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Microbial Groups (microbial + groups)
Selected AbstractsDistribution of microbial populations and their relationship with environmental parameters in the coastal waters of Qingdao, ChinaENVIRONMENTAL MICROBIOLOGY, Issue 7 2010Min Wang Summary In order to understand the large-scale distribution of microbial populations simultaneously and their relationship with environmental parameters, flow cytometry was used to analyse samples collected from 46 stations in the coastal waters of Qingdao in spring, 2007. The distribution of virus was significantly and positively correlated with heterotrophic bacteria. Two groups of picophytoplankton (Synechococcus and picoeukaryotes) were detected; however, Prochlorococcus was not found. Picoeukaryotes and nanophytoplankton were abundant in the near-shore waters, whereas Synechococcus was abundant in the off-shore areas. No variation was found in vertical distribution of virus, heterotrophic bacteria, Synechococcus and nanophytoplankton abundances, except picoeukaryotes abundance in the bottom layer was dramatically lower than that in the upper layers. Correlation analyses indicated that the relationship between abiotic variables and heterotrophic bacteria, pico- and nanophytoplankton was closer than that between abiotic variables and virioplankton. Temperature and nutrients were the synchronous factors controlling the growth of heterotrophic bacteria, pico- and nanophytoplankton in the coastal waters of Qingdao in spring. The results suggested that synergistic and antagonistic effects existed among microbial groups. [source] Substrate incorporation patterns of bacterioplankton populations in stratified and mixed waters of a humic lakeENVIRONMENTAL MICROBIOLOGY, Issue 7 2009Ulrike Buck Summary Bacterial incorporation of glucose, leucine, acetate and 4-hydroxybenzoic acid (HBA) was investigated in an artificially divided humic lake (Grosse Fuchskuhle, Germany). Two basins with contrasting influx of allochthonous organic carbon were sampled during late summer stratification (oxic and anoxic layers) and after autumn mixing. High total and cell-specific incorporation rates were observed for glucose and HBA in stratified and mixed waters respectively, but only a small fraction of bacteria visibly incorporated HBA. The oxic layer of the more humic-rich basin featured a significantly lower fraction of glucose incorporating cells and substantially higher proportions of acetate assimilating bacteria. Niche differentiation was observed in two betaproteobacterial populations: cells affiliated with the Polynucleobacter C subcluster efficiently incorporated acetate but little glucose, whereas the opposite was found for members of the R-BT065 clade. By contrast, leucine incorporation was variable in both taxa. Considering the high concentrations and rapid photochemical generation of organic acids in humic waters our results may help to explain the success of the Polynucleobacter C lineage in such habitats. Specific substrate or habitat preferences were also present in three subgroups of the actinobacterial acI lineage: The numerically dominant clade in oxic waters (acI-840-1) was absent in the anoxic zone and did not incorporate acetate. A second group (acI-840-2) was found both in the epi- and hypolimnion, whereas the third one (acI-840-3) only occurred in anoxic waters. Altogether our results suggest a constitutive preference for some substrates versus an adaptive utilization of others in the studied microbial groups. [source] Limits of life in MgCl2 -containing environments: chaotropicity defines the windowENVIRONMENTAL MICROBIOLOGY, Issue 3 2007John E. Hallsworth Summary The biosphere of planet Earth is delineated by physico-chemical conditions that are too harsh for, or inconsistent with, life processes and maintenance of the structure and function of biomolecules. To define the window of life on Earth (and perhaps gain insights into the limits that life could tolerate elsewhere), and hence understand some of the most unusual biological activities that operate at such extremes, it is necessary to understand the causes and cellular basis of systems failure beyond these windows. Because water plays such a central role in biomolecules and bioprocesses, its availability, properties and behaviour are among the key life-limiting parameters. Saline waters dominate the Earth, with the oceans holding 96.5% of the planet's water. Saline groundwater, inland seas or saltwater lakes hold another 1%, a quantity that exceeds the world's available freshwater. About one quarter of Earth's land mass is underlain by salt, often more than 100 m thick. Evaporite deposits contain hypersaline waters within and between their salt crystals, and even contain large subterranean salt lakes, and therefore represent significant microbial habitats. Salts have a major impact on the nature and extent of the biosphere, because solutes radically influence water's availability (water activity) and exert other activities that also affect biological systems (e.g. ionic, kosmotropic, chaotropic and those that affect cell turgor), and as a consequence can be major stressors of cellular systems. Despite the stressor effects of salts, hypersaline