatory sulfite reductase (DSR) gene fragments and phospholipid fatty acid (PLFA) biomarker analysis. A remarkable diversity among the DSR sequences was revealed, including sequences from F-Proteobacteria, gram-positive organisms, and the Nitrospira division. PLFA analysis detected at least,52 different mid-chain-branched saturate PLFA and included a high proportion of 10me16:0, Desulfotomaculum and Desulfotomaculum-like sequences were the most dominant DSR genes detected. Those belonging to SRB within F-Proteobacteria were mainly recovered from low-uranium (less than or equal to 302 ppb) samples. One Desulfotomaculum like sequence cluster overwhelmingly dominated high-U (> 1,500 ppb) sites. Logistic regression showed a significant influence of uranium concentration over the dominance of this cluster of sequences (P= 0.0001), This strong association indicates that Desulfotomaculum has remarkable tolerance and adaptation to high levels of uranium and suggests the organism's possible involvement in natural attenuation of uranium. The in situ activity level of Desulfotomaculum in uranium-contaminated environments and its comparison to the activities of other SRB and other functional groups should be an important area for future research
Soil microbial community structure and function responses to successive planting of Eucalyptus.
Chen, Falin; Zheng, Hua; Zhang, Kai; Ouyang, Zhiyun; Li, Huailin; Wu, Bing; Shi, Qian
2013-10-01
Many studies have shown soil degradation after the conversion of native forests to exotic Eucalyptus plantations. However, few studies have investigated the long-term impacts of short-rotation forestry practices on soil microorganisms. The impacts of Eucalyptus successive rotations on soil microbial communities were evaluated by comparing phospholipid fatty acid (PLFA) abundances, compositions, and enzyme activities of native Pinus massoniana plantations and adjacent 1st, 2nd, 3rd, 4th generation Eucalyptus plantations. The conversion from P. massoniana to Eucalyptus plantations significantly decreased soil microbial community size and enzyme activities, and increased microbial physiological stress. However, the PLFA abundances formed "u" shaped quadratic functions with Eucalyptus plantation age. Alternatively, physiological stress biomarkers, the ratios of monounsaturated to saturated fatty acid and Gram+ to Gram- bacteria, formed "n"' shaped quadratic functions, and the ratio of cy17:0 to 16:1omega7c decreased with plantation age. The activities of phenol oxidase, peroxidase, and acid phosphatase increased with Eucalyptus plantation age, while the cellobiohydrolase activity formed "u" shaped quadratic functions. Soil N:P, alkaline hydrolytic nitrogen, soil organic carbon, and understory cover largely explained the variation in PLFA profiles while soil N:P, alkaline hydrolytic nitrogen, and understory cover explained most of the variability in enzyme activity. In conclusion, soil microbial structure and function under Eucalyptus plantations were strongly impacted by plantation age. Most of the changes could be explained by altered soil resource availability and understory cover associated with successive planting of Eucalyptus. Our results highlight the importance of plantation age for assessing the impacts of plantation conversion as well as the importance of reducing disturbance for plantation management.
Directory of Open Access Journals (Sweden)
A. K. Hardison
2013-08-01
Full Text Available Microphytobenthos and benthic macroalgae play an important role in system metabolism within shallow coastal bays. However, their independent and interactive influences on sediment organic matter (SOM are not well understood. We investigated the influence of macroalgae and microphytobenthos on SOM quantity and quality in an experimental mesocosm system using bulk and molecular level (total hydrolyzable amino acids, THAA; phospholipid linked fatty acids, PLFA; pigment analyses. Our experiment used an incomplete factorial design made up of two factors, each with two levels: (1 light (ambient vs. dark and (2 macroalgae (presence vs. absence of live macroalgae. Over the course of the 42-day experiment, total organic carbon (TOC and total nitrogen (TN increased under ambient light by 173 ± 14 and 141 ± 7%, respectively, compared to in the dark (78 ± 29 and 39 ± 22%. THAA comprised a substantial fraction of SOM (~ 16% of TOC, 35% of TN and followed TOC and TN accumulation patterns. Mole percent composition of the THAA pool indicated that SOM was composed of more labile organic material (e.g., L-glutamic acid, phenylalanine under ambient light conditions while SOM in dark treatments was more degraded, with higher proportions of glycine and D-alanine. PLFA content, which represents viable biomass, made up ~ 1% of TOC and contained high levels of algal fatty acids in the light, particularly PLFA derived from diatoms. In the presence of microphytobenthos (i.e., light and macroalgae treatments, SOM lability increased, resulting in the observed increases in bacterial PLFA concentrations. Macroalgae, which were added to half of the light treatments, decreased SOM accumulation compared to light treatments without macroalgae, with TOC and TN increasing by only 130 ± 32 and 94 ± 24%, respectively. This decrease likely resulted from shading by macroalgae, which reduced production of microphytobenthos. The presence of macroalgae decreased SOM lability as
Hardison, A. K.; Canuel, E. A.; Anderson, I. C.; Tobias, C. R.; Veuger, B.; Waters, M. N.
2013-08-01
Microphytobenthos and benthic macroalgae play an important role in system metabolism within shallow coastal bays. However, their independent and interactive influences on sediment organic matter (SOM) are not well understood. We investigated the influence of macroalgae and microphytobenthos on SOM quantity and quality in an experimental mesocosm system using bulk and molecular level (total hydrolyzable amino acids, THAA; phospholipid linked fatty acids, PLFA; pigment) analyses. Our experiment used an incomplete factorial design made up of two factors, each with two levels: (1) light (ambient vs. dark) and (2) macroalgae (presence vs. absence of live macroalgae). Over the course of the 42-day experiment, total organic carbon (TOC) and total nitrogen (TN) increased under ambient light by 173 ± 14 and 141 ± 7%, respectively, compared to in the dark (78 ± 29 and 39 ± 22%). THAA comprised a substantial fraction of SOM (~ 16% of TOC, 35% of TN) and followed TOC and TN accumulation patterns. Mole percent composition of the THAA pool indicated that SOM was composed of more labile organic material (e.g., L-glutamic acid, phenylalanine) under ambient light conditions while SOM in dark treatments was more degraded, with higher proportions of glycine and D-alanine. PLFA content, which represents viable biomass, made up ~ 1% of TOC and contained high levels of algal fatty acids in the light, particularly PLFA derived from diatoms. In the presence of microphytobenthos (i.e., light and macroalgae treatments), SOM lability increased, resulting in the observed increases in bacterial PLFA concentrations. Macroalgae, which were added to half of the light treatments, decreased SOM accumulation compared to light treatments without macroalgae, with TOC and TN increasing by only 130 ± 32 and 94 ± 24%, respectively. This decrease likely resulted from shading by macroalgae, which reduced production of microphytobenthos. The presence of macroalgae decreased SOM lability as well, which
Directory of Open Access Journals (Sweden)
Armando Cavalcante Franco Dias
2012-06-01
Full Text Available Mangrove forests encompass a group of trees species that inhabit the intertidal zones, where soil is characterized by the high salinity and low availability of oxygen. The phyllosphere of these trees represent the habitat provided on the aboveground parts of plants, supporting in a global scale, a large and complex microbial community. The structure of phyllosphere communities reflects immigration, survival and growth of microbial colonizers, which is influenced by numerous environmental factors in addition to leaf physical and chemical properties. Here, a combination of culture-base methods with PCR-DGGE was applied to test whether local or plant specific factors shape the bacterial community of the phyllosphere from three plant species (Avicenia shaueriana, Laguncularia racemosa and Rhizophora mangle, found in two mangroves. The number of bacteria in the phyllosphere of these plants varied between 3.62 x 10(4 in A. schaeriana and 6.26 x 10³ in R. mangle. The results obtained by PCR-DGGE and isolation approaches were congruent and demonstrated that each plant species harbor specific bacterial communities in their leaves surfaces. Moreover, the ordination of environmental factors (mangrove and plant species, by redundancy analysis (RDA, also indicated that the selection exerted by plant species is higher than mangrove location on bacterial communities at phyllosphere.
Xu, Wei; Huang, Zhiyong; Zhang, Xiaojun; Li, Qi; Lu, Zhenming; Shi, Jinsong; Xu, Zhenghong; Ma, Yanhe
2011-09-01
Zhenjiang aromatic vinegar is one of the most famous Chinese traditional vinegars. In this study, change of the microbial community during its fermentation process was investigated. DGGE results showed that microbial community was comparatively stable, and the diversity has a disciplinary series of changes during the fermentation process. It was suggested that domestication of microbes and unique cycle-inoculation style used in the fermentation of Zhenjiang aromatic vinegar were responsible for comparatively stable of the microbial community. Furthermore, two clone libraries were constructed. The results showed that bacteria presented in the fermentation belonged to genus Lactobacillus, Acetobacter, Gluconacetobacter, Staphylococcus, Enterobacter, Pseudomonas, Flavobacterium and Sinorhizobium, while the fungi were genus Saccharomyces. DGGE combined with clone library analysis was an effective and credible technique for analyzing the microbial community during the fermentation process of Zhenjiang aromatic vinegar. Real-time PCR results suggested that the biomass showed a "system microbes self-domestication" process in the first 5 days, then reached a higher level at the 7th day before gradually decreasing until the fermentation ended at the 20th day. This is the first report to study the changes of microbial community during fermentation process of Chinese traditional solid-state fermentation of vinegar. Copyright © 2011 Elsevier Ltd. All rights reserved.
Czech Academy of Sciences Publication Activity Database
Voříšková, A.; Jansa, J.; Püschel, D.; Krüger, Manuela; Cajthaml, T.; Vosátka, M.; Janoušková, M.
2017-01-01
Roč. 27, č. 6 (2017), s. 577-585 ISSN 0940-6360 Institutional support: RVO:61389030 Keywords : Arbuscular mycorrhizal fungi * Isolate discrimination * Microsymbiont screening * Mitochondrial DNA * Molecular genetic quantification * Nuclear ribosomal DNA * plfa * Real-time PCR Subject RIV: EA - Cell Biology OBOR OECD: Cell biology Impact factor: 3.047, year: 2016
Variable effects of plant colonization on black slate uptake into microbial PLFAs
Seifert, Anne-Gret; Trumbore, Susan; Xu, Xiaomei; Zhang, Dachung; Gleixner, Gerd
2013-04-01
Microbial degradation of carbon derived from black shale and slate has been shown in vitro. However, in natural settings where other labile carbon sources are likely to exist, this has not been previously demonstrated. We investigated the uptake of ancient carbon derived from slate weathering and from recently photosynthesised organic matter by different groups of microorganisms. Therefore we isolated microbial biomarkers (phospholipid fatty acids, PLFAs) from black slates collected at a chronosequence of waste piles which differed in age and vegetation cover. We quantified the amount of PLFAs and performed stable isotope and radiocarbon measurements on individual or grouped PLFAs to quantify the fraction of slate derived carbon. We used black slate from a pile heaped in the 1950s with either uncovered black slate material (bare site) or material slightly colonized by small plants (greened site) and from a forested leaching pile (forested site) used for alum-mining in the 19th century. Colonization by plants influenced the amount and composition of the microbial community. Greater amounts of PLFAs (5410 ng PLFA/g dw) were extracted from slate sampled at the forested site as opposed to the bare site (960 ng PLFAs/g dw) or the greened (annual grasses and mosses) rock waste pile (1050 ng PLFAs/g dw). We found the highest proportion of PLFAs representing Gram-negative bacteria on the forested site and the highest proportion of PLFAs representing Gram-positive bacteria on the bare site. The fungal PLFA was most abundant at the greened site. Sites with less plant colonization (bare and greened site) tended to have more depleted δ13C values compared to the forested site. Radiocarbon measurements on PLFAs indicated that fungi and Gram-positive bacteria were best adapted to black slate carbon uptake. In the fungal PLFA (combined bare and greened waste pile sample) and in PLFAs of Gram-positive bacteria (greened site) we measured 39.7% and 28.9% ancient carbon uptake
International Nuclear Information System (INIS)
Chen, C. I.; Chuu, Y. J.; Meike, A.; Ringelberg, D.; Sawvel, A.
1998-01-01
Flow-through bioreactors are used to investigate the relationship between the supply (and limitation) of major nutrients required by microorganisms (C, N, P, S) and effluent chemistry to obtain data that can be useful to develop models of microbially mediated aqueous chemistry. The bioreactors were inoculated with crushed tuff from Yucca Mountain. Six of the 14 bioreactor experiments currently in operation have shown growth, which occurred in as few as 5 days and as much as a few months after initiation of the experiment. All of the bioreactors exhibiting growth contained glucose as a carbon source, but other nutritional components varied. Chemical signatures of each bioreactor were compared to each other and selected results were compared to computer simulations of the equivalent abiotic chemical reactions. At 21 C, the richest medium formulation produced a microbial community that lowered the effluent pH from 6.4 to as low as 3.9. The same medium formulation at 50 C produced no significant change in pH but caused a significant increase in Cl after a period of 200 days. Variations in concentrations of other elements, some of which appear to be periodic (Ca, Mg, etc.) also occur. Bioreactors fed with low C, N, P, S media showed growth, but had stabilized at lower cell densities. The room temperature bioreactor in this group exhibited a phospholipid fatty acid (PLFA) signature of sulfur- or iron-reducing bacteria, which produced a significant chemical signature in the effluent from that bioreactor. Growth had not been observed yet in the alkaline bioreactors, even in those containing glucose. The value of combining detailed chemical and community (e.g., ester-linked PLFA) analyses, long-duration experiments, and abiotic chemical models to distinguish chemical patterns is evident. Although all of the bioreactors contain the same initial microorganisms and mineral constituents, PLFA analysis demonstrates that both input chemistry and temperature determine the
Feng, Zhao; Kui-Dong, Xu; Zhao-Cui, Meng
2012-12-01
By using denaturing gradient gel electrophoresis (DGGE) and sequencing as well as Ludox-QPS method, an investigation was made on the ciliate diversity and its spatiotemporal variation in the surface sediments at three sites of Yangtze River estuary hypoxic zone in April and August 2011. The ANOSIM analysis indicated that the ciliate diversity had significant difference among the sites (R = 0.896, P = 0.0001), but less difference among seasons (R = 0.043, P = 0.207). The sequencing of 18S rDNA DGGE bands revealed that the most predominant groups were planktonic Choreotrichia and Oligotrichia. The detection by Ludox-QPS method showed that the species number and abundance of active ciliates were maintained at a higher level, and increased by 2-5 times in summer, as compared with those in spring. Both the Ludox-QPS method and the DGGE technique detected that the ciliate diversity at the three sites had the similar variation trend, and the Ludox-QPS method detected that there was a significant variation in the ciliate species number and abundance between different seasons. The species number detected by Ludox-QPS method was higher than that detected by DGGE bands. Our study indicated that the ciliates in Yangtze River estuary hypoxic zone had higher diversity and abundance, with the potential to supply food for the polyps of jellyfish.
Wu, Xueping; Gebremikael, Mesfin Tsegaye; Wu, Huijun; Cai, Dianxiong; Wang, Bisheng; Li, Baoguo; Zhang, Jiancheng; Li, Yongshan; Xi, Jilong
2018-01-01
Microbial mechanisms associated with soil organic carbon (SOC) decomposition are poorly understood. We aim to determine the effects of inorganic and organic fertilizers on soil labile carbon (C) pools, microbial community structure and C mineralization rate under an intensive wheat-maize double cropping system in Northern China. Soil samples in 0–10 cm layer were collected from a nine-year field trial involved four treatments: no fertilizer, CK; nitrogen (N) and phosphorus (P) fertilizers, NP; maize straw combined with NP fertilizers, NPS; and manure plus straw and NP fertilizers, NPSM. Soil samples were analyzed to determine labile C pools (including dissolved organic C, DOC; light free organic C, LFOC; and microbial biomass C, MBC), microbial community composition (using phospholipid fatty acid (PLFA) profiles) and SOC mineralization rate (from a 124-day incubation experiment). This study demonstrated that the application of chemical fertilizers (NP) alone did not alter labile C fractions, soil microbial communities and SOC mineralization rate from those observed in the CK treatment. Whereas the use of straw in conjunction with chemical fertilizers (NPS) became an additional labile substrate supply that decreased C limitation, stimulated growth of all PLFA-related microbial communities, and resulted in 53% higher cumulative mineralization of C compared to that of CK. The SOC and its labile fractions explained 78.7% of the variance of microbial community structure. Further addition of manure on the top of straw in the NPSM treatment did not significantly increase microbial community abundances, but it did alter microbial community structure by increasing G+/G- ratio compared to that of NPS. The cumulative mineralization of C was 85% higher under NPSM fertilization compared to that of CK. Particularly, the NPSM treatment increased the mineralization rate of the resistant pool. This has to be carefully taken into account when setting realistic and effective goals
An incubation system to trace carbon fluxes in soil - First experimental
Thiessen*, Stefany; Gleixner, Gerd; Reichstein, Markus
2010-05-01
Soils contain the largest carbon pool in terrestrial ecosystems and it is widely assumed that a considerable fraction of this pool might be mobilized by global warming. Numerous investigations have proven that soil respiration is a mixture of several source, like root rhizosphere and soil organic matter (SOM) degradation. However, little is still known about soil carbon dynamics and the influence of microbes on this process. We developed an incubation system to perform multitracer experiments to quantify the contribution of microorganisms to carbon turnover from different carbon sources. A natural 13C label was used to mark carbon sources. The old carbon in the SOM held a depleted 13C3 signal and newly added C was enriched in 13C4. Accordingly, in the experiment we quantified the relative respiration of carbon from added sugars and soil organic matter by microbial groups, with additional application of fungicide (cycloheximide). A root free arable soil was divided into three sets, all with depleted C3 soil, but varied in terms of the added material: one with C4 glucose, a second with C4 glucose combined with fungicide and the last one with water application only, as control. To characterize microbial communities and estimate microbial biomass we extract phospholipid fatty acids (PLFA). Furthermore, by measuring the isotopic ratio of the PLFA it was also possible to identify microorganisms that metabolised the traced material. Preliminary results showed that the glucose application stimulated microbial growth in the beginning, but afterwards the microbial biomass decreased again over time. However, a change in the microbial community composition could not be observed, regardless to the kind of added material. Nevertheless, the respiration response slowed down after the fungicide application, and a second respiration pulse was induced by this application. This was probably due to reactivation of the fungi, after the effect of the fungicide expired.
Directory of Open Access Journals (Sweden)
Siele Ceuppens
2015-08-01
Full Text Available Fresh herbs such as basil constitute an important food commodity worldwide. Basil provides considerable culinary and health benefits, but has also been implicated in foodborne illnesses. The naturally occurring bacterial community on basil leaves is currently unknown, so the epiphytic bacterial community was investigated using the culture-independent techniques denaturing gradient gel electrophoresis (DGGE and next-generation sequencing (NGS. Sample preparation had a major influence on the results from DGGE and NGS: Novosphingobium was the dominant genus for three different basil batches obtained by maceration of basil leaves, while washing of the leaves yielded lower numbers but more variable dominant bacterial genera including Klebsiella, Pantoea, Flavobacterium, Sphingobacterium and Pseudomonas. During storage of basil, bacterial growth and shifts in the bacterial community were observed with DGGE and NGS. Spoilage was not associated with specific bacterial groups and presumably caused by physiological tissue deterioration and visual defects, rather than by bacterial growth.
Relationships among Contrasting Measurements of Microbial Dynamics in Pasture and Organic Farm Soils
International Nuclear Information System (INIS)
Edenborn, S.L; Sexstone, A.J; Sutanto, Y; Chapman, J.A
2011-01-01
Soil bacteria exhibit short-term variations in community structure, providing an indication of anthropogenic disturbances. In this study, microbial biomass carbon (MBC), potentially mineralizable nitrogen (PMN), community level physiological profiling (CLPP), and culture-dependent DGGE (CD DGGE) fingerprinting of the 16 S r RNA gene were used to compare microbial communities in organic farm and pasture soils subjected to differing agronomic treatments. Correlation analyses revealed significant relationships between MBC, PMN, and data derived from microbial community analyses. All measures separated soil types but varied in their ability to distinguish among treatments within a soil type. Overall, MBC, PMN, and CLPP were most responsive to compost and manure amendments, while CD DGGE resolved differences in legume cropping and inorganic fertilization. The results support the hypothesis that culturable soil bacteria are a responsive fraction of the total microbial community, sensitive to agronomic perturbations and amenable to further studies aimed at linking community structure with soil functions.
Federle, T W; Ventullo, R M; White, D C
1990-12-01
The vertical distribution of microbial biomass, activity, community structure and the mineralization of xenobiotic chemicals was examined in two soil profiles in northern Wisconsin. One profile was impacted by infiltrating wastewater from a laundromat, while the other served as a control. An unconfined aquifer was present 14 meters below the surface at both sites. Biomass and community structure were determined by acridine orange direct counts and measuring concentrations of phospholipid-derived fatty acids (PLFA). Microbial activity was estimated by measuring fluorescein diacetate (FDA) hydrolysis, thymidine incorporation into DNA, and mixed amino acid (MAA) mineralization. Mineralization kinetics of linear alkylbenzene sulfonate (LAS) and linear alcohol ethoxylate (LAE) were determined at each depth. Except for MAA mineralization rates, measures of microbial biomass and activity exhibited similar patterns with depth. PLFA concentration and rates of FDA hydrolysis and thymidine incorporation decreased 10-100 fold below 3 m and then exhibited little variation with depth. Fungal fatty acid markers were found at all depths and represented from 1 to 15% of the total PLFAs. The relative proportion of tuberculostearic acid (TBS), an actinomycete marker, declined with depth and was not detected in the saturated zone. The profile impacted by wastewater exhibited higher levels of PLFA but a lower proportion of TBS than the control profile. This profile also exhibited faster rates of FDA hydrolysis and amino acid mineralization at most depths. LAS was mineralized in the upper 2 m of the vadose zone and in the saturated zone of both profiles. Little or no LAS biodegradation occurred at depths between 2 and 14 m. LAE was mineralized at all depths in both profiles, and the mineralization rate exhibited a similar pattern with depth as biomass and activity measurements. In general, biomass and biodegradative activities were much lower in groundwater than in soil samples obtained
Song, Xiaoling; Diep, Pho; Schenk, Jeannette M; Casper, Corey; Orem, Jackson; Makhoul, Zeina; Lampe, Johanna W; Neuhouser, Marian L
2016-11-01
Expressing circulating phospholipid fatty acids (PLFAs) in relative concentrations has some limitations: the total of all fatty acids are summed to 100%; therefore, the values of individual fatty acid are not independent. In this study we examined if both relative and absolute metrics could effectively measure changes in circulating PLFA concentrations in an intervention trial. 66 HIV and HHV8 infected patients in Uganda were randomized to take 3g/d of either long-chain omega-3 fatty acids (1856mg EPA and 1232mg DHA) or high-oleic safflower oil in a 12-week double-blind trial. Plasma samples were collected at baseline and end of trial. Relative weight percentage and absolute concentrations of 41 plasma PLFAs were measured using gas chromatography. Total cholesterol was also measured. Intervention-effect changes in concentrations were calculated as differences between end of 12-week trial and baseline. Pearson correlations of relative and absolute concentration changes in individual PLFAs were high (>0.6) for 37 of the 41 PLFAs analyzed. In the intervention arm, 17 PLFAs changed significantly in relative concentration and 16 in absolute concentration, 15 of which were identical. Absolute concentration of total PLFAs decreased 95.1mg/L (95% CI: 26.0, 164.2; P=0.0085), but total cholesterol did not change significantly in the intervention arm. No significant change was observed in any of the measurements in the placebo arm. Both relative weight percentage and absolute concentrations could effectively measure changes in plasma PLFA concentrations. EPA and DHA supplementation changes the concentrations of multiple plasma PLFAs besides EPA and DHA.Both relative weight percentage and absolute concentrations could effectively measure changes in plasma phospholipid fatty acid (PLFA) concentrations. Copyright © 2016 Elsevier Ltd. All rights reserved.
Zornoza, R; Guerrero, C; Mataix-Solera, J; Scow, K M; Arcenegui, V; Mataix-Beneyto, J
2008-07-01
The potential of near infrared (NIR) reflectance spectroscopy to predict various physical, chemical and biochemical properties in Mediterranean soils from SE Spain was evaluated. Soil samples (n=393) were obtained by sampling thirteen locations during three years (2003-2005 period). These samples had a wide range of soil characteristics due to variations in land use, vegetation cover and specific climatic conditions. Biochemical properties also included microbial biomarkers based on phospholipid fatty acids (PLFA). Partial least squares (PLS) regression with cross validation was used to establish relationships between the NIR spectra and the reference data from physical, chemical and biochemical analyses. Based on the values of coefficient of determination (r(2)) and the ratio of standard deviation of validation set to root mean square error of cross validation (RPD), predicted results were evaluated as excellent (r(2)>0.90 and RPD>3) for soil organic carbon, Kjeldahl nitrogen, soil moisture, cation exchange capacity, microbial biomass carbon, basal soil respiration, acid phosphatase activity, β-glucosidase activity and PLFA biomarkers for total bacteria, Gram positive bacteria, actinomycetes, vesicular-arbuscular mycorrhizal fungi and total PLFA biomass. Good predictions (0.81fungi were not accurate enough to satisfactorily estimate these variables, only permitting approximate predictions (0.66
Guo, Hai-chao; Wang, Guang-huo
2009-01-01
Annual ryegrass (Lolium multiflorum Lam.) was grown in paddy soil in pots under different phosphorus (P) fertilizer treatments to investigate changes of P fractions and microbial community of the soil. The treatments included Kunyang phosphate rock (KPR) applications at 50 mg P/kg (KPR50) and 250 mg P/kg (KPR250), mono-calcium phosphate (MCP) application at 50 mg P/kg (MCP50), and the control without P application. The results showed that KPR50, KPR250, and MCP50 applications significantly increased the dry weight of the ryegrass by 13%, 38%, and 55%, and increased P uptake by 19%, 135%, and 324%, respectively. Compared with MCP50, the relative effectiveness of KPR50 and KPR250 treatments in ryegrass production was about 23% and 68%, respectively. After one season of ryegrass growth, the KPR50, KPR250, and MCP50 applications increased soil-available P by 13.4%, 26.8%, and 55.2%, respectively. More than 80% of the applied KPR-P remained as HCl-P fraction in the soil. Phospholipid fatty acid (PLFA) analysis showed that the total and bacterial PLFAs were significantly higher in the soils with KPR250 and MCP50 treatments compared with KPR50 and control. The latter had no significant difference in the total or bacterial PLFAs. The KPR50, KPR250, and MCP50 treatments increased fungal PLFA by 69%, 103%, and 69%, respectively. Both the principal component analysis and the cluster analysis of the PLFA data suggest that P treatments altered the microbial community composition of the soils, and that P availability might be an important contributor to the changes in the microbial community structure during the ryegrass growth in the paddy soils. PMID:19817001
Di Cagno, Raffaella; Rizzello, Carlo G.; Gagliardi, Francesca; Ricciuti, Patrizia; Ndagijimana, Maurice; Francavilla, Ruggiero; Guerzoni, M. Elisabetta; Crecchio, Carmine; Gobbetti, Marco; De Angelis, Maria
2009-01-01
This study aimed at investigating the fecal microbiotas of children with celiac disease (CD) before (U-CD) and after (T-CD) they were fed a gluten-free diet and of healthy children (HC). Brothers or sisters of T-CD were enrolled as HC. Each group consisted of seven children. PCR-denaturing gradient gel electrophoresis (DGGE) analysis with V3 universal primers revealed a unique profile for each fecal sample. PCR-DGGE analysis with group- or genus-specific 16S rRNA gene primers showed that the ...
Changes in microbial community structure following herbicide (glyphosate) additions to forest soils
Alice W. Ratcliff; Matt D. Busse; Carol J. Shestak
2006-01-01
Glyphosate applied at the recommended field rate to a clay loam and a sandy loam forest soil resulted in few changes in microbial community structure. Total and culturable bacteria, fungal hyphal length, bacterial:fungal biomass, carbon utilization profiles (BIOLOG), and bacterial and fungal phospholipid fatty acids (PLFA) were unaffected 1, 3, 7, or 30 days...
Tauber, T; Berta, Brigitta; Székely, Anna J; Gyarmati, I; Kékesi, Katalin; Márialigeti, K; Tóth, Erika M
2007-03-01
The aim of the present work was to compare the microbial communities of a mesophilic and a thermophilic pilot scale anaerobe sludge digester. For studying the communities cultivation independent chemotaxonomical methods (RQ and PLFA analyses) and T-RFLP were applied. Microbial communities of the mesophilic and thermophilic pilot digesters showed considerable differences, both concerning the species present, and their abundance. A Methanosarcina sp. dominated the thermophilic, while a Methanosaeta sp. the mesophilic digester among Archaea. Species diversity of Bacteria was reduced in the thermophilic digester. Based on the quinone patterns in both digesters the dominance of sulphate reducing respiratory bacteria could be detected. The PLFA profiles of the digester communities were similar though in minor components characteristic differences were shown. Level of branched chain fatty acids is slightly lower in the thermophilic digester that reports less Gram positive bacteria. The relative ratio of fatty acids characteristic to Enterobacteriaceae, Bacteroidetes and Clostridia shows differences between the two digesters: their importance generally decreased under thermophilic conditions. The sulphate reducer marker (15:1 and 17:1) fatty acids are present in low quantity in both digesters.
Czech Academy of Sciences Publication Activity Database
Šimek, Miloslav; Virtanen, S.; Simojoki, A.; Chroňáková, Alica; Elhottová, Dana; Krištůfek, Václav; Yli-Halla, M.
2014-01-01
Roč. 466, January (2014), s. 663-672 ISSN 0048-9697 R&D Projects: GA ČR GA526/09/1570; GA MŠk LC06066 Grant - others:GAJU(CZ) GAJU 138/2010/P Institutional support: RVO:60077344 Keywords : acid sulphate soil * carbon * CARD-FISH * microorganisms * nitrogen * PLFA Subject RIV: EE - Microbiology, Virology Impact factor: 4.099, year: 2014
Czech Academy of Sciences Publication Activity Database
Byss, Marius; Elhottová, Dana; Tříska, Jan; Baldrian, Petr
2008-01-01
Roč. 2008, č. 73 (2008), s. 1518-1523 ISSN 0045-6535 R&D Projects: GA MŠk LC06066 Institutional research plan: CEZ:AV0Z60870520; CEZ:AV0Z60660521; CEZ:AV0Z50200510 Keywords : Wood-rotting basidiomycetes * Soil microbial community * PLFA, PAH Subject RIV: EH - Ecology, Behaviour Impact factor: 3.054, year: 2008
[Analysis of diversity of vaginal microbiota in healthy Chinese women by using DNA-fingerprinting].
Xiao, Bing-bing; Liao, Qin-ping
2012-04-18
To analyze the diversity of healthy women's vaginal dominant flora in different physiological states with PCR-denaturing gradient gel electrophoresis (PCR-DGGE), to establish the basis for the future study of lower genital tract infections, and to provide a theoretical basis for the development of vaginal probiotics adapted to Chinese females. Women who underwent routine gynecologic examinations in Peking University First Hospital from October 2009 to January 2010 were enrolled, including 30 at reproductive age and 30 at post menopause age. Vaginal samples were collected and then total bacterial DNA was extracted. Universal bacterial primers were used to amplify the V3 region of 16S rDNA gene. PCR products were analyzed by denatured gradient gel electrophoresis (DGGE). Featured bands on DGGE were recovered, cloned and sequenced. Alignment with known sequence was made by using Blast on GenBank to identify bacterial strains so as to analyze the diversity of healthy women's vaginal dominant flora in different physiological states. (1) Vaginal flora in healthy Chinese women at their reproductive age were relatively simple, Lactobacillus were the dominant bacteria. Common bacteria included: Lactobacillus crispatus, Lactobacillus iners,and Lactobacillus gasseri. While L. iners were the dominant vaginal bacteria that could not be recognized by traditional method. (2) Vaginal bacteria in the women at post menopause age were more complex than in those at reproductive age. Common bacteria included: Lactobacillus iners, Lactobacillus crispatus, Escherichia coli, Streptococcus agalactiae, Streptococcus gallolyticus, Veillonella sp., Streptococcus intermedius, Streptococcus anginosus, Prevotella sp., Anaerococcus lactolyticus and Bacteroides fragilis. Based on the DGGE analysis, the most common vaginal bacteria in Chinese healthy women at reproductive age are Lactobacillus crispatus, Lactobacillus iners,and Lactobacillus gasseri. the most common vaginal bacteria in healthy post
Li, Zhijian; Li, Haifeng; Bian, Ke
2016-10-03
In this study, the microbial composition of two types of Jiaozi (a dough fermentation starter in making steamed bread) was investigated using both culture-dependent and culture-independent (PCR-DGGE) methods. The numbers of the cultivable bacteria on MRS at 30°C and yeast on YPD at 28°C in the maize flour Jiaozi (MFJ) were 9.21±0.16 Log CFU/g and 9.18±0.05 Log CFU/g, respectively, which were higher than that in the rice flour Jiaozi (RFJ) (Pyeasts were isolated and identified on the basis of the sequences of their 16S rRNA gene and ITS region. The culture-dependent method showed that Acetobacter tropicalis and Enterococcus durans were the predominant bacteria strains in MFJ, and accounted for 45.7% and 25.7% of the bacteria, and Lactobacillus plantarum and Pediococcus pentosaceus represented 12.8% and 8.6%. In the RFJ sample, the most prominent isolate was P. pentosaceus (38.6%), followed by L. plantarum (24.3%), A. tropicalis (22.8%), and E. durans (5.7%). P. pentosaceus and L. plantarum were also detected in both starters by PCR-DGGE, while some bacteria species such as A. tropicalis and E. durans, recovered as pure cultures, were not detected by direct PCR-DGGE. On the other hand, Lactobacillus brevis, Weissella sp. and Lactobacillus alimentarius detected by PCR-DGGE were not recovered in any of the media and conditions used. In the MFJ sample, the isolated main yeast species were identified as Wickerhamomyces anomalus (67.2%), Saccharomyces cerevisiae (27.9%) and Torulaspora delbrueckii (4.9%). In addition to S. cerevisiae (42.9%), W. anomalus (27.0%) and T. delbrueckii (7.9%), Saccharomycopsis fibuligera was also identified as the predominant isolate in RFJ samples and accounted for 22.2%. PCR-DGGE also indicated the presence of W. anomalus and S. cerevisiae in both MFJ and RFJ starters and S. fibuligera was also detected in RFJ, but T. delbrueckii was not detected in both samples. Copyright © 2016 Elsevier B.V. All rights reserved.
Directory of Open Access Journals (Sweden)
Xiasheng Zheng
2017-09-01
Full Text Available Herbal medicine is a major component of complementary and alternative medicine, contributing significantly to the health of many people and communities. Quality control of herbal medicine is crucial to ensure that it is safe and sound for use. Here, we investigated a comprehensive quality evaluation system for a classic herbal medicine, Danggui Buxue Formula, by applying genetic-based and analytical chemistry approaches to authenticate and evaluate the quality of its samples. For authenticity, we successfully applied two novel technologies, third-generation sequencing and PCR-DGGE (denaturing gradient gel electrophoresis, to analyze the ingredient composition of the tested samples. For quality evaluation, we used high performance liquid chromatography assays to determine the content of chemical markers to help estimate the dosage relationship between its two raw materials, plant roots of Huangqi and Danggui. A series of surveys were then conducted against several exogenous contaminations, aiming to further access the efficacy and safety of the samples. In conclusion, the quality evaluation system demonstrated here can potentially address the authenticity, quality, and safety of herbal medicines, thus providing novel insight for enhancing their overall quality control.Highlight: We established a comprehensive quality evaluation system for herbal medicine, by combining two genetic-based approaches third-generation sequencing and DGGE (denaturing gradient gel electrophoresis with analytical chemistry approaches to achieve the authentication and quality connotation of the samples.
Dynamic alteration of the colonic microbiota in intestinal ischemia-reperfusion injury.
Directory of Open Access Journals (Sweden)
Fan Wang
Full Text Available Intestinal ischemia-reperfusion (I/R plays an important role in critical illnesses. Gut flora participate in the pathogenesis of the injury. This study is aimed at unraveling colonic microbiota alteration pattern and identifying specific bacterial species that differ significantly as well as observing colonic epithelium change in the same injury model during the reperfusion time course.Denaturing gradient gel electrophoresis (DGGE was used to monitor the colonic microbiota of control rats and experimental rats that underwent 0.5 hour ischemia and 1, 3, 6, 12, 24, and 72 hours following reperfusion respectively. The microbiota similarity, bacterial diversity and species that characterized the dysbiosis were estimated based on the DGGE profiles using a combination of statistical approaches. The interested bacterial species in the gel were cut and sequenced and were subsequently quantified and confirmed with real-time PCR. Meanwhile, the epithelial barrier was checked by microscopy and D-lactate analysis. Colonic flora changed early and differed significantly at 6 hours after reperfusion and then started to recover. The shifts were characterized by the increase of Escherichia coli and Prevotella oralis, and Lactobacilli proliferation together with epithelia healing.This study shows for the first time that intestinal ischemia-reperfusion results in colonic flora dysbiosis that follows epithelia damage, and identifies the bacterial species that contribute most.
Meroth, Christiane B; Hammes, Walter P; Hertel, Christian
2004-03-01
The microbiota of two industrially processed rice sourdoughs was characterised by bacteriological culture in combination with PCR-denaturing gradient gel electrophoresis (DGGE) and 16S/28S rDNA sequence analysis. Rice sourdough I was continuously propagated for several years by back-slopping every week, whereas sourdough II was processed by using a commercial starter culture and back-slopping daily for three days. In rice sourdough II Candida krusei and Saccharomyces cerevisiae as well as Lactobacillus fermentum, Lactobacillus gallinarum, Lactobacillus kimchii, Lactobacillus plantarum, and Lactobacillus pontis dominated at the first day of fermentation. RAPD analysis of lactobacilli revealed identical profiles for each of the species except for L. fermentum and L. pontis indicating the presence of different strains. Fluctuations within the LAB community during fermentation were monitored by PCR-DGGE. L. pontis decreased in numbers over time and L. curvatus became dominant after 3 days of fermentation. Rice sourdough I contained S. cerevisiae, Lactobacillus paracasei (present with three different RAPD types), Lactobacillus paralimentarius, and a Lactobacillus strain which could not be allotted to any valid species. Phylogenetic analysis based on 16S rDNA sequences revealed Lactobacillus brevis as the closest relative (97.3% sequence similarity). Differences in some phenotypic characteristics and DNA-DNA relatedness indicated that the strain represents a new Lactobacillus species, for which the name Lactobacillus spicheri is proposed.
Zheng, Xiasheng; Zhang, Peng; Liao, Baosheng; Li, Jing; Liu, Xingyun; Shi, Yuhua; Cheng, Jinle; Lai, Zhitian; Xu, Jiang; Chen, Shilin
2017-01-01
Herbal medicine is a major component of complementary and alternative medicine, contributing significantly to the health of many people and communities. Quality control of herbal medicine is crucial to ensure that it is safe and sound for use. Here, we investigated a comprehensive quality evaluation system for a classic herbal medicine, Danggui Buxue Formula, by applying genetic-based and analytical chemistry approaches to authenticate and evaluate the quality of its samples. For authenticity, we successfully applied two novel technologies, third-generation sequencing and PCR-DGGE (denaturing gradient gel electrophoresis), to analyze the ingredient composition of the tested samples. For quality evaluation, we used high performance liquid chromatography assays to determine the content of chemical markers to help estimate the dosage relationship between its two raw materials, plant roots of Huangqi and Danggui. A series of surveys were then conducted against several exogenous contaminations, aiming to further access the efficacy and safety of the samples. In conclusion, the quality evaluation system demonstrated here can potentially address the authenticity, quality, and safety of herbal medicines, thus providing novel insight for enhancing their overall quality control. Highlight : We established a comprehensive quality evaluation system for herbal medicine, by combining two genetic-based approaches third-generation sequencing and DGGE (denaturing gradient gel electrophoresis) with analytical chemistry approaches to achieve the authentication and quality connotation of the samples.
