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Sample records for active microbial population

  1. Biogeography of Metabolically Active Microbial Populations within the Subseafloor Biosphere

    NASA Astrophysics Data System (ADS)

    Reese, B. K.; Shepard, A.; St. Peter, C.; Mills, H. J.

    2011-12-01

    Microbial life in deep marine sediments is widespread, metabolically active and diverse. Evidence of prokaryotic communities in sediments as deep as 800 m below the seafloor (mbsf) have been found. By recycling carbon and nutrients through biological and geochemical processes, the deep subsurface has the potential to remain metabolically active over geologic time scales. While a vast majority of the subsurface biosphere remains under studied, recent advances in molecular techniques and an increased focus on microbiological sampling during IODP expeditions have provided the initial steps toward better characterizations of the microbial communities. Coupling of geochemistry and RNA-based molecular analysis is essential to the description of the active microbial populations within the subsurface biosphere. Studies based on DNA may describe the taxa and metabolic pathways from the total microbial community within the sediment, whether the cells sampled were metabolically active, quiescent or dead. Due to a short lifespan within a cell, only an RNA-based analysis can be used to identify linkages between active populations and observed geochemistry. This study will coalesce and compare RNA sequence and geochemical data from Expeditions 316 (Nankai Trough), 320 (Pacific Equatorial Age Transect), 325 (Great Barrier Reef) and 329 (South Pacific Gyre) to evaluate the biogeography of microbial lineages actively altering the deep subsurface. The grouping of sediments allows for a wide range of geochemical environments to be compared, including two environments limited in organic carbon. Significant to this study is the use of similar extraction, amplification and simultaneous 454 pyrosequencing on all sediment populations allowing for robust comparisons with similar protocol strengths and biases. Initial trends support previously described reduction of diversity with increasing depth. The co-localization of active reductive and oxidative lineages suggests a potential cryptic

  2. Long Live Rock! Exploring Active Microbial Populations in North Pond Subsurface Basalt

    NASA Astrophysics Data System (ADS)

    Mills, H. J.; Lehne, J.

    2014-12-01

    Microbial life should be considered as an active source for subsurface alterations of crustal material. Over the past several decades, microbial populations have been qualitatively and quantitatively characterized in marine sediments from the near shore to gyre centers, from the surface to two kilometers below the surface. Recent exploration of the underlying basement has revealed bacterial populations within the basalt. Initial cultivation-based and in situ analysis of subsurface basalt has produced some structural identification of populations that have the potential to alter the crust. Within this study, we have advanced this understanding by characterizing the metabolically active fraction of these populations. A 16S rRNA gene transcript approach was conducted using high throughput sequencing on RNA extracted from breccia, glass basalts and ultramafic basalts of the western flank of the Mid-Atlantic Ridge. Previous research has shown that the fluid within the basement is oxic. As expected, populations associated with aerobic metabolism were detected. In addition, iron-utilizing populations were observed to be metabolically active within the basalt samples characterized. Future characterization will reveal overlap between previous studies to determine the total versus metabolically active populations.

  3. Activity and growth of microbial populations in pressurized deep-sea sediment and animal gut samples.

    PubMed

    Tabor, P S; Deming, J W; Ohwada, K; Colwell, R R

    1982-08-01

    Benthic animals and sediment samples were collected at deep-sea stations in the northwest (3,600-m depth) and southeast (4,300- and 5200-m depths) Atlantic Ocean. Utilization rates of [14C]glutamate (0.67 to 0.74 nmol) in sediment suspensions incubated at in situ temperatures and pressures (3 to 5 degrees C and 360, 430, or 520 atmospheres) were relatively slow, ranging from 0.09 to 0.39 nmol g-1 day-1, whereas rates for pressurized samples of gut suspensions varied widely, ranging from no detectable activity to a rapid rate of 986 nmol g-1 day-1. Gut flora from a holothurian specimen and a fish demonstrated rapid, barophilic substrate utilization, based on relative rates calculated for pressurized samples and samples held at 1 atm (101.325 kPa). Substrate utilization by microbial populations in several sediment samples was not inhibited by in situ pressure. Deep-sea pressures did not restrict growth, measured as doubling time, of culturable bacteria present in a northwest Atlantic sediment sample and in a gut suspension prepared from an abyssal scavenging amphipod. From the results of this study, it was concluded that microbial populations in benthic environments can demonstrate significant metabolic activity under deep-ocean conditions of temperature and pressure. Furthermore, rates of microbial activity in the guts of benthic macrofauna are potentially more rapid than in surrounding deep-sea sediments. PMID:6127054

  4. Activity and growth of microbial populations in pressurized deep-sea sediment and animal gut samples.

    PubMed Central

    Tabor, P S; Deming, J W; Ohwada, K; Colwell, R R

    1982-01-01

    Benthic animals and sediment samples were collected at deep-sea stations in the northwest (3,600-m depth) and southeast (4,300- and 5200-m depths) Atlantic Ocean. Utilization rates of [14C]glutamate (0.67 to 0.74 nmol) in sediment suspensions incubated at in situ temperatures and pressures (3 to 5 degrees C and 360, 430, or 520 atmospheres) were relatively slow, ranging from 0.09 to 0.39 nmol g-1 day-1, whereas rates for pressurized samples of gut suspensions varied widely, ranging from no detectable activity to a rapid rate of 986 nmol g-1 day-1. Gut flora from a holothurian specimen and a fish demonstrated rapid, barophilic substrate utilization, based on relative rates calculated for pressurized samples and samples held at 1 atm (101.325 kPa). Substrate utilization by microbial populations in several sediment samples was not inhibited by in situ pressure. Deep-sea pressures did not restrict growth, measured as doubling time, of culturable bacteria present in a northwest Atlantic sediment sample and in a gut suspension prepared from an abyssal scavenging amphipod. From the results of this study, it was concluded that microbial populations in benthic environments can demonstrate significant metabolic activity under deep-ocean conditions of temperature and pressure. Furthermore, rates of microbial activity in the guts of benthic macrofauna are potentially more rapid than in surrounding deep-sea sediments. PMID:6127054

  5. Effects of Flavonoids on Rumen Fermentation Activity, Methane Production, and Microbial Population

    PubMed Central

    Abdullah, Norhani; Oskoueian, Armin

    2013-01-01

    This research was carried out to evaluate the effects of flavone, myricetin, naringin, catechin, rutin, quercetin, and kaempferol at the concentration of 4.5% of the substrate (dry matter basis) on the rumen microbial activity in vitro. Mixture of guinea grass and concentrate (60 : 40) was used as the substrate. The results showed that all the flavonoids except naringin and quercetin significantly (P < 0.05) decreased the dry matter degradability. The gas production significantly (P < 0.05) decreased by flavone, myricetin, and kaempferol, whereas naringin, rutin, and quercetin significantly (P < 0.05) increased the gas production. The flavonoids suppressed methane production significantly (P < 0.05). The total VFA concentration significantly (P < 0.05) decreased in the presence of flavone, myricetin, and kaempferol. All flavonoids except naringin and quercetin significantly (P < 0.05) reduced the carboxymethyl cellulase, filter paperase, xylanase, and β-glucosidase activities, purine content, and the efficiency of microbial protein synthesis. Flavone, myricetin, catechin, rutin, and kaempferol significantly (P < 0.05) reduced the population of rumen microbes. Total populations of protozoa and methanogens were significantly (P < 0.05) suppressed by naringin and quercetin. The results of this research demonstrated that naringin and quercetin at the concentration of 4.5% of the substrate (dry matter basis) were potential metabolites to suppress methane production without any negative effects on rumen microbial fermentation. PMID:24175289

  6. Effect of feed starvation on side-stream anammox activity and key microbial populations.

    PubMed

    Reeve, Petra J; Mouilleron, Irina; Chuang, Hui-Ping; Thwaites, Ben; Hyde, Kylie; Dinesh, Nirmala; Krampe, Joerg; Lin, Tsair-Fuh; van den Akker, Ben

    2016-04-15

    The anaerobic ammonium oxidation (anammox) process is widely acknowledged to be susceptible to a wide range of environmental factors given the slow growth rate of the anammox bacteria. Surprisingly there is limited experimental data regarding the susceptibility of the anammox process to feed starvations which may be encountered in full-scale applications. Therefore, a study was established to investigate the impact of feed starvations on nitritation and anammox activity in a demonstration-scale sequencing batch reactor. Three starvation periods were trialled, lasting one fortnight (15 d), one month (33 d) and two months (62 d). Regardless of the duration of the starvation period, assessment of the ammonia removal performance demonstrated nitritation and anammox activity were reinstated within one day of recovery operation. Characterisation of the community structure using 16S rRNA and functional genes specific for nitrogen-related microbes showed there was no clear impact or shift in the microbial populations between starvation and recovery phases. PMID:26861222

  7. Heterotrophic activity and biodegradation of labile and refractory compounds by groundwater and stream microbial populations.

    PubMed Central

    Ladd, T I; Ventullo, R M; Wallis, P M; Costerton, J W

    1982-01-01

    The bacteriology and heterotrophic activity of a stream and of nearby groundwater in Marmot Basin, Alberta, Canada, were studied. Acridine orange direct counts indicated that bacterial populations in the groundwater were greater than in the stream. Bacteria that were isolated from the groundwater were similar to species associated with soils. Utilization of labile dissolved organic material as measured by the heterotrophic potential technique with glutamic acid, phenylalanine, and glycolic acid as substrates was generally greater in the groundwater. In addition, specific activity indices for the populations suggested greater metabolic activity per bacterium in the groundwater. 14C-labeled lignocellulose, preferentially labeled in the lignin fraction by feeding Picea engelmannii [14C]phenylalanine, was mineralized by microorganisms in both the groundwater and the stream, but no more than 4% of the added radioactivity was lost as 14CO2 within 960 h. Up to 20% of [3'-14C]cinnamic acid was mineralized by microorganisms in both environments within 500 h. Both microbial populations appear to influence the levels of labile and recalcitrant dissolved organic material in mountain streams. PMID:7125651

  8. Microbial population, activity, and phylogenetic diversity in the subseafloor core sediment from the Sea of Okhotsk

    NASA Astrophysics Data System (ADS)

    Inagaki, F.; Suzuki, M.; Takai, K.; Nealson, K. H.; Horikoshi, K.

    2002-12-01

    Subseafloor environments has already been recognized as the largest biosphere on the planet Earth, however, the microbial diversity and activity has been still poorly understood, even in their impacts on biogeochemical processes, tectonic settings, and paleoenvironmental events. We demonstrate here the evaluation of microbial community structure and active habitats in deeply buried cold marine sediments collected from the Sea of Okhotsk by a combined use of molecular ecological surveys and culturing assays. The piston core sediment (MD01-2412) was collected by IMAGES (International Marine Global Change Study) Project from the southeastern Okhotsk Sea, June 2001. The total recovered length was about 58m. The lithology of the core sediment was mainly constructed from pelagic clay (PC) and volcanic ash layers (Ash). We collected aseptically the most inside core parts from 16 sections at different depths for microbiological study. The direct count of DAPI-stained cells revealed that the cells in Ash samples were present 1.2 to 2.2 times higher than in PC samples. The quantitative-PCR of 16S rDNA between bacterial and archaeal rDNA suggested that the increased population density in Ash layers was caused by the bacterial components. We studied approximately 650 and 550 sequences from bacterial and archaeal rDNA clone libraries, respectively. The similarity and phylogenetic analyses revealed that the microbial community structures were apparently different between in Ash layers and PC samples. From bacterial rDNA clone libraries, the members within gamma-Proteobacteria such as genera Halomonas, Shewanella, Psychromonas and Methylosinus were predominantly detected in Ash layers whereas the Dehalococcoides group and delta-Proteobacteria were major bacterial components in PC samples. From archaeal libraries, the sequences from Ash and PC samples were affiliated into the clusters represented by the environmental sequences obtained from terrestrial and deep-sea environments

  9. The Abundance and Activity of Nitrate-Reducing Microbial Populations in Estuarine Sediments

    NASA Astrophysics Data System (ADS)

    Cardarelli, E.; Francis, C. A.

    2014-12-01

    Estuaries are productive ecosystems that ameliorate nutrient and metal contaminants from surficial water supplies. At the intersection of terrestrial and aquatic environments, estuarine sediments host major microbially-mediated geochemical transformations. These include denitrification (the conversion of nitrate to nitrous oxide and/or dinitrogen) and dissimilatory nitrate reduction to ammonium (DNRA). Denitrification has historically been seen as the predominant nitrate attenuation process and functions as an effective sink for nitrate. DNRA has previously been believed to be a minor nitrate reduction process and transforms nitrate within the ecosystem to ammonium, a more biologically available N species. Recent studies have compared the two processes in coastal environments and determined fluctuating environmental conditions may suppress denitrification, supporting an increased role for DNRA in the N cycle. Nitrate availability and salinity are factors thought to influence the membership of the microbial communities present, and the nitrate reduction process that predominates. The aim of this study is to investigate how nitrate concentration and salinity alter the transcript abundances of N cycling functional gene markers for denitrification (nirK, nirS) and DNRA (nrfA) in estuarine sediments at the mouth of the hypernutrified Old Salinas River, CA. Short-term whole core incubations amended with artificial freshwater/artificial seawater (2 psu, 35 psu) and with varying NO3- concentrations (200mM, 2000mM) were conducted to assess the activity as well as the abundance of the nitrate-reducing microbial populations present. Gene expression of nirK, nirS, and nrfA at the conclusion of the incubations was quantified using reverse transcription quantitative polymerase chain reaction (RT-qPCR). High abundances of nirK, nirS, and nrfA under particular conditions coupled with the resulting geochemical data ultimately provides insight onto how the aforementioned factors

  10. Unravelling the interactions among microbial populations found in activated sludge during biofilm formation.

    PubMed

    Liébana, Raquel; Arregui, Lucía; Santos, Antonio; Murciano, Antonio; Marquina, Domingo; Serrano, Susana

    2016-09-01

    Microorganisms colonize surfaces and develop biofilms through interactions that are not yet thoroughly understood, with important implications for water and wastewater systems. This study investigated the interactions between N-acyl homoserine lactone (AHL)-producing bacteria, yeasts and protists, and their contribution to biofilm development. Sixty-one bacterial strains were isolated from activated sludge and screened for AHL production, with Aeromonas sp. found to be the dominant AHL producer. Shewanella xiamenensis, Aeromonas allosaccharophila, Acinetobacter junii and Pseudomonas aeruginosa recorded the highest adherence capabilities, with S. xiamenensis being the most effective in surface colonization. Additionally, highly significant interactions (i.e. synergic or antagonistic) were described for dual and multistrain mixtures of bacterial strains (P. aeruginosa, S. xiamenensis, A. junii and Pseudomonas stutzeri), as well as for strongly adherent bacteria co-cultured with yeasts. In this last case, the adhered biomass in co-cultures was lower than the monospecific biofilms of bacteria and yeast, with biofilm observations by microscopy suggesting that bacteria had an antagonist effect on the whole or part of the yeast population. Finally, protist predation by Euplotes sp. and Paramecium sp. on Aeromonas hydrophila biofilms not only failed to reduce biofilm formation, but also recorded unexpected results leading to the development of aggregates of high density and complexity. PMID:27306553

  11. Microbial populations in contaminant plumes

    NASA Astrophysics Data System (ADS)

    Haack, Sheridan K.; Bekins, Barbara A.

    Efficient biodegradation of subsurface contaminants requires two elements: (1) microbial populations with the necessary degradative capabilities, and (2) favorable subsurface geochemical and hydrological conditions. Practical constraints on experimental design and interpretation in both the hydrogeological and microbiological sciences have resulted in limited knowledge of the interaction between hydrogeological and microbiological features of subsurface environments. These practical constraints include: (1) inconsistencies between the scales of investigation in the hydrogeological and microbiological sciences, and (2) practical limitations on the ability to accurately define microbial populations in environmental samples. However, advances in application of small-scale sampling methods and interdisciplinary approaches to site investigations are beginning to significantly improve understanding of hydrogeological and microbiological interactions. Likewise, culture-based and molecular analyses of microbial populations in subsurface contaminant plumes have revealed significant adaptation of microbial populations to plume environmental conditions. Results of recent studies suggest that variability in subsurface geochemical and hydrological conditions significantly influences subsurface microbial-community structure. Combined investigations of site conditions and microbial-community structure provide the knowledge needed to understand interactions between subsurface microbial populations, plume geochemistry, and contaminant biodegradation. La biodégradation efficace des polluants souterrains requiert deux éléments: des populations microbiennes possédant les aptitudes nécessaires à la dégradation, et des conditions géochimiques et hydrologiques souterraines favorables. Des contraintes pratiques sur la conception et l'interprétation des expériences à la fois en microbiologie et en hydrogéologie ont conduit à une connaissance limitée des interactions entre les

  12. Identification and quantification of microbial populations in activated sludge and anaerobic digestion processes.

    PubMed

    Reyes, M; Borrás, L; Seco, A; Ferrer, J

    2015-01-01

    Eight different phenotypes were studied in an activated sludge process (AeR) and anaerobic digester (AnD) in a full-scale wastewater treatment plant by means of fluorescent in situ hybridization (FISH) and automated FISH quantification software. The phenotypes were ammonia-oxidizing bacteria, nitrite-oxidizing bacteria, denitrifying bacteria, phosphate-accumulating organisms (PAO), glycogen-accumulating organisms (GAO), sulphate-reducing bacteria (SRB), methanotrophic bacteria and methanogenic archaea. Some findings were unexpected: (a) Presence of PAO, GAO and denitrifiers in the AeR possibly due to unexpected environmental conditions caused by oxygen deficiencies or its ability to survive aerobically; (b) presence of SRB in the AeR due to high sulphate content of wastewater intake and possibly also due to digested sludge being recycled back into the primary clarifier; (c) presence of methanogenic archaea in the AeR, which can be explained by the recirculation of digested sludge and its ability to survive periods of high oxygen levels; (d) presence of denitrifying bacteria in the AnD which cannot be fully explained because the nitrate level in the AnD was not measured. However, other authors reported the existence of denitrifiers in environments where nitrate or oxygen was not present suggesting that denitrifiers can survive in nitrate-free anaerobic environments by carrying out low-level fermentation; (e) the results of this paper are relevant because of the focus on the identification of nearly all the significant bacterial and archaeal groups of microorganisms with a known phenotype involved in the biological wastewater treatment. PMID:25409582

  13. Monitoring microbial population dynamics at low densities

    NASA Astrophysics Data System (ADS)

    Julou, Thomas; Desprat, Nicolas; Bensimon, David; Croquette, Vincent

    2012-07-01

    We propose a new and simple method for the measurement of microbial concentrations in highly diluted cultures. This method is based on an analysis of the intensity fluctuations of light scattered by microbial cells under laser illumination. Two possible measurement strategies are identified and compared using simulations and measurements of the concentration of gold nanoparticles. Based on this comparison, we show that the concentration of Escherichia coli and Saccharomyces cerevisiae cultures can be easily measured in situ across a concentration range that spans five orders of magnitude. The lowest measurable concentration is three orders of magnitude (1000×) smaller than in current optical density measurements. We show further that this method can also be used to measure the concentration of fluorescent microbial cells. In practice, this new method is well suited to monitor the dynamics of population growth at early colonization of a liquid culture medium. The dynamic data thus obtained are particularly relevant for microbial ecology studies.

  14. Nonantibiotic interventions to control pathogens and undesired microbial activities in mixed microbial populations residing in the gut of food-producing animals and their excreted wastes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The intensification and industrialization of animal agriculture throughout the world has led to considerable increases in animal production efficiencies but has also led to concerns that microbial pathogens, antibiotic residues, and other chemical contaminants could be concentrated in the environmen...

  15. Impact of Fungicide Mancozeb at Different Application Rates on Soil Microbial Populations, Soil Biological Processes, and Enzyme Activities in Soil

    PubMed Central

    Mehta, Preeti; Guleria, Shiwani; Chauhan, Anjali; Shirkot, C. K.

    2014-01-01

    The use of fungicides is the continuous exercise particularly in orchard crops where fungal diseases, such as white root rot, have the potential to destroy horticultural crops rendering them unsaleable. In view of above problem, the present study examines the effect of different concentrations of mancozeb (0–2000 ppm) at different incubation periods for their harmful side effects on various microbiological processes, soil microflora, and soil enzymes in alluvial soil (pH 6.8) collected from apple orchards of Shimla in Himachal Pradesh (India). Low concentrations of mancozeb were found to be deleterious towards fungal and actinomycetes population while higher concentrations (1000 and 2000 ppm) were found to be detrimental to soil bacteria. Mancozeb impaired the process of ammonification and nitrification. Similar results were observed for nitrifying and ammonifying bacteria. Phosphorus solubilization was increased by higher concentration of mancozeb, that is, 250 ppm and above. In unamended soil, microbial biomass carbon and carbon mineralization were adversely affected by mancozeb. Soil enzymes, that is, amylase, invertase, and phosphatase showed adverse and disruptive effect when mancozeb used was above 10 ppm in unamended soil. These results conclude that, to lessen the harmful effects in soil biological processes caused by this fungicide, addition of higher amount of nitrogen based fertilizers is required. PMID:25478598

  16. Interval scanning photomicrography of microbial cell populations.

    NASA Technical Reports Server (NTRS)

    Casida, L. E., Jr.

    1972-01-01

    A single reproducible area of the preparation in a fixed focal plane is photographically scanned at intervals during incubation. The procedure can be used for evaluating the aerobic or anaerobic growth of many microbial cells simultaneously within a population. In addition, the microscope is not restricted to the viewing of any one microculture preparation, since the slide cultures are incubated separately from the microscope.

  17. Microbial populations and enzyme activities in soil in situ under transgenic corn expressing cry proteins from Bacillus thuringiensis.

    PubMed

    Icoz, I; Saxena, D; Andow, D A; Zwahlen, C; Stotzky, G

    2008-01-01

    Transgenic Bt crops produce insecticidal Cry proteins that are released to soil in plant residues, root exudates, and pollen and that may affect soil microorganisms. As a continuation of studies in the laboratory and a plant-growth room, a field study was conducted at the Rosemount Experiment Station of the University of Minnesota. Three Bt corn varieties that express the Cry1Ab protein, which is toxic to the European corn borer (Ostrinia nubilalis Hübner), and one Bt corn variety that expresses the Cry3Bb1 protein, which is toxic to the corn rootworm complex (Diabrotica spp.), and their near-isogenic non-Bt varieties were evaluated for their effects on microbial diversity by classical dilution plating and molecular (polymerase chain reaction-denaturing gradient gel electrophoresis) techniques and for the activities of some enzymes (arylsulfatases, acid and alkaline phosphatases, dehydrogenases, and proteases) involved in the degradation of plant biomass. After 4 consecutive years of corn cultivation (2003-2006), there were, in general, no consistent statistically significant differences in the numbers of different groups of microorganisms, the activities of the enzymes, and the pH between soils planted with Bt and non-Bt corn. Numbers and types of microorganisms and enzyme activities differed with season and with the varieties of corn, but these differences were not related to the presence of the Cry proteins in soil. The Cry1Ab protein of Bt corn (events Bt11 and MON810) was detected in most soils during the 4 yr, whereas the Cry3Bb1 protein was not detected in soils of Bt corn (event MON863) expressing the cry3Bb1 gene. PMID:18396552

  18. Effects of Secondary Plant Metabolites on Microbial Populations: Changes in Community Structure and Metabolic Activity in Contaminated Environments.

    PubMed

    Musilova, Lucie; Ridl, Jakub; Polivkova, Marketa; Macek, Tomas; Uhlik, Ondrej

    2016-01-01

    Secondary plant metabolites (SPMEs) play an important role in plant survival in the environment and serve to establish ecological relationships between plants and other organisms. Communication between plants and microorganisms via SPMEs contained in root exudates or derived from litter decomposition is an example of this phenomenon. In this review, the general aspects of rhizodeposition together with the significance of terpenes and phenolic compounds are discussed in detail. We focus specifically on the effect of SPMEs on microbial community structure and metabolic activity in environments contaminated by polychlorinated biphenyls (PCBs) and polyaromatic hydrocarbons (PAHs). Furthermore, a section is devoted to a complex effect of plants and/or their metabolites contained in litter on bioremediation of contaminated sites. New insights are introduced from a study evaluating the effects of SPMEs derived during decomposition of grapefruit peel, lemon peel, and pears on bacterial communities and their ability to degrade PCBs in a long-term contaminated soil. The presented review supports the "secondary compound hypothesis" and demonstrates the potential of SPMEs for increasing the effectiveness of bioremediation processes. PMID:27483244

  19. Effects of Secondary Plant Metabolites on Microbial Populations: Changes in Community Structure and Metabolic Activity in Contaminated Environments

    PubMed Central

    Musilova, Lucie; Ridl, Jakub; Polivkova, Marketa; Macek, Tomas; Uhlik, Ondrej

    2016-01-01

    Secondary plant metabolites (SPMEs) play an important role in plant survival in the environment and serve to establish ecological relationships between plants and other organisms. Communication between plants and microorganisms via SPMEs contained in root exudates or derived from litter decomposition is an example of this phenomenon. In this review, the general aspects of rhizodeposition together with the significance of terpenes and phenolic compounds are discussed in detail. We focus specifically on the effect of SPMEs on microbial community structure and metabolic activity in environments contaminated by polychlorinated biphenyls (PCBs) and polyaromatic hydrocarbons (PAHs). Furthermore, a section is devoted to a complex effect of plants and/or their metabolites contained in litter on bioremediation of contaminated sites. New insights are introduced from a study evaluating the effects of SPMEs derived during decomposition of grapefruit peel, lemon peel, and pears on bacterial communities and their ability to degrade PCBs in a long-term contaminated soil. The presented review supports the “secondary compound hypothesis” and demonstrates the potential of SPMEs for increasing the effectiveness of bioremediation processes. PMID:27483244

  20. The Microbial Database for Danish wastewater treatment plants with nutrient removal (MiDas-DK) - a tool for understanding activated sludge population dynamics and community stability.

    PubMed

    Mielczarek, A T; Saunders, A M; Larsen, P; Albertsen, M; Stevenson, M; Nielsen, J L; Nielsen, P H

    2013-01-01

    Since 2006 more than 50 Danish full-scale wastewater treatment plants with nutrient removal have been investigated in a project called 'The Microbial Database for Danish Activated Sludge Wastewater Treatment Plants with Nutrient Removal (MiDas-DK)'. Comprehensive sets of samples have been collected, analyzed and associated with extensive operational data from the plants. The community composition was analyzed by quantitative fluorescence in situ hybridization (FISH) supported by 16S rRNA amplicon sequencing and deep metagenomics. MiDas-DK has been a powerful tool to study the complex activated sludge ecosystems, and, besides many scientific articles on fundamental issues on mixed communities encompassing nitrifiers, denitrifiers, bacteria involved in P-removal, hydrolysis, fermentation, and foaming, the project has provided results that can be used to optimize the operation of full-scale plants and carry out trouble-shooting. A core microbial community has been defined comprising the majority of microorganisms present in the plants. Time series have been established, providing an overview of temporal variations in the different plants. Interestingly, although most microorganisms were present in all plants, there seemed to be plant-specific factors that controlled the population composition thereby keeping it unique in each plant over time. Statistical analyses of FISH and operational data revealed some correlations, but less than expected. MiDas-DK (www.midasdk.dk) will continue over the next years and we hope the approach can inspire others to make similar projects in other parts of the world to get a more comprehensive understanding of microbial communities in wastewater engineering. PMID:23752384

  1. Long-Term Effects of Land Application of Class B Biosolids on the Soil Microbial Populations, Pathogens, and Activity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study evaluated the influence of 20 annual land applications of Class B biosolids on the soil microbial community. The potential benefits and hazards of land application were evaluated by analysis of surface soil samples collected following the 20th land application of biosolids. The study was ...

  2. CRISPR-Induced Distributed Immunity in Microbial Populations

    PubMed Central

    Young, Mark J.; Weitz, Joshua S.; Whitaker, Rachel J.

    2014-01-01

    In bacteria and archaea, viruses are the primary infectious agents, acting as virulent, often deadly pathogens. A form of adaptive immune defense known as CRISPR-Cas enables microbial cells to acquire immunity to viral pathogens by recognizing specific sequences encoded in viral genomes. The unique biology of this system results in evolutionary dynamics of host and viral diversity that cannot be fully explained by the traditional models used to describe microbe-virus coevolutionary dynamics. Here, we show how the CRISPR-mediated adaptive immune response of hosts to invading viruses facilitates the emergence of an evolutionary mode we call distributed immunity - the coexistence of multiple, equally-fit immune alleles among individuals in a microbial population. We use an eco-evolutionary modeling framework to quantify distributed immunity and demonstrate how it emerges and fluctuates in multi-strain communities of hosts and viruses as a consequence of CRISPR-induced coevolution under conditions of low viral mutation and high relative numbers of viral protospacers. We demonstrate that distributed immunity promotes sustained diversity and stability in host communities and decreased viral population density that can lead to viral extinction. We analyze sequence diversity of experimentally coevolving populations of Streptococcus thermophilus and their viruses where CRISPR-Cas is active, and find the rapid emergence of distributed immunity in the host population, demonstrating the importance of this emergent phenomenon in evolving microbial communities. PMID:25000306

  3. BIOSORPTION OF HYDROPHOBIC ORGANIC POLLUTANTS BY MIXED MICROBIAL POPULATIONS

    EPA Science Inventory

    In recognition of the need to estimate biosorption for natural microbial populations, the variability of partition coefficients for two hydrophobic pollutants to natural populations from a variety of aquatic systems was investigated. Biosorption partition coefficients for pyrene ...

  4. Effect of oxytetracycline on biogas production and active microbial populations during batch anaerobic digestion of cow manure.

    PubMed

    Ince, Bahar; Coban, Halil; Turker, Gokhan; Ertekin, Emine; Ince, Orhan

    2013-05-01

    The aim of this study was to investigate the effect of a common veterinary antibiotic in biogas plants. 20 mg/kg of oxytetracycline was intramuscularly injected into a cow and its concentration in manure, which was sampled daily during the following 20 days, was measured. A total of 20 % of the injected oxytetracycline was detected in manure. Collected manure samples on days 1, 2, 3, 5, 10, 15, and 20 were digested in triplicate serum bottles at 37 °C for 30 days. Control serum bottles produced 255 ± 13 mL biogas, whereas 50-60 % inhibitions were obtained for the serum bottles operated with samples collected for the 5 days after medication. Multivariate statistics used for the evaluation of FISH results showed that Methanomicrobiales were the main methanogenic group responsible for most of the biogas production. Numbers of active Bacteria and Methanomicrobiales were negatively correlated with the presence of oxytetracycline, whereas Methanosarcinales and Methanobacteriales were less affected. PMID:22903595

  5. Microbial activity at gigapascal pressures.

    PubMed

    Sharma, Anurag; Scott, James H; Cody, George D; Fogel, Marilyn L; Hazen, Robert M; Hemley, Russell J; Huntress, Wesley T

    2002-02-22

    We observed physiological and metabolic activity of Shewanella oneidensis strain MR1 and Escherichia coli strain MG1655 at pressures of 68 to 1680 megapascals (MPa) in diamond anvil cells. We measured biological formate oxidation at high pressures (68 to 1060 MPa). At pressures of 1200 to 1600 MPa, living bacteria resided in fluid inclusions in ice-VI crystals and continued to be viable upon subsequent release to ambient pressures (0.1 MPa). Evidence of microbial viability and activity at these extreme pressures expands by an order of magnitude the range of conditions representing the habitable zone in the solar system. PMID:11859192

  6. Single gene-based distinction of individual microbial genomes from a mixed population of microbial cells

    PubMed Central

    Tamminen, Manu V.; Virta, Marko P. J.

    2015-01-01

    Recent progress in environmental microbiology has revealed vast populations of microbes in any given habitat that cannot be detected by conventional culturing strategies. The use of sensitive genetic detection methods such as CARD-FISH and in situ PCR have been limited by the cell wall permeabilization requirement that cannot be performed similarly on all cell types without lysing some and leaving some nonpermeabilized. Furthermore, the detection of low copy targets such as genes present in single copies in the microbial genomes, has remained problematic. We describe an emulsion-based procedure to trap individual microbial cells into picoliter-volume polyacrylamide droplets that provide a rigid support for genetic material and therefore allow complete degradation of cellular material to expose the individual genomes. The polyacrylamide droplets are subsequently converted into picoliter-scale reactors for genome amplification. The amplified genomes are labeled based on the presence of a target gene and differentiated from those that do not contain the gene by flow cytometry. Using the Escherichia coli strains XL1 and MC1061, which differ with respect to the presence (XL1), or absence (MC1061) of a single copy of a tetracycline resistance gene per genome, we demonstrate that XL1 genomes present at 0.1% of MC1061 genomes can be differentiated using this method. Using a spiked sediment microbial sample, we demonstrate that the method is applicable to highly complex environmental microbial communities as a target gene-based screen for individual microbes. The method provides a novel tool for enumerating functional cell populations in complex microbial communities. We envision that the method could be optimized for fluorescence-activated cell sorting to enrich genetic material of interest from complex environmental samples. PMID:25814987

  7. Population Education. Awareness Activities.

    ERIC Educational Resources Information Center

    Brouse, Deborah E.

    1990-01-01

    Described are awareness activities that deal with human population growth, resources, and the environment. Activities include simulations, mathematical exercises, and discussions of the topic. Specific examples of what individuals can do to help are listed. (KR)

  8. A new device for real time monitoring of microbial population dynamics during in situ and ex situ bioremediation

    SciTech Connect

    Woodward, R.E.; Malone, R.W.

    1995-12-31

    Monitoring of microbial population dynamics is an important operating parameter for successful bioremediation projects. The traditional method of plate counts or most probable number (MPN) requires 2 to 7 days for development and therefore provides a historical measurement of little real-time operational significance. Selected enzyme activity is directly proportional to microbial population density and is linear in the population range from 10{sub 4} to 10{sup 8} CFU/mL. This paper summarizes the use of this enzyme based, real-time measurement of microbial population dynamics for the management of four bioremediation projects: (1) differentiation of assimilation from nitrification during the metabolism of ammonia in an industrial waste stream, (2) treatability assessment and management of activated sludge processes during the treatment of a hazardous, petrochemical waste, (3) measurement of intrinsic microbial activity in soil cores at a spill site, and (4) non-invasive monitoring of microbial populations during in situ bioremediation of two aquifers.

  9. Characterization of Microbial Population Shifts during Sample Storage

    PubMed Central

    Mills, Heath J.; Reese, Brandi Kiel; Peter, Cruz St.

    2011-01-01

    The objective of this study was to determine shifts in the microbial community structure and potential function based on standard Integrated Ocean Drilling Program (IODP) storage procedures for sediment cores. Standard long-term storage protocols maintain sediment temperature at 4°C for mineralogy, geochemical, and/or geotechnical analysis whereas standard microbiological sampling immediately preserves sediments at −80°C. Storage at 4°C does not take into account populations may remain active over geologic time scales at temperatures similar to storage conditions. Identification of active populations within the stored core would suggest geochemical and geophysical conditions within the core change over time. To test this potential, the metabolically active fraction of the total microbial community was characterized from IODP Expedition 325 Great Barrier Reef sediment cores prior to and following a 3-month storage period. Total RNA was extracted from complementary 2, 20, and 40 m below sea floor sediment samples, reverse transcribed to complementary DNA and then sequenced using 454 FLX sequencing technology, yielding over 14,800 sequences from the six samples. Interestingly, 97.3% of the sequences detected were associated with lineages that changed in detection frequency during the storage period including key biogeochemically relevant lineages associated with nitrogen, iron, and sulfur cycling. These lineages have the potential to permanently alter the physical and chemical characteristics of the sediment promoting misleading conclusions about the in situ biogeochemical environment. In addition, the detection of new lineages after storage increases the potential for a wider range of viable lineages within the subsurface that may be underestimated during standard community characterizations. PMID:22363327

  10. Cooperation, cheating, and collapse in microbial populations

    NASA Astrophysics Data System (ADS)

    Gore, Jeff

    2012-02-01

    Natural populations can suffer catastrophic collapse in response to small changes in environmental conditions, and recovery after such a collapse can be exceedingly difficult. We have used laboratory yeast populations to study proposed early warning signals of impending extinction. Yeast cooperatively breakdown the sugar sucrose, meaning that there is a minimum number of cells required to sustain the population. We have demonstrated experimentally that the fluctuations in the population size increase in magnitude and become slower as the population approaches collapse. The cooperative nature of yeast growth on sucrose suggests that the population may be susceptible to cheater cells, which do not contribute to the public good and instead merely take advantage of the cooperative cells. We have confirmed this possibility experimentally by using a cheater yeast strain that lacks the gene encoding the cooperative behavior [1]. However, recent results in the lab demonstrate that the presence of a bacterial competitor may drive cooperation within the yeast population.[4pt] [1] Gore et al, Nature 459, 253 -- 256 (2009)

  11. Factors limiting microbial activity in volcanic tuff at Yucca Mountain

    SciTech Connect

    Kieft, T.L.; Kovacik, W.P.; Taylor, J.

    1996-09-01

    Samples of tuff aseptically collected from 10 locations in the Exploratory Shaft Facility at the site of the proposed high-level nuclear waste repository at Yucca Mountain, Nevada Test Site were analyzed for microbiological populations, activities, and factors limiting microbial activity. Radiotracer assays ({sup 14}C-labeled organic substrate mineralization), direct microscopic counts, and plate counts were used. Radiolabeled substrates were glucose, acetate, and glutamate. Radiotracer experiments were carried out with and without moisture and inorganic nutrient amendments to determine factors limiting to microbial activities. Nearly all samples showed the presence of microorganisms with the potential to mineralize organic substrates. Addition of inorganic nutrients stimulated activities in a small number of samples. The presence of viable microbial communities within the tuff has implications for transport of contaminants.