environments can be heavily populated with salt-tolerant or -dependent microbes, the halophiles. The most common salt in hypersaline environments is NaCl, but many evaporite deposits and brines are also rich in other salts, including MgCl2 (several hundred million tonnes of bischofite, MgCl2·6H2O, occur in one formation alone). Magnesium (Mg) is the third most abundant element dissolved in seawater and is ubiquitous in the Earth's crust, and throughout the Solar System, where it exists in association with a variety of anions. Magnesium chloride is exceptionally soluble in water, so can achieve high concentrations (> 5 M) in brines. However, while NaCl-dominated hypersaline environments are habitats for a rich variety of salt-adapted microbes, there are contradictory indications of life in MgCl2 -rich environments. In this work, we have sought to obtain new insights into how MgCl2 affects cellular systems, to assess whether MgCl2 can determine the window of life, and, if so, to derive a value for this window. We have dissected two relevant cellular stress-related activities of MgCl2 solutions, namely water activity reduction and chaotropicity, and analysed signatures of life at different concentrations of MgCl2 in a natural environment, namely the 0.05,5.05 M MgCl2 gradient of the seawater : hypersaline brine interface of Discovery Basin , a large, stable brine lake almost saturated with MgCl2, located on the Mediterranean Sea floor. We document here the exceptional chaotropicity of MgCl2, and show that this property, rather than water activity reduction, inhibits life by denaturing biological macromolecules. In vitro, a test enzyme was totally inhibited by MgCl2 at concentrations below 1 M; and culture medium with MgCl2 concentrations above 1.26 M inhibited the growth of microbes in samples taken from all parts of the Discovery interface. Although DNA and rRNA from key microbial groups (sulfate reducers and methanogens) were detected along the entire MgCl2 gradient of the seawater : Discovery brine interface, mRNA, a highly labile indicator of active microbes, was recovered only from the upper part of the chemocline at MgCl2 concentrations of less than 2.3 M. We also show that the extreme chaotropicity of MgCl2 at high concentrations not only denatures macromolecules, but also preserves the more stable ones: such indicator molecules, hitherto regarded as evidence of life, may thus be misleading signatures in chaotropic environments. Thus, the chaotropicity of MgCl2 would appear to be a window-of-life-determining parameter, and the results obtained here suggest that the upper MgCl2 concentration for life, in the absence of compensating (e.g. kosmotropic) solutes, is about 2.3 M. [source] Quantification of microbial communities in near-surface and deeply buried marine sediments on the Peru continental margin using real-time PCRENVIRONMENTAL MICROBIOLOGY, Issue 7 2006Axel Schippers Summary Deeply buried marine sediments harbour a large fraction of all prokaryotes on Earth but it is still unknown which phylogenetic and physiological microbial groups dominate the deep biosphere. In this study real-time PCR allowed a comparative quantitative microbial community analysis in near-surface and deeply buried marine sediments from the Peru continental margin. The 16S rRNA gene copy numbers of prokaryotes and Bacteria were almost identical with a maximum of 108,1010 copies cm,3 in the near-surface sediments. Archaea exhibited one to three orders of magnitude lower 16S rRNA gene copy numbers. The 18S rRNA gene of Eukarya was always at least three orders of magnitude less abundant than the 16S rRNA gene of prokaryotes. The 16S rRNA gene of the Fe(III)- and Mn(IV)-reducing bacterial family Geobacteraceae and the dissimilatory (bi)sulfite reductase gene (dsrA) of sulfate-reducing prokaryotes were abundant with 106,108 copies cm,3 in near-surface sediments but showed lower numbers and an irregular distribution in the deep sediments. The copy numbers of all genes decreased with sediment depth exponentially. The depth gradients were steeper for the gene copy numbers than for numbers of total prokaryotes (acridine orange direct counts), which reflects the ongoing degradation of the high-molecular-weight DNA with sediment age and depth. The occurrence of eukaryotic DNA also suggests DNA preservation in the deeply buried sediments. [source] Localization of processes involved in methanogenic degradation of rice straw in anoxic paddy soilENVIRONMENTAL MICROBIOLOGY, Issue 8 2001Kristin Glissmann In anoxic paddy soil, rice straw is decomposed to CH4 and CO2 by a complex microbial community consisting of hydrolytic, fermenting, syntrophic and methanogenic microorganisms. Here, we investigated which of these microbial groups colonized the rice straw and which were localized in the soil. After incubation of rice straw in anoxic soil slurries for different periods, the straw pieces were removed from the soil, and both slurry and straw were studied separately. Although the potential activities of polysaccharolytic enzymes were higher in the soil slurry than in the straw incubations, the actual release of reducing sugars was higher in the straw incubations. The concentrations of fermentation products, mainly acetate and