Zheng, Xiasheng; Zhang, Peng; Liao, Baosheng; Li, Jing; Liu, Xingyun; Shi, Yuhua; Cheng, Jinle; Lai, Zhitian; Xu, Jiang; Chen, Shilin
2017-01-01
Herbal medicine is a major component of complementary and alternative medicine, contributing significantly to the health of many people and communities. Quality control of herbal medicine is crucial to ensure that it is safe and sound for use. Here, we investigated a comprehensive quality evaluation system for a classic herbal medicine, Danggui Buxue Formula, by applying genetic-based and analytical chemistry approaches to authenticate and evaluate the quality of its samples. For authenticity, we successfully applied two novel technologies, third-generation sequencing and PCR-DGGE (denaturing gradient gel electrophoresis), to analyze the ingredient composition of the tested samples. For quality evaluation, we used high performance liquid chromatography assays to determine the content of chemical markers to help estimate the dosage relationship between its two raw materials, plant roots of Huangqi and Danggui. A series of surveys were then conducted against several exogenous contaminations, aiming to further access the efficacy and safety of the samples. In conclusion, the quality evaluation system demonstrated here can potentially address the authenticity, quality, and safety of herbal medicines, thus providing novel insight for enhancing their overall quality control. Highlight: We established a comprehensive quality evaluation system for herbal medicine, by combining two genetic-based approaches third-generation sequencing and DGGE (denaturing gradient gel electrophoresis) with analytical chemistry approaches to achieve the authentication and quality connotation of the samples. PMID:28955365
Pushkareva, Ekaterina; Pessi, Igor S; Namsaraev, Zorigto; Mano, Marie-Jose; Elster, Josef; Wilmotte, Annick
2018-02-07
Molecular and morphological methods were applied to study cyanobacterial community composition in biological soil crusts (BSCs) from four areas (two nunataks and two ridges) in the Sør Rondane Mountains, Antarctica. The sampling sites serve as control areas for open top chambers (OTCs) that were put in place in 2010 at the time of sample collection and will be compared with BSC samples taken from the OTCs in the future. Cyanobacterial cell biovolume was estimated using epifluorescence microscopy, which revealed the dominance of filamentous cyanobacteria in all studied sites except the Utsteinen ridge, where unicellular cyanobacteria were the most abundant. Cyanobacterial diversity was studied by a combination of molecular fingerprinting methods based on the 16S rRNA gene (denaturing gradient gel electrophoresis (DGGE) and 454 pyrosequencing) using cyanobacteria-specific primers. The number of DGGE sequences obtained per site was variable and, therefore, a high-throughput method was subsequently employed to improve the diversity coverage. Consistent with previous surveys in Antarctica, both methods showed that filamentous cyanobacteria, such as Leptolyngbya sp., Phormidium sp. and Microcoleus sp., were dominant in the studied sites. In addition, the studied localities differed in substrate type, climatic conditions and soil parameters, which probably resulted in differences in cyanobacterial community composition. Furthermore, the BSC growing on gneiss pebbles had lower cyanobacterial abundances than BSCs associated with granitic substrates. Copyright © 2018 Elsevier GmbH. All rights reserved.
Patchiness of Ciliate Communities Sampled at Varying Spatial Scales along the New England Shelf.
Directory of Open Access Journals (Sweden)
Jean-David Grattepanche
Full Text Available Although protists (microbial eukaryotes provide an important link between bacteria and Metazoa in food webs, we do not yet have a clear understanding of the spatial scales on which protist diversity varies. Here, we use a combination of DNA fingerprinting (denaturant gradient gel electrophoresis or DGGE and high-throughput sequencing (HTS to assess the ciliate community in the class Spirotrichea at varying scales of 1-3 km sampled in three locations separated by at least 25 km-offshore, midshelf and inshore-along the New England shelf. Analyses of both abundant community (DGGE and the total community (HTS members reveal that: 1 ciliate communities are patchily distributed inshore (i.e. the middle station of a transect is distinct from its two neighboring stations, whereas communities are more homogeneous among samples within the midshelf and offshore stations; 2 a ciliate closely related to Pelagostrobilidium paraepacrum 'blooms' inshore and; 3 environmental factors may differentially impact the distributions of individual ciliates (i.e. OTUs rather than the community as a whole as OTUs tend to show distinct biogeographies (e.g. some OTUs are restricted to the offshore locations, some to the surface, etc.. Together, these data show the complexity underlying the spatial distributions of marine protists, and suggest that biogeography may be a property of ciliate species rather than communities.
PCR-DGGE fingerprints of microbial successional changes during ...
African Journals Online (AJOL)
STORAGESEVER
2008-12-17
Dec 17, 2008 ... INTRODUCTION. Spontaneous lactic acid fermentation of cereal products ... tional techniques, such as cultivation of bacteria on solid media, the results are ..... the substrate, or the food matrix that is driving the process, or ...
Shin, Jung-Hun; Kim, Byung-Chun; Choi, Okkyoung; Kim, Hyunook; Sang, Byoung-In
2015-10-01
Two hollow fiber membrane biofilm reactors (HF-MBfRs) were operated for autotrophic nitrification and hydrogenotrophic denitrification for over 300 days. Oxygen and hydrogen were supplied through the hollow fiber membrane for nitrification and denitrification, respectively. During the period, the nitrogen was removed with the efficiency of 82-97% for ammonium and 87-97% for nitrate and with the nitrogen removal load of 0.09-0.26 kg NH4(+)-N/m(3)/d and 0.10-0.21 kg NO3(-)-N/m(3)/d, depending on hydraulic retention time variation by the two HF-MBfRs for autotrophic nitrification and hydrogenotrophic denitrification, respectively. Biofilms were collected from diverse topological positions in the reactors, each at different nitrogen loading rates, and the microbial communities were analyzed with partial 16S rRNA gene sequences in denaturing gradient gel electrophoresis (DGGE). Detected DGGE band sequences in the reactors were correlated with nitrification or denitrification. The profile of the DGGE bands depended on the NH4(+) or NO3(-) loading rate, but it was hard to find a major strain affecting the nitrogen removal efficiency. Nitrospira-related phylum was detected in all biofilm samples from the nitrification reactors. Paracoccus sp. and Aquaspirillum sp., which are an autohydrogenotrophic bacterium and an oligotrophic denitrifier, respectively, were observed in the denitrification reactors. The distribution of microbial communities was relatively stable at different nitrogen loading rates, and DGGE analysis based on 16S rRNA (341f /534r) could successfully detect nitrate-oxidizing and hydrogen-oxidizing bacteria but not ammonium-oxidizing bacteria in the HF-MBfRs.
Nakagawa, Tatsunori; Ishibashi, Jun-Ichiro; Maruyama, Akihiko; Yamanaka, Toshiro; Morimoto, Yusuke; Kimura, Hiroyuki; Urabe, Tetsuro; Fukui, Manabu
2004-01-01
This study describes the occurrence of unique dissimilatory sulfite reductase (DSR) genes at a depth of 1,380 m from the deep-sea hydrothermal vent field at the Suiyo Seamount, Izu-Bonin Arc, Western Pacific, Japan. The DSR genes were obtained from microbes that grew in a catheter-type in situ growth chamber deployed for 3 days on a vent and from the effluent water of drilled holes at 5 degrees C and natural vent fluids at 7 degrees C. DSR clones SUIYOdsr-A and SUIYOdsr-B were not closely related to cultivated species or environmental clones. Moreover, samples of microbial communities were examined by PCR-denaturing gradient gel electrophoresis (DGGE) analysis of the 16S rRNA gene. The sequence analysis of 16S rRNA gene fragments obtained from the vent catheter after a 3-day incubation revealed the occurrence of bacterial DGGE bands affiliated with the Aquificae and gamma- and epsilon-Proteobacteria as well as the occurrence of archaeal phylotypes affiliated with the Thermococcales and of a unique archaeon sequence that clustered with "Nanoarchaeota." The DGGE bands obtained from drilled holes and natural vent fluids from 7 to 300 degrees C were affiliated with the delta-Proteobacteria, genus Thiomicrospira, and Pelodictyon. The dominant DGGE bands retrieved from the effluent water of casing pipes at 3 and 4 degrees C were closely related to phylotypes obtained from the Arctic Ocean. Our results suggest the presence of microorganisms corresponding to a unique DSR lineage not detected previously from other geothermal environments.
International Nuclear Information System (INIS)
Takahashi, Norio; Hiyama, Keiko; Kodaira, Mieko; Satoh, Chiyoko.
1990-05-01
We have examined the feasibility of denaturing gradient gel electrophoresis (DGGE) of RNA:DNA duplexes to detect variations in genomic and cloned DNAs. The result has demonstrated that use of RNA:DNA duplexes makes DGGE much more practical for screening a large number of samples than use of DNA:DNA heteroduplexes, because preparation of RNA probes is easier than that of DNA probes. Three different 32 P-labeled RNA probes were produced. Genomic or cloned DNAs were digested with restriction enzymes and hybridized to labeled RNA probes, and resulting RNA:DNA duplexes were examined by DGGE. The presence of a mismatch(es) was detected as a difference in the mobility of bands on the gel. The experimental conditions were determined using DNA segments from cloned normal and three thalassemic human β-globin genes. The results from experiments on the cloned DNAs suggest that DGGE of RNA:DNA duplexes will detect nucleotide substitutions and deletions in DNA. In the course of these studies, a polymorphism due to a single-base substitution at position 666 of IVS2 (IVS2-666) of the human β-globin gene was directly identified using genomic DNA samples. A study of 59 unrelated Japanese from Hiroshima was undertaken in which the frequency of the allele with C at IVS2-666 was 0.48 and that of the allele with T was 0.52. This approach was found to be very effective for detecting heritable variation and should be a powerful tool for detecting fresh mutations in DNA, which occur outside the known restriction sites. (author)
DEFF Research Database (Denmark)
Ludvigsen, L.; Albrechtsen, H.-J.; Ringelberg, D.
1999-01-01
To investigate whether landfill leachates affected the microbial biomass and/or community composition of the extant microbiota, 37 samples were collected along a 305-m transect of a shallow landfill-leachate polluted aquifer. The samples were analyzed for total numbers of bacteria by use of the a......To investigate whether landfill leachates affected the microbial biomass and/or community composition of the extant microbiota, 37 samples were collected along a 305-m transect of a shallow landfill-leachate polluted aquifer. The samples were analyzed for total numbers of bacteria by use...... of the acridine orange direct count method (AODC). Numbers of dominant, specific groups of bacteria and total numbers of protozoa were measured by use of the most probable number method (MPN). Viable biomass estimates were obtained from measures of ATP and ester-linked phospholipid fatty acid (PLFA......) concentrations. The estimated numbers of total bacteria by direct counts were relatively constant throughout the aquifer, ranging from a low of 4.8 × 106 cells/g dry weight (dw) to a high of 5.3 × 107 cells/g dw. Viable biomass estimates based on PLFA concentrations were one to three orders of magnitude lower...
Morillo, J A; Aguilera, M; Antízar-Ladislao, B; Fuentes, S; Ramos-Cormenzana, A; Russell, N J; Monteoliva-Sánchez, M
2008-05-01
Two-phase olive mill waste (TPOMW) is a semisolid effluent that is rich in contaminating polyphenols and is produced in large amounts by the industry of olive oil production. Laboratory-scale bioreactors were used to investigate the biodegradation of TPOMW by its indigenous microbiota. The effect of nutrient addition (inorganic N and P) and aeration of the bioreactors was studied. Microbial changes were investigated by PCR-temperature time gradient electrophoresis (TTGE) and following the dynamics of polar lipid fatty acids (PLFA). The greatest decrease in the polyphenolic and organic matter contents of bioreactors was concomitant with an increase in the PLFA fungal/bacterial ratio. Amplicon sequences of nuclear ribosomal internal transcribed spacer region (ITS) and 16S rDNA allowed identification of fungal and bacterial types, respectively, by comparative DNA sequence analyses. Predominant fungi identified included members of the genera Penicillium, Candida, Geotrichum, Pichia, Cladosporium, and Aschochyta. A total of 14 bacterial genera were detected, with a dominance of organisms that have previously been associated with plant material. Overall, this work highlights that indigenous microbiota within the bioreactors through stimulation of the fungal fraction, is able to degrade the polyphenolic content without the inoculation of specific microorganisms.
Timmermann, Allan G
2005-01-01
Forecast combinations have frequently been found in empirical studies to produce better forecasts on average than methods based on the ex-ante best individual forecasting model. Moreover, simple combinations that ignore correlations between forecast errors often dominate more refined combination schemes aimed at estimating the theoretically optimal combination weights. In this paper we analyse theoretically the factors that determine the advantages from combining forecasts (for example, the d...
Characterization and Application of Autochthonous Starter Cultures for Fresh Cheese Production
Directory of Open Access Journals (Sweden)
Andreja Leboš Pavunc
2012-01-01
Full Text Available The use of commercial starter cultures in fresh cheese production from pasteurized milk results in the loss of typical characteristics of artisan fresh cheese due to the replacement of complex native microbiota with a defined starter culture. Hence, the aim of this research is to isolate and characterize dominant lactic acid bacteria (LAB in artisan fresh cheese and to evaluate their capacity as autochthonous starter cultures for fresh cheese production. Fifteen most prevalent Gram-positive, catalase-negative and asporogenous bacterial strains were selected for a more detailed characterization. Eleven lactic acid bacterial strains were determined to be homofermentative cocci and four heterofermentative lactobacilli. Further phenotypic and genotypic analyses revealed that those were two different LAB strains with high acidifying and proteolytic activity, identified as Lactobacillus fermentum A8 and Enterococcus faecium A7. These two autochthonous strains, alone or in combination with commercial starter, were used to produce different types of fresh cheese, which were evaluated by a panel. Conventional culturing, isolation, identification and PCR-denaturing gradient gel electrophoresis (PCR-DGGE procedures, applied to the total fresh cheese DNA extracts, were employed to define and monitor the viability of the introduced LAB strains and their effect on the final product characteristics. Production of fresh cheese using a combination of commercial starter culture and selected autochthonous strains resulted in improved sensorial properties, which were more similar to the ones of spontaneously fermented fresh cheese than to those of cheese produced with only starter culture or selected strains. After 10 days of storage, that cheese retained the best sensorial properties in comparison with all other types of cheese. The presence of inoculated autochthonous and starter cultures and their identification was demonstrated by DGGE analysis. The obtained
Noutsios, Georgios T; Papi, Rigini M; Ekateriniadou, Loukia V; Minas, Anastasios; Kyriakidis, Dimitrios A
2012-03-01
In the present study forty-four Greek endemic strains of Br. melitensis and three reference strains were genotyped by Multi locus Variable Number Tandem Repeat (ML-VNTR) analysis based on an eight-base pair tandem repeat sequence that was revealed in eight loci of Br. melitensis genome. The forty-four strains were discriminated from the vaccine strain Rev-1 by Restriction Fragment Length Polymorphism (RFLP) and Denaturant Gradient Gel Electrophoresis (DGGE). The ML-VNTR analysis revealed that endemic, reference and vaccine strains are genetically closely related, while most of the loci tested (1, 2, 4, 5 and 7) are highly polymorphic with Hunter-Gaston Genetic Diversity Index (HGDI) values in the range of 0.939 to 0.775. Analysis of ML-VNTRs loci stability through in vitro passages proved that loci 1 and 5 are non stable. Therefore, vaccine strain can be discriminated from endemic strains by allele's clusters of loci 2, 4, 6 and 7. RFLP and DGGE were also employed to analyse omp2 gene and reveled different patterns among Rev-1 and endemic strains. In RFLP, Rev-1 revealed three fragments (282, 238 and 44 bp), while endemic strains two fragments (238 and 44 bp). As for DGGE, the electrophoretic mobility of Rev-1 is different from the endemic strains due to heterologous binding of DNA chains of omp2a and omp2b gene. Overall, our data show clearly that it is feasible to genotype endemic strains of Br. melitensis and differentiate them from vaccine strain Rev-1 with ML-VNTR, RFLP and DGGE techniques. These tools can be used for conventional investigations in brucellosis outbreaks.
Ye, N-F; Lü, F; Shao, L-M; Godon, J-J; He, P-J
2007-10-01
To estimate the effect of pH on the structures of bacterial community during fermentation of vegetable wastes and to investigate the relationship between bacterial community dynamics and product distribution. The bacterial communities in five batch tests controlled at different pH values [uncontrolled (about pH 4), 5, 6, 7 and 8] were monitored by denaturing gradient gel electrophoresis (DGGE) and single-strand conformation polymorphism (SSCP). The two fingerprinting methods provided consistent results and principal component analysis indicated a close similarity of bacterial community at pH 7 and 8 in addition to those at pH 4-6. This clustering also corresponded to dominant metabolic pathway. Thus, pH 7-8 shifted from alcohol-forming to acid-forming, especially butyric acid, whereas both alcohol-forming and acid-forming dominated at pH 5-6, and at pH 4, fermentation was inhibited. Shannon-weaver index was calculated to analyse the DGGE profiles, which revealed that the bacterial diversities at pH 7 and 8 were the highest while those at pH 5 and 4 (uncontrolled) were the lowest. According to sequencing results of the bands excised from DGGE gels, lactic acid bacteria and Clostridium sp. were predominant at all pH values, but varieties in species were observed as pH changed and time prolonged. The bacterial community during fermentation was materially influenced by pH and the diverse product distribution was related to the shift of different bacterial population. The study reveals that the impact of pH on fermentation product distribution is implemented primarily by changes of bacterial community. It also provides information about the comparison of two fingerprinting methods, DGGE and SSCP.
Tok, Ezgi; Kurt, Halil; Tunga Akarsubasi, A.
2016-04-01
The microbial diversity of cave sediments which are obtained from three different caves named Insuyu, Balatini and Altınbeşik located at Southern Turkey has been investigated using molecular methods for biomineralization . The total number of 22 samples were taken in duplicates from the critical zones of the caves at where the water activity is observed all year round. Microbial communities were monitored by 16S rRNA gene based PCR-DGGE (Polymerase Chain Reaction - Denaturating Gradient Gel Electrophoresis) methodology. DNA were extracted from the samples by The PowerSoil® DNA Isolation Kit (MO BIO Laboratories inc., CA) with the modifications on the producer's protocol. The synthetic DNA molecule poly-dIdC was used to increase the yield of PCR amplification via blocking the reaction between CaCO3 and DNA molecules. Thereafter samples were amplified by using both Archaeal and Bacterial universal primers (ref). Subsequently, archaeal and bacterial diversities in cave sediments, were investigated to be able to compare with respect to their similarities by using DGGE. DGGE patterns were analysed with BioNumerics software 5.1. Similarity matrix and dendograms of the DGGE profiles were generated based on the Dice correlation coefficient (band-based) and unweighted pair-group method with arithmetic mean (UPGMA). The structural diversity of the microbial community was examined by the Shannon index of general diversity (H). Similtaneously, geochemical analyses of the sediment samples were performed within the scope of this study. Total organic carbon (TOC), x-ray diffraction spectroscopy (XRD) and x-ray fluorescence spectroscopy (XRF) analysis of sediments were also implemented. The extensive results will be obtained at the next stages of the study currently carried on.
Temporal analysis of the effect of extruded flaxseed on the swine gut microbiota.
Holman, Devin B; Baurhoo, Bushansingh; Chénier, Martin R
2014-10-01
Flaxseed is a rich source of α-linolenic acid, an essential ω-3 fatty acid reported to have beneficial health effects in humans. Feeding swine a diet supplemented with flaxseed has been found to enrich pork products with ω-3 fatty acids. However, the effect of flaxseed supplementation on the swine gut microbiota has not been assessed to date. The purpose of this study was to investigate if extruded flaxseed has any impact on the bacterial and archaeal microbiota in the feces of growing-finishing pigs over a 51-day period, using denaturing gradient gel electrophoresis (DGGE) and real-time PCR. Bacterial DGGE profile analysis revealed major temporal shifts in the bacterial microbiota with only minor ones related to diet. The archaeal microbiota was significantly less diverse than that of Bacteria. The majority of bacterial DGGE bands sequenced belonged to the Firmicutes phylum while the archaeal DGGE bands were found to consist of only 2 species, Methanobrevibacter smithii and Methanosphaera stadtmanae. The abundance of Bacteroidetes decreased significantly from day 0 to day 21 in all diet groups while the abundance of Firmicutes was relatively stable across all diet cohorts and sampling times. There was also no significant correlation between pig mass and the ratio of Firmicutes to Bacteroidetes. While the addition of extruded flaxseed to the feed of growing-finishing pigs was beneficial for improving ω-3 fatty acid content of pork, it had no detectable impact on the fecal bacterial and archaeal microbiota, suggesting that extruded flaxseed may be used to improve meat quality without adverse effect on the swine gut microbiota or animal performance.
Feng, Zhen; Gao, Wei; Ren, Dan; Chen, Xi; Li, Juan-juan
2013-04-01
Kedong sufu is a typical bacteria-fermented sufu in China. Isolation and identification of the autochthonous bacteria involved would allow the design of specific starters for this speciality. The purpose of the present study was to evaluate the bacterial flora during the ripening of Kedong sufu using polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) and culturing. In terms of bacterial diversity, 22 strains were isolated and identified and 27 strains were detected by DGGE. Regarding bacterial dynamics, the results of culturing and PCR-DGGE exhibited a similar trend towards dominant strains. Throughout the fermentation of sufu, Enterococcus avium, Enterococcus faecalis and Staphylococcus carnosus were the dominant microflora, while the secondary microflora comprised Leuconostoc mesenteroides, Staphylococcus saprophyticus, Streptococcus lutetiensis, Kocuria rosea, Kocuria kristinae, Bacillus pumilus, Bacillus cereus and Bacillus subtilis. This study is the first to reveal the bacterial flora during the ripening of Kedong sufu using both culture-dependent and culture-independent methods. This information will help in the design of autochthonous starter cultures for the production of Kedong sufu with desirable characteristic sensory profiles and shorter ripening times. © 2012 Society of Chemical Industry.
Institute of Scientific and Technical Information of China (English)
SHI Limei; CAI Yuanfeng; YANG Hualin; XING Peng; LI Pengfu; KONG Lingdong; KONG Fanxiang
2009-01-01
Interactions between bacteria and cyanobacteria have been suggested to have a potential to influence harmful algal bloom dynamics,however,little information on these interactions is reported.In this study,the bacterial communities associated with five strains of Microcystis aeruginosa,three species of other Microcystis spp.,and four representative species of non-Microcystis cyanobacteria were compared.Bacterial 16S rDNA fragments were amplified and separated by denaturing gradient gel electrophoresis (DGGE) followed DNA sequence analysis.The similarities among bacterial communities associated with these cyanobacteria were compared to the digitized DGGE profiles using the cluster analyses technique.The bacterial community structure of all cyanobacterial cultures differed.Cluster analysis showed that the similarity values among M.aeruginosa cultures were higher than those of other cyanobacterial cultures.Sequence analysis of DGGE fragments indicated the presence of bacteria including Alphaproteobacteria,Betaproteobacteria,Gammaproteobacteria,Bacteroidetes and Actinobacteria in the cyanobacterial cultures.Members of the Sphingobacteriales were the prevalent group among the Microcystis-associated bacteria.The results provided further evidence for species-specific associations between cyanoabcteria and heterotrophic bacteria,which are useful for understanding interactions between Microcystis and their associated bacteria.
Vitali, Beatrice; Pugliese, Ciro; Biagi, Elena; Candela, Marco; Turroni, Silvia; Bellen, Gert; Donders, Gilbert G. G.; Brigidi, Patrizia
2007-01-01
The microbial flora of the vagina plays a major role in preventing genital infections, including bacterial vaginosis (BV) and candidiasis (CA). An integrated approach based on PCR-denaturing gradient gel electrophoresis (PCR-DGGE) and real-time PCR was used to study the structure and dynamics of bacterial communities in vaginal fluids of healthy women and patients developing BV and CA. Universal eubacterial primers and Lactobacillus genus-specific primers, both targeted at 16S rRNA genes, were used in DGGE and real-time PCR analysis, respectively. The DGGE profiles revealed that the vaginal flora was dominated by Lactobacillus species under healthy conditions, whereas several potentially pathogenic bacteria were present in the flora of women with BV. Lactobacilli were the predominant bacterial population in the vagina for patients affected by CA, but changes in the composition of Lactobacillus species were observed. Real-time PCR analysis allowed the quantitative estimation of variations in lactobacilli associated with BV and CA diseases. A statistically significant decrease in the relative abundance of lactobacilli was found in vaginal fluids of patients with BV compared to the relative abundance of lactobacilli in the vaginal fluids of healthy women and patients with CA. PMID:17644631
Vitali, Beatrice; Pugliese, Ciro; Biagi, Elena; Candela, Marco; Turroni, Silvia; Bellen, Gert; Donders, Gilbert G G; Brigidi, Patrizia
2007-09-01
The microbial flora of the vagina plays a major role in preventing genital infections, including bacterial vaginosis (BV) and candidiasis (CA). An integrated approach based on PCR-denaturing gradient gel electrophoresis (PCR-DGGE) and real-time PCR was used to study the structure and dynamics of bacterial communities in vaginal fluids of healthy women and patients developing BV and CA. Universal eubacterial primers and Lactobacillus genus-specific primers, both targeted at 16S rRNA genes, were used in DGGE and real-time PCR analysis, respectively. The DGGE profiles revealed that the vaginal flora was dominated by Lactobacillus species under healthy conditions, whereas several potentially pathogenic bacteria were present in the flora of women with BV. Lactobacilli were the predominant bacterial population in the vagina for patients affected by CA, but changes in the composition of Lactobacillus species were observed. Real-time PCR analysis allowed the quantitative estimation of variations in lactobacilli associated with BV and CA diseases. A statistically significant decrease in the relative abundance of lactobacilli was found in vaginal fluids of patients with BV compared to the relative abundance of lactobacilli in the vaginal fluids of healthy women and patients with CA.
Suppression of Listeria monocytogenes by the Native Micro-Flora in Teewurst Sausage.
Austin-Watson, Clytrice; Grant, Ar'Quette; Brice, Michline
2013-10-21
Modern consumers are interested in the use of non-chemical methods to control pathogens when heat sterilization is not an option. Such is the case with teewurst sausage, a raw spreadable sausage and a popular German commodity. Although Listeria was not found in teewurst, the optimal microbial growing conditions of teewurst coupled with the ubiquity of L. monocytogenes in nature, makes the possibility of contamination of products very possible. This pilot study was conducted to examine teewurst's native micro-flora's ability to suppress the outgrowth of L. monocytogenes at 10 °C using standard plate counts and PCR-DGGE. Traditional plating methods showed L. monocytogenes growth significantly decreased when in competition with the teewurst's native micro-flora ( p flora of the teewurst suppressed the overall growth of L. monocytogenes by an average of two logs, under these conditions. Denaturing Gradient Gel Electrophoresis (DGGE) amplicons with unique banding patterns were extracted from DGGE gel for identification. Brochothrix thermosphacta and Lactobacillus curvatus were identified as a part of the teewurst's native micro-flora. Although the native micro-flora did not decrease L. monocytogenes to below limits of detection, it was enough of a decrease to warrant further investigation.
Breulmann, Marc; Masyutenko, Nina Petrovna; Kogut, Boris Maratovich; Schroll, Reiner; Dörfler, Ulrike; Buscot, François; Schulz, Elke
2014-11-01
The quality, stability and availability of organic carbon (OC) in soil organic matter (SOM) can vary widely between differently managed ecosystems. Several approaches have been developed for isolating SOM fractions to examine their ecological roles, but links between the bioavailability of the OC of size-density fractions and soil microbial communities have not been previously explored. Thus, in the presented laboratory study we investigated the potential bioavailability of OC and the structure of associated microbial communities in different particle-size and density fractions of SOM. For this we used samples from four grassland ecosystems with contrasting management intensity regimes and two soil types: a Haplic Cambisol and a typical Chernozem. A combined size-density fractionation protocol was applied to separate clay-associated SOM fractions (CF1, <1 μm; CF2, 1-2 μm) from light SOM fractions (LF1, <1.8 g cm(-3); LF2, 1.8-2.0 g cm(-3)). These fractions were used as carbon sources in a respiration experiment to determine their potential bioavailability. Measured CO2-release was used as an index of substrate accessibility and linked to the soil microbial community structure, as determined by phospholipid fatty acids (PLFA) analysis. Several key factors controlling decomposition processes, and thus the potential bioavailability of OC, were identified: management intensity and the plant community composition of the grasslands (both of which affect the chemical composition and turnover of OC) and specific properties of individual SOM fractions. The PLFA patterns highlighted differences in the composition of microbial communities associated with the examined grasslands, and SOM fractions, providing the first broad insights into their active microbial communities. From observed interactions between abiotic and biotic factors affecting the decomposition of SOM fractions we demonstrate that increasing management intensity could enhance the potential bioavailability of
International Nuclear Information System (INIS)
Veyrinas, Kevin
2015-01-01
This is thesis is dedicated to the study and the use of the remarkable properties of the molecular frame photoelectron angular distribution (MFPAD). This observable is a very sensitive probe of both the photoionization (PI) processes in small molecules, through the determination of the magnitudes and relative phases of the dipole matrix elements, and the polarization state of the ionizing light, which is entirely encoded in the MFPAD in terms of the Stokes parameters (s1, s2, s3). MFPAD measurements take advantage of dissociative photoionization (DPI) processes by combining an electron-ion 3D momentum spectroscopy technique with the use of different radiation facilities: SOLEIL synchrotron (DESIRS and PLEIADES beamlines) and the XUV PLFA beamline (SLIC, LIDyL Attophysics group, CEA Saclay) based on the interaction of a strong laser field with a gaseous target called high harmonic generation (HHG). The first part of the thesis is devoted to the complete characterization of the polarization state of an incoming radiation. In this context, an original 'molecular polarimetry' method is introduced and demonstrated by comparison with a VUV optical polarimeter available on the DESIRS beamline. Using this method to determine the full polarization ellipse of HHG radiation generated in different conditions on the XUV PLFA facility leads to original results that include the challenging disentanglement of the circular and unpolarized components of the studied radiation. The second part deals with the study of DPI of the H 2 , D 2 and HD molecules induced by circularly polarized light at resonance with the doubly excited states Q1 and Q2. In this energy region (30-35 eV) where direct ionization, autoionization and dissociation compete on a femtosecond timescale, the photonic excitation gives rise to complex ultrafast electronic and nuclear coupled dynamics. The remarkable asymmetries observed in the circular dichroism in the molecular frame, compared to quantum
Quéméneur, Marianne; Cébron, Aurélie; Billard, Patrick; Battaglia-Brunet, Fabienne; Garrido, Francis; Leyval, Corinne; Joulian, Catherine
2010-01-01
Denaturing gradient gel electrophoresis (DGGE) and quantitative real-time PCR (qPCR) were successfully developed to monitor functional aoxB genes as markers of aerobic arsenite oxidizers. DGGE profiles showed a shift in the structure of the aoxB-carrying bacterial population, composed of members of the Alpha-, Beta- and Gammaproteobacteria, depending on arsenic (As) and Eh levels in Upper Isle River Basin waters. The highest aoxB gene densities were found in the most As-polluted oxic surface waters but without any significant correlation with environmental factors. Arsenite oxidizers seem to play a key role in As mobility in As-impacted waters. PMID:20453153
Spielvogel, Sandra; Steingräber, Laura; Schleuß, Per; Kuzyakov, Yakov; Guggenberger, Georg
2015-04-01
Kobresia pastures of the Tibetan Plateau represent the world's largest alpine ecosystem. Moderate husbandry on Kobresia pastures is beneficial for the storage of soil organic carbon (OC), nitrogen (N) and other nutrients and prevents erosion by establishment of sedge-turf root mats with high OC allocation rates below ground. However, undisturbed root mats are affected by freezing and thawing processes, which cause initial ice cracks. As a consequence decomposition of root mat layers will be accelerated and current sedentarization programs with concomitant increased grazing intensity may additionally enhance root mat degradation. Finally, cracks are enlarged by water and wind erosion as well as pika activities until bare soil surface areas without root mat horizons occur. The aim of this study was to understand the impact of the root mat layer on soil organic carbon stabilization and microbial functioning depending on soil depths and to predict future changes (OC, N and nutrient losses, soil microbial functioning in SOM transformation) by overgrazing and climate change. We investigated the mineral soil below Kobresia root mats along a false time degradation sequence ranging from stage 1 (intact root mat) to stage 4 (mats with large cracks and bare soil patches). Vertical gradients of δ13C values, neutral sugar, cutin and suberin contents as well as microbial biomass estimated by total phospholipid fatty acid (PLFA), microbial community composition (PLFA profiles) and activities of six extracellular enzymes involved in the C, N, and P cycle were assessed. Soil OC and N contents as well as C/N ratios indicate an increasing illuviation of topsoil material into the subsoil with advancing root mat degradation. This was confirmed by more negative δ13C values as well as significantly (p ≤ 0.05) increasing contributions of cutin derived hydroxy fatty acids to OC in the subsoils from degradation stages 1 to 4. PLFA profiles were surprisingly similar in the subsoils of
Ledder, Ruth G; Sreenivasan, Prem K; DeVizio, William; McBain, Andrew J
2010-12-01
The microbiological effects of biocidal products used for the enhancement of oral hygiene relate to the active compound(s) as well as other formulation components. Here, we test the specificities of selected actives in the absence of multiple excipients. Salivary ecosystems were maintained in tissue culture plate-based hydroxyapatite disc models (HDMs) and modified drip-flow biofilm reactors (MDFRs). Test compounds stannous fluoride (SF), SDS, triclosan (TCS), zinc lactate (ZL) and ZL with SF in combination (ZLSF) were delivered to the HDMs once and four times daily for 6 days to MDFRs. Plaques were characterized by differential viable counting and PCR-denaturing gradient gel electrophoresis (DGGE). TCS and SDS were the most effective compounds against HDM plaques, significantly reducing total viable counts (P<0.05), whilst SF, ZL and ZLSF were comparatively ineffective. TCS exhibited specificity for streptococci (P<0.01) and Gram-negative anaerobes (P<0.01) following a single dosing and also on repeated dosing in MDFRs. In contrast to single exposures, multiple dosing with ZLSF also significantly reduced all bacterial groups, whilst SF and ZL caused significant but transient reductions. According to PCR-DGGE analyses, significant (P<0.05) reductions in eubacterial diversity occurred following 6 day dosing with both TCS and ZLSF. Concordance of MDFR eubacterial profiles with salivary inocula ranged between 58 and 97%. TCS and ZL(SF) exhibited similar specificities to those reported for formulations. TCS was the most potent antibacterial, after single and multiple dosage regimens.
Czech Academy of Sciences Publication Activity Database
Kotas, Petr; Chroma, M.; Šantrůčková, H.; Lepš, Jan; Tříska, Jan; Kaštovská, E.
2017-01-01
Roč. 20, č. 2 (2017), s. 354-367 ISSN 1432-9840 R&D Projects: GA ČR GA13-17118S Institutional support: RVO:67179843 ; RVO:60077344 Keywords : dominant removal * fertilization * grassland * microbial community structure * mowing * pH * PLFA Subject RIV: EH - Ecology, Behaviour; EG - Zoology (ENTU-I) OBOR OECD: Environmental sciences (social aspects to be 5.7); Entomology (ENTU-I) Impact factor: 4.198, year: 2016
Symbol Stream Combining Versus Baseband Combining for Telemetry Arraying
Divsalar, D.
1983-01-01
The objectives of this article are to investigate and analyze the problem of combining symbol streams from many Deep Space Network stations to enhance bit signal-to-noise ratio and to compare the performance of this combining technique with baseband combining. Symbol stream combining (SSC) has some advantages and some disadvantages over baseband combining (BBC). The SSC suffers almost no loss in combining the digital data and no loss due to the transmission of the digital data by microwave links between the stations. The BBC suffers 0.2 dB loss due to alignment and combining the IF signals and 0.2 dB loss due to transmission of signals by microwave links. On the other hand, the losses in the subcarrier demodulation assembly (SDA) and in the symbol synchronization assembly (SSA) for SSC are more than the losses in the SDA and SSA for BBC. It is shown that SSC outperforms BBC by about 0.35 dB (in terms of the required bit energy-to-noise spectral density for a bit error rate of 1,000) for an array of three DSN antennas, namely 64 m, 34m(T/R) and 34m(R).
Soil microbial community structure across a thermal gradient following a geothermal heating event.
Norris, Tracy B; Wraith, Jon M; Castenholz, Richard W; McDermott, Timothy R
2002-12-01
In this study microbial species diversity was assessed across a landscape in Yellowstone National Park, where an abrupt increase in soil temperature had occurred due to recent geothermal activity. Soil temperatures were measured, and samples were taken across a temperature gradient (35 to 65 degrees C at a 15-cm depth) that spanned geothermally disturbed and unimpacted soils; thermally perturbed soils were visually apparent by the occurrence of dead or dying lodgepole pine trees. Changes in soil microbial diversity across the temperature gradient were qualitatively assessed based on 16S rRNA sequence variation as detected by denaturing gradient gel electrophoresis (DGGE) using both ribosomal DNA (rDNA) and rRNA as PCR templates and primers specific for the Bacteria or Archaea domain. The impact of the major heating disturbance was apparent in that DGGE profiles from heated soils appeared less complex than those from the unaffected soils. Phylogenetic analysis of a bacterial 16S rDNA PCR clone library from a recently heated soil showed that a majority of the clones belonged to the Acidobacterium (51%) and Planctomyces (18%) divisions. Agar plate counts of soil suspensions cultured on dilute yeast extract and R2A agar media incubated at 25 or 50 degrees C revealed that thermophile populations were two to three orders of magnitude greater in the recently heated soil. A soil microcosm laboratory experiment simulated the geothermal heating event. As determined by both RNA- and DNA-based PCR coupled with DGGE, changes in community structure (marked change in the DGGE profile) of soils incubated at 50 degrees C occurred within 1 week and appeared to stabilize after 3 weeks. The results of our molecular and culture data suggest that thermophiles or thermotolerant species are randomly distributed in this area within Yellowstone National Park and that localized thermal activity selects for them.
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.
Directory of Open Access Journals (Sweden)
Ruoyang He
Full Text Available Forest land-use changes have long been suggested to profoundly affect soil microbial communities. However, how forest type conversion influences soil microbial properties remains unclear in Tibetan boreal forests. The aim of this study was to explore variations of soil microbial profiles in the surface organic layer and subsurface mineral soil among three contrasting forests (natural coniferous forest, NF; secondary birch forest, SF and spruce plantation, PT. Soil microbial biomass, activity and community structure of the two layers were investigated by chloroform fumigation, substrate respiration and phospholipid fatty acid analysis (PLFA, respectively. In the organic layer, both NF and SF exhibited higher soil nutrient levels (carbon, nitrogen and phosphorus, microbial biomass carbon and nitrogen, microbial respiration, PLFA contents as compared to PT. However, the measured parameters in the mineral soils often did not differ following forest type conversion. Irrespective of forest types, the microbial indexes generally were greater in the organic layer than in the mineral soil. PLFAs biomarkers were significantly correlated with soil substrate pools. Taken together, forest land-use change remarkably altered microbial community in the organic layer but often did not affect them in the mineral soil. The microbial responses to forest land-use change depend on soil layer, with organic horizons being more sensitive to forest conversion.
Directory of Open Access Journals (Sweden)
Hongwei Xie
Full Text Available Methyl bromide (MB and other alternatives were evaluated for suppression of Fusarium spp., Phytophthora spp., and Meloidogyne spp. and their influence on soil microbial communities. Both Fusarium spp. and Phytophthora spp. were significantly reduced by the MB (30.74 mg kg-1, methyl iodide (MI: 45.58 mg kg-1, metham sodium (MS: 53.92 mg kg-1 treatments. MS exhibited comparable effectiveness to MB in controlling Meloidogyne spp. and total nematodes, followed by MI at the tested rate. By contrast, sulfuryl fluoride (SF: 33.04 mg kg-1 and chloroform (CF: 23.68 mg kg-1 showed low efficacy in controlling Fusarium spp., Phytophthora spp., and Meloidogyne spp. MB, MI and MS significantly lowered the abundance of different microbial populations and microbial biomass in soil, whereas SF and CF had limited influence on them compared with the control. Diversity indices in Biolog studies decreased in response to fumigation, but no significant difference was found among treatments in PLFA studies. Principal component and cluster analyses of Biolog and PLFA data sets revealed that MB and MI treatments greatly influenced the soil microbial community functional and structural diversity compared with SF treatment. These results suggest that fumigants with high effectiveness in suppressing soil-borne disease could significantly influence soil microbial community.
