scholarly journals Diversity, Dynamics, and Distribution ofBdellovibrioand Like Organisms in Perialpine Lakes

2019 ◽  
Vol 85 (6) ◽  
Author(s):  
Benoit Paix ◽  
Jade A. Ezzedine ◽  
Stéphan Jacquet
Keyword(s):  
Denaturing Gradient Gel Electrophoresis ◽  
Single Species ◽  
Abundance Distribution ◽  
Near Surface ◽  
Content Type ◽  
Perialpine Lakes ◽  
Gradient Gel Electrophoresis ◽  
Different Depths ◽  
Diversity Dynamics ◽  
Quantitative Importance

ABSTRACTMicrobes drive a variety of ecosystem processes and services, but many of them remain largely unexplored because of a lack of knowledge on both the diversity and functionality of some potentially crucial microbiological compartments. This is the case with and within the group of bacterial predators collectively known asBdellovibrioand like organisms (BALOs). Here, we report the abundance, distribution, and diversity of three families of these obligate predatory Gram-negative bacteria in three perialpine lakes (Lakes Annecy, Bourget, and Geneva). The study was conducted at different depths (near-surface versus 45 or 50 m) from August 2015 to January 2016. Using PCR-denaturing gradient gel electrophoresis (PCR-DGGE) and cloning-sequencing approaches, we show that the diversity of BALOs is relatively low and very specific to freshwaters or even the lakes themselves. While thePeredibacteraceaefamily was represented mainly by a single species (Peredibacter starrii), it could represent up to 7% of the total bacterial cell abundances. Comparatively, the abundances of the two other families (BdellovibrionaceaeandBacteriovoracaceae) were significantly lower. In addition, the distributions in the water column were very different between the three groups, suggesting various life strategies/niches, as follows:Peredibacteraceaedominated near the surface, whileBdellovibrionaceaeandBacteriovoracaceaewere more abundant at greater depths. Statistical analyses revealed that BALOs seem mainly to be driven by depth and temperature. Finally, this original study was also the opportunity to design new quantitative PCR (qPCR) primers forPeredibacteraceaequantification.IMPORTANCEThis study highlights the abundance, distribution, and diversity of a poorly known microbial compartment in natural aquatic ecosystems, theBdellovibrioand like organisms (BALOs). These obligate bacterial predators of other bacteria may have an important functional role. This study shows the relative quantitative importance of the three main families of this group, with the design of a new primer pair, and their diversity. While both the diversity and the abundances of these BALOs were globally low, it is noteworthy that the abundance of thePeredibacteraceaecould reach important values.

scholarly journals Bdellovibrio and like organisms bacterial predators are not equally distributed in peri-alpine lakes

2017 ◽  
Author(s):  
Benoit Paix ◽  
Stéphan Jacquet
Keyword(s):  
Single Species ◽  
Ecosystem Processes ◽  
Alpine Lakes ◽  
Gram Negative Bacteria ◽  
Prokaryotic Community ◽  
Abundance Distribution ◽  
Near Surface ◽  
Gram Negative ◽  
Different Depths ◽  
First Time

Microbes drive a variety of ecosystem processes and services but still many of them remain largely unexplored because of our lack of knowledge on both diversity and functionality of some potentially key microbiological compartments. This is typically the case with and within the group of bacterial predators collectively known as Bdellovibrio and like organisms (BALOs). Here we report for the first time the abundance, distribution and diversity of the three main families of these natural and obligatory predators of gram negative bacteria in three peri-alpine lakes (e.g. lakes Annecy, Bourget and Geneva) at different depths (surface vs. 45 or 50 m) and along a few months (from August 2015 to January 2016). We show that, using PCR-DGGE and cloning-sequencing approaches, the diversity appeared relatively low and very specific to fresh waters or even of the lakes themselves. While the Peredibacteraceae family was represented mainly by a single species (i.e. Peredibacter starii), it could constitute up to 7% of the total bacterial cell abundances. Comparati vel y, the abundances of the two other families (referred to as Bdellovibrionaceae and Bacteriovaracaceae) were significantly lower. More interestingly, the distribution in the water column was very different between the three groups suggesting various life strategies/niches for each of them: Peredibactereacea dominated near surface while the Bdellovibrionaceae and the Bacteriovaracaceae were more abundant at depth. All in all, our results suggest that these bacterial predators are likely to play a significant role in mortality, carbon fluxes and prokaryotic community structure in lakes.

