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Microbial Ecology (microbial + ecology)
Selected AbstractsAquatic Microbial Ecology: Water Desert, Microcosm, Ecosystem.INTERNATIONAL REVIEW OF HYDROBIOLOGY, Issue 4-5 2008What's Next? Abstract Aquatic microbial ecology aims at nothing less than explaining the world from "ecological scratch". It develops theories, concepts and models about the small and invisible living world that is at the bottom of every macroscopic aquatic system. In this paper we propose to look at the development of Aquatic Microbial Ecology as a reiteration of classical (eukaryotic) limnology and oceanography. This was conceptualized moving historically from the so-called water desert to microcosm to ecosystem. Each of these concepts characterizes a particular historical field of knowledge that embraces also practices and theories about living beings in aquatic environments. Concerning the question of "who is there", however, Aquatic Microbial Ecology historically developed in reverse order. Repetition, reiteration and replication notwithstanding, Aquatic Microbial Ecology has contributed new ideas, theories and methods to the whole field of ecology as well as to microbiology. The disciplining of Aquatic Microbial Ecology happened in the larger field of plankton biology, and it is still attached to this biological domain, even conceiving of itself very self-consciously as a discipline of its own. Today, Aquatic Microbial Ecology as a discipline is much broader than plankton ecology ever was, for it includes not only oceans and freshwaters but also benthic, interstitial and groundwater systems. The success of Aquatic Microbial Ecology is expressed by its influence on other fields in ecology. The challenge is to further develop its theoretical and methodological features while at the same time contributing to current pressing problems such as climate change or the management of global water resources. And then it may not be fanciful to suppose that even in the year nineteen hundred and nineteen a great number of minds are still only partially lit up by the cold light of knowledge. It is the most capricious illuminant. They are still apt to ruminate, without an overpowering bias to the truth, whether a kingfisher's body shows which way the wind blows; whether an ostrich digests iron; whether owls and ravens herald ill-fortune; and the spilling of salt bad luck; what the tingling of ears forebodes, and even to toy pleasantly with more curious speculations as to the joints of elephants and the politics of storks, which came within the province of the more fertile and better-informed brain of the author (1919) Virginia Woolf from the essay "Reading", In: Leonard Woolf (ed.), 1950: The Captain's Death Bed and Other Essays, , London: Hogarth Press, p. 157. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Microbial ecology of corals, sponges, and algae in mesophotic coral environmentsFEMS MICROBIOLOGY ECOLOGY, Issue 1 2010Julie B. Olson Abstract Mesophotic coral ecosystems that occur at depths from 30 to 200 m have historically been understudied and yet appear to support a diverse biological community. The microbiology of these systems is particularly poorly understood, especially with regard to the communities associated with corals, sponges, and algae. This lack of information is partly due to the problems associated with gaining access to these environments and poor reproducibility across sampling methods. To summarize what is known about the microbiology of these ecosystems and to highlight areas where research is urgently needed, an overview of the current state of knowledge is presented. Emphasis is placed on the characterization of microbial populations, both prokaryotic and eukaryotic, associated with corals, sponges, and algae and the factors that influence microbial community structure. In topic areas where virtually nothing is known from mesophotic environments, the knowledge pertaining to shallow-water ecosystems is summarized to provide a starting point for a discussion on what might be expected in the mesophotic zone. [source] Applications of the rep-PCR DNA fingerprinting technique to study microbial diversity, ecology and evolutionENVIRONMENTAL MICROBIOLOGY, Issue 4 2009Satoshi Ishii Summary A large number of repetitive DNA sequences are found in multiple sites in the genomes of numerous bacteria, archaea and eukarya. While the functions of many of these repetitive sequence elements are unknown, they have proven to be useful as the basis of several powerful tools for use in molecular diagnostics, medical microbiology, epidemiological analyses and environmental microbiology. The repetitive sequence-based PCR or rep-PCR DNA fingerprint technique uses primers targeting several of these repetitive elements and PCR to