Energy Technology Data Exchange (ETDEWEB)
Antizar-Ladislao, B.; Spanova, K.; Beck, A.J.; Russell, N.J. [University of London Imperial College for Science Technology & Medicine, Ashford (United Kingdom)
2008-06-15
The microbial community structure changes of an aged-coal-tar soil contaminated with polycyclic aromatic hydrocarbons (PAHs) were investigated during simulated bioremediation at the laboratory-scale using an in-vessel composting approach. The composting reactors were operated using a logistic three-factor factorial design with three temperatures (T = 38, 55 or 70 {sup o}C), four soil to green-waste amendment ratios (S:GW = 0.6:1, 0.7:1, 0.8:1 or 0.9:1 on a dry weight basis) and three moisture contents (MC = 40%, 60% or 80%). Relative changes in microbial populations were investigated by following the dynamics of phospholipid fatty acid (PLFA) signatures using a {sup 13}C-labeled palmitic acid internal standard and sensitive GC/MS analysis during in-vessel composting over 98 days. The results of this investigation indicated that fungal to bacterial PLFA ratios were significantly influenced by temperature (p<0.05), and Gram-positive to Gram-negative bacterial ratios were significantly influenced by temperature (p<0.001) and S:GW ratio (p<0.01) during in-vessel composting. Additionally, the Gram-positive to Gram-negative bacterial ratios were correlated to the extent of PAH losses)<0.005) at 70{sup o}C.
The impact of zero-valent iron nanoparticles upon soil microbial communities is context dependent.
Pawlett, Mark; Ritz, Karl; Dorey, Robert A; Rocks, Sophie; Ramsden, Jeremy; Harris, Jim A
2013-02-01
Nanosized zero-valent iron (nZVI) is an effective land remediation tool, but there remains little information regarding its impact upon and interactions with the soil microbial community. nZVI stabilised with sodium carboxymethyl cellulose was applied to soils of three contrasting textures and organic matter contents to determine impacts on soil microbial biomass, phenotypic (phospholipid fatty acid (PLFA)), and functional (multiple substrate-induced respiration (MSIR)) profiles. The nZVI significantly reduced microbial biomass by 29 % but only where soil was amended with 5 % straw. Effects of nZVI on MSIR profiles were only evident in the clay soils and were independent of organic matter content. PLFA profiling indicated that the soil microbial community structure in sandy soils were apparently the most, and clay soils the least, vulnerable to nZVI suggesting a protective effect imparted by clays. Evidence of nZVI bactericidal effects on Gram-negative bacteria and a potential reduction of arbuscular mycorrhizal fungi are presented. Data imply that the impact of nZVI on soil microbial communities is dependent on organic matter content and soil mineral type. Thereby, evaluations of nZVI toxicity on soil microbial communities should consider context. The reduction of AM fungi following nZVI application may have implications for land remediation.
Directory of Open Access Journals (Sweden)
A. Lombao
2013-01-01
Full Text Available Studies concerning the microbial communities in burnt soils have been focused on biochemical properties and, despite its interest, information about the microbial community structure is scarce. The aim of this study was to evaluate the short- and medium- term effects produced by a high severity fire and the application of post-fire stabilization methods (mulching and seeding in the structure of soil microbial population, determined by means of the analysis of phospholipid fatty acids (PLFA. The study was performed in a forest ecosystem affected by a high severity wildfire and highly susceptible to post-fire soil erosion (Laza, NW Spain. Samples were collected from the A horizon (0-2 cm immediately and 4, 8 and 12 months after the wildfire. The results of principal component analysis carried out with PLFA data make possible to differentiate between burnt and unburnt samples, indicating a clear effect of the wildfire on composition of microbial communities. Unburnt samples were characterized by the presence of fungal fatty acid as 18:2ω6, 18:1ω9 o 16:ω5, whereas fatty acid characteristics of actinomycetes tended to be higher in burnt samples than in the corresponding unburnt samples. The structure of microbial communities also varied with sampling time, confirming seasonal fluctuations of soil microbial parameters.
Dippold, Michaela; Kuzyakov, Yakov
2015-04-01
Understanding the soil organic matter (SOM) dynamics is one of the most important challenges in soil science. Transformation of low molecular weight organic substances (LMWOS) is a key step in biogeochemical cycles because 1) all high molecular substances pass this stage during their decomposition and 2) only LMWOS will be taken up by microorganisms. Previous studies on LMWOS were focused on determining net fluxes through the LMWOS pool, but they rarely identified transformations. As LMWOS are the preferred C and energy source for microorganisms, the transformations of LMWOS are dominated by biochemical pathways of the soil microorganisms. Thus, understanding fluxes and transformations in soils requires a detailed knowledge on the biochemical pathways and its controlling factors. Tracing C fate in soil by isotopes became on of the most applied and promising biogeochemistry tools. Up to now, studies on LMWOS were nearly exclusively based on uniformly labeled organic substances i.e. all C atoms in the molecules were labeled with 13C or 14C. However, this classical approach did not allow the differentiation between use of intact initial substances in any process, or whether they were transformed to metabolites. The novel tool of position-specific labeling enables to trace molecule atoms separately and thus to determine the cleavage of molecules - a prerequisite for metabolic tracing. Position-specific labeling of LMWOS and quantification of 13CO2 and 13C in bulk soil enabled following the basic metabolic pathways of soil microorganisms. However, only the combination of position-specific 13C labeling with compound-specific isotope analysis of microbial biomarkers and metabolites allowed 1) tracing specific anabolic pathways in diverse microbial communities in soils and 2) identification of specific pathways of individual functional microbial groups. So, these are the prerequisites for soil fluxomics. Our studies combining position-specific labeled glucose with amino
Tanaka, Yasushi; Watanabe, Jun; Mogi, Yoshinobu
2012-08-01
Soy sauce is a traditional seasoning produced through the fermentation of soybeans and wheat using microbes. In this study, the microbial communities involved in the soy sauce manufacturing process were analyzed by PCR-Denaturing Gradient Gel Electrophoresis (PCR-DGGE). The bacterial DGGE profile indicated that the bacterial microbes in the koji were Weissella cibaria (Weissella confusa, Weissella kimchii, Weissella salipiscis, Lactobacillus fermentum, Lactobacillus plantarum, Lactobacillus iners, or Streptococcus thermophilus), Staphylococcus gallinarum (or Staphylococcus xylosus), and Staphylococcus kloosii. In addition to these bacteria, Tetragenococcus halophilus was also detected in the mash during lactic acid fermentation. The fungal DGGE profile indicated that the fungal microbes in the koji were not only Aspergillus oryzae but also several yeasts. In the mash, Zygosaccharomyces rouxii appeared in the early fermentation stage, Candida etchellsii (or Candida nodaensis) and Candida versatilis were detected at the middle fermentation stage, and Candida etchellsii was detected at the mature fermentation stage. These results suggest that the microbial communities present during the soy sauce manufacturing process change drastically throughout its production. This is the first report to reveal the microbial communities involved in the soy sauce manufacturing process using a culture-independent method. Crown Copyright © 2012. Published by Elsevier Ltd. All rights reserved.
Directory of Open Access Journals (Sweden)
Arianna Buccioni
2017-01-01
Full Text Available Ruminants derived products have a prominent role in diets and economy worldwide; therefore, the capability to control the rumen microbial ecosystem, for ameliorating their quality, is of fundamental importance in the livestock sector. The aim of this study was to evaluate the effect of dietary supplementation with chestnut and quebracho tannins on microbial community and fatty acid profile, in the rumen fluid of dairy ewes. Multivariate analysis of PCR-DGGE profiles of rumen microbial communities showed a correlation among the presence of chestnut or quebracho in the diet, the specific Butyrivibrio group DGGE profiles, the increase in 18:3 cis9, cis12, and cis15; 18:2 cis9 and cis12; 18:2 cis9 and trans11; 18:2 trans11 and cis15; and 18:1 trans11 content, and the decrease in 18:0 concentration. Phylogenetic analysis of DGGE band sequences revealed the presence of bacteria representatives related to the genera Hungatella, Ruminococcus, and Eubacterium and unclassified Lachnospiraceae family members, suggesting that these taxa could be affected by tannins presence in the diets. The results of this study showed that tannins from chestnut and quebracho can reduce the biohydrogenation of unsaturated fatty acids through changes in rumen microbial communities.
Suppression of Listeria monocytogenes by the Native Micro-Flora in Teewurst Sausage
Directory of Open Access Journals (Sweden)
Michline Brice
2013-10-01
Full Text Available Modern consumers are interested in the use of non-chemical methods to control pathogens when heat sterilization is not an option. Such is the case with teewurst sausage, a raw spreadable sausage and a popular German commodity. Although Listeria was not found in teewurst, the optimal microbial growing conditions of teewurst coupled with the ubiquity of L. monocytogenes in nature, makes the possibility of contamination of products very possible. This pilot study was conducted to examine teewurst’s native micro-flora’s ability to suppress the outgrowth of L. monocytogenes at 10 °C using standard plate counts and PCR-DGGE. Traditional plating methods showed L. monocytogenes growth significantly decreased when in competition with the teewurst’s native micro-flora (p < 0.05. The native micro-flora of the teewurst suppressed the overall growth of L. monocytogenes by an average of two logs, under these conditions. Denaturing Gradient Gel Electrophoresis (DGGE amplicons with unique banding patterns were extracted from DGGE gel for identification. Brochothrix thermosphacta and Lactobacillus curvatus were identified as a part of the teewurst’s native micro-flora. Although the native micro-flora did not decrease L. monocytogenes to below limits of detection, it was enough of a decrease to warrant further investigation.
International Nuclear Information System (INIS)
Kirk, Jennifer L.; Klironomos, John N.; Lee, Hung; Trevors, Jack T.
2005-01-01
Enhanced rhizosphere degradation uses plants to stimulate the rhizosphere microbial community to degrade organic contaminants. We measured changes in microbial communities caused by the addition of two species of plants in a soil contaminated with 31,000 ppm of total petroleum hydrocarbons. Perennial ryegrass and/or alfalfa increased the number of rhizosphere bacteria in the hydrocarbon-contaminated soil. These plants also increased the number of bacteria capable of petroleum degradation as estimated by the most probable number (MPN) method. Eco-Biolog plates did not detect changes in metabolic diversity between bulk and rhizosphere samples but denaturing gradient gel electrophoresis (DGGE) analysis of PCR-amplified partial 16S rDNA sequences indicated a shift in the bacterial community in the rhizosphere samples. Dice coefficient matrices derived from DGGE profiles showed similarities between the rhizospheres of alfalfa and perennial ryegrass/alfalfa mixture in the contaminated soil at week seven. Perennial ryegrass and perennial ryegrass/alfalfa mixture caused the greatest change in the rhizosphere bacterial community as determined by DGGE analysis. We concluded that plants altered the microbial population; these changes were plant-specific and could contribute to degradation of petroleum hydrocarbons in contaminated soil. - Plant-specific changes in microbial populations on roots affect degradation of petroleum hydrocarbons in contaminated soil
Shi, Shengjing; Bending, Gary D
2007-04-01
The phenyl-urea herbicide isoproturon is a major contaminant of surface and ground-water in agricultural catchments. Earlier work suggested that within-field spatial variation of isoproturon degradation rate resulted from interactions between catabolizing Sphingomonas spp. and pH. In the current study, changes to the structure of Sphingomonas communities during isoproturon catabolism were investigated using Sphingomonas-specific 16S rRNA gene primers. Growth-linked catabolism at high-pH (>7.5) sites was associated with the appearance of multiple new denaturing gradient gel electrophoresis (DGGE) bands. At low-pH sites, there was no change in DGGE banding at sites in which there was cometabolism, but at sites in which there was growth-linked catabolism, degradation was associated with the appearance of a new band not present at high pH sites. Sequencing of DGGE bands indicated that a strain related to Sphingomonas mali proliferated at low pH sites, while strain Sphingomonas sp. SRS2, a catabolic strain identified in earlier work, together with several further Sphingomonas spp., proliferated at high-pH sites. The data indicate that degradation was associated with complex changes to the structure of Sphingomonas spp. communities, the precise nature of which was spatially variable.
Hoyles, Lesley; Clear, Jessica A; McCartney, Anne L
2013-08-01
With the exceptions of the bifidobacteria, propionibacteria and coriobacteria, the Actinobacteria associated with the human gastrointestinal tract have received little attention. This has been due to the seeming absence of these bacteria from most clone libraries. In addition, many of these bacteria have fastidious growth and atmospheric requirements. A recent cultivation-based study has shown that the Actinobacteria of the human gut may be more diverse than previously thought. The aim of this study was to develop a denaturing gradient gel electrophoresis (DGGE) approach for characterizing Actinobacteria present in faecal samples. Amount of DNA added to the Actinobacteria-specific PCR used to generate strong PCR products of equal intensity from faecal samples of five infants, nine adults and eight elderly adults was anti-correlated with counts of bacteria obtained using fluorescence in situ hybridization probe HGC69A. A nested PCR using Actinobacteria-specific and universal PCR-DGGE primers was used to generate profiles for the Actinobacteria. Cloning of sequences from the DGGE bands confirmed the specificity of the Actinobacteria-specific primers. In addition to members of the genus Bifidobacterium, species belonging to the genera Propionibacterium, Microbacterium, Brevibacterium, Actinomyces and Corynebacterium were found to be part of the faecal microbiota of healthy humans. Copyright © 2013 Elsevier Ltd. All rights reserved.
Changes in soil microbial communities as affected by intensive cattle husbandry
Czech Academy of Sciences Publication Activity Database
Elhottová, Dana; Koubová, Anna; Šimek, Miloslav; Cajthaml, Tomáš; Jirout, Jiří; Esperschuetz, J.; Schloter, M.; Gattinger, A.
2012-01-01
Roč. 58, July (2012), s. 56-65 ISSN 0929-1393 R&D Projects: GA MŠk LC06066; GA ČR GA526/09/1570; GA ČR GAP504/10/2077 Grant - others:Akademie věd ČR(CZ) D-CZ 45:05/06 Institutional support: RVO:60077344 ; RVO:61388971 Keywords : outdoor husbandry * PLFA/PLEL * organic matter pyrolysis Subject RIV: EH - Ecology, Behaviour Impact factor: 2.106, year: 2012
Miyatake, T.; Moerdijk-Poortvliet, T.C.W.; Stal, L.J.; Boschker, H.T.S.
2014-01-01
Carbon flow from benthic diatoms to heterotrophic bacterial was traced in an intertidal sediment for 5 consecutive days. 13C-labeled bicarbonate was sprayed onto the sediment surface during low tide and 13C-label incorporation in major carbon pools, intermediate metabolites, and biomarkers were monitored. Phospholipid-derived fatty acid (PLFA) and ribosomal ribonucleic acid (rRNA) were used to identify the responsible members of the microbial community at class and family phylogenetic resolut...
Influence of technological treatments on bacterial communities in ...
African Journals Online (AJOL)
Influence of technological treatments on bacterial communities in tilapia ( Oreochromis niloticus ) as determined by 16S rDNA fingerprinting using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE)
Cui, Zhisong; Shao, Zongze
2009-07-01
In order to identify the predominant strains of polycyclic aromatic hydrocarbon (PAH)-degrading consortia harboring in sea water and surface sediment collected from deep sea of the Middle Atlantic Ridge. We employed enrichment method and spread-plate method to isolate cultivable bacteria and PAHs degraders from deep sea samples. Phylogenetic analysis was conducted by 16S rRNA gene sequencing of the bacteria. Then we analyzed the dominant bacteria in the PAHs-degrading consortia by denaturing gradient gel electrophoresis (DGGE) combined with DNA sequencing. Altogether 16 cultivable bacteria were obtained, including one PAHs degrader Novosphingobium sp. 4D. Phylogenetic analysis showed that strains closely related to Alcanivorax dieselolei NO1A (5/16) and Tistrella mobilis TISTR 1108T (5/16) constituted two biggest groups among the cultivable bacteria. DGGE analysis showed that strain 4L (also 4M and 4N, Alcanivorax dieselolei NO1A, 99.21%), 4D (Novosphingobium pentaromativorans US6-1(T), 97.07%) and 4B (also 4E, 4H and 4K, Tistrella mobilis TISTR 1108T, > 99%) dominated the consortium MC2D. While in consortium MC3CO, the predominant strains were strain 5C (also 5H, Alcanivorax dieselolei NO1A, > 99%), uncultivable strain represented by band 5-8 (Novosphingobium aromaticivorans DSM 12444T, 99.41%), 5J (Tistrella mobilis TISTR 1108T, 99.52%) and 5F (also 5G, Thalassospira lucentensis DSM 14000T, degrading consortia in sea water and surface sediment of Middle Atlantic Ridge deep sea, with Novosphingobium spp. as their main PAHs degraders.
Chen, Lie-zhong; Li, Yan-li; Yu, Yun-long
2014-01-01
Chlorpyrifos is a widely used insecticide in recent years, and it will produce adverse effects on soil when applied on crops or mixed with soil. In this study, nested polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE) were combined to explore the bacterial and fungal community successions in soil treated with 5 and 20 mg/kg of chlorpyrifos. Furthermore, isolates capable of efficiently decomposing chlorpyrifos were molecular-typed using enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR). Under the experimental conditions, degradation of chlorpyrifos in soil was interpreted with the first-order kinetics, and the half-lives of chlorpyrifos at 5 and 20 mg/kg doses were calculated to be 8.25 and 8.29 d, respectively. DGGE fingerprint and principal component analysis (PCA) indicated that the composition of the fungal community was obviously changed with the chlorpyrifos treatment, and that samples of chlorpyrifos treatment were significantly separated from those of the control from the beginning to the end. While for the bacterial community, chlorpyrifos-treated soil samples were apparently different in the first 30 d and recovered to a similar level of the control up until 60 d, and the distance in the PCA between the chlorpyrifos-treated samples and the control was getting shorter through time and was finally clustered into one group. Together, our results demonstrated that the application of chlorpyrifos could affect the fungal community structure in a quick and lasting way, while only affecting the bacterial community in a temporary way. Finally, nine typical ERIC types of chlorpyrifos-degrading isolates were screened. PMID:24711353
DEFF Research Database (Denmark)
Criscuolo, Paola; Laursen, Keld; Reichstein, Toke
2018-01-01
examine the effectiveness of different combinations of knowledge sources for achieving innovative performance. We suggest that combinations involving integrative search strategies – combining internal and external knowledge – are the most likely to generate product and process innovation. In this context......, we present the idea that cognitively distant knowledge sources are helpful for innovation only when used in conjunction with knowledge sources that are closer to the focal firm. We also find important differences between product and process innovation, with the former associated with broader searches......Searching for the most rewarding sources of innovative ideas remains a key challenge in management of technological innovation. Yet, little is known about which combinations of internal and external knowledge sources are triggers for innovation. Extending theories about searching for innovation, we...
Fan, Li; Ni, Jinren; Wu, Yanjun; Zhang, Yongyong
2009-03-15
The wastewater originated from the production of bromoamine acid was treated in a sequential system of micro-electrolysis (ME) and biological aerobic filter (BAF). Decolorization and COD(Cr) removal rate of the proposed system was investigated with full consideration of the influence of two major controlling factors such as organic loading rate (OLR) and hydraulic retention time (HRT). The removal rate of COD(Cr) was 81.2% and that of chrominance could be up to 96.6% at an OLR of 0.56 kg m(-3)d(-1) when the total HRT was 43.4h. Most of the chrominance was removed by the ME treatment, however, the BAF process was more effective for COD(Cr) removal. The GC-MS and HPLC-MS analysis of the contaminants revealed that 1-aminoanthraquinone, bromoamine acid and mono-sulfonated 1,2-dichlorobenzene were the main organic components in the wastewater. The reductive transformation of the anthraquinone derivatives in the ME reactor improved the biodegradability of the wastewater, and rendered the decolorization. After long-term of operation, it was observed that the predominant microorganisms immobilized on the BAF carriers were rod-shaped and globular. Four bacterial strains with apparent 16S rDNA fragments in the Denaturing Gradient Gel Electrophoresis (DGGE) profiles of BAF samples were identified as Variovorax sp., Sphingomonas sp., Mycobacterium sp., and Microbacterium sp.
Energy Technology Data Exchange (ETDEWEB)
Fan Li [Shenzhen Graduate School, Peking University, Key Laboratory for Environmental and Urban Sciences, Guang Dong 518055 (China); Department of Environmental Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871 (China); Ni Jinren [Shenzhen Graduate School, Peking University, Key Laboratory for Environmental and Urban Sciences, Guang Dong 518055 (China); Department of Environmental Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871 (China)], E-mail: nijinren@iee.pku.edu.cn; Wu Yanjun; Zhang Yongyong [Shenzhen Graduate School, Peking University, Key Laboratory for Environmental and Urban Sciences, Guang Dong 518055 (China); Department of Environmental Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871 (China)
2009-03-15
The wastewater originated from the production of bromoamine acid was treated in a sequential system of micro-electrolysis (ME) and biological aerobic filter (BAF). Decolorization and COD{sub Cr} removal rate of the proposed system was investigated with full consideration of the influence of two major controlling factors such as organic loading rate (OLR) and hydraulic retention time (HRT). The removal rate of COD{sub Cr} was 81.2% and that of chrominance could be up to 96.6% at an OLR of 0.56 kg m{sup -3} d{sup -1} when the total HRT was 43.4 h. Most of the chrominance was removed by the ME treatment, however, the BAF process was more effective for COD{sub Cr} removal. The GC-MS and HPLC-MS analysis of the contaminants revealed that 1-aminoanthraquinone, bromoamine acid and mono-sulfonated 1,2-dichlorobenzene were the main organic components in the wastewater. The reductive transformation of the anthraquinone derivatives in the ME reactor improved the biodegradability of the wastewater, and rendered the decolorization. After long-term of operation, it was observed that the predominant microorganisms immobilized on the BAF carriers were rod-shaped and globular. Four bacterial strains with apparent 16S rDNA fragments in the Denaturing Gradient Gel Electrophoresis (DGGE) profiles of BAF samples were identified as Variovorax sp., Sphingomonas sp., Mycobacterium sp., and Microbacterium sp.
International Nuclear Information System (INIS)
Fan Li; Ni Jinren; Wu Yanjun; Zhang Yongyong
2009-01-01
The wastewater originated from the production of bromoamine acid was treated in a sequential system of micro-electrolysis (ME) and biological aerobic filter (BAF). Decolorization and COD Cr removal rate of the proposed system was investigated with full consideration of the influence of two major controlling factors such as organic loading rate (OLR) and hydraulic retention time (HRT). The removal rate of COD Cr was 81.2% and that of chrominance could be up to 96.6% at an OLR of 0.56 kg m -3 d -1 when the total HRT was 43.4 h. Most of the chrominance was removed by the ME treatment, however, the BAF process was more effective for COD Cr removal. The GC-MS and HPLC-MS analysis of the contaminants revealed that 1-aminoanthraquinone, bromoamine acid and mono-sulfonated 1,2-dichlorobenzene were the main organic components in the wastewater. The reductive transformation of the anthraquinone derivatives in the ME reactor improved the biodegradability of the wastewater, and rendered the decolorization. After long-term of operation, it was observed that the predominant microorganisms immobilized on the BAF carriers were rod-shaped and globular. Four bacterial strains with apparent 16S rDNA fragments in the Denaturing Gradient Gel Electrophoresis (DGGE) profiles of BAF samples were identified as Variovorax sp., Sphingomonas sp., Mycobacterium sp., and Microbacterium sp
Ercolini, D; Moschetti, G; Blaiotta, G; Coppola, S
2001-03-01
Separation of amplified V3 region from 16S rDNA by denaturing gradient gel electrophoresis (DGGE) was tested as a tool for differentiation of lactic acid bacteria commonly isolated from food. Variable V3 regions of 21 reference strains and 34 wild strains referred to species belonging to the genera Pediococcus, Enterococcus, Lactococcus, Lactobacillus, Leuconostoc, Weissella, and Streptococcus were analyzed. DGGE profiles obtained were species-specific for most of the cultures tested. Moreover, it was possible to group the remaining LAB reference strains according to the migration of their 16S V3 region in the denaturing gel. The results are discussed with reference to their potential in the analysis of LAB communities in food, besides shedding light on taxonomic aspects.
Microbial ecology of two hot springs of Sikkim: Predominate population and geochemistry.
Najar, Ishfaq Nabi; Sherpa, Mingma Thundu; Das, Sayak; Das, Saurav; Thakur, Nagendra
2018-10-01
Northeastern regions of India are known for their floral and faunal biodiversity. Especially the state of Sikkim lies in the eastern Himalayan ecological hotspot region. The state harbors many sulfur rich hot springs which have therapeutic and spiritual values. However, these hot springs are yet to be explored for their microbial ecology. The development of neo generation techniques such as metagenomics has provided an opportunity for inclusive study of microbial community of different environment. The present study describes the microbial diversity in two hot springs of Sikkim that is Polok and Borong with the assist of culture dependent and culture independent approaches. The culture independent techniques used in this study were next generation sequencing (NGS) and Phospholipid Fatty Acid Analysis (PLFA). Having relatively distinct geochemistry both the hot springs are thermophilic environments with the temperature range of 50-77 °C and pH range of 5-8. Metagenomic data revealed the dominance of bacteria over archaea. The most abundant phyla were Proteobacteria and Bacteroidetes although other phyla were also present such as Acidobacteria, Nitrospirae, Firmicutes, Proteobacteria, Parcubacteria and Spirochaetes. The PLFA studies have shown the abundance of Gram Positive bacteria followed by Gram negative bacteria. The culture dependent technique was correlative with PLFA studies. Most abundant bacteria as isolated and identified were Gram-positive genus Geobacillus and Anoxybacillus. The genus Geobacillus has been reported for the first time in North-Eastern states of India. The Geobacillus species obtained from the concerned hot springs were Geobacillus toebii, Geobacillus lituanicus, Geobacillus Kaustophillus and the Anoxybacillus species includes Anoxybacillus gonensis and Anoxybacillus Caldiproteolyticus. The distribution of major genera and their statistical correlation analyses with the geochemistry of the springs predicted that the temperature, p
Competition between roots and microorganisms for phosphorus: A novel 33P labeling approach
Zilla, Thomas; Kuzyakov, Yakov; Zavišiæ, Aljoša; Polle, Andrea
2015-04-01
While organic N mineralization exhibits clear seasonal uptake dynamics, knowledge about seasonal variation in microbial P uptake and mineralization is scarce. We hypothesize that the dynamics of P uptake and mineralization by microorganisms in temperate forest soils exhibit a seasonality anti-cyclic to plant P uptake. Therefore, the ratio of microbial P to labile P increases by the transition from acquiring ecosystems (in spring) to recycling ones (in fall). To investigate this, intact soil-plant mesocosms containing Ah horizon with 1 year old F. sylvatica were removed from the P-rich field site Bad Brueckenau and the P-depleted field site Luess in Germany. During incubation under controlled conditions, seasonal pulse labeling by 33P-orthophosphate was performed at 5 time points over the course of one year. 33P recovery in microbial compounds of organic and mineral soil horizons was determined 7 and 30 days after the labeling. This procedure will account for temporal changes in P allocation and also considers the rather slow P transport from the mycorrhiza into the plants and other microorganisms. For the first time we analyzed the 33P incorporation into total PLFA and consequently provide a new technique for the analysis of P uptake by microorganisms, which has clear advantages compared to P quantification after chloroform fumigation. Polar lipids are hereby extracted with a Frostegård-modified Bligh-and-Dyer buffer, i.e. a single phase mixture of chloroform, methanol and citrate buffer (0.8:1:2, v:v:v). Phospholipids (PLFA) are isolated and purified by solid phase extraction via a silica gel column chromatography. Subsequently, PLFA are hydrolyzed and the resulting fatty acids derivatized by methylation. The fatty acid methyl esters were extracted with n-hexane and measured by GC/MS to investigate the composition of the microbial community. The remaining extract, containing head groups, phosphate units and glycerol backbones, was used to determine 33P activity
The application of polymerase chain reaction-denaturing gradient ...
African Journals Online (AJOL)
Jane
2011-05-23
May 23, 2011 ... dominance in microbial ecology if the corresponding environment samples had been provided. This ... yeast peptone dextrose; PCR, polymerase chain reaction. method, DGGE method ..... Two nuclear mutations that block.
Piwat, S; Teanpaisan, R
2013-01-01
This study aimed to develop a 16S rRNA PCR-denaturing gradient gel electrophoresis (DGGE) to identify the species level of Lactobacillus casei group and to investigate their characteristics of acid production and inhibitory effect. PCR-DGGE has been developed based on the 16S rRNA gene, and a set of HDA-1-GC and HDA-2, designed at V2-V3 region, and another set of CARP-1-GC and CARP-2, designed at V1 region, have been used. The bacterial strains included L. casei ATCC 393, L. paracasei CCUG 32212, L. rhamnosus ATCC 7469, L. zeae CCUG 35515, and 46 clinical strains of L. casei/paracasei/rhamnosus. Inhibitory effect against Streptococcus mutans and acid production were examined. Results revealed that each type species strain and identified clinical isolate showed its own unique DGGE pattern using CARP1-GC and CARP2 primers. HDA1-GC and HDA2 primers could distinguish the strains of L. paracasei from L. casei. It was found that inhibitory effect of L. paracasei was stronger than L. casei and L. rhamnosus. The acid production of L. paracasei was lower than L. casei and L. rhamnosus. In conclusion, the technique has been proven to be able to differentiate between closely related species in L. casei group and thus provide reliable information of their phenotypic appearances.
Gabarró, J; Hernández-Del Amo, E; Gich, F; Ruscalleda, M; Balaguer, M D; Colprim, J
2013-12-01
This study investigates the microbial community dynamics in an intermittently aerated partial nitritation (PN) SBR treating landfill leachate, with emphasis to the nosZ encoding gene. PN was successfully achieved and high effluent stability and suitability for a later anammox reactor was ensured. Anoxic feedings allowed denitrifying activity in the reactor. The influent composition influenced the mixed liquor suspended solids concentration leading to variations of specific operational rates. The bacterial community was low diverse due to the stringent conditions in the reactor, and was mostly enriched by members of Betaproteobacteria and Bacteroidetes as determined by 16S rRNA sequencing from excised DGGE melting types. The qPCR analysis for nitrogen cycle-related enzymes (amoA, nirS, nirK and nosZ) demonstrated high amoA enrichment but being nirS the most relatively abundant gene. nosZ was also enriched from the seed sludge. Linear correlation was found mostly between nirS and the organic specific rates. Finally, Bacteroidetes sequenced in this study by 16S rRNA DGGE were not sequenced for nosZ DGGE, indicating that not all denitrifiers deal with complete denitrification. However, nosZ encoding gene bacteria was found during the whole experiment indicating the genetic potential to reduce N2O. Copyright © 2013 Elsevier Ltd. All rights reserved.
Energy Technology Data Exchange (ETDEWEB)
Doi, Tetsuya [Field Production Science Center, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Nishitokyo, Tokyo 188-0002 (Japan); Nishihara Environment Technology Inc., Tokyo 108-0023 (Japan); Matsumoto, Hisami [Nishihara Environment Technology Inc., Tokyo 108-0023 (Japan); Abe, Jun [AE-Bio, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo 113-8657 (Japan); Morita, Shigenori [Field Production Science Center, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Nishitokyo, Tokyo 188-0002 (Japan)
2009-02-15
We performed an experiment of continuous anaerobic hydrogen fermentation as a pilot-plant-scale test, in which waste from a bread factory was fermented by microflora of rice rhizosphere origin. The community structure of microflora during anaerobic hydrogen fermentation was analyzed using PCR-DGGE, FISH, and quinone profiles. The relation of those results to hydrogen generation was discussed. Results show that a suitable condition was a reactor temperature of 35 C, with HRT 12-36 h, volume load of 30-70 kg-COD{sub Cr}/m{sup 3} day, and maximum hydrogen production rate of 1.30 mol-H{sub 2}/mol-hexose. Regarding characteristics of microflora during fermentation, PCR-DGGE results show specific 16S rDNA band patterns; Megasphaera elsdenii and Clostridium sp. of the hydrogen-producing bacteria were identified. M. elsdenii was detected throughout the fermentation period, while Clostridium sp. of hydrogen-producing bacteria was detected on the 46th day. Furthermore, FISH revealed large amounts of Clostridium spp. in the sample. The quinone profile showed that the dominant molecular species of quinone is MK-7. Because Clostridium spp. belong to MK-7, results suggest that the quinone profile result agrees with the results of PCR-DGGE and FISH. Microflora in the rhizosphere of rice plants can be a possible resource for effective bacteria of biohydrogen production. (author)
Directory of Open Access Journals (Sweden)
Anne A M J Becker
Full Text Available Understanding the symbiotic relationship between gut microbes and their animal host requires characterization of the core microbiota across populations and in time. Especially in captive populations of endangered wildlife species such as the cheetah (Acinonyx jubatus, this knowledge is a key element to enhance feeding strategies and reduce gastrointestinal disorders. In order to investigate the temporal stability of the intestinal microbiota in cheetahs under human care, we conducted a longitudinal study over a 3-year period with bimonthly faecal sampling of 5 cheetahs housed in two European zoos. For this purpose, an integrated 16S rRNA DGGE-clone library approach was used in combination with a series of real-time PCR assays. Our findings disclosed a stable faecal microbiota, beyond intestinal community variations that were detected between zoo sample sets or between animals. The core of this microbiota was dominated by members of Clostridium clusters I, XI and XIVa, with mean concentrations ranging from 7.5-9.2 log10 CFU/g faeces and with significant positive correlations between these clusters (P<0.05, and by Lactobacillaceae. Moving window analysis of DGGE profiles revealed 23.3-25.6% change between consecutive samples for four of the cheetahs. The fifth animal in the study suffered from intermediate episodes of vomiting and diarrhea during the monitoring period and exhibited remarkably more change (39.4%. This observation may reflect the temporary impact of perturbations such as the animal's compromised health, antibiotic administration or a combination thereof, which temporarily altered the relative proportions of Clostridium clusters I and XIVa. In conclusion, this first long-term monitoring study of the faecal microbiota in feline strict carnivores not only reveals a remarkable compositional stability of this ecosystem, but also shows a qualitative and quantitative similarity in a defined set of faecal bacterial lineages across the five
Liu, Xingmei; Zhou, Jian; Li, Wanlu; Xu, Jianming; Brookes, Philip C
2014-05-01
Our aim was to test the effects of simulated acid rain (SAR) at different pHs, when applied to fertilized and unfertilized soils, on the leaching of soil cations (K, Ca, Mg, Na) and Al. Their effects on soil pH, exchangeable H(+) and Al(3+) and microbial community structure were also determined. A Paleudalfs soil was incubated for 30 days, with and without an initial application of urea (200 mg N kg(-1)soil) as nitrogen (N) fertilizer. The soil was held in columns and leached with SAR at three pH levels. Six treatments were tested: SAR of pH 2.5, 4.0 and 5.6 leaching on unfertilized soil (T1, T2 and T3), and on soils fertilized with urea (T4, T5 and T6). Increasing acid inputs proportionally increased cation leaching in both unfertilized and fertilized soils. Urea application increased the initial Ca and Mg leaching, but had no effect on the total concentrations of Ca, Mg and K leached. There was no significant difference for the amount of Na leached between the different treatments. The SAR pH and urea application had significant effects on soil pH, exchangeable H(+) and Al(3+). Urea application, SAR treated with various pH, and the interactions between them all had significant impacts on total phospholipid fatty acids (PLFAs). The highest concentration of total PLFAs occurred in fertilized soils with SAR pH5.6 and the lowest in soils leached with the lowest SAR pH. Soils pretreated with urea then leached with SARs of pH 4.0 and 5.6 had larger total PLFA concentrations than soil without urea. Bacterial, fungal, actinomycete, Gram-negative and Gram-positive bacterial PLFAs had generally similar trends to total PLFAs.
Sverdrup, Line E; Linjordet, Roar; Strømman, Gjermund; Hagen, Snorre B; van Gestel, Cornelis A M; Frostegård, Sa; Sørheim, Roald
2006-12-01
The effect of zinc on soil nitrification and composition of the microbial community in soil was investigated using a full factorial experiment with five zinc concentrations and four levels of biological complexity (microbes only, microbes and earthworms (Eisenia fetida), microbes and Italian ryegrass (Lolium multiflorum var. Macho), and microbes, ryegrass and earthworms). After 6 weeks of exposure, the activity of soil nitrifying bacteria was measured and the microbial community structure was characterized by phospholipid fatty acid (PLFA) analysis. Soil nitrification and several PLFA markers were significantly influenced by either zinc addition and/or the presence of earthworms or ryegrass, and one of the most pronounced changes was the increase of fungi and decrease of bacteria with increasing concentrations of zinc. Of particular interest, however, was the potential interaction between the presence of plants and/or earthworms and the effect of zinc, which the factorial study design allowed us to explore. Such an effect was observed in two cases: Earthworms reduced the positive effect of zinc on the fungal biomass (ANOVA, p=0.03), and the effect of earthworms on the soil nitrification activity depended on zinc concentration (ANOVA, p<0.05). The effect of earthworm presence was not very large, but it does show that multispecies tests might give information about metal toxicity or bioavailability that cannot be predicted from single-species tests.
Peltoniemi, Krista; Laiho, Raija; Juottonen, Heli; Kiikkilä, Oili; Mäkiranta, Päivi; Minkkinen, Kari; Pennanen, Taina; Penttilä, Timo; Sarjala, Tytti; Tuittila, Eeva-Stiina; Tuomivirta, Tero; Fritze, Hannu
2015-07-01
Impacts of warming with open-top chambers on microbial communities in wet conditions and in conditions resulting from moderate water-level drawdown (WLD) were studied across 0-50 cm depth in northern and southern boreal sedge fens. Warming alone decreased microbial biomass especially in the northern fen. Impact of warming on microbial PLFA and fungal ITS composition was more obvious in the northern fen and linked to moisture regime and sample depth. Fungal-specific PLFA increased in the surface peat in the drier regime and decreased in layers below 10 cm in the wet regime after warming. OTUs representing Tomentella and Lactarius were observed in drier regime and Mortierella in wet regime after warming in the northern fen. The ectomycorrhizal fungi responded only to WLD. Interestingly, warming together with WLD decreased archaeal 16S rRNA copy numbers in general, and fungal ITS copy numbers in the northern fen. Expectedly, many results indicated that microbial response on warming may be linked to the moisture regime. Results indicated that microbial community in the northern fen representing Arctic soils would be more sensitive to environmental changes. The response to future climate change clearly may vary even within a habitat type, exemplified here by boreal sedge fen. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
Responses of Soil Microbial Community Structure and Diversity to Agricultural Deintensification
Institute of Scientific and Technical Information of China (English)
ZHANG Wei-Jian; S.HU; RUI Wen-Yi; C.TU; H.G.DIAB; F.J.LOUWS; J.P.MUELLER; N.CREAMER; M.BELL; M.G.WAGGER
2005-01-01
Using a scheme of agricultural fields with progressively less intensive management (deintensification), different management practices in six agroecosystems located near Goldsboro, NC, USA were tested in a large-scale experiment, including two cash-grain cropping systems employing either tillage (CT) or no-tillage (NT), an organic farming system (OR), an integrated cropping system with animals (IN), a successional field (SU), and a plantation woodlot (WO). Microbial phospholipid fatty acid (PLFA) profiles and substrate utilization patterns (BIOLOG ECO plates) were measured to examine the effects of deintensification on the structure and diversity of soil microbial communities. Principle component analyses of PLFA and BIOLOG data showed that the microbial community structure diverged among the soils of the six systems.Lower microbial diversity was found in lowly managed ecosystem than that in intensive and moderately managed agroecosystems, and both fungal contribution to the total identified PLFAs and the ratio of microbial biomass C/N increased along with agricultural deintensification. Significantly higher ratios of C/N (P < 0.05) were found in the WO and SU systems, and for fungal/bacterial PLFAs in the WO system (P < 0.05). There were also significant decreases (P < 0.05)along with agricultural deintensification for contributions of total bacterial and gram positive (G+) bacterial PLFAs.Agricultural deintensification could facilitate the development of microbial communities that favor soil fungi over bacteria.