scholarly journals Efficacy of Rifaximin Vaginal Tablets in Treatment of Bacterial Vaginosis: a Molecular Characterization of the Vaginal Microbiota

2012 ◽  
Vol 56 (8) ◽  
pp. 4062-4070 ◽  
Author(s):  
Federica Cruciani ◽  
Patrizia Brigidi ◽  
Fiorella Calanni ◽  
Vittoria Lauro ◽  
Raffaella Tacchi ◽  
...  
Keyword(s):  
Bacterial Vaginosis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Vaginal Microbiota ◽  
Controlled Study ◽  
Double Blind ◽  
Content Type ◽  
Sexually Transmitted ◽  
Gradient Gel Electrophoresis ◽  
Adverse Pregnancy ◽  
The Impact

ABSTRACTBacterial vaginosis (BV) is a common vaginal disorder characterized by an alteration of the vaginal bacterial morphotypes, associated with sexually transmitted infections and adverse pregnancy outcomes. The purpose of the present study was to evaluate the impact of different doses of rifaximin vaginal tablets (100 mg/day for 5 days, 25 mg/day for 5 days, and 100 mg/day for 2 days) on the vaginal microbiota of 102 European patients with BV enrolled in a multicenter, double-blind, randomized, placebo-controlled study. An integrated molecular approach based on quantitative PCR (qPCR) and PCR-denaturing gradient gel electrophoresis (PCR-DGGE) was used to investigate the effects of vaginal tablets containing the antibiotic. An increase in members of the genusLactobacillusand a decrease in the BV-related bacterial groups after the antibiotic treatment were demonstrated by qPCR. PCR-DGGE profiles confirmed the capability of rifaximin to modulate the composition of the vaginal microbial communities and to reduce their complexity. This molecular analysis supported the clinical observation that rifaximin at 25 mg/day for 5 days represents an effective treatment to be used in future pivotal studies for the treatment of BV.

scholarly journals Microbial Ecology Dynamics during Rye and Wheat Sourdough Preparation

2013 ◽  
Vol 79 (24) ◽  
pp. 7827-7836 ◽  
Author(s):  
Danilo Ercolini ◽  
Erica Pontonio ◽  
Francesca De Filippis ◽  
Fabio Minervini ◽  
Antonietta La Storia ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Microbial Ecology ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Diversity Indices ◽  
Rrna Gene ◽  
Content Type ◽  
Gradient Gel Electrophoresis ◽  
Plate Counts ◽  
Relative Abundances

ABSTRACTThe bacterial ecology during rye and wheat sourdough preparation was described by 16S rRNA gene pyrosequencing. Viable plate counts of presumptive lactic acid bacteria, the ratio between lactic acid bacteria and yeasts, the rate of acidification, a permutation analysis based on biochemical and microbial features, the number of operational taxonomic units (OTUs), and diversity indices all together demonstrated the maturity of the sourdoughs during 5 to 7 days of propagation. Flours were mainly contaminated by metabolically active genera (Acinetobacter,Pantoea,Pseudomonas,Comamonas,Enterobacter,Erwinia, andSphingomonas) belonging to the phylumProteobacteriaorBacteroidetes(genusChryseobacterium). Their relative abundances varied with the flour. Soon after 1 day of propagation, this population was almost completely inhibited except for theEnterobacteriaceae. Although members of the phylumFirmicuteswere present at very low or intermediate relative abundances in the flours, they became dominant soon after 1 day of propagation. Lactic acid bacteria were almost exclusively representative of theFirmicutesby this time.Weissellaspp. were already dominant in rye flour and stably persisted, though they were later flanked by theLactobacillus sakeigroup. There was a succession of species during 10 days of propagation of wheat sourdoughs. The fluctuation between dominating and subdominating populations ofL. sakeigroup,Leuconostocspp.,Weissellaspp., andLactococcus lactiswas demonstrated. Other subdominant species such asLactobacillus plantarumwere detectable throughout propagation. As shown by PCR-denaturing gradient gel electrophoresis (PCR-DGGE) analysis,Saccharomyces cerevisiaedominated throughout the sourdough propagation. Notwithstanding variations due to environmental and technology determinants, the results of this study represent a clear example of how the microbial ecology evolves during sourdough preparation.