generate unique DNA profiles or ,fingerprints' of individual microbial strains. Although this technique has been extensively used to examine diversity among variety of prokaryotic microorganisms, rep-PCR DNA fingerprinting can also be applied to microbial ecology and microbial evolution studies since it has the power to distinguish microbes at the strain or isolate level. Recent advancement in rep-PCR methodology has resulted in increased accuracy, reproducibility and throughput. In this minireview, we summarize recent improvements in rep-PCR DNA fingerprinting methodology, and discuss its applications to address fundamentally important questions in microbial ecology and evolution. [source] Microbial diversity , insights from population geneticsENVIRONMENTAL MICROBIOLOGY, Issue 1 2008Ted H. M. Mes Summary Although many environmental microbial populations are large and genetically diverse, both the level of diversity and the extent to which it is ecologically relevant remain enigmatic. Because the effective (or long-term) population size, Ne, is one of the parameters that determines population genetic diversity, tests and simulations that assume selectively neutral mutations may help to identify the processes that have shaped microbial diversity. Using ecologically important genes, tests of selective neutrality suggest that adaptive as well as non-adaptive types of selection act and that departure from neutrality may be widespread or restricted to small groups of genotypes. Population genetic simulations using population sizes between 103 and 107 suggest extremely high levels of microbial diversity in environments that sustain large populations. However, census and effective population sizes may differ considerably, and because we know nothing of the evolutionary history of environmental microbial populations, we also have no idea what Ne of environmental populations is. On the one hand, this reflects our ignorance of the microbial world. On the other hand, the tests and simulations illustrate interactions between microbial diversity and microbial population genetics that should inform our thinking in microbial ecology. Because of the different views on microbial diversity across these disciplines, such interactions are crucial if we are to understand the role of genes in microbial communities. [source] Ecological control analysis: being(s) in control of mass flux and metabolite concentrations in anaerobic degradation processesENVIRONMENTAL MICROBIOLOGY, Issue 2 2007Wilfred F. M. Röling Summary Identification of the functional groups of microorganisms that are predominantly in control of fluxes through, and concentrations in, microbial networks would benefit microbial ecology and environmental biotechnology: the properties of those controlling microorganisms could be studied or monitored specifically or their activity could be modulated in attempts to manipulate the behaviour of such networks. Herein we present ecological control analysis (ECA) as a versatile mathematical framework that allows for the quantification of the control of each functional group in a microbial network on its process rates and concentrations of intermediates. In contrast to current views, we show that rates of flow of matter are not always limited by a single functional group; rather flux control can be distributed over several groups. Also, control over intermediate concentrations is always shared. Because of indirect interactions, through other functional groups, the concentration of an intermediate can also be controlled by functional groups not producing or consuming it. Ecological control analysis is illustrated by a case study on the anaerobic degradation of organic matter, using experimental data obtained from the literature. During anaerobic degradation, fermenting microorganisms interact with terminal electron-accepting microorganisms (e.g. halorespirers, methanogens). The analysis indicates that flux control mainly resides with fermenting microorganisms, but can shift to the terminal electron-accepting microorganisms under less favourable redox conditions. Paradoxically, halorespiring microorganisms do not control the rate of perchloroethylene and trichloroethylene degradation even though they catalyse those processes themselves. [source] The searchlight and the bucket of microbial ecologyENVIRONMENTAL MICROBIOLOGY, Issue 1 2007Nicole Dubilier No abstract is available for this article. [source] The human microbiome: eliminating the biomedical/environmental dichotomy in microbial ecologyENVIRONMENTAL MICROBIOLOGY, Issue 1 2007Ruth E. Ley No abstract is available for this article. [source] Impact of animal waste lagoon effluents on chlorpyrifos degradation in soilsENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 12 2000Xinjiang Huang Abstract Animal-derived