Mangal, Vaughn; Stock, Naomi L; Guéguen, Celine
2016-03-01
Orbitrap high resolution mass spectrometry (HRMS) with electrospray ionization in both positive and negative polarity was conducted on Suwannee River fulvic acid (SRFA), Pony Lake fulvic acid (PLFA) standards, and dissolved organic matter (DOM) released by freshwater phytoplankton (Scenedesmus obliquus, Euglena mutabilis, and Euglena gracilis). Three-dimensional van Krevelen diagrams expressing various oxygenation states of sulfur molecules and abundance plots of sulfur-containing species were constructed. Orbitrap HRMS analysis of SRFA found a high density of peaks in the lignin region (77 %) and low density of protein material (6.53 %), whereas for PLFA, 25 % of the total peaks were lignin related compared to 56 % of peaks in protein regions, comparable with other HRMS studies. Phytoplankton-derived DOM of S. obliquus, E. mutabilis, and E. gracilis was dominated by protein molecules at respective percentages of 36, 46, and 49 %, and is consistent with previous experiments examining phytoplankton-derived DOM composition. The normalized percentage of SO-containing compounds was determined among the three phytoplankton to be 56 % for Scenedesmus, 54 % for E. mutabilis, and 47 % for E. gracilis, suggesting variation between sulfur content in phytoplankton-derived DOM and differences in metal binding capacities. These results suggest the level of resolution by Orbitrap mass spectrometry is sufficient for preliminary characterization of phytoplankton DOM at an affordable cost relative to other HRMS techniques.
Deng, Qi; Hui, Dafeng; Chu, Guowei; Han, Xi; Zhang, Quanfa
2017-07-17
Rain-induced soil CO 2 pulse, a rapid excitation in soil CO 2 flux after rain, is ubiquitously observed in terrestrial ecosystems, yet the underlying mechanisms in tropical forests are still not clear. We conducted a rain simulation experiment to quantify rain-induced changes in soil CO 2 flux and microbial community composition in a tropical forest. Soil CO 2 flux rapidly increased by ~83% after rains, accompanied by increases in both bacterial (~51%) and fungal (~58%) Phospholipid Fatty Acids (PLFA) biomass. However, soil CO 2 flux and microbial community in the plots without litters showed limited response to rains. Direct releases of CO 2 from litter layer only accounted for ~19% increases in soil CO 2 flux, suggesting that the leaching of dissolved organic carbon (DOC) from litter layer to the topsoil is the major cause of rain-induced soil CO 2 pulse. In addition, rain-induced changes in soil CO 2 flux and microbial PLFA biomass decreased with increasing rain sizes, but they were positively correlated with litter-leached DOC concentration rather than total DOC flux. Our findings reveal an important role of litter-leached DOC input in regulating rain-induced soil CO 2 pulses and microbial community composition, and may have significant implications for CO 2 losses from tropical forest soils under future rainfall changes.
Farm system management affects community structure of arbuscular mycorrhizal fungi
Czech Academy of Sciences Publication Activity Database
Schneider, K. D.; Lynch, D. H.; Dunfield, K.; Khosla, K.; Jansa, Jan; Voroney, R. P.
2015-01-01
Roč. 96, NOV 2015 (2015), s. 192-200 ISSN 0929-1393 Institutional support: RVO:61388971 Keywords : Organic agriculture * PCR-DGGE * Phosphorus availability Subject RIV: EE - Microbiology, Virology Impact factor: 2.670, year: 2015
Microbial Succession in Co-Composting of Chipped-Ground Oil Palm Frond and Palm Oil Mill Effluent
International Nuclear Information System (INIS)
Mohd Najib Ahmad; Siti Ramlah Ahmad Ali; Mohd Ali Hassan
2016-01-01
Succession and phylogenetic profile of microbial communities during co-composting of chipped-ground oil palm frond (CG-OPF) and palm oil mill effluent (POME) were studied by apply-ing polymerase chain reaction-denaturant gel gradient electrophoresis (PCR-DGGE) analysis. The results indicated that the dominant microbial community detected was γ-Pro bacteria such as Pseudomonas sp. at almost throughout the composting process. Whilst Bacillales such as Bacillus psychrodurans were found toward the end of the composting process. Bacteroidetes such as Pedobacter solani were detected at the final stage of composting. This study contributed to a better understanding of microbial shifting and functioning throughout CG-OPF composting. Therefore, PCR-DGGE is recommended to be used as a tool to identify potential microbes that can contribute to a better performance of composting process. (author)
DEFF Research Database (Denmark)
Paltsi, Jordi; Illa, J.; Prenafeta-Boldu, F.X.
2010-01-01
Biomass samples taken during the continuous operation of thermophilic anaerobic digestors fed with manure and exposed to successive inhibitory pulses of long-chain fatty acids (LCFA) were characterized in terms of specific metabolic activities and 16S rDNA DGGE profiling of the microbial community....... Population profiles of eubacterial and archaeal 16S rDNA genes revealed that no significant shift on microbial community composition took place upon biomass exposure to LCFA. DNA sequencing of predominant DGGE bands showed close phylogenetic affinity to ribotypes characteristic from specific beta...... kinetics considering the relation between LCFA inhibitory substrate concentration and specific biomass content, as an approximation to the adsorption process, improved the model fitting and provided a better insight on the physical nature of the LCFA inhibition process. (C) 2009 Elsevier Ltd. All rights...
Shimomura, Yumi; Morimoto, Sho; Hoshino, Yuko Takada; Uchida, Yoshitaka; Akiyama, Hiroko; Hayatsu, Masahito
2012-01-01
Ammonia monooxygenase subunit A gene (amoA) is frequently used as a functional gene marker for diversity analysis of ammonia-oxidizing bacteria (AOB). To select a suitable amoA primer for real-time PCR and PCR-denaturing gradient gel electrophoresis (DGGE), three reverse primers (degenerate primer amoA-2R; non-degenerate primers amoA-2R-GG and amoA-2IR) were examined. No significant differences were observed among the three primers in terms of quantitative values of amoA from environmental samples using real-time PCR. We found that PCR-DGGE analysis with the amoA-2IR primer gave the best results in this studied soil. These results indicate that amoA-2IR is a suitable primer for community analysis of AOB in the environment. PMID:22075625
Bu, Yufen; Shao, Wei; Huang, Weijing; Ji, Qianlong; Yao, Yuncong
2016-01-01
Plant growth can be promoted by the application of apple fruit fermentation (AFF), despite unclear of the underlying mechanisms, the effects involved in AFF on rhizosphere microorganisms have been hypothesized. We investigated the consequences of applying AFF alone or in combination with Bacillus licheniformis to strawberry tissue culture seedlings in vitro, the analyses of Denaturing Gradient Gel Electrophoresis (DGGE) and 16S rDNA were performed to determine AFF effects on rhizosphere. Moreover, the growth index and antioxidant enzyme activities were determined 30 days after treatments. We identified five dominant bacteria in AFF: Coprinus atramentarius, Bacillus megaterium, Bacillus licheniformis, Weissella and B. subtilis. The greatest number of bacterial species were observed in the rhizosphere of control matrix (water treated), and the lowest diversity appeared in the rhizosphere soil treated with 108 cfu/mL B. licheniformis alone. Combining AFF plus B. licheniformis in one treatment resulted in the largest leaf area, plant height, root length, plant weight, and the markedly higher activities of antioxidant enzymes. We conclude that a combination of AFF plus B. licheniformis treatment to matrix can increase antioxidant enzymes activities in strawberry seedlings, optimize the status of rhizosphere microbial, and promote plant growth. PMID:27755580
Modifiable Combining Functions
Cohen, Paul; Shafer, Glenn; Shenoy, Prakash P.
2013-01-01
Modifiable combining functions are a synthesis of two common approaches to combining evidence. They offer many of the advantages of these approaches and avoid some disadvantages. Because they facilitate the acquisition, representation, explanation, and modification of knowledge about combinations of evidence, they are proposed as a tool for knowledge engineers who build systems that reason under uncertainty, not as a normative theory of evidence.
16S rRNA targeted DGGE fingerprinting of microbial communities
Tzeneva, V.A.; Heilig, G.H.J.; Vliet, van W.M.; Akkermans, A.D.L.; Vos, de W.M.; Smidt, H.
2008-01-01
The past decades have seen the staggering development of molecular microbial ecology as a discipline that uses the detection of so-called biomarkers to monitor microbial communities in environment samples. A variety of molecules can be used as biomarkers, including cell-wall components, proteins,
Morison, W L
1985-08-01
Various adjunctive treatments are now frequently used in combination with PUVA therapy with the aims of limiting adverse effects, improving efficacy and decreasing the cost of treatment. In the management of psoriasis, PUVA plus retinoids, PUVA plus methotrexate and PUVA plus UVB phototherapy are the most frequently used combinations. PUVA plus topical corticosteroids and PUVA plus anthralin are also efficacious but adverse effects and poor acceptance by patients are limiting factors. Combinations of PUVA plus nitrogen mustard and ionizing radiation are used in mycosis fungoides to treat tumors and residual disease in secluded sites. In the management of photodermatoses with PUVA therapy, prednisone is often required to prevent exacerbation of disease. A combination of prednisone and PUVA therapy can also be useful in lichen planus and atopic eczema. The selection of a suitable combination treatment, will depend upon the preferences of the clinician, the disease being treated, and the characteristics of the patient.
International Nuclear Information System (INIS)
Bhunia, C.T.
2007-07-01
Packet combining scheme is a well defined simple error correction scheme for the detection and correction of errors at the receiver. Although it permits a higher throughput when compared to other basic ARQ protocols, packet combining (PC) scheme fails to correct errors when errors occur in the same bit locations of copies. In a previous work, a scheme known as Packet Reversed Packet Combining (PRPC) Scheme that will correct errors which occur at the same bit location of erroneous copies, was studied however PRPC does not handle a situation where a packet has more than 1 error bit. The Modified Packet Combining (MPC) Scheme that can correct double or higher bit errors was studied elsewhere. Both PRPC and MPC schemes are believed to offer higher throughput in previous studies, however neither adequate investigation nor exact analysis was done to substantiate this claim of higher throughput. In this work, an exact analysis of both PRPC and MPC is carried out and the results reported. A combined protocol (PRPC and MPC) is proposed and the analysis shows that it is capable of offering even higher throughput and better error correction capability at high bit error rate (BER) and larger packet size. (author)
Development of two dimensional electrophoresis method using single chain DNA
International Nuclear Information System (INIS)
Ikeda, Junichi; Hidaka, So
1998-01-01
By combining a separation method due to molecular weight and a method to distinguish difference of mono-bases, it was aimed to develop a two dimensional single chain DNA labeled with Radioisotope (RI). From electrophoretic pattern difference of parent and variant strands, it was investigated to isolate the root module implantation control gene. At first, a Single Strand Conformation Polymorphism (SSCP) method using concentration gradient gel was investigated. As a result, it was formed that intervals between double chain and single chain DNAs expanded, but intervals of both single chain DNAs did not expand. On next, combination of non-modified acrylic amide electrophoresis method and Denaturing Gradient-Gel Electrophoresis (DGGE) method was examined. As a result, hybrid DNA developed by two dimensional electrophoresis arranged on two lines. But, among them a band of DNA modified by high concentration of urea could not be found. Therefore, in this fiscal year's experiments, no preferable result could be obtained. By the used method, it was thought to be impossible to detect the differences. (G.K.)
Application of rice rhizosphere microflora for hydrogen production from apple pomace
Energy Technology Data Exchange (ETDEWEB)
Doi, Tetsuya [Institute for Sustainable Agro-ecosystem Services (ISAS), Graduate School of Agriculture and Life Sciences, The University of Tokyo, Nishitokyo, Tokyo 188-0002 (Japan); Nishihara Environment Technology Inc., Tokyo 108-0023 (Japan); Matsumoto, Hisami [Nishihara Environment Technology Inc., Tokyo 108-0023 (Japan); Abe, Jun [AE-Bio, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo 113-8657 (Japan); Morita, Shigenori [Institute for Sustainable Agro-ecosystem Services (ISAS), Graduate School of Agriculture and Life Sciences, The University of Tokyo, Nishitokyo, Tokyo 188-0002 (Japan)
2010-07-15
The combination of substrate materials and bacteria is an important factor affecting conversion technology for biological hydrogen production. We performed anaerobic hydrogen fermentation of apple pomace wastes using rhizosphere bacterial microflora of rice as the parent inoculum. In the vial test, the optimal condition for hydrogen fermentation was initial pH 6.0, 35 C, and 73.4 g pomace per liter of medium (equivalent to 10 g-hexose/L). In the batch experiment (pH 6.0, temperature 35 C) the hydrogen yield reached 2.3 mol-H{sub 2}/mol-hexose. The time course of biogas production and PCR-DGGE analysis suggest that Clostridium spp. decomposed degradable carbohydrates rapidly and a part of the refractory carbohydrate (e.g. pectin) gradually in the apple pomace slurry. In addition to hydrogen, volatile fatty acids (VFAs) were produced in the anaerobic fermentation of apple pomace, which can be a substrate for methane fermentation. The rice rhizosphere can be a promising source of inoculum bacteria for hydrogen fermentation in combination with plant material waste like apple pomace. (author)
Propagating Class and Method Combination
DEFF Research Database (Denmark)
Ernst, Erik
1999-01-01
number of implicit combinations. For example, it is possible to specify separate aspects of a family of classes, and then combine several aspects into a full-fledged class family. The combination expressions would explicitly combine whole-family aspects, and by propagation implicitly combine the aspects...
Zhang, Dan; Wang, Chuan; Zhang, Liping; Xu, Dong; Liu, Biyun; Zhou, Qiaohong; Wu, Zhenbin
2016-06-01
Long-term use of chlorpyrifos poses a potential threat to the environment that cannot be ignored, yet little is known about the succession of substrate microbial communities in constructed wetlands (CWs) under chlorpyrifos stress. Six pilot-scale CW systems receiving artificial wastewater containing 1mg/L chlorpyrifos were established to investigate the effects of chlorpyrifos and wetland vegetation on the microbial metabolism pattern of carbon sources and community structure, using BIOLOG and denaturing gradient gel electrophoresis (DGGE) approaches. Based on our samples, BIOLOG showed that Shannon diversity (H') and richness (S) values distinctly increased after 30days when chlorpyrifos was added. At the same time, differences between the vegetated and the non-vegetated systems disappeared. DGGE profiles indicated that H' and S had no significant differences among four different treatments. The effect of chlorpyrifos on the microbial community was mainly reflected at the physiological level. Principal component analysis (PCA) of both BIOLOG and DGGE showed that added chlorpyrifos made a difference on test results. Meanwhile, there was no difference between the vegetation and no-vegetation treatments after addition of chlorpyrifos at the physiological level. Moreover, the vegetation had no significant effect on the microbial community at the genetic level. Comparisons were made between bacteria in this experiment and other known chlorpyrifos-degrading bacteria. The potential chlorpyrifos-degrading ability of bacteria in situ may be considerable. Copyright © 2016. Published by Elsevier B.V.
Rezaei Somee, Maryam; Shavandi, Mahmoud; Dastgheib, Seyed Mohammad Mehdi; Amoozegar, Mohammad Ali
2018-05-01
Oil-based drill cuttings are hazardous wastes containing complex hydrocarbons, heavy metals, and brine. Their remediation is a crucial step before release to the environment. In this work, we enriched a halophilic consortium, from oil-polluted saline soil, which is capable of degrading diesel as the main pollutant of oil-based drill cuttings. The degradation ability of the consortium was evaluated in microcosms using two different diluting agents (fine sand and biologically active soil). During the bioremediation process, the bacterial community dynamics of the microcosms was surveyed using PCR amplification of a fragment of 16S rRNA gene followed by denaturing gradient gel electrophoresis (DGGE). The diesel degradation rates were monitored by total petroleum hydrocarbon (TPH) measurement and the total count of heterotrophic and diesel-degrading bacteria. After 3 months, the microcosm containing fine sand and drill cuttings with the ratio of 1:1 (initial TPH of 36,000 mg/kg) showed the highest TPH removal (40%) and its dominant bacterial isolates belonged to the genera Dietzia, Arthrobacter , and Halomonas . DGGE results also confirmed the role of these genera in drill cuttings remediation. DGGE analysis of the bacterial diversity showed that Propionibacterium, Salinimicrobium, Marinobacter , and Dietzia are dominant in active soil microcosm; whereas Bacillus, Salinibacillus , and Marinobacter are abundant in sand microcosm. Our results suggest that the bioaugmentation strategy would be more successful if the diluting agent does not contain a complex microbial community.
Directory of Open Access Journals (Sweden)
Juan Ling
2015-06-01
Full Text Available Seagrass meadows represent one of the highest productive marine ecosystems and are of great ecological and economic values. Recently, they have been confronted with worldwide decline. Fungi play important roles in sustaining the ecosystem health as degraders of polycyclic aromatic hydrocarbons (PAHs, but fewer studies have been conducted in seagrass ecosystems. Hence, we investigated the dynamic variations of the fungal community succession under PAH stress in rhizosphere sediment of seagrasses Enhalus acoroides in this study. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE, quantitative PCR (qPCR and a clone library have been employed to analyze the fungal community’s shifts. Sequencing results of DGGE and the clone library showed that the predominant species belong to phyla Ascomycota and Basidiomycota. The abundance of three groups decreased sharply over the incubation period, whereas they demonstrated different fungal diversity patterns. Both the exposure time and the PAH concentrations affected the microbial diversity as assessed by PCR-DGGE analysis. Redundancy analysis (RDA indicated that significant factors driving community shifts were ammonium and pH (p < 0.05. Significant amounts of the variations (31.1% were explained by pH and ammonium, illustrating that those two parameters were the most likely ones to influence or be influenced by the fungal communities’ changes. Investigation results also indicated that fungal communities in seagrass meadow were very sensitive to PAH-induced stress and may be used as potential indicators for the PAH contamination.
[Bacterial diversity in the oral cavity of adolescents with different caries susceptibilities].
Yangyang, Zhang; Jinzhi, He; Xin, Xu; Xuedong, Zhou
2015-12-01
To analyze the differences between the bacterial diversities in the saliva of caries-free and caries-susceptible adolescents through polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE). Twenty adolescent subjects aged 12-18 years were recruited and subdivided into two groups: caries-free adolescents (n = 10) and caries-susceptible adolescents (n = 10). Saliva samples were collected. Total DNA was isolated directly from each sample. A portion of the 16S rRNA gene locus was PCR-amplified by using universal primers. Microbial diversity was analyzed through PCR-DGGE. Analyzing the DGGE profile, we found that the composition of the saliva microbiome exhibited great intra-individual differences; the average band numbers of the caries-free adolescent group and the caries-susceptible adolescent group were 32.5 ± 3.7 and 27.3 ± 3.4, respectively. The differences between the groups were statistically significant (P = 0.008). Shannon-Wiener's indexes of the caries-susceptible adolescent group and the caries-free adolescent group were 2.5 ± 0.2 and 2.6 ± 0.2, respectively, but the differences between the groups were not significant (P = 0.405). Clustering analysis results suggested that most of the samples in the same group clustered together; this observation showed a high community structure similarity. The microbial diversity and complexity of bacteria in saliva are significantly higher in caries-free adolescents than in caries-susceptible adolescents. During caries development, bacterial diversity in the saliva likely decreases.
Comparison of DNA extraction protocols for microbial communities from soil treated with biochar
Leite, D.C.A.; Balieiro, F.C.; Pires, C.A.; Madari, B.E.; Rosado, A.S.; Coutinho, H.L.C.; Peixoto, R.S.
2014-01-01
Many studies have evaluated the effects of biochar application on soil structure and plant growth. However, there are very few studies describing the effect of biochar on native soil microbial communities. Microbial analysis of environmental samples requires accurate and reproducible methods for the extraction of DNA from samples. Because of the variety among microbial species and the strong adsorption of the phosphate backbone of the DNA molecule to biochar, extracting and purifying high quality microbial DNA from biochar-amended soil is not a trivial process and can be considerably more difficult than the extraction of DNA from other environmental samples. The aim of this study was to compare the relative efficacies of three commercial DNA extraction kits, the FastDNA® SPIN Kit for Soil (FD kit), the PowerSoil® DNA Isolation Kit (PS kit) and the ZR Soil Microbe DNA Kit Miniprep™ (ZR kit), for extracting microbial genomic DNA from sand treated with different types of biochar. The methods were evaluated by comparing the DNA yields and purity and by analysing the bacterial and fungal community profiles generated by PCR-DGGE. Our results showed that the PCR-DGGE profiles for bacterial and fungal communities were highly affected by the purity and yield of the different DNA extracts. Among the tested kits, the PS kit was the most efficient with respect to the amount and purity of recovered DNA and considering the complexity of the generated DGGE microbial fingerprint from the sand-biochar samples. PMID:24948928
African Journal of Biotechnology - Vol 3, No 3 (2004)
African Journals Online (AJOL)
Screening cowpea [Vigna unguiculata (L.) Walp.] ... be distinguished by DGGE analysis of PCR-amplified 18S rDNA fragments · EMAIL FREE FULL ... Isolation of a kernel oleoyl-ACP thioesterase gene from the oil palm Elaeis guineensis Jacq.
Czech Academy of Sciences Publication Activity Database
Kopečný, Jan; Novotný, M.; Kmeť, V.
2004-01-01
Roč. 13, - (2004), s. 35-36 ISSN 1210-3209 Grant - others:Science and Technology Assistance Agency(SK) APVT-20-026102 Institutional research plan: CEZ:AV0Z5045916 Keywords : marmot * DGGE * Tatras Subject RIV: EE - Microbiology, Virology
Rodriguez, E.; Lopes, A.; Fdz-Polanco, M.; Stams, A.J.M.; Garcia Encina, P.A.
2012-01-01
The microbial communities (Bacteria and Archaea) established in an anaerobic fluidized bed reactor used to treat synthetic vinasse (betaine, glucose, acetate, propionate, and butyrate) were characterized by denaturing gradient gel electrophoresis (DGGE) and phylogenetic analysis. This study was
Comparison between different bio-treatments of a hydrocarbon ...
African Journals Online (AJOL)
We investigated the bio-remediation of a hydrocarbon contaminated soil pile that ... Nutrient and microbial amendments did not confer any long-term benefit on the ... Denaturing gradient gel electrophoresis (DGGE) analyses of 16S rDNA and ...
Ishii, Satoshi; Kadota, Koji; Senoo, Keishi
2009-09-01
DNA fingerprinting analysis such as amplified ribosomal DNA restriction analysis (ARDRA), repetitive extragenic palindromic PCR (rep-PCR), ribosomal intergenic spacer analysis (RISA), and denaturing gradient gel electrophoresis (DGGE) are frequently used in various fields of microbiology. The major difficulty in DNA fingerprinting data analysis is the alignment of multiple peak sets. We report here an R program for a clustering-based peak alignment algorithm, and its application to analyze various DNA fingerprinting data, such as ARDRA, rep-PCR, RISA, and DGGE data. The results obtained by our clustering algorithm and by BioNumerics software showed high similarity. Since several R packages have been established to statistically analyze various biological data, the distance matrix obtained by our R program can be used for subsequent statistical analyses, some of which were not previously performed but are useful in DNA fingerprinting studies.
Sahan, E.; Sabbe, K.; Creach, V.; Hernandez-Raquet, G.; Vyverman, W.; Stal, L.J.; Muyzer, G.
2007-01-01
The composition and seasonal dynamics of biofilm-associated eukaryotic communities were analysed at the metre and kilometre scale along a salinity gradient in the Westerschelde estuary (The Netherlands), using microscopy and a genetic fingerprinting technique (PCR-DGGE). Microphytobenthic biomass,
Lee, O. O.; Chui, P. Y.; Wong, Y. H.; Pawlik, J. R.; Qian, P.-Y.
2009-01-01
to progeny are largely unknown. In this study, both a 16S rRNA gene-based fingerprinting technique (denaturing gradient gel electrophoresis [DGGE]) and clone library analysis were applied to compare the bacterial communities associated with adults and embryos
DEFF Research Database (Denmark)
Bernbom, Nete; Nørrung, Birgit; Saadbye, Peter
2006-01-01
and specific pathogen free (SPF). or human flora associated (HFA). A higher variation (p animals. Analysis of DGGE and T-RFLP profiles of fecal microbiota from SPF and HFA rats revealed that variation over time was less significant than...
Combination N-Way Power Divider/Combiner and Noninvasive Reflected Power Detection
National Oceanic and Atmospheric Administration, Department of Commerce — An N-way RF/microwave power divider/combiner utilizes one input and N outputs, or conversely N inputs and one output to divide (or combine) RF/microwave power while...
Effective Nutritional Supplement Combinations
Cooke, Matt; Cribb, Paul J.
Few supplement combinations that are marketed to athletes are supported by scientific evidence of their effectiveness. Quite often, under the rigor of scientific investigation, the patented combination fails to provide any greater benefit than a group given the active (generic) ingredient. The focus of this chapter is supplement combinations and dosing strategies that are effective at promoting an acute physiological response that may improve/enhance exercise performance or influence chronic adaptations desired from training. In recent years, there has been a particular focus on two nutritional ergogenic aids—creatine monohydrate and protein/amino acids—in combination with specific nutrients in an effort to augment or add to their already established independent ergogenic effects. These combinations and others are discussed in this chapter.
Improving Griffith's protocol for co-extraction of microbial DNA and RNA in adsorptive soils
DEFF Research Database (Denmark)
Paulin, Mélanie Marie; Nicolaisen, Mette Haubjerg; Jacobsen, Carsten Suhr
2013-01-01
Quantification of microbial gene expression is increasingly being used to study key functions in soil microbial communities, yet major limitations still exist for efficient extraction of nucleic acids, especially RNA for transcript analysis, from this complex matrix. We present an improved......-time PCR on both the RNA (after conversion to cDNA) and the DNA fraction of the extracts. Non-adsorptive soils were characterized by low clay content and/or high phosphate content, whereas adsorptive soils had clay contents above 20% and/or a strong presence of divalent Ca in combination with high p......H. Modifications to the co-extraction protocol improved nucleic acid extraction efficiency from all adsorptive soils and were successfully validated by DGGE analysis of the indigenous community based on 16S rRNA gene and transcripts in soils representing low biomass and/or high clay content. This new approach...
Identification of the Bacterial Community Responsible for ...
African Journals Online (AJOL)
Identification of bacteria community responsible for decontaminating Eleme petrochemical industrial effluent using 16S PCR denaturing gradient gel electrophoresis (DGGE) was determined. Gene profiles were determined by extracting DNA from bacterial isolates and amplified by polymerase chain reaction (PCR) using ...
Microbiota of Tayohounta , a fermented baobab flavour food of Benin
African Journals Online (AJOL)
Tayohounta was also investigated using culture independent techniques, direct DNA extraction, polymerase chain reaction - denaturing gradient gel electrophoresis (PCR-DGGE) and cloning. Isolated microorganisms were tested for their functionality in baobab seed kernels fermentation. Total viable counts were around 9 ...
Bacterial populations concomitant with Sclerotium rolfsii sclerotia in ...
African Journals Online (AJOL)
SARAH
2015-09-30
Sep 30, 2015 ... (2003) plated on culture media S. rolfsii sclerotia recovered from ... replicated four times (36 pots). All 36 pots were ... DGGE analysis and sequencing: A FastDNA Spin Kit for soil (Qbiogene ...... Wiley, New York, pp. 115-175.
All-fiber 7x1 signal combiner for incoherent laser beam combining
Noordegraaf, D.; Maack, M. D.; Skovgaard, P. M. W.; Johansen, J.; Becker, F.; Belke, S.; Blomqvist, M.; Laegsgaard, J.
2011-02-01
We demonstrate an all-fiber 7x1 signal combiner for incoherent laser beam combining. This is a potential key component for reaching several kW of stabile laser output power. The combiner couples the output from 7 single-mode (SM) fiber lasers into a single multi-mode (MM) fiber. The input signal fibers have a core diameter of 17 μm and the output MM fiber has a core diameter of 100 μm. In a tapered section light gradually leaks out of the SM fibers and is captured by a surrounding fluorine-doped cladding. The combiner is tested up to 2.5 kW of combined output power and only a minor increase in device temperature is observed. At an intermediate power level of 600 W a beam parameter product (BPP) of 2.22 mm x mrad is measured, corresponding to an M2 value of 6.5. These values are approaching the theoretical limit dictated by brightness conservation.
International Nuclear Information System (INIS)
Hahn, K.
1994-03-01
In a heavy ion inertial fusion (HIF) driver, the beam energy and current are increased several orders of magnitude from the injector to the final focus system. At low and high energy stages of the driver, electrostatic and magnetic focusing transport channels, respectively, can be used. At the electric-to-magnetic transition point, the beams may be combined to reduce the transverse dimensions of the system, which could have significant impact on the driver cost. In a presently envisioned combiner, four beams are brought together transversely into a single transport channel. A matching section follows the combiner in order to provide a smooth transition to the subsequent magnetic transport channel. This report summarizes a conceptual design study of possible combiner configurations for the proposed Introduction Linac Systems Experiment (ILSE). The conceptual design study includes subjects such as the expected technical difficulties, predicted emittance growth, particle loss, effect of geometric and chromatic aberrations, and the sensitivity of emittance growth on the initial beam position and angle errors
Optical Communications Channel Combiner
Quirk, Kevin J.; Quirk, Kevin J.; Nguyen, Danh H.; Nguyen, Huy
2012-01-01
NASA has identified deep-space optical communications links as an integral part of a unified space communication network in order to provide data rates in excess of 100 Mb/s. The distances and limited power inherent in a deep-space optical downlink necessitate the use of photon-counting detectors and a power-efficient modulation such as pulse position modulation (PPM). For the output of each photodetector, whether from a separate telescope or a portion of the detection area, a communication receiver estimates a log-likelihood ratio for each PPM slot. To realize the full effective aperture of these receivers, their outputs must be combined prior to information decoding. A channel combiner was developed to synchronize the log-likelihood ratio (LLR) sequences of multiple receivers, and then combines these into a single LLR sequence for information decoding. The channel combiner synchronizes the LLR sequences of up to three receivers and then combines these into a single LLR sequence for output. The channel combiner has three channel inputs, each of which takes as input a sequence of four-bit LLRs for each PPM slot in a codeword via a XAUI 10 Gb/s quad optical fiber interface. The cross-correlation between the channels LLR time series are calculated and used to synchronize the sequences prior to combining. The output of the channel combiner is a sequence of four-bit LLRs for each PPM slot in a codeword via a XAUI 10 Gb/s quad optical fiber interface. The unit is controlled through a 1 Gb/s Ethernet UDP/IP interface. A deep-space optical communication link has not yet been demonstrated. This ground-station channel combiner was developed to demonstrate this capability and is unique in its ability to process such a signal.
Margesin, Rosa; Siles, José A; Cajthaml, Tomas; Öhlinger, Birgit; Kistler, Erich
2017-05-01
Microbial ecology has been recognized as useful in archaeological studies. At Archaic Monte Iato in Western Sicily, a native (indigenous) building was discovered. The objective of this study was the first examination of soil microbial communities related to this building. Soil samples were collected from archaeological layers at a ritual deposit (food waste disposal) in the main room and above the fireplace in the annex. Microbial soil characterization included abundance (cellular phospholipid fatty acids (PLFA), viable bacterial counts), activity (physiological profiles, enzyme activities of viable bacteria), diversity, and community structure (bacterial and fungal Illumina amplicon sequencing, identification of viable bacteria). PLFA-derived microbial abundance was lower in soils from the fireplace than in soils from the deposit; the opposite was observed with culturable bacteria. Microbial communities in soils from the fireplace had a higher ability to metabolize carboxylic and acetic acids, while those in soils from the deposit metabolized preferentially carbohydrates. The lower deposit layer was characterized by higher total microbial and bacterial abundance and bacterial richness and by a different carbohydrate metabolization profile compared to the upper deposit layer. Microbial community structures in the fireplace were similar and could be distinguished from those in the two deposit layers, which had different microbial communities. Our data confirmed our hypothesis that human consumption habits left traces on microbiota in the archaeological evidence; therefore, microbiological residues as part of the so-called ecofacts are, like artifacts, key indicators of consumer behavior in the past.
Smith, A Peyton; Marín-Spiotta, Erika; Balser, Teri
2015-09-01
Soil microorganisms regulate fundamental biochemical processes in plant litter decomposition and soil organic matter (SOM) transformations. Understanding how microbial communities respond to changes in vegetation is critical for improving predictions of how land-cover change affects belowground carbon storage and nutrient availability. We measured intra- and interannual variability in soil and forest litter microbial community composition and activity via phospholipid fatty acid analysis (PLFA) and extracellular enzyme activity across a well-replicated, long-term chronosequence of secondary forests growing on abandoned pastures in the wet subtropical forest life zone of Puerto Rico. Microbial community PLFA structure differed between young secondary forests and older secondary and primary forests, following successional shifts in tree species composition. These successional patterns held across seasons, but the microbial groups driving these patterns differed over time. Microbial community composition from the forest litter differed greatly from those in the soil, but did not show the same successional trends. Extracellular enzyme activity did not differ with forest succession, but varied by season with greater rates of potential activity in the dry seasons. We found few robust significant relationships among microbial community parameters and soil pH, moisture, carbon, and nitrogen concentrations. Observed inter- and intrannual variability in microbial community structure and activity reveal the importance of a multiple, temporal sampling strategy when investigating microbial community dynamics with land-use change. Successional control over microbial composition with forest recovery suggests strong links between above and belowground communities. © 2015 John Wiley & Sons Ltd.
Direct and indirect photolysis of triclocarban in the presence of dissolved organic matter
Directory of Open Access Journals (Sweden)
Tamara D. Trouts
2015-05-01
Full Text Available Abstract Photolysis is an important attenuation pathway for the removal of wastewater effluent organic micropollutants from surface waters. In this work, direct and indirect processes leading to the degradation of the disinfectant, triclocarban were studied. Photo-irradiation experiments were conducted in water collected from Old Woman Creek (OWC a tributary of Lake Erie near Huron, OH, USA and in solutions of fulvic acids isolated from the Suwannee River, Georgia, USA (SRFA, Old Woman Creek (OWCFA and Pony Lake, Antarctica (PLFA. Photodegradation of triclocarban proceeded faster in the presence of all three fulvic acids relative to deionized water. PLFA, an autochthonous dissolved organic matter (DOM was found to be more reactive than the other fulvic acids, while the mostly allochthonous SRFA exhibited the lowest reactivity toward triclocarban. The later observation can be in part explained by anti-oxidant moieties present in SRFA. Photosensitized triclocarban degradation in whole water DOM from OWC was entirely attributable to the fulvic acid fraction and suggests that this component is the most photo-reactive fraction of the DOM. Anoxic and methanol-quenched experiments revealed unexpected results whereby the former suggests oxidation through reaction with triplet DOM, while the later is indicative of reaction with photo-generated hydroxyl radicals. It is possible that methanol can quench excited DOM species, which would shut down the triplet oxidation pathway. Finally, we observed no enhancement of triclocarban-photosensitized degradation through the addition of iron.
Šimek, M; Elhottová, D; Mench, M; Giagnoni, L; Nannipieri, P; Renella, G
2017-11-02
Phytomanagement of trace element-contaminated soils can reduce soil toxicity and restore soil ecological functions, including the soil gas exchange with the atmosphere. We studied the emission rate of the greenhouse gases (GHGs) CO 2 , CH 4 , and N 2 O; the potential CH 4 oxidation; denitrification enzyme activity (DEA), and glucose mineralization of a Cu-contaminated soil amended with dolomitic limestone and compost, alone or in combination, after a 2-year phytomanagement with a mixed stand of Populus nigra, Salix viminalis, S. caprea, and Amorpha fruticosa. Soil microbial biomass and microbial community composition after analysis of the phospholipid fatty acids (PLFA) profile were determined. Phytomanagement significantly reduced Cu availability and soil toxicity, increased soil microbial biomass and glucose mineralization capacity, changed the composition of soil microbial communities, and increased the CO 2 and N 2 O emission rates and DEA. Despite such increases, microbial communities were evolving toward less GHG emission per unit of microbial biomass than in untreated soils. Overall, the aided phytostabilization option would allow methanotrophic populations to establish in the remediated soils due to decreased soil toxicity and increased nutrient availability.
Liu, WT; Linning, KD; Nakamura, K; Mino, T; Matsuo, T; Forney, LJ
Biomarkers (respiratory quinones and cellular fatty acids) and denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA genes were used to characterize the microbial community structure of lab-scale enhanced biological phosphate-removal (EBPR) systems in response to altering sludge
DEFF Research Database (Denmark)
Holmsgaard, Peter N.; Dealtry, Simone; Dunon, Vincent
2017-01-01
positively during the course of the season. Furthermore, a banding-pattern analysis of 16S rRNA gene-based DGGE fingerprinting, targeting the Alpha- and Betaproteobacteria as well as the Actinobacteria, indicated that the Betaproteobacteria might play an important role. Interestingly, a decrease...
Generator of combined logical signals
International Nuclear Information System (INIS)
Laviron, Andre; Berard, Claude.
1982-01-01
The invention concerns a generator of combined logical signals to form combinations of two outputs at logical level 1 and N-2 outputs at logical level 0, among N generator outputs. This generator is characterized in that it includes a set of N means for storing combinations. Means enable the N storage means to be loaded with the logical levels corresponding to a pre-set starting combination, to control the operations for shifting the contents of the storage means and to control, by transfer facilities, the transfers of contents between these storage means. Controls enable the storage means to be actuated in order to obtain combinations of logical levels 1 and 0. The generation of combinations can be stopped after another pre-set combination. Application is for testing of safety circuits for nuclear power stations [fr
Jang, Hyun Min; Lee, Jae Won; Ha, Jeong Hyub; Park, Jong Moon
2013-11-01
To evaluate the applicability of single-stage thermophilic aerobic digestion (TAD) process treating high-strength food wastewater (FWW), TAD process was operated at four organic loading rates (OLRs) from 9.2 to 37.2 kg COD/m(3)d. The effects of OLRs on microbial community changes were also examined. The highest volumetric removal rate (13.3 kg COD/m(3)d) and the highest thermo-stable protease activity (0.95 unit/mL) were detected at OLR=18.6 kg COD/m(3)d. Denaturing gradient gel electrophoresis (DGGE) profiles and quantitative PCR (qPCR) results showed significant microbial community shifts in response to changes in OLR. In particular, DGGE and phylogenetic analysis demonstrate that the presence of Bacillus sp. (phylum of Firmicutes) was strongly correlated with efficient removal of organic particulates from high-strength food wastewater. Copyright © 2013 Elsevier Ltd. All rights reserved.
DEFF Research Database (Denmark)
Licht, Tine Rask; Hansen, Max; Bergström, Anders
2010-01-01
Background: Our study was part of the large European project ISAFRUIT aiming to reveal the biological explanations for the epidemiologically well-established health effects of fruits. The objective was to identify effects of apple and apple product consumption on the composition of the cecal...... microbial community in rats, as well as on a number of cecal parameters, which may be influenced by a changed microbiota. Results: Principal Component Analysis (PCA) of cecal microbiota profiles obtained by PCR-DGGE targeting bacterial 16S rRNA genes showed an effect of whole apples in a long-term feeding...... study (14 weeks), while no effects of apple juice, puree or pomace on microbial composition in cecum were observed. Administration of either 0.33 or 3.3% apple pectin in the diet resulted in considerable changes in the DGGE profiles. A 2-fold increase in the activity of beta-glucuronidase was observed...
Microbial diversity in fecal samples depends on DNA extraction method
DEFF Research Database (Denmark)
Mirsepasi, Hengameh; Persson, Søren; Struve, Carsten
2014-01-01
was to evaluate two different DNA extraction methods in order to choose the most efficient method for studying intestinal bacterial diversity using Denaturing Gradient Gel Electrophoresis (DGGE). FINDINGS: In this study, a semi-automatic DNA extraction system (easyMag®, BioMérieux, Marcy I'Etoile, France......BACKGROUND: There are challenges, when extracting bacterial DNA from specimens for molecular diagnostics, since fecal samples also contain DNA from human cells and many different substances derived from food, cell residues and medication that can inhibit downstream PCR. The purpose of the study...... by easyMag® from the same fecal samples. Furthermore, DNA extracts obtained using easyMag® seemed to contain inhibitory compounds, since in order to perform a successful PCR-analysis, the sample should be diluted at least 10 times. DGGE performed on PCR from DNA extracted by QIAamp DNA Stool Mini Kit DNA...
