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At least 307 records · Page 17Linked to original sources
PubMed2006

Microbial community in black rust exposed to hot ridge flank crustal fluids.

During Integrated Ocean Drilling Program Expedition 301, we obtained a sample of black rust from a circulation obviation retrofit kit (CORK) observatory at a borehole on the eastern flank of Juan de Fuca Ridge. Due to overpressure, the CORK had failed to seal the borehole. Hot fluids from oceanic crust had discharged to the overlying bottom seawater and resulted in the formation of black rust analogous to a hydrothermal chimney deposit. Both culture-dependent and culture-independent analyses indicated that the black-rust-associated community differed from communities reported from other microbial habitats, including hydrothermal vents at seafloor spreading centers, while it shared phylotypes with communities previously detected in crustal fluids from the same borehole. The most frequently retrieved sequences of bacterial and archaeal 16S rRNA genes were related to the genera Ammonifex and Methanothermococcus, respectively. Most phylotypes, including phylotypes previously detected in crustal fluids, were isolated in pure culture, and their metabolic traits were determined. Quantification of the dissimilatory sulfite reductase (dsrAB) genes, together with stable sulfur isotopic and electron microscopic analyses, strongly suggested the prevalence of sulfate reduction, potentially by the Ammonifex group of bacteria. Stable carbon isotopic analyses suggested that the bulk of the microbial community was trophically reliant upon photosynthesis-derived organic matter. This report provides important insights into the phylogenetic, physiological, and trophic characteristics of subseafloor microbial ecosystems in warm ridge flank crusts.

Archaea↗
PubMed2005

Evolution of a microbial nitrilase gene family: a comparative and environmental genomics study.

BACKGROUND: Completed genomes and environmental genomic sequences are bringing a significant contribution to understanding the evolution of gene families, microbial metabolism and community eco-physiology. Here, we used comparative genomics and phylogenetic analyses in conjunction with enzymatic data to probe the evolution and functions of a microbial nitrilase gene family. Nitrilases are relatively rare in bacterial genomes, their biological function being unclear. RESULTS: We examined the genetic neighborhood of the different subfamily genes and discovered conserved gene clusters or operons associated with specific nitrilase clades. The inferred evolutionary transitions that separate nitrilases which belong to different gene clusters correlated with changes in their enzymatic properties. We present evidence that Darwinian adaptation acted during one of those transitions and identified sites in the enzyme that may have been under positive selection. CONCLUSION: Changes in the observed biochemical properties of the nitrilases associated with the different gene clusters are consistent with a hypothesis that those enzymes have been recruited to a novel metabolic pathway following gene duplication and neofunctionalization. These results demonstrate the benefits of combining environmental genomic sampling and completed genomes data with evolutionary and biochemical analyses in the study of gene families. They also open new directions for studying the functions of nitrilases and the genes they are associated with.

Aminohydrolases↗
PubMed2005

Risk factors of mortality for nosocomial pneumonia: importance of initial anti-microbial therapy.

Nosocomial pneumonia is a common nosocomial infection and has high mortality rate. Risk factors of mortality of nosocomial pneumonia were studied in 132 hospitalised patients who developed nosocomial pneumonia. The overall mortality rate was 64/132, 48.5%. Of the 11 risk factors univariately associated with mortality due to nosocomial pneumonia, only the inappropriate initial anti-microbial therapy, high simplified acute physiology score and multiple organ failures remained significant after stepwise logistic regression. Gram-negative bacilli were still the most pre-dominant causative microbiologic agents of nosocomial pneumonia with Pseudomonas aeruginosa (20.3%), Acinetobacter baumannii (18.6%) and Escherichia coli (5.9%) being the three most predominant pathogens. A. baumannii were significantly more predominant among non-survivors than survivors (13.56 vs. 5.08%, p=0.0418). The incidence rate of methicillin-resistant Staphylococcus aureus was 19.5% higher than previous reports. We conclude that inappropriate initial anti-microbial therapy for nosocomial pneumonia is associated with the mortality rate of nosocomial pneumonia, and appropriate anti-microbial therapy improves outcome of nosocomial pneumonia.

Aged↗
PubMed2005

Chemical modulation of physiological adaptation and cross-protective responses against oxidative stress in soil bacterium and phytopathogen, Xanthomonas.