lagoon effluents are a good source of inorganic nutrients and organic matter; however, they may impact the degradation and transport of soil-applied pesticides. The degradation of chlorpyrifos in poultry-, swine-, and cow-derived effluents and effluent-soil matrices were studied using batch and column incubation studies. Chlorpyrifos was degraded by aerobic microbial processes in animal-derived lagoon effluents. Microbial community analysis by denaturing gradient gel electrophoresis of polymerase chain reaction-amplified 16S ribosomal ribonucleic acid genes showed that a single band became dominant in effluent during chlorpyrifos degradation. In soils, both biotic and abiotic degradation contributed significantly to the overall dissipation of chlorpyrifos. Large differences in degradation rates were observed between soils, with the fastest rate observed in soil with higher pH and cation-exchange capacity. Effluents appeared to have only a minor effect on chlorpyrifos degradation in soils, although effluent-induced increases in soil-solution pH over time may enhance hydrolysis by a few percent in low-pH soils. Soil properties, not effluent properties, appear to control chlorpyrifos degradation under laboratory conditions; however, the impact on changes in soil properties and microbial ecology with long-term effluent irrigation warrants further investigation. [source] Size and phenotypic structure of microbial communities within soil profiles in relation to different playing areas on a UK golf courseEUROPEAN JOURNAL OF SOIL SCIENCE, Issue 5 2008M. D. Bartlett Summary Amenity turf accounts for up to 4% of land-use in urban areas, providing key refuges for both above- and below-ground biodiversity. Golf courses occupy the largest surface area of all sports facilities; however, only a limited amount of microbial ecology has been carried out to investigate differences in the size and structure of microbial communities of the soil. The soil microbial community is a key agent in nutrient cycling and delivery of other ecosystem goods and services; however, there has been little work focused on amenity turf ecosystems in the UK. A study of soil microbial community size and structure, on the range of playing areas maintained for the game of golf at a single golf course in relation to depth through the soil profile, was carried out. Soil from different playing areas showed significant differences in the size (measured using chloroform fumigation extraction) of the microbial community (P < 0.01), with a greater concentration of microbial biomass at 0,75 mm from the surface, compared with deeper zones (P < 0.01). Principal component analysis of phospholipid fatty acid (PLFA) biomarkers indicated that the community structure was significantly different at 0,75 mm from the surface on all areas of the golf course investigated (P < 0.05, in all cases). The PLFA biomarkers consistently associated with such discrimination were 16:0 and 18:1,9 c. These findings suggest that there is a consistently larger and similarly structured microbial community associated with the surface thatch layer, commonly found in amenity turf. [source] Soil microbial community structure in cucumber rhizosphere of different resistance cultivars to fusarium wiltFEMS MICROBIOLOGY ECOLOGY, Issue 3 2010Huaiying Yao Abstract Cucumber fusarium wilt is a common soil-borne disease. We hypothesize that there is a relationship between the severity of disease and soil microbial ecology. In this work, culturable microbial populations, lipid fatty acid and community-level physiological profiles (CLPP) from rhizosphere soils of four different cucumber cultivars were investigated. Comparatively higher actinomycetes, mycorrhizal colonization and higher ratios of bacteria to fungi were found in the two resistant cultivars compared with the two susceptible cultivars. CLPP analysis showed that catabolic diversity indices were higher in the presence of two resistant cultivars. Phospholipid fatty acid (PLFA) profiles suggested that fungal (18:2,6,9c) PLFA was enriched in the rhizosphere soils of the two susceptible cultivars, but some bacterial (16:0 and 15:0a) PLFAs were found in a lower relative abundance in these soils. The neutral lipid fatty acid 16:1,5, which is an indicator of arbuscular mycorrhizal fungi, was enriched in the rhizosphere soils of the two resistant cultivars. All the three methods suggested that plant genotype had a significant impact on the soil microbial community composition and activity, and the differences in the rhizosphere microbial community may result in the differences in the resistance to fusarium wilt. [source] Reproducibility of a microbial river water community to self-organize upon perturbation with the natural chemical enantiomers, R - and S -carvoneFEMS MICROBIOLOGY