Tuan, Nguyen Ngoc; Chang, Yi-Chia; Yu, Chang-Ping; Huang, Shir-Ly
2014-01-01
In this study, the first survey of microbial community in thermophilic anaerobic digester using swine manure as sole feedstock was performed by multiple approaches including denaturing gradient gel electrophoresis (DGGE), clone library and pyrosequencing techniques. The integrated analysis of 21 DGGE bands, 126 clones and 8506 pyrosequencing read sequences revealed that Clostridia from the phylum Firmicutes account for the most dominant Bacteria. In addition, our analysis also identified additional taxa that were missed by the previous researches, including members of the bacterial phyla Synergistetes, Planctomycetes, Armatimonadetes, Chloroflexi and Nitrospira which might also play a role in thermophilic anaerobic digester. Most archaeal 16S rRNA sequences could be assigned to the order Methanobacteriales instead of Methanomicrobiales comparing to previous studies. In addition, this study reported that the member of Methanothermobacter genus was firstly found in thermophilic anaerobic digester. Copyright © 2014 Elsevier GmbH. All rights reserved.
Conceptual Combination During Sentence Comprehension
Swinney, David; Love, Tracy; Walenski, Matthew; Smith, Edward E.
2008-01-01
This experiment examined the time course of integration of modifier-noun (conceptual) combinations during auditory sentence comprehension using cross-modal lexical priming. The study revealed that during ongoing comprehension, there is initial activation of features of the noun prior to activation of (emergent) features of the entire conceptual combination. These results support compositionality in conceptual combination; that is, they indicate that features of the individual words constituting a conceptual combination are activated prior to combination of the words into a new concept. PMID:17576278
Secondary combined suicide pact.
Jayanth, S H; Girish Chandra, Y P; Hugar, Basappa S; Kainoor, Sunilkumar
2014-03-01
This article reports a combined suicide pact, where in a young couple; a 26 year old male and a 20 year old female committed suicide by using two methods. The couple had resorted to hanging and self-immolation to prevent failure of single method alone. In secondary combined suicides, several other methods of suicide are tried after the first method chosen has failed. It is primary combined suicide only when two or more methods are used simultaneously. Both types of combined suicide by one individual is well reported in the literature whereas the same by two persons together is rare. In this report, the deceased were disappointed lovers, poor and the family members were against their marriage. The investigation of scene, methods employed to commit suicide, autopsy findings and the interview with their relatives altogether suggested that it was a secondary combined suicide pact. Copyright © 2014 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.
Priha, Outi; Nyyssönen, Mari; Bomberg, Malin; Laitila, Arja; Simell, Jaakko; Kapanen, Anu; Juvonen, Riikka
2013-09-01
Sulfate-reducing bacteria (SRB) participate in microbially induced corrosion (MIC) of equipment and H2S-driven reservoir souring in oil field sites. Successful management of industrial processes requires methods that allow robust monitoring of microbial communities. This study investigated the applicability of denaturing high-performance liquid chromatography (DHPLC) targeting the dissimilatory sulfite reductase ß-subunit (dsrB) gene for monitoring SRB communities in oil field samples from the North Sea, the United States, and Brazil. Fifteen of the 28 screened samples gave a positive result in real-time PCR assays, containing 9 × 10(1) to 6 × 10(5) dsrB gene copies ml(-1). DHPLC and denaturing gradient gel electrophoresis (DGGE) community profiles of the PCR-positive samples shared an overall similarity; both methods revealed the same samples to have the lowest and highest diversity. The SRB communities were diverse, and different dsrB compositions were detected at different geographical locations. The identified dsrB gene sequences belonged to several phylogenetic groups, such as Desulfovibrio, Desulfococcus, Desulfomicrobium, Desulfobulbus, Desulfotignum, Desulfonatronovibrio, and Desulfonauticus. DHPLC showed an advantage over DGGE in that the community profiles were very reproducible from run to run, and the resolved gene fragments could be collected using an automated fraction collector and sequenced without a further purification step. DGGE, on the other hand, included casting of gradient gels, and several rounds of rerunning, excising, and reamplification of bands were needed for successful sequencing. In summary, DHPLC proved to be a suitable tool for routine monitoring of the diversity of SRB communities in oil field samples.
Comparison of DNA extraction protocols for microbial communities from soil treated with biochar
Directory of Open Access Journals (Sweden)
D.C.A. Leite
2014-01-01
Full Text Available Many studies have evaluated the effects of biochar application on soil structure and plant growth. However, there are very few studies describing the effect of biochar on native soil microbial communities. Microbial analysis of environmental samples requires accurate and reproducible methods for the extraction of DNA from samples. Because of the variety among microbial species and the strong adsorption of the phosphate backbone of the DNA molecule to biochar, extracting and purifying high quality microbial DNA from biochar-amended soil is not a trivial process and can be considerably more difficult than the extraction of DNA from other environmental samples. The aim of this study was to compare the relative efficacies of three commercial DNA extraction kits, the FastDNA® SPIN Kit for Soil (FD kit, the PowerSoil® DNA Isolation Kit (PS kit and the ZR Soil Microbe DNA Kit MiniprepTM (ZR kit, for extracting microbial genomic DNA from sand treated with different types of biochar. The methods were evaluated by comparing the DNA yields and purity and by analysing the bacterial and fungal community profiles generated by PCR-DGGE. Our results showed that the PCR-DGGE profiles for bacterial and fungal communities were highly affected by the purity and yield of the different DNA extracts. Among the tested kits, the PS kit was the most efficient with respect to the amount and purity of recovered DNA and considering the complexity of the generated DGGE microbial fingerprint from the sand-biochar samples.
Directory of Open Access Journals (Sweden)
Szacawa Ewelina
2015-09-01
Full Text Available The aim of the study was to evaluate the presence of Mycoplasma bovis infection and co-infections with other Mycoplasma spp. infections in cattle. The tested population was one in the eastern region of Poland containing 66 dairy cows and 23 calves showing different clinical signs and suffering from pneumonia, mastitis, and arthritis. The incidence of M. bovis in co-infections with other Mycoplasma spp. was examined using serological traditional mycoplasma culture methods, and the molecular methods - PCR and polymerase chain reaction/denaturing gradient gel electrophoresis (PCR/DGGE. The PCR/DGGE method for detecting Mycoplasma spp. in cattle was used for the first time in Poland. The seroprevalence of M. bovis in the affected cattle herds in the eastern region of Poland was 47.8% in calves and 19.7% in dairy cows. The direct detection and identification of M. bovis from nasopharyngeal swabs by PCR revealed that 56.5% of calves were positive, but all of the dairy cows were negative. The PCR/DGGE identified eight (34.8% instances of M. arginini and eight (26.1% instances of M. bovirhinis co-infecting with M. bovis in ten calves. The seroprevalence of M. bovis in the tested population was 33.7%. Any future attempts to control mycoplasma infections require an insight into the current epidemiological situation of M. bovis infection and its relationship to other mycoplasmas in causing clinical disease in cattle. Using these diagnostic methods we have demonstrated that mycoplasmal infections are often caused by multiple species of Mycoplasma and not just the primary M. bovis pathogen.
de-Bashan, Luz E.; Hernandez, Juan-Pablo; Nelson, Karis N.; Bashan, Yoav
2010-01-01
Mine tailing deposits in semiarid and arid environments frequently remain devoid of vegetation due to the toxicity of the substrate and the absence of a diverse soil microbial community capable of supporting seed germination and plant growth. The contribution of the plant growth promoting bacterium (PGPB) Azospirillum brasilense Sp6 to the growth of quailbush in compost-amended, moderately acidic, high-metal content mine tailings using an irrigation-based reclamation strategy was examined along with its influence on the rhizosphere bacterial community. Sp6 inoculation resulted in a significant (2.2-fold) increase in plant biomass production. The data suggest that the inoculum successfully colonized the root surface and persisted throughout the 60-day experiment in both the rhizosphere, as demonstrated by excision and sequencing of the appropriate denaturing gradient gel electrophoresis (DGGE) band, and the rhizoplane, as indicated by fluorescent in situ hybridization of root surfaces. Changes in rhizosphere community structure in response to Sp6 inoculation were evaluated after 15, 30, and 60 days using DGGE analysis of 16S rRNA polymerase chain reaction amplicons. A comparison of DGGE profiles using canonical correspondence analysis revealed a significant treatment effect (Sp6-inoculated vs. uninoculated plants vs. unplanted) on bacterial community structure at 15, 30, and 60 days (p<0.05). These data indicate that in an extremely stressed environment such as acid mine tailings, an inoculated plant growth promoting bacterium not only can persist and stimulate plant growth but also can directly or indirectly influence rhizobacterial community development. PMID:20632001
Bacteria and yeast microbiota in milk kefir grains from different Italian regions.
Garofalo, Cristiana; Osimani, Andrea; Milanović, Vesna; Aquilanti, Lucia; De Filippis, Francesca; Stellato, Giuseppina; Di Mauro, Simone; Turchetti, Benedetta; Buzzini, Pietro; Ercolini, Danilo; Clementi, Francesca
2015-08-01
Kefir grains are a unique symbiotic association of different microrganisms, mainly lactic acid bacteria, yeasts and occasionally acetic acid bacteria, cohabiting in a natural polysaccharide and a protein matrix. The microbial composition of kefir grains can be considered as extremely variable since it is strongly influenced by the geographical origin of the grains and by the sub-culturing method used. The aim of this study was to elucidate the bacteria and yeast species occurring in milk kefir grains collected in some Italian regions by combining the results of scanning electron microscopy analysis, viable counts on selective culture media, PCR-DGGE and pyrosequencing. The main bacterial species found was Lactobacillus kefiranofaciens while Dekkera anomala was the predominant yeast. The presence of sub-dominant species ascribed to Streptococcus thermophilus, Lactococcus lactis and Acetobacter genera was also highlighted. In addition, Lc. lactis, Enterococcus sp., Bacillus sp., Acetobacter fabarum, Acetobacter lovaniensis and Acetobacter orientalis were identified as part of the cultivable community. This work further confirms both the importance of combining culture-independent and culture-dependent approaches to study microbial diversity in food and how the combination of multiple 16S rRNA gene targets strengthens taxonomic identification using sequence-based identification approaches. Copyright © 2015 Elsevier Ltd. All rights reserved.
Touceda-González, M; Prieto-Fernández, Á; Renella, G; Giagnoni, L; Sessitsch, A; Brader, G; Kumpiene, J; Dimitriou, I; Eriksson, J; Friesl-Hanl, W; Galazka, R; Janssen, J; Mench, M; Müller, I; Neu, S; Puschenreiter, M; Siebielec, G; Vangronsveld, J; Kidd, P S
2017-12-01
Gentle remediation options (GRO) are based on the combined use of plants, associated microorganisms and soil amendments, which can potentially restore soil functions and quality. We studied the effects of three GRO (aided-phytostabilisation, in situ stabilisation and phytoexclusion, and aided-phytoextraction) on the soil microbial biomass and respiration, the activities of hydrolase enzymes involved in the biogeochemical cycles of C, N, P, and S, and bacterial community structure of trace element contaminated soils (TECS) from six field trials across Europe. Community structure was studied using denaturing gradient gel electrophoresis (DGGE) fingerprinting of Bacteria, α- and β-Proteobacteria, Actinobacteria and Streptomycetaceae, and sequencing of DGGE bands characteristic of specific treatments. The number of copies of genes involved in ammonia oxidation and denitrification were determined by qPCR. Phytomanagement increased soil microbial biomass at three sites and respiration at the Biogeco site (France). Enzyme activities were consistently higher in treated soils compared to untreated soils at the Biogeco site. At this site, microbial biomass increased from 696 to 2352 mg ATP kg -1 soil, respiration increased from 7.4 to 40.1 mg C-CO 2 kg -1 soil d -1 , and enzyme activities were 2-11-fold higher in treated soils compared to untreated soil. Phytomanagement induced shifts in the bacterial community structure at both, the total community and functional group levels, and generally increased the number of copies of genes involved in the N cycle (nirK, nirS, nosZ, and amoA). The influence of the main soil physico-chemical properties and trace element availability were assessed and eventual site-specific effects elucidated. Overall, our results demonstrate that phytomanagement of TECS influences soil biological activity in the long term. Copyright © 2017 Elsevier Ltd. All rights reserved.
Solís-Domínguez, Fernando A.; Valentín-Vargas, Alexis; Chorover, Jon; Maier, Raina M.
2011-01-01
Mine tailings in arid and semi-arid environments are barren of vegetation and subject to eolian dispersion and water erosion. Revegetation is a cost-effective strategy to reduce erosion processes and has wide public acceptance. A major cost of revegetation is the addition of amendments, such as compost, to allow plant establishment. In this paper we explore whether arbuscular mycorrhizal fungi (AMF) can help support plant growth in tailings at a reduced compost concentration. A greenhouse experiment was performed to determine the effects of three AMF inocula on biomass, shoot accumulation of heavy metals, and changes in the rhizosphere microbial community structure of the native plant Prosopis juliflora (mesquite). Plants were grown in an acidic lead/zinc mine tailings amended with 10% (w/w) compost amendment, which is slightly sub-optimal for plant growth in these tailings. After two months, AMF-inoculated plants showed increased dry biomass and root length (p tailings. Mesquite shoot tissue lead and zinc concentrations did not exceed domestic animal toxicity limits regardless of whether AMF inoculation was used. The rhizosphere microbial community structure was assessed using denaturing gradient gel electrophoresis (DGGE) profiles of the small subunit RNA gene for bacteria and fungi. Canonical correspondence analysis (CCA) of DGGE profiles showed that the rhizosphere fungal community structure at the end of the experiment was significantly different from the community structure in the tailings, compost, and AMF inocula prior to planting. Further, CCA showed that AMF inoculation significantly influenced the development of both the fungal and bacterial rhizosphere community structures after two months. The changes observed in the rhizosphere microbial community structure may be either a direct effect of the AMF inocula, caused by changes in plant physiology induced by AMF, or a combination of both mechanisms. PMID:21211826
LENUS (Irish Health Repository)
Zhou, Ping
2011-08-03
Abstract Background To simplify the methodology for the isolation of Campylobacter spp. from retail broiler meat, we evaluated 108 samples (breasts and thighs) using an unpaired sample design. The enrichment broths were incubated under aerobic conditions (subsamples A) and for comparison under microaerobic conditions (subsamples M) as recommended by current reference protocols. Sensors were used to measure the dissolved oxygen (DO) in the broth and the percentage of oxygen (O2) in the head space of the bags used for enrichment. Campylobacter isolates were identified with multiplex PCR assays and typed using pulsed-field gel electrophoresis (PFGE). Ribosomal intergenic spacer analyses (RISA) and denaturing gradient gel electrophoresis (DGGE) were used to study the bacterial communities of subsamples M and A after 48 h enrichment. Results The number of Campylobacter positive subsamples were similar for A and M when all samples were combined (P = 0.81) and when samples were analyzed by product (breast: P = 0.75; thigh: P = 1.00). Oxygen sensors showed that DO values in the broth were around 6 ppm and O2 values in the head space were 14-16% throughout incubation. PFGE demonstrated high genomic similarity of isolates in the majority of the samples in which isolates were obtained from subsamples A and M. RISA and DGGE results showed a large variability in the bacterial populations that could be attributed to sample-to-sample variations and not enrichment conditions (aerobic or microaerobic). These data also suggested that current sampling protocols are not optimized to determine the true number of Campylobacter positive samples in retail boiler meat. Conclusions Decreased DO in enrichment broths is naturally achieved. This simplified, cost-effective enrichment protocol with aerobic incubation could be incorporated into reference methods for the isolation of Campylobacter spp. from retail broiler meat.
Patra, A K; Yu, Z
2013-03-01
Coconut (CO) and fish (FO) oils were previously shown to inhibit rumen methanogenesis and biohydrogenation, which mitigates methane emission and helps improve beneficial fatty acids in meat and milk. This study aimed at investigating the comparative effects of CO and FO on the methanogenesis, fermentation, and microbial abundances and diversity in vitro rumen cultures containing different doses (0, 3.1, and 6.2 mL/L) of each oil and 400mg feed substrate using rumen fluid from lactating dairy cows as inocula. Increasing doses of CO and FO quadratically decreased concentrations of methane, but hydrogen concentrations were only increased quadratically by CO. Both oils linearly decreased dry matter and neutral detergent fiber digestibility of feeds but did not affect the concentration of total volatile fatty acids. However, CO reduced acetate percentage and acetate to propionate ratio and increased the percentages of propionate and butyrate to a greater extent than FO. Ammonia concentration was greater for CO than FO. As determined by quantitative real-time PCR, FO had greater inhibition to methanogens than CO, but the opposite was true for protozoal, Ruminococcus flavefaciens, and Fibrobacter succinogenes. Ruminococcus albus was not affected by either oil. Denaturing gradient gel electrophoresis (DGGE) profiles revealed that bacterial and archaeal community composition were changed differently by oil type. Based on Pareto-Lorenz evenness curve analysis of the DGGE profiles, CO noticeably changed the functional organization of archaea compared with FO. In conclusion, although both CO and FO decreased methane concentrations to a similar extent, the mode of reduction and the effect on abundances and diversity of archaeal and bacterial populations differed between the oils. Thus, the use of combination of CO and FO at a low dose may additively lower methanogenesis in the rumen while having little adverse effect on rumen fermentation. Copyright © 2013 American Dairy
Hongpattarakere, Tipparat; Buntin, Nirunya; Nuylert, Aem
2016-01-01
Histamine formation and bacteriological changes caused by temperature abuse commonly occurring in the manufacturing process of standard canned tuna was assessed in microbiologically challenged tonggol (Thunnus tonggol). The in situ challenge was performed by water-soaking at 26-28 °C for 7 h to ensure the multiplication and active phase of fish microflora. Right after pre-cooking to back-bone temperature (BBT) of 50-52 °C, histamine dropped to 5.17 ± 2.71 ppm, and slowly reached 6.84 ± 1.69 ppm at 16 h abuse. On the contrary, histamine was reduced to 2.87 ± 1.23 ppm and eventually reached 5.01 ± 1.32 ppm at 24 h abuse in the pre-cooked fish previously frozen. The numbers of total aerobic bacteria, Enterobactericeae, psychrotroph, histamine forming bacteria (HFB) and diversity of fish microflora were revealed by cultural and nested PCR-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) techniques. Interestingly, frozen storage effectively halted histamine formation in raw fish throughout 16 h abuse despite the presence of HFB. These included the prolific strains of Morganella morganii, Proteus penneri, Proteus mirabilin, Citrobacter spp. The nested PCR-DGGE profile confirmed the presence of M. morganii and Citrobacter spp. in raw fish. These prolific strains were hardly observed in the precooked fish previously frozen. Frozen storage did not only promote even histamine distribution throughout fish muscle but also enhanced histamine loss during thawing and pre-cooking. Therefore, pre-cooking and frozen storage were proven to be the effective combined hurdles not only to reduce but also prolong histamine formation of the challenged toggol throughout 24 h of temperature abuse during canning process.
A designated centre for people with disabilities operated by Health Service Executive, Meath
LENUS (Irish Health Repository)
Zhou, Ping
2011-08-03
Abstract Background To simplify the methodology for the isolation of Campylobacter spp. from retail broiler meat, we evaluated 108 samples (breasts and thighs) using an unpaired sample design. The enrichment broths were incubated under aerobic conditions (subsamples A) and for comparison under microaerobic conditions (subsamples M) as recommended by current reference protocols. Sensors were used to measure the dissolved oxygen (DO) in the broth and the percentage of oxygen (O2) in the head space of the bags used for enrichment. Campylobacter isolates were identified with multiplex PCR assays and typed using pulsed-field gel electrophoresis (PFGE). Ribosomal intergenic spacer analyses (RISA) and denaturing gradient gel electrophoresis (DGGE) were used to study the bacterial communities of subsamples M and A after 48 h enrichment. Results The number of Campylobacter positive subsamples were similar for A and M when all samples were combined (P = 0.81) and when samples were analyzed by product (breast: P = 0.75; thigh: P = 1.00). Oxygen sensors showed that DO values in the broth were around 6 ppm and O2 values in the head space were 14-16% throughout incubation. PFGE demonstrated high genomic similarity of isolates in the majority of the samples in which isolates were obtained from subsamples A and M. RISA and DGGE results showed a large variability in the bacterial populations that could be attributed to sample-to-sample variations and not enrichment conditions (aerobic or microaerobic). These data also suggested that current sampling protocols are not optimized to determine the true number of Campylobacter positive samples in retail boiler meat. Conclusions Decreased DO in enrichment broths is naturally achieved. This simplified, cost-effective enrichment protocol with aerobic incubation could be incorporated into reference methods for the isolation of Campylobacter spp. from retail broiler meat.
Melview Nursing Home, Prior Park, Clonmel, Tipperary.
LENUS (Irish Health Repository)
Zhou, Ping
2011-08-03
Abstract Background To simplify the methodology for the isolation of Campylobacter spp. from retail broiler meat, we evaluated 108 samples (breasts and thighs) using an unpaired sample design. The enrichment broths were incubated under aerobic conditions (subsamples A) and for comparison under microaerobic conditions (subsamples M) as recommended by current reference protocols. Sensors were used to measure the dissolved oxygen (DO) in the broth and the percentage of oxygen (O2) in the head space of the bags used for enrichment. Campylobacter isolates were identified with multiplex PCR assays and typed using pulsed-field gel electrophoresis (PFGE). Ribosomal intergenic spacer analyses (RISA) and denaturing gradient gel electrophoresis (DGGE) were used to study the bacterial communities of subsamples M and A after 48 h enrichment. Results The number of Campylobacter positive subsamples were similar for A and M when all samples were combined (P = 0.81) and when samples were analyzed by product (breast: P = 0.75; thigh: P = 1.00). Oxygen sensors showed that DO values in the broth were around 6 ppm and O2 values in the head space were 14-16% throughout incubation. PFGE demonstrated high genomic similarity of isolates in the majority of the samples in which isolates were obtained from subsamples A and M. RISA and DGGE results showed a large variability in the bacterial populations that could be attributed to sample-to-sample variations and not enrichment conditions (aerobic or microaerobic). These data also suggested that current sampling protocols are not optimized to determine the true number of Campylobacter positive samples in retail boiler meat. Conclusions Decreased DO in enrichment broths is naturally achieved. This simplified, cost-effective enrichment protocol with aerobic incubation could be incorporated into reference methods for the isolation of Campylobacter spp. from retail broiler meat.
Buried straw layer and plastic mulching increase microlfora diversity in salinized soil
Institute of Scientific and Technical Information of China (English)
LI Yu-yi; PANG Huan-cheng; HAN Xiu-fang; YAN Shou-wei; ZHAO Yong-gan; WANG Jing; ZHAI Zhen; ZHANG Jian-li
2016-01-01
Salt stress has been increasingly constraining crop productivity in arid lands of the world. In our recent study, salt stress was aleviated and crop productivity was improved remarkably by straw layer burial plus plastic iflm mulching in a saline soil. However, its impact on the microlfora diversity is not wel documented. Field micro-plot experiments were conducted from 2010 to 2011 using four tilage methods: (i) deep tilage with plastic iflm mulching (CK), (i) straw layer burial at 40 cm (S), (ii) straw layer burial plus surface soil mulching with straw material (S+S), and (iv) plastic iflm mulching plus buried straw layer (P+S). Culturable microbes and predominant bacterial communities were studied; based on 16S rDNA, bacterial com-munity structure and abundance were characterized using denaturing gradient gel electrophoresis (DGGE) and polymerase chain reaction (PCR). Results showed that P+S was the most favorable for culturable bacteria, actinomyces and fungi and induced the most diverse genera of bacteria compared to other tilage methods. Soil temperature had signiifcant positive correlations with the number of bacteria, actinomyces and fungi (P<0.01). However, soil water was poorly correlated with any of the microbes. Salt content had a signiifcant negative correlation with the number of microbers, especialy for bacteria and fungi (P<0.01). DGGE analysis showed that the P+S exhibited the highest diversity of bacteria with 20 visible bands folowed by S+S, S and CK. Moreover, P+S had the highest similarity (68%) of bacterial communities with CK. The major bacterial genera in al soil samples wereFirmicutes,Proteobacteria andActinobacteria. Given the considerable increase in microbial growth, the combined use of straw layer burial and plastic iflm mulching could be a practical option for aleviating salt stress effects on soil microbial community and thereby improving crop production in arid saline soils.
LENUS (Irish Health Repository)
Zhou, Ping
2011-08-03
Abstract Background To simplify the methodology for the isolation of Campylobacter spp. from retail broiler meat, we evaluated 108 samples (breasts and thighs) using an unpaired sample design. The enrichment broths were incubated under aerobic conditions (subsamples A) and for comparison under microaerobic conditions (subsamples M) as recommended by current reference protocols. Sensors were used to measure the dissolved oxygen (DO) in the broth and the percentage of oxygen (O2) in the head space of the bags used for enrichment. Campylobacter isolates were identified with multiplex PCR assays and typed using pulsed-field gel electrophoresis (PFGE). Ribosomal intergenic spacer analyses (RISA) and denaturing gradient gel electrophoresis (DGGE) were used to study the bacterial communities of subsamples M and A after 48 h enrichment. Results The number of Campylobacter positive subsamples were similar for A and M when all samples were combined (P = 0.81) and when samples were analyzed by product (breast: P = 0.75; thigh: P = 1.00). Oxygen sensors showed that DO values in the broth were around 6 ppm and O2 values in the head space were 14-16% throughout incubation. PFGE demonstrated high genomic similarity of isolates in the majority of the samples in which isolates were obtained from subsamples A and M. RISA and DGGE results showed a large variability in the bacterial populations that could be attributed to sample-to-sample variations and not enrichment conditions (aerobic or microaerobic). These data also suggested that current sampling protocols are not optimized to determine the true number of Campylobacter positive samples in retail boiler meat. Conclusions Decreased DO in enrichment broths is naturally achieved. This simplified, cost-effective enrichment protocol with aerobic incubation could be incorporated into reference methods for the isolation of Campylobacter spp. from retail broiler meat.
Janzcyk, P.; Pieper, R.; Smidt, H.; Souffrant, W.B.
2007-01-01
Our study aimed to provide a comprehensive characterization of changes in porcine intestinal Lactobacillus populations around the time of weaning based on 16S rRNA gene amplification and denaturing gradient gel electrophoresis (DGGE). DNA was extracted from the ileal contents of piglets at weaning
Microbial Community Strucure of a Tropical Wastewater Stabilization Pond (Cajati, Brazil)
DEFF Research Database (Denmark)
Nishio, Sandra; Schramm, Andreas; Pellizari, V.
seasons. CARD-FISH successfully detected 55-85% and 40-50% of all cells in the water and sludge samples, respectively, and generally confirmed the DGGE results. The bacterial community was dominated by unicellular cyanobacteria, followed by either Beta- or Alphaproteobacteria, depending on the season...
Wu, Y; Hayes, VM; Osinga, J; Mulder, IM; Looman, MWG; Buys, CHCM; Hofstra, RMW
1998-01-01
Denaturing gradient gel electrophoresis (DGGE) is one of the most powerful methods for mutation detection currently available. For successful application the appropriate selection of PCR fragments and PCR primers is crucial. The sequence of interest should always be within the domain with the lowest
Czech Academy of Sciences Publication Activity Database
Jirout, Jiří; Pižl, Václav
2014-01-01
Roč. 76, September (2014), s. 249-256 ISSN 0038-0717 R&D Projects: GA ČR GAP504/12/0536 Institutional support: RVO:60077344 Keywords : bacteria * archaea * fungi * community composition * DGGE * earthworm Subject RIV: EH - Ecology, Behaviour Impact factor: 3.932, year: 2014
Enhanced selection of micro-aerobic pentachlorophenol degrading granular sludge
Energy Technology Data Exchange (ETDEWEB)
Lv, Yuancai, E-mail: donkey1204@hotmail.com [State Key Laboratory of Pulp and Paper Engineering, College of Light Industry and Food Science, South China University of Technology, Guangzhou 510640 (China); Chen, Yuancai, E-mail: chenyc@scut.edu.cn [State Key Laboratory of Pulp and Paper Engineering, College of Light Industry and Food Science, South China University of Technology, Guangzhou 510640 (China); Ministry of Education Key Laboratory of Pollution Control and Ecological Remediation for Industrial Agglomeration Area, College of Environment and Energy, South China University of Technology, Guangzhou 510006 (China); Song, Wenzhe, E-mail: songwenzhe007@126.com [Ministry of Education Key Laboratory of Pollution Control and Ecological Remediation for Industrial Agglomeration Area, College of Environment and Energy, South China University of Technology, Guangzhou 510006 (China); Hu, Yongyou, E-mail: ppyyhu@scut.edu.cn [State Key Laboratory of Pulp and Paper Engineering, College of Light Industry and Food Science, South China University of Technology, Guangzhou 510640 (China); Ministry of Education Key Laboratory of Pollution Control and Ecological Remediation for Industrial Agglomeration Area, College of Environment and Energy, South China University of Technology, Guangzhou 510006 (China)
2014-09-15
Graphical abstract: In this work, an aerobic column reactor was placed before the USB to maintain micro-oxygen condition in the reactor and the micro-aerobic pentachlorophenol (PCP) degrading granular sludge under oxygen-limited conditions (0.1–0.2 mg L{sup −1}) was successfully obtained. PCP degradation by the micro-aerobic system was studied and the variance of microbial community was also discussed by using PCR-DGGE analysis. - Highlights: • Micro-aerobic granular sludge was cultivated in column-type combined reactors. • PCP biodegradation, VFA accumulation and biogas production were studied. • The function of Methanogenic archaeon in the system was investigated. • Fluctuation and diversity of microbial community were discussed by DGGE analysis. • The dominated microorganisms were identified by 16S rDNA sequences. - Abstract: Column-type combined reactors were designed to cultivate micro-aerobic pentachlorophenol (PCP) degrading granular sludge under oxygen-limited conditions (0.1–0.2 mg L{sup −1}) over 39-day experimental period. Micro-aerobic granular had both anaerobic activity (SMA: 2.34 mMCH{sub 4}/h g VSS) and aerobic activity (SOUR: 2.21 mMO{sub 2}/h g VSS). Metabolite analysis results revealed that PCP was sequentially dechlorinated to TCP, DCP, and eventually to MCP. Methanogens were not directly involved in the dechlorination of PCP, but might played a vital role in stabilizing the overall structure of the granule sludge. For Eubacteria, the Shannon Index (2.09 in inoculated granular sludge) increased both in micro-aerobic granular sludge (2.61) and PCP-degradation granular sludge (2.55). However, for Archaea, it decreased from 2.53 to 1.85 and 1.84, respectively. Although the Shannon Index demonstrated slight difference between micro-aerobic granular sludge and PCP-degradation granular sludge, the Principal Component Analysis (PCA) indicated obvious variance of the microbial composition, revealing significant effect of micro
Enhanced selection of micro-aerobic pentachlorophenol degrading granular sludge
International Nuclear Information System (INIS)
Lv, Yuancai; Chen, Yuancai; Song, Wenzhe; Hu, Yongyou
2014-01-01
Graphical abstract: In this work, an aerobic column reactor was placed before the USB to maintain micro-oxygen condition in the reactor and the micro-aerobic pentachlorophenol (PCP) degrading granular sludge under oxygen-limited conditions (0.1–0.2 mg L −1 ) was successfully obtained. PCP degradation by the micro-aerobic system was studied and the variance of microbial community was also discussed by using PCR-DGGE analysis. - Highlights: • Micro-aerobic granular sludge was cultivated in column-type combined reactors. • PCP biodegradation, VFA accumulation and biogas production were studied. • The function of Methanogenic archaeon in the system was investigated. • Fluctuation and diversity of microbial community were discussed by DGGE analysis. • The dominated microorganisms were identified by 16S rDNA sequences. - Abstract: Column-type combined reactors were designed to cultivate micro-aerobic pentachlorophenol (PCP) degrading granular sludge under oxygen-limited conditions (0.1–0.2 mg L −1 ) over 39-day experimental period. Micro-aerobic granular had both anaerobic activity (SMA: 2.34 mMCH 4 /h g VSS) and aerobic activity (SOUR: 2.21 mMO 2 /h g VSS). Metabolite analysis results revealed that PCP was sequentially dechlorinated to TCP, DCP, and eventually to MCP. Methanogens were not directly involved in the dechlorination of PCP, but might played a vital role in stabilizing the overall structure of the granule sludge. For Eubacteria, the Shannon Index (2.09 in inoculated granular sludge) increased both in micro-aerobic granular sludge (2.61) and PCP-degradation granular sludge (2.55). However, for Archaea, it decreased from 2.53 to 1.85 and 1.84, respectively. Although the Shannon Index demonstrated slight difference between micro-aerobic granular sludge and PCP-degradation granular sludge, the Principal Component Analysis (PCA) indicated obvious variance of the microbial composition, revealing significant effect of micro-aerobic condition and
All-fiber 7x1 signal combiner for incoherent laser beam combining
DEFF Research Database (Denmark)
Noordegraaf, Danny; Maack, Martin D.; Skovgaard, Peter M. W.
2011-01-01
We demonstrate an all-fiber 7x1 signal combiner for incoherent laser beam combining. This is a potential key component for reaching several kW of stabile laser output power. The combiner couples the output from 7 single-mode (SM) fiber lasers into a single multi-mode (MM) fiber. The input signal ...... in device temperature is observed. At an intermediate power level of 600 W a beam parameter product (BPP) of 2.22 mm x mrad is measured, corresponding to an M2 value of 6.5. These values are approaching the theoretical limit dictated by brightness conservation....
Birth control pills - combination
... page: //medlineplus.gov/ency/patientinstructions/000655.htm Birth control pills - combination To use the sharing features on ... both progestin and estrogen. What Are Combination Birth Control Pills? Birth control pills help keep you from ...
Spatial and vertical distribution of bacteria in the Pearl River estuary ...
African Journals Online (AJOL)
In order to investigate the spatial and vertical change of bacteria community structure in the Pearl River estuary sediment, denaturing gradient gel electrophoresis (DGGE) and multivariate statistical analyses were carried out in this study. Results of multidimensional scaling analyses (MDS) were in good agreement with the ...
Bacterial community structure in the Cerasus sachalinensis Kom ...
African Journals Online (AJOL)
Jane
2011-07-21
Jul 21, 2011 ... The bacterial community structures of the Cerasus sachalinensis Kom. rhizosphere in wild and cultivated soil were studied and the community changes in different growth stages were analyzed by the PCR-denaturing gradient gel electrophoresis (PCR-DGGE) method. The results showed that the bacterial ...
DEFF Research Database (Denmark)
Bernbom, Nete; Jelle, N.B.; Brogren, C.-H.
2009-01-01
microbiota was in all treatments dominated by lactic acid bacteria and coliforms and no changes in the rat commensal microbiota were detected after ingestion of either of the two L plantarum strains as determined by both culturable methods and molecular methods (DGGE). Both strains were detected...
Analysis of bacterial and fungal community structure in replant ...
African Journals Online (AJOL)
High quality DNA is the basis of analyzing bacterial and fungal community structure in replant strawberry rhizosphere soil with the method of denaturing gradient gel electrophoresis (DGGE). DNA of soil microorganisms was extracted from the rhizosphere soil of strawberries planted in different replanted years (0, two, ...
Bacterial diversity in agricultural soils during litter decomposition
Dilly, O.; Bloem, J.; Vos, A.; Munch, J.C.
2004-01-01
Denaturing gradient gel electrophoresis (DGGE) of amplified fragments of genes coding for 16S rRNA was used to study the development of bacterial communities during decomposition of crop residues in agricultural soils. Ten strains were tested, and eight of these strains produced a single band.
Bassin, J.P.; Pronk, M.; Muyzer, G.; Kleerebezem, R.; Dezotti, M.; Van Loosdrecht, M.C.M.
2011-01-01
The long- and short-term effects of salt on biological nitrogen and phosphorus removal processes were studied in an aerobic granular sludge reactor. The microbial community structure was investigated by PCR-denaturing gradient gel electrophoresis (DGGE) on 16S rRNA and amoA genes. PCR products
Sustainable nitrification in fluidised bed reactor with immobilised ...
African Journals Online (AJOL)
TOC concentration above 800 mg·ℓ-1 was not able to cause the inhibition of the heterotrophs over the nitrifiers. PCR-DGGE results indicated the presence of Nitrosomonas (ammonia-oxidising bacteria) and Nitrobacter (nitrite-oxidising bacteria) in the immobilised pellets. Keywords: bioimmobilisation, ammonium, partial ...
Practical, general parser combinators
A. Izmaylova (Anastasia); A. Afroozeh (Ali); T. van der Storm (Tijs)
2016-01-01
textabstractParser combinators are a popular approach to parsing where contextfree grammars are represented as executable code. However, conventional parser combinators do not support left recursion, and can have worst-case exponential runtime. These limitations hinder the expressivity and
Zeng, Guangming; Zhang, Jiachao; Chen, Yaoning; Yu, Zhen; Yu, Man; Li, Hui; Liu, Zhifeng; Chen, Ming; Lu, Lunhui; Hu, Chunxiao
2011-10-01
The aim of this study was to compare the relative contribution of ammonia-oxidizing archaea (AOA) and bacteria (AOB) to nitrification during agricultural waste composting. The AOA and AOB amoA gene abundance and composition were determined by quantitative PCR and denaturing gradient gel electrophoresis (DGGE), respectively. The results showed that the archaeal amoA gene was abundant throughout the composting process, while the bacterial amoA gene abundance decreased to undetectable level during the thermophilic and cooling stages. DGGE showed more diverse archaeal amoA gene composition when the potential ammonia oxidation (PAO) rate reached peak values. A significant positive relationship was observed between the PAO rate and the archaeal amoA gene abundance (R²=0.554; Parchaea dominated ammonia oxidation during the thermophilic and cooling stages. Bacteria were also related to ammonia oxidation activity (R²=0.503; P=0.03) especially during the mesophilic and maturation stages. Copyright © 2011 Elsevier Ltd. All rights reserved.
Randazzo, C L; Pitino, I; De Luca, S; Scifò, G O; Caggia, C
2008-03-20
The effect of six wild strains on the volatile profile of the PS cheese was investigated and compared to that generated from industrial starters generally used to produce PS cheese. All cheeses were subjected to microbiological, physicochemical, and volatile compounds analyses. The DGGE of the 16S rDNA analysis was also applied. The volatile compounds generated during ripening were studied through the SPME and the GC-MS methods. No difference was detected between the experimental and control cheeses throughout chemical and microbiological analyses, while the DGGE results showed the presence of Streptococcus thermophilus in all cheeses, and the dominance of Enterococcus durans, Lactobacillus rhamnosus, and Lactobacillus casei in most of the experimental cheeses. Moreover, the presence of Lactococcus lactis species as in the control and in the experimental P2 and P4 cheeses was also revealed. The SPME results showed more pronounced volatile compounds in the experimental cheese samples than in the control ones.
Elgueta, Sebastian; Correa, Arturo; Campo, Marco; Gallardo, Felipe; Karpouzas, Dimitrios; Diez, Maria Cristina
2017-09-02
The use of biopurification systems can mitigate the effects of pesticide contamination on farms. The primary aim of this study was to evaluate the effect of pesticide dissipation on microbial communities in a pilot biopurification system. The pesticide dissipation of atrazine, chlorpyrifos and iprodione (35 mg kg -1 active ingredient [a.i.]) and biological activity were determined for 40 days. The microbial communities (bacteria, actinomycetes and fungi) were analyzed using denaturing gradient gel electrophoresis (DGGE). In general, pesticide dissipation was the highest by day 5 and reached 95%. The pesticides did not affect biological activity during the experiment. The structure of the actinomycete and bacterial communities in the rhizosphere was more stable during the evaluation than that in the communities in the control without pesticides. The rhizosphere fungal communities, detected using DGGE, showed small and transitory shifts with time. To conclude, rhizosphere microbial communities were not affected during pesticide dissipation in a pilot biopurification system.
Guan, Le Luo; Nkrumah, Joshua D; Basarab, John A; Moore, Stephen S
2008-11-01
Linkage of rumen microbial structure to host phenotypical traits may enhance the understanding of host-microbial interactions in livestock species. This study used culture-independent PCR-denaturing gradient gel electrophoresis (PCR-DGGE) to investigate the microbial profiles in the rumen of cattle differing in feed efficiency. The analysis of detectable bacterial PCR-DGGE profiles showed that the profiles generated from efficient steers clustered together and were clearly separated from those obtained from inefficient steers, indicating that specific bacterial groups may only inhabit in efficient steers. In addition, the bacterial profiles were more likely clustered within a certain breed, suggesting that host genetics may play an important role in rumen microbial structure. The correlations between the concentrations of volatile fatty acids and feed efficiency traits were also observed. Significantly higher concentrations of butyrate (P < 0.001) and valerate (P = 0.006) were detected in the efficient steers. Our results revealed potential associations between the detectable rumen microbiota and its fermentation parameters with the feed efficiency of cattle.