scholarly journals Bacterial Chitinolytic Communities Respond to Chitin and pH Alteration in Soil

2012 ◽  
Vol 79 (1) ◽  
pp. 263-272 ◽  
Author(s):  
Anna M. Kielak ◽  
Mariana Silvia Cretoiu ◽  
Alexander V. Semenov ◽  
Søren J. Sørensen ◽  
Jan Dirk van Elsas
Keyword(s):  
16S Rrna ◽  
Bacterial Communities ◽  
Plant Pathogens ◽  
Structural Changes ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Acid Soil ◽  
Rrna Gene ◽  
Content Type ◽  
Soil Suppressiveness ◽  
Gradient Gel Electrophoresis

ABSTRACTChitin amendment is a promising soil management strategy that may enhance the suppressiveness of soil toward plant pathogens. However, we understand very little of the effects of added chitin, including the putative successions that take place in the degradative process. We performed an experiment in moderately acid soil in which the level of chitin, next to the pH, was altered. Examination of chitinase activities revealed fast responses to the added crude chitin, with peaks of enzymatic activity occurring on day 7. PCR-denaturing gradient gel electrophoresis (DGGE)-based analyses of 16S rRNA andchiAgenes showed structural changes of the phylogenetically and functionally based bacterial communities following chitin addition and pH alteration. Pyrosequencing analysis indicated (i) that the diversity ofchiAgene types in soil is enormous and (i) that differentchiAgene types are selected by the addition of chitin at different prevailing soil pH values. Interestingly, a major role of Gram-negative bacteria versus a minor one ofActinobacteriain the immediate response to the added chitin (based on 16S rRNA gene abundance andchiAgene types) was indicated. The results of this study enhance our understanding of the response of the soil bacterial communities to chitin and are of use for both the understanding of soil suppressiveness and the possible mining of soil for novel enzymes.

scholarly journals Changes in Bacterial Diversity Associated with Epithelial Tissue in the Beef Cow Rumen during the Transition to a High-Grain Diet

2011 ◽  
Vol 77 (16) ◽  
pp. 5770-5781 ◽  
Author(s):  
Yanhong Chen ◽  
Gregory B. Penner ◽  
Meiju Li ◽  
Masahito Oba ◽  
Le Luo Guan
Keyword(s):  
Bacterial Diversity ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Pcr Analysis ◽  
Control Group ◽  
Epithelial Tissue ◽  
Rrna Gene ◽  
Content Type ◽  
Beef Cow ◽  
Dietary Transition ◽  
Gradient Gel Electrophoresis