  12. Temporal variation in airborne microbial populations and microbially-derived allergens in a tropical urban landscape

    NASA Astrophysics Data System (ADS)

    Woo, Anthony C.; Brar, Manreetpal S.; Chan, Yuki; Lau, Maggie C. Y.; Leung, Frederick C. C.; Scott, James A.; Vrijmoed, Lilian L. P.; Zawar-Reza, Peyman; Pointing, Stephen B.

    2013-08-01

    The microbial component of outdoor aerosols was assessed along a gradient of urban development from inner-city to rural in the seasonal-tropical metropolis of Hong Kong. Sampling over a continuous one-year period was conducted, with molecular analyses to characterize bacterial and eukaryal microbial populations, immuno-assays to detect microbially-derived allergens and extensive environmental and meteorological observations. The data revealed bio-aerosol populations were not significantly impacted by the level of urban development as measured by anthropogenic pollutants and human population levels, but instead exhibited a strong seasonal trend related to general climatic variables. We applied back-trajectory analysis to establish sources of air masses and this allowed further explanation of urban bio-aerosols largely in terms of summer-marine and winter-continental origins. We also evaluated bio-aerosols for the potential to detect human health threats. Many samples supported bacterial and fungal phylotypes indicative of known pathogenic taxa, together with common indicators of human presence. The occurrence of allergenic endotoxins and beta-glucans generally tracked trends in microbial populations, with levels known to induce symptoms detected during summer months when microbial loading was higher. This strengthens calls for bio-aerosols to be considered in future risk assessments and surveillance of air quality, along with existing chemical and particulate indices.

  13. 2007 Microbial Population Biology (July 22-26, 2007)

    SciTech Connect

    Anthony M. Dean Nancy Ryan Gray

    2008-04-01

    Microbial Population Biology covers a diverse range of cutting edge issues in the microbial sciences and beyond. Firmly founded in evolutionary biology and with a strongly integrative approach, past meetings have covered topics ranging from the dynamics and genetics of adaptation to the evolution of mutation rate, community ecology, evolutionary genomics, altruism, and epidemiology. This meeting is never dull: some of the most significant and contentious issues in biology have been thrashed out here. We anticipate the 2007 meeting being no exception. The final form of the 2007 meeting is yet to be decided, but the following topics are likely to be included: evolutionary emergence of infectious disease and antibiotic resistance, genetic architecture and implications for the evolution of microbial populations, ageing in bacteria, biogeography, evolution of symbioses, the role of microbes in ecosystem function, and ecological genomics.

  14. Experimental demonstration of an Allee effect in microbial populations.

    PubMed

    Kaul, RajReni B; Kramer, Andrew M; Dobbs, Fred C; Drake, John M

    2016-04-01

    Microbial populations can be dispersal limited. However, microorganisms that successfully disperse into physiologically ideal environments are not guaranteed to establish. This observation contradicts the Baas-Becking tenet: 'Everything is everywhere, but the environment selects'. Allee effects, which manifest in the relationship between initial population density and probability of establishment, could explain this observation. Here, we experimentally demonstrate that small populations ofVibrio fischeriare subject to an intrinsic demographic Allee effect. Populations subjected to predation by the bacterivoreCafeteria roenbergensisdisplay both intrinsic and extrinsic demographic Allee effects. The estimated critical threshold required to escape positive density-dependence is around 5, 20 or 90 cells ml(-1)under conditions of high carbon resources, low carbon resources or low carbon resources with predation, respectively. This work builds on the foundations of modern microbial ecology, demonstrating that mechanisms controlling macroorganisms apply to microorganisms, and provides a statistical method to detect Allee effects in data. PMID:27048467

  15. MICROBIAL POPULATION ANALYSIS AS A MEASURE OF ECOSYSTEM RESTORATION

    EPA Science Inventory

    During a controlled oil spill study in a freshwater wetland, four methods were used to track changes in microbial populations in response to in situ remediation treatments, including nutrient amendments and the removal of surface vegetation. Most probable number (MPN) esimates o...

  16. Microbial activity at Yucca Mountain

    SciTech Connect

    Horn, J.M.; Meike, A.

    1995-09-25

    The U.S. Department of Energy is engaged in a suitability study for a potential geological repository at Yucca Mountain, Nevada, for the containment and storage of commercially generated spent fuel and defense high-level nuclear waste. There is growing recognition of the role that biotic factors could play in this repository, either directly through microbially induced corrosion (MIC), or indirectly by altering the chemical environment or contributing to the transport of radionuclides. As a first step toward describing and predicting these processes, a workshop was held on April 10-12, 1995, in Lafayette, California. The immediate aims of the workshop were: (1) To identify microbially related processes relevant to the design of a radioactive waste repository under conditions similar to those at Yucca Mountain. (2) To determine parameters that are critical to the evaluation of a disturbed subterranean environment. (3) To define the most effective means of investigating the factors thus identified.

  17. Molecular Characterization of Water Column Microbial Populations within the Northern Gulf of Mexico Hypoxic Zone

    NASA Astrophysics Data System (ADS)

    Mills, H. J.; Reese, B. K.; Romero, B.

    2012-12-01

    The Gulf of Mexico hypoxic zone displays spatial and temporal variability on seasonal, diurnal, and hourly timescales. The highly dynamic geochemistry can be a result of physical and chemical factors as well as pelagic microbial populations. As part of an ongoing project to determine the mechanisms controlling hypoxia and understand the biological factors within this region, shifts in the composition of the metabolically active microbial populations within the water column were characterized. Understanding these shifts provide information on microbial populations that have the potential to decrease oxygen concentrations through respiration and increase oxygen through photosynthesis. Temporal and spatial variations of metabolically active microbial populations were investigated along a well-studied 20 m isobath extending east of Terrebonne Bay to a location offshore from the Atchafalaya Bay. An RNA-based molecular characterization of the microbial population was used to determine the distribution of the metabolically active lineages. Bacterial SSU rRNA were pyrosequenced (Roche 454 FLX) providing over 700,000 sequences with an average read length of more than 400 bases. Known photosynthetic lineages varied in frequency of detection at depth and time of sampling, as was expected. Additional lineages with the capacity for suboxic metabolic processes were detected mid-water column associated with hypoxic water formation. These data suggest hypoxic conditions persist long enough in the mid-water to promote a physiological response within the microbial populations. In addition, temporal switches between photosynthesis and respiration should be considered when analyzing the extent of hypoxia. The techniques used provide a unique view of the biological mechanisms controlling hypoxia within the northern Gulf of Mexico.

  18. Evolutionary Dynamics and Diversity in Microbial Populations

    NASA Astrophysics Data System (ADS)

    Thompson, Joel; Fisher, Daniel

    2013-03-01

    Diseases such as flu and cancer adapt at an astonishing rate. In large part, viruses and cancers are so difficult to prevent because they are continually evolving. Controlling such ``evolutionary diseases'' requires a better understanding of the underlying evolutionary dynamics. It is conventionally assumed that adaptive mutations are rare and therefore will occur and sweep through the population in succession. Recent experiments using modern sequencing technologies have illuminated the many ways in which real population sequence data does not conform to the predictions of conventional theory. We consider a very simple model of asexual evolution and perform simulations in a range of parameters thought to be relevant for microbes and cancer. Simulation results reveal complex evolutionary dynamics typified by competition between lineages with different sets of adaptive mutations. This dynamical process leads to a distribution of mutant gene frequencies different than expected under the conventional assumption that adaptive mutations are rare. Simulated gene frequencies share several conspicuous features with data collected from laboratory-evolved yeast and the worldwide population of influenza.

  19. Strain-level microbial epidemiology and population genomics from shotgun metagenomics.

    PubMed

    Scholz, Matthias; Ward, Doyle V; Pasolli, Edoardo; Tolio, Thomas; Zolfo, Moreno; Asnicar, Francesco; Truong, Duy Tin; Tett, Adrian; Morrow, Ardythe L; Segata, Nicola

    2016-05-01

    Identifying microbial strains and characterizing their functional potential is essential for pathogen discovery, epidemiology and population genomics. We present pangenome-based phylogenomic analysis (PanPhlAn; http://segatalab.cibio.unitn.it/tools/panphlan), a tool that uses metagenomic data to achieve strain-level microbial profiling resolution. PanPhlAn recognized outbreak strains, produced the largest strain-level population genomic study of human-associated bacteria and, in combination with metatranscriptomics, profiled the transcriptional activity of strains in complex communities. PMID:26999001

  20. Effect of Gamma radiation on microbial population of natural casings

    NASA Astrophysics Data System (ADS)

    Trigo, M. J.; Fraqueza, M. J.

    1998-06-01

    The high microbial load of fresh and dry natural casings increases the risk of meat product contamination with pathogenic microorganisms, agents of foodborn diseases. The aim of this work is to evaluate the killing effect of gamma radiation of the resident microbial population of pork and beef casings, to improve their hygiene and safety. Portions of fresh pork (small intestines and colon) and dry beef casings were irradiated in a Cobalt 60 source with with absorbed doses of 1,2,5 and 10 kGy. The D 10 values of total aerobic microorganisms in the pork casings were 1.65 kGy for colon and 1.54 kGy for small intestine. The D 10 value found in beef dry casings (small intestine) was 10.17 kGy. Radurization with 5 kGy was able to reduce, at least, 6 logs the coliform bacteria in pork casings. The killing effect over faecal Streptococci was 4 logs for pork fresh casings and 2 logs for beef dry casings. Gamma radiation with 5 kGy proved to be a convenient method to reduce substantially the microbial population of pork fresh casings. Otherwise, the microbial population of beef dry casings still resisted to 10 kGy.

  1. Strongly Deterministic Population Dynamics in Closed Microbial Communities

    NASA Astrophysics Data System (ADS)

    Frentz, Zak; Kuehn, Seppe; Leibler, Stanislas

    2015-10-01

    Biological systems are influenced by random processes at all scales, including molecular, demographic, and behavioral fluctuations, as well as by their interactions with a fluctuating environment. We previously established microbial closed ecosystems (CES) as model systems for studying the role of random events and the emergent statistical laws governing population dynamics. Here, we present long-term measurements of population dynamics using replicate digital holographic microscopes that maintain CES under precisely controlled external conditions while automatically measuring abundances of three microbial species via single-cell imaging. With this system, we measure spatiotemporal population dynamics in more than 60 replicate CES over periods of months. In contrast to previous studies, we observe strongly deterministic population dynamics in replicate systems. Furthermore, we show that previously discovered statistical structure in abundance fluctuations across replicate CES is driven by variation in external conditions, such as illumination. In particular, we confirm the existence of stable ecomodes governing the correlations in population abundances of three species. The observation of strongly deterministic dynamics, together with stable structure of correlations in response to external perturbations, points towards a possibility of simple macroscopic laws governing microbial systems despite numerous stochastic events present on microscopic levels.

  2. Self-driven jamming in growing microbial populations

    NASA Astrophysics Data System (ADS)

    Delarue, Morgan; Hartung, Jörn; Schreck, Carl; Gniewek, Pawel; Hu, Lucy; Herminghaus, Stephan; Hallatschek, Oskar

    2016-08-01

    In natural settings, microbes tend to grow in dense populations where they need to push against their surroundings to accommodate space for new cells. The associated contact forces play a critical role in a variety of population-level processes, including biofilm formation, the colonization of porous media, and the invasion of biological tissues. Although mechanical forces have been characterized at the single-cell level, it remains elusive how collective pushing forces result from the combination of single-cell forces. Here, we reveal a collective mechanism of confinement, which we call self-driven jamming, that promotes the build-up of large mechanical pressures in microbial populations. Microfluidic experiments on budding yeast populations in space-limited environments show that self-driven jamming arises from the gradual formation and sudden collapse of force chains driven by microbial proliferation, extending the framework of driven granular matter. The resulting contact pressures can become large enough to slow down cell growth, to delay the cell cycle in the G1 phase, and to strain or even destroy the micro-environment through crack propagation. Our results suggest that self-driven jamming and build-up of large mechanical pressures is a natural tendency of microbes growing in confined spaces, contributing to microbial pathogenesis and biofouling.

  3. Self-Driven Jamming of Growing Microbial Populations

    NASA Astrophysics Data System (ADS)

    Schreck, Carl; Delarue, Morgan; Gneiwek, Pawel; Hallatschek, Oskar

    When cells grow in confined spaces, they assemble into dense populations that interact both chemically and physically. Although in recent years scientists have uncovered a previously hidden layer of mechanical regulation in mammalian tissues that impacts gene expression and development, little is known about the consequences of mechanical constraints on single-celled microbes. This is largely due to a lack of appropriate culturing techniques and accurate computational models. Using physically explicit computer models that are developed alongside microfluidic experiments, we address two fundamental questions: (1) what structures self-assemble in confined geometries due to the cell growth and division process? and (2) how do those structures and associated stresses feed back on to cell physiology? We find that microbial growth in confinement can lead to jamming, heterogeneous stress fields, and intermittent flow that in turn result in spatially and temporally heterogeneous physiological responses. With computer simulations, we further explore the differences between this 'active' flow that is driven internally by cell growth and 'inactive' flow, such as shear and hopper flow, that is driven externally.

  4. Growth dynamics and the evolution of cooperation in microbial populations

    NASA Astrophysics Data System (ADS)

    Cremer, Jonas; Melbinger, Anna; Frey, Erwin

    2012-02-01

    Microbes providing public goods are widespread in nature despite running the risk of being exploited by free-riders. However, the precise ecological factors supporting cooperation are still puzzling. Following recent experiments, we consider the role of population growth and the repetitive fragmentation of populations into new colonies mimicking simple microbial life-cycles. Individual-based modeling reveals that demographic fluctuations, which lead to a large variance in the composition of colonies, promote cooperation. Biased by population dynamics these fluctuations result in two qualitatively distinct regimes of robust cooperation under repetitive fragmentation into groups. First, if the level of cooperation exceeds a threshold, cooperators will take over the whole population. Second, cooperators can also emerge from a single mutant leading to a robust coexistence between cooperators and free-riders. We find frequency and size of population bottlenecks, and growth dynamics to be the major ecological factors determining the regimes and thereby the evolutionary pathway towards cooperation.

  5. Microbial activities in deep subsurface environments

    SciTech Connect

    Phelps, T.J.; Raione, E.G.; White, D.C. |; Fliermans, C.B.

    1988-12-31

    Activities of microorganisms residing in terrestrial deep subsurface sediments were examined in forty-six sediment samples from three aseptically sampled boreholes. Radiolabeled time course experiments assessing in situ microbial activities were initiated within 30 minutes of core recovery. [{sup 14}C-1-] Acetate incorporation into lipids. [methyl-{sup 3}H-]thymidine incorporation into DNA, [{sup 14}C-2-]acetate and [{sup 14}C-U-]glucose mineralization in addition to microbial enrichment and enumeration studies were examined in surface and subsurface sediments. Surface soils contained the greatest biomass and activities followed by the shallow aquifer zones. Water saturated subsurface sediments exhibited three to four orders of magnitude greater activity and culturable microorganisms than the dense clay zones. Regardless of depth, sediments which contained more than 20% clays exhibited the lowest activities and culturable microorganisms.

  6. Distributions of microbial activities in deep subseafloor sediments

    NASA Technical Reports Server (NTRS)

    D'Hondt, Steven; Jorgensen, Bo Barker; Miller, D. Jay; Batzke, Anja; Blake, Ruth; Cragg, Barry A.; Cypionka, Heribert; Dickens, Gerald R.; Ferdelman, Timothy; Hinrichs, Kai-Uwe; Holm, Nils G.; Mitterer, Richard; Spivack, Arthur; Wang, Guizhi; Bekins, Barbara; Engelen, Bert; Ford, Kathryn; Gettemy, Glen; Rutherford, Scott D.; Sass, Henrik; Skilbeck, C. Gregory; Aiello, Ivano W.; Guerin, Gilles; House, Christopher H.; Inagaki, Fumio

    2004-01-01

    Diverse microbial communities and numerous energy-yielding activities occur in deeply buried sediments of the eastern Pacific Ocean. Distributions of metabolic activities often deviate from the standard model. Rates of activities, cell concentrations, and populations of cultured bacteria vary consistently from one subseafloor environment to another. Net rates of major activities principally rely on electron acceptors and electron donors from the photosynthetic surface world. At open-ocean sites, nitrate and oxygen are supplied to the deepest sedimentary communities through the underlying basaltic aquifer. In turn, these sedimentary communities may supply dissolved electron donors and nutrients to the underlying crustal biosphere.

  7. Facilitation as Attenuating of Environmental Stress among Structured Microbial Populations

    PubMed Central

    Santaella, Sandra Tédde; Martins, Claudia Miranda; Martins, Rogério Parentoni

    2016-01-01

    There is currently an intense debate in microbial societies on whether evolution in complex communities is driven by competition or cooperation. Since Darwin, competition for scarce food resources has been considered the main ecological interaction shaping population dynamics and community structure both in vivo and in vitro. However, facilitation may be widespread across several animal and plant species. This could also be true in microbial strains growing under environmental stress. Pure and mixed strains of Serratia marcescens and Candida rugosa were grown in mineral culture media containing phenol. Growth rates were estimated as the angular coefficients computed from linearized growth curves. Fitness index was estimated as the quotient between growth rates computed for lineages grown in isolation and in mixed cultures. The growth rates were significantly higher in associated cultures than in pure cultures and fitness index was greater than 1 for both microbial species showing that the interaction between Serratia marcescens and Candida rugosa yielded more efficient phenol utilization by both lineages. This result corroborates the hypothesis that facilitation between microbial strains can increase their fitness and performance in environmental bioremediation. PMID:26904719

  8. Facilitation as Attenuating of Environmental Stress among Structured Microbial Populations.

    PubMed

    Martins, Suzana Cláudia Silveira; Santaella, Sandra Tédde; Martins, Claudia Miranda; Martins, Rogério Parentoni

    2016-01-01

    There is currently an intense debate in microbial societies on whether evolution in complex communities is driven by competition or cooperation. Since Darwin, competition for scarce food resources has been considered the main ecological interaction shaping population dynamics and community structure both in vivo and in vitro. However, facilitation may be widespread across several animal and plant species. This could also be true in microbial strains growing under environmental stress. Pure and mixed strains of Serratia marcescens and Candida rugosa were grown in mineral culture media containing phenol. Growth rates were estimated as the angular coefficients computed from linearized growth curves. Fitness index was estimated as the quotient between growth rates computed for lineages grown in isolation and in mixed cultures. The growth rates were significantly higher in associated cultures than in pure cultures and fitness index was greater than 1 for both microbial species showing that the interaction between Serratia marcescens and Candida rugosa yielded more efficient phenol utilization by both lineages. This result corroborates the hypothesis that facilitation between microbial strains can increase their fitness and performance in environmental bioremediation. PMID:26904719

  9. Addition of activated switchgrass biochar to an aridic subsoil increases microbial nitrogen cycling gene abundances

    Technology Transfer Automated Retrieval System (TEKTRAN)

    It has been demonstrated that soil amended with biochar, designed specifically for use as a soil conditioner, results in changes to the microbial populations that reside therein. These changes have been reflected in studies measuring variations in microbial activity, biomass, and community structure...

  10. The bacteriocin bactofencin A subtly modulates gut microbial populations.

    PubMed

    Guinane, Caitriona M; Lawton, Elaine M; O'Connor, Paula M; O'Sullivan, Órla; Hill, Colin; Ross, R Paul; Cotter, Paul D

    2016-08-01

    The diverse and dynamic microbiota of the gastrointestinal tract represents a vast source of bioactive substances. These include bacteriocins, which are antimicrobial peptides with the potential to modulate gut populations to impact positively on human health. Although several gut-derived bacteriocins have been isolated, there remain only a few exceptional studies in which their influence on microbial populations within the gut has been investigated. To facilitate such investigations, in vitro faecal fermentation systems can be used to simulate the anaerobic environment of the colon. In this instance, such a system was employed to explore the impact of bactofencin A, a novel broad spectrum class IId bacteriocin produced by gut isolates of Lactobacillus salivarius, on intestinal populations and overall microbial diversity. The study reveals that, although bactofencin A is a broad spectrum bacteriocin, it has a relatively subtle influence on intestinal communities, with a potentially positive impact on anaerobic populations such as Bacteroides, Clostridium and Bifidibacterium spp. The strategy taken is an important first step in investigating the merits of using bactofencin A to manipulate the gut microbiota in a beneficial way for health. PMID:27154638

  11. Linking Toluene Degradation with Specific Microbial Populations in Soil

    PubMed Central

    Hanson, Jessica R.; Macalady, Jennifer L.; Harris, David; Scow, Kate M.

    1999-01-01

    Phospholipid fatty acid (PLFA) analysis of a soil microbial community was coupled with 13C isotope tracer analysis to measure the community’s response to addition of 35 μg of [13C]toluene ml of soil solution−1. After 119 h of incubation with toluene, 96% of the incorporated 13C was detected in only 16 of the total 59 PLFAs (27%) extracted from the soil. Of the total 13C-enriched PLFAs, 85% were identical to the PLFAs contained in a toluene-metabolizing bacterium isolated from the same soil. In contrast, the majority of the soil PLFAs (91%) became labeled when the same soil was incubated with [13C]glucose. Our study showed that coupling 13C tracer analysis with PLFA analysis is an effective technique for distinguishing a specific microbial population involved in metabolism of a labeled substrate in complex environments such as soil. PMID:10583996

  12. Milankovitch-scale correlations between deeply buried microbial populations and biogenic ooze lithology

    USGS Publications Warehouse

    Aiello, I.W.; Bekins, B.A.

    2010-01-01

    The recent discoveries of large, active populations of microbes in the subseafloor of the world's oceans supports the impact of the deep biosphere biota on global biogeochemical cycles and raises important questions concerning the functioning of these extreme environments for life. These investigations demonstrated that subseafloor microbes are unevenly distributed and that cell abundances and metabolic activities are often independent from sediment depths, with increased prokaryotic activity at geochemical and/or sedimentary interfaces. In this study we demonstrate that microbial populations vary at the scale of individual beds in the biogenic oozes of a drill site in the eastern equatorial Pacific (Ocean Drilling Program Leg 201, Site 1226). We relate bedding-scale changes in biogenic ooze sediment composition to organic carbon (OC) and microbial cell concentrations using high-resolution color reflectance data as proxy for lithology. Our analyses demonstrate that microbial concentrations are an order of magnitude higher in the more organic-rich diatom oozes than in the nannofossil oozes. The variations mimic small-scale variations in diatom abundance and OC, indicating that the modern distribution of microbial biomass is ultimately controlled by Milankovitch-frequency variations in past oceanographic conditions. ?? 2010 Geological Society of America.

  13. Metabolic Differences in Microbial Cell Populations Revealed by Nanophotonic Ionization

    SciTech Connect

    Walker, Bennett; Antonakos, Cory; Retterer, Scott T; Vertes, Akos

    2013-01-01

    ellular differences are linked to cell differentiation, the proliferation of cancer and to the development of drug resistance in microbial infections. Due to sensitivity limitations, however, large- scale metabolic analysis at the single cell level is only available for cells significantly larger in volume than Saccharomyces cerevisiae (~30 fL). Here we demonstrate that by a nanophotonic ionization platform and mass spectrometry, over one hundred up to 108 metabolites, or up to 18% of the known S. cerevisiae metabolome, can be identified in very small cell populations (n < 100). Under ideal conditions, r Relative quantitation of up to 4% of the metabolites is achieved at the single cell level.

  14. Management and control of microbial populations' development in LSS of missions of different durations.

    PubMed

    Somova, L A; Pechurkin, N S

    2005-01-01

    The problem of interaction between man and microorganisms in closed habitats is an inextricable part of the whole problem of co-existence between macro- and microorganisms. Concerning the support of human life in closed habitat, we can, conventionally, divide microorganisms, acting in life support system (LSS) into three groups: useful, neutral and harmful. The tasks, for human beings for optimal coexistence with microhabitants seem to be trivial: (1) to increase the activity of useful forms, (2) decrease the activity harmful forms, (3) not allow the neutral forms to become the harmful ones and even to help them to gain useful activity. The task of efficient management and control of microbial population's development in LSS highly depends on mission duration. As for short-term missions without recycling, the proper hygienic procedures are developed. For longer missions, the probability of transformation of the neutral forms into the harmful ones is becoming more dangerous. The LSS for long-term missions are to use cycling-recycling systems, including system with biological recycling. In these systems, microbial populations as regenerative link should be useful and active agents. Some problems of microbial populations control and management are discussed in the paper. PMID:16175696

  15. Monomethylhydrazine degradation and its effect on carbon dioxide evolution and microbial populations in soil

    SciTech Connect

    Ou, L.T.; Street, J.J.

    1988-09-01

    Monomethylhydrazine (MMH), along with hydrazine and 1,1-dimethylhydrazine are the main components of hydrazine fuels. Information on the fate of MMH in soil and its overall effect on soil microbial activity is not known, though MMH is known to be toxic to a number of soil bacteria. Despite the fact that axenic bacterial cultures are inhibited by the three hydrazines, Ou and Street reported that soil respiration, and total bacterial and fungal populations in soil, were not inhibited by hydrazine at concentrations of 100 ..mu..g/g and lower. Even at 500 ..mu..g/g, only total bacterial populations in soil were inhibited by the presence of hydrazine. They also reported that hydrazine rapidly disappeared in soil. The authors initiated this study to investigate the effect of MMH on soil microbial activity and on degradation of the chemical in soil.

  16. Microbial Community Structure and Enzyme Activities in Semiarid Agricultural Soils

    NASA Astrophysics Data System (ADS)

    Acosta-Martinez, V. A.; Zobeck, T. M.; Gill, T. E.; Kennedy, A. C.

    2002-12-01

    The effect of agricultural management practices on the microbial community structure and enzyme activities of semiarid soils of different textures in the Southern High Plains of Texas were investigated. The soils (sandy clay loam, fine sandy loam and loam) were under continuous cotton (Gossypium hirsutum L.) or in rotations with peanut (Arachis hypogaea L.), sorghum (Sorghum bicolor L.) or wheat (Triticum aestivum L.), and had different water management (irrigated or dryland) and tillage (conservation or conventional). Microbial community structure was investigated using fatty acid methyl ester (FAME) analysis by gas chromatography and enzyme activities, involved in C, N, P and S cycling of soils, were measured (mg product released per kg soil per h). The activities of b-glucosidase, b-glucosaminidase, alkaline phosphatase, and arylsulfatase were significantly (P<0.05) increased in soils under cotton rotated with sorghum or wheat, and due to conservation tillage in comparison to continuous cotton under conventional tillage. Principal component analysis showed FAME profiles of these soils separated distinctly along PC1 (20 %) and PC2 (13 %) due to their differences in soil texture and management. No significant differences were detected in FAME profiles due to management practices for the same soils in this sampling period. Enzyme activities provide early indications of the benefits in microbial populations and activities and soil organic matter under crop rotations and conservation tillage in comparison to the typical practices in semiarid regions of continuous cotton and conventional tillage.

  17. Microbial populations and activities in the rhizoplane of rock-weathering desert plants. I. Root colonization and weathering of igneous rocks.

    PubMed

    Puente, M E; Bashan, Y; Li, C Y; Lebsky, V K

    2004-09-01

    Dense layers of bacteria and fungi in the rhizoplane of three species of cactus (Pachycereus pringlei, Stenocereus thurberi, Opuntia cholla) and a wild fig tree (Ficus palmeri) growing in rocks devoid of soil were revealed by bright-field and fluorescence microscopy and field emission scanning electron microscopy. These desert plants are responsible for rock weathering in an ancient lava flow at La Purisima-San Isidro and in sedimentary rock in the Sierra de La Paz, both in Baja California Sur, Mexico. The dominant bacterial groups colonizing the rhizoplane were fluorescent pseudomonads and bacilli. Seven of these bacterial species were identified by the 16S rRNA molecular method. Unidentified fungal and actimomycete species were also present. Some of the root-colonizing microorganisms fixed in vitro N(2), produced volatile and non-volatile organic acids that subsequently reduced the pH of the rock medium in which the bacteria grew, and significantly dissolved insoluble phosphates, extrusive igneous rock, marble, and limestone. The bacteria were able to release significant amounts of useful minerals, such as P, K, Mg, Mn, Fe, Cu, and Zn from the rocks and were thermo-tolerant, halo-tolerant, and drought-tolerant. The microbial community survived in the rhizoplane of cacti during the annual 10-month dry season. This study indicates that rhizoplane bacteria on cacti roots in rock may be involved in chemical weathering in hot, subtropical deserts. PMID:15375735

  18. Microbial Population Changes During Bioremediation of an Experimental Oil Spill

    SciTech Connect

    Chang, Y.J.; Davis, G.A.; Macnaughton, S.J.; Stephen, J.R.; Venosa, A.D.; White, D.C.

    1998-08-08

    A field experiment was conducted in Delaware (USA) to evaluate three crude oil bioremediation techniques. Four treatments were studied: no oil control, oil alone, oil + nutrients, and oil + nutrients + an indigenous inoculum. The microbial populations were monitored by standard MPN techniques, PLFA profile analysis, and 16S rDNA DGGE analysis for species definition. Viable MPN estimates showed high but steadily declining microbial numbers and no significant differences among treatments during the 14-weeks. Regarding the PLFA results, the communities shifted over the 14-week period from being composed primarily of eukaryotes to Gram-negative bacteria. The Gram-negative communities shifted from the exponential to the stationary phase of growth after week 0. All Gram-negative communities showed evidence of environmental stress. The 16S rDNA DGGE profile of all plots revealed eight prominent bands at time zero. The untreated control plots revealed a simple, dynamic dominant population structure throughout the experiment. The original banding pattern disappeared rapidly in all oiled plots, indicating that the dominant species diversity changed and increased substantially over 14 weeks. The nature of this change was altered by nutrient-addition and the addition of the indigenous inoculum.

  19. Population dynamics of microbial communities in the zebrafish gut

    NASA Astrophysics Data System (ADS)

    Jemielita, Matthew; Taormina, Michael; Burns, Adam; Hampton, Jennifer; Rolig, Annah; Wiles, Travis; Guillemin, Karen; Parthasarathy, Raghuveer

    2015-03-01

    The vertebrate intestine is home to a diverse microbial community, which plays a crucial role in the development and health of its host. Little is known about the population dynamics and spatial structure of this ecosystem, including mechanisms of growth and interactions between species. We have constructed an experimental model system with which to explore these issues, using initially germ-free larval zebrafish inoculated with defined communities of fluorescently tagged bacteria. Using light sheet fluorescence microscopy combined with computational image analysis we observe and quantify the entire bacterial community of the intestine during the first 24 hours of colonization, during which time the bacterial population grows from tens to tens of thousands of bacteria. We identify both individual bacteria and clusters of bacteria, and quantify the growth rate and spatial distribution of these distinct subpopulations. We find that clusters of bacteria grow considerably faster than individuals and are located in specific regions of the intestine. Imaging colonization by two species reveals spatial segregation and competition. These data and their analysis highlight the importance of spatial organization in the establishment of gut microbial communities, and can provide inputs to physical models of real-world ecological dynamics.

  20. Metalliferous Biosignatures for Deep Subsurface Microbial Activity.

    PubMed

    Parnell, John; Brolly, Connor; Spinks, Sam; Bowden, Stephen

    2016-03-01

    The interaction of microbes and metals is widely assumed to have occurred in surface or very shallow subsurface environments. However new evidence suggests that much microbial activity occurs in the deep subsurface. Fluvial, lacustrine and aeolian 'red beds' contain widespread centimetre-scale reduction spheroids in which a pale reduced spheroid in otherwise red rocks contains a metalliferous core. Most of the reduction of Fe (III) in sediments is caused by Fe (III) reducing bacteria. They have the potential to reduce a range of metals and metalloids, including V, Cu, Mo, U and Se, by substituting them for Fe (III) as electron acceptors, which are all elements common in reduction spheroids. The spheroidal morphology indicates that they were formed at depth, after compaction, which is consistent with a microbial formation. Given that the consequences of Fe (III) reduction have a visual expression, they are potential biosignatures during exploration of the terrestrial and extraterrestrial geological record. There is debate about the energy available from Fe (III) reduction on Mars, but the abundance of iron in Martian soils makes it one of the most valuable prospects for life there. Entrapment of the microbes themselves as fossils is possible, but a more realistic target during the exploration of Mars would be the colour contrasts reflecting selective reduction or oxidation. This can be achieved by analysing quartz grains across a reduction spheroid using Raman spectroscopy, which demonstrates its suitability for life detection in subsurface environments. Microbial action is the most suitable explanation for the formation of reduction spheroids and may act as metalliferous biosignatures for deep subsurface microbial activity. PMID:26376912

  1. Metalliferous Biosignatures for Deep Subsurface Microbial Activity

    NASA Astrophysics Data System (ADS)

    Parnell, John; Brolly, Connor; Spinks, Sam; Bowden, Stephen

    2016-03-01

    The interaction of microbes and metals is widely assumed to have occurred in surface or very shallow subsurface environments. However new evidence suggests that much microbial activity occurs in the deep subsurface. Fluvial, lacustrine and aeolian `red beds' contain widespread centimetre-scale reduction spheroids in which a pale reduced spheroid in otherwise red rocks contains a metalliferous core. Most of the reduction of Fe (III) in sediments is caused by Fe (III) reducing bacteria. They have the potential to reduce a range of metals and metalloids, including V, Cu, Mo, U and Se, by substituting them for Fe (III) as electron acceptors, which are all elements common in reduction spheroids. The spheroidal morphology indicates that they were formed at depth, after compaction, which is consistent with a microbial formation. Given that the consequences of Fe (III) reduction have a visual expression, they are potential biosignatures during exploration of the terrestrial and extraterrestrial geological record. There is debate about the energy available from Fe (III) reduction on Mars, but the abundance of iron in Martian soils makes it one of the most valuable prospects for life there. Entrapment of the microbes themselves as fossils is possible, but a more realistic target during the exploration of Mars would be the colour contrasts reflecting selective reduction or oxidation. This can be achieved by analysing quartz grains across a reduction spheroid using Raman spectroscopy, which demonstrates its suitability for life detection in subsurface environments. Microbial action is the most suitable explanation for the formation of reduction spheroids and may act as metalliferous biosignatures for deep subsurface microbial activity.

  2. Active laser tweezers microrheometry of microbial biofilms

    NASA Astrophysics Data System (ADS)

    Osterman, N.; Slapar, V.; Boric, M.; Stopar, D.; Babič, D.; Poberaj, I.

    2010-08-01

    Microbial biofilms are present on biotic and abiotic surfaces and have a significant impact on many fields in industry, health care and technology. Thus, a better understanding of processes that lead to development of biofilms and their chemical and mechanical properties is needed. In the following paper we report the results of active laser tweezers microrheology study of optically inhomogeneous extracellular matrix secreted by Visbrio sp. bacteria. One particle and two particle active microrheology were used in experiments. Both methods exhibited high enough sensitivity to detect viscosity changes at early stages of bacterial growth. We also showed that both methods can be used in mature samples where optical inhomogeneity becomes significant.

  3. Uranium Biomineralization By Natural Microbial Phosphatase Activities in the Subsurface

    SciTech Connect

    Taillefert, Martial

    2015-04-01

    This project investigated the geochemical and microbial processes associated with the biomineralization of radionuclides in subsurface soils. During this study, it was determined that microbial communities from the Oak Ridge Field Research subsurface are able to express phosphatase activities that hydrolyze exogenous organophosphate compounds and result in the non-reductive bioimmobilization of U(VI) phosphate minerals in both aerobic and anaerobic conditions. The changes of the microbial community structure associated with the biomineralization of U(VI) was determined to identify the main organisms involved in the biomineralization process, and the complete genome of two isolates was sequenced. In addition, it was determined that both phytate, the main source of natural organophosphate compounds in natural environments, and polyphosphate accumulated in cells could also be hydrolyzed by native microbial population to liberate enough orthophosphate and precipitate uranium phosphate minerals. Finally, the minerals produced during this process are stable in low pH conditions or environments where the production of dissolved inorganic carbon is moderate. These findings suggest that the biomineralization of U(VI) phosphate minerals is an attractive bioremediation strategy to uranium bioreduction in low pH uranium-contaminated environments. These efforts support the goals of the SBR long-term performance measure by providing key information on "biological processes influencing the form and mobility of DOE contaminants in the subsurface".

  4. Microbial growth associated with granular activated carbon in a pilot water treatment facility.

    PubMed Central

    Wilcox, D P; Chang, E; Dickson, K L; Johansson, K R

    1983-01-01

    The microbial dynamics associated with granular activated carbon (GAC) in a pilot water treatment plant were investigated over a period of 16 months. Microbial populations were monitored in the influent and effluent waters and on the GAC particles by means of total plate counts and ATP assays. Microbial populations between the influent and effluent waters of the GAC columns generally increased, indicating microbial growth. The dominant genera of microorganisms isolated from interstitial waters and GAC particles were Achromobacter, Acinetobacter, Aeromonas, Alcaligenes, Bacillus, Chromobacterium, Corynebacterium, Micrococcus, Microcyclus, Paracoccus, and Pseudomonas. Coliform bacteria were found in small numbers in the effluents from some of the GAC columns in the later months of the study. Oxidation of influent waters with ozone and maintenance of aerobic conditions on the GAC columns failed to appreciably enhance the microbial growth on GAC. PMID:6625567

  5. Dynamics of organic matter and microbial populations in amended soil: a multidisciplinary approach

    NASA Astrophysics Data System (ADS)

    Gigliotti, Giovanni; Pezzolla, Daniela; Zadra, Claudia; Albertini, Emidio; Marconi, Gianpiero; Turchetti, Benedetta; Buzzini, Pietro

    2013-04-01

    The application of organic amendments to soils, such as pig slurry, sewage sludge and compost is considered a tool for improving soil fertility and enhancing C stock. The addition of these different organic materials allows a good supply of nutrients for plants but also contributes to C sequestration, affects the microbial activity and the transformation of soil organic matter (SOM). Moreover, the addition of organic amendment has gained importance as a source of greenhouse gas (GHG) emissions and then as a cause of the "Global Warming". Therefore, it is important to investigate the factors controlling the SOM mineralization in order to improve soil C sequestration and decreasing at the same time the GHG emissions. The quality of organic matter added to the soil will play an important role in these dynamics, affecting the microbial activity and the changes in microbial community structure. A laboratory, multidisciplinary experiment was carried out to test the effect of the amendment by anaerobic digested livestock-derived organic materials on labile organic matter evolution and on dynamics of microbial population, this latter both in terms of consistence of microbial biomass, as well as in terms of microbial biodiversity. Different approaches were used to study the microbial community structure: chemical (CO2 fluxes, WEOC, C-biomass, PLFA), microbiological (microbial enumeration) and molecular (DNA extraction and Roche 454, Next Generation Sequencing, NGS). The application of fresh digestate, derived from the anaerobic treatment of animal wastes, affected the short-term dynamics of microbial community, as reflected by the increase of CO2 emissions immediately after the amendment compared to the control soil. This is probably due to the addition of easily available C added with the digestate, demonstrating that this organic material was only partially stabilized by the anaerobic process. In fact, the digestate contained a high amounts of available C, which led to

  6. MICROBIAL DEGRADATION OF SEVEN AMIDES BY SUSPENDED BACTERIAL POPULATIONS

    EPA Science Inventory

    Microbial transformation rate constants were determined for seven amides in natural pond water. A second-order mathematical rate expression served as the model for describing the microbial transformation. Also investigated was the relationship between the infrared spectra and the...