Szirányi, Barbara; Krett, Gergely; Kosáros, Tünde; Janurik, Endre; Pekár, Ferenc; Márialigeti, Károly; Borsodi, Andrea K
2017-12-01
Disposal of used geothermal waters in Hungary often means temporary storage in reservoir lakes to reduce temperature and improve water quality. In this study, the physical and chemical properties and changes in the bacterial community structure of a reservoir lake system in southeast region of Hungary were monitored and compared through 2 years, respectively. The values of biological oxygen demand, concentrations of ammonium ion, total inorganic nitrogen, total phosphorous, and total phenol decreased, whereas oxygen saturation, total organic nitrogen, pH, and conductivity increased during the storage period. Bacterial community structure of water and sediment samples was compared by denaturing gradient gel electrophoresis (DGGE) following the amplification of the 16S rRNA gene. According to the DGGE patterns, greater seasonal than spatial differences of bacterial communities were revealed in both water and sediment of the lakes. Representatives of the genera Arthrospira and Anabaenopsis (cyanobacteria) were identified as permanent and dominant members of the bacterial communities.
Intrinsic bioremediation potential of a chronically polluted marine coastal area.
Catania, Valentina; Santisi, Santina; Signa, Geraldina; Vizzini, Salvatrice; Mazzola, Antonio; Cappello, Simone; Yakimov, Michail M; Quatrini, Paola
2015-10-15
A microbiological survey of the Priolo Bay (eastern coast of Sicily, Ionian Sea), a chronically polluted marine coastal area, was carried out in order to discern its intrinsic bioremediation potential. Microbiological analysis, 16S rDNA-based DGGE fingerprinting and PLFAs analysis were performed on seawater and sediment samples from six stations on two transects. Higher diversity and variability among stations was detected by DGGE in sediment than in water samples although seawater revealed higher diversity of culturable hydrocarbon-degrading bacteria. The most polluted sediment hosted higher total bacterial diversity and higher abundance and diversity of culturable HC degraders. Alkane- and PAH-degrading bacteria were isolated from all stations and assigned to Alcanivorax, Marinobacter, Thalassospira, Alteromonas and Oleibacter (first isolation from the Mediterranean area). High total microbial diversity associated to a large selection of HC degraders is believed to contribute to natural attenuation of the area, provided that new contaminant contributions are avoided. Copyright © 2015 Elsevier Ltd. All rights reserved.
Sun, Jiajun; Qian, Xun; Gu, Jie; Wang, Xiaojuan; Gao, Hua
2016-09-01
The effects of oxytetracycline (OTC) on nitrogen-fixing bacterial communities were investigated during cattle manure composting. The abundance and community structure of nitrogen-fixing bacteria were determined by qPCR and denaturing gradient gel electrophoresis (DGGE), respectively. The matrix was spiked with OTC at four levels: no OTC, 10mg/kg dry weight (DW) OTC (L), 60mg/kg DW OTC (M), and 200mg/kg DW OTC (H). The high temperature period of composting was shorter with M and H, and the decline in temperature during the cooling stage was accelerated by OTC. OTC had a concentration-dependent inhibitory effect on the nitrogenase activity during early composting, and the nifH gene abundance declined significantly during the later composting stage. The DGGE profile and statistical analysis showed that OTC changed the nitrogen-fixing bacterial community succession and reduced the community richness and dominance. The nitrogen-fixing bacterial community structure was affected greatly by the high level of OTC. Copyright © 2016. Published by Elsevier Ltd.
Binocular Combination of Second-Order Stimuli
Zhou, Jiawei; Liu, Rong; Zhou, Yifeng; Hess, Robert F.
2014-01-01
Phase information is a fundamental aspect of visual stimuli. However, the nature of the binocular combination of stimuli defined by modulations in contrast, so-called second-order stimuli, is presently not clear. To address this issue, we measured binocular combination for first- (luminance modulated) and second-order (contrast modulated) stimuli using a binocular phase combination paradigm in seven normal adults. We found that the binocular perceived phase of second-order gratings depends on the interocular signal ratio as has been previously shown for their first order counterparts; the interocular signal ratios when the two eyes were balanced was close to 1 in both first- and second-order phase combinations. However, second-order combination is more linear than previously found for first-order combination. Furthermore, binocular combination of second-order stimuli was similar regardless of whether the carriers in the two eyes were correlated, anti-correlated, or uncorrelated. This suggests that, in normal adults, the binocular phase combination of second-order stimuli occurs after the monocular extracting of the second-order modulations. The sensory balance associated with this second-order combination can be obtained from binocular phase combination measurements. PMID:24404180
Combination contraceptives: effects on weight.
Gallo, Maria F; Lopez, Laureen M; Grimes, David A; Carayon, Florence; Schulz, Kenneth F; Helmerhorst, Frans M
2014-01-29
Weight gain is often considered a side effect of combination hormonal contraceptives, and many women and clinicians believe that an association exists. Concern about weight gain can limit the use of this highly effective method of contraception by deterring the initiation of its use and causing early discontinuation among users. However, a causal relationship between combination contraceptives and weight gain has not been established. The aim of the review was to evaluate the potential association between combination contraceptive use and changes in weight. In November 2013, we searched the computerized databases CENTRAL (The Cochrane Library), MEDLINE, POPLINE, EMBASE, and LILACS for studies of combination contraceptives, as well as ClinicalTrials.gov and International Clinical Trials Registry Platform (ICTRP). For the initial review, we also wrote to known investigators and manufacturers to request information about other published or unpublished trials not discovered in our search. All English-language, randomized controlled trials were eligible if they had at least three treatment cycles and compared a combination contraceptive to a placebo or to a combination contraceptive that differed in drug, dosage, regimen, or study length. All titles and abstracts located in the literature searches were assessed. Data were entered and analyzed with RevMan. A second author verified the data entered. For continuous data, we calculated the mean difference and 95% confidence interval (CI) for the mean change in weight between baseline and post-treatment measurements using a fixed-effect model. For categorical data, such as the proportion of women who gained or lost more than a specified amount of weight, the Peto odds ratio with 95% CI was calculated. We found 49 trials that met our inclusion criteria. The trials included 85 weight change comparisons for 52 distinct contraceptive pairs (or placebos). The four trials with a placebo or no intervention group did not find
This paper outlines a life-cycle cost analysis comparing a green (rain gardens) and gray (tunnels) infrastructure combination to a gray-only option to control combined sewer overflow in the Turkey Creek Combined Sewer Overflow Basin, in Kansas City, MO. The plan area of this Bas...
Packet reversed packet combining scheme
International Nuclear Information System (INIS)
Bhunia, C.T.
2006-07-01
The packet combining scheme is a well defined simple error correction scheme with erroneous copies at the receiver. It offers higher throughput combined with ARQ protocols in networks than that of basic ARQ protocols. But packet combining scheme fails to correct errors when the errors occur in the same bit locations of two erroneous copies. In the present work, we propose a scheme that will correct error if the errors occur at the same bit location of the erroneous copies. The proposed scheme when combined with ARQ protocol will offer higher throughput. (author)
Exploring Microbial Iron Oxidation in Wetland Soils
Wang, J.; Muyzer, G.; Bodelier, P. L. E.; den Oudsten, F.; Laanbroek, H. J.
2009-04-01
Iron is one of the most abundant elements on earth and is essential for life. Because of its importance, iron cycling and its interaction with other chemical and microbial processes has been the focus of many studies. Iron-oxidizing bacteria (FeOB) have been detected in a wide variety of environments. Among those is the rhizosphere of wetland plants roots which release oxygen into the soil creating suboxic conditions required by these organisms. It has been reported that in these rhizosphere microbial iron oxidation proceeds up to four orders of magnitude faster than strictly abiotic oxidation. On the roots of these wetland plants iron plaques are formed by microbial iron oxidation which are involved in the sequestering of heavy metals as well organic pollutants, which of great environmental significance.Despite their important role being catalysts of iron-cycling in wetland environments, little is known about the diversity and distribution of iron-oxidizing bacteria in various environments. This study aimed at developing a PCR-DGGE assay enabling the detection of iron oxidizers in wetland habitats. Gradient tubes were used to enrich iron-oxidizing bacteria. From these enrichments, a clone library was established based on the almost complete 16s rRNA gene using the universal bacterial primers 27f and 1492r. This clone library consisted of mainly α- and β-Proteobacteria, among which two major clusters were closely related to Gallionella spp. Specific probes and primers were developed on the basis of this 16S rRNA gene clone library. The newly designed Gallionella-specific 16S rRNA gene primer set 122f/998r was applied to community DNA obtained from three contrasting wetland environments, and the PCR products were used in denaturing gradient gel electrophoresis (DGGE) analysis. A second 16S rRNA gene clone library was constructed using the PCR products from one of our sampling sites amplified with the newly developed primer set 122f/998r. The cloned 16S rRNA gene
Physical Conditions Regulate the Fungal to Bacterial Ratios of a Tropical Suspended Soil
Directory of Open Access Journals (Sweden)
Julian Donald
2017-12-01
Full Text Available As a source of ‘suspended soils’, epiphytes contribute large amounts of organic matter to the canopy of tropical rain forests. Microbes associated with epiphytes are responsible for much of the nutrient cycling taking place in rain forest canopies. However, soils suspended far above the ground in living organisms differ from soil on the forest floor, and traditional predictors of soil microbial community composition and functioning (nutrient availability and the activity of soil organisms are likely to be less important. We conducted an experiment in the rain forest biome at the Eden Project in the U.K. to explore how biotic and abiotic conditions determine microbial community composition and functioning in a suspended soil. To simulate their natural epiphytic lifestyle, bird’s nest ferns (Asplenium nidus were placed on a custom-built canopy platform suspended 8 m above the ground. Ammonium nitrate and earthworm treatments were applied to ferns in a factorial design. Extracellular enzyme activity and Phospholipid Fatty Acid (PLFA profiles were determined at zero, three and six months. We observed no significant differences in either enzyme activity or PLFA profiles between any of the treatments. Instead, we observed decreases in β-glucosidase and N-acetyl-glucosaminidase activity, and an increase in phenol oxidase activity across all treatments and controls over time. An increase in the relative abundance of fungi during the experiment meant that the microbial communities in the Eden Project ferns after six months were comparable with ferns sampled from primary tropical rain forest in Borneo.
Czech Academy of Sciences Publication Activity Database
Bougnom, B.P.; Knapp, B.A.; Elhottová, Dana; Koubová, Anna; Etoa, F.X.; Insam, H.
2010-01-01
Roč. 45, č. 3 (2010), s. 319-324 ISSN 0929-1393 R&D Projects: GA MŠk LC06066; GA MŠk MEB060814 Institutional research plan: CEZ:AV0Z60660521 Keywords : CLPPs * compost * DGGE Subject RIV: EH - Ecology, Behaviour Impact factor: 2.399, year: 2010
Molecular monitoring of succession of bacterial communities in human neonates
Favier, C.; Vaughan, E.E.; Vos, de W.M.; Akkermans, A.D.L.
2002-01-01
The establishment of bacterial communities in two healthy babies was examined for more than the first 10 months of life by monitoring 16S ribosomal DNA (rDNA) diversity in fecal samples by PCR and denaturing gradient gel electrophoresis (DGGE) and by analyzing the sequences of the major ribotypes.
Langlois, Michel; Peillex-Delphe, Guy
2005-01-01
Particle accelerators need radio frequency sources. Above 300 MHz, the amplifiers mostly used high power klystrons developed for this sole purpose. As for military equipment, users are drawn to buy "off the shelf" components rather than dedicated devices. IOTs have replaced most klystrons in TV transmitters and find their way in particle accelerators. They are less bulky, easier to replace, more efficient at reduced power. They are also far less powerful. What is the benefit of very compact sources if huge 3 dB couplers are needed to combine the power? To alleviate this drawback, we investigated a resonant combiner, operating in TM010 mode, able to combine 3 to 5 IOTs. Our IOTs being able to deliver 80 kW C.W. apiece, combined power would reach 400 kW minus the minor insertion loss. Values for matching and insertion loss are given. The behavior of the system in case of IOT failure is analyzed.
Andreolli, Marco; Albertarelli, Nicola; Lampis, Silvia; Brignoli, Pierlorenzo; Khoei, Nazaninalsadat Seyed; Vallini, Giovanni
2016-01-01
The present study reports on a real case of contamination due to the chronic leakage of diesel fuel from an underground tank at a dismissed service station. Speciation of the microbial community according to both lateral and vertical gradients from the origin of the contaminant release was analyzed by means of the PCR-DGGE technique. Moreover, the effects of a landfarming treatment on both the microbial community structure and the abatement of contamination were analyzed. The concentration of total petrol hydrocarbons (TPHs) decreased along the horizontal gradient (from 7042.2 ± 521.9 to 112.2 ± 24.3 mg kg(-1)), while increased downwards from the position of the tank (from 502.6 ± 43.7 to 4972.5 ± 275.3 mg kg(-1)). PCR-DGGE analyses and further statistical treatment of the data indicated a correlation between structure of the bacterial communities and amount of diesel fuel contamination. On the other hand, level of contamination, soil texture and depth were shown to affect the fungal community. Chloroflexi and Ascomycota were the most abundant microbes ascertained through culture-independent procedures. Landfarming promoted 91.6 % reduction of TPHs in 75 days. Furthermore, PCR-DGGE analyses evidenced that both bacterial and fungal communities of the treated soil were restored to the pristine conditions of uncontaminated topsoil. The present study demonstrated that bacterial and fungal communities were affected differently by soil factors such as level of hydrocarbon contamination as well as soil depth and texture. This report shows that a well-planned landfarming treatment can drive the restoration of the soil in terms of both abatement of the contaminants and resilience of the microbial community structure.
Bacterial Exposures and Associations with Atopy and Asthma in Children.
Directory of Open Access Journals (Sweden)
Maria Valkonen
Full Text Available The increase in prevalence of asthma and atopic diseases in Western countries has been linked to aspects of microbial exposure patterns of people. It remains unclear which microbial aspects contribute to the protective farm effect.The objective of this study was to identify bacterial groups associated with prevalence of asthma and atopy, and to quantify indoor exposure to some of these bacterial groups.A DNA fingerprinting technique, denaturing gradient gel electrophoresis (DGGE, was applied to mattress dust samples of farm children and control children in the context of the GABRIEL Advanced study. Associations between signals in DGGE and atopy, asthma and other allergic health outcomes were analyzed. Quantitative DNA based assays (qPCR for four bacterial groups were applied on the dust samples to seek quantitative confirmation of associations indicated in DNA fingerprinting.Several statistically significant associations between individual bacterial signals and also bacterial diversity in DGGE and health outcomes in children were observed. The majority of these associations showed inverse relationships with atopy, less so with asthma. Also, in a subsequent confirmation study using a quantitative method (qPCR, higher mattress levels of specifically targeted bacterial groups - Mycobacterium spp., Bifidobacteriaceae spp. and two different clusters of Clostridium spp. - were associated with a lower prevalence of atopy.DNA fingerprinting proved useful in identifying bacterial signals that were associated with atopy in particular. These findings were quantitatively confirmed for selected bacterial groups with a second method. High correlations between the different bacterial exposures impede a clear attribution of protective effects to one specific bacterial group. More diverse bacterial flora in mattress dust may link to microbial exposure patterns that protect against development of atopic diseases.
Zhou, Wenting; Nan, Xiaoning; Zheng, Zhou; Wei, Cong; He, Hong
2015-01-01
Intestinal bacterial community plays a crucial role in the nutrition, development, survival, and reproduction of insects. When compared with other insects with piercing-sucking mouthparts, the habitats of cicada nymphs and adults are totally different. However, little is known about the differences in the gut bacterial communities in the nymphs and adults within any cicada species. The diversity of bacteria in the gut of nymphs and adults of both genders of Meimuna mongolica (Distant) was studied using the denaturing gradient gel electrophoresis (DGGE) method. Few inter-individual variations among gut microbiota were observed, suggesting that M. mongolica typically harbors a limited and consistent suite of bacterial species. Bacteria in the genera Pseudomonas and Enterobacter were the predominant components of the gut microflora of M. mongolica at all life stages. Bacteria of Pantoea, Streptococcus, and Uruburuella were also widespread in the cicada samples but at relatively lower concentrations. The relative stability and similarity of the PCR-DGGE patterns indicate that all individuals of this cicada species harbor a characteristic bacterial community which is independent from developmental stages and genders. Related endosymbionts that could be harbored in bacteromes of cicadas were not detected in any gut samples, which could be related to the cicada species and the distribution of these endosymbionts in the cicada cavity, or due to some of the possible limitations of PCR-DGGE community profiling. It is worthwhile to further address if related cicada endosymbiont clades distribute in the alimentary canals and other internal organs through diagnostic PCR using group-specific primer sets. © The Author 2015. Published by Oxford University Press on behalf of the Entomological Society of America.
Energy Technology Data Exchange (ETDEWEB)
Kumaraswamy, Raji; Ebert, Sara; Fedorak, Phillip M.; Foght, Julia M. [Alberta Univ., Edmonton, AB (Canada). Biological Sciences; Gray, Murray R. [Alberta Univ., Edmonton, AB (Canada). Chemical and Materials Engineering
2011-03-15
Nitrate injection into oil fields is an alternative to biocide addition for controlling sulfide production ('souring') caused by sulfate-reducing bacteria (SRB). This study examined the suitability of several cultivation-dependent and cultivation-independent methods to assess potential microbial activities (sulfidogenesis and nitrate reduction) and the impact of nitrate amendment on oil field microbiota. Microcosms containing produced waters from two Western Canadian oil fields exhibited sulfidogenesis that was inhibited by nitrate amendment. Most probable number (MPN) and fluorescent in situ hybridization (FISH) analyses of uncultivated produced waters showed low cell numbers ({<=}10{sup 3} MPN/ml) dominated by SRB (>95% relative abundance). MPN analysis also detected nitrate-reducing sulfide-oxidizing bacteria (NRSOB) and heterotrophic nitrate-reducing bacteria (HNRB) at numbers too low to be detected by FISH or denaturing gradient gel electrophoresis (DGGE). In microcosms containing produced water fortified with sulfate, near-stoichiometric concentrations of sulfide were produced. FISH analyses of the microcosms after 55 days of incubation revealed that Gammaproteobacteria increased from undetectable levels to 5-20% abundance, resulting in a decreased proportion of Deltaproteobacteria (50-60% abundance). DGGE analysis confirmed the presence of Delta- and Gammaproteobacteria and also detected Bacteroidetes. When sulfate-fortified produced waters were amended with nitrate, sulfidogenesis was inhibited and Deltaproteobacteria decreased to levels undetectable by FISH, with a concomitant increase in Gammaproteobacteria from below detection to 50-60% abundance. DGGE analysis of these microcosms yielded sequences of Gamma- and Epsilonproteobacteria related to presumptive HNRB and NRSOB (Halomonas, Marinobacterium, Marinobacter, Pseudomonas and Arcobacter), thus supporting chemical data indicating that nitrate-reducing bacteria out-compete SRB when nitrate is
Cardinali, Federica; Osimani, Andrea; Taccari, Manuela; Milanović, Vesna; Garofalo, Cristiana; Clementi, Francesca; Polverigiani, Serena; Zitti, Silvia; Raffaelli, Nadia; Mozzon, Massimo; Foligni, Roberta; Franciosi, Elena; Tuohy, Kieran; Aquilanti, Lucia
2017-08-16
Caciofiore della Sibilla is an Italian specialty soft cheese manufactured with Sopravissana raw ewes' milk and thistle rennet prepared with young fresh leaves and stems of Carlina acanthifolia All. subsp. acanthifolia, according to an ancient tradition deeply rooted in the territory of origin (mountainous hinterland of the Marche region, Central Italy). In this study, the impact of thistle rennet on the bacterial dynamics and diversity of Caciofiore della Sibilla cheese was investigated by applying a polyphasic approach based on culture and DNA-based techniques (Illumina sequencing and PCR-DGGE). A control cheese manufactured with the same batch of ewes' raw milk and commercial animal rennet was analyzed in parallel. Overall, a large number of bacterial taxa were identified, including spoilage, environmental and pro-technological bacteria, primarily ascribed to Lactobacillales. Thistle rennet was observed clearly to affect the early bacterial dynamics of Caciofiore della Sibilla cheese with Lactobacillus alimentarius/paralimentarius and Lactobacillus plantarum/paraplantarum/pentosus being detected in the phyllosphere of C. acanthifolia All., thistle rennet and curd obtained with thistle rennet. Other bacterial taxa, hypothetically originating from the vegetable coagulant (Enterococcus faecium, Lactobacillus brevis, Lactobacillus delbrueckii, Leuconostoc mesenteroides/pseudomesenteroides), were exclusively found in Caciofiore della Sibilla cheese by PCR-DGGE. At the end of the maturation period, Illumina sequencing demonstrated that both cheeses were dominated by Lactobacillales; however curd and cheese produced with thistle rennet were co-dominated by Lactobacillus and Leuconostoc, whereas Lactoccous prevailed in curd and cheese produced with commercial animal rennet followed by Lactobacillus. Differences in the bacterial composition between the two cheeses at the end of their maturation period were confirmed by PCR-DGGE analysis. Copyright © 2017 Elsevier B
Energy Technology Data Exchange (ETDEWEB)
White, J.; Gilbert, J. A.; Hill, G.; Hill, E.; Huse, S. M.; Weightman, A. J.; Mahenthiralingam, E. (CLS-CI); (Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University); (ECHA Microbiology Ltd.); (Josephine Bay Paul Centre for Comparative Molecular Biology and Evolution)
2011-07-01
Bacterial diversity in contaminated fuels has not been systematically investigated using cultivation-independent methods. The fuel industry relies on phenotypic cultivation-based contaminant identification, which may lack accuracy and neglect difficult-to-culture taxa. By the use of industry practice aerobic cultivation, 16S rRNA gene sequencing, and strain genotyping, a collection of 152 unique contaminant isolates from 54 fuel samples was assembled, and a dominance of Pseudomonas (21%), Burkholderia (7%), and Bacillus (7%) was demonstrated. Denaturing gradient gel electrophoresis (DGGE) of 15 samples revealed Proteobacteria and Firmicutes to be the most abundant phyla. When 16S rRNA V6 gene pyrosequencing of four selected fuel samples (indicated by 'JW') was performed, Betaproteobacteria (42.8%) and Gammaproteobacteria (30.6%) formed the largest proportion of reads; the most abundant genera were Marinobacter (15.4%; JW57), Achromobacter (41.6%; JW63), Burkholderia (80.7%; JW76), and Halomonas (66.2%; JW78), all of which were also observed by DGGE. However, the Clostridia (38.5%) and Deltaproteobacteria (11.1%) identified by pyrosequencing in sample JW57 were not observed by DGGE or aerobic culture. Genotyping revealed three instances where identical strains were found: (i) a Pseudomonas sp. strain recovered from 2 different diesel fuel tanks at a single industrial site; (ii) a Mangroveibacter sp. strain isolated from 3 biodiesel tanks at a single refinery site; and (iii) a Burkholderia vietnamiensis strain present in two unrelated automotive diesel samples. Overall, aerobic cultivation of fuel contaminants recovered isolates broadly representative of the phyla and classes present but lacked accuracy by overrepresenting members of certain groups such as Pseudomonas.
Combined eye-atmosphere visibility model
Kaufman, Y. J.
1981-01-01
Existing models of the optical characteristics of the eye are combined with a recent model of optical characteristics of the atmosphere given by its modulation transfer function. This combination results in the combined eye-atmosphere performance given by the product of their modulation transfer functions. An application for the calculation of visibility thresholds in the case of a two-halves field is given.
Trendwatch combining expert opinion
Hendrix, E.M.T.; Kornelis, M.; Pegge, S.M.; Galen, van M.A.
2006-01-01
In this study, focus is on a systematic way to detect future changes in trends that may effect the dynamics in the agro-food sector, and on the combination of opinions of experts. For the combination of expert opinions, the usefulness of multilevel models is investigated. Bayesian data analysis is
Modified Aggressive Packet Combining Scheme
International Nuclear Information System (INIS)
Bhunia, C.T.
2010-06-01
In this letter, a few schemes are presented to improve the performance of aggressive packet combining scheme (APC). To combat error in computer/data communication networks, ARQ (Automatic Repeat Request) techniques are used. Several modifications to improve the performance of ARQ are suggested by recent research and are found in literature. The important modifications are majority packet combining scheme (MjPC proposed by Wicker), packet combining scheme (PC proposed by Chakraborty), modified packet combining scheme (MPC proposed by Bhunia), and packet reversed packet combining (PRPC proposed by Bhunia) scheme. These modifications are appropriate for improving throughput of conventional ARQ protocols. Leung proposed an idea of APC for error control in wireless networks with the basic objective of error control in uplink wireless data network. We suggest a few modifications of APC to improve its performance in terms of higher throughput, lower delay and higher error correction capability. (author)
Directory of Open Access Journals (Sweden)
Vladimir G. Panov
2015-01-01
Full Text Available In this article, we check and develop further some postulates of the theory and mathematical modeling of combined toxic effect that we proposed earlier [1]. To this end, we have analyzed the results of an experiment on rats exposed during 6 weeks to repeated intraperitoneal injections of lead acetate, sodium fluoride or both. The development of intoxication was estimated quantitatively with 54 functional, biochemical and morphometric indices. For mathematical description of the effect that lead and fluorine doses produced alone or in combination, we used a response surface regression model containing linear and cross terms (hyperbolic paraboloid. It is shown that the combination of lead and fluoride features the same 10 types of combined effect that we found previously for the lead and cadmium combination. Special attention is given to indices on which lead and fluorine produce an opposite effect.
Directory of Open Access Journals (Sweden)
Slović Živana
2017-01-01
Full Text Available Introduction: Combined homicide is a combination of two or more different modes of killing. These homicides occur when multiple perpetrators have different mode of killing, to hide the true manner of death, or when an initially unsuccessful attack with one weapon is abandoned and changed by another mode which is more successful, or due to availability of weapons at the scene of homicide, or unexpected appearance of possible eyewitness, or else. Case report: This case report is about 65-year old woman who was found in her residence on the floor next to the bed lying on her back with two kitchen knives in her neck. Autopsy revealed an abrasion on the frontal part of the neck and a bruise of the soft tissues of the neck with a double fracture of both greater horns of the hyoid bone and a fracture of both superior horns of the thyroid cartilage. The cause of death was exsanguination into right half of the thoracic cavity from the left subclavian artery which was cut, on the spot of stab wound in the neck. Conclusion: Hemorrhage in the soft tissue near broken hyoid bone and thyroid cartilage indicate that the victim was first strangulated and then stabbed with kitchen knives. Combined homicides are caused by one or more killers in order to accelerate the killing, or to be sure to provide the fatal outcome. This case is also interesting because the killer left weapon in the victim's neck.
African Journals Online (AJOL)
rbr
of the idiomatic expression as a whole" (Crystal 2003: 225-226). Idiomatic .... nations and idioms.11 Nonetheless, free combinations of words have not been .... those who thronged Emmett place last night wanted to see the film, and they.
Belladonna Alkaloid Combinations and Phenobarbital
Donnatal® Elixir (as a combination product containing Atropine, Hyoscyamine, Phenobarbital, Scopolamine) ... PB Hyos® Elixir (as a combination product containing Atropine, Hyoscyamine, Phenobarbital, Scopolamine)
OT-Combiners Via Secure Computation
DEFF Research Database (Denmark)
Harnik, Danny; Ishai, Yuval; Kushilevitz, Eyal
2008-01-01
of faulty candidates (t = Ω(n)). Previous OT-combiners required either ω(n) or poly(k) calls to the n candidates, where k is a security parameter, and produced only a single secure OT. We demonstrate the usefulness of the latter result by presenting several applications that are of independent interest......An OT-combiner implements a secure oblivious transfer (OT) protocol using oracle access to n OT-candidates of which at most t may be faulty. We introduce a new general approach for combining OTs by making a simple and modular use of protocols for secure computation. Specifically, we obtain an OT......, strengthen the security, and improve the efficiency of previous OT-combiners. In particular, we obtain the first constant-rate OT-combiners in which the number of secure OTs being produced is a constant fraction of the total number of calls to the OT-candidates, while still tolerating a constant fraction...
Czech Academy of Sciences Publication Activity Database
Valášková, Vendula; Baldrian, Petr
2009-01-01
Roč. 55, č. 10 (2009), s. 413-423 ISSN 1214-1178 R&D Projects: GA ČR GA526/08/0751; GA MŠk LC06066 Institutional research plan: CEZ:AV0Z50200510 Keywords : DGGE * bacteria * fungi Subject RIV: EE - Microbiology, Virology Impact factor: 0.697, year: 2009
16S rRNA gene sequence and phylogenetic tree of lactobacillus ...
African Journals Online (AJOL)
... processed by denaturing gradient gel electrophoresis (DGGE). Phylogenetic tree was constructed with the sequences of the V2-V3 region of 16S rRNA gene. Results show two distinct divisions among the Lactobacillus species. The study presents a new understanding of the nature of the Lactobacillus vaginal microbiota ...
Molecular method to assess the diversity of Burkholderia species in environmental samples
Salles, J.; Souza, de F.A.; Elsas, van J.D.
2002-01-01
In spite of the importance of many members of the genus Burkholderia in the soil microbial community, no direct method to assess the diversity of this genus has been developed so far. The aim of this work was the development of soil DNA-based PCR-denaturing gradient gel electrophoresis (DGGE), a
Molecular method to assess the diversity of Burkholderia species in environmental samples
Salles, Joanna; De Souza, F.A.; Van Elsas, J.D.
2002-01-01
In spite of the importance of many members of the genus Burkholderia in the soil microbial community, no direct method to assess the diversity of this genus has been developed so far. The aim of this work was the development of soil DNA-based PCR-denaturing gradient get electrophoresis (DGGE), a
Atypical combinations and scientific impact.
Uzzi, Brian; Mukherjee, Satyam; Stringer, Michael; Jones, Ben
2013-10-25
Novelty is an essential feature of creative ideas, yet the building blocks of new ideas are often embodied in existing knowledge. From this perspective, balancing atypical knowledge with conventional knowledge may be critical to the link between innovativeness and impact. Our analysis of 17.9 million papers spanning all scientific fields suggests that science follows a nearly universal pattern: The highest-impact science is primarily grounded in exceptionally conventional combinations of prior work yet simultaneously features an intrusion of unusual combinations. Papers of this type were twice as likely to be highly cited works. Novel combinations of prior work are rare, yet teams are 37.7% more likely than solo authors to insert novel combinations into familiar knowledge domains.
The comparative evaluation of film-screen combinations
International Nuclear Information System (INIS)
Choi, Gyung Ja; Choi, Syng Kyu
1988-01-01
This study was to compare the quality of image by different screen and film combinations. Using the sensitometer measured the speed and average gradient of blue sensitive films and orthochromatic films. The films was combined with rare earth screen LR, Lm, LF and conventional screen OM, OH, XOR, OKa and exposed the stepwedge to impulse 2, 3, 4, 6, 10, 15, 24, 38, 60 and measured the density. The following results were obtained: 1. The density of film and film-screen combinations showed significant difference, then in film-screen combinations was significantly different by the screens than films. 2. The speed of blue sensitive films was little different, the TMG of orthochromatic films producted high speed, and the AX films was high average gradient. 3. The relative speed of film-screen combinations showed significant difference, and was high in the OKa of the conventional screens and in the LR of the rare earth screens, especially that of LR screen in the combination with blue sensitive films was high. 4. The average gradient of film-screen combinations showed no significant difference, and was high in the OKa screen and LR/OG combination, and that of OKa/AX combination was highest. 5. The latitude of film-screen combinations showed significant difference by screens, and was high in the LM screen in combination with blue sensitive films and in the OM screen in combination with orthochromatic films. 6. The subject contrast of film-screen combinations showed significant difference by screen, and was high in the LR screen in combination with blue sensitive AX film and orthochromatic TMG film.
Wang, Ting; Sun, Hongwen; Ren, Xinhao; Li, Bing; Mao, Hongjun
2017-09-21
Two kinds of biochars, one derived from corn straw and one from pig manure, were studied as carriers of a mutant genotype from Bacillus subtilis (B38) for heavy metal contaminated soil remediation. After amendment with biochar, the heavy metal bioavailability decreased. Moreover, the heavy metal immobilization ability of the biochar was enhanced by combining it with B38. The simultaneous application of B38 and pig manure-derived biochar exhibited a superior effect on the promotion of plant growth and the immobilization of heavy metals in soil. The plant biomass increased by 37.9% and heavy metal concentrations in the edible part of lettuce decreased by 69.9-96.1%. The polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) profiles revealed that pig manure-derived biochar could enhance the proliferation of both exotic B38 and native microbes. These results suggest that B38 carried by pig manure-derived biochar may be a promising candidate for the remediation of soils contaminated by multiple heavy metals.
Russian Kefir Grains Microbial Composition and Its Changes during Production Process.
Kotova, I B; Cherdyntseva, T A; Netrusov, A I
2016-01-01
By combining DGGE-PCR method, classical microbiological analysis and light- and electron microscopic observations, it was found that the composition of microbial communities of central Russia regions kefir grains, starter and kefir drink include bacteria of the genera Lactobacillus, Leuconostoc and Lactococcus, and yeast anamorphs of the genera Saccharomyces, Kazachstania and Gibellulopsis. Fifteen prokaryotic and four eukaryotic pure cultures of microorganisms were isolated and identified from kefir grains. It has been shown that members of the genus Lactobacillus prevailed in kefir grains, whereas strains Leuconostoc pseudomesenteroides and Lactococcus lactis dominated in the final product - kefir drink. Yeasts contained in kefir grains in small amounts have reached a significant number of cells in the process of development of this dairy product. The possibility of reverse cell aggregation has been attempted in a mixed cultivation of all isolated pure cultures, but full formation kefir grains is not yet observed after 1.5 years of observation and reinoculations.
Aditiawati, Pingkan; Yohandini, Heni; Madayanti, Fida; Akhmaloka
2009-01-01
Microbial communities in an acidic hot spring, namely Kawah Hujan B, at Kamojang geothermal field, West Java-Indonesia was examined using culture dependent and culture independent strategies. Chemical analysis of the hot spring water showed a characteristic of acidic-sulfate geothermal activity that contained high sulfate concentrations and low pH values (pH 1.8 to 1.9). Microbial community present in the spring was characterized by 16S rRNA gene combined with denaturing gradient gel electrophoresis (DGGE) analysis. The majority of the sequences recovered from culture-independent method were closely related to Crenarchaeota and Proteobacteria phyla. However, detail comparison among the member of Crenarchaeota showing some sequences variation compared to that the published data especially on the hypervariable and variable regions. In addition, the sequences did not belong to certain genus. Meanwhile, the 16S Rdna sequences from culture-dependent samples revealed mostly close to Firmicute and gamma Proteobacteria.
DEFF Research Database (Denmark)
Offersen, Birgitte Vrou; Alsner, Jan; Olsen, Karen Ege
2008-01-01
: Tumour sections were stained for HER2, CD34, and MIB-1. HER2 scores were based on staining intensity, 3+ being considered HER2+. Angiogenesis was scored by the Chalkley method. MIB-1 was evaluated using systematic random sampling. PAI-1 was measured by ELISA. TP53 mutations were evaluated by DGGE...
DEFF Research Database (Denmark)
De Abreu, Angela Alexandra Valente; Karakashev, Dimitar Borisov; Angelidaki, Irini
2012-01-01
.0 LH2 L-1 d-1 and hydrogen yield of 1.10 and 0.75 molH2 mol-1substrate for Rarab and Rgluc, respectively). Lower hydrogen production in Rgluc was associated with higher lactate production. DGGE results revealed no significant difference on the bacterial community composition between operational periods...
A molecular analysis of fecal and mucosal bacterial communities in irritable bowel syndrome.
LENUS (Irish Health Repository)
Codling, Caroline
2010-02-01
The objectives of this study were, firstly, to determine the diversity of the host\\'s gut microbiota in irritable bowel syndrome (IBS) using a culture-independent method (DGGE of the 16S rRNA gene) and, secondly, to examine mucosal biopsies of IBS patients and compare them to their own fecal microbiota.
McIntyre, R. E.; Grierson, P. F.; Adams, M. A.
2005-05-01
Riparian systems are hotspots in dryland landscapes for nutrient supply and transformation. Biogeochemical fluxes in riparian systems are closely coupled to hydrological flowpaths, which, in dryland regions, are characterised by catastrophic flooding and long periods of erratic or no flow. Re-wetting of soils stimulates soil microbial processes that drive mineralization of nutrients necessary for plant growth. We present here the first data of a 3-year research project investigating biogeochemical processes in riparian systems in the semi-arid Pilbara region of Western Australia. Spatial patterns of nitrogen, phosphorus and carbon were closely related to topographic zone (across floodplain and channels) and vegetation type. NO3- and PCi concentrations were four-fold higher in channel, bank and riparian soils than in soils of floodplain and riparian-floodplain transition zones. Nitrogen distribution was highly heterogeneous in riparian soils (NO3- CV=102%, NH4+ CV=84%) while phosphorus was particularly heterogeneous in floodplain soils (PCi CV=153%, PCo CV=266%), in comparison to other zones. Phospholipid fatty acid (PLFA) and enzymatic profiles will be used to assess microbial functional groups, combined with mineralisation experiments and stable isotope studies (15N and 13C). These data will improve understanding of biogeochemical cycling in dryland riparian systems, and contribute to improved regional management of water resources.
Jiao, Haihua; Luo, Jinxue; Zhang, Yiming; Xu, Shengjun; Bai, Zhihui; Huang, Zhanbin
2015-09-01
Bio-augmentation is a promising technique for remediation of polluted soils. This study aimed to evaluate the bio-augmentation effect of Rhodobacter sphaeroides biofertilizer (RBF) on the bioremediation of total petroleum hydrocarbons (TPH) contaminated soil. A greenhouse pot experiment was conducted over a period of 120 days, three methods for enhancing bio-augmentation were tested on TPH contaminated soils, including single addition RBF, planting, and combining of RBF and three crop species, such as wheat (W), cabbage (C) and spinach (S), respectively. The results demonstrated that the best removal of TPH from contaminated soil in the RBF bio-augmentation rhizosphere soils was found to be 46.2%, 65.4%, 67.5% for W+RBF, C+RBF, S+RBF rhizosphere soils respectively. RBF supply impacted on the microbial community diversity (phospholipid fatty acids, PLFA) and the activity of soil enzymes, such as dehydrogenase (DH), alkaline phosphatase (AP) and urease (UR). There were significant difference among the soil only containing crude oil (CK), W, C and S rhizosphere soils and RBF bio-augmentation soils. Moreover, the changes were significantly distinct depended on crops species. It was concluded that the RBF is a valuable material for improving effect of remediation of TPH polluted soils.
Transfer function combinations
Zhou, Liang; Schott, Mathias; Hansen, Charles
2012-01-01
Direct volume rendering has been an active area of research for over two decades. Transfer function design remains a difficult task since current methods, such as traditional 1D and 2D transfer functions, are not always effective for all data sets. Various 1D or 2D transfer function spaces have been proposed to improve classification exploiting different aspects, such as using the gradient magnitude for boundary location and statistical, occlusion, or size metrics. In this paper, we present a novel transfer function method which can provide more specificity for data classification by combining different transfer function spaces. In this work, a 2D transfer function can be combined with 1D transfer functions which improve the classification. Specifically, we use the traditional 2D scalar/gradient magnitude, 2D statistical, and 2D occlusion spectrum transfer functions and combine these with occlusion and/or size-based transfer functions to provide better specificity. We demonstrate the usefulness of the new method by comparing to the following previous techniques: 2D gradient magnitude, 2D occlusion spectrum, 2D statistical transfer functions and 2D size based transfer functions. © 2012 Elsevier Ltd.