ECOLOGY, Issue 2 2008Katja Lehmann Abstract A river water microbial community was studied in response to perturbation with the monoterpene enantiomers R - and S -carvone. The microbial community structure and function was also evaluated after enantiomers exposure was switched. Microbial communities were evaluated by length heterogeneity PCR. The addition of R - and S -carvone enriched for a range of functionally different communities: enantiomer-selective, racemic and ones that contain both. After 5 days incubation, the R - and S -carvone treatments developed a range of dominant microbial communities, which were increasingly dissimilar from the ones in which no carvone degradation had taken place (R -values: R -carvone 0.743, S -carvone 0.5007). There was an increase in the evenness of the microbial community structure upon carvone depletion. After the cross-over, the rate of carvone utilization was significantly faster than after the first carvone addition (P=0.008) as demonstrated by concomitant carvone and oxygen depletion. The main R -degrading community (450,456 bp) appeared enantioselective and largely unable to degrade S -carvone, whereas the S -carvone-degrading community (502,508 bp) appeared to have racemic catabolic capacity. In conclusion, chemical perturbations, such as enantiomers, might generate a significant shift in the river microbial ecology that can have implications for the function of a river in both a spatial and temporal context. [source] New directions and interactions in metagenomics researchFEMS MICROBIOLOGY ECOLOGY, Issue 3 2006Naomi Ward Abstract Metagenomics, which aims to access the genomic potential of an environmental sample directly, is a burgeoning area that is generating enormous amounts of biological information. An examination of recent metagenomics literature reveals the discipline to be heading in new and interesting directions, including the investigation of the normal flora of mammals, analysis of ancient genomes, and exploration of the distribution of novel pathways. In addition, the development of new bioinformatics approaches and tools is allowing innovative mining of both existing and new data. Finally, there are indications that the integration of metagenomics with complementary approaches in microbial ecology is beginning. [source] Bacteria in the cold deep-sea benthic boundary layer and sediment,water interface of the NE AtlanticFEMS MICROBIOLOGY ECOLOGY, Issue 2 2000Carol Turley Abstract This is a short review of the current understanding of the role of microorganisms in the biogeochemistry in the deep-sea benthic boundary layer (BBL) and sediment,water interface (SWI) of the NE Atlantic, the gaps in our knowledge and some suggestions of future directions. The BBL is the layer of water, often tens of meters thick, adjacent to the sea bed and with homogenous properties of temperature and salinity, which sometimes contains resuspended detrital particles. The SWI is the bioreactive interface between the water column and the upper 1 cm of sediment and can include a large layer of detrital material composed of aggregates that have sedimented from the upper mixed layer of the ocean. This material is biologically transformed, over a wide range of time scales, eventually forming the sedimentary record. To understand the microbial ecology of deep-sea bacteria, we need to appreciate the food supply in the upper ocean, its packaging, passage and transformation during the delivery to the sea bed, the seasonality of variability of the supply and the environmental conditions under which the deep-sea bacteria grow. We also need to put into a microbial context recent geochemical findings of vast reservoirs of intrinsically labile organic material sorped onto sediments. These may well become desorped, and once again available to microorganisms, during resuspension events caused by deep ocean currents. As biotechnologists apply their tools in the deep oceans in search of unique bacteria, an increasing knowledge and understanding of the natural processes undertaken and environmental conditions experienced by deep-sea bacteria will facilitate this exploitation. [source] Linkage of microbial ecology to phenotype: correlation of rumen microbial ecology to cattle's feed efficiencyFEMS MICROBIOLOGY LETTERS, Issue 1 2008Le Luo Guan Abstract 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. [source] Ribosomal RNA-targeted nucleic acid probes for studies in microbial ecologyFEMS MICROBIOLOGY REVIEWS, Issue 5 2000Rudolf Amann Abstract With readily applicable hybridization assays, mainly based on rRNA-targeted nucleic acid probes, and direct, cultivation-independent sequence retrieval, microbiologists can for the first time determine the true composition of microbial communities. Phylogenetic identification and exact spatiotemporal