Soil bacteria need to adapt quickly to changes in the environmental conditions. Physiological adaptation plays an important role in microbial survival, especially under stressful conditions. Here the abilities of chemicals and pesticides to modulate physiological adaptive and cross-protective responses, that make the bacteria more resistant to oxidative stress, are examined in the soil bacterium and phytopathogen, Xanthomonas. The genetic basis for the observed stress resistance, as well as the regulatory mechanisms controlling gene expression during the process, has begun to be elucidated.

Adaptation, Physiological↗
PubMed1998

Effect of some physiological factors on nitrogenase activity and nitrogenase mediated hydrogen evolution by mixed microbial culture.

Fermentative H2 evolution, nitrogenase activity (acetylene reduction) and nitrogenase mediated H2 evolution was studied in free cells of mixed microbial population of H2 producers. At 3% glucose level, the cells produced 8.35 l H2/mol glucose utilized. The role of nitrogenase system in H2 generation was evident by derepressed nitrogenase activity (0.46 nmoles C2H4 produced/mg protein/h) under defined in vitro conditions. For maximum expression of the activity, the cells required preactivation under anaerobic conditions by incubating at 40 degrees C for 20-24 h with 0.2% glucose in the culture medium. At an O2 level of more than 0.25%, the acetylene reduction activity decreased significantly and could not be detected at a level of 20%. Nitrogenase activity development was higher at acetylene: inoculum ratio between 4.2-6.25. H2 evolution was lower when the mixed cells were incubated under an atmosphere of 10% C2H2 and 5% CO gas. This decrease in H2 evolution was also evident at 2.5-6.5 mM NaNO3 and KNO3 concentrations in the liquid culture medium thus establishing more than 50% H2 evolution through nitrogenase.

Acetylene↗
PubMed2003

Activity assessment of microorganisms eluted from sediments using 5-cyano-2,3-ditolyl tetrazolium chloride: a quantitative comparison of flow cytometry to epifluorescent microscopy.

Enhanced natural recovery may be successfully implemented at contaminated sediment sites, which are often characterized by large volumes of sediments with low to moderate levels of contamination to cost-effectively reduce human and ecological risks. In order to evaluate the potential for microbial contribution to remediation strategies, physiological assessment of indigenous microorganisms is essential. We report here a method for rapid and accurate assessment of metabolically (5-cyano-2,3-ditolyl tetrazolium chloride [CTC]) active microorganisms eluted from sediment, based on flow cytometry (FCM). Microorganisms eluted from sediment and suspended in estuarine medium were stained with CTC and counterstained with the DNA stain Picogreen (PG). Optimal stain concentrations and incubation times were employed. FCM quantification of the dual-stained microorganisms was not statistically different (paired t test; alpha=0.05; df=10) from enumeration (total or active numbers) by an established method (fluorescent microscopy) over two orders of magnitude (approximately 10(4)-10(6)/ml). This research suggests that FCM, which allows the collection and analysis of multiple parameters (light scatter and fluorescence emission), is a good candidate for microbial characterization in complex environmental matrices, such as sediments, across a broad range of activity levels (approximately 2% to 84% of total). Potential applications for this FCM-based method include the rapid assessment of changes in sediment microbial activity in response to enhanced bioremediation strategies.

DNA, Bacterial↗
PubMed2006

Influence of the diet components on the symbiotic microorganisms community in hindgut of Coptotermes formosanus Shiraki.

Artificial diet was developed for rearing of lower termites (workers) Coptotermes formosanus. C. formosanus was fed with either wood powder of Japanese red pine, cellulose, cellobiose, or glucose for 30 days. The effect of carbon sources in the diet on the structure and function of the symbiotic intestinal microbial community and on the physiological activity of C. formosanus was studied. Three symbiont protozoa, Pseudotrichonympha grassi, Holomastigotoides hartmanni, and Spirotrichonympha leidyi, were found in the hindgut of C. formosanus that fed on the diets containing carbon sources with high molecular weight (MW). However, when artificial diets containing carbohydrate with low MW were used, both P. grassi and H. hartmanni disappeared, and only few S. leidyi were alive. This suggested that both P. grassi and H. hartmanni play important roles in the digestion and utilization of carbohydrate with high MW. The denaturing gradient gel electrophoresis analysis of bacterial community in the hindgut of termites showed that the similarity between intestinal bacteria community in termites fed with diets containing high-MW carbon sources and those with low MW was only about 40%. It was apparent that changes in diets resulted to changes in intestinal microbial community, and this in turn affected cellulase activity in C. formosanus.