  7. Evidence of ancient microbial activity on Mars

    NASA Astrophysics Data System (ADS)

    Wallis, Jamie; Wickramasinghe, N. C.; Wallis, Daryl H.; Miyake, Nori; Wallis, M. K.; Hoover, Richard B.

    2015-09-01

    We report for the first time in situ observations of a relatively rare secondary iron arsenate-sulphate mineral named bukovskýite - Fe3+ 2(As5+O4)(S6+O4)(OH)•7(H2O) - found in a shock melt vein of the Tissint Martian meteorite. It is hypothesised that the mineral formed when high concentrations of aqueous H+, Fe(III), SO4 and AsO4 were maintained for long periods of time in microenvironments created within wet subsurface Martian clays. The aqueous H+, Fe(III), SO4 and AsO4 species arose from the microbial oxidation of FeS2 with concurrent release of sequestrated As. The availability of aqueous AsO4 would also be complemented by dissolution by-products of the microbial reduction of Feoxides influenced by dissolved organic matter that alters the redox state and the complexation of As, thus shifting As partitioning in favour of the solute phase. This hypothesis is substantially supported by SEM analysis of a 15μm spherical structure comprising of a carbonaceous outer coating with a inner core of FeS2 (pyrite) that showed the pyrite surface with spherical pits, and chains of pits, with morphologies distinct from abiotic alteration features. The pits and channels have a clustered, geometric distribution, typical of microbial activity, and are closely comparable to biologically mediated microstructures created by Fe- and S-oxidising microbes in the laboratory. These microstructures are interpreted as trace fossils resulting from the attachment of bacteria to the pyrite surfaces.

  8. Spatial Shifts in Microbial Population Structure Within Poultry Litter Associated with Physicochemical Properties

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microbial populations within poultry litter have been largely ignored with the exception of potential human or livestock pathogens. A better understanding of the community structure and identity of the microbial populations within poultry litter could aid in the development of management practices t...

  9. Energy and power limits for microbial activity

    NASA Astrophysics Data System (ADS)

    LaRowe, D.; Amend, J.

    2014-12-01

    The goal of this presentation is to describe a quantitative framework for determining how energy limits microbial activity, biomass and, ultimately, biogeochemical processes. Although this model can be applied to any environment, its utility is demonstrated in marine sediments, which are an attractive test habitat because they encompass a broad spectrum of energy levels, varying amounts of biomass and are ubiquitous. The potential number of active microbial cells in Arkonas Basin (Baltic Sea) sediments are estimated as a function of depth by quantifying the amount of energy that is available to them and the rate at which it is supplied: power. The amount of power supplied per cubic centimeter of sediment is determined by calculating the Gibbs energy of fermentation and sulfate reduction in combination with the rate of particulate organic carbon, POC, degradation. The Reactive Continuum Model (Boudreau and Ruddick, 1991), RCM, is used to determine the rate at which POC is made available for microbial consumption. The RCM represents POC as containing a range of different types of organic compounds whose ability to be consumed by microorganisms varies as a function of the age of the sediment and on the distribution of compound types that were initially deposited. The sediment age model and RCM parameters determined by (Mogollon et al., 2012) are used. The power available for fermentation and sulfate reduction coupled to H2 and acetate oxidation varies from 10-8 W cm-3 at the sediment water interface to between 10-11 - 10-12 W cm-3 at 3.5 meters below the seafloor, mbsf. Using values of maintenance powers for each of these catabolic activities taken from the literature, the total number of active cells in these sediments similarly decreases from just less than 108 cell cm-3 at the SWI to 4.6 x 104 cells cm-3 at 3.5 mbsf. The number of moles of POC decreases from 2.6 x 10-5 to 9.5 x 10-6, also becoming more recalcitrant with depth. Boudreau, B. P. and Ruddick, B. R

  10. Negative frequency-dependent interactions can underlie phenotypic heterogeneity in a clonal microbial population.

    PubMed

    Healey, David; Axelrod, Kevin; Gore, Jeff

    2016-01-01

    Genetically identical cells in microbial populations often exhibit a remarkable degree of phenotypic heterogeneity even in homogenous environments. Such heterogeneity is commonly thought to represent a bet-hedging strategy against environmental uncertainty. However, evolutionary game theory predicts that phenotypic heterogeneity may also be a response to negative frequency-dependent interactions that favor rare phenotypes over common ones. Here we provide experimental evidence for this alternative explanation in the context of the well-studied yeast GAL network. In an environment containing the two sugars glucose and galactose, the yeast GAL network displays stochastic bimodal activation. We show that in this mixed sugar environment, GAL-ON and GAL-OFF phenotypes can each invade the opposite phenotype when rare and that there exists a resulting stable mix of phenotypes. Consistent with theoretical predictions, the resulting stable mix of phenotypes is not necessarily optimal for population growth. We find that the wild-type mixed strategist GAL network can invade populations of both pure strategists while remaining uninvasible by either. Lastly, using laboratory evolution we show that this mixed resource environment can directly drive the de novo evolution of clonal phenotypic heterogeneity from a pure strategist population. Taken together, our results provide experimental evidence that negative frequency-dependent interactions can underlie the phenotypic heterogeneity found in clonal microbial populations. PMID:27487817

  11. Microbial Population of Feedlot Waste and Associated Sites

    PubMed Central

    Rhodes, R. A.; Hrubant, G. R.

    1972-01-01

    A quantitative determination was made every 2 months for a year of the microflora of beef cattle waste and runoff at a medium-sized midwestern feedlot. Counts were obtained for selected groups of organisms in waste taken from paved areas of pens cleaned daily and, therefore, reflect the flora of raw waste. Overall, in terms of viable count per gram dry weight, the feedlot waste contained 1010 total organisms, 109 anaerobes, 108 gram-negative bacteria, 107 coliforms, 106 sporeformers, and 105 yeasts, fungi, and streptomycetes. The specific numbers and pattern of these groups of organisms varied only slightly during the study in spite of a wide variation in weather. Data indicate that little microbial growth occurs in the waste as it exists in the feedlot. Runoff from the pens contained the same general population pattern but with greater variation attributable to volume of liquid. Comparable determinations of an associated field disposal area (before and after cropping), stockpiled waste, and elevated dirt areas in the pens indicate that fungi, and especially streptomycetes, are the aerobic organisms most associated with final stabilization of the waste. Yeasts, which are the dominant type of organism in the ensiled corn fed the cattle, do not occur in large numbers in the animal waste. Large ditches receiving runoff and subsurface water from the fields have a population similar to the runoff but with fewer coliforms. PMID:16349931

  12. Effects of Alkaline Phosphatase Activity on Nucleotide Measurements in Aquatic Microbial Communities †

    PubMed Central

    Karl, D. M.; Craven, D. B.

    1980-01-01

    Alkaline phosphatase (APase) activity was detected in aquatic microbial assemblages from the subtropics to Antarctica. The occurrence of APase in environmental nucleotide extracts was shown to significantly affect the measured concentrations of cellular nucleotides (adenosine triphosphate, adenosine diphosphate, adenosine monophosphate, guanosine triphosphate, uridine triphosphate, and cytidine triphosphate), adenylate energy charge, and guanosine triphosphate/adenosine triphosphate ratios, when conventional methods of nucleotide extraction were employed. Under the reaction conditions specified in this report, the initial rate of hydrolysis of adenosine triphosphate was directly proportional to the activity of APase in the sample extracts and consequently can be used as a sensitive measure of APase activity. A method was devised for obtaining reliable nucleotide measurements in naturally occurring microbial populations containing elevated levels of APase activity. The metabolic significance of APase activity in microbial cells is discussed, and it is concluded that the occurrence and regulation of APase in nature is dependent upon microscale inorganic phosphate limitation of the autochthonous microbial communities. PMID:16345634

  13. Community Analysis of Dynamic Microbial Mat Communities from Actively Erupting Seamounts (Invited)

    NASA Astrophysics Data System (ADS)

    Davis, R.; Tebo, B.; Moyer, C. L.

    2009-12-01

    The actively erupting deep-sea volcanoes NW Rota-1 and W Mata have multiple diffuse low-temperature (Tmax= 20-30 degrees) vent sites which harbor dense populations of microbial mat communities driven by chemoautotrophy. These microbial mats were often composed of white filamentous bacteria growing in close proximity to focused hydrothermal flow. Eight microbial mats were sampled from discrete hydrothermal vents on NW Rota-1 and W Mata volcanoes in 2009. The microbial mat communities were analyzed with quantitative PCR (Q-PCR) and terminal-restriction fragment length polymorphism (T-RFLP) community fingerprinting. All of the sampled microbial mats were dominated by the class Epsilonproteobacteria. The microbial mat at Iceberg Vent contained 13.5% Archaea, while all other microbial mats contained less than 1% Archaea. Bacterial community fingerprints from NW Rota-1 and W Mata formed distinct clusters that were well separated from clusters formed by hydrothermal communities from Axial and Eifuku Seamounts that were also dominated by Epsilonproteobacteria. Iceberg vent communities from NW Rota-1 have transitioned from being dominated by Caminibacter phylotypes to Sulfuimonas group phylotypes since 2004. These data suggest that microbial communities found on actively erupting volcanoes are geographically distinct and provide a natural laboratory to study microbial colonization and community succession at hydrothermal systems.

  14. Effects of Potassium Permanganate Oxidation on Subsurface Microbial Activity

    NASA Technical Reports Server (NTRS)

    Rowland, Martin A.; Brubaker, Gaylen R.; Westray, Mark; Morris, Damon; Kohler, Keisha; McCool, Alex (Technical Monitor)

    2001-01-01

    In situ chemical oxidation has the potential for degrading large quantities of organic contaminants and can be more effective and timely than traditional ex situ treatment methods. However, there is a need to better characterize the potential effects of this treatment on natural processes. This study focuses on potential inhibition to anaerobic dechlorination of trichloroethene (TCE) in soils from a large manufacturing facility as a result of in situ oxidation using potassium permanganate (KMn04)Previous microcosm studies established that natural attenuation occurs on-site and that it is enhanced by the addition of ethanol to the system. A potential remediation scheme for the site involves the use of potassium permanganate to reduce levels of TCE in heavily contaminated areas, then to inject ethanol into the system to "neutralize" excess oxidant and enhance microbial degradation. However, it is currently unknown whether the exposure of indigenous microbial populations to potassium permanganate may adversely affect biological reductive dechlorination by these microorganisms. Consequently, additional microcosm studies were conducted to evaluate this remediation scheme and assess the effect of potassium permanganate addition on biological reductive dechlorination of TCE. Samples of subsurface soil and groundwater were collected from a TCE-impacted area of the site. A portion of the soil was pretreated with nutrients and ethanol to stimulate microbial activity, while the remainder of the soil was left unamended. Soil/groundwater microcosms were prepared in sealed vials using the nutrient-amended and unamended soils, and the effects of potassium permanganate addition were evaluated using two permanganate concentrations (0.8 and 2.4 percent) and two contact times (1 and 3 weeks). TCE was then re-added to each microcosm and TCE and dichloroethene (DCE) concentrations were monitored to determine the degree to which microbial dechlorination occurred following chemical

  15. New Methods for Analysis of Spatial Distribution and Coaggregation of Microbial Populations in Complex Biofilms

    PubMed Central

    Almstrand, Robert; Daims, Holger; Persson, Frank; Sörensson, Fred

    2013-01-01

    In biofilms, microbial activities form gradients of substrates and electron acceptors, creating a complex landscape of microhabitats, often resulting in structured localization of the microbial populations present. To understand the dynamic interplay between and within these populations, quantitative measurements and statistical analysis of their localization patterns within the biofilms are necessary, and adequate automated tools for such analyses are needed. We have designed and applied new methods for fluorescence in situ hybridization (FISH) and digital image analysis of directionally dependent (anisotropic) multispecies biofilms. A sequential-FISH approach allowed multiple populations to be detected in a biofilm sample. This was combined with an automated tool for vertical-distribution analysis by generating in silico biofilm slices and the recently developed Inflate algorithm for coaggregation analysis of microbial populations in anisotropic biofilms. As a proof of principle, we show distinct stratification patterns of the ammonia oxidizers Nitrosomonas oligotropha subclusters I and II and the nitrite oxidizer Nitrospira sublineage I in three different types of wastewater biofilms, suggesting niche differentiation between the N. oligotropha subclusters, which could explain their coexistence in the same biofilms. Coaggregation analysis showed that N. oligotropha subcluster II aggregated closer to Nitrospira than did N. oligotropha subcluster I in a pilot plant nitrifying trickling filter (NTF) and a moving-bed biofilm reactor (MBBR), but not in a full-scale NTF, indicating important ecophysiological differences between these phylogenetically closely related subclusters. By using high-resolution quantitative methods applicable to any multispecies biofilm in general, the ecological interactions of these complex ecosystems can be understood in more detail. PMID:23892743

  16. Effects of biochar amendments on soil microbial biomass and activity.

    PubMed

    Zhang, H; Voroney, R P; Price, G W

    2014-11-01

    Environmental benefits reported in the literature of using biochar as a soil amendment are generally increased microbial activity and reduced greenhouse gas (GHG) emissions. This study determined the effects of amendment with biomass feedstocks (spent coffee grounds, wood pellets, and horse bedding compost) and that of biochars (700°C) produced from these feedstocks on soil microbial biomass (C and N) and activity. Soils were amended with these substrates at 0.75% by weight and incubated for up to 175 d under laboratory conditions. Biochar residual effects on soil microbial activity were also studied by amending these soils with either ammonium nitrate (NHNO, 35 mg N kg) or with glucose (864 mg C kg) plus NHNO. Soil microbial biomass C and N, net N mineralization, and CO, NO, and CH emissions were measured. Amendment with biomass feedstocks significantly increased soil microbial biomass and activity, whereas amendment with the biochars had no significant effect. Also, biochar amendment had no significant effect on either net N mineralization or NO and CH emissions from soil. These results indicate that production of biochars at this high temperature eliminated potential substrates. Microbial biomass C in biochar-amended and unamended soils was not significantly different following additions of NHNO or glucose plus NHNO, suggesting that microbial access to otherwise labile C and N was not affected. This study shows that biochars produced at 700°C, regardless of feedstock source, do not enhance soil microbial biomass or activity. PMID:25602227

  17. The Dynamic Arctic Snow Pack: An Unexplored Environment for Microbial Diversity and Activity

    PubMed Central

    Larose, Catherine; Dommergue, Aurélien; Vogel, Timothy M.

    2013-01-01

    The Arctic environment is undergoing changes due to climate shifts, receiving contaminants from distant sources and experiencing increased human activity. Climate change may alter microbial functioning by increasing growth rates and substrate use due to increased temperature. This may lead to changes of process rates and shifts in the structure of microbial communities. Biodiversity may increase as the Arctic warms and population shifts occur as psychrophilic/psychrotolerant species disappear in favor of more mesophylic ones. In order to predict how ecological processes will evolve as a function of global change, it is essential to identify which populations participate in each process, how they vary physiologically, and how the relative abundance, activity and community structure will change under altered environmental conditions. This review covers aspects of the importance and implication of snowpack in microbial ecology emphasizing the diversity and activity of these critical members of cold zone ecosystems. PMID:24832663

  18. Microbial populations related to PAH biodegradation in an aged biostimulated creosote-contaminated soil.

    PubMed

    Lladó, Salvador; Jiménez, Nuria; Viñas, Marc; Solanas, Anna Maria

    2009-09-01

    A previous bioremediation survey on a creosote-contaminated soil showed that aeration and optimal humidity promoted depletion of three-ringed polycyclic aromatic hydrocarbons (PAHs), but residual concentrations of four-ringed benzo(a)anthracene (B(a)A) and chrysene (Chry) remained. In order to explain the lack of further degradation of heavier PAHs such as four-ringed PAHs and to analyze the microbial population responsible for PAH biodegradation, a chemical and microbial molecular approach was used. Using a slurry incubation strategy, soil in liquid mineral medium with and without additional B(a)A and Chry was found to contain a powerful PAH-degrading microbial community that eliminated 89% and 53% of the added B(a)A and Chry, respectively. It is hypothesized that the lack of PAH bioavailability hampered their further biodegradation in the unspiked soil. According to the results of the culture-dependent and independent techniques Mycobacterium parmense, Pseudomonas mexicana, and Sphingobacterials group could control B(a)A and Chry degradation in combination with several microorganisms with secondary metabolic activity. PMID:19153811

  19. Effect of electrokinetic remediation on indigenous microbial activity and community within diesel contaminated soil.

    PubMed

    Kim, Seong-Hye; Han, Hyo-Yeol; Lee, You-Jin; Kim, Chul Woong; Yang, Ji-Won

    2010-07-15

    Electrokinetic remediation has been successfully used to remove organic contaminants and heavy metals within soil. The electrokinetic process changes basic soil properties, but little is known about the impact of this remediation technology on indigenous soil microbial activities. This study reports on the effects of electrokinetic remediation on indigenous microbial activity and community within diesel contaminated soil. The main removal mechanism of diesel was electroosmosis and most of the bacteria were transported by electroosmosis. After 25 days of electrokinetic remediation (0.63 mA cm(-2)), soil pH developed from pH 3.5 near the anode to pH 10.8 near the cathode. The soil pH change by electrokinetics reduced microbial cell number and microbial diversity. Especially the number of culturable bacteria decreased significantly and only Bacillus and strains in Bacillales were found as culturable bacteria. The use of EDTA as an electrolyte seemed to have detrimental effects on the soil microbial activity, particularly in the soil near the cathode. On the other hand, the soil dehydrogenase activity was enhanced close to the anode and the analysis of microbial community structure showed the increase of several microbial populations after electrokinetics. It is thought that the main causes of changes in microbial activities were soil pH and direct electric current. The results described here suggest that the application of electrokinetics can be a promising soil remediation technology if soil parameters, electric current, and electrolyte are suitably controlled based on the understanding of interaction between electrokinetics, contaminants, and indigenous microbial community. PMID:20452646

  20. Representation of Dormant and Active Microbial Dynamics for Ecosystem Modeling

    SciTech Connect

    Wang, Gangsheng; Mayes, Melanie; Gu, Lianhong; Schadt, Christopher Warren

    2014-01-01

    Dormancy is an essential strategy for microorganisms to cope with environmental stress. However, global ecosystem models typically ignore microbial dormancy, resulting in notable model uncertainties. To facilitate the consideration of dormancy in these large-scale models, we propose a new microbial physiology component that works for a wide range of substrate availabilities. This new model is based on microbial physiological states and the major parameters are the maximum specific growth and maintenance rates of active microbes and the ratio of dormant to active maintenance rates. A major improvement of our model over extant models is that it can explain the low active microbial fractions commonly observed in undisturbed soils. Our new model shows that the exponentially-increasing respiration from substrate-induced respiration experiments can only be used to determine the maximum specific growth rate and initial active microbial biomass, while the respiration data representing both exponentially-increasing and non-exponentially-increasing phases can robustly determine a range of key parameters including the initial total live biomass, initial active fraction, the maximum specific growth and maintenance rates, and the half-saturation constant. Our new model can be incorporated into existing ecosystem models to account for dormancy in microbially-driven processes and to provide improved estimates of microbial activities.

  1. Molecular Characterization of Swine Manure Lagoon Microbial and Antibiotic Resistant Populations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: The differences in swine manure lagoon effluent based on differing management styles or approaches such as different stages of swine rearing determines the presence of variable antibiotic resistance determinants and functional microbial populations. These concerns determine the suitabil...

  2. The subzero microbiome: microbial activity in frozen and thawing soils.

    PubMed

    Nikrad, Mrinalini P; Kerkhof, Lee J; Häggblom, Max M

    2016-06-01

    Most of the Earth's biosphere is characterized by low temperatures (<5°C) and cold-adapted microorganisms are widespread. These psychrophiles have evolved a complex range of adaptations of all cellular constituents to counteract the potentially deleterious effects of low kinetic energy environments and the freezing of water. Microbial life continues into the subzero temperature range, and this activity contributes to carbon and nitrogen flux in and out of ecosystems, ultimately affecting global processes. Microbial responses to climate warming and, in particular, thawing of frozen soils are not yet well understood, although the threat of microbial contribution to positive feedback of carbon flux is substantial. To date, several studies have examined microbial community dynamics in frozen soils and permafrost due to changing environmental conditions, and some have undertaken the complicated task of characterizing microbial functional groups and how their activity changes with changing conditions, either in situ or by isolating and characterizing macromolecules. With increasing temperature and wetter conditions microbial activity of key microbes and subsequent efflux of greenhouse gases also increase. In this review, we aim to provide an overview of microbial activity in seasonally frozen soils and permafrost. With a more detailed understanding of the microbiological activities in these vulnerable soil ecosystems, we can begin to predict and model future expectations for carbon release and climate change. PMID:27106051

  3. Microbial ecology of terrestrial Antarctica: Are microbial systems at risk from human activities?

    SciTech Connect

    White, G.J.

    1996-08-01

    Many of the ecological systems found in continental Antarctica are comprised entirely of microbial species. Concerns have arisen that these microbial systems might be at risk either directly through the actions of humans or indirectly through increased competition from introduced species. Although protection of native biota is covered by the Protocol on Environmental Protection to the Antarctic Treaty, strict measures for preventing the introduction on non-native species or for protecting microbial habitats may be impractical. This report summarizes the research conducted to date on microbial ecosystems in continental Antarctica and discusses the need for protecting these ecosystems. The focus is on communities inhabiting soil and rock surfaces in non-coastal areas of continental Antarctica. Although current polices regarding waste management and other operations in Antarctic research stations serve to reduce the introduction on non- native microbial species, importation cannot be eliminated entirely. Increased awareness of microbial habitats by field personnel and protection of certain unique habitats from physical destruction by humans may be necessary. At present, small-scale impacts from human activities are occurring in certain areas both in terms of introduced species and destruction of habitat. On a large scale, however, it is questionable whether the introduction of non-native microbial species to terrestrial Antarctica merits concern.

  4. Temporal variation of microbial population in a thermophilic biofilter for SO₂ removal.

    PubMed

    Zhang, Jingying; Li, Lin; Liu, Junxin

    2016-01-01

    The performance of a biofilter relies on the activity of microorganisms during the gas contaminant treatment process. In this study, SO2 was treated using a laboratory-scale biofilter packed with polyurethane foam cubes (PUFC), on which thermophilic desulfurization bacteria were attached. The thermophilic biofilter effectively reduced SO2 within 10months of operation time, with a maximum elimination capacity of 48.29 g/m(3)/hr. Temporal shifts in the microbial population in the thermophilic biofilter were determined through polymerase chain reaction-denaturing gradient gel electrophoresis and deoxyribonucleic acid (DNA) sequence analysis. The substrate species and environmental conditions in the biofilter influenced the microbial population. Oxygen distribution in the PUFC was analyzed using a microelectrode. When the water-containing rate in PUFC was over 98%, the oxygen distribution presented aerobic-anoxic-aerobic states along the test route on the PUFC. The appearance of sulfate-reducing bacteria was caused by the anaerobic conditions and sulfate formation after 4months of operation. PMID:26899638

  5. Microbial diversity differences within aerobic granular sludge and activated sludge flocs.

    PubMed

    Winkler, M-K H; Kleerebezem, R; de Bruin, L M M; Verheijen, P J T; Abbas, B; Habermacher, J; van Loosdrecht, M C M

    2013-08-01

    In this study, we investigated during 400 days the microbial community variations as observed from 16S DNA gene DGGE banding patterns from an aerobic granular sludge pilot plant as well as the from a full-scale activated sludge treatment plant in Epe, the Netherlands. Both plants obtained the same wastewater and had the same relative hydraulic variations and run stable over time. For the total bacterial population, a similarity analysis was conducted showing that the community composition of both sludge types was very dissimilar. Despite this difference, general bacterial population of both systems had on average comparable species richness, entropy, and evenness, suggesting that different bacteria were sharing the same functionality. Moreover, multi-dimensional scaling analysis revealed that the microbial populations of the flocculent sludge system moved closely around the initial population, whereas the bacterial population in the aerobic granular sludge moved away from its initial population representing a permanent change. In addition, the ammonium-oxidizing community of both sludge systems was studied in detail showing more unevenness than the general bacterial community. Nitrosomonas was the dominant AOB in flocculent sludge, whereas in granular sludge, Nitrosomonas and Nitrosospira were present in equal amounts. A correlation analysis of process data and microbial data from DGGE gels showed that the microbial diversity shift in ammonium-oxidizing bacteria clearly correlated with fluctuations in temperature. PMID:23064482

  6. Microbial Biomass and Activity Distribution in an Anoxic, Hypersaline Basin

    PubMed Central

    LaRock, Paul A.; Lauer, Ray D.; Schwarz, John R.; Watanabe, Kathleen K.; Wiesenburg, Denis A.

    1979-01-01

    The Orca Basin is a hypersaline depression in the northern Gulf of Mexico with anoxic conditions observed in the lower 200 m of the water column. Measurements of adenosine 5′-triphosphate, heterotrophic potential, and uridine uptake made above and across the interface into the anoxic zone revealed the presence of an active microbial population approximately 100 m above the interface. Biomass and activity decreased at and just below the interface but increased near the bottom, consistent with similar observations made in the Cariaco Trench. The maximum adenosine 5′-triphosphate concentration above the interface of 5.9 ng/liter (2,173 m) is about eight times greater than the value found in oxygenated waters of corresponding depth in the absence of an anoxic zone. The maximum adenosine 5′-triphosphate concentration in the anoxic zone is approximately 15 times greater than that found in oxygenated water of similar depth, suggesting anoxia will support the development of a larger bacterial population. Our findings suggest that autotrophic bacteria may be the dominant physiological group in the region just above the interface. PMID:16345355

  7. Microbial biomass and activity distribution in an anoxic, hypersaline basin.

    PubMed

    Larock, P A; Lauer, R D; Schwarz, J R; Watanabe, K K; Wiesenburg, D A

    1979-03-01

    The Orca Basin is a hypersaline depression in the northern Gulf of Mexico with anoxic conditions observed in the lower 200 m of the water column. Measurements of adenosine 5'-triphosphate, heterotrophic potential, and uridine uptake made above and across the interface into the anoxic zone revealed the presence of an active microbial population approximately 100 m above the interface. Biomass and activity decreased at and just below the interface but increased near the bottom, consistent with similar observations made in the Cariaco Trench. The maximum adenosine 5'-triphosphate concentration above the interface of 5.9 ng/liter (2,173 m) is about eight times greater than the value found in oxygenated waters of corresponding depth in the absence of an anoxic zone. The maximum adenosine 5'-triphosphate concentration in the anoxic zone is approximately 15 times greater than that found in oxygenated water of similar depth, suggesting anoxia will support the development of a larger bacterial population. Our findings suggest that autotrophic bacteria may be the dominant physiological group in the region just above the interface. PMID:16345355

  8. Ileal and cecal microbial populations in broilers given specific essential oil blends and probiotics in two consecutive grow-outs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Digestive microbial populations (MP) are key components for sustained healthy broiler production. Specific essential oil (EO) blends and probiotics used as feed additives have shown to promote healthy digestive microbials, resulting in improved poultry production. Two consecutive experiments were ...

  9. Population information activities in Hungary.

    PubMed

    Csahok, I

    1984-12-01

    The focal point for all population information activities in Hungary is the Central Statistical Office which is responsible for the organization and implementation of the decennial population censuses and of the intercensal population surveys and other data collection activities. The Central Statistical Office publishes a large volume of population information. The results of the censuses are presented partly in special census volumes and partly in statistical yearbooks. The Demographic Yearbook and other publications present results of population studies and Hungarian statistics. The Demographic Research Institute, which is part of the Central Statistical Office, is primarily responsible for research activity. The main task of the Institute is to study and analyze population processes and phenomena, as well as explore main demographic trends, carried out by using Hungarian and international demographic data. Demografia and serial publications present results of research activities of the Institute. The Library and Documentation Service, also part of the Central Statistical Office, provides conventional library services. Its main activity is the collection of both Hungarian and foreign and international official statistical publications, as well as theoretical and methodological works. Of a stock of 650,000 volumes covering a wide range of social and economic sciences, in addition to data material, the library has nearly 120,000 official statistical publications consisting mainly of population statistics and demographic data. Another activity of the Library is the processing and dissemination of documentation and it acts as a 2dary source of both Hungarian and foreign publications, especially on demography. The documentation consists of translating articles, book chapters or documents of international organizations, editing annotated bibliographies and disseminating custom-made, user-oriented profiles. This computerized information retrieval system uses Text

  10. Metagenomic Approach for Understanding Microbial Population from Petroleum Muck

    PubMed Central

    Joshi, M. N.; Dhebar, S. V.; Dhebar, S. V.; Bhargava, P.; Pandit, A. S.; Patel, R. P.; Saxena, A. K.

    2014-01-01

    Petroleum products play a major role in fueling the economy of the world but the pollution they create has become a critical issue. Understanding the diversity present in pipeline muck will help with the exploration of new microbial strains with better hydrocarbon degrading capacities for bioremediation of polluted sites. This study provides an analysis of petroleum muck using next generation sequencing. PMID:24874664

  11. Metagenomic approach for understanding microbial population from petroleum muck.

    PubMed

    Joshi, M N; Dhebar, S V; Dhebar, S V; Bhargava, P; Pandit, A S; Patel, R P; Saxena, A K; Bagatharia, S B

    2014-01-01

    Petroleum products play a major role in fueling the economy of the world but the pollution they create has become a critical issue. Understanding the diversity present in pipeline muck will help with the exploration of new microbial strains with better hydrocarbon degrading capacities for bioremediation of polluted sites. This study provides an analysis of petroleum muck using next generation sequencing. PMID:24874664

  12. MICROBIAL POPULATION CHANGES DURING BIOREMEDIATION OF AN EXPERIMENTAL OIL SPILL

    EPA Science Inventory

    Three crude oil bioremediation techniques were applied in a randomized block field experiment simulating a coastal oil-spill. Four treatments (no oil control, oil alone, oil + nutrients, and oil + nutrients + an indigenous inoculum) were applied. In-situ microbial community str...

  13. Measurements of Microbial Community Activities in Individual Soil Macroaggregates

    SciTech Connect

    Bailey, Vanessa L.; Bilskis, Christina L.; Fansler, Sarah J.; McCue, Lee Ann; Smith, Jeff L.; Konopka, Allan

    2012-05-01

    The functional potential of single soil aggregates may provide insights into the localized distribution of microbial activities better than traditional assays conducted on bulk quantities of soil. Thus, we scaled down enzyme assays for {beta}-glucosidase, N-acetyl-{beta}-D-glucosaminidase, lipase, and leucine aminopeptidase to measure of the enzyme potential of individual aggregates (250-1000 {mu}m diameter). Across all enzymes, the smallest aggregates had the greatest activity and the range of enzyme activities observed in all aggregates supports the hypothesis that functional potential in soil may be distributed in a patchy fashion. Paired analyses of ATP as a surrogate for active microbial biomass and {beta}-glucosidase on the same aggregates suggest the presence of both extracellular {beta}-glucosidase functioning in aggregates with no detectable ATP and also of relatively active microbial communities (high ATP) that have low {beta}-glucosidase potentials. Studying function at a scale more consistent with microbial habitat presents greater opportunity to link microbial community structure to microbial community function.

  14. Influence of packaging conditions on natural microbial population growth of endive.

    PubMed

    Charles, Florence; Rugani, Nathalie; Gontard, Nathalie

    2005-05-01

    The influence of three packaging conditions, i.e., unmodified atmosphere packaging (UAP), passive modified atmosphere packaging (MAP), and active MAP, on the natural microbial population growth of endive was investigated at 20 degrees C. For UAP, endive was placed in macroperforated oriented polypropylene pouches that maintained gas composition close to that of air (21 kPa O2 and 0 kPa CO2) but also limited superficial product dehydration. For MAP, endive was placed in low-density polyethylene pouches that induced a 3 kPa O2 and 5 kPa CO2 equilibrium atmosphere composition. Steady state was reached after 25 h of storage with an oxygen absorbing packet (active MAP) compared with 100 h without the packet (passive MAP) and was maintained for 200 h. After 312 h of storage, both active and passive MAP reduced total aerobic mesophile, yeast, and mold population growth compared with endive in UAP. Active MAP accelerated and improved the inhibition of Pseudomonas spp. and Enterobacteriaceae, respectively, probably because of the rapid O2 depletion during the transition period. A shift in the Enterobacteriaceae subpopulation from Rhanella aquatilis to Enterobacter agglomerans was observed for both passive and active MAP. PMID:15895736

  15. Ecological perspectives on synthetic biology: insights from microbial population biology

    PubMed Central

    Escalante, Ana E.; Rebolleda-Gómez, María; Benítez, Mariana; Travisano, Michael

    2015-01-01

    The metabolic capabilities of microbes are the basis for many major biotechnological advances, exploiting microbial diversity by selection or engineering of single strains. However, there are limits to the advances that can be achieved with single strains, and attention has turned toward the metabolic potential of consortia and the field of synthetic ecology. The main challenge for the synthetic ecology is that consortia are frequently unstable, largely because evolution by constituent members affects their interactions, which are the basis of collective metabolic functionality. Current practices in modeling consortia largely consider interactions as fixed circuits of chemical reactions, which greatly increases their tractability. This simplification comes at the cost of essential biological realism, stripping out the ecological context in which the metabolic actions occur and the potential for evolutionary change. In other words, evolutionary stability is not engineered into the system. This realization highlights the necessity to better identify the key components that influence the stable coexistence of microorganisms. Inclusion of ecological and evolutionary principles, in addition to biophysical variables and stoichiometric modeling of metabolism, is critical for microbial consortia design. This review aims to bring ecological and evolutionary concepts to the discussion on the stability of microbial consortia. In particular, we focus on the combined effect of spatial structure (connectivity of molecules and cells within the system) and ecological interactions (reciprocal and non-reciprocal) on the persistence of microbial consortia. We discuss exemplary cases to illustrate these ideas from published studies in evolutionary biology and biotechnology. We conclude by making clear the relevance of incorporating evolutionary and ecological principles to the design of microbial consortia, as a way of achieving evolutionarily stable and sustainable systems. PMID

  16. Ecological perspectives on synthetic biology: insights from microbial population biology.

    PubMed

    Escalante, Ana E; Rebolleda-Gómez, María; Benítez, Mariana; Travisano, Michael

    2015-01-01

    The metabolic capabilities of microbes are the basis for many major biotechnological advances, exploiting microbial diversity by selection or engineering of single strains. However, there are limits to the advances that can be achieved with single strains, and attention has turned toward the metabolic potential of consortia and the field of synthetic ecology. The main challenge for the synthetic ecology is that consortia are frequently unstable, largely because evolution by constituent members affects their interactions, which are the basis of collective metabolic functionality. Current practices in modeling consortia largely consider interactions as fixed circuits of chemical reactions, which greatly increases their tractability. This simplification comes at the cost of essential biological realism, stripping out the ecological context in which the metabolic actions occur and the potential for evolutionary change. In other words, evolutionary stability is not engineered into the system. This realization highlights the necessity to better identify the key components that influence the stable coexistence of microorganisms. Inclusion of ecological and evolutionary principles, in addition to biophysical variables and stoichiometric modeling of metabolism, is critical for microbial consortia design. This review aims to bring ecological and evolutionary concepts to the discussion on the stability of microbial consortia. In particular, we focus on the combined effect of spatial structure (connectivity of molecules and cells within the system) and ecological interactions (reciprocal and non-reciprocal) on the persistence of microbial consortia. We discuss exemplary cases to illustrate these ideas from published studies in evolutionary biology and biotechnology. We conclude by making clear the relevance of incorporating evolutionary and ecological principles to the design of microbial consortia, as a way of achieving evolutionarily stable and sustainable systems. PMID

  17. Oxygen Effects on Thermophilic Microbial Populations in Biofilters Treating Nitric Oxide Containing Off-Gas Streams

    SciTech Connect

    Lee, Brady Douglas; Apel, William Arnold; Smith, William Aaron

    2004-04-01

    Electricity generation from coal has increased by an average of 51 billion kWh per year over the past 3 years. For this reason cost-effective strategies to control nitrogen oxides (NOx) from coal-fired power plant combustion gases must be developed. Compost biofilters operated at 55°C at an empty bed contact time (EBCT) of 13 seconds were shown to be feasible for removal of nitric oxide (NO) from synthetic flue gas. Denitrifying microbial populations in these biofilters were shown to reduce influent NO feeds by 90 to 95% at inlet NO concentrations of 500 ppmv. Oxygen was shown to have a significant effect on the NO removal efficiency demonstrated by these biofilters. Two biofilters were set up under identical conditions for the purpose of monitoring NO removal as well as changes in the microbial population in the bed medium under anaerobic and aerobic conditions. Changes in the microbial population were monitored to determine the maximum oxygen tolerance of a denitrifying biofilter as well as methods of optimizing microbial populations capable of denitrification in the presence of low oxygen concentrations. Nitric oxide removal dropped to between 10 and 20% when oxygen was present in the influent stream. The inactive compost used to pack the biofilters may have also caused the decreased NO removal efficiency compared to previous biofiltration experiments. Analysis of the bed medium microbial population using environmental scanning electron microscopy indicated significant increases in biomass populating the surface of the compost when compared to unacclimated compost.