quantification of microorganisms will in the future become prerequisites for high quality studies in microbial ecology just as good taxonomy and solid quantification have always been for macroecology. This review is intended to give a short history of the development of rRNA-targeted nucleic acid probes and probe technologies, as well as of their application in microbial ecology. The current state of the art is described, and we will try to look into the future. Over the last decade, rRNA-targeted probes have become a handy tool for microbial ecologists. In order to speed up the transformation of microbial ecology from a mostly descriptive to a hypothesis-driven, experimental science more intense use must be made of the taxonomic precision and quantitativeness of rRNA-targeted probes. [source] Aquatic Microbial Ecology: Water Desert, Microcosm, Ecosystem.INTERNATIONAL REVIEW OF HYDROBIOLOGY, Issue 4-5 2008What's Next? Abstract Aquatic microbial ecology aims at nothing less than explaining the world from "ecological scratch". It develops theories, concepts and models about the small and invisible living world that is at the bottom of every macroscopic aquatic system. In this paper we propose to look at the development of Aquatic Microbial Ecology as a reiteration of classical (eukaryotic) limnology and oceanography. This was conceptualized moving historically from the so-called water desert to microcosm to ecosystem. Each of these concepts characterizes a particular historical field of knowledge that embraces also practices and theories about living beings in aquatic environments. Concerning the question of "who is there", however, Aquatic Microbial Ecology historically developed in reverse order. Repetition, reiteration and replication notwithstanding, Aquatic Microbial Ecology has contributed new ideas, theories and methods to the whole field of ecology as well as to microbiology. The disciplining of Aquatic Microbial Ecology happened in the larger field of plankton biology, and it is still attached to this biological domain, even conceiving of itself very self-consciously as a discipline of its own. Today, Aquatic Microbial Ecology as a discipline is much broader than plankton ecology ever was, for it includes not only oceans and freshwaters but also benthic, interstitial and groundwater systems. The success of Aquatic Microbial Ecology is expressed by its influence on other fields in ecology. The challenge is to further develop its theoretical and methodological features while at the same time contributing to current pressing problems such as climate change or the management of global water resources. And then it may not be fanciful to suppose that even in the year nineteen hundred and nineteen a great number of minds are still only partially lit up by the cold light of knowledge. It is the most capricious illuminant. They are still apt to ruminate, without an overpowering bias to the truth, whether a kingfisher's body shows which way the wind blows; whether an ostrich digests iron; whether owls and ravens herald ill-fortune; and the spilling of salt bad luck; what the tingling of ears forebodes, and even to toy pleasantly with more curious speculations as to the joints of elephants and the politics of storks, which came within the province of the more fertile and better-informed brain of the author (1919) Virginia Woolf from the essay "Reading", In: Leonard Woolf (ed.), 1950: The Captain's Death Bed and Other Essays, , London: Hogarth Press, p. 157. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Which are the polyphosphate accumulating organisms in full-scale activated sludge enhanced biological phosphate removal systems in Australia?JOURNAL OF APPLIED MICROBIOLOGY, Issue 2 2006M. Beer Abstract Aims:, To see if the compositions of the microbial communities in full scale enhanced biological phosphorus removal activated sludge systems were the same as those from laboratory scale sequencing batch reactors fed a synthetic sewage. Methods:, Biomass samples taken from nine full scale enhanced biological phosphate removal (EBPR) activated sludge plants in the eastern states of Australia were analysed for their populations of polyphosphate (polyP)-accumulating organisms (PAO) using semi-quantitative fluorescence in situ hybridization (FISH) in combination with DAPI (4,-6-diamidino-2-phenylindole) staining for polyP. Results:, Very few betaproteobacterial Rhodocyclus related organisms could be detected by FISH in most of the plants examined, and even where present, not all these cells even within a single cluster, stained positively for polyP with DAPI. In some plants in samples from aerobic reactors the Actinobacteria dominated populations containing polyP. Conclusions:, The PAO populations in full-scale EBPR systems often differ to those