Animals↗
PubMed2006

Diagnostic microbial microarrays in soil ecology.

Soil microbial communities are responsible for important physiological and metabolic processes. In the last decade soil microorganisms have been frequently analysed by cultivation-independent techniques because only a minority of the natural microbial communities are accessible by cultivation. Cultivation-independent community analyses have revolutionized our understanding of soil microbial diversity and population dynamics. Nevertheless, many methods are still laborious and time-consuming, and high-throughput methods have to be applied in order to understand population shifts at a finer level and to be better able to link microbial diversity with ecosystems functioning. Microbial diagnostic microarrays (MDMs) represent a powerful tool for the parallel, high-throughput identification of many microorganisms. Three categories of MDMs have been defined based on the nature of the probe and target molecules used: phylogenetic oligonucleotide microarrays with short oligonucleotides against a phylogenetic marker gene; functional gene arrays containing probes targeting genes encoding specific functions; and community genome arrays employing whole genomes as probes. In this review, important methodological developments relevant to the application of the different types of diagnostic microarrays in soil ecology will be addressed and new approaches, needs and future directions will be identified, which might lead to a better insight into the functional activities of soil microbial communities.

Bacteria↗
PubMed2006

Dynamics of multiple symbiont density regulation during host development: tsetse fly and its microbial flora.

Symbiotic associations often enhance hosts' physiological capabilities, allowing them to expand into restricted terrains, thus leading to biological diversification. Stable maintenance of partners is essential for the overall biological system to succeed. The viviparous tsetse fly (Diptera: Glossinidae) offers an exceptional system to examine factors that influence the maintenance of multiple symbiotic organisms within a single eukaryotic host. This insect harbours three different symbionts representing diverse associations, coevolutionary histories and transmission modes. The enterics, obligate mutualist Wigglesworthia and beneficial Sodalis, are maternally transmitted to the intrauterine larvae, while parasitic Wolbachia infects the developing oocyte. In this study, the population dynamics of these three symbionts were examined through host development and during potentially disruptive events, including host immune challenge, the presence of third parties (such as African trypanosomes) and environmental perturbations (such as fluctuating humidity levels). While mutualistic partners exhibited well-regulated density profiles over different host developmental stages, parasitic Wolbachia infections varied in individual hosts. Host immune status and the presence of trypanosome infections did not impact the steady-state density levels observed for mutualistic microbes in either sex, while these factors resulted in an increase in Wolbachia density in males. Interestingly, perturbation of the maternal environment resulted in the deposition of progeny harbouring greater overall symbiont loads. The regulation of symbiont density, arising from coadaptive processes, may be an important mechanism driving inter-specific relations to ensure their competitive survival and to promote specialization of beneficial associations.

Animals↗
PubMed2005

Distribution, phylogenetic diversity and physiological characteristics of epsilon-Proteobacteria in a deep-sea hydrothermal field.

Epsilon-Proteobacteria is increasingly recognized as an ecologically significant group of bacteria, particularly in deep-sea hydrothermal environments. In this study, we studied the spatial distribution, diversity and physiological characteristics of the epsilon-Proteobacteria in various microbial habitats in the vicinity of a deep-sea hydrothermal vent occurring in the Iheya North field in the Mid-Okinawa Trough, by using culture-dependent and -independent approaches. The habitats studied were inside and outside hydrothermal plume, and annelid polychaete tubes. In addition, we deployed colonization devices near the vent emission. The polychaete tubes harboured physiologically and phylogenetically diverse microbial community. The in situ samplers were predominantly colonized by epsilon-Proteobacteria. Energy metabolism of epsilon-Proteobacteria isolates was highly versatile. Tree topology generated from the metabolic traits was significantly different (P = 0.000) from that of 16S rRNA tree, indicating current 16S rRNA gene-based analyses do not provide sufficient information to infer the physiological characteristics of epsilon-Proteobacteria. Nevertheless, culturability of epsilon-Proteobacteria in various microbial habitats differed among the phylogenetic subgroups. Members of Sulfurimonas were characterized by the robust culturability, and the other phylogenetic subgroups appeared to lose culturability in seawater, probably because of the sensitivity to oxygen. These results provide new insight into the ecophysiological characteristics of the deep-sea hydrothermal vent epsilon-Proteobacteria, which has never been assessed by comparative analysis of the 16S rRNA genes.