ABSTRACTOur understanding of the ruminal epithelial tissue-associated bacterial (defined as epimural bacteria in this study) community is limited. In this study, we aimed to determine whether diet influences the diversity of the epimural bacterial community in the bovine rumen. Twenty-four beef heifers were randomly assigned to either a rapid grain adaptation (RGA) treatment (n= 18) in which the heifers were allowed to adapt from a diet containing 97% hay to a diet containing 8% hay over 29 days or to the control group (n= 6), which was fed 97% hay. Rumen papillae were collected when the heifers were fed 97%, 25%, and 8% hay diets. PCR-denaturing gradient gel electrophoresis (DGGE) and quantitative real-time PCR analysis were used to characterize rumen epimural bacterial diversity and to estimate the total epimural bacterial population (copy numbers of the 16S rRNA gene). The epimural bacterial diversity from RGA heifers changed (P= 0.01) in response to the rapid dietary transition, whereas it was not affected in control heifers. A total of 88 PCR-DGGE bands were detected, and 44 were identified from phyla includingFirmicutes,Bacteroidetes, andProteobacteria. The bacteriaTreponemasp.,Ruminobactersp., andLachnospiraceaesp. were detected only when heifers were fed 25% and 8% hay diets, suggesting the presence of these bacteria is the result of adaptation to the high-grain diets. In addition, the total estimated population of rumen epimural bacteria was positively correlated with molar proportions of acetate, isobutyrate, and isovalerate, suggesting that they may play a role in volatile fatty acid metabolism in the rumen.

scholarly journals Influence of Artisan Bakery- or Laboratory-Propagated Sourdoughs on the Diversity of Lactic Acid Bacterium and Yeast Microbiotas

2012 ◽  
Vol 78 (15) ◽  
pp. 5328-5340 ◽  
Author(s):  
Fabio Minervini ◽  
Anna Lattanzi ◽  
Maria De Angelis ◽  
Raffaella Di Cagno ◽  
Marco Gobbetti
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Lactic Acid Bacterium ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Type I ◽  
Content Type ◽  
Stable Species ◽  
Mature Type ◽  
Gradient Gel Electrophoresis ◽  
Permutation Analysis

ABSTRACTSeven mature type I sourdoughs were comparatively back-slopped (80 days) at artisan bakery and laboratory levels under constant technology parameters. The cell density of presumptive lactic acid bacteria and related biochemical features were not affected by the environment of propagation. On the contrary, the number of yeasts markedly decreased from artisan bakery to laboratory propagation. During late laboratory propagation, denaturing gradient gel electrophoresis (DGGE) showed that the DNA band corresponding toSaccharomyces cerevisiaewas no longer detectable in several sourdoughs. Twelve species of lactic acid bacteria were variously identified through a culture-dependent approach. All sourdoughs harbored a certain number of species and strains, which were dominant throughout time and, in several cases, varied depending on the environment of propagation. As shown by statistical permutation analysis, the lactic acid bacterium populations differed among sourdoughs propagated at artisan bakery and laboratory levels.Lactobacillus plantarum,Lactobacillus sakei, andWeissella cibariadominated in only some sourdoughs back-slopped at artisan bakeries, andLeuconostoc citreumseemed to be more persistent under laboratory conditions. Strains ofLactobacillus sanfranciscensiswere indifferently found in some sourdoughs. Together with the other stable species and strains, other lactic acid bacteria temporarily contaminated the sourdoughs and largely differed between artisan bakery and laboratory levels. The environment of propagation has an undoubted influence on the composition of sourdough yeast and lactic acid bacterium microbiotas.

scholarly journals Gastrointestinal Colonization with a Cephalosporinase-Producing Bacteroides Species Preserves Colonization Resistance against Vancomycin-Resistant Enterococcus and Clostridium difficile in Cephalosporin-Treated Mice

2014 ◽  
Vol 58 (8) ◽  
pp. 4535-4542 ◽  
Author(s):  
Usha Stiefel ◽  
Michelle M. Nerandzic ◽  
Michael J. Pultz ◽  
Curtis J. Donskey
Keyword(s):  
Clostridium Difficile ◽  
Intestinal Tract ◽  
Denaturing Gradient Gel Electrophoresis ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Content Type ◽  
Antibiotic Effect ◽  
Gradient Gel Electrophoresis ◽  
Vancomycin Resistant