seen in laboratory scale reactors fed artificial sewage, and Rhodocyclus related organisms, dominating these latter communities may not be as important in full-scale systems. Instead Actinobacteria may be the major PAO. Significance and Impact of the Study:, These findings illustrate how little is still known about the microbial ecology of EBPR processes and that more emphasis should now be placed on analysis of full-scale plants if microbiological methods are to be applied to monitoring their performances. [source] Failure of the ammonia oxidation process in two pharmaceutical wastewater treatment plants is linked to shifts in the bacterial communitiesJOURNAL OF APPLIED MICROBIOLOGY, Issue 5 2005L. Wittebolle Abstract Aims:, To investigate whether two different wastewater treatment plants (WWTPs) , treating the same pharmaceutical influent , select for a different bacterial and/or ammonia oxidizing bacterial (AOB) community. Methods and Results:, Molecular fingerprinting demonstrated that each WWTP had its own total bacterial and AOB community structure, but Nitrosomonas eutropha and N. europea were dominant in both WWTP A and B. The DNA and RNA analysis of the AOB communities revealed different patterns; so the most abundant species may not necessarily be the most active ones. Nitritation failures, monitored by chemical parameter analysis, were reflected as AOB community shifts and visualized by denaturing gradient gel electrophoresis (DGGE)-based moving window analysis. Conclusions:, This research demonstrated the link between functional performance (nitritation parameters) and the presence and activity of a specific microbial ecology (AOB). Clustering and moving window analysis based on DGGE showed to be valuable to monitor community shifts in both WWTPs. Significance and Impact of the Study:, This study of specific community shifts together with functional parameter analysis has potential as a tool for relating functional instability (such as operational failures) to specific-bacterial community shifts. [source] Use of RAPD and killer toxin sensitivity in Saccharomyces cerevisiae strain typingJOURNAL OF APPLIED MICROBIOLOGY, Issue 3 2005L. Corte Abstract Aims:, Two different strain characterization techniques, random amplified polymorphic DNA (RAPD) and killer toxin sensitivity (KTS), were compared to assess their typing performance using a set of 30 certified Saccharomyces cerevisiae strains. Methods and Results:, A sequential random resampling procedure was employed to subdivide the 32 descriptors in eight sets, in order to compare the differential performances of the two techniques with diverse number of characters. Results showed that RAPD performs better than killer, although the complete differentiation of the strains under study could be obtained only by combining profiles from the two techniques Conclusions:, The combination of different typing techniques was useful when discriminating similar organisms. In such cases, the introduction of a second typing technique can be more advantageous than increasing the number of characters obtained with a single method. Significance and Impact of the Study:, The distribution of among-strains pairwise distances and the relative performance of the two techniques has implications for the study of biodiversity, taxonomy and microbial ecology. [source] A Genomic Study of Leuconostoc mesenteroides and the Molecular Ecology of Sauerkraut FermentationsJOURNAL OF FOOD SCIENCE, Issue 1 2004F. BREIDT JR. ABSTRACT: Most vegetable fermentations are carried out without the use of starter cultures, using a technology that has remained virtually unchanged for centuries. As the scale of industrial vegetable fermentations increases worldwide, the disposal of salt (chloride) waste, which is generated during processing of these products, has become a major problem. The development of new technology to reduce the amount of salt used in vegetable fermentations may require a greater understanding of the microbial ecology of these fermentations, and may also require the use of starter cultures. [source] Effects of areca nut extracts on the functions of human neutrophils in vitroJOURNAL OF PERIODONTAL RESEARCH, Issue 4 2000Shan-Ling Hung Aqueous extracts of ripe areca nut without husk (ripe ANE) and fresh and tender areca nut with husk (tender ANE) were examined for their effects on the defensive functions of human neutrophils. Exposure of peripheral blood neutrophils to ripe ANE and tender ANE inhibited their bactericidal activity against oral pathogens, including Actinobacillus actinomycetemcomitans and Streptococcus mutans, in a dose-dependent manner. At the concentrations tested, ripe and tender ANEs did not significantly affect the viability of neutrophils as verified by their ability to exclude trypan blue