Transfer function combinations
Zhou, Liang
2012-10-01
Direct volume rendering has been an active area of research for over two decades. Transfer function design remains a difficult task since current methods, such as traditional 1D and 2D transfer functions, are not always effective for all data sets. Various 1D or 2D transfer function spaces have been proposed to improve classification exploiting different aspects, such as using the gradient magnitude for boundary location and statistical, occlusion, or size metrics. In this paper, we present a novel transfer function method which can provide more specificity for data classification by combining different transfer function spaces. In this work, a 2D transfer function can be combined with 1D transfer functions which improve the classification. Specifically, we use the traditional 2D scalar/gradient magnitude, 2D statistical, and 2D occlusion spectrum transfer functions and combine these with occlusion and/or size-based transfer functions to provide better specificity. We demonstrate the usefulness of the new method by comparing to the following previous techniques: 2D gradient magnitude, 2D occlusion spectrum, 2D statistical transfer functions and 2D size based transfer functions. © 2012 Elsevier Ltd.
Energy Technology Data Exchange (ETDEWEB)
Wlachovsky, I; Bartos, J
1980-02-15
A design is presented for a coal combine, equipped with two drum operational units, on whose both ends of the upper surface of the body, two coal saws are mounted with the help of a lever system. These saws, found in an operational position, form a gap in the block of the coal block, which is not embraced by the drum operational unit. The coal block, found between the gap and the support, falls down onto the longwall scraper conveyor. The lever system of each coal saw is controlled by two hydraulic jacks. One of the jacks is mounted vertically on the facial wall of the body of the combine and is used for the hoisting for the required height of the horizontal arm of the lever, reinforced by one end in the hinge on the body of the combine. On the ''free'' end of that lever, a coal saw is mounted in a hinge-like fashion and which is connected by the hydraulic jack to the horizontal arm of the lever system. This hydraulic jack is used for the clamping of the coal saw to the face.
Spectral coherent combination of ultrashort pulses
International Nuclear Information System (INIS)
Ursescu, D.; Banici, R.; Ionel, L.; Rusen, L.; Sandel, S.; Blanaru, C.
2010-01-01
Complete text of publication follows. The coherent beam combination was chosen in several laser systems, including ELI, as a solution to increase the final attainable intensity. However, the coherent beam combination it is also a difficult technique while it has to combine coherently in space and in time several beams amplified in different laser chains. That means in particular that the beams should be in phase in every point of the amplified beam so the spatial beam profiling techniques have to be mastered with high accuracy for all the combined beams. Here it is proposed an alternative coherent beam combination than the use of identical ultrashort pulses. The idea is to spectrally combine laser pulses with complementary spectra. Collinear and non-collinear approaches have been modelled. Ongoing experimental development, including the demonstration of the rephasing for two spectrally complementary ultrashort pulses will be presented. Acknowledgements. The research leading to these results has received funding from the EC's Seventh Framework Programme (LASERLAB-EUROPE, grant agreement no. 228334).
International Nuclear Information System (INIS)
Manente, Giovanni
2016-01-01
Highlights: • Off-design model of a 390 MW_e three pressure combined cycle developed and validated. • The off-design model is used to evaluate different hybridization schemes with solar. • Power boosting and fuel saving with different design modifications are considered. • Maximum solar share of total electricity is only 1% with the existing equipment. • The maximum incremental solar radiation-to-electrical efficiency approaches 29%. - Abstract: The integration of solar energy into natural gas combined cycles has been successfully demonstrated in several integrated solar combined cycles since the beginning of this decade in many countries. There are many motivations that drive investments on integrated solar combined cycles which are primarily the repowering of existing power plants, the compliance with more severe environmental laws on emissions and the mitigation of risks associated with large solar projects. Integrated solar combined cycles are usually developed as brownfield facilities by retrofitting existing natural gas combined cycles and keeping the existing equipment to minimize costs. In this work a detailed off-design model of a 390 MW_e three pressure level natural gas combined cycle is built to evaluate different integration schemes of solar energy which either keep the equipment of the combined cycle unchanged or include new equipment (steam turbine, heat recovery steam generator). Both power boosting and fuel saving operation strategies are analyzed in the search for the highest annual efficiency and solar share. Results show that the maximum incremental power output from solar at design solar irradiance is limited to 19 MW_e without modifications to the existing equipment. Higher values are attainable only including a larger steam turbine. High solar radiation-to-electrical efficiencies in the range 24–29% can be achieved in the integrated solar combined cycle depending on solar share and extension of tube banks in the heat recovery
Mode Combinations and International Operations
DEFF Research Database (Denmark)
Benito, Gabriel R. G.; Petersen, Bent; Welch, Lawrence S.
2011-01-01
reveals that companies tend to combine modes of operation; thereby producing unique foreign operation mode “packages” for given activities and/or countries, and that the packages are liable to be modified over time – providing a potentially important optional path for international expansion. Our data...... key markets (China, UK and USA) as the basis for an exploration of the extent to which, and how and why, companies combine clearly different foreign operation modes. We examine their use of foreign operation mode combinations within given value activities as well as within given countries. The study...
Meyer, Joana Beatrice; Song-Wilson, Yi; Foetzki, Andrea; Luginbühl, Carolin; Winzeler, Michael; Kneubühler, Yvan; Matasci, Caterina; Mascher-Frutschi, Fabio; Kalinina, Olena; Boller, Thomas; Keel, Christoph; Maurhofer, Monika
2013-01-01
This study aimed to evaluate the impact of genetically modified (GM) wheat with introduced pm3b mildew resistance transgene, on two types of root-colonizing microorganisms, namely pseudomonads and arbuscular mycorrhizal fungi (AMF). Our investigations were carried out in field trials over three field seasons and at two locations. Serial dilution in selective King's B medium and microscopy were used to assess the abundance of cultivable pseudomonads and AMF, respectively. We developed a denaturing gradient gel electrophoresis (DGGE) method to characterize the diversity of the pqqC gene, which is involved in Pseudomonas phosphate solubilization. A major result was that in the first field season Pseudomonas abundances and diversity on roots of GM pm3b lines, but also on non-GM sister lines were different from those of the parental lines and conventional wheat cultivars. This indicates a strong effect of the procedures by which these plants were created, as GM and sister lines were generated via tissue cultures and propagated in the greenhouse. Moreover, Pseudomonas population sizes and DGGE profiles varied considerably between individual GM lines with different genomic locations of the pm3b transgene. At individual time points, differences in Pseudomonas and AMF accumulation between GM and control lines were detected, but they were not consistent and much less pronounced than differences detected between young and old plants, different conventional wheat cultivars or at different locations and field seasons. Thus, we conclude that impacts of GM wheat on plant-beneficial root-colonizing microorganisms are minor and not of ecological importance. The cultivation-independent pqqC-DGGE approach proved to be a useful tool for monitoring the dynamics of Pseudomonas populations in a wheat field and even sensitive enough for detecting population responses to altered plant physiology.
Are we biologically safe with snow precipitation? A case study in beijing.
Directory of Open Access Journals (Sweden)
Fangxia Shen
Full Text Available In this study, the bacterial and fungal abundances, diversities, conductance levels as well as total organic carbon (TOC were investigated in the snow samples collected from five different snow occurrences in Beijing between January and March, 2010. The collected snow samples were melted and cultured at three different temperatures (4, 26 and 37°C. The culturable bacterial concentrations were manually counted and the resulting colony forming units (CFUs at 26°C were further studied using V3 region of 16 S rRNA gene-targeted polymerase chain reaction -denaturing gradient gel electrophoresis (PCR-DGGE. The clone library was constructed after the liquid culturing of snow samples at 26°C. And microscopic method was employed to investigate the fungal diversity in the samples. In addition, outdoor air samples were also collected using mixed cellulose ester (MCE filters and compared with snow samples with respect to described characteristics. The results revealed that snow samples had bacterial concentrations as much as 16000 CFU/ml for those cultured at 26°C, and the conductance levels ranged from 5.6×10(-6 to 2.4×10(-5 S. PCR-DGGE, sequencing and microscopic analysis revealed remarkable bacterial and fungal diversity differences between the snow samples and the outdoor air samples. In addition, DGGE banding profiles for the snow samples collected were also shown distinctly different from one another. Absent from the outdoor air, certain human, plant, and insect fungal pathogens were found in the snow samples. By calculation, culturable bacteria accounted for an average of 3.38% (±1.96% of TOC for the snow samples, and 0.01% for that of outdoor air samples. The results here suggest that snow precipitations are important sources of fungal pathogens and ice nucleators, thus could affect local climate, human health and agriculture security.
Effect of rice beer on gut bacteria
Directory of Open Access Journals (Sweden)
Bhuwan Bhaskar
2017-10-01
Full Text Available The human gut is colonized by trillions of bacteria, called microbiota influences human health and is effected by several host factors. The studies in humans and model organisms have clearly demonstrated that out of several important factors, diet has the most dominant role in regulation of the gut microbiota. Additionally, with an increase in the knowledge on the microbiota, the connections between microbial actions on dietary consumption are being revealed. Consumption of fermented beverages holds a long tradition and accounts for approximately one-third of the human diet globally. In various societies, fermentation has not only been well established as a process for food preservation, human nutrition, traditional medicine and culture but also for the improving the sensorial characteristics, such as texture, flavor and aroma and most importantly for the magnification of the nutritional values. Consumption of rice beer is an essential part of the socio-cultural life of several tribes of North-East India. It is believed to be effective against several ailments such as ameboisis, acidity, vomiting and has health modulating effects including cholesterol reduction and endocrine function. Effect of rice beer was tested on mice model. 17 healthy Swiss albino mice were taken for the study and divided into two groups: control and treated. Rice beer was fed to the treated group once daily and fecal samples were collected. Metagenomic DNA from stool samples was extracted and V6 - V8 region of the 16S rDNA gene was amplified, followed by Denaturing Gradient Gel Electrophoresis (DGGE.The DGGE gel was scored using GelCompar II software. Gas Chromatography Mass Spectrometry (GCMS analysis of stool samples was also carried out. Multidimensional scaling (MDS plot of the DGGE profiles showed distinct clustering of control and treated groups, indicating the effect of rice beer consumption on gut microbes.
Babin, Doreen; Vogel, Cordula; Zühlke, Sebastian; Schloter, Michael; Pronk, Geertje Johanna; Heister, Katja; Spiteller, Michael; Kögel-Knabner, Ingrid; Smalla, Kornelia
2014-01-01
The fate of polycyclic aromatic hydrocarbons (PAHs) in soil is determined by a suite of biotic and abiotic factors, and disentangling their role in the complex soil interaction network remains challenging. Here, we investigate the influence of soil composition on the microbial community structure and its response to the spiked model PAH compound phenanthrene and plant litter. We used long-term matured artificial soils differing in type of clay mineral (illite, montmorillonite) and presence of charcoal or ferrihydrite. The soils received an identical soil microbial fraction and were incubated for more than two years with two sterile manure additions. The matured artificial soils and a natural soil were subjected to the following spiking treatments: (I) phenanthrene, (II) litter, (III) litter + phenanthrene, (IV) unspiked control. Total community DNA was extracted from soil sampled on the day of spiking, 7, 21, and 63 days after spiking. Bacterial 16S rRNA gene and fungal internal transcribed spacer amplicons were quantified by qPCR and subjected to denaturing gradient gel electrophoresis (DGGE). DGGE analysis revealed that the bacterial community composition, which was strongly shaped by clay minerals after more than two years of incubation, changed in response to spiked phenanthrene and added litter. DGGE and qPCR showed that soil composition significantly influenced the microbial response to spiking. While fungal communities responded only in presence of litter to phenanthrene spiking, the response of the bacterial communities to phenanthrene was less pronounced when litter was present. Interestingly, microbial communities in all artificial soils were more strongly affected by spiking than in the natural soil, which might indicate the importance of higher microbial diversity to compensate perturbations. This study showed the influence of soil composition on the microbiota and their response to phenanthrene and litter, which may increase our understanding of
Directory of Open Access Journals (Sweden)
Joana Beatrice Meyer
Full Text Available This study aimed to evaluate the impact of genetically modified (GM wheat with introduced pm3b mildew resistance transgene, on two types of root-colonizing microorganisms, namely pseudomonads and arbuscular mycorrhizal fungi (AMF. Our investigations were carried out in field trials over three field seasons and at two locations. Serial dilution in selective King's B medium and microscopy were used to assess the abundance of cultivable pseudomonads and AMF, respectively. We developed a denaturing gradient gel electrophoresis (DGGE method to characterize the diversity of the pqqC gene, which is involved in Pseudomonas phosphate solubilization. A major result was that in the first field season Pseudomonas abundances and diversity on roots of GM pm3b lines, but also on non-GM sister lines were different from those of the parental lines and conventional wheat cultivars. This indicates a strong effect of the procedures by which these plants were created, as GM and sister lines were generated via tissue cultures and propagated in the greenhouse. Moreover, Pseudomonas population sizes and DGGE profiles varied considerably between individual GM lines with different genomic locations of the pm3b transgene. At individual time points, differences in Pseudomonas and AMF accumulation between GM and control lines were detected, but they were not consistent and much less pronounced than differences detected between young and old plants, different conventional wheat cultivars or at different locations and field seasons. Thus, we conclude that impacts of GM wheat on plant-beneficial root-colonizing microorganisms are minor and not of ecological importance. The cultivation-independent pqqC-DGGE approach proved to be a useful tool for monitoring the dynamics of Pseudomonas populations in a wheat field and even sensitive enough for detecting population responses to altered plant physiology.
Tapia-Paniagua, S T; Vidal, S; Lobo, C; García de la Banda, I; Esteban, M A; Balebona, M C; Moriñigo, M A
2015-10-01
Few antimicrobials are currently authorised in the aquaculture industry to treat infectious diseases. Among them, oxytetracycline (OTC) is one of the first-choice drugs for nearly all bacterial diseases. The objective of this study was to evaluate the effect of the dietary administration of OTC both alone and jointly with the probiotic Shewanella putrefaciens Pdp11 (SpPdp11) on the intestinal microbiota and hepatic expression of genes related to immunity in Senegalese sole (Solea senegalensis) juveniles. The results demonstrated that the richness and diversity of the intestinal microbiota of fish treated with OTC decreased compared with those of the control group but that these effects were lessened by the simultaneous administration of SpPdp11. In addition, specimens that received OTC and SpPdp11 jointly showed a decreased intensity of the Denaturing Gradient Gel Electrophoresis (DGGE) bands related to Vibrio genus and the presence of DGGE bands related to Lactobacillus and Shewanella genera. The relationship among the intestinal microbiota of fish fed with control and OTC diets and the expression of the NADPH oxidase and CASPASE-6 genes was demonstrated by a Principal Components Analysis (PCA) carried out in this study. In contrast, a close relationship between the transcription of genes, such as NKEF, IGF-β, HSP70 and GP96, and the DGGE bands of fish treated jointly with OTC and SpPdp11 was observed in the PCA study. In summary, the results obtained in this study demonstrate that the administration of OTC results in the up-regulation of genes related to apoptosis but that the joint administration of OTC and S. putrefaciens Pdp11 increases the transcription of genes related to antiapoptotic effects and oxidative stress regulation. Further, a clear relationship between these changes and those detected in the intestinal microbiota is established. Copyright © 2015 Elsevier Ltd. All rights reserved.
Yang, Zhenping; Yang, Wenping; Li, Shengcai; Hao, Jiaomin; Su, Zhifeng; Sun, Min; Gao, Zhiqiang; Zhang, Chunlai
2016-01-01
As the major crops in north China, spring crops are usually planted from April through May every spring and harvested in fall. Wheat is also a very common crop traditionally planted in fall or spring and harvested in summer year by year. This continuous cropping system exhibited the disadvantages of reducing the fertility of soil through decreasing microbial diversity. Thus, management of microbial diversity in the rhizosphere plays a vital role in sustainable crop production. In this study, ten common spring crops in north China were chosen sole-cropped and four were chosen intercropped with peanut in wheat fields after harvest. Denaturing gradient gel electrophoresis (DGGE) and DNA sequencing of one 16S rDNA fragment were used to analyze the bacterial diversity and species identification. DGGE profiles showed the bacterial community diversity in rhizosphere soil samples varied among various crops under different cropping systems, more diverse under intercropping system than under sole-cropping. Some intercropping-specific bands in DGGE profiles suggested that several bacterial species were stimulated by intercropping systems specifically. Furthermore, the identification of these dominant and functional bacteria by DNA sequencing indicated that intercropping systems are more beneficial to improve soil fertility. Compared to intercropping systems, we also observed changes in microbial community of rhizosphere soil under sole-crops. The rhizosphere bacterial community structure in spring crops showed a strong crop species-specific pattern. More importantly, Empedobacter brevis, a typical plant pathogen, was only found in the carrot rhizosphere, suggesting carrot should be sown prudently. In conclusion, our study demonstrated that crop species and cropping systems had significant effects on bacterial community diversity in the rhizosphere soils. We strongly suggest sorghum, glutinous millet and buckwheat could be taken into account as intercropping crops with peanut
Chikere, Chioma B; Surridge, Karen; Okpokwasili, Gideon C; Cloete, Thomas E
2012-03-01
Bacterial population dynamics were examined during bioremediation of an African soil contaminated with Arabian light crude oil and nutrient enrichment (biostimulation). Polymerase chain reaction followed by denaturing gradient gel electrophoresis (DGGE) were used to generate bacterial community fingerprints of the different treatments employing the 16S ribosomal ribonucleic acid (rRNA) gene as molecular marker. The DGGE patterns of the nutrient-amended soils indicated the presence of distinguishable bands corresponding to the oil-contaminated-nutrient-enriched soils, which were not present in the oil-contaminated and pristine control soils. Further characterization of the dominant DGGE bands after excision, reamplification and sequencing revealed that Corynebacterium spp., Dietzia spp., Rhodococcus erythropolis sp., Nocardioides sp., Low G+C (guanine plus cytosine) Gram positive bacterial clones and several uncultured bacterial clones were the dominant bacterial groups after biostimulation. Prominent Corynebacterium sp. IC10 sequence was detected across all nutrient-amended soils but not in oil-contaminated control soil. Total heterotrophic and hydrocarbon utilizing bacterial counts increased significantly in the nutrient-amended soils 2 weeks post contamination whereas oil-contaminated and pristine control soils remained fairly stable throughout the experimental period. Gas chromatographic analysis of residual hydrocarbons in biostimulated soils showed marked attenuation of contaminants starting from the second to the sixth week after contamination whereas no significant reduction in hydrocarbon peaks were seen in the oil-contaminated control soil throughout the 6-week experimental period. Results obtained indicated that nutrient amendment of oil-contaminated soil selected and enriched the bacterial communities mainly of the Actinobacteria phylogenetic group capable of surviving in toxic contamination with concomitant biodegradation of the hydrocarbons. The
el Fantroussi, S; Verschuere, L; Verstraete, W; Top, E M
1999-03-01
The effect of three phenyl urea herbicides (diuron, linuron, and chlorotoluron) on soil microbial communities was studied by using soil samples with a 10-year history of treatment. Denaturing gradient gel electrophoresis (DGGE) was used for the analysis of 16S rRNA genes (16S rDNA). The degree of similarity between the 16S rDNA profiles of the communities was quantified by numerically analysing the DGGE band patterns. Similarity dendrograms showed that the microbial community structures of the herbicide-treated and nontreated soils were significantly different. Moreover, the bacterial diversity seemed to decrease in soils treated with urea herbicides, and sequence determination of several DGGE fragments showed that the most affected species in the soils treated with diuron and linuron belonged to an uncultivated bacterial group. As well as the 16S rDNA fingerprints, the substrate utilization patterns of the microbial communities were compared. Principal-component analysis performed on BIOLOG data showed that the functional abilities of the soil microbial communities were altered by the application of the herbicides. In addition, enrichment cultures of the different soils in medium with the urea herbicides as the sole carbon and nitrogen source showed that there was no difference between treated and nontreated soil in the rate of transformation of diuron and chlorotoluron but that there was a strong difference in the case of linuron. In the enrichment cultures with linuron-treated soil, linuron disappeared completely after 1 week whereas no significant transformation was observed in cultures inoculated with nontreated soil even after 4 weeks. In conclusion, this study showed that both the structure and metabolic potential of soil microbial communities were clearly affected by a long-term application of urea herbicides.
Scheirlinck, Ilse; Van der Meulen, Roel; Van Schoor, Ann; Vancanneyt, Marc; De Vuyst, Luc; Vandamme, Peter; Huys, Geert
2008-04-01
A total of 39 traditional sourdoughs were sampled at 11 bakeries located throughout Belgium which were visited twice with a 1-year interval. The taxonomic structure and stability of the bacterial communities occurring in these traditional sourdoughs were assessed using both culture-dependent and culture-independent methods. A total of 1,194 potential lactic acid bacterium (LAB) isolates were tentatively grouped and identified by repetitive element sequence-based PCR, followed by sequence-based identification using 16S rRNA and pheS genes from a selection of genotypically unique LAB isolates. In parallel, all samples were analyzed by denaturing gradient gel electrophoresis (DGGE) of V3-16S rRNA gene amplicons. In addition, extensive metabolite target analysis of more than 100 different compounds was performed. Both culturing and DGGE analysis showed that the species Lactobacillus sanfranciscensis, Lactobacillus paralimentarius, Lactobacillus plantarum, and Lactobacillus pontis dominated the LAB population of Belgian type I sourdoughs. In addition, DGGE band sequence analysis demonstrated the presence of Acetobacter sp. and a member of the Erwinia/Enterobacter/Pantoea group in some samples. Overall, the culture-dependent and culture-independent approaches each exhibited intrinsic limitations in assessing bacterial LAB diversity in Belgian sourdoughs. Irrespective of the LAB biodiversity, a large majority of the sugar and amino acid metabolites were detected in all sourdough samples. Principal component-based analysis of biodiversity and metabolic data revealed only little variation among the two samples of the sourdoughs produced at the same bakery. The rare cases of instability observed could generally be linked with variations in technological parameters or differences in detection capacity between culture-dependent and culture-independent approaches. Within a sampling interval of 1 year, this study reinforces previous observations that the bakery environment
Scheirlinck, Ilse; Van der Meulen, Roel; Van Schoor, Ann; Vancanneyt, Marc; De Vuyst, Luc; Vandamme, Peter; Huys, Geert
2008-01-01
A total of 39 traditional sourdoughs were sampled at 11 bakeries located throughout Belgium which were visited twice with a 1-year interval. The taxonomic structure and stability of the bacterial communities occurring in these traditional sourdoughs were assessed using both culture-dependent and culture-independent methods. A total of 1,194 potential lactic acid bacterium (LAB) isolates were tentatively grouped and identified by repetitive element sequence-based PCR, followed by sequence-based identification using 16S rRNA and pheS genes from a selection of genotypically unique LAB isolates. In parallel, all samples were analyzed by denaturing gradient gel electrophoresis (DGGE) of V3-16S rRNA gene amplicons. In addition, extensive metabolite target analysis of more than 100 different compounds was performed. Both culturing and DGGE analysis showed that the species Lactobacillus sanfranciscensis, Lactobacillus paralimentarius, Lactobacillus plantarum, and Lactobacillus pontis dominated the LAB population of Belgian type I sourdoughs. In addition, DGGE band sequence analysis demonstrated the presence of Acetobacter sp. and a member of the Erwinia/Enterobacter/Pantoea group in some samples. Overall, the culture-dependent and culture-independent approaches each exhibited intrinsic limitations in assessing bacterial LAB diversity in Belgian sourdoughs. Irrespective of the LAB biodiversity, a large majority of the sugar and amino acid metabolites were detected in all sourdough samples. Principal component-based analysis of biodiversity and metabolic data revealed only little variation among the two samples of the sourdoughs produced at the same bakery. The rare cases of instability observed could generally be linked with variations in technological parameters or differences in detection capacity between culture-dependent and culture-independent approaches. Within a sampling interval of 1 year, this study reinforces previous observations that the bakery environment
Are We Biologically Safe with Snow Precipitation? A Case Study in Beijing
Shen, Fangxia; Yao, Maosheng
2013-01-01
In this study, the bacterial and fungal abundances, diversities, conductance levels as well as total organic carbon (TOC) were investigated in the snow samples collected from five different snow occurrences in Beijing between January and March, 2010. The collected snow samples were melted and cultured at three different temperatures (4, 26 and 37°C). The culturable bacterial concentrations were manually counted and the resulting colony forming units (CFUs) at 26°C were further studied using V3 region of 16 S rRNA gene-targeted polymerase chain reaction -denaturing gradient gel electrophoresis (PCR-DGGE). The clone library was constructed after the liquid culturing of snow samples at 26°C. And microscopic method was employed to investigate the fungal diversity in the samples. In addition, outdoor air samples were also collected using mixed cellulose ester (MCE) filters and compared with snow samples with respect to described characteristics. The results revealed that snow samples had bacterial concentrations as much as 16000 CFU/ml for those cultured at 26°C, and the conductance levels ranged from 5.6×10−6 to 2.4×10−5 S. PCR-DGGE, sequencing and microscopic analysis revealed remarkable bacterial and fungal diversity differences between the snow samples and the outdoor air samples. In addition, DGGE banding profiles for the snow samples collected were also shown distinctly different from one another. Absent from the outdoor air, certain human, plant, and insect fungal pathogens were found in the snow samples. By calculation, culturable bacteria accounted for an average of 3.38% (±1.96%) of TOC for the snow samples, and 0.01% for that of outdoor air samples. The results here suggest that snow precipitations are important sources of fungal pathogens and ice nucleators, thus could affect local climate, human health and agriculture security. PMID:23762327
Energy Technology Data Exchange (ETDEWEB)
Vinas, M.; Sabate, J.; Solanas, A.M. [Barcelona Univ., Barcelona (Spain). Dept. of Microbiology; Guasp, C.; Lalucat, J. [Illes Balears Univ., Palma de Mallorca (Spain). Dept. of Biology
2005-11-15
Microbial consortia are used in the decontamination of polluted environmental sites. A microbial consortium obtained by batch enrichment culture is a closed system with controlled conditions in which micro-organisms with a potentially high growth rate are selected and become dominant. The aim of this study was to identify the members of consortium AM, in which earlier batch enrichment work had shown high biodegradation rates of the aromatic fraction of polycyclic aromatic hydrocarbon (PAH). The AM consortium was obtained by sequential enrichment in liquid culture with a PAH mixture of 3- and 4- ringed PAHs as the sole source of carbon and energy. The consortium was examined using a triple approach method based on various cultivation strategies, denaturing gradient electrophoresis (DGGE) and the screening of 16S and 18S rRNA gene clone libraries. Eleven different sequences by culture-dependent techniques and 7 by both DGGE and clone libraries were obtained, yielding 19 different microbial components. Proteobacteria were the dominant group, representing 83 per cent of the total, while the Cytophaga-Flexibactor-Bacteroides group (CFB) was 11 per cent, and Ascomycota fungi were 6 per cent. It was determined that {beta}-Proteobacteria were predominant in the DGGE and clone library methods, whereas they were a minority in culturable strains. The highest diversity and number of noncoincident sequences was achieved by the cultivation method that showed members of the {alpha},{beta}, and {gamma}-Proteobacteria, CFB bacterial group, and Ascomycota fungi. Only 6 of the 11 strains isolated showed PAH-degrading capability. The bacterial strain (AMS7) and the fungal strain (AMF1) achieved the greatest PAH depletion. Results indicated that polyphasic assessment is necessary for a proper understanding of the composition of a microbial consortium. It was concluded that microbial consortia are more complex than previously realized. 54 refs., 3 tabs., 3 figs.
Bending, Gary D.; Lincoln, Suzanne D.; Sørensen, Sebastian R.; Morgan, J. Alun W.; Aamand, Jens; Walker, Allan
2003-01-01
Substantial spatial variability in the degradation rate of the phenyl-urea herbicide isoproturon (IPU) [3-(4-isopropylphenyl)-1,1-dimethylurea] has been shown to occur within agricultural fields, with implications for the longevity of the compound in the soil, and its movement to ground- and surface water. The microbial mechanisms underlying such spatial variability in degradation rate were investigated at Deep Slade field in Warwickshire, United Kingdom. Most-probable-number analysis showed that rapid degradation of IPU was associated with proliferation of IPU-degrading organisms. Slow degradation of IPU was linked to either a delay in the proliferation of IPU-degrading organisms or apparent cometabolic degradation. Using enrichment techniques, an IPU-degrading bacterial culture (designated strain F35) was isolated from fast-degrading soil, and partial 16S rRNA sequencing placed it within the Sphingomonas group. Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified bacterial community 16S rRNA revealed two bands that increased in intensity in soil during growth-linked metabolism of IPU, and sequencing of the excised bands showed high sequence homology to the Sphingomonas group. However, while F35 was not closely related to either DGGE band, one of the DGGE bands showed 100% partial 16S rRNA sequence homology to an IPU-degrading Sphingomonas sp. (strain SRS2) isolated from Deep Slade field in an earlier study. Experiments with strains SRS2 and F35 in soil and liquid culture showed that the isolates had a narrow pH optimum (7 to 7.5) for metabolism of IPU. The pH requirements of IPU-degrading strains of Sphingomonas spp. could largely account for the spatial variation of IPU degradation rates across the field. PMID:12571001
Screening of micro-organisms for Venturia inaequalis control by means of DGGE
Speksnijder, A.G.C.L.; Lombaers-van der Plas, C.H.; Köhl, J.
2006-01-01
Venturia inaequalis causes apple scab. The control of the disease in organic apple production depends on the use of copper which will be restricted in future for environmental reasons. In the search for environmental friendly microbial biocontrol agents and stimulation of antagonistic populations in
Combined radiotherapy-chemotherapy
International Nuclear Information System (INIS)
Steel, G.G.
1989-01-01
This paper presents the clinically confirmed benefits of combined chemotherapy-radiotherapy. They have been found in a small group of diseases that respond to chemotherapy alone. According to the author, only when a drug or drug combination has the ability to eradicate occult disease or substantially to reduce the size of objectively measurable disease is there likely to be an demonstrable benefit from its use in conjunction with radiotherapy. It is the author's belief that the immediate future lies in selecting drugs and patients in which a good chemotherapeutic response can be expected, avoiding drugs that seriously enhance radiation damage to normal tissues and keeping drug and radiation treatments far enough apart in time to minimize interactions
Autonomous grain combine control system
Hoskinson, Reed L.; Kenney, Kevin L.; Lucas, James R.; Prickel, Marvin A.
2013-06-25
A system for controlling a grain combine having a rotor/cylinder, a sieve, a fan, a concave, a feeder, a header, an engine, and a control system. The feeder of the grain combine is engaged and the header is lowered. A separator loss target, engine load target, and a sieve loss target are selected. Grain is harvested with the lowered header passing the grain through the engaged feeder. Separator loss, sieve loss, engine load and ground speed of the grain combine are continuously monitored during the harvesting. If the monitored separator loss exceeds the selected separator loss target, the speed of the rotor/cylinder, the concave setting, the engine load target, or a combination thereof is adjusted. If the monitored sieve loss exceeds the selected sieve loss target, the speed of the fan, the size of the sieve openings, or the engine load target is adjusted.
Directory of Open Access Journals (Sweden)
Gary S. Bañuelos
2016-08-01
Full Text Available Selenium (Se biofortification has been practiced in Se-deficient regions throughout the world primarily by adding inorganic sources of Se to the soil. Considering the use of adding organic sources of Se could be useful as an alternative Se amendment for the production of Se-biofortified food crops. In this multi-year micro-plot study, we investigate growing carrots and broccoli in soils that had been previously amended with Se-enriched Stanleya pinnata Pursh (Britton three and four years prior to planting one and two, respectively. Results showed that total and extractable Se concentrations in soils (0-30 cm were 1.65 mg kg-1 and 88 µg L-1, and 0.92 mg kg-1 and 48.6 µg L-1 at the beginning of the growing season for planting one and two, respectively. After each respective growing season, total Se concentrations in the broccoli florets and carrots ranged from 6.99 to 7.83 mg kg-1 and 3.15 to 6.25 mg kg-1 in planting one and two, respectively. In broccoli and carrot plant tissues, SeMet (selenomethionine was the predominant selenoamino acid identified in Se aqueous extracts. In postharvest soils from planting one, phospholipid analyses (PLFA showed that amending the soil with S. pinnata exerted no effect on the microbial biomass, AMF (arbuscular mycorrhizal fungi, actinomycetes and Gram-positive and bacterial PLFA at both 0-5 and 0-30 cm, respectively, three years later. Successfully producing Se-enriched broccoli and carrots three and four years later after amending soil with Se-enriched S. pinnata clearly demonstrates its potential source as an organic Se enriched fertilizer for Se-deficient regions.
Dissipation of sulfamethoxazole in pasture soils as affected by soil and environmental factors.
Srinivasan, Prakash; Sarmah, Ajit K
2014-05-01
The dissipation of sulfamethoxazole (SMO) antibiotic in three different soils was investigated through laboratory incubation studies. The experiments were conducted under different incubation conditions such as initial chemical concentration, soil depth, temperature, and with sterilisation. The results indicate that SMO dissipated rapidly in New Zealand pasture soils, and the 50% dissipation times (DT50) in Hamilton, Te Kowhai and Horotiu soils under non-sterile conditions were 9.24, 4.3 and 13.33 days respectively. During the incubation period for each sampling event the soil dehydrogenase activity (DHA) and the variation in microbial community were monitored thorough phospholipid fatty acid extraction analysis (PLFA). The DHA data correlated well with the dissipation rate constants of SMO antibiotic, an increase in the DHA activity resulted in faster antibiotic dissipation. The PLFA analysis was indicative of higher bacterial presence as compared to fungal community, highlighting the type of microbial community responsible for dissipation. The results indicate that with increasing soil depth, SMO dissipation in soil was slower (except for Horotiu) while with increase in temperature the antibiotic loss was faster, and was noticeable in all the soils. Both the degree of biological activity and the temperature of the soil influenced overall SMO dissipation. SMO is not likely to persist more than 5-6 months in all three soils suggesting that natural biodegradation may be sufficient for the removal of these contaminants from the soil. Its dissipation in sterile soils indicated abiotic factors such as strong sorption onto soil components to play a role in the dissipation of SMO. Copyright © 2014 Elsevier B.V. All rights reserved.
Microbial biomass, community structure and metal tolerance of a naturally Pb-enriched forest soil.
Bååth, E; Díaz-Raviña, M; Bakken, L R
2005-11-01
The effect of long-term elevated soil Pb levels on soil microbiota was studied at a forest site in Norway, where the soil has been severely contaminated with Pb since the last period of glaciation (several thousand years). Up to 10% Pb (total amount, w/w) has been found in the top layer. The microbial community was drastically affected, as judged from changes in the phospholipid fatty acid (PLFA) pattern. Specific PLFAs that were high in Pb-enriched soil were branched (especially br17:0 and br18:0), whereas PLFAs common in eukaryotic organisms such as fungi (18:2omega6,9 and 20:4) were low compared with levels at adjacent, uncontaminated sites. Congruent changes in the PLFA pattern were found upon analyzing the culturable part of the bacterial community. The high Pb concentrations in the soil resulted in increased tolerance to Pb of the bacterial community, measured using both thymidine incorporation and plate counts. Furthermore, changes in tolerance were correlated to changes in the community structure. The bacterial community of the most contaminated soils showed higher specific activity (thymidine and leucine incorporation rates) and higher culturability than that of control soils. Fungal colony forming units (CFUs) were 10 times lower in the most Pb-enriched soils, the species composition was widely different from that in control soils, and the isolated fungi had high Pb tolerance. The most commonly isolated fungus in Pb-enriched soils was Tolypocladium inflatum. Comparison of isolates from Pb-enriched soil and isolates from unpolluted soils showed that T. inflatum was intrinsically Pb-tolerant, and that the prolonged conditions with high Pb had not selected for any increased tolerance.
Directory of Open Access Journals (Sweden)
Alberto F Rubio-Guerra
2009-11-01
Full Text Available Alberto F Rubio-Guerra1, David Castro-Serna2, Cesar I Elizalde Barrera2, Luz M Ramos-Brizuela21Metabolic and Research Clinic, 2Internal Medicine Department, Hospital General de Ticomán SS DF, MéxicoAbstract: Recent guidelines for the management of hypertension recommend target blood pressures <140/90 mmHg in hypertensive patients, or <130/80 mmHg in subjects with diabetes, chronic kidney disease, or coronary artery disease. Despite the availability and efficacy of antihypertensive drugs, most hypertensive patients do not reach the recommended treatment targets with monotherapy, making combination therapy necessary to achieve the therapeutic goal. Combination therapy with 2 or more agents is the most effective method for achieving strict blood pressure goals. Fixed-dose combination simplifies treatment, reduces costs, and improves adherence. There are many drug choices for combination therapy, but few data are available about the efficacy and safety of some specific combinations. Combination therapy of calcium antagonists and inhibitors of the renin-angiotensin-aldosterone system (RAAS are efficacious and safe, and have been considered rational by both the JNC 7 and the 2007 European Society of Hypertension – European Society of Cardiology guidelines for the management of arterial hypertension. The aim of this review is to discuss some relevant issues about the use of combinations with calcium channel blockers and RAAS inhibitors in the treatment of hypertension.Keywords: hypertension, calcium channel blockers, renin-angiotensin-aldosterone system inhibitors, fixed-dose combination, adherence
Effects of imidacloprid on soil microbial communities in different saline soils.
Zhang, Qingming; Xue, Changhui; Wang, Caixia
2015-12-01
The effects of imidacloprid in the soil environment are a worldwide concern. However, the impact of imidacloprid on soil microorganisms under salt stress is almost unknown. Therefore, an indoor incubation test was performed, and the denaturing gradient gel electrophoresis (DGGE) approach was used to determine the response of different saline soil bacterial and fungal community structures to the presence of imidacloprid (0.4, 2, 10 mg kg(-1)). The results showed that the soil bacterial diversity slightly declined with increasing imidacloprid concentration in soils with low salinity. In moderately saline soils, a new band in the DGGE profile suggested that imidacloprid could improve the soil bacterial diversity to some degree. An analysis of variance indicated that the measured soil bacterial diversity parameters were significantly affected by dose and incubation time. Compared with the control, the soil fungal community structure showed no obvious changes in low and moderately saline soils treated with imidacloprid. The results of these observations provide a basic understanding of the potential ecological effects of imidacloprid on different microorganisms in saline soils.
Seasonal variation of plankton communities influenced by environmental factors in an artificial lake
Li, Xuemei; Yu, Yuhe; Zhang, Tanglin; Feng, Weisong; Ao, Hongyi; Yan, Qingyun
2012-05-01
We evaluated the seasonal variation in plankton community composition in an artificial lake. We conducted microscopic analysis and denaturing gradient gel electrophoresis (DGGE) of PCR-amplified partial 16S rRNA and 18S rRNA genes to characterize the plankton community. The clustering of unweighted pair group method with arithmetic mean (UPGMA) was then used to investigate the similarity of these plankton communities. DGGE fingerprinting revealed that samples collected at the different sites within a season shared high similarity and were generally grouped together. In contrast, we did not observe any seasonal variation based on microscopic analysis. Redundancy analysis (RDA) of the plankton operational taxonomic units (OTUs) in relation to environmental factors revealed that transparency was negatively correlated with the first axis ( R=-0.931), and temperature and total phosphorus (TP) were positively correlated with the first axis ( R=0.736 and R=0.660, respectively). In conclusion, plankton communities in the artificial lake exhibited significant seasonal variation. Transparency, phosphorus and temperature appear to be the major factors driving the differences in plankton composition.
Energy Technology Data Exchange (ETDEWEB)
Satoh, Chiyoko; Takahashi, Norio; Asakawa, Junichi; Hiyama, Keiko; Kodaira, Meiko (Radiation Effects Research Foundation, Hiroshima (Japan))
1993-01-01
In the course of feasibility studies to examine the efficiencies and practicalities of various techniques for screening for genetic variations, the human coagulation factor IX (F9) genes of 63 Japanese families were examined by PCR-denaturing gradient gel electrophoresis (PCR-DGGE). Four target sequences with lengths of 983-2,891 bp from the F9 genes of 126 unrelated individuals from Hiroshima and their 100 children were amplified by PCR, digested with restriction enzymes to approximately 500-bp fragments, and examined by DGGE - a total of 6,724 bp being examined per individual. GC-rich sequences (GC-clamps) of 40 bp were attached to both ends of the target sequences, as far as was feasible. Eleven types of new nucleotide substitutions were detected in the population, none of which produced RFLPs or caused hemophilia B. By examining two target sequences in a single lane, approximately 8,000 bp in a diploid individual could be examined. This approach is very effective for the detection of variations in DNA and is applicable to large-scale population studies. 46 refs., 3 figs., 1 tab.