Culture Media↗
PubMed1984

Impact of an oil field effluent on microbial activities in a Wyoming river.

The survival, functions, and physiological diversity of autochthonous sediment microbiota were examined in situ at five stations along the Little Popo Agie River, WY; one station above, one at, and three below a discharge point for oil wastewater from Union Oil Company's Dallas Field. Below the oil wastewater discharge point there were increases in electron-transport activity, carbon dioxide production, and microbial populations of heterotrophs, ammonifiers, hexadecane degraders, starch hydrolyzers, protein hydrolyzers, and sulfate reducers. At a station 1420 m below the discharge point, however, overall sediment microbial activities and all of the physiological groups of bacteria, except hexadecane-degrading microbiota, were at levels comparable with those at the control station above the discharge point. Similarly, mineralization of glucose, amino acids, hexanoic acid, and hexadecane was elevated at stations directly below the discharge point, but appeared to subside rapidly. Xenobiotic biodegradation potential of the sediments varied with the chemical and the sample location and was not directly related to oil residue levels in the sediment. Microorganisms thus appeared to maintain physiological diversity and increased in numbers and activity in a riverine environment that contained petroleum hydrocarbon concentrations known to be deleterious to freshwater fish and macrobenthic communities.

Alkanes↗
PubMed2004

Heavy-metal and microbial depuration of the clam Ruditapes decussatus and its effect on bivalve behavior and physiology.

The bivalve Ruditapes decussatus was evaluated as a possible biomonitor of heavy-metal contamination. Concentrations of copper (Cu), cobalt (Co), iron (Fe), nickel (Ni), and manganese (Mn) were measured in R. decussatus. Water and sediment samples were collected at two stations of Timsah Lake in Ismailia, Egypt, from October to November 2002, using atomic absorption spectrophotometry (AAS). Results from the heavy-metal and microbial analyses indicated that site II was less contaminated than site I. The bivalve showed accumulation of metals, with a bioaccumulation factor (BAF) greater than 4. The bioaccumulation of metals varied strongly according to the sampling site. After 48 h of depuration, Fe, Ni, Co, Cu, and Mn were reduced significantly, to 46.8% and 47.7%, 19.9% and 20.3%, 27.3% and 27.9%, 35.9% and 36.6%, and 18.2% and 26.6%, compared with the initial concentrations, in clam tissue at the two stations. In bivalves from site II the counts of total bacteria, fecal coliforms, and bacterial pathogens were reduced by more than 90%, whereas phage counts were only reduced by 56% after 4 days of depuration. The depuration of bivalves collected from the heavily polluted site (I) was not effective, as coliforms were reduced only by 85% after 4 days, whereas counts of pathogens and pathogenic indicators such as Vibrio, fecal Streptococcus, and coliphage decreased to less than 50% of the initial concentration. The time necessary to decrease contamination to 10%, 50%, and 90% for clams at both stations was consistently shorter for heavy metals than for microorganisms. Investigation of the effects of heavy-metal and microbiological depuration on valve movement and physiological rates (oxygen consumption and ammonia excretion) was carried out on R. decussatus to test the utility of physiological stress indices in assessing the health of depurated animals. Clams in the experimental tanks exhibited various states of activity, which were rated by identifying and scoring (0-4) the different parameters, including shell gap, siphon extension, and foot protrusion. Moreover, an increase in ammonia excretion was usually associated with an increase in respiration rate. The oxygen-to-nitrogen ratio provided a sensitive indicator of bivalve health. It can be concluded that shellfish monitoring and depuration data depended on the initial concentration of the pollutants. There were differences in the physiological responses of clams from the two sites during the periods of pre- and postdepuration of the contaminants. There was a significant correlation between reduction of metal concentration in clam tissue and enhancement of valve movement, as well as activity and increasing respiration rate.

Ammonia↗
PubMed2005

Recovery of microbially mediated processes in soil augmented with a pentachlorophenol-mineralizing bacterium.