ABSTRACTAntibiotics that are excreted into the intestinal tract may disrupt the indigenous intestinal microbiota and promote colonization by health care-associated pathogens. β-Lactam, or penicillin-type, antibiotics are among the most widely utilized antibiotics worldwide and may also adversely affect the microbiota. Many bacteria are capable, however, of producing β-lactamase enzymes that inactivate β-lactam antibiotics. We hypothesized that prior establishment of intestinal colonization with a β-lactamase-producing anaerobe might prevent these adverse effects of β-lactam antibiotics, by inactivating the portion of antibiotic that is excreted into the intestinal tract. Here, mice with a previously abolished microbiota received either oral normal saline or an oral cephalosporinase-producing strain ofBacteroides thetaiotaomicronfor 3 days. Mice then received 3 days of subcutaneous ceftriaxone, followed by either oral administration of vancomycin-resistantEnterococcus(VRE) or sacrifice and assessment ofin vitrogrowth of epidemic and nonepidemic strains ofClostridium difficilein murine cecal contents. Stool concentrations of VRE and ceftriaxone were measured, cecal levels ofC. difficile24 h after incubation were quantified, and denaturing gradient gel electrophoresis (DGGE) of microbial 16S rRNA genes was performed to evaluate the antibiotic effect on the microbiota. The results demonstrated that establishment of prior colonization with a β-lactamase-producing intestinal anaerobe inactivated intraintestinal ceftriaxone during treatment with this antibiotic, allowed recovery of the normal microbiota despite systemic ceftriaxone, and prevented overgrowth with VRE and epidemic and nonepidemic strains ofC. difficilein mice. These findings describe a novel probiotic strategy to potentially prevent pathogen colonization in hospitalized patients.

scholarly journals Evaluation of a Parchment Document, the 13th Century Incorporation Charter for the City of Krakow, Poland, for Microbial Hazards

2016 ◽  
Vol 82 (9) ◽  
pp. 2620-2631 ◽  
Author(s):  
Tomasz Lech
Keyword(s):  
Denaturing Gradient Gel Electrophoresis ◽  
Genetic Identification ◽  
13Th Century ◽  
Content Type ◽  
Microbiological Methods ◽  
Gradient Gel Electrophoresis ◽  
Identification Of Bacteria ◽  
Bacteria And Fungi ◽  
The City ◽  
Destructive Potential

ABSTRACTThe literature of environmental microbiology broadly discusses issues associated with microbial hazards in archives, but these publications are mainly devoted to paper documents. There are few articles on historical parchment documents, which used to be very important for the development of literature and the art of writing. These studies present a broad spectrum of methods for the assessment of biodeterioration hazards of the parchment document in question. They are based on both conventional microbiological methods and advanced techniques of molecular biology. Here, a qualitative analysis was conducted, based on genetic identification of bacteria and fungi present on the document as well as denaturing gradient gel electrophoresis profiling and examining the destructive potential of isolated microbes. Moreover, the study involved a quantitative and qualitative microbiological assessment of the indoor air in the room where the parchment was kept. The microbes with the highest destructive potential that were isolated from the investigated item wereBacillus cereusandAcinetobacter lwoffiibacteria andPenicillium chrysogenum,Chaetomium globosum, andTrichoderma longibrachiatumfungi. The presence of theB. cereusstrain was particularly interesting since, under appropriate conditions, it leads to complete parchment degradation within several days.

scholarly journals amoAGene Abundances and Nitrification Potential Rates Suggest that Benthic Ammonia-Oxidizing Bacteria and Not Archaea Dominate N Cycling in the Colne Estuary, United Kingdom