dye. However, both ANEs inhibited the production of bactericidal superoxide anion by neutrophils as measured by cytochrome c reduction. Moreover, the ripe ANE inhibited neutrophils more effectively than did tender ANE. Arecoline, a major alkaloid of areca nut, only exhibited an inhibitory effect on the functions of neutrophils when high concentrations were used. Therefore, arecoline could not be used to explain the inhibitory effects observed for ANEs. In conclusion, our results demonstrated that ripe and tender ANEs reduced the antibacterial activity and the superoxide anion production of neutrophils. This effect may contribute to a less efficient elimination of bacteria from the periodontal environment. Inhibition of the antimicrobial functions of neutrophils may alter the microbial ecology of the oral cavity, and this may be one possible mechanism by which areca nut compromises the oral health of users of areca nut products. [source] In vitro effects of phlorotannins from Ascophyllum nodosum (brown seaweed) on rumen bacterial populations and fermentationJOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE, Issue 13 2009Yuxi Wang Abstract BACKGROUND: Use of brown algae (seaweed) in ruminant diets is increasing, but the effects of its phlorotannins (PT) on rumen microbial ecology have not been determined. Mixed forage (50:25:25 ground barley silage,alfalfa hay,grass hay) was used as substrate in a batch culture ruminal incubation that included PT extracted from Ascophyllum nodosum, with and without polyethylene glycol. Principal ruminal bacteria were quantified using real-time polymerase chain reaction. RESULTS: At 500 µg mL,1, PT reduced growth of Fibrobacter succinogenes by 78%, 83% and 65% at 6, 12 and 24 h (P < 0.001), Ruminococcus albus at 24 h only (P < 0.01) and did not affect R. flavefaciens. Non-cellulolytic bacteria Selenomonas ruminantium, Ruminobacter amylophilus and Prevotella bryantii were increased (P < 0.001) by PT at 12 and 24 h. Effects of PT on fermentation products (gas production, volatile fatty acid profiles and ammonia accumulation) were consistent with alterations in rumen microbial populations. CONCLUSION: The effects of PT on ruminal bacteria were species-dependent, which suggests that diet may mediate PT effects on animal performance. The variation in sensitivity of ruminal bacteria to PT reflects previously reported effects of condensed tannins from terrestrial plants on microbial populations. Copyright © 2009 Crown in the right of Canada. Published by John Wiley & Sons, Ltd [source] Quorum sensing and signal interference: diverse implicationsMOLECULAR MICROBIOLOGY, Issue 6 2004Lian-Hui Zhang Summary Quorum sensing (QS) is a community genetic regulation mechanism that controls microbiological functions of medical, agricultural and industrial importance. Discovery of microbial QS signals and the signalling mechanisms led to identification of numerous enzymatic and non-enzymatic signal interference mechanisms that quench microbial QS signalling. Evidence is accumulating that such signal interference mechanisms can be developed as promising approaches to control microbial infection and biofilm formation. In addition, these mechanisms exist not only in microorganisms but also in the host organisms of bacterial pathogens, highlighting their potential implications in microbial ecology and in host,pathogen interactions. Investigation of QS and signal interference mechanisms might significantly broaden the scope of research in microbiology. [source] DNA reassociation kinetics and diversity indices: richness is not rich enoughOIKOS, Issue 2 2008Bart Haegeman DNA reassociation kinetics, also known as Cot curves, were recently used by Gans and co-workers to estimate the number of bacterial species present in soil samples. By reanalysing the mathematical model we show that rather than the number of species, Simpson and Shannon diversity indices are encoded in the experimental data. Our main tool to establish this result are the so-called Rényi diversities, closely related to Hill numbers, illustrating the power of these concepts in interpreting ecological data. We argue that the huge diversity encountered in microbial ecology can be quantified more informatively by diversity indices than by number of species. [source] Technical considerations for RNA-based stable isotope probing: an approach to associating microbial diversity with microbial community function,RAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 23 2002Mike Manefield An ongoing challenge within microbial ecology is the development of methodologies that attribute microbial community functions to microbial diversity. One approach, involving the incorporation of stable isotopes from labelled tracer compounds into biological signature molecules (biomarkers), may overcome