  18. Which Members of the Microbial Communities Are Active? Microarrays

    NASA Astrophysics Data System (ADS)

    Morris, Brandon E. L.

    only at the early stages of understanding the microbial processes that occur in petroliferous formations and the surrounding subterranean environment. Important first steps in characterising the microbiology of oilfield systems involve identifying the microbial community structure and determining how population diversity changes are affected by the overall geochemical and biological parameters of the system. This is relatively easy to do today by using general 16S rRNA primers for PCR and building clone libraries. For example, previous studies using molecular methods characterised many dominant prokaryotes in petroleum reservoirs (Orphan et al., 2000) and in two Alaskan North Slope oil facilities (Duncan et al., 2009; Pham et al., 2009). However, the problem is that more traditional molecular biology approaches, such as 16S clone libraries, fail to detect large portions of the community perhaps missing up to half of the biodiversity (see Hong et al., 2009) and require significant laboratory time to construct large libraries necessary to increase the probability of detecting the majority of even bacterial biodiversity. In the energy sector, the overarching desire would be to quickly assess the extent of in situ hydrocarbon biodegradation or to disrupt detrimental processes such as biofouling, and in these cases it may not be necessary to identify specific microbial species. Rather, it would be more critical to evaluate metabolic processes or monitor gene products that are implicated in the specific activity of interest. Research goals such as these are well suited for a tailored application of microarray technology.

  19. Soil Bacteria Population Dynamics Following Stimulation for Ureolytic Microbial-Induced CaCO3 Precipitation.

    PubMed

    Gat, Daniella; Ronen, Zeev; Tsesarsky, Michael

    2016-01-19

    Microbial-induced CaCO3 precipitation (MICP) via urea-hydrolysis (ureolysis) is an emerging soil improvement technique for various civil engineering and environmental applications. In-situ application of MICP in soils is performed either by augmenting the site with ureolytic bacteria or by stimulating indigenous ureolytic bacteria. Both of these approaches may lead to changes in the indigenous bacterial population composition and to the accumulation of large quantities of ammonium. In this batch study, effective ureolysis was stimulated in coastal sand from a semiarid environment, with low initial ureolytic bacteria abundance. Two different carbon sources were used: yeast-extract and molasses. No ureolysis was observed in their absence. Ureolysis was achieved using both carbon sources, with a higher rate in the yeast-extract enrichment resulting from increased bacterial growth. The changes to the indigenous bacterial population following biostimulation of ureolysis were significant: Bacilli class abundancy increased from 5% in the native sand up to 99% in the yeast-extract treatment. The sand was also enriched with ammonium-chloride, where ammonia-oxidation was observed after 27 days, but was not reflected in the bacterial population composition. These results suggest that biostimulation of ureolytic bacteria can be applied even in a semiarid and nutrient-poor environment using a simple carbon source, that is, molasses. The significant changes to bacterial population composition following ureolysis stimulation could result in a decrease in trophic activity and diversity in the treated site, thus they require further attention. PMID:26689904

  20. Integral structural-functional method for characterizing microbial populations

    NASA Astrophysics Data System (ADS)

    Yakushev, A. V.

    2015-04-01

    An original integral structural-functional method has been proposed for characterizing microbial communities. The novelty of the approach is the in situ study of microorganisms based on the growth kinetics of microbial associations in liquid nutrient broth media under selective conditions rather than on the level of taxa or large functional groups. The method involves the analysis of the integral growth model of a periodic culture. The kinetic parameters of such associations reflect their capacity of growing on different media, i.e., their physiological diversity, and the metabolic capacity of the microorganisms for growth on a nutrient medium. Therefore, the obtained parameters are determined by the features of the microbial ecological strategies. The inoculation of a dense medium from the original inoculate allows characterizing the taxonomic composition of the dominants in the soil community. The inoculation from the associations developed on selective media characterizes the composition of syntrophic groups, which fulfill a specific function in nature. This method is of greater information value than the classical methods of inoculation on selective media.

  1. Microbial population dynamics during fed-batch operation of commercially available garbage composters.

    PubMed

    Narihiro, T; Abe, T; Yamanaka, Y; Hiraishi, A

    2004-09-01

    Microbial populations in terms of quantity, quality, and activity were monitored during 2 months of start-up operation of commercially available composters for fed-batch treatment of household biowaste. All the reactors, operated at a waste-loading rate of 0.7 kg day(-1) (wet wt), showed a mass reduction efficiency of 88-93%. The core temperature in the reactors fluctuated between 31 degrees C and 58 degrees C due to self-heating. The pH declined during the early stage of operation and steadied at pH 7.4-9.3 during the fully acclimated stage. The moisture content was 48-63% early in the process and 30-40% at the steady state. Both direct total counts and plate counts of bacteria increased via two phases (designated phases I, II) and reached an order of magnitude of 10(11) cells g(-1) (dry wt) at the steady state. Microbial community changes during the start-up period were studied by culture-independent quinone profiling and denatured gradient gel electrophoresis (DGGE) of PCR-amplified 16S rDNA. In all the reactors, ubiquinones predominated during phase I, whereas partially saturated menaquinones became predominant during phase II. This suggested that there was a drastic population shift from ubiquinone-containing Proteobacteria to Actinobacteria during the start-up period. The DGGE analysis of the bacterial community in one of the reactors also demonstrated a drastic population shift during phase I and the predominance of members of the phyla Proteobacteria and Bacteroidetes during the overall period. But this molecular analysis failed to detect actinobacterial clones from the reactor at any stage. PMID:15480624

  2. The effect of D123 wheat as a companion crop on soil enzyme activities, microbial biomass and microbial communities in the rhizosphere of watermelon

    PubMed Central

    Xu, Weihui; Wang, Zhigang; Wu, Fengzhi

    2015-01-01

    The growth of watermelon is often threatened by Fusarium oxysporum f. sp. niveum (Fon) in successively monocultured soil, which results in economic loss. The objective of this study was to investigate the effect of D123 wheat as a companion crop on soil enzyme activities, microbial biomass and microbial communities in the rhizosphere of watermelon and to explore the relationship between the effect and the incidence of wilt caused by Fon. The results showed that the activities of soil polyphenol oxidase, urease and invertase were increased, the microbial biomass nitrogen (MBN) and microbial biomass phosphorus (MBP) were significantly increased, and the ratio of MBC/MBN was decreased (P < 0.05). Real-time PCR analysis showed that the Fon population declined significantly in the watermelon/wheat companion system compared with the monoculture system (P < 0.05). The analysis of microbial communities showed that the relative abundance of microbial communities was changed in the rhizosphere of watermelon. Compared with the monoculture system, the relative abundances of Alphaproteobacteria, Actinobacteria, Gemmatimonadetes and Sordariomycetes were increased, and the relative abundances of Gammaproteobacteria, Sphingobacteria, Cytophagia, Pezizomycetes, and Eurotiomycetes were decreased in the rhizosphere of watermelon in the watermelon/wheat companion system; importantly, the incidence of Fusarium wilt was also decreased in the watermelon/wheat companion system. In conclusion, this study indicated that D123 wheat as a companion crop increased soil enzyme activities and microbial biomass, decreased the Fon population, and changed the relative abundance of microbial communities in the rhizosphere of watermelon, which may be related to the reduction of Fusarium wilt in the watermelon/wheat companion system. PMID:26388851

  3. Visualizing the population dynamics of microbial communities in the larval zebrafish gut

    NASA Astrophysics Data System (ADS)

    Parthasarathy, Raghuveer

    In each of our digestive tracts, trillions of microbes representing hundreds of different species colonize local environments, reproduce, and compete with one another. The resulting ecosystems influence many aspects their host's development and health. Little is known about how gut microbial communities vary in space and time: how they grow, fluctuate, and respond to various perturbations. To address this and investigate microbial colonization of the vertebrate gut, we apply light sheet fluorescence microscopy to a model system that combines a realistic in vivo environment with a high degree of experimental control: larval zebrafish with defined subsets of commensal bacterial species. Light sheet microscopy enables three-dimensional imaging with high resolution over the entire intestine, providing visualizations that would be difficult or impossible to achieve with other techniques. Quantitative analysis of image data enables measurement of bacterial abundances and distributions. I will describe this approach and focus especially on recent experiments in which a colonizing bacterial species is challenged by the invasion of a second species, which leads to the decline of the first group. Imaging reveals dramatic population collapses that differentially affect the two species due to their different biogeographies and morphologies. The collapses are driven by the peristaltic motion of the zebrafish intestine, indicating that the physical activity of the host environment can play a major role in mediating inter-species competition. role in mediating inter-species competition. Supported by the National Science Foundation under Grant No. 0922951 and the National Institutes of Health under Award Number 1P50GM098911.

  4. Hydrazine degradation and its effect on microbial activity in soil

    SciTech Connect

    Ou, L.T.; Street, J.J.

    1987-01-01

    Considerable information has been accumulated on the toxicity of hydrazine to soil bacterial cultures and on the degradation of hydrazne by soil bacterial cultures. The activities of the autotrophic nitrifiers Nitrosomonas and Nitrobacter and of denitrifying bacteria, and the growth of Enterobacter cloacae, were all inhibited by hydrazine. An enzyme system has been found in heterotrophic N/sub 2/-fixing bacteria capable of degrading hydrazine. Information concerning the effect of hydrazine on microbial activity in soils is not available, however. Accidental spills to soil can occur during transportation and storage. Therefore, this study was initiated to determine degradation rates of hydrazine in soils and its effect on soil microbial activity.

  5. The Biodiversity Changes in the Microbial Population of Soils Contaminated with Crude Oil.

    PubMed

    Abbasian, Firouz; Lockington, Robin; Megharaj, Mallavarapu; Naidu, Ravi

    2016-06-01

    Crude oil spills resulting from excavation, transportation and downstream processes can cause intensive damage to living organisms and result in changes in the microbial population of that environment. In this study, we used a pyrosequencing analysis to investigate changes in the microbial population of soils contaminated with crude oil. Crude oil contamination in soil resulted in the creation of a more homogenous population of microorganisms dominated by members of the Actinomycetales, Clostridiales and Bacillales (all belonging to Gram-positive bacteria) as well as Flavobacteriales, Pseudomonadales, Burkholderiales, Rhizobiales and Sphingomonadales (all belonging to Gram-negative bacteria). These changes in the biodiversity decreased the ratios of chemoheterotrophic bacteria at higher concentrations of crude oil contamination, with these being replaced by photoheterotrophic bacteria, mainly Rhodospirillales. Several of the dominant microbial orders in the crude oil contaminated soils are able to degrade crude oil hydrocarbons and therefore are potentially useful for remediation of crude oil in contaminated sites. PMID:26858133

  6. Large-scale distribution of microbial and viral populations in the South Atlantic Ocean.

    PubMed

    De Corte, Daniele; Sintes, Eva; Yokokawa, Taichi; Lekunberri, Itziar; Herndl, Gerhard J

    2016-04-01

    Viruses are abundant, diverse and dynamic components of the marine environments and play a significant role in the ocean biogeochemical cycles. To assess potential variations in the relation between viruses and microbes in different geographic regions and depths, viral and microbial abundance and production were determined throughout the water column along a latitudinal transect in the South Atlantic Ocean. Path analysis was used to examine the relationships between several abiotic and biotic parameters and the different microbial and viral populations distinguished by flow cytometry. The depth-integrated contribution of microbial and viral abundance to the total microbial and viral biomass differed significantly among the different provinces. Additionally, the virus-to-microbe ratio increased with depth and decreased laterally towards the more productive regions. Our data revealed that the abundance of phytoplankton and microbes is the main controlling factor of the viral populations in the euphotic and mesopelagic layers, whereas in the bathypelagic realm, viral abundance was only weakly related to the biotic and abiotic variables. The relative contribution of the three viral populations distinguished by flow cytometry showed a clear geographical pattern throughout the water column, suggesting that these populations are composed of distinct taxa able to infect specific hosts. Overall, our data indicate the presence of distinct microbial patterns along the latitudinal transect. This variability is not limited to the euphotic layer but also detectable in the meso- and bathypelagic layers. PMID:26765966

  7. Large‐scale distribution of microbial and viral populations in the South Atlantic Ocean

    PubMed Central

    Sintes, Eva; Yokokawa, Taichi; Lekunberri, Itziar; Herndl, Gerhard J.

    2016-01-01

    Summary Viruses are abundant, diverse and dynamic components of the marine environments and play a significant role in the ocean biogeochemical cycles. To assess potential variations in the relation between viruses and microbes in different geographic regions and depths, viral and microbial abundance and production were determined throughout the water column along a latitudinal transect in the South Atlantic Ocean. Path analysis was used to examine the relationships between several abiotic and biotic parameters and the different microbial and viral populations distinguished by flow cytometry. The depth‐integrated contribution of microbial and viral abundance to the total microbial and viral biomass differed significantly among the different provinces. Additionally, the virus‐to‐microbe ratio increased with depth and decreased laterally towards the more productive regions. Our data revealed that the abundance of phytoplankton and microbes is the main controlling factor of the viral populations in the euphotic and mesopelagic layers, whereas in the bathypelagic realm, viral abundance was only weakly related to the biotic and abiotic variables. The relative contribution of the three viral populations distinguished by flow cytometry showed a clear geographical pattern throughout the water column, suggesting that these populations are composed of distinct taxa able to infect specific hosts. Overall, our data indicate the presence of distinct microbial patterns along the latitudinal transect. This variability is not limited to the euphotic layer but also detectable in the meso‐ and bathypelagic layers. PMID:26765966

  8. Microbial Species Richness and Metabolic Activities in Hypersaline Microbial Mats: Insight into Biosignature Formation Through Lithification

    NASA Astrophysics Data System (ADS)

    Baumgartner, Laura K.; Dupraz, Christophe; Buckley, Daniel H.; Spear, John R.; Pace, Norman R.; Visscher, Pieter T.

    2009-11-01

    Microbial mats in the hypersaline lake of Salt Pan, Eleuthera, Bahamas, display a gradient of lithification along a transect from the center to the shore of the lake. These mats exist under similar geochemical conditions, with light quantity and quality as the sole major environmental difference. Therefore, we hypothesized that the microbial community may be driving the differences in lithification and, by extension, mineral biosignature formation. The lithifying and non-lithifying mat communities were compared (via 16S rRNA gene sequencing, 485 and 464 sequences, respectively) over both temporal and spatial scales. Seven bacterial groups dominated in all the microbial mat libraries: bacteriodetes, alphaproteobacteria, deltaproetobacteria, chloroflexi, spirochaetes, cyanobacteria, and planctomycetes. The mat communities were all significantly different over space, time, and lithification state. Species richness is significantly higher in the non-lithifying mats, potentially due to differences in mat structure and activity. This increased richness may impact lithification and, hence, biosignature production.

  9. Range expansions transition from pulled to pushed waves with increasing cooperativity in an experimental microbial population

    NASA Astrophysics Data System (ADS)

    Gandhi, Saurabh; Yurtsev, Eugene; Korolev, Kirill; Gore, Jeff

    Range expansions are becoming more frequent due to environmental changes and rare long distance dispersal, often facilitated by anthropogenic activities. Simple models in theoretical ecology explain many emergent properties of range expansions, such as a constant expansion velocity, in terms of organism-level properties such as growth and dispersal rates. Testing these quantitative predictions in natural populations is difficult because of large environmental variability. Here, we used a controlled microbial model system to study range expansions of populations with and without intra-specific cooperativity. For non-cooperative growth, the expansion dynamics were dominated by population growth at the low-density front, which pulled the expansion forward. We found these expansions to be in close quantitative agreement with the classical theory of pulled waves by Fisher and Skellam, suitably adapted to our experimental system. However, as cooperativity increased, the expansions transitioned to being pushed, i.e. controlled by growth in the bulk as well as in the front. Although both pulled and pushed waves expand at a constant velocity and appear otherwise similar, their distinct dynamics leads to very different evolutionary consequences. Given the prevalence of cooperative growth in nature, understanding the effects of cooperativity is essential to managing invading species and understanding their evolution.

  10. Response of microbial activities and diversity to PAHs contamination at coal tar contaminated land

    NASA Astrophysics Data System (ADS)

    Zhao, Xiaohui; Sun, Yujiao; Ding, Aizhong; Zhang, Dan; Zhang, Dayi

    2015-04-01

    Coal tar is one of the most hazardous and concerned organic pollutants and the main hazards are polycyclic aromatic hydrocarbons (PAHs). The indigenous microorganisms in soils are capable to degrade PAHs, with essential roles in biochemical process for PAHs natural attenuation. This study investigated 48 soil samples (from 8 depths of 6 boreholes) in Beijing coking and chemistry plant (China) and revealed the correlation between PAHs contamination, soil enzyme activities and microbial community structure, by 16S rRNA denaturing gradient gel electrophoresis (DGGE). At the site, the key contaminants were identified as naphthalene, acenaphthylene, acenaphthene, fluorene, phenanthrene and anthracene, and the total PAHs concentration ranged from 0.1 to 923.9 mg/kg dry soil. The total PAHs contamination level was positively correlated (p<0.05) with the bacteria count (0.9×107-14.2×107 CFU/mL), catalase activities (0.554-6.230 mL 0.02 M KMnO4/g•h) and dehydrogenase activities (1.9-30.4 TF μg/g•h soil), showing the significant response of microbial population and degrading functions to the organic contamination in soils. The PAHs contamination stimulated the PAHs degrading microbes and promoted their biochemical roles in situ. The positive relationship between bacteria count and dehydrogenase activities (p<0.05) suggested the dominancy of PAHs degrading bacteria in the microbial community. More interestingly, the microbial community deterioration was uncovered via the decline of microbial biodiversity (richness from 16S rRNA DGGE) against total PAHs concentration (p<0.05). Our research described the spatial profiles of PAHs contamination and soil microbial functions at the PAHs heavily contaminated sites, offering deeper understanding on the roles of indigenous microbial community in natural attenuation process.

  11. Deep-Subterranean Microbial Habitats in the Hishikari Epithermal Gold Mine: Active Thermophilic Microbial Communities and Endolithic Ancient Microbial Relicts.

    NASA Astrophysics Data System (ADS)

    Hirayama, H.; Takai, K.; Inagaki, F.; Horikoshi, K.

    2001-12-01

    Deep subterranean microbial community structures in an epithermal gold-silver deposit, Hishikari gold mine, southern part of Kyusyu Japan, were evaluated through the combined use of enrichment culture methods and culture-independent molecular surveys. The geologic setting of the Hishikari deposit is composed of three lithologies; basement oceanic sediments of the Cretaceous Shimanto Supergroup, Quaternary andesites, and auriferous quartz vein. We studied the drilled core rock of these, and the geothermal hot waters from the basement aquifers collected by means of the dewatering system located at the deepest level in the mining sites. Culture-independent molecular phylogenetic analyses of PCR-amplified ribosomal DNA (rDNA) recovered from drilled cores suggested that the deep-sea oceanic microbial communities were present as ancient indigenous relicts confined in the Shimanto basement. On the other hand, genetic signals of active thermophilic microbial communities, mainly consisting of thermophilic hydrogen-oxidizer within Aquificales, thermophilic methanotroph within g-Proteobacteria and yet-uncultivated bacterium OPB37 within b-Proteobacteria, were detected with these of oceanic relicts from the subterranean geothermal hot aquifers (temp. 70-100ºC). Successful cultivation and FISH analyses strongly supported that these thermophilic lithotrophic microorganisms could be exactly active and they grew using geochemically produced hydrogen and methane gasses as nutrients. Based on these results, the deep-subsurface biosphere occurring in the Hishikari epithermal gold mine was delineated as endolithic ancient microbial relicts and modern habitats raising active lithotrophic thermophiles associated with the geological and geochemical features of the epithermal gold deposit.

  12. Genetic Diversity Affects the Daily Transcriptional Oscillations of Marine Microbial Populations

    PubMed Central

    Shilova, Irina N.; Robidart, Julie C.; DeLong, Edward F.; Zehr, Jonathan P.

    2016-01-01

    Marine microbial communities are genetically diverse but have robust synchronized daily transcriptional patterns at the genus level that are similar across a wide variety of oceanic regions. We developed a microarray-inspired gene-centric approach to resolve transcription of closely-related but distinct strains/ecotypes in high-throughput sequence data. Applying this approach to the existing metatranscriptomics datasets collected from two different oceanic regions, we found unique and variable patterns of transcription by individual taxa within the abundant picocyanobacteria Prochlorococcus and Synechococcus, the alpha Proteobacterium Pelagibacter and the eukaryotic picophytoplankton Ostreococcus. The results demonstrate that marine microbial taxa respond differentially to variability in space and time in the ocean. These intra-genus individual transcriptional patterns underlie whole microbial community responses, and the approach developed here facilitates deeper insights into microbial population dynamics. PMID:26751368

  13. Radiation resistance of the natural microbial population in buffer materials

    SciTech Connect

    Stroes-Gascoyne, S.; Lucht, L.M.; Borsa, J.; Delaney, T.L.; Haveman, S.A.; Hamon, C.J.

    1995-12-31

    The radiation sensitivity of naturally occurring microorganisms in buffer materials was investigated as well as the sensitivity of Bacillus subtillis spores and Acinetobacter radioresistens in a buffer matrix. The D{sub 10} values obtained in these radiation experiments varied from 0.34 to 1.68 kGy and it was calculated that the surface of a nuclear fuel waste container would be sterilized in 9 to 33 d after emplacement, depending on the type of container, and the initial bioburden. This suggests that formation of biofilms and microbially influenced corrosion would not be of concern of some time after emplacement. The results also indicated that sterilization throughout a 25 cm thick buffer layer is unlikely and that repopulation of the container surface after some time is a possibility, depending on the mobility of microbes in compacted buffer material.

  14. Controlling Salmonella infection in weanling pigs through water delivery of direct-fed microbials or organic acids; Part I. Effects on growth performance, microbial populations and immune status

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Pigs (n=88) weaned at 19 ± 2 d of age were used in a 14 d study to evaluate the effects of water-delivered direct-fed microbials (DFM) or organic acids on immune status, Salmonella infection and shedding, and intestinal microbial populations following a Salmonella Typhimurium challenge. Pigs were ch...

  15. Organic matter mineralization in frozen boreal soils-environmental constraints on catabolic and anabolic microbial activity

    NASA Astrophysics Data System (ADS)

    Oquist, Mats G.; Sparrman, Tobias; Schleucher, Jürgen; Nilsson, Mats B.

    2014-05-01

    Heterotrophic microbial mineralization of soil organic matter (SOM) and associated production and emission of atmospheric trace gases proceed during the winter months in the frozen soils of high latitude ecosystems. However, in what ways this microbial activity is constrained by the environmental conditions prevailing in a frozen soil matrix is uncertain. This presentation will address how temperature, water availability and substrate availability combine to regulate rates of microbial activity at below freezing temperatures and the implications of this activity for SOM mineralization in the surface layers of boreal forest soils experiencing seasonal freezing. We show that the amount and availability of liquid water is an integral factor regulating rates of microbial activity in the frozen soil matrix and can also explain frequently observed deviations in the temperature responses of biogenic CO2 production in frozen soils, as compared to unfrozen soils. Using stable isotope labeling (13C) we also show that the partitioning of substrate carbon, in the form of monomeric sugar (glucose), for catabolic and anabolic metabolism remain constant in the temperature range of -4C to 9C. This confirms that microbial growth may proceed even when soils are frozen. In addition we present corresponding data for organisms metabolizing polymeric substrates (cellulose) requiring exoenzymatic activity prior to substrate uptake. We conclude that the metabolic response of soil microorganism to controlling factors may change substantially across the freezing point of soil water, and also the patterns of interaction among controlling factors are affected. Thus, it is evident that metabolic response functions derived from investigations of unfrozen soils cannot be superimposed on frozen soils. Nonetheless, the soil microbial population appear very adapted to seasonal freezing with respect to their metabolic performance.

  16. USE OF ARISA TO MONITOR SHIFTS IN RUMEN MICROBIAL POPULATIONS CAUSED BY CHANGES IN DIET

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective was to determine whether automated ribosomal intergenic spacer analysis (ARISA) is sensitive enough to detect shifts in rumen microbial populations caused by dietary changes. Six ruminally cannulated, non-lactating, non-pregnant Holstein cows were sampled for rumen contents in a random...

  17. Profiling the Change in Fecal Microbial Populations of Mares and Foals Over Time

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The gastrointestinal tract of the mature horse contains a complex community of microorganisms, many of which aid in digestion. Little information is available concerning the establishment of these microbial populations in young horses. The limited research that has been conducted has utilized cultur...

  18. IN SITU APPARENT CONDUCTIVITY MEASUREMENTS AND MICROBIAL POPULATION DISTRIBUTION AT A HYDROCARBON CONTAMINATED SITE

    EPA Science Inventory

    We investigated the bulk electrical conductivity and microbial population distribution in sediments at a site contaminated with light non-aqueous phase liquid (LNAPL). The bulk conductivity was measured using in situ vertical resistivity probes, while the most probable number met...

  19. Aerobic Microbial Community of Insectary Population of Phlebotomus papatasi

    PubMed Central

    Maleki-Ravasan, Naseh; Oshaghi, Mohammad Ali; Hajikhani, Sara; Saeidi, Zahra; Akhavan, Amir Ahmad; Gerami-Shoar, Mohsen; Shirazi, Mohammad Hasan; Yakhchali, Bagher; Rassi, Yavar; Afshar, Davoud

    2014-01-01

    Background: Microbes particularly bacteria presenting in the gut of haematophagous insects may have an important role in the epidemiology of human infectious disease. Methods: The microbial flora of gut and surrounding environmental of a laboratory strain of Phlebotomus papatasi, the main vector of Zoonotic Cutaneous Leishmaniasis (ZCL) in the old world, was investigated. Biochemical reactions and 16s rDNA sequencing of the isolated bacteria against 24 sugars and amino acids were used for bacteria species identification. Common mycological media used for fungi identification as well. Results: Most isolates belonged to the Enterobacteriaceae, a large, heterogeneous group of gram-negative rods whose natural habitat is the intestinal tract of humans and animals. Enterobacteriaceae groups included Edwardsiella, Enterobacter, Escherichia, Klebsiella, Kluyvera, Leminorella, Pantoea, Proteus, Providencia, Rahnella, Serratia, Shigella, Tatumella, and Yersinia and non Enterobacteriaceae groups included Bacillus, Staphylococcus and Pseudomonas. The most prevalent isolates were Proteus mirabilis and P. vulgaris. These saprophytic and swarming motile bacteria were isolated from all immature, pupae, and mature fed or unfed male or female sand flies as well as from larval and adult food sources. Five fungi species were also isolated from sand flies, their food sources and colonization materials where Candida sp. was common in all mentioned sources. Conclusion: Midgut microbiota are increasingly seen as an important factor for modulating vector competence in insect vectors so their possible effects of the mirobiota on the biology of P. papatasi and their roles in the sandfly-Leishmania interaction are discussed. PMID:25629067

  20. Tracking dynamics of plant biomass composting by changes in substrate structure, microbial community, and enzyme activity

    PubMed Central

    2012-01-01

    Background Understanding the dynamics of the microbial communities that, along with their secreted enzymes, are involved in the natural process of biomass composting may hold the key to breaking the major bottleneck in biomass-to-biofuels conversion technology, which is the still-costly deconstruction of polymeric biomass carbohydrates to fermentable sugars. However, the complexity of both the structure of plant biomass and its counterpart microbial degradation communities makes it difficult to investigate the composting process. Results In this study, a composter was set up with a mix of yellow poplar (Liriodendron tulipifera) wood-chips and mown lawn grass clippings (85:15 in dry-weight) and used as a model system. The microbial rDNA abundance data obtained from analyzing weekly-withdrawn composted samples suggested population-shifts from bacteria-dominated to fungus-dominated communities. Further analyses by an array of optical microscopic, transcriptional and enzyme-activity techniques yielded correlated results, suggesting that such population shifts occurred along with early removal of hemicellulose followed by attack on the consequently uncovered cellulose as the composting progressed. Conclusion The observed shifts in dominance by representative microbial groups, along with the observed different patterns in the gene expression and enzymatic activities between cellulases, hemicellulases, and ligninases during the composting process, provide new perspectives for biomass-derived biotechnology such as consolidated bioprocessing (CBP) and solid-state fermentation for the production of cellulolytic enzymes and biofuels. PMID:22490508

  1. Tracking Dynamics of Plant Biomass Composting by Changes in Substrate Structure, Microbial Community, and Enzyme Activity

    SciTech Connect

    Wei, H.; Tucker, M. P.; Baker, J. O.; Harris, M.; Luo, Y. H.; Xu, Q.; Himmel, M. E.; Ding, S. Y.

    2012-04-01

    Understanding the dynamics of the microbial communities that, along with their secreted enzymes, are involved in the natural process of biomass composting may hold the key to breaking the major bottleneck in biomass-to-biofuels conversion technology, which is the still-costly deconstruction of polymeric biomass carbohydrates to fermentable sugars. However, the complexity of both the structure of plant biomass and its counterpart microbial degradation communities makes it difficult to investigate the composting process. In this study, a composter was set up with a mix of yellow poplar (Liriodendron tulipifera) wood-chips and mown lawn grass clippings (85:15 in dry-weight) and used as a model system. The microbial rDNA abundance data obtained from analyzing weekly-withdrawn composted samples suggested population-shifts from bacteria-dominated to fungus-dominated communities. Further analyses by an array of optical microscopic, transcriptional and enzyme-activity techniques yielded correlated results, suggesting that such population shifts occurred along with early removal of hemicellulose followed by attack on the consequently uncovered cellulose as the composting progressed. The observed shifts in dominance by representative microbial groups, along with the observed different patterns in the gene expression and enzymatic activities between cellulases, hemicellulases, and ligninases during the composting process, provide new perspectives for biomass-derived biotechnology such as consolidated bioprocessing (CBP) and solid-state fermentation for the production of cellulolytic enzymes and biofuels.

  2. Physical Properties and Microbial Activity in Forest Residual Substrate

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Many growers in the horticulture industry have expressed concern that switching from a pine bark-based substrate to one with a significant wood content will increase microbial activity, resulting in nitrogen (N) immobilization. This study evaluated four growth substrates (pine bark, peat moss and tw...

  3. MICROBIAL COMMUNITY STRUCTURE AND ENZYME ACTIVITIES IN SEMIARID AGRICULTURAL SOILS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The effect of management on the microbial community structure and enzyme activities of three semiarid soils from Southern High Plains of Texas were investigated. The soils (sandy clay loam, fine sandy loam and loam) were under continuous cotton (Gossypium hirsutum L.) or in cotton -peanut (Arachis h...

  4. Measurements of microbial community activities in individual soil macroaggregates

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The functional potential of single soil aggregates may provide insights into the localized distribution of microbial activities better than traditional assays conducted on bulk quantities of soil. Thus, we scaled down enzyme assays for ß-glucosidase, N-acetyl-ß-D-glucosaminidase, lipase, and leucine...

  5. ACID RAIN AND SOIL MICROBIAL ACTIVITY: EFFECTS AND THEIR MECHANISMS

    EPA Science Inventory

    In the investigation, our aim was to determine if acid rain affects soil microbial activity and to identify possible mechanisms of observed effects. A Sierran forest soil (pH 6.4) planted with Ponderosa pine seedlings was exposed to simulated rain (pH 2.0, 3.0, 4.0 and 5.6) with ...

  6. Soil disturbance increases soil microbial enzymatic activity in arid ecoregion

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Functional diversity of the soil microbial community is commonly used in the assessment of soil health as it relates to the activity of soil microflora involved in carbon cycling. Soil microbes in different microenvironments will have varying responses to different substrates, thus catabolic fingerp...

  7. Plant diversity increases soil microbial activity and soil carbon storage.

    PubMed

    Lange, Markus; Eisenhauer, Nico; Sierra, Carlos A; Bessler, Holger; Engels, Christoph; Griffiths, Robert I; Mellado-Vázquez, Perla G; Malik, Ashish A; Roy, Jacques; Scheu, Stefan; Steinbeiss, Sibylle; Thomson, Bruce C; Trumbore, Susan E; Gleixner, Gerd

    2015-01-01

    Plant diversity strongly influences ecosystem functions and services, such as soil carbon storage. However, the mechanisms underlying the positive plant diversity effects on soil carbon storage are poorly understood. We explored this relationship using long-term data from a grassland biodiversity experiment (The Jena Experiment) and radiocarbon ((14)C) modelling. Here we show that higher plant diversity increases rhizosphere carbon inputs into the microbial community resulting in both increased microbial activity and carbon storage. Increases in soil carbon were related to the enhanced accumulation of recently fixed carbon in high-diversity plots, while plant diversity had less pronounced effects on the decomposition rate of existing carbon. The present study shows that elevated carbon storage at high plant diversity is a direct function of the soil microbial community, indicating that the increase in carbon storage is mainly limited by the integration of new carbon into soil and less by the decomposition of existing soil carbon. PMID:25848862

  8. Microbial activity in the marine deep biosphere: progress and prospects

    PubMed Central

    Orcutt, Beth N.; LaRowe, Douglas E.; Biddle, Jennifer F.; Colwell, Frederick S.; Glazer, Brian T.; Reese, Brandi Kiel; Kirkpatrick, John B.; Lapham, Laura L.; Mills, Heath J.; Sylvan, Jason B.; Wankel, Scott D.; Wheat, C. Geoff

    2013-01-01

    The vast marine deep biosphere consists of microbial habitats within sediment, pore waters, upper basaltic crust and the fluids that circulate throughout it. A wide range of temperature, pressure, pH, and electron donor and acceptor conditions exists—all of which can combine to affect carbon and nutrient cycling and result in gradients on spatial scales ranging from millimeters to kilometers. Diverse and mostly uncharacterized microorganisms live in these habitats, and potentially play a role in mediating global scale biogeochemical processes. Quantifying the rates at which microbial activity in the subsurface occurs is a challenging endeavor, yet developing an understanding of these rates is essential to determine the impact of subsurface life on Earth's global biogeochemical cycles, and for understanding how microorganisms in these “extreme” environments survive (or even thrive). Here, we synthesize recent advances and discoveries pertaining to microbial activity in the marine deep subsurface, and we highlight topics about which there is still little understanding and suggest potential paths forward to address them. This publication is the result of a workshop held in August 2012 by the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) “theme team” on microbial activity (www.darkenergybiosphere.org). PMID:23874326

  9. Effect of hybrid poplar trees on microbial populations important to hazardous waste bioremediation

    SciTech Connect

    Jordahl, J.L.; Foster, L.; Schnoor, J.L.; Alvarez, P.J.J.

    1997-06-01

    Microbial concentrations of denitrifiers, pseudomonads, and monoaromatic petroleum hydrocarbon (BTX) degraders were significantly higher (p < 0.1) in soil samples from the rhizosphere of poplar trees than in adjacent agricultural soils, and atrazine degraders were found only in one rhizosphere sample. The relative abundance of these phenotypes (as a fraction of total heterotrophs) was not significantly different between rhizosphere and surrounding soils. Therefore, the poplar rhizosphere enhanced the growth of microbial populations that participate in natural bioremediation without exerting selective pressure for them.

  10. Chronic impact of sulfamethoxazole on acetate utilization kinetics and population dynamics of fast growing microbial culture.