Directory of Open Access Journals (Sweden)
V. Gowdaman
2015-04-01
Full Text Available Anaerobic digestion is gaining enormous attention due to the ability to covert organic wastes into biogas, an alternative sustainable energy. Methanogenic community plays a significant role in biogas production and also for proficient functioning of the anaerobic digester. Therefore, this study was carried out to investigate the methanogen diversity of a food waste anaerobic digester. After endogenous respiration, the digester samples were supplemented with isotopes of acetate to enrich methanogen population, and were analyzed using DNA-SIP (Stable-Isotope Probing. Following separation and fractionation of heavy (13C and light (12C DNA, PCR amplification was carried out using archaeal 16S rRNA gene followed by DGGE analysis. Sequencing of the prominent DGGE bands revealed the dominance of Methanocorpusculum labreanum species belonging to hydrogenotrophic Methanomicrobiales, which can produce methane in the presence of H2/CO2 and requires acetate for its growth. This is the first instance where Methanocorpusculum labreanum is being reported as a dominant species in an anaerobic digester operative on food waste.
The oral microbial community of gingivitis and lumpy jaw in captive macropods.
Antiabong, John F; Boardman, Wayne; Moore, Robert B; Brown, Melissa H; Ball, Andrew S
2013-12-01
Gingivitis and lumpy jaw are diseases of polymicrobial aetiology. Although Fusobacterium necrophorum has been associated with these diseases in macropods, little is known about other organisms associated with these diseases in this animal species. PCR-DGGE analysis revealed the potential pathogens associated with gingivitis and lumpy jaw in macropods. PCR-DGGE profile comparison between the healthy and disease groups indicated a shift in the oral bacterial community structures with similarity coefficients of 48% and 35% for gingivitis and lumpy jaw respectively. Moreover, gingivitis was associated with increase in bacterial diversity (Shannon index = 2.87; PL curve = 45%) while lumpy jaw resulted in a decline in bacterial diversity (Shannon index = 2.47; PL curve = 74%). This study suggest that the establishment of gingivitis and lumpy jaw diseases follows the ecological plaque hypothesis. This forms the basis for an expanded investigation in an epidemiological scale and suggests the need for the appropriate choice of antimicrobial agent(s) and for the effective management and control of polymicrobial diseases. Copyright © 2013 Elsevier Ltd. All rights reserved.
Dietary carbohydrate source influences molecular fingerprints of the rat faecal microbiota
DEFF Research Database (Denmark)
Licht, Tine Rask; Hansen, Max; Poulsen, Morten
2006-01-01
Background: A study was designed to elucidate effects of selected carbohydrates on composition and activity of the intestinal microbiota. Five groups of eight rats were fed a western type diet containing cornstarch (reference group), sucrose, potato starch, inulin (a long-chained fructan) or olig......Background: A study was designed to elucidate effects of selected carbohydrates on composition and activity of the intestinal microbiota. Five groups of eight rats were fed a western type diet containing cornstarch (reference group), sucrose, potato starch, inulin (a long-chained fructan...... of coliform bacteria in faeces. In the inulin and oligofructose groups, higher levels of butyrate and propionate, respectively, were measured. Principal Component Analysis of profiles of the faecal microbiota obtained by Denaturing Gradient Gel Electrophoresis (DGGE) of PCR amplified bacterial 16S rRNA genes...... and are not expected to reach the large intestine, the DGGE band patterns obtained indicated that these carbohydrates indeed affected the composition of bacteria in the large gut. Also the two fructans resulted in completely different molecular fingerprints of the faecal microbiota, indicating that even though...
Kim, Jaisoo; Koo, So-Yeon; Kim, Ji-Young; Lee, Eun-Hee; Lee, Sang-Don; Ko, Kyung-Seok; Ko, Dong-Chan; Cho, Kyung-Suk
2009-10-01
The effects of acid mine drainage (AMD) in a stream and groundwater near an abandoned copper mine were characterized by physicochemical properties, bacterial community structure using denaturing gel gradient electrophoresis (DGGE), and microbial activity/diversity using Ecoplate technique. Based on DGGE fingerprints, the eubacterial community structures grouped into the stream water (GRS1, GRS2 and GRS3) and groundwater samples (GW1 and GW2), apparently based on differences in water temperature and the concentrations of dissolved oxygen, nitrate and sulfate. The most highly AMD-contaminated sample (GRS1) had additional α-Proteobacteria whereas the groundwater samples included additional β-Proteobacteria, suggesting the development of populations resistant to AMD toxicity under aerobic and anaerobic conditions, respectively. Community level physiological activities on the 31 Ecoplate substrates suggested that the activities decreased with increasing concentrations of sulfate and heavy metals derived from AMD. The Shannon index showed that microbial diversity was greatest in GRS2, and lowest in GRS1, and was probably related to the level of AMD.
Thermophilic biofiltration of benzene and toluene.
Cho, Kyung-Suk; Yoo, Sun-Kyung; Ryu, Hee Wook
2007-12-01
In the current studies, we characterized the degradation of a hot mixture of benzene and toluene (BT) gases by a thermophilic biofilter using polyurethane as packing material and high-temperature compost as a microbial source. We also examined the effect of supplementing the biofilter with yeast extract (YE). We found that YE substantially enhanced microbial activity in the thermophilic biofilter. The degrading activity of the biofilter supplied with YE was stable during long-term operation (approximately 100 d) without accumulating excess biomass. The maximum elimination capacity (1,650 g x m(-3) h(-1)) in the biofilter supplemented with YE was 3.5 times higher than that in the biofilter without YE (470 g g x m(-3) h(-1)). At similar retention times, the capacity to eliminate BT for the YE-supplemented biofilter was higher than for previously reported mesophilic biofilters. Thus, thermophilic biofiltration can be used to degrade hydrophobic compounds such as a BT mixture. Finally, 16S rDNA polymerase chain reaction-DGGE (PCR-DGGE) fingerprinting revealed that the thermophilic bacteria in the biofilter included Rubrobacter sp. and Mycobacterium sp.
[Fungal community structure in phase II composting of Volvariella volvacea].
Chen, Changqing; Li, Tong; Jiang, Yun; Li, Yu
2014-12-04
To understand the fungal community succession during the phase II of Volvariella volvacea compost and clarify the predominant fungi in different fermentation stages, to monitor the dynamic compost at the molecular level accurately and quickly, and reveal the mechanism. The 18S rDNA-denaturing gradient gel electrophoresis (DGGE) and sequencing methods were used to analyze the fungal community structure during the course of compost. The DGGE profile shows that there were differences in the diversity of fungal community with the fermentation progress. The diversity was higher in the stages of high temperature. And the dynamic changes of predominant community and relative intensity was observed. Among the 20 predominant clone strains, 9 were unknown eukaryote and fungi, the others were Eurotiales, Aspergillus sp., Melanocarpus albomyces, Colletotrichum sp., Rhizomucor sp., Verticillium sp., Penicillium commune, Microascus trigonosporus and Trichosporon lactis. The 14 clone strains were detected in the stages of high and durative temperature. The fungal community structure and predominant community have taken dynamic succession during the phase II of Volvariella volvacea compost.
Lau, Evan; Nash, C. Z.; Vogler, D. R.; Cullings, K.; DeVincenzi, Donald (Technical Monitor)
2002-01-01
Denaturing Gradient Gel Electrophoresis (DGGE) of partial 16S rRNA gene sequences was used to investigate the molecular biodiversity of cyanobacterial communities inhabiting various lithified morpho-structures in two hotsprings of Yellowstone National Park. These morpho-structures - flat-topped columns, columnar cones, and ridged cones - resemble ancient stromatolites, which are possibly biogenic in origin. The top, middle and bottom sections of these lithified morpho-structures, as well as surrounding non-lithified mats were analyzed to determine the vertical and spatial distribution of cyanobacterial communities. Results from DGGE indicate that the cyanobacterial community composition of lithified morpho-structures (flat-topped columns, columnar cones, and ridged cones) were largely similar in vertical distribution as well as among the morpho-structures being studied. Preliminary results indicate that the cyanobacterial communities in these lithified morpho-structures were significantly different from communities in surrounding non-lithified mats. These results provide additional support to the theory that certain Phormidium/Leptolyngbya species are involved in the morphogenesis of lithifying morpho-structures in hotsprings and may have played a role in the formation of ancient stromatolites.
Yang, Yang; Wu, Feng-zhi
2011-10-01
A pot experiment was conducted to study the effects of intercropping various Chinese onion cultivars of different allelopathic potential on the cucumber growth and rhizospheric soil environment. When intercropped with high allelopathic Chinese onion cultivars, the EC value and peroxidase activity of cucumber rhizospheric soil decreased, while the pH value, invertase and catalase activities, and bacterial community diversity increased. The cloning and sequencing results indicated that most DGGE bands amplified from cucumber rhizospheric soil samples showed a high homology to uncultured bacterial species. The common bands were affiliated with Actinobacteria and Proteobacteria, and the differential bacteria bands were affiliated with Proteobacteria and Anaerolineaceae. Rhodospirillales and Acidobacteria were only found in the cucumber rhizospheric soil intercropped with low allelopathic Chinese onion cultivars. Correlation analysis showed that there were significant positive correlations between rhizospheric soil urease activity and cucumber seedlings height, total dry biomass, leaf area, and DGGE band number. It was suggested that intercropping high allelopathic Chinese onion cultivars could establish a good rhizospheric soil micro-environment for cucumber growth, and promote the growth of cucumber seedlings markedly.
Influence of long-term repeated prescribed burning on mycelial communities of ectomycorrhizal fungi.
Bastias, Brigitte A; Xu, Zhihong; Cairney, John W G
2006-01-01
To demonstrate the efficacy of direct DNA extraction from hyphal ingrowth bags for community profiling of ectomycorrhizal (ECM) mycelia in soil, we applied the method to investigate the influence of long-term repeated prescribed burning on an ECM fungal community. DNA was extracted from hyphal ingrowth bags buried in forest plots that received different prescribed burning treatments for 30 yr, and denaturing gradient gel electrophoresis (DGGE) profiles of partial fungal rDNA internal transcribed spacer (ITS) regions were compared. Restriction fragment length polymorphism (RFLP) and sequence analyses were also used to compare clone assemblages between the treatments. The majority of sequences derived from the ingrowth bags were apparently those of ECM fungi. DGGE profiles for biennially burned plots were significantly different from those of quadrennially burned and unburned control plots. Analysis of clone assemblages indicated that this reflected altered ECM fungal community composition. The results indicate that hyphal ingrowth bags represent a useful method for investigation of ECM mycelial communities, and that frequent long-term prescribed burning can influence below-ground ECM fungal communities.
EGSIEM combination service: combination of GRACE monthly K-band solutions on normal equation level
Meyer, Ulrich; Jean, Yoomin; Arnold, Daniel; Jäggi, Adrian
2017-04-01
The European Gravity Service for Improved Emergency Management (EGSIEM) project offers a scientific combination service, combining for the first time monthly GRACE gravity fields of different analysis centers (ACs) on normal equation (NEQ) level and thus taking all correlations between the gravity field coefficients and pre-eliminated orbit and instrument parameters correctly into account. Optimal weights for the individual NEQs are commonly derived by variance component estimation (VCE), as is the case for the products of the International VLBI Service (IVS) or the DTRF2008 reference frame realisation that are also derived by combination on NEQ-level. But variance factors are based on post-fit residuals and strongly depend on observation sampling and noise modeling, which both are very diverse in case of the individual EGSIEM ACs. These variance factors do not necessarily represent the true error levels of the estimated gravity field parameters that are still governed by analysis noise. We present a combination approach where weights are derived on solution level, thereby taking the analysis noise into account.
Mode Combinations and International Operations
DEFF Research Database (Denmark)
Benito, Gabriel R. G.; Petersen, Bent; Welch, Lawrence S.
2011-01-01
reveals that companies tend to combine modes of operation; thereby producing unique foreign operation mode “packages” for given activities and/or countries, and that the packages are liable to be modified over time—providing a potentially important optional path for international expansion. The data show...... markets (China, UK and USA) is used as the basis for an exploration of the extent to which, and how and why, companies combine clearly different foreign operation modes. We examine their use of foreign operation mode combinations within given value activities as well as within given countries. The study...
Directory of Open Access Journals (Sweden)
Uolevi Lehtinen
2013-07-01
Full Text Available The objectives of this article strive to describe the idea and rationale of combining i.e. why, when and how to develop theoretically new combined approaches. Then business administration, especially marketing is used as a theoretical and empirical illustrative area. Methodology is inductive and deductive logic and in the empirical examples surveys, case analysis and utilization of secondary data. This article introduce a new promising way, in the long run, to develop new comprehensive approaches and even paradigms for different disciplines, subdisciplines and branches of subdiciplines. Therefore, the ultimate message of the article is to challenge the researchers to put the idea and rationale for combing to the test in their own research field and to build new combined and comprehensive approaches if possible in the field. This message is rather multidisciplinary concerning for example economics, social sciences and political sciences in addition to business administration.
Revised Accounting for Business Combinations
Wilson, Arlette C.; Key, Kimberly
2008-01-01
The Financial Accounting Standards Board (FASB) has recently issued Statement of Financial Accounting Standards No. 141 (Revised 2007) Business Combinations. The object of this Statement is to improve the relevance, representational faithfulness, and comparability of reported information about a business combination and its effects. This Statement…
DEFF Research Database (Denmark)
Haglind, Fredrik
2011-01-01
The part-load performance of combined cycles intended for naval use is of great importance, and it is influenced by the gas turbine configuration and load control strategy. This paper is aimed at quantifying the effects of variable geometry gas turbines on the part-load efficiency for combined...... cycles used for ship propulsion. Moreover, the paper is aimed at developing methodologies and deriving models for part-load simulations suitable for energy system analysis of various components within combined cycle power plants. Two different gas turbine configurations are studied, a two-shaft aero......-derivative configuration and a single-shaft industrial configuration. The results suggest that by the use of variable geometry gas turbines, the combined cycle part-load performance can be improved. In order to minimise the voyage fuel consumption, a combined cycle featuring two-shaft gas turbines with VAN control...
Investigations on combined injuries. Pt. 24
International Nuclear Information System (INIS)
Sedlmeier, H.; Lehner, K.; Werdan, K.; Messerschmidt, O.
1979-01-01
Combined injuries were inflicted upon NMRI-mice, hurting each with an open skin wound subsequent to sublethal exposition to X-rays. Lethality among animals with combined injuries was between 40 and 60%, while animals only irradiated and those with only a skin wound had lethalities between 10 and 20% and 0%, respectively. Blood circulation and respiration of animals injured with combined lesions were studied in an attempt to understand the cause of the high lethality in this group. The blood volume and the oxygen transport capacity were drastically reduced in animals with combined injuries as compared to those in animals only irradiated, although plasma volume, vascular permeability and distribution of the blood volume remained similar in both groups. Analyses of gases and acid/base composition of blood revealed neither respiratory nor metabolic acidosis. These findings indicate that combined injuries hardly impair blood circulation and respiratory function. (orig.) [de
Directory of Open Access Journals (Sweden)
Chenlong Deng
2018-02-01
Full Text Available Considering the influence of the ionosphere, troposphere, and other systematic errors on double-differenced ambiguity resolution (AR, we present an optimal triple-frequency code-phase combination determination method driven by both the model and the real data. The new method makes full use of triple-frequency code measurements (especially the low-noise of the code on the B3 signal to minimize the total noise level and achieve the largest AR success rate (model-driven under different ionosphere residual situations (data-driven, thus speeding up the AR by directly rounding. With the triple-frequency Beidou Navigation Satellite System (BDS data collected at five stations from a continuously-operating reference station network in Guangdong Province of China, different testing scenarios are defined (a medium baseline, whose distance is between 20 km and 50 km; a medium-long baseline, whose distance is between 50 km and 100 km; and a long baseline, whose distance is larger than 100 km. The efficiency of the optimal code-phase combination on the AR success rate was compared with that of the geometry-free and ionosphere-free (GIF combination and the Hatch-Melbourne-Wübbena (HMW combination. Results show that the optimal combinations can always achieve better results than the HMW combination with B2 and B3 signals, especially when the satellite elevation angle is larger than 45°. For the wide-lane AR which aims to obtain decimeter-level kinematic positioning service, the standard deviation (STD of ambiguity residuals for the suboptimal combination are only about 0.2 cycles, and the AR success rate by directly rounding can be up to 99%. Compared with the HMW combinations using B1 and B2 signals and using B1 and B3 signals, the suboptimal combination achieves the best results in all baselines, with an overall improvement of about 40% and 20%, respectively. Additionally, the STD difference between the optimal and the GIF code-phase combinations decreases
Uniportal anatomic combined unusual segmentectomies.
González-Rivas, Diego; Lirio, Francisco; Sesma, Julio
2017-01-01
Nowadays, sublobar anatomic resections are gaining momentum as a valid alternative for early stage lung cancer. Despite being technically demanding, anatomic segmentectomies can be performed by uniportal video-assisted thoracic surgery (VATS) approach to combine the benefits of minimally invasiveness with the maximum lung sparing. This procedure can be even more complex if a combined resection of multiple segments from different lobes has to be done. Here we report five cases of combined and unusual segmentectomies done by the same experienced surgeon in high volume institutions to show uniportal VATS is a feasible approach for these complex resections and to share an excellent educational resource.
Combined oral contraceptives: venous thrombosis.
de Bastos, Marcos; Stegeman, Bernardine H; Rosendaal, Frits R; Van Hylckama Vlieg, Astrid; Helmerhorst, Frans M; Stijnen, Theo; Dekkers, Olaf M
2014-03-03
Combined oral contraceptive (COC) use has been associated with venous thrombosis (VT) (i.e., deep venous thrombosis and pulmonary embolism). The VT risk has been evaluated for many estrogen doses and progestagen types contained in COC but no comprehensive comparison involving commonly used COC is available. To provide a comprehensive overview of the risk of venous thrombosis in women using different combined oral contraceptives. Electronic databases (Pubmed, Embase, Web of Science, Cochrane, CINAHL, Academic Search Premier and ScienceDirect) were searched in 22 April 2013 for eligible studies, without language restrictions. We selected studies including healthy women taking COC with VT as outcome. The primary outcome of interest was a fatal or non-fatal first event of venous thrombosis with the main focus on deep venous thrombosis or pulmonary embolism. Publications with at least 10 events in total were eligible. The network meta-analysis was performed using an extension of frequentist random effects models for mixed multiple treatment comparisons. Unadjusted relative risks with 95% confidence intervals were reported.Two independent reviewers extracted data from selected studies. 3110 publications were retrieved through a search strategy; 25 publications reporting on 26 studies were included. Incidence of venous thrombosis in non-users from two included cohorts was 0.19 and 0.37 per 1 000 person years, in line with previously reported incidences of 0,16 per 1 000 person years. Use of combined oral contraceptives increased the risk of venous thrombosis compared with non-use (relative risk 3.5, 95% confidence interval 2.9 to 4.3). The relative risk of venous thrombosis for combined oral contraceptives with 30-35 μg ethinylestradiol and gestodene, desogestrel, cyproterone acetate, or drospirenone were similar and about 50-80% higher than for combined oral contraceptives with levonorgestrel. A dose related effect of ethinylestradiol was observed for gestodene
Combinations of genetic variants associated with bipolar disorder
DEFF Research Database (Denmark)
Mellerup, Erling; Andreassen, Ole A; Bennike, Bente
2017-01-01
The main objective of the study was to find genetic variants that in combination are significantly associated with bipolar disorder. In previous studies of bipolar disorder, combinations of three and four single nucleotide polymorphisms (SNP) genotypes taken from 803 SNPs were analyzed, and five...... clusters of combinations were found to be significantly associated with bipolar disorder. In the present study, combinations of ten SNP genotypes taken from the same 803 SNPs were analyzed, and one cluster of combinations was found to be significantly associated with bipolar disorder. Combinations from......, heterozygote or variant homozygote. In the combinations containing 10 SNP genotypes almost all the genotypes were the normal homozygote. Such a finding may indicate that accumulation in the genome of combinations containing few SNP genotypes may be a risk factor for bipolar disorder when those combinations...
DEFF Research Database (Denmark)
Ludvigsen, Liselotte; Albrechtsen, Hans-Jørgen; Rootzén, Helle
1997-01-01
Different multivariate statistical analyses were applied to phospholipid fatty acids representing the biomass composition and to different biogeochemical parameters measured in 37 samples from a landfill contaminated aquifer at Grindsted Landfill (Denmark). Principal component analysis...... and correspondence analysis were used to identify groups of samples showing similar patterns with respect to biogeochemical variables and phospholipid fatty acid composition. The principal component analysis revealed that for the biogeochemical parameters the first principal component was linked to the pollution...... was used to allocate samples of phospholipid fatty acids into predefined classes. A large percentages of samples were classified correctly when discriminating samples into groups of dissolved organic carbon and specific conductivity, indicating that the biomass is highly influenced by the pollution...
International Nuclear Information System (INIS)
Schaudy, R.
1978-02-01
A review on wood-plastic combinations is given including the production (wood and plastic component, radiation hardening, curing), the obtained properties, present applications and prospects for the future of these materials. (author)
IPTV program recommendation based on combination strategies
Directory of Open Access Journals (Sweden)
Li Hao
2018-01-01
Full Text Available As a new interactive service technology, IPTV has been extensively studying in the field of TV pro-gram recommendation, but the sparse of the user-program rating matrix and the cold-start problem is a bottleneck that the program recommended accurately. In this paper, a flexible combination of two recommendation strategies proposed, which explored the sparse and cold-start problem as well as the issue of user interest change over time. This paper achieved content-based filtering section and collaborative filtering section according to the two combination strategies, which effectively solved the cold-start program and over the sparse problem and the problem of users interest change over time. The experimental results showed that this combinational recommendation system in optimal parameters compared by using any one of two combination strategies or not using any combination strategy at all, and the reducing range of MAE is [2.7%,3%].The increasing range of precision and recall is [13.8%95.5%] and [0,97.8%], respectively. The experiment showed better results when using combinational recommendation system in optimal parameters than using each combination strategies individually or not using any combination strategy.
Bifuel coal-gas combined cycles
International Nuclear Information System (INIS)
Chmielniak, Tadeusz; Kotowicz, Janusz; Lyczko, Jacek
1997-01-01
This paper describes basic ways of realization of bi fuel cool-gas combined cycles. The criterion of classification of the systems specification is a joint of the gas pail with the steam part: a) The gas turbine flue gases are introduced into the steam boiler combustion chamber (the serial, hot wind box). b) Bypass of the beat exchangers at the steam turbine unit and/or the steam boiler, by use the waste heat exchangers, or waste boiler at the gas turbine unit (the parallel-coupled). c) The mixed, it's a combination of the two upper. The analysis of the parallel system has been specially presented. In derived formulas for the total efficiency of the bi fuel parallel combined cycle balance equations have been used. This formulas can be used for planning new combined cycle power plants and for modernization existing steam power plants. It was made a discussion about influence of the ratio the gas and the steam turbine electric power on the cycle efficiency in care of the full and the part load of the bi fuel combined cycle power plant. The various systems of the joint of the gas part with the steam part have been examined. The selected results of the calculations have been attached. The models and the numerical simulations have been based on data from the existing steam power plants and real gas turbine units. (Author)
Combinators for Paraconsistent Attitudes
DEFF Research Database (Denmark)
Villadsen, Jørgen
2001-01-01
In order to analyse the semantics of natural language sentences a translation into a partial type logic using lexical and logical combinators is presented. The sentences cover a fragment of English with propositional attitudes like knowledge, belief and assertion. A combinator is a closed term...... used for embedded sentences expressing propositional attitudes, thereby allowing for inconsistency without explosion (also called paraconsistency), and is based on a few key equalities for the connectives giving four truth values (truth, falsehood, and undefinedness with negative and positive polarity...
[Discussion on combined periodontic-endodontic lesion type].
Wang, Kai; Zhou, Li
2008-02-01
Combined the elaboration on periodontic-endodontic lesion in the textbook Periodontics with the deficiencies existed in the clinical and teaching work and demonstrated the understanding on the type of the combined periodontic-endodontic lesion, and suggested the viewpoint of no sub-type of combined periodontic-endodontic lesion. Only regard the type of pulp disease that induced by periodontal disease as genuine combined periodontic-endodontic lesion.
Qiu, Guanglei; Song, Yonghui; Zeng, Ping; Duan, Liang; Xiao, Shuhu
2013-02-15
Berberine is a broad-spectrum antibiotic extensively used in personal medication. The production of berberine results in the generation of wastewater containing concentrated residual berberine. However, few related studies up to date focus on berberine removal from wastewaters. In this study, a lab-scale upflow anaerobic sludge blanket (UASB)-membrane bioreactor (MBR) process was developed for berberine removal from synthetic wastewater. The performance of the UASB-MBR system on berberine, COD and NH(4)(+)--N removal was investigated at different berberine loadings. And the effects of berberine on bacterial communities were evaluated using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). Results showed that, as the increase of berberine loadings, UASB performance was affected remarkably, whereas, efficient and stable performance of MBR ensured the overall removal rates of berberine, COD and NH(4)(+)--N consistently reached up to 99%, 98% and 98%, respectively. Significant shifts of bacterial community structures were detected in both UASB and MBR, especially in the initial operations. Along with the increase of berberine loadings, high antibiotic resisting species and some functional species, i.e. Acinetobacter sp., Clostridium sp., Propionibacterium sp., and Sphingomonas sp. in UASB, as well as Sphingomonas sp., Methylocystis sp., Hydrogenophaga sp. and Flavobacterium sp. in MBR were enriched in succession. Copyright © 2013 Elsevier B.V. All rights reserved.
Combined enteral and parenteral nutrition.
Wernerman, Jan
2012-03-01
To review and discuss the evidence and arguments to combine enteral nutrition and parenteral nutrition in the ICU, in particular with reference to the Early Parenteral Nutrition Completing Enteral Nutrition in Adult Critically Ill Patients (EPaNIC) study. The EPaNIC study shows an advantage in terms of discharges alive from the ICU when parenteral nutrition is delayed to day 8 as compared with combining enteral nutrition and parenteral nutrition from day 3 of ICU stay. The difference between the guidelines from the European Society of Enteral and Parenteral Nutrition in Europe and American Society for Parenteral and Enteral Nutrition/Society of Critical Care Medicine in North America concerning the combination of enteral nutrition and parenteral nutrition during the initial week of ICU stay was reviewed. The EPaNIC study clearly demonstrates that early parenteral nutrition in the ICU is not in the best interests of most patients. Exactly at what time point the combination of enteral nutrition and parenteral nutrition should be considered is still an open question.
Combinations of Genetic Variants Occurring Exclusively in Patients
Directory of Open Access Journals (Sweden)
Erling Mellerup
Full Text Available In studies of polygenic disorders, scanning the genetic variants can be used to identify variant combinations. Combinations that are exclusively found in patients can be separated from those combinations occurring in control persons. Statistical analyses can be performed to determine whether the combinations that occur exclusively among patients are significantly associated with the investigated disorder. This research strategy has been applied in materials from various polygenic disorders, identifying clusters of patient-specific genetic variant combinations that are significant associated with the investigated disorders. Combinations from these clusters are found in the genomes of up to 55% of investigated patients, and are not present in the genomes of any control persons. Keywords: Genetic variants, Polygenic disorder, Combinations of genetic variants, Patient-specific combinations
Food irradiation and combination processes
International Nuclear Information System (INIS)
Campbell-Platt, G.; Grandison, A.S.
1990-01-01
International approval of food irradiation is being given for the use of low and medium doses. Uses are being permitted for different categories of foods with maximum levels being set between 1 and 10 kGy. To maximize the effectiveness of these mild irradiation treatments while minimizing any organoleptic quality changes, combination processes of other technologies with irradiation will be useful. Combinations most likely to be exploited in optimal food processing include the use of heat, low temperature, and modified-atmosphere packaging. Because irradiation does not have a residual effect, the food packaging itself becomes an important component of a successful process. These combination processes provide promising alternatives to the use of chemical preservatives or harsher processing techniques. (author)
Directory of Open Access Journals (Sweden)
Eugene Thomas Cloete
2011-08-01
Full Text Available Bioremediation of hydrocarbon pollutants is advantageous owing to the cost-effectiveness of the technology and the ubiquity of hydrocarbon degrading microorganisms in the soil. Soil microbial diversity is affected by hydrocarbon perturbation thus selective enrichment of hydrocarbon utilizers occurs. Hydrocarbons interact with the soil matrix and soil microorganisms determining the fate of the contaminants relative to their chemical nature and microbial degradative capabilities respectively. Bacterial dynamics in crude oil-polluted soil microcosms undergoing bioremediation were investigated over a 42-day period. Four out of the five microcosms containing 4kg of pristine soil each were contaminated with 4% Arabian light crude oil. Three microcosms were amended with either 25g of NPK fertilizer, calcium ammonium nitrate or poultry droppings respectively while the fourth designated oil-contaminated control was unamended. The fifth microcosm had only pristine soil and was set up to ascertain indigenous bacterial community structure pre-contamination. Biostimulated soils were periodically tilled and watered. Hydrocarbon degradation was measured throughout the experimental period by gas chromatography. Gas chromatographic tracing of residual hydrocarbons in biostimulated soils showed marked attenuation of contaminants starting from the second (day 14 till the sixth (day 42 week after contamination whereas no significant reduction in hydrocarbon peaks was seen in the oil contaminated control soil throughout the 6-week experimental period. Molecular fingerprints of bacterial communities involved in aerobic biodegradation of crude oil hydrocarbons in biostimulated soils and controls were generated with DGGE using PCR-amplification of 16S rRNA gene obtained from extracted total soil community DNA. DGGE fingerprints demonstrated that NPK, calcium ammonium nitrate and poultry droppings selected different bacterial populations during the active phase of oil
Zhang, Ming; Qiao, Xuewei; Zhao, Liang; Jiang, Lu; Ren, Fazheng
2011-12-01
Probiotics and carcinogens both have a significant effect on the microfloral composition of the human intestine. The objective of this study was to investigate the impact of an important carcinogen, 4-Nitroquinoline-1-Oxide on colonic microflora and the efficacy of the probiotic Lactobacillus salivarius REN as an agent of counteracting these effects. Using denaturing gradient gel electrophoresis (DGGE) combined with redundancy analysis, we demonstrated that both 4-Nitroquinoline-1-Oxide and L. salivarius REN significantly altered the bacterial communities of rat colons. A total of 27 bacterial strains were identified as being affected by treatment with 4-Nitroquinoline-1-Oxide or L. salivarius REN using a t-value biplot combined with band sequencing. 4-Nitroquinoline-1-Oxide treatment increased the abundance of two potential pathogens (one Helicobacter strain and one Desulfovibrio strain), as well as reducing the abundance of two potentially beneficial strains (one Ruminococcaceae strain and one Rumen bacteria). The Helicobacter strain was initally detected in carcinogen-treated rat intestinal microflora, but L. salivarius REN treatment effectively suppressed the growth of the Helicobacter strain. These results suggested that L. salivarius REN may be a potential probiotic, efficiently acting against the initial infection with, and the growth of pathogenic bacteria.
Marzorati, Massimo; Maignien, Lois; Verhelst, An; Luta, Gabriela; Sinnott, Robert; Kerckhof, Frederiek Maarten; Boon, Nico; Van de Wiele, Tom; Possemiers, Sam
2013-02-01
The combination of a Simulator of the Human Intestinal Microbial Ecosystem with ad hoc molecular techniques (i.e. pyrosequencing, denaturing gradient gel electrophoresis and quantitative PCR) allowed an evaluation of the extent to which two plant polysaccharide supplements could modify a complex gut microbial community. The presence of Aloe vera gel powder and algae extract in product B as compared to the standard blend (product A) improved its fermentation along the entire simulated colon. The potential extended effect of product B in the simulated distal colon, as compared to product A, was confirmed by: (i) the separate clustering of the samples before and after the treatment in the phylogenetic-based dendrogram and OTU-based PCoA plot only for product B; (ii) a higher richness estimator (+33 vs. -36 % of product A); and (iii) a higher dynamic parameter (21 vs. 13 %). These data show that the combination of well designed in vitro simulators with barcoded pyrosequencing is a powerful tool for characterizing changes occurring in the gut microbiota following a treatment. However, for the quantification of low-abundance species-of interest because of their relationship to potential positive health effects (i.e. bifidobacteria or lactobacilli)-conventional molecular ecological approaches, such as PCR-DGGE and qPCR, still remain a very useful complementary tool.
Directory of Open Access Journals (Sweden)
Pawinee Chaiprasert
2017-01-01
Full Text Available Various anaerobic starter seeds from different sources were investigated for their efficacies in treatment of different types of wastewater. Six combinations of starter seeds and wastewaters were selected out of 25 combination batch experiments and operated in semicontinuous reactors. It was noticed that the efficacies of various anaerobic starter seeds for biogas production from different types of wastewater in terms of reactor performance and stability were depended on wastewater characteristics and F/M ratio affecting microbial community and their microbial activities. However, exogenous starter seed can be used across different types of wastewater with or without acclimatization. Four reactors reached the targeted OLR of 2 kg COD/m3·d with high performance and stability except for concentrated rubber wastewater (RBw, even using high active starter seeds of cassava starch (CSs and palm oil (POs. The toxic compounds in RBw such as ammonia and sulfate might also adversely affect methanogenic activity in CSsRBw and POsRBw reactors. DGGE analysis showed that propionate utilizers, Smithella propionica strain LYP and Syntrophus sp., were detected in all samples. For Archaea domain, methylotrophic, hydrogenotrophic, and acetoclastic methanogens were also detected. Syntrophic relationships were assumed between propionate utilizers and methanogens as acetate/H2 producers and utilizers, respectively.
Directory of Open Access Journals (Sweden)
Thiago M A Santos
Full Text Available The diversity of the uterine bacterial composition in dairy cows is still poorly understood, although the emerging picture has shown to be increasingly complex. Understanding the complexity and ecology of microorganisms in the uterus of postpartum dairy cows is critical for developing strategies to block their action in reproductive disorders, such as metritis/endometritis. Here, we used PCR-Denaturing Gradient Gel Electrophoresis (DGGE and DNA pyrosequencing to provide a comprehensive description of the uterine bacterial diversity and compare its succession in healthy, metritic and endometritic Holstein dairy cows at three intervals following calving. Samples were collected from 16 dairy cows housed in a dairy farm located in upstate New York. PCR-DGGE revealed a complex profile with extensive differences in the community structure. With few exceptions, clustering analysis grouped samples from cows presenting the same health status. Analysis of >65,000 high-quality 16S rRNA gene sequences showed that the uterine bacterial consortia, regardless of the health status, is mainly composed of members of the phyla Bacteroidetes, Fusobacteria, Firmicutes, Proteobacteria, and Tenericutes. In addition to these co-dominant phyla, sequences from Spirochaetes, Synergistetes, and Actinobacteria appear less frequently. It is possible that some sequences detected in the uterine fluid resulted from the presence of fecal or vaginal contaminants. Overall, the bacterial core community was different in uterine fluid of healthy cows, when compared to cows suffering from postpartum diseases, and the phylogenetic diversity in all the combined samples changed gradually over time. Particularly at the 34-36 days postpartum (DPP, the core community seemed to be specific for each health status. Our finding reveals that the uterine microbiota in dairy cows varies according with health status and DPP. Also, it adds further support to the hypothesis that there is uterine
Solís-Domínguez, Fernando A; Valentín-Vargas, Alexis; Chorover, Jon; Maier, Raina M
2011-02-15
Mine tailings in arid and semi-arid environments are barren of vegetation and subject to eolian dispersion and water erosion. Revegetation is a cost-effective strategy to reduce erosion processes and has wide public acceptance. A major cost of revegetation is the addition of amendments, such as compost, to allow plant establishment. In this paper we explore whether arbuscular mycorrhizal fungi (AMF) can help support plant growth in tailings at a reduced compost concentration. A greenhouse experiment was performed to determine the effects of three AMF inocula on biomass, shoot accumulation of heavy metals, and changes in the rhizosphere microbial community structure of the native plant Prosopis juliflora (mesquite). Plants were grown in an acidic lead/zinc mine tailings amended with 10% (w/w) compost amendment, which is slightly sub-optimal for plant growth in these tailings. After two months, AMF-inoculated plants showed increased dry biomass and root length (p<0.05) and effective AMF colonization compared to controls grown in uninoculated compost-amended tailings. Mesquite shoot tissue lead and zinc concentrations did not exceed domestic animal toxicity limits regardless of whether AMF inoculation was used. The rhizosphere microbial community structure was assessed using denaturing gradient gel electrophoresis (DGGE) profiles of the small subunit RNA gene for bacteria and fungi. Canonical correspondence analysis (CCA) of DGGE profiles showed that the rhizosphere fungal community structure at the end of the experiment was significantly different from the community structure in the tailings, compost, and AMF inocula prior to planting. Further, CCA showed that AMF inoculation significantly influenced the development of both the fungal and bacterial rhizosphere community structures after two months. The changes observed in the rhizosphere microbial community structure may be either a direct effect of the AMF inocula, caused by changes in plant physiology induced by
Combined precut in difficult biliary cannulation
Directory of Open Access Journals (Sweden)
Jesús Espinel-Díez
2013-06-01
Full Text Available Aim: precut sphincterotomy refers to a variety of endoscopic techniques that are used in order to access the bile duct when conventional methods of cannulation have failed. There are not significant data (such as efficacy, safety about the use of different techniques of precutting at the same session. We have described our experience with combined precut sphincterotomy (CPS and we have compared our results to the use of an isolated precut. Patients and methods: we have performed 247 precuts of a total of 2.390 ERCPs. Patients were distributed according to the type of precut practiced: Needle-knife, transpancreatic and combined precut sphincterotomies. "Combined precut" consisted in performing first a transpancreatic sphincterotomy and, if the access was not achieved, then performing a needle-knife sphincterotomy in the same session. The data about safety and efficacy were prospectively collected. The complications were defined according to the consensus criteria. Results: we performed precutting techniques in 247 patients. Needle-knife, transpancreatic, and combined precuts were performed in 125 (6.9%, 74 (4.1% and 48 (2.6% patients, respectively. Bile duct cannulation was successful in 48 patients (100% in the group of combined precut, 121 patients (96.8% in the transpancreatic group, and 67 patients (90.5% in the needle-knife group (p = 0.03. There were not differences in complications rates between the three groups. There was no pancreatitis in the combined precut group. The complications were successfully managed with conservative treatment. Conclusions: combined precut sphincterotomy seems to be a safe and successful technique in those cases of difficult bile duct cannulation.
Combination of the LEP II ffbar Results
Geweniger, C; Elsing, M; Goy, C; Holt, J; Liebig, W; Minard, M N; Renton, P B; Riemann, S; Sachs, K; Ward, P; Wynhoff, S
2002-01-01
Preliminary combinations of measurements of the 4 LEP collaborations of the process e+e-->ffbar at LEP-II are presented, using data from the full LEP-II data set where available. Cross-sections and forward-backward asymmetry measurements are combined for the full LEP-II data set. Combined differential cross-sections $\\frac{{\\rm d}\\sigma}{{\\rm d}\\cos\\theta}$ for electron-pairs, muon pair and tau-pair final states are presented. Measurements of the production of heavy flavours are combined. The combined results are interpreted in terms of contact interactions and the exchange Z' bosons and leptoquarks, and within models of low scale gravity in large extra dimensions.
GLONASS orbit/clock combination in VNIIFTRI
Bezmenov, I.; Pasynok, S.
2015-08-01
An algorithm and a program for GLONASS satellites orbit/clock combination based on daily precise orbits submitted by several Analytic Centers were developed. Some theoretical estimates for combine orbit positions RMS were derived. It was shown that under condition that RMS of satellite orbits provided by the Analytic Centers during a long time interval are commensurable the RMS of combine orbit positions is no greater than RMS of other satellite positions estimated by any of the Analytic Centers.
Combining semantics with non-standard interpreter hierarchies
DEFF Research Database (Denmark)
Abramov, Sergei M.; Glück, Robert
2000-01-01
This paper reports on results concerning the combination of non-standard semantics via interpreters. We define what a semantics combination means and identify under which conditions a combination can be realized by computer programs (robustness, safely combinable). We develop the underlying mathe...... mathematical theory and examine the meaning of several non-standard interpreter towers. Our results suggest a technique for the implementation of a certain class of programming language dialects by composing a hierarchy of non-standard interpreters....