propionate, increased steadily in the straw incubations, whereas only a little CH4 was formed. In the soil slurries, on the other hand, fermentation products were low, whereas CH4 production was more pronounced. The production of CH4 or of fermentation products in the separated straw and soil incubations accounted in sum for 54,82% of the CH4 formed when straw was not removed from the soil. Syntrophic propionate degradation to acetate, CO2 and H2 was thermodynamically more favourable in the soil than in the straw fraction. These results show that hydrolysis and primary fermentation reactions were mainly localized on the straw pieces, whereas the syntrophic and methanogenic reactions were mainly localized in the soil. The percentage of bacterial relative to total microbial 16S rRNA content was higher on the straw than in the soil, whereas it was the opposite for the archaeal 16S rRNA content. It appears that rice straw is mainly colonized by hydrolytic and fermenting bacteria that release their fermentation products into the soil pore water where they are further degraded to CH4. Hence, complete methanogenic degradation of straw in rice soil seems to involve compartmentalization. [source] Multiple profiling of soil microbial communities identifies potential genetic markers of metal-enriched sewage sludgeFEMS MICROBIOLOGY ECOLOGY, Issue 3 2008Catriona A. Macdonald Abstract The long-term impacts of Cu- and Zn-rich sewage sludge additions on the structure of the microbial community in a field under pasture were investigated using a combination of multiplex-terminal restriction fragment length polymorphism (M-TRFLP) and T-RFLP profiling approaches. Changes in the community structure of bacteria, fungi, archaea and actinobacteria were observed in soils that had previously received Cu- (50,200 mg kg,1 soil) and Zn- (150,450 mg kg,1 soil) rich sewage sludge additions. Changes in the structure of all microbial groups measured were observed at Cu and Zn rates below the current EU guidelines (135 mg kg,1 Cu and 300 mg kg,1 Zn). The response of the fungal community, and to a lesser extent the bacterial and archaeal community, to Cu was dose dependent. The fungal community also showed a dose-dependent response to Zn, which was not observed in the other microbial groups assessed. Redundancy analysis demonstrated that individual terminal restriction fragments responded to both Cu and Zn and these may have potential as genetic markers of long-term metal effects in soil. [source] Linking microbial activity and soil organic matter transformations in forest soils under elevated CO2GLOBAL CHANGE BIOLOGY, Issue 2 2005S. A. Billings Abstract Soil organic matter (SOM) dynamics ultimately govern the ability of soil to provide long-term C sequestration and the nutrients required for ecosystem productivity. Predicting belowground responses to elevated CO2 requires an integrated understanding of SOM transformations and the microbial activity that governs them. It remains unclear how the microorganisms upon which these transformations depend will function in an elevated CO2 world. This study examines SOM transformations and microbial metabolism in soils from the Duke Free Air Carbon Enrichment site in North Carolina, USA. We assessed microbial respiration and net nitrogen (N) mineralization in soils with and without elevated CO2 exposure during a 100-day incubation. We also traced the depleted C isotopic signature of the supplemental CO2 into SOM and the soils' phospholipid fatty acids (PLFA), which serve as biomarkers for living cells. Cumulative net N mineralization in elevated CO2 soils was 50% that in control soils after a 100-day incubation. Respiration was not altered with elevated CO2. C : N ratios of bulk SOM did not change with elevated CO2, but incubation data suggest that the C : N ratios of mineralized organic matter increased with elevated CO2. Values of SOM ,13C were depleted with elevated CO2 (,26.7±0.2 vs. ,30.2±0.3,), reflecting the depleted signature of the supplemental CO2. We compared ,13C of individual PLFA with the ,13C of SOM to discern incorporation of the depleted C isotopic signature into soil microbial groups in elevated CO2 plots. PLFA i15:0, a15:0, and 10Met18:0 reflected significant incorporation of recently produced photosynthate, suggesting that the bacterial groups defined by these biomarkers are active metabolizers in elevated CO2 soils. At least one of these groups (actinomycetes, 10Met18:0) specializes in metabolizing less labile substrates. Because control plots did not receive an equivalent 13C tracer, we cannot determine from these data whether this group of organisms was stimulated by elevated CO2 compared with these organisms in control soils. Stimulation of this group, if it occurred in the elevated CO2 plot, would be consistent with a decline in the availability of mineralizable organic matter with elevated CO2, which incubation data suggest may be the case in these soils. [source] Technological characterization of the natural lactic acid bacteria of artisanal Turkish White Pickled cheeseINTERNATIONAL JOURNAL OF DAIRY TECHNOLOGY, Issue 2 2008ELIF DAGDEMIR The aim of this study was to characterize the lactic acid bacteria (LAB) isolated from White Pickled cheeses produced