    PubMed

    Kor-Bicakci, G; Pala-Ozkok, I; Rehman, A; Jonas, D; Ubay-Cokgor, E; Orhon, D

    2014-08-01

    The study evaluated the chronic impact of sulfamethoxazole on metabolic activities of fast growing microbial culture. It focused on changes induced on utilization kinetics of acetate and composition of the microbial community. The experiments involved a fill and draw reactor, fed with acetate and continuous sulfamethoxazole dosing of 50 mg/L. The evaluation relied on model evaluation of the oxygen uptake rate profiles, with parallel assessment of microbial community structure by 454-pyrosequencing. Continuous sulfamethoxazole dosing inflicted a retardation effect on acetate utilization in a way commonly interpreted as competitive inhibition, blocked substrate storage and accelerated endogenous respiration. A fraction of acetate was utilized at a much lower rate with partial biodegradation of sulfamethoxazole. Results of pyrosequencing with a replacement mechanism within a richer more diversified microbial culture, through inactivation of vulnerable fractions in favor of species resistant to antibiotic, which made them capable of surviving and competing even with a slower metabolic response. PMID:24908607

  11. Microbial production of sensory-active miraculin.

    PubMed

    Ito, Keisuke; Asakura, Tomiko; Morita, Yuji; Nakajima, Ken-ichiro; Koizumi, Ayako; Shimizu-Ibuka, Akiko; Masuda, Katsuyoshi; Ishiguro, Masaji; Terada, Tohru; Maruyama, Jun-ichi; Kitamoto, Katsuhiko; Misaka, Takumi; Abe, Keiko

    2007-08-24

    Miraculin (MCL), a tropical fruit protein, is unique in that it has taste-modifying activity to convert sourness to sweetness, though flat in taste at neutral pH. To obtain a sufficient amount of MCL to examine the mechanism involved in this sensory event at the molecular level, we transformed Aspergillus oryzae by introducing the MCL gene. Transformants were expressed and secreted a sensory-active form of MCL yielding 2 mg/L. Recombinant MCL resembled native MCL in the secondary structure and the taste-modifying activity to generate sweetness at acidic pH. Since the observed pH-sweetness relation seemed to reflect the imidazole titration curve, suggesting that histidine residues might be involved in the taste-modifying activity. H30A and H30,60A mutants were generated using the A. oryzae-mediated expression system. Both mutants found to have lost the taste-modifying activity. The result suggests that the histidine-30 residue is important for the taste-modifying activity of MCL. PMID:17592723

  12. Active and total microbial communities in forest soil are largely different and highly stratified during decomposition

    PubMed Central

    Baldrian, Petr; Kolařík, Miroslav; Štursová, Martina; Kopecký, Jan; Valášková, Vendula; Větrovský, Tomáš; Žifčáková, Lucia; Šnajdr, Jaroslav; Rídl, Jakub; Vlček, Čestmír; Voříšková, Jana

    2012-01-01

    Soils of coniferous forest ecosystems are important for the global carbon cycle, and the identification of active microbial decomposers is essential for understanding organic matter transformation in these ecosystems. By the independent analysis of DNA and RNA, whole communities of bacteria and fungi and its active members were compared in topsoil of a Picea abies forest during a period of organic matter decomposition. Fungi quantitatively dominate the microbial community in the litter horizon, while the organic horizon shows comparable amount of fungal and bacterial biomasses. Active microbial populations obtained by RNA analysis exhibit similar diversity as DNA-derived populations, but significantly differ in the composition of microbial taxa. Several highly active taxa, especially fungal ones, show low abundance or even absence in the DNA pool. Bacteria and especially fungi are often distinctly associated with a particular soil horizon. Fungal communities are less even than bacterial ones and show higher relative abundances of dominant species. While dominant bacterial species are distributed across the studied ecosystem, distribution of dominant fungi is often spatially restricted as they are only recovered at some locations. The sequences of cbhI gene encoding for cellobiohydrolase (exocellulase), an essential enzyme for cellulose decomposition, were compared in soil metagenome and metatranscriptome and assigned to their producers. Litter horizon exhibits higher diversity and higher proportion of expressed sequences than organic horizon. Cellulose decomposition is mediated by highly diverse fungal populations largely distinct between soil horizons. The results indicate that low-abundance species make an important contribution to decomposition processes in soils. PMID:21776033

  13. Promoting uranium immobilization by the activities of microbial phophatases

    SciTech Connect

    Sobecky, Patricia A.; Martial Taillefert

    2006-06-01

    The following is a summary of progress in our project ''Promoting uranium immobilization by the activities of microbial phosphatases'' during the second year of the project. (1). Assignment of microbial phosphatases to molecular classes. One objective of this project is to determine the relationship of phosphatase activity to metal resistance in subsurface strains and possible contributions of horizontal gene transfer (HGT) to the dissemination of nonspecific acid phosphatase genes. Non-specific acid phosphohydrolases are a broad group of secreted microbial phosphatases that function in acidic-to-neutral pH ranges and utilize a wide range of organophosphate substrates. To address this objective we have designed a collection of PCR primer sets based on known microbial acid phosphatase sequences. Genomic DNA is extracted from subsurface FRC isolates and amplicons of the expected sizes are sequenced and searched for conserved signature motifs. During this reporting period we have successfully designed and tested a suite of PCR primers for gram-positive and gram-negative groups of the following phosphatase classes: (1) Class A; (2) Class B; and (3) Class C (gram negative). We have obtained specific PCR products for each of the classes using the primers we have designed using control strains as well as with subsurface isolates.

  14. Microbial Dioxygenase Gene Population Shifts during Polycyclic Aromatic Hydrocarbon Biodegradation

    PubMed Central

    Ní Chadhain, Sinéad M.; Norman, R. Sean; Pesce, Karen V.; Kukor, Jerome J.; Zylstra, Gerben J.

    2006-01-01

    The degradation of polycyclic aromatic hydrocarbons (PAHs) by bacteria has been widely studied. While many pure cultures have been isolated and characterized for their ability to grow on PAHs, limited information is available on the diversity of microbes involved in PAH degradation in the environment. We have designed generic PCR primers targeting the gene fragment encoding the Rieske iron sulfur center common to all PAH dioxygenase enzymes. These Rieske primers were employed to track dioxygenase gene population shifts in soil enrichment cultures following exposure to naphthalene, phenanthrene, or pyrene. PAH degradation was monitored by gas chromatograph with flame ionization detection. DNA was extracted from the enrichment cultures following PAH degradation. 16S rRNA and Rieske gene fragments were PCR amplified from DNA extracted from each enrichment culture and an unamended treatment. The PCR products were cloned and sequenced. Molecular monitoring of the enrichment cultures before and after PAH degradation using denaturing gradient gel electrophoresis and 16S rRNA gene libraries suggests that specific phylotypes of bacteria were associated with the degradation of each PAH. Sequencing of the cloned Rieske gene fragments showed that different suites of genes were present in soil microbe populations under each enrichment culture condition. Many of the Rieske gene fragment sequences fell into clades which are distinct from the reference dioxygenase gene sequences used to design the PCR primers. The ability to profile not only the bacterial community but also the dioxygenases which they encode provides a powerful tool for both assessing bioremediation potential in the environment and for the discovery of novel dioxygenase genes. PMID:16751518

  15. Soil microbial activity as influenced by compaction and straw mulching

    NASA Astrophysics Data System (ADS)

    Siczek, A.; Frąc, M.

    2012-02-01

    Field study was performed on Haplic Luvisol soil to determine the effects of soil compaction and straw mulching on microbial parameters of soil under soybean. Treatments with different compaction were established on unmulched and mulched with straw soil. The effect of soil compaction and straw mulching on the total bacteria number and activities of dehydrogenases, protease, alkaline and acid phosphatases was studied. The results of study indicated the decrease of enzymes activities in strongly compacted soil and their increase in medium compacted soil as compared to no-compacted treatment. Mulch application caused stimulation of the bacteria total number and enzymatic activity in the soil under all compaction levels. Compaction and mulch effects were significant for all analyzed microbial parameters (P<0.001).

  16. Effect of Elevated Salt Concentrations on the Aerobic Granular Sludge Process: Linking Microbial Activity with Microbial Community Structure▿

    PubMed Central

    Bassin, J. P.; Pronk, M.; Muyzer, G.; Kleerebezem, R.; Dezotti, M.; van Loosdrecht, M. C. M.

    2011-01-01

    The long- and short-term effects of salt on biological nitrogen and phosphorus removal processes were studied in an aerobic granular sludge reactor. The microbial community structure was investigated by PCR-denaturing gradient gel electrophoresis (DGGE) on 16S rRNA and amoA genes. PCR products obtained from genomic DNA and from rRNA after reverse transcription were compared to determine the presence of bacteria as well as the metabolically active fraction of bacteria. Fluorescence in situ hybridization (FISH) was used to validate the PCR-based results and to quantify the dominant bacterial populations. The results demonstrated that ammonium removal efficiency was not affected by salt concentrations up to 33 g/liter NaCl. Conversely, a high accumulation of nitrite was observed above 22 g/liter NaCl, which coincided with the disappearance of Nitrospira sp. Phosphorus removal was severely affected by gradual salt increase. No P release or uptake was observed at steady-state operation at 33 g/liter NaCl, exactly when the polyphosphate-accumulating organisms (PAOs), “Candidatus Accumulibacter phosphatis” bacteria, were no longer detected by PCR-DGGE or FISH. Batch experiments confirmed that P removal still could occur at 30 g/liter NaCl, but the long exposure of the biomass to this salinity level was detrimental for PAOs, which were outcompeted by glycogen-accumulating organisms (GAOs) in the bioreactor. GAOs became the dominant microorganisms at increasing salt concentrations, especially at 33 g/liter NaCl. In the comparative analysis of the diversity (DNA-derived pattern) and the activity (cDNA-derived pattern) of the microbial population, the highly metabolically active microorganisms were observed to be those related to ammonia (Nitrosomonas sp.) and phosphate removal (“Candidatus Accumulibacter”). PMID:21926194

  17. Seasonal distribution of microbial activity in bioaerosols in the outdoor environment of the Qingdao coastal region

    NASA Astrophysics Data System (ADS)

    Zhong, Xi; Qi, Jianhua; Li, Hongtao; Dong, Lijie; Gao, Dongmei

    2016-09-01

    Microbial activities in the atmosphere can indicate the physiological processes of microorganisms and can indirectly affect cloud formation and environmental health. In this study, the microbial activity in bioaerosols collected in the Qingdao coastal region was investigated using the fluorescein diacetate (FDA) hydrolysis method to detect the enzyme activity of microorganisms. The results showed that the microbial activity ranged from 5.49 to 102 ng/m3 sodium fluorescein from March 2013 to February 2014; the average value was 34.4 ng/m3. Microbial activity has no statistical correlation with total microbial quantity. Multiple linear regression analysis showed that meteorological factors such as atmospheric temperature, relative humidity and wind speed accounted for approximately 35.7% of the variation of the microbial activity, although their individual impacts on microbial activity varied. According to the correlation analysis, atmospheric temperature and wind speed had a significant positive and negative influence on microbial activity, respectively, whereas relative humidity and wind direction had no significant influence. The seasonal distribution of microbial activity in bioaerosols was in the order of summer > autumn > winter > spring, with high fluctuations in the summer and autumn. Microbial activity in bioaerosols differed in different weather conditions such as the sunny, foggy, and hazy days of different seasons. Further in situ observations in different weather conditions at different times and places are needed to understand the seasonal distribution characteristics of microbial activity in bioaerosols and the influence factors of microbial activity.

  18. Targeted Proteomics Approaches To Monitor Microbial Activity In Basalt Aquifer

    NASA Astrophysics Data System (ADS)

    Paszczynski, A. J.; Paidisetti, R.

    2007-12-01

    Microorganisms play a major role in biogeochemical cycles of the Earth. Information regarding microbial community composition can be very useful for environmental monitoring since the short generation times of microorganisms allows them to respond rapidly to changing environmental conditions. Microbial mediated attenuation of toxic chemicals offers great potential for the restoration of contaminated environments in an ecologically acceptable manner. Current knowledge regarding the structure and functional activities of microbial communities is limited, but more information is being acquired every day through many genomic- and proteomic- based methods. As of today, only a small fraction of the Earth's microorganisms has been cultured, and so most of the information regarding the biodegradation and therapeutic potentials of these uncultured microorganisms remains unknown. Sequence analysis of DNA and/or RNA has been used for identifying specific microorganisms, to study the community composition, and to monitor gene expression providing limited information about metabolic state of given microbial system. Proteomic studies can reveal information regarding the real-time metabolic state of the microbial communities thereby aiding in understanding their interaction with the environment. In research described here the involvement of microbial communities in the degradation of anthropogenic contaminants such as trichloroethylene (TCE) was studied using mass spectrometry-based proteomics. The co- metabolic degradation of TCE in the groundwater of the Snake River Plain Aquifer at the Test Area North (TAN) site of Idaho National Laboratory (INL) was monitored by the characterization of peptide sequences of enzymes such as methane monooxygenases (MMOs). MMOs, expressed by methanotrophic bacteria are involved in the oxidation of methane and non-specific co-metabolic oxidation of TCE. We developed a time- course cell lysis method to release proteins from complex microbial

  19. Effect of oenological practices on microbial populations using culture-independent techniques.

    PubMed

    Andorrà, Imma; Landi, Sara; Mas, Albert; Guillamón, José M; Esteve-Zarzoso, Braulio

    2008-10-01

    Sulphur dioxide (SO(2)) addition and yeast inoculation are well-established practices in winemaking for restricting the growth of indigenous yeasts and bacterial populations. The effect of these oenological practices on wine microbial populations has been evaluated using culture-independent methods. These are quantitative PCR (qPCR) for the enumeration of yeasts, lactic acid bacteria (LAB) and acetic acid bacteria (AAB), and PCR-DGGE to determine the yeast and bacteria species diversity. The PCR-DGGE method detected a low yeast and bacteria species diversity. On the contrary, the specificity of the primers designed for the qPCR allowed that minor microbial groups such as Hanseniaspora were accurately quantified regardless of a large presence of other microbial groups such as Saccharomyces. From an oenological point of view, inoculation increased the proportion of Saccharomyces vs. non-Saccharomyces in a shorter time. Hanseniaspora increased during the first phase and decreased during the latter phases of the process, especially in the sulphited fermentations. Both yeast inoculation and SO(2) kept the LAB populations at very low level, while the AAB populations were hardly affected by these two practices. PMID:18721672

  20. Population-reaction model and microbial experimental ecosystems for understanding hierarchical dynamics of ecosystems.

    PubMed

    Hosoda, Kazufumi; Tsuda, Soichiro; Kadowaki, Kohmei; Nakamura, Yutaka; Nakano, Tadashi; Ishii, Kojiro

    2016-02-01

    Understanding ecosystem dynamics is crucial as contemporary human societies face ecosystem degradation. One of the challenges that needs to be recognized is the complex hierarchical dynamics. Conventional dynamic models in ecology often represent only the population level and have yet to include the dynamics of the sub-organism level, which makes an ecosystem a complex adaptive system that shows characteristic behaviors such as resilience and regime shifts. The neglect of the sub-organism level in the conventional dynamic models would be because integrating multiple hierarchical levels makes the models unnecessarily complex unless supporting experimental data are present. Now that large amounts of molecular and ecological data are increasingly accessible in microbial experimental ecosystems, it is worthwhile to tackle the questions of their complex hierarchical dynamics. Here, we propose an approach that combines microbial experimental ecosystems and a hierarchical dynamic model named population-reaction model. We present a simple microbial experimental ecosystem as an example and show how the system can be analyzed by a population-reaction model. We also show that population-reaction models can be applied to various ecological concepts, such as predator-prey interactions, climate change, evolution, and stability of diversity. Our approach will reveal a path to the general understanding of various ecosystems and organisms. PMID:26747638

  1. Microbial Genomics of a Host-Associated Commensal Bacterium in Fragmented Populations of Endangered Takahe.

    PubMed

    Grange, Zoë L; Gartrell, Brett D; Biggs, Patrick J; Nelson, Nicola J; Anderson, Marti; French, Nigel P

    2016-05-01

    Isolation of wildlife into fragmented populations as a consequence of anthropogenic-mediated environmental change may alter host-pathogen relationships. Our understanding of some of the epidemiological features of infectious disease in vulnerable populations can be enhanced by the use of commensal bacteria as a proxy for invasive pathogens in natural ecosystems. The distinctive population structure of a well-described meta-population of a New Zealand endangered flightless bird, the takahe (Porphyrio hochstetteri), provided a unique opportunity to investigate the influence of host isolation on enteric microbial diversity. The genomic epidemiology of a prevalent rail-associated endemic commensal bacterium was explored using core genome and ribosomal multilocus sequence typing (rMLST) of 70 Campylobacter sp. nova 1 isolated from one third of the takahe population resident in multiple locations. While there was evidence of recombination between lineages, bacterial divergence appears to have occurred and multivariate analysis of 52 rMLST genes revealed location-associated differentiation of C. sp. nova 1 sequence types. Our results indicate that fragmentation and anthropogenic manipulation of populations can influence host-microbial relationships, with potential implications for niche adaptation and the evolution of micro-organisms in remote environments. This study provides a novel framework in which to explore the complex genomic epidemiology of micro-organisms in wildlife populations. PMID:26707136

  2. Spatial patterns of microbial diversity and activity in an aged creosote-contaminated site

    PubMed Central

    Mukherjee, Shinjini; Juottonen, Heli; Siivonen, Pauli; Lloret Quesada, Cosme; Tuomi, Pirjo; Pulkkinen, Pertti; Yrjälä, Kim

    2014-01-01

    Restoration of polluted sites via in situ bioremediation relies heavily on the indigenous microbes and their activities. Spatial heterogeneity of microbial populations, contaminants and soil chemical parameters on such sites is a major hurdle in optimizing and implementing an appropriate bioremediation regime. We performed a grid-based sampling of an aged creosote-contaminated site followed by geostatistical modelling to illustrate the spatial patterns of microbial diversity and activity and to relate these patterns to the distribution of pollutants. Spatial distribution of bacterial groups unveiled patterns of niche differentiation regulated by patchy distribution of pollutants and an east-to-west pH gradient at the studied site. Proteobacteria clearly dominated in the hot spots of creosote pollution, whereas the abundance of Actinobacteria, TM7 and Planctomycetes was considerably reduced from the hot spots. The pH preferences of proteobacterial groups dominating in pollution could be recognized by examining the order and family-level responses. Acidobacterial classes came across as generalists in hydrocarbon pollution whose spatial distribution seemed to be regulated solely by the pH gradient. Although the community evenness decreased in the heavily polluted zones, basal respiration and fluorescein diacetate hydrolysis rates were higher, indicating the adaptation of specific indigenous microbial populations to hydrocarbon pollution. Combining the information from the kriged maps of microbial and soil chemistry data provided a comprehensive understanding of the long-term impacts of creosote pollution on the subsurface microbial communities. This study also highlighted the prospect of interpreting taxa-specific spatial patterns and applying them as indicators or proxies for monitoring polluted sites. PMID:25105905

  3. Spatial patterns of microbial diversity and activity in an aged creosote-contaminated site.

    PubMed

    Mukherjee, Shinjini; Juottonen, Heli; Siivonen, Pauli; Lloret Quesada, Cosme; Tuomi, Pirjo; Pulkkinen, Pertti; Yrjälä, Kim

    2014-10-01

    Restoration of polluted sites via in situ bioremediation relies heavily on the indigenous microbes and their activities. Spatial heterogeneity of microbial populations, contaminants and soil chemical parameters on such sites is a major hurdle in optimizing and implementing an appropriate bioremediation regime. We performed a grid-based sampling of an aged creosote-contaminated site followed by geostatistical modelling to illustrate the spatial patterns of microbial diversity and activity and to relate these patterns to the distribution of pollutants. Spatial distribution of bacterial groups unveiled patterns of niche differentiation regulated by patchy distribution of pollutants and an east-to-west pH gradient at the studied site. Proteobacteria clearly dominated in the hot spots of creosote pollution, whereas the abundance of Actinobacteria, TM7 and Planctomycetes was considerably reduced from the hot spots. The pH preferences of proteobacterial groups dominating in pollution could be recognized by examining the order and family-level responses. Acidobacterial classes came across as generalists in hydrocarbon pollution whose spatial distribution seemed to be regulated solely by the pH gradient. Although the community evenness decreased in the heavily polluted zones, basal respiration and fluorescein diacetate hydrolysis rates were higher, indicating the adaptation of specific indigenous microbial populations to hydrocarbon pollution. Combining the information from the kriged maps of microbial and soil chemistry data provided a comprehensive understanding of the long-term impacts of creosote pollution on the subsurface microbial communities. This study also highlighted the prospect of interpreting taxa-specific spatial patterns and applying them as indicators or proxies for monitoring polluted sites. PMID:25105905

  4. Midgut Microbial Community of Culex quinquefasciatus Mosquito Populations from India

    PubMed Central

    Chandel, Kshitij; Mendki, Murlidhar J.; Parikh, Rasesh Y.; Kulkarni, Girish; Tikar, Sachin N.; Sukumaran, Devanathan; Prakash, Shri; Parashar, Brahma D.; Shouche, Yogesh S.; Veer, Vijay

    2013-01-01

    The mosquito Culex quinquefasciatus is a ubiquitous species that serves as a major vector for west nile virus and lymphatic filariasis. Ingestion of bloodmeal by females triggers a series of physiological processes in the midgut and also exposes them to infection by these pathogens. The bacteria normally harbored in the midgut are known to influence physiology and can also alter the response to various pathogens. The midgut bacteria in female Cx. quinquefasciatus mosquitoes collected over a large geographical area from India was studied. Examination of 16S ribosomal DNA amplicons from culturable microflora revealed the presence of 83 bacterial species belonging to 31 bacterial genera. All of these species belong to three phyla i.e. Proteobacteria, Firmicutes and Actinobacteria. Phylum Proteobacteria was the most dominant phylum (37 species), followed by Firmicutes (33 species) and Actinobacteria (13 species). Phylum Proteobacteria, was dominated by members of γ-proteobacteria class. The genus Staphylococcus was the largest genus represented by 11 species whereas Enterobacter was the most prevalent genus and recovered from all the field stations except Leh. Highest bacterial prevalence was observed from Bhuj (22 species) followed by Nagrota (18 species), Masimpur (18 species) and Hathigarh (16 species). Whereas, least species were observed from Leh (8 species). It has been observed that individual mosquito harbor extremely diverse gut bacteria and have very small overlap bacterial taxa in their gut. This variation in midgut microbiota may be one of the factors responsible for variation in disease transmission rates or vector competence within mosquito population. The present data strongly encourage further investigations to verify the potential role of the detected bacteria in mosquito for the transmission of lymphatic filariasis and west nile virus. To the best of our knowledge this is the first study on midgut microbiota of wild Cx. quinquefasciatus from over a

  5. Microbial Diversity and Population Structure of Extremely Acidic Sulfur-Oxidizing Biofilms From Sulfidic Caves

    NASA Astrophysics Data System (ADS)

    Jones, D.; Stoffer, T.; Lyon, E. H.; Macalady, J. L.

    2005-12-01

    Extremely acidic (pH 0-1) microbial biofilms called snottites form on the walls of sulfidic caves where gypsum replacement crusts isolate sulfur-oxidizing microorganisms from the buffering action of limestone host rock. We investigated the phylogeny and population structure of snottites from sulfidic caves in central Italy using full cycle rRNA methods. A small subunit rRNA bacterial clone library from a Frasassi cave complex snottite sample contained a single sequence group (>60 clones) similar to Acidithiobacillus thiooxidans. Bacterial and universal rRNA clone libraries from other Frasassi snottites were only slightly more diverse, containing a maximum of 4 bacterial species and probably 2 archaeal species. Fluorescence in situ hybridization (FISH) of snottites from Frasassi and from the much warmer Rio Garrafo cave complex revealed that all of the communities are simple (low-diversity) and dominated by Acidithiobacillus and/or Ferroplasma species, with smaller populations of an Acidimicrobium species, filamentous fungi, and protists. Our results suggest that sulfidic cave snottites will be excellent model microbial ecosystems suited for ecological and metagenomic studies aimed at elucidating geochemical and ecological controls on microbial diversity, and at mapping the spatial history of microbial evolutionary events such as adaptations, recombinations and gene transfers.

  6. Quantifying the metabolic activities of human-associated microbial communities across multiple ecological scales

    PubMed Central

    Maurice, Corinne Ferrier; Turnbaugh, Peter James

    2013-01-01

    Humans are home to complex microbial communities, whose aggregate genomes and their encoded metabolic activities are referred to as the human microbiome. Recently, researchers have begun to appreciate that different human body habitats and the activities of their resident microorganisms can be better understood in ecological terms, as a range of spatial scales encompassing single cells, guilds of microorganisms responsive to a similar substrate, microbial communities, body habitats, and host populations. However, the bulk of the work to date has focused on studies of culturable microorganisms in isolation or on DNA sequencing-based surveys of microbial diversity in small to moderately sized cohorts of individuals. Here, we discuss recent work that highlights the potential for assessing the human microbiome at a range of spatial scales, and for developing novel techniques that bridge multiple levels: for example, through the combination of single cell methods and metagenomic sequencing. These studies promise to not only provide a much-needed epidemiological and ecological context for mechanistic studies of culturable and genetically tractable microorganisms, but may also lead to the discovery of fundamental rules that govern the assembly and function of host-associated microbial communities. PMID:23550823

  7. Direct Experimental Assessment of Microbial Activity in North Pond Sediments

    NASA Astrophysics Data System (ADS)

    Ferdelman, T. G.; Picard, A.; Morando, M.; Ziebis, W.

    2009-12-01

    North Pond, an isolated sediment pond located at 22°45’N on the western flank of the Mid-Atlantic Ridge, offered the opportunity to study microbial activities in deeply-buried low-activity sediments. About 8 x 15 km in size with sediment maximum thickness of about 300 m, North Pond is completely surrounded by exposed 7 Ma old basement. North Pond lies above the carbonate compensation depth at a water depth about 4500 m; hydrostatic pressure at the seafloor is about 45 MPa and the temperature is near 2°C. During the a R/V MS Merian cruise (MSM-11/1) in February -March 2009, 14 gravity cores of up to 9 m length were successfully obtained, from which samples were taken with 1-m resolution for experimental activity measurements. The goal of the experimental work was 1) to examine potential metabolic pathways in North Pond sediments and carbon assimilation pathways in this low-energy environment, and 2) explore the effects of pressure on microbial metabolic activities. As dissolved oxygen penetrated through all depths, sediments were aerobically sampled, processed and incubated at 4°C. Selected samples were immediately stored at in situ pressure until further use. The microbial uptake of both organic and inorganic carbon in selected North Pond sediment samples was investigated by following the fate of 14C in radio-labeled organic and organic compounds in North Pond sediment slurry incubations. Shipboard and on-shore experiments using 14C-leucine, 14C-glucose and 14C-bicarbonate were performed on selected cores. Day- to month- incubations were performed at 4°C. Parallel incubations were conducted at atmospheric pressure (0.1 MPa) and in situ pressure (~45 MPa). Either whole cell extraction (Kallmeyer et al., Limnol. Oceanogr.: Methods 6, 2008, 238-245) or protein-DNA extraction was carried on after various incubations to determine the fraction of 14C incorporated into cellular components. Formation of 14C-labeled CO2 was determined on samples incubated with 14C

  8. Direct Observations Of Microbial Activity At Extreme Pressures

    NASA Astrophysics Data System (ADS)

    Sharma, A.; Scott, J. H.; Cody, G. D.; Fogel, M.; Hazen, R. M.; Hemley, R. J.; Huntress, W. T.

    2002-12-01

    Microbial communities adapt to a wide range of pressures, temperatures, salinities, pH, and oxidation states. Although, significant attention has been focused on the effects of high and low temperature on physiology, there is some evidence that elevated pressure may also manifest interesting effects on cellular physiology, such as enzyme inactivation, cell-membrane breach, and suppression of protein interactions with various substrates. However, exactly how these factors affect intact cells is not well understood. In this study, we have adapted diamond anvil cells to explore the effects of high pressure on microbial life. We used the rate of microbial formate oxidation as a probe of metabolic viability. The utilization of formate by microorganisms is a fundamental metabolic process in anaerobic environments. We monitored in-situ microbial formate oxidation via molecular spectroscopy for Shewanella oneidensis strain MR1 and Escherichia coli strain MG1655 at high pressures (68 to 1060 MPa). At pressures of 1200 to 1600 MPa, living bacteria resided in fluid inclusions in ice-VI crystals and continued to be viable upon subsequent release to ambient pressures (0.1 MPa). Furthermore, direct microscopic observations indicate that these cells maintain their ability for cellular division upon decompression from such high pressures. Evidence of microbial viability and activity at these extreme pressures expands by an order of magnitude the range of conditions representing the habitable zone in the solar system. These results imply that pressure may not be a significant impediment to life. The maximum pressure explored in this work is equivalent to a depth of ~ 50 km below Earth's crust, or ~ 160 km in a hypothetical ocean. The pressures encountered at the depths of thick ice caps and deep crustal subsurface may not be a limiting factor for the existence of life. This suggests that deep (water/ice) layers of Europa, Callisto, or Ganymede, subduction zones on Earth, and the

  9. Temperature and Microbial Activity Effects on Soil Carbon Stabilization

    NASA Astrophysics Data System (ADS)

    Fissore, C.; van Diepen, L.; Wixon, D.; Marin-Spiotta, E.; Giardina, C. P.

    2014-12-01

    Uncertainties on the importance of environmental controls on soil C stabilization and turnover limit accurate predictions of the rate and magnitude of the response of soils to climate change. Here we report results from a study of interactions among vegetation and soil microbial communities in North American forests across a highly constrained, 22OC gradient mean annual temperature (MAT) as a proxy for understanding changes with climate. Previous work indicated that turnover and amount of labile SOC responded negatively to MAT, whereas stable SOC was insensitive to temperature variation. Hardwood forests stored a larger amount of stable SOC, but with shorter mean residence times than paired pine forests. Our findings suggest that the interaction between vegetation composition and microbial communities may affect SOC accumulation and stabilization responses to rising temperature. To investigate these relationships, we characterized the microbial communities with Phospholipid Fatty Acid (PLFA) analysis. PLFA analyses indicate complex microbial responses to increased MAT and vegetation composition. Microbial biomass declined with MAT in conifer forests and increased in hardwood forests. Relative abundance of actinomycetes increased with MAT for both forest types, and was correlated with amount and turnover of active SOC. The relative abundance of fungi decreased with increasing MAT, while gram+ bacteria increased, such that fungi:bacteria ratio decreased with MAT, with this trend being more pronounced for hardwood cover type. These results are consistent with a long-term warming experiment in a hardwood forest at the Harvard Forest LTER site, where after 12 years of warming the relative abundance of gram positive bacteria and actinomycetes increased, while fungal biomass decreased. In contrast, relationships between microbial groups and the stable fraction of SOC along the gradient were only observed in conifers. Increases in mean residence time of stable SOC were

  10. From field barley to malt: detection and specification of microbial activity for quality aspects.

    PubMed

    Noots, I; Delcour, J A; Michiels, C W

    1999-01-01

    Barley grain carries a numerous, variable, and complex microbial population that mainly consists of bacteria, yeasts, and filamentous fungi and that can partly be detected and quantified using plating methods and microscopic and molecular techniques. The extent and the activity of this microflora are determined by the altering state of the grain and the environmental conditions in the malt production chain. Three ecological systems can be distinguished: the growing cereal in the field, the dry barley grain under storage, and the germinating barley kernel during actual malting. Microorganisms interact with the malting process both by their presence and by their metabolic activity. In this respect, interference with the oxygen uptake by the barley grain and secretion of enzymes, hormones, toxins, and acids that may affect the plant physiological processes have been studied. As a result of the interaction, microorganisms can cause important losses and influence malt quality as measured by brewhouse performance and beer quality. Of particular concern is the occurrence of mycotoxins that may affect the safety of malt. The development of the microflora during malt production can to a certain extent be controlled by the selection of appropriate process conditions. Physical and chemical treatments to inactivate the microbial population on the barley grain are suggested. Recent developments, however, aim to control the microbial activity during malt production by promoting the growth of desirable microbial cultures, selected either as biocontrol agents inhibiting mycotoxin-producing molds or as starter cultures actively contributing to malt modification. Such techniques may offer natural opportunities to improve the quality and safety of malt. PMID:10405796

  11. Multiple microbial activities for volatile organic compounds reduction by biofiltration.

    PubMed

    Civilini, Marcello

    2006-07-01

    In the northeast of Italy, high volatile organic carbon (VOC) emissions originate from small-medium companies producing furniture. In these conditions it is difficult to propose a single, efficient, and economic system to reduce pollution. Among the various choices, the biofiltration method could be a good solution, because microbial populations possess multiple VOC degradation potentials used to oxidize these compounds to CO2. Starting from the air emissions of a typical industrial wood-painting plant, a series of experiments studied in vitro microbial degradation of each individual VOC. Isolated strains were then added to a laboratory-scale biofiltration apparatus filled with an organic matrix, and the different VOC behavior demonstrated the potential of single and/or synergic microbial removal actions. When a single substrate was fed, the removal efficiency of a Pseudomonas aeruginosa inoculated reactor was 1.1, 1.17, and 0.33 g m(-3) hr(-1), respectively, for xylene, toluene, and ethoxy propyl acetate. A VOC mixture composed of butyl acetate, ethyl acetate, diacetin alcohol, ethoxy propanol acetate, methyl ethyl ketone, methyl isobutyl ketone, toluene, and xylene was then fed into a 2-m(3) reactor treating 100 m3 hr(-1) of contaminated air. The reactor was filled with the same mixture of organic matrix, enriched with all of the isolated strains together. During reactor study, different VOC loading rates were used, and the behavior was evaluated continuously. After a short acclimation period, the removal efficiency was > 65% at VOC load of 150-200 g m(-3) hr(-1). Quantification of removal efficiencies and VOC speciation confirmed the relationship among removal efficiencies, compound biodegradability, and the dynamic transport of each mixture component within the organic matrix. Samples of the fixed bed were withdrawn at different intervals and the heterogeneous microbial community evaluated for both total and differential compound counts. PMID:16878585

  12. Assessing Microbial Activity in Marcellus Shale Hydraulic Fracturing Fluids

    NASA Astrophysics Data System (ADS)

    Wishart, J. R.; Morono, Y.; Itoh, M.; Ijiri, A.; Hoshino, T.; Inagaki, F.; Verba, C.; Torres, M. E.; Colwell, F. S.

    2014-12-01

    Hydraulic fracturing (HF) produces millions of gallons of waste fluid which contains a microbial community adapted to harsh conditions such as high temperatures, high salinities and the presence of heavy metals and radionuclides. Here we present evidence for microbial activity in HF production fluids. Fluids collected from a Marcellus shale HF well were supplemented with 13C-labeled carbon sources and 15N-labeled ammonium at 25°C under aerobic or anaerobic conditions. Samples were analyzed for 13C and 15N incorporation at sub-micrometer scale by ion imaging with the JAMSTEC NanoSIMS to determine percent carbon and nitrogen assimilation in individual cells. Headspace CO2 and CH4 were analyzed for 13C enrichment using irm-GC/MS. At 32 days incubation carbon assimilation was observed in samples containing 1 mM 13C-labeled glucose under aerobic and anaerobic conditions with a maximum of 10.4 and 6.5% total carbon, respectively. Nitrogen assimilation of 15N ammonium observed in these samples were 0.3 and 0.8% of total nitrogen, respectively. Head space gas analysis showed 13C enrichment in CH4 in anaerobic samples incubated with 1mM 13C-labeled bicarbonate (2227 ‰) or methanol (98943 ‰). Lesser 13C enrichment of CO2 was observed in anaerobic samples containing 1 mM 13C-labeled acetate (13.7 ‰), methanol (29.9 ‰) or glucose (85.4 ‰). These results indicate metabolic activity and diversity in microbial communities present in HF flowback fluids. The assimilation of 13C-labeled glucose demonstrates the production of biomass, a critical part of cell replication. The production of 13CO2 and 13CH4 demonstrate microbial metabolism in the forms of respiration and methanogenesis, respectively. Methanogenesis additionally indicates the presence of an active archaeal community. This research shows that HF production fluid chemistry does not entirely inhibit microbial activity or growth and encourages further research regarding biogeochemical processes occurring in

  13. Microbial Populations Associated with Treatment of an Industrial Dye Effluent in an Anaerobic Baffled Reactor

    PubMed Central

    Plumb, Jason J.; Bell, Joanne; Stuckey, David C.

    2001-01-01

    Fluorescent in situ hybridization (FISH) using 16S and 23S rRNA-targeted probes together with construction of an archaeal 16S ribosomal DNA (rDNA) clone library was used to characterize the microbial populations of an anaerobic baffled reactor successfully treating industrial dye waste. Wastewater produced during the manufacture of food dyes containing several different azo and other dye compounds was decolorized and degraded under sulfidogenic and methanogenic conditions. Use of molecular methods to describe microbial populations showed that a diverse group of Bacteria and Archaea was involved in this treatment process. FISH enumeration showed that members of the gamma subclass of the class Proteobacteria and bacteria in the Cytophaga-Flexibacter-Bacteroides phylum, together with sulfate-reducing bacteria, were prominent members of a mixed bacterial population. A combination of FISH probing and analysis of 98 archaeal 16S rDNA clone inserts revealed that together with the bacterial population, a methanogenic population dominated by Methanosaeta species and containing species of Methanobacterium and Methanospirillum and a relatively unstudied methanogen, Methanomethylovorans hollandica, contributed to successful anaerobic treatment of the industrial waste. We suggest that sulfate reducers, or more accurately sulfidogenic bacteria, together with M. hollandica contribute considerably to the treatment process through metabolism of dye-associated sulfonate groups and subsequent conversion of sulfur compounds to carbon dioxide and methane. PMID:11425746

  14. Microbial Population and Community Dynamics on Plant Roots and Their Feedbacks on Plant Communities

    PubMed Central

    Bever, James D.; Platt, Thomas G.; Morton, Elise R.

    2012-01-01

    The composition of the soil microbial community can be altered dramatically due to association with individual plant species, and these effects on the microbial community can have important feedbacks on plant ecology. Negative plant-soil feedback plays primary roles in maintaining plant community diversity, whereas positive plant-soil feedback may cause community conversion. Host-specific differentiation of the microbial community results from the trade-offs associated with overcoming plant defense and the specific benefits associated with plant rewards. Accumulation of host-specific pathogens likely generates negative feedback on the plant, while changes in the density of microbial mutualists likely generate positive feedback. However, the competitive dynamics among microbes depends on the multidimensional costs of virulence and mutualism, the fine-scale spatial structure within plant roots, and active plant allocation and localized defense. Because of this, incorporating a full view of microbial dynamics is essential to explaining the dynamics of plant-soil feedbacks and therefore plant community ecology. PMID:22726216

  15. [Effects of the Vital Activity of Soil Insect Larvae on Microbial Processes in the Soil].