Specific physiological groups can be used to evaluate the recovery of soil microbial communities following disturbance. In this study, soil was contaminated with pentachlorophenol (PCP) to assess the resiliency of microorganisms responsible for carbon and nitrogen cycling. Methane fluxes were monitored in soil microcosms to evaluate the effects of contamination and augmentation on microbial populations involved in carbon cycling. The addition of a PCP-mineralizing bacterium, Sphingomonas chlorophenolica strain RA2, enhanced the recovery of methane-oxidizing capacity relative to uninoculated treatments when soil was contaminated with low concentrations of PCP (10 and 50 microg/g soil, ppm). At the highest level of PCP contamination tested (300 ppm), there was no recovery of methane-oxidizing capacity whether or not the PCP-mineralizing bacterium was added to soil. The nitrogen-cycling capacity of contaminated and augmented soil was tested by measuring nitrification potentials. The addition of PCP resulted in a concentration-dependent reduction in nitrification rates. After three months of incubation, all augmented soils had nitrification rates equivalent to the uncontaminated control, and the uninoculated soils contaminated with 100 and 300 ppm PCP still were impaired in their nitrification potentials. These results indicate that biological removal of a contaminant has the potential to restore microbially mediated processes to levels observed prior to contamination.

Ammonia↗
PubMed2005

Microbe-surface interactions in biofouling and biocorrosion processes.

The presence of microorganisms on material surfaces can have a profound effect on materials performance. Surface-associated microbial growth, i.e. a biofilm, is known to instigate biofouling. The presence of biofilms may promote interfacial physico-chemical reactions that are not favored under abiotic conditions. In the case of metallic materials, undesirable changes in material properties due to a biofilm (or a biofouling layer) are referred to as biocorrosion or microbially influenced corrosion (MIC). Biofouling and biocorrosion occur in aquatic and terrestrial habitats varying in nutrient content, temperature, pressure and pH. Interfacial chemistry in such systems reflects a wide variety of physiological activities carried out by diverse microbial populations thriving within biofilms. Biocorrosion can be viewed as a consequence of coupled biological and abiotic electron-transfer reactions, i.e. redox reactions of metals, enabled by microbial ecology. Microbially produced extracellular polymeric substances (EPS), which comprise different macromolecules, mediate initial cell adhesion to the material surface and constitute a biofilm matrix. Despite their unquestionable importance in biofilm development, the extent to which EPS contribute to biocorrosion is not well-understood. This review offers a current perspective on material/microbe interactions pertinent to biocorrosion and biofouling, with EPS as a focal point, while emphasizing the role atomic force spectroscopy and mass spectrometry techniques can play in elucidating such interactions.

Bacterial Physiological Phenomena↗
PubMed2006

Immunobiology of human NKG2D and its ligands.

The NKG2D-DAP10 receptor complex activates natural killer (NK) cells and costimulates effector T cell subsets upon engagement of ligands that can be conditionally expressed under physiologically harmful conditions such as microbial infections and malignancies. These characteristics have given rise to the widely embraced concept of immunorecognition of "induced or damaged self," complementing the "missing self" paradigm that is represented by MHC class I allotypes and their interactions with inhibitory receptors on NK cells. However, this notion may only be partially sustainable, as various patterns of constitutive tissue distributions have become apparent among members of one NKG2D ligand family. This review summarizes the biological properties of NKG2D and its ligands and discusses the interactions and regulation of these molecules with emphasis of their significance in microbial infections, tumor immunology, and autoimmune disease.

Autoimmune Diseases↗
PubMed1990

Physiology of aliphatic hydrocarbon-degrading microorganisms.

This paper reviews aspects of the physiology and biochemistry of the microbial biodegradation of alkanes larger than methane, alkenes and alkynes with particular emphasis upon recent developments. Subject areas discussed include: substrate uptake; metabolic pathways for alkenes and straight and branched-chain alkanes; the genetics and regulation of pathways; co-oxidation of aliphatic hydrocarbons; the potential for anaerobic aliphatic hydrocarbon degradation; the potential deployment of aliphatic hydrocarbon-degrading microorganisms in biotechnology.

Anaerobiosis↗
PubMed1988

Seminalplasmin: a protein with many biological properties.

Proteins present in the seminal plasma of mammals are known to influence functions associated with ejaculated spermatozoa such as motility, capacitation, acrosome reaction and fertilising ability. The proteins isolated and characterised so far influence only one of the above functions of spermatozoa. Seminalplasmin, a protein isolated from the seminal plasma of bull is exceptional in that it influences many of the above spermatozoal functions. It is also a potent antimicrobial protein and capable of lysing microbial and mammalian cells. The physiological function of seminalplasmin as nature's own antifertility agent is discussed.

Acrosome↗