with traditional methods; and to improve the quality of cheesemaking with a selection of bacterial cultures from artisanal White cheeses. LAB were isolated and identified from 30 White Pickled cheese samples collected from various cities in Turkey. Also, the numbers of several microbial groups (total aerobic mesophilic bacteria, LAB, enterococci, coliforms, moulds and yeasts) of cheese samples were enumerated. Lactobacilli, lactococci and enterococci were the most abundant microbial groups. The numbers of Enterococcus and Lactobacillus isolates were higher than those of the other LAB. Enterococcus faecalis (24.43%), Enterococcus faecium (17.61%) and Lactobacillus fermentum (19.88%) isolates were the most frequently isolated species. Lactococcus strains showed the highest acidifying activity, followed by Enterococcus and Lactobacillus strains. Proteolytic activity of Enterococcus faecalis strains was higher than that of the other enterococci species, except Enterococcus avium strains. Within lactobacilli strains, the highest mean proteolytic activity was that of Lactobacillus bifermentans, Lactobacillus brevis and Lactobacillus casei strains. [source] THE EFFECT of MODIFIED ATMOSPHERE PACKAGING ON the MICROBIAL ECOLOGY IN REQUEIJÃO, A PORTUGUESE WHEY CHEESEJOURNAL OF FOOD PROCESSING AND PRESERVATION, Issue 2 2000MANUELA E. PINTADO The effects of modified atmosphere packaging on growth of adventitious microorganisms in Portuguese whey cheese (Requeijão) were studied following a response surface methodology using storage time (2, 6, 10 and 15 days), storage temperature (4, 12 and 18C) and fraction of CO2 in the overhead gaseous mixture also containing nitrogen (0, 50 and 100%) as manipulated variables. the viable numbers of Enterobacteriacea, staphylococci, yeasts and spore-forming bacteria in the experimental whey cheeses did not increase within 15 days when storage was at 4C under 100% CO2; those of enterococci increased significantly after 6 days under similar conditions, and a similar inhibiting effect was observed against Bacillus, pseudomonads, lactobacilli and streptococci. It was observed that 100% N2 at 4C was able to completely inhibit growth of staphylococci, lactobacilli and Bacillus for 2 days. the loci (and the nature) of the optima in terms of manipulated variables were obtained for all microbial groups studied. No true overall minimum was found, but storage conditions preset at 4C and 100% CO2 led to a 15 day extension of the shelf-life of Requeijão. [source] Changes in the rRNA levels of specific microbial groups in activated sludge during sample handling and storageLETTERS IN APPLIED MICROBIOLOGY, Issue 2 2005J.E. Keith Abstract Aims:, To quantitatively analyse the changes in group-specific rRNA levels in activated sludge as a function of sample handling and storage procedure. Methods and Results:, Quantitative membrane hybridizations with 32P-labelled oligonucleotide probes were used to analyse the effects of different sample handling and storage conditions on the relative rRNA levels of the alpha, beta, and gamma-Proteobacteria, the Cytophaga-Flavobacteria group, and the mycolic acid-containing actinomycetes in activated sludge. Group-specific rRNA levels, expressed as percentages of total 16S rRNA detected with a universal probe, in samples maintained at room temperature significantly changed after 48 h. Group-specific rRNA levels in samples treated with chloramphenicol showed significant change after 72 h. Conclusions:, Sample storage at room temperature is a viable option if freezing or analysis can be performed within 24 h, while treatment with chlorampenicol can extend that time to at least 48 h. Significance and Impact of the Study:, Handling, shipping, and storage of environmental samples under several conditions may result in inaccurate determination of the microbial populations in microbial ecology studies. [source] Pilot-scale evaluation of in situ cometabolic bioremediation of TCE in groundwater using PHOSter® technologyREMEDIATION, Issue 2 2008Karl W. Eggers A study was conducted to evaluate the efficacy of PHOSter® technology for treating groundwater contaminated with trichloroethene (TCE) at Edwards Air Force Base, California. The technology consists of injecting a gaseous mixture of air, methane, and nutrients into groundwater with the objective of stimulating the growth of methanotrophs, a naturally occurring microbial group that is capable of catalyzing the aerobic degradation of chlorinated solvents into nontoxic products. Injection operations were performed at one well for a period of three months. Six monitoring wells were utilized for groundwater and wellhead vapor monitoring and for groundwater and microbial sampling. In the five monitoring wells located within 44 feet of the injection well, the following results were observed: dissolved oxygen concentrations increased to a range between 6 and 8 milligrams per liter (,g/L); the biomass of target microbial groups increased by one to five orders of magnitude; and TCE concentrations decreased by an average of 92 percent, and to below the California primary maximum contaminant level (MCL; 5 micrograms per liter [µg/L]) in the well closest to the injection well. © 2008 Wiley Periodicals, Inc., [source] |