    PubMed

    Samoilova, E S; Kostina, N V; Striganova, B R

    2015-01-01

    The effects of Elateridae larvae (wireworms) on the structure, functional diversity, and tolerance of the soil microbial population in steppe ecosystems have been investigated. The trophic and locomotor activity of wireworms leads to an appreciable increase in bacterial abundance and suppression of fungal activity. The fungal hyphae in the presence of wireworms are significantly damaged, which can be related to the feeding activity of Elateridae. The increase of bacterial abundance on the background of exclusion of the fungal component shifts the microbial succession to the acceleration of organic matter mineralization. The microbial consumption of mono- and oligosaccharides, alcohols, and water-soluble compounds increases in the presence of wireworms (multisubstrate test). The effect of Elateridae larvae on the microorganisms transforming nitrogen compounds is species-specific. Agriotes obscurus activity decreases their consumption of urea and creatinine by 2.1-2.5 times, and Selatosomus aeneus increases it by 1.3 and 2.5 times, respectively. The intensity of actual nitrogen fixation in the soil increases in the presence of wireworms by almost 4 times, but the losses of gaseous nitrogen do not increase because of the decrease in both the denitrification and methanogenesis rates PMID:26852485

  16. Improving rumen ecology and microbial population by dried rumen digesta in beef cattle.

    PubMed

    Cherdthong, Anusorn; Wanapat, Metha; Saenkamsorn, Anuthida; Supapong, Chanadol; Anantasook, Nirawan; Gunun, Pongsatorn

    2015-06-01

    Four Thai native beef cattle with initial body weight (BW) of 91.8 ± 4.75 kg were randomly assigned according to a 4 × 4 Latin square design to receive four concentrates replacement levels of soybean meal (SBM) by dried rumen digesta (DRD) at 0, 33, 67, and 100 % on dry matter (DM) basis. All cattle were fed rice straw ad libitum while additional concentrate was fed at 0.5 % BW daily. The experiment was conducted for four periods of 21 days. Rumen fluid was analyzed for predominant cellulolytic bacterial population by using real-time PCR technique. Increasing levels of DRD did not alter total feed intake, ruminal pH and temperature, and plasma urea nitrogen (P > 0.05). Protozoa and fungal population were not differed by DRD supplementation while population of bacteria at 4 h post feeding was increased when SBM was replaced with DRD at 66 and 100 % DM. Population of total bacteria and R. flavefaciens at 4 h post feeding were significantly highest with inclusion of 100 % of DRD in the ration. The experimental diets has no effect on excretion and absorption of purine derivatives (P > 0.05), while microbial crude protein and efficiency of microbial N synthesis were significantly increased with DRD inclusion in the diet and highest with 100 % DRD replacement (P > 0.05). Replacement of SBM by DRD at 100 % DM improved the rumen ecology and microbial population in beef cattle fed on rice straw. PMID:25851930

  17. Microbial Community Dynamics and Activity Link to Indigo Production from Indole in Bioaugmented Activated Sludge Systems

    PubMed Central

    Deng, Jie; Deng, Ye; Van Nostrand, Joy D.; Wu, Liyou; He, Zhili; Qin, Yujia; Zhou, Jiti; Zhou, Jizhong

    2015-01-01

    Biosynthesis of the popular dyestuff indigo from indole has been comprehensively studied using pure cultures, but less has been done to characterize the indigo production by microbial communities. In our previous studies, a wild strain Comamonas sp. MQ was isolated from activated sludge and the recombinant Escherichia coli nagAc carrying the naphthalene dioxygenase gene (nag) from strain MQ was constructed, both of which were capable of producing indigo from indole. Herein, three activated sludge systems, G1 (non-augmented control), G2 (augmented with Comamonas sp. MQ), and G3 (augmented with recombinant E. coli nagAc), were constructed to investigate indigo production. After 132-day operation, G3 produced the highest yields of indigo (99.5 ± 3.0 mg/l), followed by G2 (27.3 ± 1.3 mg/l) and G1 (19.2 ± 1.2 mg/l). The microbial community dynamics and activities associated with indigo production were analyzed by Illumina Miseq sequencing of 16S rRNA gene amplicons. The inoculated strain MQ survived for at least 30 days, whereas E. coli nagAc was undetectable shortly after inoculation. Quantitative real-time PCR analysis suggested the abundance of naphthalene dioxygenase gene (nagAc) from both inoculated strains was strongly correlated with indigo yields in early stages (0–30 days) (P < 0.001) but not in later stages (30–132 days) (P > 0.10) of operation. Based on detrended correspondence analysis (DCA) and dissimilarity test results, the communities underwent a noticeable shift during the operation. Among the four major genera (> 1% on average), the commonly reported indigo-producing populations Comamonas and Pseudomonas showed no positive relationship with indigo yields (P > 0.05) based on Pearson correlation test, while Alcaligenes and Aquamicrobium, rarely reported for indigo production, were positively correlated with indigo yields (P < 0.05). This study should provide new insights into our understanding of indigo bio-production by microbial communities

  18. Microbial population dynamics in a thermophilic methane digester fed with garbage.

    PubMed

    Cheon, J; Hong, F; Hidaka, T; Koshikawa, H; Tsuno, H

    2007-01-01

    The diversity of microbial communities in three full-scale thermophilic anaerobic digesters which treated garbage, sewage sludge and livestock wastes (hereafter called TGD, TSD and TLD, respectively) was investigated using 16S rDNA clone libraries in triplicate. The population dynamics of TGD were also studied. The purposes were to show the microbial diversity in each reactor and to suggest which key microbes in a thermophilic methane digester fed with garbage, including a check of reproducibility and the suggestion of an error range in this molecular biology method. 736 clones were identified, and the maximum error was estimated to be around +/-10% for the same OTU (operational taxonomic unit) and for most detected OTUs. The most frequently detected OTU shows a close relationship to Uncultured bacterium clone MBA08, Unidentified bacterium clone TUG22 and Uncultured archaeal symbiont PA204 in TGD, TSD and TLD, respectively. The microbial population dynamics in TGD were studied over a period of 90 days, and the occupying ratios of Bacillus infernus and Methanothermobacter wolfeii were shown to change with the change in VFA concentration. From the dynamic change and characteristics of the microbes, it is concluded that Bacillus infernus and Methanothermobacter wolfeii played an important role and were recommended as key microbes in TGD. PMID:17564383

  19. [Nutrient contents and microbial populations of aeolian sandy soil in Sanjiangyuan region of Qinghai Province].

    PubMed

    Lin, Chao-feng; Chen, Zhan-quan; Xue, Quan-hong; Lai, Hang-xian; Chen, Lai-sheng; Zhang, Deng-shan

    2007-01-01

    Sanjiangyuan region (the headstream of three rivers) in Qinghai Province of China is the highest and largest inland alpine wetland in the world. The study on the nutrient contents and microbial populations of aeolian sandy soils in this region showed that soil organic matter content increased with the evolution of aeolian sand dunes from un-stabilized to stabilized state, being 5.9 and 3.8 times higher in stabilized sand dune than in mobile and semi-stabilized sand dunes, respectively. Soil nitrogen and phosphorus contents increased in line with the amount of organic matter, while potassium content and pH value varied slightly. The microbial populations changed markedly with the development of vegetation, fixing of mobile sand, and increase of soil nutrients. The quantities of soil bacteria, fungi and actinomycetes were 4.0 and 2.8 times, 19.6 and 6.3 times, and 12.4 and 2.6 times higher in stabilized and semi-stabilized sand dunes than in mobile sand dune, respectively, indicating that soil microbial bio-diversity was increased with the evolution of aeolian sand dunes from mobile to stabilized state. In addition, the quantities of soil microbes were closely correlated with the contents of soil organic matter, total nitrogen, and available nitrogen and phosphorus, but not correlated with soil total phosphorus, total and available potassium, or pH value. PMID:17396507

  20. Geochemical Attributes and Gradients Within Geothermal Systems Define the Distribution of Specific Microbial Populations

    NASA Astrophysics Data System (ADS)

    Inskeep, W. P.; Macur, R. E.; Korf, S.; Taylor, W. P.; Ackerman, G.; Kozubal, M.; Nagy, A.

    2006-12-01

    Microorganisms in natural habitats interact with mineral surfaces in many different respects. For example, microorganisms are known to enhance the dissolution rates of some minerals via the production of organic acids and other exudates, but at the same time, may mineralize solid phases as a direct or indirect result of metabolic processes. It is also well-established that many microorganisms form biofilms on mineral surfaces, and may preferentially attach to surfaces rich in necessary nutrients or in elements used for energy conservation. In part due to the complexity of natural soil, water and sediments systems, it is generally difficult to ascertain mechanisms controlling the distribution of organisms on mineral surfaces and their role in mineral precipitation-dissolution reactions. Geothermal microbial communities are often less diverse than surface soils and sediments and offer opportunities for understanding relationships among specific microbial populations and geochemical processes that define the biogeochemical cycles of individual elements. We have investigated numerous acidic and near-neutral geothermal sites in Yellowstone National Park, and have performed a number of complimentary chemical and microbiological analyses to ascertain the role of microorganisms in S, Fe, As and Sb cycling in geothermal systems. Our results demonstrate the importance of microbiota in the formation of various Fe(III) oxide phases with variable anion chemistry, and the importance of chemolithotrophic metabolisms in Fe, S and As cycling. Where possible, these metabolisms are linked to specific microbial populations identified via molecular methods, and in some cases confirmed using isolation and characterization of individual organisms.

  1. Microbial diversity in European alpine permafrost and active layers.

    PubMed

    Frey, Beat; Rime, Thomas; Phillips, Marcia; Stierli, Beat; Hajdas, Irka; Widmer, Franco; Hartmann, Martin

    2016-03-01

    Permafrost represents a largely understudied genetic resource. Thawing of permafrost with global warming will not only promote microbial carbon turnover with direct feedback on greenhouse gases, but also unlock an unknown microbial diversity. Pioneering metagenomic efforts have shed light on the permafrost microbiome in polar regions, but temperate mountain permafrost is largely understudied. We applied a unique experimental design coupled to high-throughput sequencing of ribosomal markers to characterize the microbiota at the long-term alpine permafrost study site 'Muot-da-Barba-Peider' in eastern Switzerland with an approximate radiocarbon age of 12 000 years. Compared to the active layers, the permafrost community was more diverse and enriched with members of the superphylum Patescibacteria (OD1, TM7, GN02 and OP11). These understudied phyla with no cultured representatives proposedly feature small streamlined genomes with reduced metabolic capabilities, adaptations to anaerobic fermentative metabolisms and potential ectosymbiotic lifestyles. The permafrost microbiota was also enriched with yeasts and lichenized fungi known to harbour various structural and functional adaptation mechanisms to survive under extreme sub-zero conditions. These data yield an unprecedented view on microbial life in temperate mountain permafrost, which is increasingly important for understanding the biological dynamics of permafrost in order to anticipate potential ecological trajectories in a warming world. PMID:26832204

  2. Temperature affects microbial abundance, activity and interactions in anaerobic digestion.

    PubMed

    Lin, Qiang; De Vrieze, Jo; Li, Jiabao; Li, Xiangzhen

    2016-06-01

    Temperature is a major factor determining the performance of the anaerobic digestion process. The microbial abundance, activity and interactional networks were investigated under a temperature gradient from 25°C to 55°C through amplicon sequencing, using 16S ribosomal RNA and 16S rRNA gene-based approaches. Comparative analysis of past accumulative elements presented by 16S rRNA gene-based analysis, and the in-situ conditions presented by 16S rRNA-based analysis, provided new insights concerning the identification of microbial functional roles and interactions. The daily methane production and total biogas production increased with temperature up to 50°C, but decreased at 55°C. Increased methanogenesis and hydrolysis at 50°C were main factors causing higher methane production which was also closely related with more well-defined methanogenic and/or related modules with comprehensive interactions and increased functional orderliness referred to more microorganisms participating in interactions. This research demonstrated the importance of evaluating functional roles and interactions of microbial community. PMID:26970926

  3. Leaf Associated Microbial Activities in a Stream Affected by Acid Mine Drainage

    NASA Astrophysics Data System (ADS)

    Schlief, Jeanette

    2004-11-01

    Microbial activity was assessed on birch leaves and plastic strips during 140 days of exposure at three sites in an acidic stream of the Lusatian post-mining landscape, Germany. The sites differed in their degrees of ochre deposition and acidification. The aim of the study was (1) to follow the microbial activities during leaf colonization, (2) to compare the effect of different environmental conditions on leaf associated microbial activities, and (3) to test the microbial availability of leaf litter in acidic mining waters. The activity peaked after 49 days and subsequently decreased gradually at all sites. A formation of iron plaques on leaf surfaces influenced associated microbial activity. It seemed that these plaques inhibit the microbial availability of leaf litter and serve as a microbial habitat by itself. (

  4. Heterotrophic and Autotrophic Microbial Populations in Cold Perennial Springs of the High Arctic ▿ †

    PubMed Central

    Perreault, Nancy N.; Greer, Charles W.; Andersen, Dale T.; Tille, Stefanie; Lacrampe-Couloume, Georges; Lollar, Barbara Sherwood; Whyte, Lyle G.

    2008-01-01

    The saline springs of Gypsum Hill in the Canadian high Arctic are a rare example of cold springs originating from deep groundwater and rising to the surface through thick permafrost. The heterotrophic bacteria and autotrophic sulfur-oxidizing bacteria (up to 40% of the total microbial community) isolated from the spring waters and sediments were classified into four phyla (Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria) based on 16S rRNA gene analysis; heterotrophic isolates were primarily psychrotolerant, salt-tolerant, facultative anaerobes. Some of the isolates contained genes for thiosulfate oxidation (soxB) and anoxygenic photosynthesis (pufM), possibly enabling the strains to better compete in these sulfur-rich environments subject to long periods of illumination in the Arctic summer. Although leucine uptake by the spring water microbial community was low, CO2 uptake was relatively high under dark incubation, reinforcing the idea that primary production by chemoautotrophs is an important process in the springs. The small amounts of hydrocarbons in gases exsolving from the springs (0.38 to 0.51% CH4) were compositionally and isotopically consistent with microbial methanogenesis and possible methanotrophy. Anaerobic heterotrophic sulfur oxidation and aerobic autotrophic sulfur oxidation activities were demonstrated in sediment slurries. Overall, our results describe an active microbial community capable of sustainability in an extreme environment that experiences prolonged periods of continuous light or darkness, low temperatures, and moderate salinity, where life seems to rely on chemolithoautotrophy. PMID:18805995

  5. Biofuel intercropping effects on soil carbon and microbial activity.

    PubMed

    Strickland, Michael S; Leggett, Zakiya H; Sucre, Eric B; Bradford, Mark A

    2015-01-01

    Biofuels will help meet rising demands for energy and, ideally, limit climate change associated with carbon losses from the biosphere to atmosphere. Biofuel management must therefore maximize energy production and maintain ecosystem carbon stocks. Increasingly, there is interest in intercropping biofuels with other crops, partly because biofuel production on arable land might reduce availability and increase the price of food. One intercropping approach involves growing biofuel grasses in forest plantations. Grasses differ from trees in both their organic inputs to soils and microbial associations. These differences are associated with losses of soil carbon when grasses become abundant in forests. We investigated how intercropping switchgrass (Panicum virgalum), a major candidate for cellulosic biomass production, in loblolly pine (Pinus taeda) plantations affects soil carbon, nitrogen, and microbial dynamics. Our design involved four treatments: two pine management regimes where harvest residues (i.e., biomass) were left in place or removed, and two switchgrass regimes where the grass was grown with pine under the same two biomass scenarios (left or removed). Soil variables were measured in four 1-ha replicate plots in the first and second year following switchgrass planting. Under switchgrass intercropping, pools of mineralizable and particulate organic matter carbon were 42% and 33% lower, respectively. These declines translated into a 21% decrease in total soil carbon in the upper 15 cm of the soil profile, during early stand development. The switchgrass effect, however, was isolated to the interbed region where switchgrass is planted. In these regions, switchgrass-induced reductions in soil carbon pools with 29%, 43%, and 24% declines in mineralizable, particulate, and total soil carbon, respectively. Our results support the idea that grass inputs to forests can prime the activity of soil organic carbon degrading microbes, leading to net reductions in stocks

  6. Variation in microbial population during composting of agro-industrial waste.

    PubMed

    Coelho, Luísa; Reis, Mário; Dionísio, Lídia

    2013-05-01

    Two compost piles were prepared, using two ventilation systems: forced ventilation and ventilation through mechanical turning. The material to compost was a mixture of orange waste, olive pomace, and grass clippings (2:1:1 v/v). During the composting period (375 days), samples were periodically taken from both piles, and the enumeration of fungi, actinomycetes, and heterotrophic bacteria was carried out. All studied microorganisms were incubated at 25 and 55 °C after inoculation in appropriate growth media. Fungi were dominant in the early stages of both composting processes; heterotrophic bacteria proliferated mainly during the thermophilic stage, and actinomycetes were more abundant in the final stage of the composting process. Our results showed that the physical and chemical parameters: temperature, pH, moisture, and aeration influenced the variation of the microbial population along the composting process. This study demonstrated that composting of these types of wastes, despite the prolonged mesophilic stage, provided an expected microbial variation. PMID:22699450

  7. Geobacter, Anaeromyxobacter and Anaerolineae populations are enriched on anodes of root exudate-driven microbial fuel cells in rice field soil.

    PubMed

    Cabezas, Angela; Pommerenke, Bianca; Boon, Nico; Friedrich, Michael W

    2015-06-01

    Plant-based sediment microbial fuel cells (PMFCs) couple the oxidation of root exudates in living rice plants to current production. We analysed the composition of the microbial community on anodes from PMFC with natural rice field soil as substratum for rice by analysing 16S rRNA as an indicator of microbial activity and diversity. Terminal restriction fragment length polymorphism (TRFLP) analysis indicated that the active bacterial community on anodes from PMFCs differed strongly compared with controls. Moreover, clones related to Deltaproteobacteria and Chloroflexi were highly abundant (49% and 21%, respectively) on PMFCs anodes. Geobacter (19%), Anaeromyxobacter (15%) and Anaerolineae (17%) populations were predominant on anodes with natural rice field soil and differed strongly from those previously detected with potting soil. In open circuit (OC) control PMFCs, not allowing electron transfer, Deltaproteobacteria (33%), Betaproteobacteria (20%), Chloroflexi (12%), Alphaproteobacteria (10%) and Firmicutes (10%) were detected. The presence of an electron accepting anode also had a strong influence on methanogenic archaea. Hydrogenotrophic methanogens were more active on PMFC (21%) than on OC controls (10%), whereas acetoclastic Methanosaetaceae were more active on OC controls (31%) compared with PMFCs (9%). In conclusion, electron accepting anodes and rice root exudates selected for distinct potential anode-reducing microbial populations in rice soil inoculated PMFC. PMID:25683328

  8. Representing Microbial Dormancy in Soil Decomposition Models Improves Model Performance and Reveals Key Ecosystem Controls on Microbial Activity

    NASA Astrophysics Data System (ADS)

    He, Y.; Yang, J.; Zhuang, Q.; Wang, G.; Liu, Y.

    2014-12-01

    Climate feedbacks from soils can result from environmental change and subsequent responses of plant and microbial communities and nutrient cycling. Explicit consideration of microbial life history traits and strategy may be necessary to predict climate feedbacks due to microbial physiology and community changes and their associated effect on carbon cycling. In this study, we developed an explicit microbial-enzyme decomposition model and examined model performance with and without representation of dormancy at six temperate forest sites with observed soil efflux ranged from 4 to 10 years across different forest types. We then extrapolated the model to all temperate forests in the Northern Hemisphere (25-50°N) to investigate spatial controls on microbial and soil C dynamics. Both models captured the observed soil heterotrophic respiration (RH), yet no-dormancy model consistently exhibited large seasonal amplitude and overestimation in microbial biomass. Spatially, the total RH from temperate forests based on dormancy model amounts to 6.88PgC/yr, and 7.99PgC/yr based on no-dormancy model. However, no-dormancy model notably overestimated the ratio of microbial biomass to SOC. Spatial correlation analysis revealed key controls of soil C:N ratio on the active proportion of microbial biomass, whereas local dormancy is primarily controlled by soil moisture and temperature, indicating scale-dependent environmental and biotic controls on microbial and SOC dynamics. These developments should provide essential support to modeling future soil carbon dynamics and enhance the avenue for collaboration between empirical soil experiment and modeling in the sense that more microbial physiological measurements are needed to better constrain and evaluate the models.

  9. Large-Scale In-situ Experiments to Determine Geochemical Alterations and Microbial Activities at the Geological Repository

    NASA Astrophysics Data System (ADS)

    Choung, S.; Francis, A. J.; Um, W.; Choi, S.; Kim, S.; Park, J.; Kim, S.

    2013-12-01

    The countries that have generated nuclear power have facing problems on the disposal of accumulated radioactive wastes. Geological disposal method has been chosen in many countries including Korea. A safety issue after the closure of geological repository has been raised, because microbial activities lead overpressure in the underground facilities through gas production. In particular, biodegradable organic materials derived from low- and intermediate-level radioactive wastes play important role on microbial activities in the geological repository. This study performed large scale in-situ experiments using organic wastes and groundwater, and investigated geochemical alteration and microbial activities at early stage (~63 days) as representative of the period, after closure of the geological repository. The geochemical alteration controlled significantly the microorganism types and populations. Database of the biogeochemical alteration facilitates prediction of radionuclides' mobility and establishment of remedial strategy against unpredictable accidents and hazards at early stage right after closure of the geological repository.

  10. Quantitative Modeling of Microbial Population Responses to Chronic Irradiation Combined with Other Stressors

    PubMed Central

    Shuryak, Igor; Dadachova, Ekaterina

    2016-01-01

    Microbial population responses to combined effects of chronic irradiation and other stressors (chemical contaminants, other sub-optimal conditions) are important for ecosystem functioning and bioremediation in radionuclide-contaminated areas. Quantitative mathematical modeling can improve our understanding of these phenomena. To identify general patterns of microbial responses to multiple stressors in radioactive environments, we analyzed three data sets on: (1) bacteria isolated from soil contaminated by nuclear waste at the Hanford site (USA); (2) fungi isolated from the Chernobyl nuclear-power plant (Ukraine) buildings after the accident; (3) yeast subjected to continuous γ-irradiation in the laboratory, where radiation dose rate and cell removal rate were independently varied. We applied generalized linear mixed-effects models to describe the first two data sets, whereas the third data set was amenable to mechanistic modeling using differential equations. Machine learning and information-theoretic approaches were used to select the best-supported formalism(s) among biologically-plausible alternatives. Our analysis suggests the following: (1) Both radionuclides and co-occurring chemical contaminants (e.g. NO2) are important for explaining microbial responses to radioactive contamination. (2) Radionuclides may produce non-monotonic dose responses: stimulation of microbial growth at low concentrations vs. inhibition at higher ones. (3) The extinction-defining critical radiation dose rate is dramatically lowered by additional stressors. (4) Reproduction suppression by radiation can be more important for determining the critical dose rate, than radiation-induced cell mortality. In conclusion, the modeling approaches used here on three diverse data sets provide insight into explaining and predicting multi-stressor effects on microbial communities: (1) the most severe effects (e.g. extinction) on microbial populations may occur when unfavorable environmental

  11. Quantitative Modeling of Microbial Population Responses to Chronic Irradiation Combined with Other Stressors.

    PubMed

    Shuryak, Igor; Dadachova, Ekaterina

    2016-01-01

    Microbial population responses to combined effects of chronic irradiation and other stressors (chemical contaminants, other sub-optimal conditions) are important for ecosystem functioning and bioremediation in radionuclide-contaminated areas. Quantitative mathematical modeling can improve our understanding of these phenomena. To identify general patterns of microbial responses to multiple stressors in radioactive environments, we analyzed three data sets on: (1) bacteria isolated from soil contaminated by nuclear waste at the Hanford site (USA); (2) fungi isolated from the Chernobyl nuclear-power plant (Ukraine) buildings after the accident; (3) yeast subjected to continuous γ-irradiation in the laboratory, where radiation dose rate and cell removal rate were independently varied. We applied generalized linear mixed-effects models to describe the first two data sets, whereas the third data set was amenable to mechanistic modeling using differential equations. Machine learning and information-theoretic approaches were used to select the best-supported formalism(s) among biologically-plausible alternatives. Our analysis suggests the following: (1) Both radionuclides and co-occurring chemical contaminants (e.g. NO2) are important for explaining microbial responses to radioactive contamination. (2) Radionuclides may produce non-monotonic dose responses: stimulation of microbial growth at low concentrations vs. inhibition at higher ones. (3) The extinction-defining critical radiation dose rate is dramatically lowered by additional stressors. (4) Reproduction suppression by radiation can be more important for determining the critical dose rate, than radiation-induced cell mortality. In conclusion, the modeling approaches used here on three diverse data sets provide insight into explaining and predicting multi-stressor effects on microbial communities: (1) the most severe effects (e.g. extinction) on microbial populations may occur when unfavorable environmental

  12. Changes in the Size of the Active Microbial Pool Explain Short-Term Soil Respiratory Responses to Temperature and Moisture

    PubMed Central

    Salazar-Villegas, Alejandro; Blagodatskaya, Evgenia; Dukes, Jeffrey S.

    2016-01-01

    Heterotrophic respiration contributes a substantial fraction of the carbon flux from soil to atmosphere, and responds strongly to environmental conditions. However, the mechanisms through which short-term changes in environmental conditions affect microbial respiration still remain unclear. Microorganisms cope with adverse environmental conditions by transitioning into and out of dormancy, a state in which they minimize rates of metabolism and respiration. These transitions are poorly characterized in soil and are generally omitted from decomposition models. Most current approaches to model microbial control over soil CO2 production relate responses to total microbial biomass (TMB) and do not differentiate between microorganisms in active and dormant physiological states. Indeed, few data for active microbial biomass (AMB) exist with which to compare model output. Here, we tested the hypothesis that differences in soil microbial respiration rates across various environmental conditions are more closely related to differences in AMB (e.g., due to activation of dormant microorganisms) than in TMB. We measured basal respiration (SBR) of soil incubated for a week at two temperatures (24 and 33°C) and two moisture levels (10 and 20% soil dry weight [SDW]), and then determined TMB, AMB, microbial specific growth rate, and the lag time before microbial growth (tlag) using the Substrate-Induced Growth Response (SIGR) method. As expected, SBR was more strongly correlated with AMB than with TMB. This relationship indicated that each g active biomass C contributed ~0.04 g CO2-C h−1 of SBR. TMB responded very little to short-term changes in temperature and soil moisture and did not explain differences in SBR among the treatments. Maximum specific growth rate did not respond to environmental conditions, suggesting that the dominant microbial populations remained similar. However, warmer temperatures and increased soil moisture both reduced tlag, indicating that favorable

  13. Changes in the Size of the Active Microbial Pool Explain Short-Term Soil Respiratory Responses to Temperature and Moisture.

    PubMed

    Salazar-Villegas, Alejandro; Blagodatskaya, Evgenia; Dukes, Jeffrey S

    2016-01-01

    Heterotrophic respiration contributes a substantial fraction of the carbon flux from soil to atmosphere, and responds strongly to environmental conditions. However, the mechanisms through which short-term changes in environmental conditions affect microbial respiration still remain unclear. Microorganisms cope with adverse environmental conditions by transitioning into and out of dormancy, a state in which they minimize rates of metabolism and respiration. These transitions are poorly characterized in soil and are generally omitted from decomposition models. Most current approaches to model microbial control over soil CO2 production relate responses to total microbial biomass (TMB) and do not differentiate between microorganisms in active and dormant physiological states. Indeed, few data for active microbial biomass (AMB) exist with which to compare model output. Here, we tested the hypothesis that differences in soil microbial respiration rates across various environmental conditions are more closely related to differences in AMB (e.g., due to activation of dormant microorganisms) than in TMB. We measured basal respiration (SBR) of soil incubated for a week at two temperatures (24 and 33°C) and two moisture levels (10 and 20% soil dry weight [SDW]), and then determined TMB, AMB, microbial specific growth rate, and the lag time before microbial growth (t lag ) using the Substrate-Induced Growth Response (SIGR) method. As expected, SBR was more strongly correlated with AMB than with TMB. This relationship indicated that each g active biomass C contributed ~0.04 g CO2-C h(-1) of SBR. TMB responded very little to short-term changes in temperature and soil moisture and did not explain differences in SBR among the treatments. Maximum specific growth rate did not respond to environmental conditions, suggesting that the dominant microbial populations remained similar. However, warmer temperatures and increased soil moisture both reduced t lag , indicating that favorable

  14. Inflammasome Activity in Non-Microbial Lung Inflammation

    PubMed Central

    Ather, Jennifer L.; Martin, Rebecca A.; Ckless, Karina; Poynter, Matthew E.

    2015-01-01

    The understanding of interleukin-1 (IL-1) family cytokines in inflammatory disease has rapidly developed, due in part to the discovery and characterization of inflammasomes, which are multi-subunit intracellular protein scaffolds principally enabling recognition of a myriad of cellular stimuli, leading to the activation of caspase-1 and the processing of IL-1β and IL-18. Studies continue to elucidate the role of inflammasomes in immune responses induced by both microbes and environmental factors. This review focuses on the current understanding of inflammasome activity in the lung, with particular focus on the non-microbial instigators of inflammasome activation, including inhaled antigens, oxidants, cigarette smoke, diesel exhaust particles, mineral fibers, and engineered nanomaterials, as well as exposure to trauma and pre-existing inflammatory conditions such as metabolic syndrome. Inflammasome activity in these sterile inflammatory states contribute to diseases including asthma, chronic obstructive disease, acute lung injury, ventilator-induced lung injury, pulmonary fibrosis, and lung cancer. PMID:25642415

  15. Evaluation of Potential Impacts of Microbial Activity on Drift Chemistry

    SciTech Connect

    Y. Wang

    2004-11-18

    ''Evaluation of Potential Impacts of Microbial Activity on Drift Chemistry'' focuses on the potential for microbial communities that could be active in repository emplacement drifts to influence the in-drift bulk chemical environment. This report feeds analyses to support the inclusion or exclusion of features, events, and processes (FEPs) in the total system performance assessment (TSPA) for the license application (LA), but this work is not expected to generate direct feeds to the TSPA-LA. The purpose was specified by, and the evaluation was performed and is documented in accordance with, ''Technical Work Plan For: Near-Field Environment and Transport In-Drift Geochemistry Analyses'' (BSC 2004 [DIRS 172402], Section 2.1). This report addresses all of the FEPs assigned by the technical work plan (TWP), including the development of exclusion arguments for FEPs that are not carried forward to the TSPA-LA. Except for an editorial correction noted in Section 6.2, there were no other deviations from the TWP. This report documents the completion of all assigned tasks, as follows (BSC 2004 DIRS 172402, Section 1.2.1): (1) Perform analyses to evaluate the potential for microbial activity in the waste emplacement drift under the constraints of anticipated physical and chemical conditions. (2) Evaluate uncertainties associated with these analyses. (3) Determine whether the potential for microbes warrants a feed to TSPA-LA to account for predicted effects on repository performance. (4) Provide information to address the ''Yucca Mountain Review Plan, Final Report'' (NUREG-1804) (NRC 2003 [DIRS 163274]) and Key Technical Issues and agreements, as appropriate. (5) Develop information for inclusion or exclusion of FEPs.

  16. Microbial solar cells: applying photosynthetic and electrochemically active organisms.

    PubMed

    Strik, David P B T B; Timmers, Ruud A; Helder, Marjolein; Steinbusch, Kirsten J J; Hamelers, Hubertus V M; Buisman, Cees J N

    2011-01-01

    Microbial solar cells (MSCs) are recently developed technologies that utilize solar energy to produce electricity or chemicals. MSCs use photoautotrophic microorganisms or higher plants to harvest solar energy, and use electrochemically active microorganisms in the bioelectrochemical system to generate electrical current. Here, we review the principles and performance of various MSCs in an effort to identify the most promising systems, as well as the bottlenecks and potential solutions, for "real-life" MSC applications. We present an outlook on future applications based on the intrinsic advantages of MSCs, specifically highlighting how these living energy systems can facilitate the development of an electricity-producing green roof. PMID:21067833

  17. Chromium Isotope Behaviour During Aerobic Microbial Reduction Activities

    NASA Astrophysics Data System (ADS)

    Zhang, Q.; Amor, K.; Porcelli, D.; Thompson, I.

    2014-12-01

    Microbial activity is a very important, and possibly even the dominant, reduction mechanism for many metals in natural water systems. Isotope fractionations during microbial metal reduction can reflect one major mechanism in metal cycling in the environment, and isotopic signatures can be used to identify and quantify reduction processes during biogeochemical cycling in the present environment as well as in the past. There are many Cr (VI)-reducing bacteria that have been discovered and isolated from the environment, and Cr isotopes were found to be fractionated during microbial reduction processes. In this study, Cr reduction experiments have been undertaken to determine the conditions under which Cr is reduced and the corresponding isotope signals that are generated. The experiments have been done with a facultative bacteria Pseudomonas fluorescens LB 300, and several parameters that have potential impact on reduction mechanisms have been investigated. Electron donors are important for bacteria growth and metabolism. One factor that can control the rate of Cr reduction is the nature of the electron donor. The results show that using citrate as an electron donor can stimulate bacteria reduction activity to a large extent; the reduction rate is much higher (15.10 mgˑL-1hour-1) compared with experiments using glucose (6.65 mgˑL-1ˑhour-1), acetate (4.88 mgˑL-1hour-1) or propionate (4.85 mgˑL-1hour-1) as electron donors. Groups with higher electron donor concentrations have higher reduction rates. Chromium is toxic, and when increasing Cr concentrations in the medium, the bacteria reduction rate is also higher, which reflects bacteria adapting to the toxic environment. In the natural environment, under different pH conditions, bacteria may metabolise in different ways. In our experiments with pH, bacteria performed better in reducing Cr (VI) when pH = 8, and there are no significant differences between groups with pH = 4 or pH = 6. To investigate this further, Cr

  18. Uranium Biomineralization by Natural Microbial Phosphatase Activities in the Subsurface

    SciTech Connect

    Sobecky, Patricia A.

    2015-04-06

    In this project, inter-disciplinary research activities were conducted in collaboration among investigators at The University of Alabama (UA), Georgia Institute of Technology (GT), Lawrence Berkeley National Laboratory (LBNL), Brookhaven National Laboratory (BNL), the DOE Joint Genome Institute (JGI), and the Stanford Synchrotron Radiation Light source (SSRL) to: (i) confirm that phosphatase activities of subsurface bacteria in Area 2 and 3 from the Oak Ridge Field Research Center result in solid U-phosphate precipitation in aerobic and anaerobic conditions; (ii) investigate the eventual competition between uranium biomineralization via U-phosphate precipitation and uranium bioreduction; (iii) determine subsurface microbial community structure changes of Area 2 soils following organophosphate amendments; (iv) obtain the complete genome sequences of the Rahnella sp. Y9-602 and the type-strain Rahnella aquatilis ATCC 33071 isolated from these soils; (v) determine if polyphosphate accumulation and phytate hydrolysis can be used to promote U(VI) biomineralization in subsurface sediments; (vi) characterize the effect of uranium on phytate hydrolysis by a new microorganism isolated from uranium-contaminated sediments; (vii) utilize positron-emission tomography to label and track metabolically-active bacteria in soil columns, and (viii) study the stability of the uranium phosphate mineral product. Microarray analyses and mineral precipitation characterizations were conducted in collaboration with DOE SBR-funded investigators at LBNL. Thus, microbial phosphorus metabolism has been shown to have a contributing role to uranium immobilization in the subsurface.

  19. Metaproteomic analysis reveals microbial metabolic activities in the deep ocean

    NASA Astrophysics Data System (ADS)

    Wang, Da-Zhi; Xie, Zhang-Xian; Zhang, Shu-Feng; Wang, Ming-Hua; Zhang, Hao; Kong, Ling-Fen; Lin, Lin

    2016-04-01

    The deep sea is the largest habitat on earth and holds many and varied microbial life forms. However, little is known about their metabolic activities in the deep ocean. Here, we characterized protein profiles of particulate (>0.22 μm) and dissolved (between 10 kDa and 0.22 μm) fractions collected from the deep South China Sea using a shotgun proteomic approach. SAR324, Alteromonadales and SAR11 were the most abundant groups, while Prasinophyte contributed most to eukaryotes and cyanophage to viruses. The dominant heterotrophic activity was evidenced by the abundant transporters (33%). Proteins participating in nitrification, methanogenesis, methyltrophy and CO2 fixation were detected. Notably, the predominance of unique cellular proteins in dissolved fraction suggested the presence of membrane structures. Moreover, the detection of translation proteins related to phytoplankton indicated that other process rather than sinking particles might be the downward export of living cells. Our study implied that novel extracellular activities and the interaction of deep water with its overlying water could be crucial to the microbial world of deep sea.

  20. An ecosystem analysis of the activated sludge microbial community.

    PubMed

    Yiannakopoulou, Trissevyene V

    2010-01-01

    This study was undertaken (i) to investigate the interactions of the activated sludge microbial community in a chemostat with the "environment", such as the substrate composition and variations, (ii) to investigate how these interactions affect the quality of the treated effluent and (iii) to determine the limits or applicability conditions to the indicators and to the prediction potential of the treated effluent quality. This work presents (a) the experimental results obtained from a reactor fed municipal wastewater (Data Set2-DS2) concerning the reactor's operating conditions and the microbial community of the sludge (b) comparisons between DS2 and an older Data Set (DS1) obtained when the reactor was fed synthetic substrate, all other experimental conditions being identical, and (c) simulation results and sensitivity analyses of two model runs (R1 and R2, corresponding to DS1 and DS2). The first trophic level (P(1)) of the DS2 microbial community consisted of bacteria, the second trophic level (P(2)) of bacteria-eating protozoa, rotifers and nematodes and the third trophic level (P(3)) of carnivorous protozoa and arthropods. Rotifers were an important constituent of the DS2 microbial community. The DS1 and DS1 communities differed in total size, trophic level sizes and species composition. Correlations between the major microbial groups of DS2 community and either loading rates or effluent quality attributes were generally low, but the correlation of bacteria with SVI and ammonia in the effluent was better. Also, the ratio of rotifers to protozoa in P(2) was correlated to BOD in the effluent. The results of this work indicate that predictions of the treated effluent quality based only on protozoa may not be safe. Sensitivity analysis of R2 run indicate that, when variation in Y and K(d) biokinetic coefficients of the sludge are combined with fluctuations in composition and quality of municipal wastewater entering the reactor, then sufficient significant

  1. Promoting Physical Activity among Underserved Populations.

    PubMed

    Mendoza-Vasconez, Andrea S; Linke, Sarah; Muñoz, Mario; Pekmezi, Dori; Ainsworth, Cole; Cano, Mayra; Williams, Victoria; Marcus, Bess H; Larsen, Britta A

    2016-01-01

    Underserved populations, including racial/ethnic minorities, individuals with low socioeconomic status, and individuals with physical disabilities, are less likely to engage in sufficient moderate to vigorous physical activity (MVPA) and are thus at increased risk of morbidity and mortality. These populations face unique challenges to engaging in MVPA. Learning how to overcome these challenges is a necessary first step in achieving health equity through health promotion research. In this review of the literature, we discuss issues and strategies that have been used to promote MVPA among individuals from underserved populations, focusing on recruitment, intervention delivery, and the use of technology in interventions. Physical activity promotion research among these vulnerable populations is scarce. Nevertheless, there is preliminary evidence of efficacy in the use of certain recruitment and intervention strategies including tailoring, cultural adaptation, incorporation of new technologies, and multilevel and community-based approaches for physical activity promotion among different underserved populations. PMID:27399827

  2. Effects of repeated applications of chlorimuron-ethyl on the soil microbial biomass, activity and microbial community in the greenhouse.