2014 ◽  
Vol 81 (1) ◽  
pp. 159-165 ◽  
Author(s):  
Jialin Li ◽  
David B. Nedwell ◽  
Jessica Beddow ◽  
Alex J. Dumbrell ◽  
Boyd A. McKew ◽  
...  
Keyword(s):  
Denaturing Gradient Gel Electrophoresis ◽  
Dry Weight ◽  
Estuarine Sediments ◽  
Ammonia Oxidizer ◽  
Ammonia Oxidizing Bacteria ◽  
Content Type ◽  
Gene Abundance ◽  
Nitrification Potential ◽  
Gradient Gel Electrophoresis ◽  
Colne Estuary

ABSTRACTNitrification, mediated by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), is important in global nitrogen cycling. In estuaries where gradients of salinity and ammonia concentrations occur, there may be differential selections for ammonia-oxidizer populations. The aim of this study was to examine the activity, abundance, and diversity of AOA and AOB in surface oxic sediments of a highly nutrified estuary that exhibits gradients of salinity and ammonium. AOB and AOA communities were investigated by measuring ammonia monooxygenase (amoA) gene abundance and nitrification potentials both spatially and temporally. Nitrification potentials differed along the estuary and over time, with the greatest nitrification potentials occurring mid-estuary (8.2 μmol N grams dry weight [gdw]−1day−1in June, increasing to 37.4 μmol N gdw−1day−1in January). At the estuary head, the nitrification potential was 4.3 μmol N gdw−1day−1in June, increasing to 11.7 μmol N gdw−1day−1in January. At the estuary head and mouth, nitrification potentials fluctuated throughout the year. AOBamoAgene abundances were significantly greater (by 100-fold) than those of AOA both spatially and temporally.Nitrosomonasspp. were detected along the estuary by denaturing gradient gel electrophoresis (DGGE) band sequence analysis. In conclusion, AOB dominated over AOA in the estuarine sediments, with the ratio of AOB/AOAamoAgene abundance increasing from the upper (freshwater) to lower (marine) regions of the Colne estuary. These findings suggest that in this nutrified estuary, AOB (possiblyNitrosomonasspp.) were of major significance in nitrification.

scholarly journals Denaturing Gradient Gel Electrophoresis and Barcoded Pyrosequencing Reveal Unprecedented Archaeal Diversity in Mangrove Sediment and Rhizosphere Samples

2012 ◽  
Vol 78 (16) ◽  
pp. 5520-5528 ◽  
Author(s):  
Ana C. C. Pires ◽  
Daniel F. R. Cleary ◽  
Adelaide Almeida ◽  
Ângela Cunha ◽  
Simone Dealtry ◽  
...  
Keyword(s):  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Mangrove Sediment ◽  
Bulk Sediment ◽  
Archaeal Diversity ◽  
Mangrove Species ◽  
Content Type ◽  
Gradient Gel Electrophoresis

ABSTRACTMangroves are complex ecosystems that regulate nutrient and sediment fluxes to the open sea. The importance of bacteria and fungi in regulating nutrient cycles has led to an interest in their diversity and composition in mangroves. However, very few studies have assessedArchaeain mangroves, and virtually nothing is known about whether mangrove rhizospheres affect archaeal diversity and composition. Here, we studied the diversity and composition ofArchaeain mangrove bulk sediment and the rhizospheres of two mangrove trees,Rhizophora mangleandLaguncularia racemosa, using denaturing gradient gel electrophoresis (DGGE) and pyrosequencing of archaeal 16S rRNA genes with a nested-amplification approach. DGGE profiles revealed significant structural differences between bulk sediment and rhizosphere samples, suggesting that roots of both mangrove species influence the sediment archaeal community. Nearly all of the detected sequences obtained with pyrosequencing were identified asArchaea, but most were unclassified at the level of phylum or below. Archaeal richness was, furthermore, the highest in theL. racemosarhizosphere, intermediate in bulk sediment, and the lowest in theR. manglerhizosphere. This study shows that rhizosphere microhabitats ofR. mangleandL. racemosa, common plants in subtropical mangroves located in Rio de Janeiro, Brazil, hosted distinct archaeal assemblages.

Sign in / Sign up

Export Citation Format

Share Document