this current limitation. To examine the potential of RNA as the biomarker in stable isotope probing we have generated a series of atom % 13C-enriched RNA samples through exploitation of the anabolic abilities of a phenol-degrading environmental isolate. Isotope ratio mass spectrometry was used to determine the atom % 13C of each RNA sample (ca. 1,100%). The corresponding buoyant density (1.755,1.795,g,mL,1) was determined by equilibrium density gradient centrifugation and agarose gel electrophoresis. This empirically defined relationship between the atom % 13C of RNA and its buoyant density suggests ribonucleic acids with atom % 13C enrichments greater than 10% can be isolated by equilibrium density centrifugation. The processing and analysis of isolated RNA by reverse transcription polymerase chain reaction, denaturing gradient gel electrophoresis, cloning and sequencing are discussed. The RNA-based stable isotope probing protocol presented here will find particular utility in assessing the roles of microbial community members in the biodegradation of natural and anthropogenic xenobiotic compounds. Copyright © 2002 John Wiley & Sons, Ltd. [source] Bacterial diversity in various coastal mariculture ponds in Southeast China and in diseased eels as revealed by culture and culture-independent molecular techniquesAQUACULTURE RESEARCH, Issue 9 2010Yonghui Zeng Abstract Mariculture ponds are widely distributed in Chinese coasts and have become a threat to the health of coastal ecosystems. In order to improve our understanding on the microbial composition in mariculture environments, we sampled a variety of ponds farming different animals or plants around the Dongshan Island and Xiamen Island in Southeast China and isolated cultures from the tissues of diseased eels. Analysis by polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE), clone library and direct culturing methods revealed highly diverse bacterial communities in these samples. Bacterial communities in the Dongshan samples were dominated by Alphaproteobacteria, Gammaproteobacteria and Bacteroidetes. The Gracilaria verrucosa pond harbours the most abundant species (20 DGGE bands), followed by Epinephelus diacanthus pond (18 bands), Haliotis diversicolor supertexta pond I (18 bands) and Penaeus vannamei pond (11 bands). In comparison with surface waters, Penacus orientalis pond sediment showed a much more complex bacterial community, from which only sequences affiliated with Deltaproteobacteria, Firmicutes, Acidobacteria and candidate phylum TM6 were found. Bacterial cultures in diseased eels were closely related to two pathogenic genera, Aeromonas in Gammaproteobacteria and Bacillus, in Firmicutes. Clones affiliated with another two genera, Escherichia and Vibrio, that have pathogenic potentials were also identified. Phylogenetic analysis of a total of 131 sequences showed that 48.9% of the sequences were clustered into Gammaproteobacteria and formed the most abundant group, followed by Alphaproteobacteria (19.1%), Firmicutes (7.6%), Bacteroidetes (5.3%), Deltaproteobacteria (5.3%), Actinobacteria (4.6%), Chloroplast (3.8%), Acidobacteria (2.3%), Cyanobacteria (1.5%), Betaproteobacteria (0.7%) and TM6 (0.7%). 43.7% (28/64) of the phylogenetic clusters cannot be classified into any known genus and 44.3% (58/131) of the sequences show <95% similarity to public database records, suggesting that abundant novel species exist in mariculture ponds. Gathering bacterial diversity data in mariculture ponds and diseased fish is meaningful for the prevention and control of fish diseases and for the improvement of our understanding of microbial ecology in a pond environment. [source] Biotec Visions 2009, November,DecemberBIOTECHNOLOGY JOURNAL, Issue 11 2009Article first published online: 13 NOV 200 Nobel Prizes 2009: Ribosomes , Telomeres and telomerases Encyclopaedia of Life Sciences: SNP genotyping technologies , Molecular mimicry Special issues: Chinese microbial ecology , Advances in yeast proteomics , MALDI-TOF "Flip-flop" drug susceptibility test News: Phytophthora infestans genome , Sequencing bacterial transcriptomes , Stem cells from fat , Selecting green clones , Endogenous mutagenic force , Green batteries , Tobacco-produced vaccine , O2 transport in artificial liver , Endolysins instead of antibiotics , Quick switch key for mitochondria , Climate change shrinks algae , Bacteria degrade microcystins Opinion: Will biotech banish wrinkles forever? Most Read Synthetic biology Tips and tricks: Trypsinizing cells Biotech round the world: Kenya Writing Tips: IMRAD or RAMID? Briefs: Metabolic Engineering award , Mosquitoes , from foe to friend , Mobile phone microscope Test your Knowledge: Do you recognize this? In Brief: The horse pathogen Rhodococcus equi [source] | ||||||||||||||||||||||||||||