    PubMed

    Xu, Jun; Zhang, Ying; Dong, Fengshou; Liu, Xingang; Wu, Xiaohu; Zheng, Yongquan

    2014-02-01

    The impacts of repeated chlorimuron-ethyl applications on soil microbial community structure and function were studied under greenhouse conditions. Chlorimuron-ethyl was applied to soil samples at three different doses [1-,10-,100-fold of recommended field rate (T1, T10, T100)] for 3 years. The half-lives of chlorimuron-ethyl were 37.1-54.6 days. The soil microbial biomass (microbial biomass carbon and total phospholipid fatty acid), the microbial activity (basal respiration and average well color development), the ratio of Gram-negative/Gram-positive bacteria and Shannon index were stimulated by chlorimuron-ethyl during the initial period. Except for T100, the other treatments recovered to the untreated level. The ratio of fungi/bacteria decreased during the initial period and then recovered in the end. Principal component analysis of phospholipid fatty acid showed that chlorimuron-ethyl altered the microbial community structure. Except got T100, T1 and T10 were not different from the control at the end of experiment. These results suggested a dosage effect of chlorimuron-ethyl on the living microbial biomass and the microbial community. PMID:24264144

  3. Effect of temperature decrease on the microbial population and process performance of a mesophilic anaerobic bioreactor.

    PubMed

    Bohn, I; Björnsson, L; Mattiasson, B

    2007-08-01

    The effect of a temperature decrease from 33 degrees C to 12 degrees C was investigated for anaerobic digestion of crop residues. A laboratory-scale reactor (R0) was inoculated with mesophilic sludge and operated as continuously stirred fed-batch system at temperatures of 12 degrees C, 18 degrees C and 33 degrees C. Changes in the microbial populations of the sludge were followed by means of fluorescence in situ hybridization analysis. Methane was produced in R0 at all temperatures. Stable long-term operation at 18 degress C was achieved yielding 151 mlCH4 gVS(added(-1) at a rate of 108 mlCH4 l(R)(-1)d(-1) once the microbial populations of the sludge had adapted to this temperature. After operation at 18 degrees C, the contents of R0 was mixed and distributed into three smaller reactors, which were operated at 18 degrees C (R18), 25 degrees C (R25) and 37 degrees C (R37), respectively. Methane production rates for R37 and R25 were 366 and 310 mlCH4 l(R)(-1)d(-1), respectively, which were higher than the 215 mlCH4 l(R)(-1)d(-1) obtained in R0 when this was operated at 33 degrees C. Hydrolysis was found to decrease when temperature was decreased and especially below 25 degrees C. At temperatures below 16 degrees C, acidogenesis and methanogenesis were the rate-limiting steps. Adaptation of the mesophilic sludge to 18 degrees C was indicated by an increase in the ratio of Bacteria to total prokaryotes (sum of Archaea and Bacteria). This was thought to be caused by enrichment of Bacteria in the sludge, which appeared to be an important adaptation mechanism. During the adaptation, the Methanomicrobiales and Methanosarcinaceae populations increased relative to the total Archaea population whereas the Methanosaeta population decreased. The population changes were reflected by reactor performance. PMID:17879853

  4. Characterization of Microbial Population Structures in Recreational Waters and Primary Sources of Fecal Pollution with a Next-Generation Sequencing Approach

    EPA Science Inventory

    The invention of new approaches to DNA sequencing commonly referred to as next generation sequencing technologies is revolutionizing the study of microbial diversity. In this chapter, we discuss the characterization of microbial population structures in recreational waters and p...

  5. ECOLOGICALLY SIGNIFICANT EFFECTS OF #PSEUDOMONAS PUTIDA# PP0103 (PR0103), GENETICALLY ENGINEERED TO DEGRADE 2,4-DICHLOROPHENOXYACETATE, ON MICROBIAL POPULATIONS AND PROCESSES IN SOIL

    EPA Science Inventory

    Genetically engineered microorganisms (GEMS) released to the environment may perturb microbial populations and their processes in soil. hanges in microbial communities, biogeochemical processes, and the physiochemical characteristics of soil might result from the introduction of ...

  6. Growth performance and intestinal microbial populations of growing pigs fed diets containing sucrose thermal oligosaccharide caramel.

    PubMed

    Orban, J I; Patterson, J A; Adeola, O; Sutton, A L; Richards, G N

    1997-01-01

    Four experiments were conducted to determine growth performance and changes in intestinal microbial populations of growing pigs fed diets containing sucrose thermal oligosaccharide caramel (STOC). Ninety-six barrows and 96 gilts were group-fed experimental nursery diets for 32 d after weaning in both Exp. 1 and 2. For each experiment, pigs were divided into four groups of 48 pigs and were fed either control, antibiotic (Apramycin sulfate, 34 mg/kg), 1% STOC, or 2% STOC diets for 32 d after weaning. Each diet was replicated six times with eight pigs per replication. Pigs were either orally gavaged (Exp 1) with water of STOC (2 g per pig) or pigs were creep-fed (Exp 2) either a control diet or a 2% STOC diet for 5 d before weaning (33 d). At the end of Exp 1 and 2, cecal material was collected for enumeration of total aerobes, total anaerobes, coliforms, lactobacilli, and bifidobacteria. Gilts (96 per experiment) used in Exp. 3 and 4 were weaned at 26 d and fed experimental nursery diets for 32 d. They were fed either a control or 1% STOC diet and were otherwise treated as previously described. There were no significant effects of STOC or antibiotic on ADG, ADFI, feed efficiency, or cecal microbial populations in pigs in this study. Feeding diets containing either antibiotic of STOC did not improve animal performance or change intestinal bacterial populations in the present study. PMID:9027562

  7. Unsupervised discovery of microbial population structure within metagenomes using nucleotide base composition

    PubMed Central

    Saeed, Isaam; Tang, Sen-Lin; Halgamuge, Saman K.

    2012-01-01

    An approach to infer the unknown microbial population structure within a metagenome is to cluster nucleotide sequences based on common patterns in base composition, otherwise referred to as binning. When functional roles are assigned to the identified populations, a deeper understanding of microbial communities can be attained, more so than gene-centric approaches that explore overall functionality. In this study, we propose an unsupervised, model-based binning method with two clustering tiers, which uses a novel transformation of the oligonucleotide frequency-derived error gradient and GC content to generate coarse groups at the first tier of clustering; and tetranucleotide frequency to refine these groups at the secondary clustering tier. The proposed method has a demonstrated improvement over PhyloPythia, S-GSOM, TACOA and TaxSOM on all three benchmarks that were used for evaluation in this study. The proposed method is then applied to a pyrosequenced metagenomic library of mud volcano sediment sampled in southwestern Taiwan, with the inferred population structure validated against complementary sequencing of 16S ribosomal RNA marker genes. Finally, the proposed method was further validated against four publicly available metagenomes, including a highly complex Antarctic whale-fall bone sample, which was previously assumed to be too complex for binning prior to functional analysis. PMID:22180538

  8. Effect of pyrene and cadmium on microbial activity and community structure in soil.

    PubMed

    Lu, Mang; Xu, Kui; Chen, Jun

    2013-04-01

    In this study, a greenhouse experiment was conducted to investigate interactive effects of cadmium (Cd) × pyrene × plant treatments on soil microbial activity and community structure. The results demonstrated that the basal respiration, microbial biomass carbon and metabolic quotient in both unplanted and rhizosphere soil were significantly influenced by interaction of Cd and pyrene. The combined application of Cd and pyrene caused a significantly greater biocidal influence on the soil microorganisms than the single spiking of Cd or pyrene. The soil basal respiration increased with the spiking of 2.5 mg kg(-1) Cd in both unplanted and rhizosphere soil. The eco-physiological index of Cd-tolerant populations was significantly different among the unplanted soil, rhizoplane and rhizosphere soil of tall fescue, indicating a slightly uneven distribution of fast- and slow-growing tolerant bacteria. Obvious differences in microbial activity were observed among treatments due to different physicochemical characteristics of the rhizosphere soils depending on the plant species. PMID:23290945

  9. Nanocalorimetric Characterization of Microbial Activity in Deep Subsurface Oceanic Crustal Fluids

    PubMed Central

    Robador, Alberto; LaRowe, Douglas E.; Jungbluth, Sean P.; Lin, Huei-Ting; Rappé, Michael S.; Nealson, Kenneth H.; Amend, Jan P.

    2016-01-01

    Although fluids within the upper oceanic basaltic crust harbor a substantial fraction of the total prokaryotic cells on Earth, the energy needs of this microbial population are unknown. In this study, a nanocalorimeter (sensitivity down to 1.2 nW ml-1) was used to measure the enthalpy of microbially catalyzed reactions as a function of temperature in samples from two distinct crustal fluid aquifers. Microorganisms in unamended, warm (63°C) and geochemically altered anoxic fluids taken from 292 meters sub-basement (msb) near the Juan de Fuca Ridge produced 267.3 mJ of heat over the course of 97 h during a step-wise isothermal scan from 35.5 to 85.0°C. Most of this heat signal likely stems from the germination of thermophilic endospores (6.66 × 104 cells ml-1FLUID) and their subsequent metabolic activity at temperatures greater than 50°C. The average cellular energy consumption (5.68 pW cell-1) reveals the high metabolic potential of a dormant community transported by fluids circulating through the ocean crust. By contrast, samples taken from 293 msb from cooler (3.8°C), relatively unaltered oxic fluids, produced 12.8 mJ of heat over the course of 14 h as temperature ramped from 34.8 to 43.0°C. Corresponding cell-specific energy turnover rates (0.18 pW cell-1) were converted to oxygen uptake rates of 24.5 nmol O2 ml-1FLUID d-1, validating previous model predictions of microbial activity in this environment. Given that the investigated fluids are characteristic of expansive areas of the upper oceanic crust, the measured metabolic heat rates can be used to constrain boundaries of habitability and microbial activity in the oceanic crust. PMID:27092118

  10. Nanocalorimetric Characterization of Microbial Activity in Deep Subsurface Oceanic Crustal Fluids.

    PubMed

    Robador, Alberto; LaRowe, Douglas E; Jungbluth, Sean P; Lin, Huei-Ting; Rappé, Michael S; Nealson, Kenneth H; Amend, Jan P

    2016-01-01

    Although fluids within the upper oceanic basaltic crust harbor a substantial fraction of the total prokaryotic cells on Earth, the energy needs of this microbial population are unknown. In this study, a nanocalorimeter (sensitivity down to 1.2 nW ml(-1)) was used to measure the enthalpy of microbially catalyzed reactions as a function of temperature in samples from two distinct crustal fluid aquifers. Microorganisms in unamended, warm (63°C) and geochemically altered anoxic fluids taken from 292 meters sub-basement (msb) near the Juan de Fuca Ridge produced 267.3 mJ of heat over the course of 97 h during a step-wise isothermal scan from 35.5 to 85.0°C. Most of this heat signal likely stems from the germination of thermophilic endospores (6.66 × 10(4) cells ml(-1) FLUID) and their subsequent metabolic activity at temperatures greater than 50°C. The average cellular energy consumption (5.68 pW cell(-1)) reveals the high metabolic potential of a dormant community transported by fluids circulating through the ocean crust. By contrast, samples taken from 293 msb from cooler (3.8°C), relatively unaltered oxic fluids, produced 12.8 mJ of heat over the course of 14 h as temperature ramped from 34.8 to 43.0°C. Corresponding cell-specific energy turnover rates (0.18 pW cell(-1)) were converted to oxygen uptake rates of 24.5 nmol O2 ml(-1) FLUID d(-1), validating previous model predictions of microbial activity in this environment. Given that the investigated fluids are characteristic of expansive areas of the upper oceanic crust, the measured metabolic heat rates can be used to constrain boundaries of habitability and microbial activity in the oceanic crust. PMID:27092118

  11. Study on Biodegradation Process of Polyethylene Glycol with Exponential Glowth of Microbial Population

    NASA Astrophysics Data System (ADS)

    Watanabe, Masaji; Kawai, Fusako

    Biodegradation of polyethylene glycol is studied mathematically. A mathematical model for depolymerization process of exogenous type is described. When a degradation rate is a product of a time factor and a molecular factor, a time dependent model can be transformed into a time independent model, and techniques developed in previous studies can be applied to the time independent model to determine the molecular factor. The time factor can be determined assuming the exponential growth of the microbial population. Those techniques are described, and numerical results are presented. A comparison between a numerical result and an experimental result shows that the mathematical method is appropriate for practical applications.

  12. Uncharted Microbial World: Microbes and Their Activities in the Environment

    SciTech Connect

    Harwood, Caroline; Buckley, Merry.

    2007-12-31

    Microbes are the foundation for all of life. From the air we breathe to the soil we rely on for farming to the water we drink, everything humans need to survive is intimately coupled with the activities of microbes. Major advances have been made in the understanding of disease and the use of microorganisms in the industrial production of drugs, food products and wastewater treatment. However, our understanding of many complicated microbial environments (the gut and teeth), soil fertility, and biogeochemical cycles of the elements is lagging behind due to their enormous complexity. Inadequate technology and limited resources have stymied many lines of investigation. Today, most environmental microorganisms have yet to be isolated and identified, let alone rigorously studied. The American Academy of Microbiology convened a colloquium in Seattle, Washington, in February 2007, to deliberate the way forward in the study of microorganisms and microbial activities in the environment. Researchers in microbiology, marine science, pathobiology, evolutionary biology, medicine, engineering, and other fields discussed ways to build on and extend recent successes in microbiology. The participants made specific recommendations for targeting future research, improving methodologies and techniques, and enhancing training and collaboration in the field. Microbiology has made a great deal of progress in the past 100 years, and the useful applications for these new discoveries are numerous. Microorganisms and microbial products are now used in industrial capacities ranging from bioremediation of toxic chemicals to probiotic therapies for humans and livestock. On the medical front, studies of microbial communities have revealed, among other things, new ways for controlling human pathogens. The immediate future for research in this field is extremely promising. In order to optimize the effectiveness of community research efforts in the future, scientists should include manageable

  13. Ecological distribution and population physiology defined by proteomics in a natural microbial community

    USGS Publications Warehouse

    Mueller, Ryan S.; Denef, Vincent J.; Kalnejais, Linda H.; Suttle, K. Blake; Thomas, Brian C.; Wilmes, Paul; Smith, Richard L.; Nordstrom, D Kirk; McCleskey, R. Blaine; Shah, Menesh B.; VerBekmoes, Nathan C.; Hettich, Robert L.; Banfield, Jillian F.

    2010-01-01

    An important challenge in microbial ecology is developing methods that simultaneously examine the physiology of organisms at the molecular level and their ecosystem level interactions in complex natural systems. We integrated extensive proteomic, geochemical, and biological information from 28 microbial communities collected from an acid mine drainage environment and representing a range of biofilm development stages and geochemical conditions to evaluate how the physiologies of the dominant and less abundant organisms change along environmental gradients. The initial colonist dominates across all environments, but its proteome changes between two stable states as communities diversify, implying that interspecies interactions affect this organism's metabolism. Its overall physiology is robust to abiotic environmental factors, but strong correlations exist between these factors and certain subsets of proteins, possibly accounting for its wide environmental distribution. Lower abundance populations are patchier in their distribution, and proteomic data indicate that their environmental niches may be constrained by specific sets of abiotic environmental factors. This research establishes an effective strategy to investigate ecological relationships between microbial physiology and the environment for whole communities in situ.

  14. Ecological distribution and population physiology defined by proteomics in a natural microbial community

    PubMed Central

    Mueller, Ryan S; Denef, Vincent J; Kalnejais, Linda H; Suttle, K Blake; Thomas, Brian C; Wilmes, Paul; Smith, Richard L; Nordstrom, D Kirk; McCleskey, R Blaine; Shah, Manesh B; VerBerkmoes, Nathan C; Hettich, Robert L; Banfield, Jillian F

    2010-01-01

    An important challenge in microbial ecology is developing methods that simultaneously examine the physiology of organisms at the molecular level and their ecosystem level interactions in complex natural systems. We integrated extensive proteomic, geochemical, and biological information from 28 microbial communities collected from an acid mine drainage environment and representing a range of biofilm development stages and geochemical conditions to evaluate how the physiologies of the dominant and less abundant organisms change along environmental gradients. The initial colonist dominates across all environments, but its proteome changes between two stable states as communities diversify, implying that interspecies interactions affect this organism's metabolism. Its overall physiology is robust to abiotic environmental factors, but strong correlations exist between these factors and certain subsets of proteins, possibly accounting for its wide environmental distribution. Lower abundance populations are patchier in their distribution, and proteomic data indicate that their environmental niches may be constrained by specific sets of abiotic environmental factors. This research establishes an effective strategy to investigate ecological relationships between microbial physiology and the environment for whole communities in situ. PMID:20531404

  15. Ecological distribution and population physiology defined by proteomics in a natural microbial community

    SciTech Connect

    Muller, R; Denef, Vincent; Kalnejals, Linda; Suttle, K Blake; Thomas, Brian; Wilmes, P; Smith, Richard L.; Nordstrom, D Kirk; McCleskey, R Blaine; Shah, Manesh B; Verberkmoes, Nathan C; Hettich, Robert {Bob} L; Banfield, Jillian F.

    2010-01-01

    An important challenge in microbial ecology is developing methods that simultaneously examine the physiology of organisms at the molecular level and their ecosystem level interactions in complex natural systems.We integrated extensive proteomic, geochemical, and biological information from 28 microbial communities collected from an acid mine drainage environment and representing a range of biofilm development stages and geochemical conditions to evaluate how the physiologies of the dominant and less abundant organisms change along environmental gradients. The initial colonist dominates across all environments, but its proteome changes between two stable states as communities diversify, implying that interspecies interactions affect this organism s metabolism. Its overall physiology is robust to abiotic environmental factors, but strong correlations exist between these factors and certain subsets of proteins, possibly accounting for its wide environmental distribution. Lower abundance populations are patchier in their distribution, and proteomic data indicate that their environmental niches may be constrained by specific sets of abiotic environmental factors. This research establishes an effective strategy to investigate ecological relationships between microbial physiology and the environment for whole communities in situ

  16. Development of a microbial population within a hot-drinks vending machine and the microbial load of vended hot chocolate drink.

    PubMed

    Hall, A; Short, K; Saltmarsh, M; Fielding, L; Peters, A

    2007-09-01

    In order to understand the development of the microbial population within a hot-drinks vending machine a new machine was placed in a staff area of a university campus vending only hot chocolate. The machine was cleaned weekly using a detergent based protocol. Samples from the mixing bowl, dispense area, and drink were taken over a 19-wk period and enumerated using plate count agar. Bacillus cereus was identified using biochemical methods. Vended drinks were sampled at 0, 3, 6, and 9 min after vending; the hot chocolate powder was also sampled. Over the 1st 8 wk, a significant increase in the microbial load of the machine components was observed. By the end of the study, levels within the vended drink had also increased significantly. Inactivation of the automatic flush over a subsequent 5-wk period led to a statistically but not operationally significant increase in the microbial load of the dispense area and vended drink. The simple weekly clean had a significant impact on the microbial load of the machine components and the vended drink. This study demonstrated that a weekly, detergent-based cleaning protocol was sufficient to maintain the microbial population of the mixing bowl and dispense point in a quasi-steady state below 3.5 log CFU/cm2 ensuring that the microbial load of the vended drinks was maintained below 3.4 log CFU/mL. The microbial load of the drinks showed no significant changes over 9 min after vending, suggesting only spores are present in the final product. PMID:17995650

  17. Molecular Analysis of Surfactant-Driven Microbial Population Shifts in Hydrocarbon-Contaminated Soil†

    PubMed Central

    Colores, Gregory M.; Macur, Richard E.; Ward, David M.; Inskeep, William P.

    2000-01-01

    We analyzed the impact of surfactant addition on hydrocarbon mineralization kinetics and the associated population shifts of hydrocarbon-degrading microorganisms in soil. A mixture of radiolabeled hexadecane and phenanthrene was added to batch soil vessels. Witconol SN70 (a nonionic, alcohol ethoxylate) was added in concentrations that bracketed the critical micelle concentration (CMC) in soil (CMC′) (determined to be 13 mg g−1). Addition of the surfactant at a concentration below the CMC′ (2 mg g−1) did not affect the mineralization rates of either hydrocarbon. However, when surfactant was added at a concentration approaching the CMC′ (10 mg g−1), hexadecane mineralization was delayed and phenanthrene mineralization was completely inhibited. Addition of surfactant at concentrations above the CMC′ (40 mg g−1) completely inhibited mineralization of both phenanthrene and hexadecane. Denaturing gradient gel electrophoresis of 16S rRNA gene segments showed that hydrocarbon amendment stimulated Rhodococcus and Nocardia populations that were displaced by Pseudomonas and Alcaligenes populations at elevated surfactant levels. Parallel cultivation studies revealed that the Rhodococcus population can utilize hexadecane and that the Pseudomonas and Alcaligenes populations can utilize both Witconol SN70 and hexadecane for growth. The results suggest that surfactant applications necessary to achieve the CMC alter the microbial populations responsible for hydrocarbon mineralization. PMID:10877792

  18. Mapping the Centimeter-Scale Spatial Variability of PAHs and Microbial Populations in the Rhizosphere of Two Plants.

    PubMed

    Bourceret, Amélia; Leyval, Corinne; de Fouquet, Chantal; Cébron, Aurélie

    2015-01-01

    Rhizoremediation uses root development and exudation to favor microbial activity. Thus it can enhance polycyclic aromatic hydrocarbon (PAH) biodegradation in contaminated soils. Spatial heterogeneity of rhizosphere processes, mainly linked to the root development stage and to the plant species, could explain the contrasted rhizoremediation efficiency levels reported in the literature. Aim of the present study was to test if spatial variability in the whole plant rhizosphere, explored at the centimetre-scale, would influence the abundance of microorganisms (bacteria and fungi), and the abundance and activity of PAH-degrading bacteria, leading to spatial variability in PAH concentrations. Two contrasted rhizospheres were compared after 37 days of alfalfa or ryegrass growth in independent rhizotron devices. Almost all spiked PAHs were degraded, and the density of the PAH-degrading bacterial populations increased in both rhizospheres during the incubation period. Mapping of multiparametric data through geostatistical estimation (kriging) revealed that although root biomass was spatially structured, PAH distribution was not. However a greater variability of the PAH content was observed in the rhizosphere of alfalfa. Yet, in the ryegrass-planted rhizotron, the Gram-positive PAH-degraders followed a reverse depth gradient to root biomass, but were positively correlated to the soil pH and carbohydrate concentrations. The two rhizospheres structured the microbial community differently: a fungus-to-bacterium depth gradient similar to the root biomass gradient only formed in the alfalfa rhizotron. PMID:26599438

  19. Mapping the Centimeter-Scale Spatial Variability of PAHs and Microbial Populations in the Rhizosphere of Two Plants

    PubMed Central

    Bourceret, Amélia; Leyval, Corinne; de Fouquet, Chantal; Cébron, Aurélie

    2015-01-01

    Rhizoremediation uses root development and exudation to favor microbial activity. Thus it can enhance polycyclic aromatic hydrocarbon (PAH) biodegradation in contaminated soils. Spatial heterogeneity of rhizosphere processes, mainly linked to the root development stage and to the plant species, could explain the contrasted rhizoremediation efficiency levels reported in the literature. Aim of the present study was to test if spatial variability in the whole plant rhizosphere, explored at the centimetre-scale, would influence the abundance of microorganisms (bacteria and fungi), and the abundance and activity of PAH-degrading bacteria, leading to spatial variability in PAH concentrations. Two contrasted rhizospheres were compared after 37 days of alfalfa or ryegrass growth in independent rhizotron devices. Almost all spiked PAHs were degraded, and the density of the PAH-degrading bacterial populations increased in both rhizospheres during the incubation period. Mapping of multiparametric data through geostatistical estimation (kriging) revealed that although root biomass was spatially structured, PAH distribution was not. However a greater variability of the PAH content was observed in the rhizosphere of alfalfa. Yet, in the ryegrass-planted rhizotron, the Gram-positive PAH-degraders followed a reverse depth gradient to root biomass, but were positively correlated to the soil pH and carbohydrate concentrations. The two rhizospheres structured the microbial community differently: a fungus-to-bacterium depth gradient similar to the root biomass gradient only formed in the alfalfa rhizotron. PMID:26599438

  20. Flow cytometry and cell sorting of heterogeneous microbial populations: the importance of single-cell analyses.

    PubMed Central

    Davey, H M; Kell, D B

    1996-01-01

    The most fundamental questions such as whether a cell is alive, in the sense of being able to divide or to form a colony, may sometimes be very hard to answer, since even axenic microbial cultures are extremely heterogeneous. Analyses that seek to correlate such things as viability, which is a property of an individual cell, with macroscopic measurements of culture variables such as ATP content, respiratory activity, and so on, must inevitably fail. It is therefore necessary to make physiological measurements on individual cells. Flow cytometry is such a technique, which allows one to analyze cells rapidly and individually and permits the quantitative analysis of microbial heterogeneity. It therefore offers many advantages over conventional measurements for both routine and more exploratory analyses of microbial properties. While the technique has been widely applied to the study of mammalian cells, is use in microbiology has until recently been much more limited, largely because of the smaller size of microbes and the consequently smaller optical signals obtainable from them. Since these technical barriers no longer hold, flow cytometry with appropriate stains has been used for the rapid discrimination and identification of microbial cells, for the rapid assessment of viability and of the heterogeneous distributions of a wealth of other more detailed physiological properties, for the analysis of antimicrobial drug-cell interactions, and for the isolation of high-yielding strains of biotechnological interest. Flow cytometric analyses provide an abundance of multivariate data, and special methods have been devised to exploit these. Ongoing advances mean that modern flow cytometers may now be used by nonspecialists to effect a renaissance in our understanding of microbial heterogeneity. PMID:8987359

  1. Microbial biomass and activity in soils with different moisture content heated at high temperatures

    NASA Astrophysics Data System (ADS)

    Barreiro, Ana; Lombao, Alba; Martin, Angela; Cancelo-González, Javier; Carballas, Tarsy; Díaz-Raviña, Montserrat

    2015-04-01

    It is well known that soil properties determining the thermal transmissivity (moisture, texture, organic matter, etc.) and the duration and temperatures reached during soil heating are key factors driving the fire-induced changes in soil microbial communities. However, despite its interest, the information about this topic is scarce. The aim of the present study is to analyze, under laboratory conditions, the impact of the thermal shock (infrared lamps reaching temperatures of 100 °C, 200 °C and 400 °C) on microbial communities of three acid soils under different moisture level (0 %, 25 % and 50 % per soil volume). Soil temperature was measured with thermocouples and the impact of soil heating was evaluated by means of the analysis of the temperature-time curves calculating the maximum temperature reached (Tmax) and the degree-hours (GH) as an estimation of the amount of heat supplied to the samples (fire severity). The bacterial growth (leucine incorporation) and the total microbial biomass (PLFA) were measured immediately after the heating and one month after the incubation of reinoculated soils. The results showed clearly the importance of moisture level in the transmission of heat through the soil and hence in the further direct impact of high temperatures on microorganisms living in soil. In general, the values of microbial parameters analyzed were low, particularly immediately after soil heating at higher temperatures; the bacterial activity measurements (leucine incorporation technique) being more sensitive to detect the thermal shock showed than total biomass measurements (PLFA). After 1 month incubation, soil microbial communities tend to recover due to the proliferation of surviving population using as substrate the dead microorganisms (soil sterilization). Thus, time elapsed after the heating was found to be decisive when examining the relationships between the microbial properties and the soil heating parameters (GH, Tmax). Analysis of results also

  2. Geophysical Monitoring of Microbial Activity within a Wetland Soil

    NASA Astrophysics Data System (ADS)

    O'Brien, M.; Zhang, C.; Ntarlagiannis, D.; Slater, L.; Yee, N.

    2007-05-01

    We performed Induced Polarization (IP) and Self Potential (SP) measurements to record the geoelectrical signatures of microbial activity within a wetland soil. The experiment was conducted in laboratory, utilizing an open flow column set up. Soil samples from Kearny Marsh (KM), a shallow water wetland, were collected and stored at 4o Celsius prior to the start of the experiment. Two columns were dry packed with a mix of KM soil and sterile Ottawa sand (50% by weight). One column was sterilized and used as a control while the other column retained the biologically active soil sample. Both columns were saturated with a minimal salts medium capable of supporting microbial life; after saturation, a steady flow rate of one pore volume per day was maintained throughout the experiment. Ambient temperature and pressure changes (at the inflow and outflow of each column) were continuously monitored throughout the experiment. Common geochemical parameters, such as Eh, pH, and fluid conductivity were measured at the inflow and outflow of each column at regular intervals. IP and SP responses were continuously recorded on both columns utilizing a series of electrodes along the column length; additionally for the SP measurements we used a reference electrode at the inflow tube. Strong SP anomalies were observed for all the locations along the active column. Black visible mineral precipitant also formed in the active column. The observed precipitation coincided with the times that SP anomalies developed at each electrode position. These responses are associated with microbial induced sulfide mineralization. We interpret the SP signal as the result of redox processes associated with this mineralization driven by gradients in ionic concentration and mobility within the column, similar to a galvanic cell mechanism. IP measurements show no correlation with these visual and SP responses. Destructive analysis of the samples followed the termination of the experiment. Scanning electron

  3. Microbial population and functional dynamics associated with surface potential and carbon metabolism

    PubMed Central

    Ishii, Shun'ichi; Suzuki, Shino; Norden-Krichmar, Trina M; Phan, Tony; Wanger, Greg; Nealson, Kenneth H; Sekiguchi, Yuji; Gorby, Yuri A; Bretschger, Orianna

    2014-01-01

    Microbial extracellular electron transfer (EET) to solid surfaces is an important reaction for metal reduction occurring in various anoxic environments. However, it is challenging to accurately characterize EET-active microbial communities and each member's contribution to EET reactions because of changes in composition and concentrations of electron donors and solid-phase acceptors. Here, we used bioelectrochemical systems to systematically evaluate the synergistic effects of carbon source and surface redox potential on EET-active microbial community development, metabolic networks and overall electron transfer rates. The results indicate that faster biocatalytic rates were observed under electropositive electrode surface potential conditions, and under fatty acid-fed conditions. Temporal 16S rRNA-based microbial community analyses showed that Geobacter phylotypes were highly diverse and apparently dependent on surface potentials. The well-known electrogenic microbes affiliated with the Geobacter metallireducens clade were associated with lower surface potentials and less current generation, whereas Geobacter subsurface clades 1 and 2 were associated with higher surface potentials and greater current generation. An association was also observed between specific fermentative phylotypes and Geobacter phylotypes at specific surface potentials. When sugars were present, Tolumonas and Aeromonas phylotypes were preferentially associated with lower surface potentials, whereas Lactococcus phylotypes were found to be closely associated with Geobacter subsurface clades 1 and 2 phylotypes under higher surface potential conditions. Collectively, these results suggest that surface potentials provide a strong selective pressure, at the species and strain level, for both solid surface respirators and fermentative microbes throughout the EET-active community development. PMID:24351938

  4. Specific microbial populations thrive under fluctuating redox conditions in tropical soils

    NASA Astrophysics Data System (ADS)

    Deangelis, K. M.; Silver, W. L.; Thompson, A.; Firestone, M. K.

    2008-12-01

    The highly weathered soils of upland humid tropical forests are characterized by rapidly fluctuating redox conditions, dominated by Fe-oxide mineralogy, and have relatively low sulfate availability. To assess how fluctuating redox conditions and accompanying biogeochemistry impact microbial community structure and function, we collected soil cores from the Luquillo LTER forest in Puerto Rico and incubated them for 32 days under one of three redox regimes: static oxic, static anoxic, and 4-day fluctuating redox. Over this time course we measured CO2, CH4, and N2O production, amorphous iron and Fe(II), and microbial community structure by high density microarray (PhyloChip) analysis. Static oxic, anoxic, and fluctuating redox soils all had statistically indistinguishable respiration rates over the course of the experiment. Fluctuating redox conditions permitted simultaneous methanogenesis, N2O production, and iron reduction, all accompanied by steady CO2 production. We analyzed the standing and active microbial community using the 16S ribosomal DNA and RNA biomarkers, identifying 2489 taxa in these soils. Ordination analysis showed significant separation between the active (RNA-based) and standing (DNA-based) communities, with much more variation in the active community compared to the standing community. Fluctuating redox conditions maintained a microbial community structure similar to that of the pre-incubation samples, while static anaerobic conditions had the most profound effect on the communities. Finally, there was considerable overlap between the taxa that were the most highly correlated with production of CH4 and Fe(II). Association of groups of taxa with specific biogeochemical processes begins to identify organisms potentially responsible for field biogeochemical processing.

  5. Influence of benomyl and prometryn on the soil microbial activities and community structures in pasture grasslands of Slovakia.

    PubMed

    Javoreková, Sona; Svrceková, Ivana; Maková, Jana

    2010-10-01

    The effects of pesticides (a herbicide and a fungicide) on the microbial community structure and their activity were analyzed in soil from four alpine pasture grasslands in Slovakia. Specifically, the effects of the herbicide, Gesagard (prometryn active ingredient), and fungicide, Fundazol 50 WP (benomyl active ingredient), on the microbial respiration activity (CO2 production), the numbers of selective microbial physiological groups (CFU.g(-1)) and the structure (relative abundance) of soil microbial communities [(phospholipid fatty acid (PLFA)] were analyzed under controlled laboratory conditions. All treatments including the treatments with pesticides increased (statistically significantly) the production of CO2 in all fields during 21 days of incubation and posed a statistically insignificant negative influence on the numbers of the observed physiological groups of microorganisms. The significantly negative influence was evaluated only in the numbers of two physiological groups; spores of bacteria utilizing organic nitrogen and bacteria, and their spores utilizing inorganic nitrogen. A shift in the microbial composition was evident when the PLFA patterns of samples from different sites and treatments were compared by the Principal Component Analysis (PCA). According to the second component PCA 2 (15.95 %) the locations were grouped into two clusters. The first one involved the Donovaly and Dubakovo sites and the second one contained the Velka Fatra and Mala Fatra locations. The PLFA composition of the soils showed important changes after the treatment with pesticides according to PCA 1 (66.06 %). Other treatments had not had a significant effect on the soil microbial community with the exception of the population of fungi. The lower relative abundance (significant effect) of Gram-positive bacteria, actinomycetes and general group of bacteria were determined in samples treated by the herbicide Gesagard. The application of fungicide Fundazol decreased

  6. Influence of the activity of Allobophora molleri in microbial activity and metal availability of arsenic-polluted soils.

    PubMed

    Tejada, Manuel; Gómez, Isidoro; Hernández, Teresa; García, Carlos

    2013-10-01

    We investigate the use of Allolobophora molleri as a biomarker of arsenic (As)-polluted soils and study the influence of A. molleri on the metabolic activity and microbial biodiversity of soil polluted with As. Because there are no experimental data available regarding the effect of the pollutant rate of As on A. molleri, we determined the LC₅₀ that was 143.5 mg As kg(-1). Sodium arsenite was added at two rates, equivalent to 143.5 and 71.8 mg As kg(-1) soil, to a soil that was then maintained with and without worms for 120 days. In addition, a nonpolluted soil without and with earthworms was used as the control. The As concentration in the soil was measured after 7 and 120 and the worm weight and As concentration after 120 days of exposure. Soil enzymatic activities and the structure of the soil microbial community, by analysis of phospholipid fatty acids, were determined. At the end of the experiment, the highest earthworm As contents were found in soils polluted with the highest rate of As. Earthworm weights significantly decreased in soil polluted with 143.5 or 71.8 mg As kg(-1), by 49.9 and 29.8% of initial weight, because the worm consumption rate decreased. These results suggest that A. molleri can be used as a good biomarker of the As toxicity. The As available fraction decreased in polluted soil with worms because the metal was accumulated in worm tissues. However, this assimilation was lower than other worms such as L. rubbellus or L. terrestris. Soil enzymatic activities were decreased in As-polluted soils but were increased significantly by the presence of earthworms. The earthworms modified the soil microbial diversity. In this respect, A. molleri significantly increased (p < 0.05) the bacterial and fungal populations. Soil As pollution decreased microbial biodiversity but to a lesser extent in the presence of A. molleri. PMID:23703122

  7. Mapping Microbial Populations Relative to Sites of Ongoing Serpentinization: Results from the Tablelands Ophiolite Complex, Canada

    NASA Astrophysics Data System (ADS)

    Schrenk, M. O.; Brazelton, W. J.; Woodruff, Q.; Szponar, N.; Morrill, P. L.

    2010-12-01

    The aqueous alteration of ultramafic rocks (serpentinization) has been suggested to be a favorable process for the habitability of astrobodies in our solar system including subsurface environments of Mars and Europa. Serpentinization produces copious quantities of hydrogen and small organic molecules, and leads to highly reducing, highly alkaline conditions (up to pH 12) and a lack of dissolved inorganic carbon, which both stimulates and challenges microbial activities. Several environments on Earth provide insight into the relationships between serpentinization and microbial life including slow-spreading mid-ocean ridges, subduction zones, and ophiolite materials emplaced along continental margins. The Tablelands, an ophiolite in western Newfoundland, Canada provides an opportunity to carefully document and map the relationships between geochemical energy, microbial growth, and physiology. Alkaline fluids at the Tablelands originate from 500-million year old oceanic crust and accumulate in shallow pools or seep from beneath serpentinized talus. Fluids, rocks, and gases were collected from the Tablelands during a series of field excursions in 2009 and 2010, and geochemical, microscopic, molecular, and cultivation-based approaches were used to study the serpentinite microbial ecosystem. These samples provide an opportunity to generate a comprehensive map of microbial communities and their activities in space and time. Data indicate that a low but detectable stock of microorganisms inhabit high pH pools associated with end-member serpentinite fluids. Enrichment cultures yielded brightly pigmented colonies related to Alphaproteobacteria, presumably carrying out anoxygenic photosynthesis, and Firmicutes, presumably catalyzing the fermentation of organic matter. Culture-independent analyses of SSU rRNA using T-RFLP indicated low diversity communities of Firmicutes and Archaea in standing alkaline pools, communities of Beta- and Gammaproteobacteria at high pH seeps, and

  8. Microbial Activation of Wooden Vats Used for Traditional Cheese Production and Evolution of Neoformed Biofilms

    PubMed Central

    Gaglio, Raimondo; Cruciata, Margherita; Di Gerlando, Rosalia; Scatassa, Maria Luisa; Cardamone, Cinzia; Mancuso, Isabella; Sardina, Maria Teresa; Moschetti, Giancarlo; Portolano, Baldassare

    2015-01-01

    Three Lactococcus lactis subsp. cremoris strains were used to develop ad hoc biofilms on the surfaces of virgin wooden vats used for cheese production. Two vats (TZ) were tested under controlled conditions (pilot plant), and two vats (TA) were tested under uncontrolled conditions (industrial plant). In each plant, one vat (TA1 and TZ1) was used for the control, traditional production of PDO Vastedda della Valle del Belìce (Vastedda) cheese, and one (TA2 and TZ2) was used for experimental production performed after lactococcal biofilm activation and the daily addition of a natural whey starter culture (NWSC). Microbiological and scanning electron microscopy analyses showed differences in terms of microbial levels and composition of the neoformed biofilms. The levels of the microbial groups investigated during cheese production showed significant differences between the control trials and between the control and experimental trials, but the differences were not particularly marked between the TA2 and TZ2 productions, which showed the largest numbers of mesophilic lactic acid bacterium (LAB) cocci. LAB populations were characterized phenotypically and genotypically, and 44 dominant strains belonging to 10 species were identified. Direct comparison of the polymorphic profiles of the LAB collected during cheese making showed that the addition of the NWSC reduced their biodiversity. Sensory evaluation showed that the microbial activation of the wooden vats with the multistrain Lactococcus culture generated cheeses with sensory attributes comparable to those of commercial cheese. Thus, neoformed biofilms enable a reduction of microbial variability and stabilize the sensorial attributes of Vastedda cheese. PMID:26546430

  9. Uranium Biomineralization by Natural Microbial Phosphatase Activities in the Subsurface

    NASA Astrophysics Data System (ADS)

    Martinez, R.; Wu, C. H.; Beazley, M. J.; Andersen, G. L.; Hazen, T. C.; Taillefert, M.; Sobecky, P. A.

    2011-12-01

    Soils and groundwater contaminated with heavy metals and radionuclides remain a legacy of Cold War nuclear weapons development. Due to the scale of environmental contamination, in situ sequestration of heavy metals and radionuclides remain the most cost-effective strategy for remediation. We are currently investigating a remediation approach that utilizes periplasmic and extracellular microbial phosphatase activity of soil bacteria capable promoting in situ uranium phosphate sequestration. Our studies focus on the contaminated soils from the DOE Field Research Center (ORFRC) in Oak Ridge, TN. We have previously demonstrated that ORFRC strains with phosphatase-positive phenotypes were capable of promoting the precpitation of >95% U(VI) as a low solubility phosphate mineral during growth on glycerol phosphate as a sole carbon and phosphorus source. Here we present culture-independent soil slurry studies aimed at understanding microbial community dynamics resulting from exogenous organophosphate additions. Soil slurries containing glycerol-2-phosphate (G2P) or glycerol-3-phosphate (G3P) and nitrate as the sole C, P and N sources were incubated under oxic growth conditions at pH 5.5 or pH 6.8. Following treatments, total DNA was extracted and prokaryotic diversity was assessed using high-density 16S oligonucleotide microarray (PhyloChip) analysis. Treatments at pH 5.5 and pH 6.8 amended with G2P required 36 days to accumulate 4.8mM and 2.2 mM phosphate, respectively. In contrast, treatments at pH 5.5 and pH 6.8 amended with G3P accumulated 8.9 mM and 8.7 mM phosphate, respectively, after 20 days. A total of 2120 unique taxa representing 46 phyla, 66 classes, 110 orders, and 186 families were detected among all treatment conditions. The phyla that significantly (P<0.05) increased in abundance relative to incubations lacking organophosphate amendments included: Crenarchaeota, Euryarchaeota, Bacteroidetes, and Proteobacteria. Members from the classes Bacteroidetes

  10. Archaeal populations in hypersaline sediments underlying orange microbial mats in the Napoli mud volcano.

    PubMed

    Lazar, Cassandre Sara; L'haridon, Stéphane; Pignet, Patricia; Toffin, Laurent

    2011-05-01

    Microbial mats in marine cold seeps are known to be associated with ascending sulfide- and methane-rich fluids. Hence, they could be visible indicators of anaerobic oxidation of methane (AOM) and methane cycling processes in underlying sediments. The Napoli mud volcano is situated in the Olimpi Area that lies on saline deposits; from there, brine fluids migrate upward to the seafloor. Sediments associated with a brine pool and microbial orange mats of the Napoli mud volcano were recovered during the Medeco cruise. Based on analysis of RNA-derived sequences, the "active" archaeal community was composed of many uncultured lineages, such as rice cluster V or marine benthic group D. Function methyl coenzyme M reductase (mcrA) genes were affiliated with the anaerobic methanotrophic Archaea (ANME) of the ANME-1, ANME-2a, and ANME-2c groups, suggesting that AOM occurred in these sediment layers. Enrichment cultures showed the presence of viable marine methylotrophic Methanococcoides in shallow sediment layers. Thus, the archaeal community diversity seems to show that active methane cycling took place in the hypersaline microbial mat-associated sediments of the Napoli mud volcano. PMID:21335391

  11. Microbial populations stimulated for hexavalent uranium reduction in uranium mine sediment.

    SciTech Connect

    Suzuki, Y.; Kelly, S. D.; Kemner, K. M.; Banfield, J. F.; Environmental Research; Univ. of Wisconsin-Madison; Univ. of California-Berkeley

    2003-03-01

    Uranium-contaminated sediment and water collected from an inactive uranium mine were incubated anaerobically with organic substrates. Stimulated microbial populations removed U almost entirely from solution within 1 month. X-ray absorption near-edge structure analysis showed that U(VI) was reduced to U(IV) during the incubation. Observations by transmission electron microscopy, selected area diffraction pattern analysis, and energy-dispersive X-ray spectroscopic analysis showed two distinct types of prokaryotic cells that precipitated only a U(IV) mineral uraninite (UO{sub 2}) or both uraninite and metal sulfides. Prokaryotic cells associated with uraninite and metal sulfides were inferred to be sulfate-reducing bacteria. Phylogenetic analysis of 16S ribosomal DNA obtained from the original and incubated sediments revealed that microbial populations were changed from microaerophilic Proteobacteria to anaerobic low-G+C gram-positive sporeforming bacteria by the incubation. Forty-two out of 94 clones from the incubated sediment were related to sulfate-reducing Desulfosporosinus spp., and 23 were related to fermentative Clostridium spp. The results suggest that, if in situ bioremediation were attempted in the uranium mine ponds, Desulfosporosinus spp. would be a major contributor to U(VI) and sulfate reduction and Clostridium spp. to U(VI) reduction.

  12. Microbial Populations Stimulated for Hexavalent Uranium Reduction in Uranium Mine Sediment

    PubMed Central

    Suzuki, Yohey; Kelly, Shelly D.; Kemner, Kenneth M.; Banfield, Jillian F.

    2003-01-01

    Uranium-contaminated sediment and water collected from an inactive uranium mine were incubated anaerobically with organic substrates. Stimulated microbial populations removed U almost entirely from solution within 1 month. X-ray absorption near-edge structure analysis showed that U(VI) was reduced to U(IV) during the incubation. Observations by transmission electron microscopy, selected area diffraction pattern analysis, and energy-dispersive X-ray spectroscopic analysis showed two distinct types of prokaryotic cells that precipitated only a U(IV) mineral uraninite (UO2) or both uraninite and metal sulfides. Prokaryotic cells associated with uraninite and metal sulfides were inferred to be sulfate-reducing bacteria. Phylogenetic analysis of 16S ribosomal DNA obtained from the original and incubated sediments revealed that microbial populations were changed from microaerophilic Proteobacteria to anaerobic low-G+C gram-positive sporeforming bacteria by the incubation. Forty-two out of 94 clones from the incubated sediment were related to sulfate-reducing Desulfosporosinus spp., and 23 were related to fermentative Clostridium spp. The results suggest that, if in situ bioremediation were attempted in the uranium mine ponds, Desulfosporosinus spp. would be a major contributor to U(VI) and sulfate reduction and Clostridium spp. to U(VI) reduction. PMID:12620814

  13. Effects of different sources of physically effective fiber on rumen microbial populations.

    PubMed

    Shaw, C N; Kim, M; Eastridge, M L; Yu, Z

    2016-03-01

    Physically effective fiber is needed by dairy cattle to prevent ruminal acidosis. This study aimed to examine the effects of different sources of physically effective fiber on the populations of fibrolytic bacteria and methanogens. Five ruminally cannulated Holstein cows were each fed five diets differing in physically effective fiber sources over 15 weeks (21 days/period) in a Latin Square design: (1) 44.1% corn silage, (2) 34.0% corn silage plus 11.5% alfalfa hay, (3) 34.0% corn silage plus 5.1% wheat straw, (4) 36.1% corn silage plus 10.1% wheat straw, and (5) 34.0% corn silage plus 5.5% corn stover. The impact of the physically effective fiber sources on total bacteria and archaea were examined using denaturing gradient gel electrophoresis. Specific real-time PCR assays were used to quantify total bacteria, total archaea, the genus Butyrivibrio, Fibrobacter succinogenes, Ruminococcus albus, Ruminococcus flavefaciens and three uncultured rumen bacteria that were identified from adhering ruminal fractions in a previous study. No significant differences were observed among the different sources of physical effective fiber with respect to the microbial populations quantified. Any of the physically effective fiber sources may be fed to dairy cattle without negative impact on the ruminal microbial community. PMID:26365790

  14. Roots shaping their microbiome: global hotspots for microbial activity.

    PubMed

    Reinhold-Hurek, Barbara; Bünger, Wiebke; Burbano, Claudia Sofía; Sabale, Mugdha; Hurek, Thomas

    2015-01-01

    Land plants interact with microbes primarily at roots. Despite the importance of root microbial communities for health and nutrient uptake, the current understanding of the complex plant-microbe interactions in the rhizosphere is still in its infancy. Roots provide different microhabitats at the soil-root interface: rhizosphere soil, rhizoplane, and endorhizosphere. We discuss technical aspects of their differentiation that are relevant for the functional analysis of their different microbiomes, and we assess PCR (polymerase chain reaction)-based methods to analyze plant-associated bacterial communities. Development of novel primers will allow a less biased and more quantitative view of these global hotspots of microbial activity. Based on comparison of microbiome data for the different root-soil compartments and on knowledge of bacterial functions, a three-step enrichment model for shifts in community structure from bulk soil toward roots is presented. To unravel how plants shape their microbiome, a major research field is likely to be the coupling of reductionist and molecular ecological approaches, particularly for specific plant genotypes and mutants, to clarify causal relationships in complex root communities. PMID:26243728

  15. Microbial Population Differentials between Mucosal and Submucosal Intestinal Tissues in Advanced Crohn's Disease of the Ileum

    PubMed Central

    Chiodini, Rodrick J.; Dowd, Scot E.; Chamberlin, William M.; Galandiuk, Susan; Davis, Brian; Glassing, Angela

    2015-01-01

    Since Crohn's disease is a transmural disease, we hypothesized that examination of deep submucosal tissues directly involved in the inflammatory disease process may provide unique insights into bacterial populations transgressing intestinal barriers and bacterial populations more representative of the causes and agents of the disease. We performed deep 16s microbiota sequencing on isolated ilea mucosal and submucosal tissues on 20 patients with Crohn's disease and 15 non-inflammatory bowel disease controls with a depth of coverage averaging 81,500 sequences in each of the 70 DNA samples yielding an overall resolution down to 0.0001% of the bacterial population. Of the 4,802,328 total sequences generated, 98.9% or 4,749,183 sequences aligned with the Kingdom Bacteria that clustered into 8545 unique sequences with <3% divergence or operational taxonomic units enabling the identification of 401 genera and 698 tentative bacterial species. There were significant differences in all taxonomic levels between the submucosal microbiota in Crohn's disease compared to controls, including organisms of the Order Desulfovibrionales that were present within the submucosal tissues of most Crohn's disease patients but absent in the control group. A variety of organisms of the Phylum Firmicutes were increased in the subjacent submucosa as compared to the parallel mucosal tissue including Ruminococcus spp., Oscillospira spp., Pseudobutyrivibrio spp., and Tumebacillus spp. In addition, Propionibacterium spp. and Cloacibacterium spp. were increased as well as large increases in Proteobacteria including Parasutterella spp. and Methylobacterium spp. This is the first study to examine the microbial populations within submucosal tissues of patients with Crohn's disease and to compare microbial communities found deep within the submucosal tissues with those present on mucosal surfaces. Our data demonstrate the existence of a distinct submucosal microbiome and ecosystem that is not well

  16. Promoting Uranium Immobilization by the Activities of Microbial Phosphatases

    SciTech Connect

    Martinez, Robert J.; Beazley, Melanie J.; Wilson, Jarad J.; Taillefert, Martial; Sobecky, Patricia A.

    2005-04-05

    amplified phosphatases are being analyzed to determine whether or not there is evidence for the horizontal transfer of such genes amongst subsurface microbial populations. Microbially precipitated U(VI) phosphate minerals will be further analyzed via capillary electrophoresis and extended x-ray absorption fine structure spectroscopy to determine uranium speciation.

  17. Microbial Biomass and Population Densities of Non-Sorted Circles in High Arctic Ecosystems

    NASA Astrophysics Data System (ADS)

    Rivera-Figueroa, F.; González, G.; Gould, W. A.; Cantrell, S.; Pérez, J.

    2006-12-01

    Non-sorted circles are small patterned-ground features that occur in arctic soils as a result of intensive frost heave action. This tundra feature has been extensively described. However, little is known about the ecological relationships between this pattern and above- and belowground organisms. In this study, we compare the biomass and populaton densities of microbes in non-sorted circles and the vegetated surrounding soils (inter-circles) in the High Arctic. We collected soil samples during the summer of 2004 and 2005 on Banks and Prince Patrick and Ellef Ringnes Islands, Canada. Soil samples (0-10 cm) were gathered from non- sorted circles and inter-circles along a topographic sequence: dry (ridge), mesic (mid slope) and wet (valley) and along three transects in zonal (mesic) sites on each island. We estimated total microbial biomass and bacterial population densities using substrate induce respiration (SIR) and the most probable number method (MPN), respectively. We also isolated soil fungi using Rose Bengal and Saboraud Dextrose culture media. We are in the process of analyzing the catena samples using a terminal restriction fragment length polymorphism (TRFLP) technique of PCR-amplified 16S rRNA. Based on the SIR trials, the average microbial biomass at the mid slope position in the Banks site (Green Cabin) was 0.49 mg C g-1 dry soil in the non- sorted circles and 0.95 mg C g-1 dry soil in the inter-circles. At Prince Patrick Island (Mould Bay) the microbial biomass was 0.54 mg C g-1 dry soil in the non-sorted circles and 0.74 mg C g-1 dry soil in the inter-circles. In Ellef Ringnes (Isachsen) the microbial biomass was 0.09 mg C g-1 dry soil in the non- sorted circles and 0.14 mg C g-1 dry soil in the inter-circles. At the mesic site at Green Cabin, bacteria vary from 2.92 x 106 cell g-1 dry soil in the non-sorted circles to 6.74 x 106 cell g-1 dry soil in the inter-circles. At Mould Bay the range was 7.67 x 105 cells g-1 dry soil in the non-sorted circles

  18. Impact of Nano-Silver Exposure on Microbial Activity

    NASA Astrophysics Data System (ADS)

    Morales, V. L.; Braga, R. A., Jr.; Spiers, A. J.

    2012-04-01

    A key gap in environmental impact assessments of emerging contaminants is the change in biological activity of microorganisms exposed to toxic substances. Silver-nanoparticles are among the top cytotoxic nanomaterials suspected to threaten microbial functions of natural and engineered systems. In this study, a novel light-interference technique termed 'bio-speckle' is employed to determine real-time biological activity of monocultures and biologically complex samples. Bio-speckle uses laser illumination of biological samples to create interference patterns of the scattered light that can be used to quantify intracellular organelle movement as a measurement of biological activity. To test the potential of bio-speckle technique for toxicity assays, filter paper microcosms of the model environmental bacterium Pseudomonas fluorescens strain SBW25 were exposed to uncoated nano-silver suspensions for 2, 24, 48, and 72 hours. At the end of each exposure period, biological activity was quantitatively determined as the dynamic speckle pattern's moment of inertia. Results suggest that the biological activity of bacteria decreases exponentially with the time of exposure of the colonies to the silver nanoparticles.

  19. Promoting uranium immobilization by the activities of microbial phophatases

    SciTech Connect

    Sobecky, Patricia A.

    2005-06-01

    The first objective of this project is to determine the relationship of phosphatase activity to metal resistance in subsurface strains and the role of lateral gene transfer (LGT) in dissemination of nonspecific acid phosphatase genes. Nonspecific acid phosphohydrolases are a broad group of secreted microbial phosphatases that function in acidic-to-neutral pH ranges and utilize a wide range of organophosphate substrates. We have previously shown that PO43- accumulation during growth on a model organophosphorus compound was attributable to the overproduction of alkaline phosphatase by genetically modified subsurface pseudomonads [Powers et al. (2002) FEMS Microbiol. Ecol. 41:115-123]. During this report period, we have extended these results to include indigenous metal resistant subsurface microorganisms cultivated from the Field Research Center (FRC), in Oak Ridge Tennessee.

  20. Quantification of Microbial Activities in Near-Surface Soils

    NASA Astrophysics Data System (ADS)

    Schroth, M. H.; Nauer, P.; Zeyer, J.

    2007-12-01

    Microbial processes in near-surface soils play an important role in carbon and nutrient cycling, and specifically in the turnover of greenhouse gases such as CO2 and CH4. We modified a recently developed technique, the gas push-pull test (GPPT), to allow for the in-situ quantification of microbial activities in near-surface soils. A GPPT consists of the controlled injection of a gas mixture containing reactive gases (e.g., CH4, O2, CO2) and nonreactive tracer gases (e.g., Ar, Ne) into the soil, followed by the extraction of the gas mixture/soil-air blend from the same location. Rates of microbial activities are computed from the gases" breakthrough curves obtained during the GPPT's extraction phase. For a GPPT to be applied successfully, it is important that sufficient mass of the injected gases can be recovered during the test, even after prolonged incubation in soil. But this may be difficult to achieve during GPPTs performed in near- surface soils, where gas loss to the atmosphere can be substantial. Our modification consisted of performing GPPTs within a steel cylinder (8.4-cm radius), which was previously driven into the soil to a depth of 50 cm. During the GPPTs, the cylinder was temporarily closed with a removable lid to minimize gas loss to the atmosphere. We performed a series of numerical simulations as well as laboratory experiments to test the usefulness of this modification. Numerical simulations confirmed that without use of the cylinder, typical near- surface GPPTs (e.g., injection/extraction depth 20 cm below soil surface) are subject to extensive gas loss to the atmosphere (mass recovery < 20% for most gases), whereas mass recovery of injected gases increased dramatically when the cylinder was employed (mass recovery > 90% for most gases). Results from laboratory experiments confirmed this observation. We will also present results of a first field application, in which a near- surface GPPT was successfully conducted in a sandy soil to quantify in

  1. In vitro utilization of gold and green kiwifruit oligosaccharides by human gut microbial populations.

    PubMed

    Parkar, Shanthi G; Rosendale, Doug; Paturi, Gunaranjan; Herath, Thanuja D; Stoklosinski, Halina; Phipps, Janet E; Hedderley, Duncan; Ansell, Juliet

    2012-09-01

    We examined the effects of whole kiwifruit on gut microbiota using an in vitro batch model of gastric-ileal digestion and colonic fermentation. Faecal fermentations of gold and green kiwifruit, inulin and water (control) digests were performed for up to 48 h. As compared to the control, gold and green kiwifruit increased Bifidobacterium spp. by 0.9 and 0.8 log(10) cfu/ml, respectively (P < 0.001), and the Bacteroides-Prevotella-Porphyromonas group by 0.4 and 0.5 log(10) cfu/ml, respectively. Inulin only had a bifidogenic effect (+0.4 log(10) cfu/ml). This was accompanied with increases in microbial glycosidases, especially those with substrate specificities relating to the breakdown of kiwifruit oligosaccharides, and with increased generation of short chain fatty acids. The microbial metabolic activity was sustained for up to 48 h, which we attribute to the complexity of the carbohydrate substrate provided by whole kiwifruit. Kiwifruit fermenta supernatant was also separately shown to affect the in vitro proliferation of Bifidobacterium longum, and its adhesion to Caco-2 intestinal epithelial cells. Collectively, these data suggest that whole kiwifruit may modulate human gut microbial composition and metabolism to produce metabolites conducive to increased bifidobacteria-host association. PMID:22576129

  2. Electrodic voltages in the presence of dissolved sulfide: Implications for monitoring natural microbial activity

    SciTech Connect

    Slater, L.; Ntarlagiannis, D.; Yee, N.; O'Brien, M.; Zhang, C.; Williams, K. H.

    2008-10-01

    There is growing interest in the development of new monitoring strategies for obtaining spatially extensive data diagnostic of microbial processes occurring in the earth. Open-circuit potentials arising from variable redox conditions in the fluid local-to-electrode surfaces (electrodic potentials) were recorded for a pair of silver-silver chloride electrodes in a column experiment, whereby a natural wetland soil containing a known community of sulfate reducers was continuously fed with a sulfate-rich nutrient medium. Measurements were made between five electrodes equally spaced along the column and a reference electrode placed on the column inflow. The presence of a sulfate reducing microbial population, coupled with observations of decreasing sulfate levels, formation of black precipitate (likely iron sulfide),elevated solid phase sulfide, and a characteristic sulfurous smell, suggest microbial-driven sulfate reduction (sulfide generation) in our column. Based on the known sensitivity of a silver electrode to dissolved sulfide concentration, we interpret the electrodic potentials approaching 700 mV recorded in this experiment as an indicator of the bisulfide (HS-) concentration gradients in the column. The measurement of the spatial and temporal variation in these electrodic potentials provides a simple and rapid method for monitoring patterns of relative HS- concentration that are indicative of the activity of sulfate-reducing bacteria. Our measurements have implications both for the autonomous monitoring of anaerobic microbial processes in the subsurface and the performance of self-potential electrodes, where it is critical to isolate, and perhaps quantify, electrochemical interfaces contributing to observed potentials.

  3. Range expansions transition from pulled to pushed waves as growth becomes more cooperative in an experimental microbial population.

    PubMed

    Gandhi, Saurabh R; Yurtsev, Eugene Anatoly; Korolev, Kirill S; Gore, Jeff

    2016-06-21

    Range expansions are becoming more frequent due to environmental changes and rare long-distance dispersal, often facilitated by anthropogenic activities. Simple models in theoretical ecology explain many emergent properties of range expansions, such as a constant expansion velocity, in terms of organism-level properties such as growth and dispersal rates. Testing these quantitative predictions in natural populations is difficult because of large environmental variability. Here, we used a controlled microbial model system to study range expansions of populations with and without intraspecific cooperativity. For noncooperative growth, the expansion dynamics were dominated by population growth at the low-density front, which pulled the expansion forward. We found these expansions to be in close quantitative agreement with the classical theory of pulled waves by Fisher [Fisher RA (1937) Ann Eugen 7(4):355-369] and Skellam [Skellam JG (1951) Biometrika 38(1-2):196-218], suitably adapted to our experimental system. However, as cooperativity increased, the expansions transitioned to being pushed, that is, controlled by growth and dispersal in the bulk as well as in the front. Given the prevalence of cooperative growth in nature, understanding the effects of cooperativity is essential to managing invading species and understanding their evolution. PMID:27185918

  4. Range expansions transition from pulled to pushed waves as growth becomes more cooperative in an experimental microbial population

    PubMed Central

    Yurtsev, Eugene Anatoly; Korolev, Kirill S.; Gore, Jeff

    2016-01-01

    Range expansions are becoming more frequent due to environmental changes and rare long-distance dispersal, often facilitated by anthropogenic activities. Simple models in theoretical ecology explain many emergent properties of range expansions, such as a constant expansion velocity, in terms of organism-level properties such as growth and dispersal rates. Testing these quantitative predictions in natural populations is difficult because of large environmental variability. Here, we used a controlled microbial model system to study range expansions of populations with and without intraspecific cooperativity. For noncooperative growth, the expansion dynamics were dominated by population growth at the low-density front, which pulled the expansion forward. We found these expansions to be in close quantitative agreement with the classical theory of pulled waves by Fisher [Fisher RA (1937) Ann Eugen 7(4):355–369] and Skellam [Skellam JG (1951) Biometrika 38(1-2):196–218], suitably adapted to our experimental system. However, as cooperativity increased, the expansions transitioned to being pushed, that is, controlled by growth and dispersal in the bulk as well as in the front. Given the prevalence of cooperative growth in nature, understanding the effects of cooperativity is essential to managing invading species and understanding their evolution. PMID:27185918

  5. High throughput sequencing reveals distinct microbial populations within the mucosal and luminal niches in healthy individuals

    PubMed Central

    Ringel, Yehuda; Maharshak, Nitsan; Ringel-Kulka, Tamar; Wolber, Elizabeth Ashley; Sartor, R Balfour; Carroll, Ian M

    2015-01-01

    Background: The intestinal microbiota is associated with human health and diseases. The luminal microbiota (LM) and the mucosal-associated microbiota (MAM) are 2 distinct ecosystems with different metabolic and immunological functions. Aim: To characterize the intestinal LM and MAM in humans using high throughput sequencing of the 16S rRNA gene. Methods: Fresh fecal samples and distal colonic mucosal biopsies collected from 24 healthy subjects before (fecal) and during (mucosa) a flexible sigmoidoscopy of an un-prepared bowel. High throughput sequencing of the 16S rRNA gene was used to characterize bacterial communities. Sequences were processed using the QIIME pipeline. Results: LM and MAM populations were significantly different (ANOSIM: R = 0.49, P = 0.001). The LM displayed tighter clustering compared to the MAM (average weighted UniFrac distances 0.27 ± 0.05 vs. 0.43 ± 0.09, P < 0.001, respectively), and showed higher diversity (Shannon diversity index: 4.96 ± 0.37 vs 4.14 ± 0.56, respectively, P < 0.001). The dominant phyla in the LM and MAM were significantly different: Firmicutes (41.4% vs. 29.1%, FDR < 0.0001, respectively), Bacteroidetes (20.2% vs. 26.3%, FDR < 0.05, respectively), Actinobacteria (22% vs. 12.6%, FDR < 0.0001, respectively) and Proteobacteria (9.3% vs. 19.3%, FDR < 0.0001, respectively). The abundance of 56 genera differed significantly (FDR < 0.1) between the 2 niches. All of the genera in the fecal microbiota were present in the MAM while 10 genera were found to be unique to the MAM. Conclusion: The LM and MAM are distinct microbial ecosystems that differ significantly from each other in microbial diversity and composition. These two microbial niches should be investigated independently to better understand the role of the intestinal microbiota in health and disease. PMID:25915459

  6. Distribution of microbial populations and their relationship with environmental variables in the North Yellow Sea, China

    NASA Astrophysics Data System (ADS)

    Bai, Xiaoge; Wang, Min; Liang, Yantao; Zhang, Zhifeng; Wang, Fang; Jiang, Xuejiao

    2012-03-01

    In order to understand the large-scale spatial distribution characteristics of picoplankton, nanophytoplankton and virioplankton and their relationship with environmental variables in coastal and offshore waters, flow cytometry (FCM) was used to analyze microbial abundance of samples collected in summer from four depths at 36 stations in the North Yellow Sea (NYS). The data revealed spatial heterogeneity in microbial populations in the offshore and near-shore waters of the NYS during the summer. For the surface layer, picoeukaryotes were abundant in the near-shore waters, Synechococcus was abundant in the offshore areas, and bacterial and viral abundances were high in the near-shore waters around the Liaodong peninsula. In the near-shore waters, no significant vertical variation of picophytoplankton (0.2-2μm) abundance was found. However, the nanophytoplankton abundance was higher in the upper layers (from the surface to 10 m depth) than in the bottom layer. For the offshore waters, both pico- and nanophytoplankton (2-20μm) abundance decreased sharply with depth in the North Yellow Sea Cold Water Mass (NYSCWM). But, for the vertical distribution of virus and bacteria abundance, no significant variation was observed in both near-shore and offshore waters. Autotrophic microbes were more sensitive to environmental change than heterotrophic microbes and viruses. Viruses showed a positive correlation with bacterial abundance, suggesting that the bacteriophage might be prominent for virioplankton (about 0.45μm) in summer in the NYS and that viral abundance might play an important role in microbial loop functions.

  7. Correlating microbial community compositions with environmental factors in activated sludge from four full-scale municipal wastewater treatment plants in Shanghai, China.

    PubMed

    Gao, Pin; Xu, Wenli; Sontag, Philip; Li, Xiang; Xue, Gang; Liu, Tong; Sun, Weimin

    2016-05-01

    Activated sludge system is an important process of domestic and industrial wastewater treatment containing highly diverse microbial communities. In this study, high-throughput sequencing was applied to examine the microbial community composition and diversity of activated sludge samples from four full-scale municipal wastewater treatment plants (WWTPs) in Shanghai. A relationship between microbial communities and environmental variables was examined. Proteobacteria was the most dominant phylogenetic group, followed by Bacteroidetes and Firmicutes. A total of 166 genera were commonly shared by all seven sludge samples, including Zoogloea, Dechloromonas, Thauera, Nitrospira, Arcobacter, etc. Besides these shared populations, certain unique bacterial populations were found abundant in individual sludge sample. Canonical correspondence analysis (CCA) indicated that influent COD and pH had the greatest influence on microbial community compositions, whereas dissolved oxygen (DO) exhibited the least influence. The operating process was likely to foster diversity of the microbial communities inhabiting the wastewater treatment facilities. Alternative operation methods including a fluctuation of anoxic, oxic, and anaerobic conditions were favorable for promoting the growth of diverse microbial populations in activated sludge systems. PMID:26795962

  8. Long-term effects of timber harvesting on hemicellulolytic microbial populations in coniferous forest soils.

    PubMed

    Leung, Hilary T C; Maas, Kendra R; Wilhelm, Roland C; Mohn, William W

    2016-02-01

    Forest ecosystems need to be sustainably managed, as they are major reservoirs of biodiversity, provide important economic resources and modulate global climate. We have a poor knowledge of populations responsible for key biomass degradation processes in forest soils and the effects of forest harvesting on these populations. Here, we investigated the effects of three timber-harvesting methods, varying in the degree of organic matter removal, on putatively hemicellulolytic bacterial and fungal populations 10 or more years after harvesting and replanting. We used stable-isotope probing to identify populations that incorporated (13)C from labeled hemicellulose, analyzing (13)C-enriched phospholipid fatty acids, bacterial 16 S rRNA genes and fungal ITS regions. In soil microcosms, we identified 104 bacterial and 52 fungal hemicellulolytic operational taxonomic units (OTUs). Several of these OTUs are affiliated with taxa not previously reported to degrade hemicellulose, including the bacterial genera Methylibium, Pelomonas and Rhodoferax, and the fungal genera Cladosporium, Pseudeurotiaceae, Capronia, Xenopolyscytalum and Venturia. The effect of harvesting on hemicellulolytic populations was evaluated based on in situ bacterial and fungal OTUs. Harvesting treatments had significant but modest long-term effects on relative abundances of hemicellulolytic populations, which differed in strength between two ecozones and between soil layers. For soils incubated in microcosms, prior harvesting treatments did not affect the rate of incorporation of hemicellulose carbon into microbial biomass. In six ecozones across North America, distributions of the bacterial hemicellulolytic OTUs were similar, whereas distributions of fungal ones differed. Our work demonstrates that diverse taxa in soil are hemicellulolytic, many of which are differentially affected by the impact of harvesting on environmental conditions. However, the hemicellulolytic capacity of soil communities appears

  9. Acinetobacter, Aeromonas, and Trichococcus populations dominate the microbial community within urban sewer infrastructure

    PubMed Central

    VandeWalle, J. L.; Goetz, G.W.; Huse, S.M.; Morrison, H. G.; Sogin, M.L.; Hoffmann, R.G.; Yan, K.; McLellan, S.L.

    2012-01-01

    We evaluated the population structure and temporal dynamics of the dominant community members within sewage influent from two wastewater treatment plants (WWTPs) in Milwaukee, WI. We generated >1.1M bacterial pyrotag sequences from the V6 hypervariable region of 16S rRNA genes from 38 influent samples and two samples taken upstream in the sanitary sewer system. Only a small fraction of pyrotags from influent samples (~15%) matched sequences from human fecal samples. The fecal components of the sewage samples included enriched pyrotag populations from Lactococcus and Enterobacteriaceae relative to their fractional representation in human fecal samples. In contrast to the large number of distinct pyrotags that represent fecal bacteria such as Lachnospiraceae and Bacteroides, only one or two unique V6 sequences represented Acinetobacter, Trichococcus and Aeromonas, which collectively account for nearly 35% of the total sewage community. Two dominant Acinetobacter V6 pyrotags (designated Acineto tag 1 and Acineto tag 2) fluctuated inversely with a seasonal pattern over a 3-year period, suggesting two distinct Acinetobacter populations respond differently to ecological forcings in the system. A single nucleotide change in the V6 pyrotags accounted for the difference in these populations and corresponded to two phylogenically distinct clades based on full-length sequences. Analysis of wavelet functions, derived from a mathematical model of temporal fluctuations, demonstrated that other abundant sewer associated populations including Trichococcus and Aeromonas had temporal patterns similar to either Acineto tag 1 or Acineto tag 2. Populations with related temporal fluctuations were found to significantly correlate with the same WWTP variables (5-day BOD, flow, ammonia, total phosphorous, and suspended solids). These findings illustrate that small differences in V6 sequences can represent phylogenetically and ecologically distinct taxa. This work provides insight into

  10. 2009 MICROBIAL POPULATION BIOLOGY GORDON RESEARCH CONFERENCES JULY 19-24,2009

    SciTech Connect

    ANTHONY DEAN

    2009-07-24

    The 2009 Gordon Conference on Microbial Population Biology will cover a diverse range of cutting edge issues in the microbial sciences and beyond. Firmly founded in evolutionary biology and with a strongly integrative approach, past Conferences have covered a range of topics from the dynamics and genetics of adaptation to the evolution of mutation rate, community ecology, evolutionary genomics, altruism, and epidemiology. The 2009 Conference is no exception, and will include sessions on the evolution of infectious diseases, social evolution, the evolution of symbioses, experimental evolution, adaptive landscapes, community dynamics, and the evolution of protein structure and function. While genomic approaches continue to make inroads, broadening our knowledge and encompassing new questions, the conference will also emphasize the use of experimental approaches to test hypotheses decisively. As in the past, this Conference provides young scientists and graduate students opportunities to present their work in poster format and exchange ideas with leading investigators from a broad spectrum of disciplines. This meeting is never dull: some of the most significant and contentious issues in biology have been thrashed out here. The 2009 meeting will be no exception.

  11. Ecological differentiation in planktonic and sediment-associated chemotrophic microbial populations in Yellowstone hot springs.

    PubMed

    Colman, Daniel R; Feyhl-Buska, Jayme; Robinson, Kirtland J; Fecteau, Kristopher M; Xu, Huifang; Shock, Everett L; Boyd, Eric S

    2016-09-01

    Chemosynthetic sediment and planktonic community composition and sizes, aqueous geochemistry and sediment mineralogy were determined in 15 non-photosynthetic hot springs in Yellowstone National Park (YNP). These data were used to evaluate the hypothesis that differences in the availability of dissolved or mineral substrates in the bulk fluids or sediments within springs coincides with ecologically differentiated microbial communities and their populations. Planktonic and sediment-associated communities exhibited differing ecological characteristics including community sizes, evenness and richness. pH and temperature influenced microbial community composition among springs, but within-spring partitioning of taxa into sediment or planktonic communities was widespread, statistically supported (P < 0.05) and could be best explained by the inferred metabolic strategies of the partitioned taxa. Microaerophilic genera of the Aquificales predominated in many of the planktonic communities. In contrast, taxa capable of mineral-based metabolism such as S(o) oxidation/reduction or Fe-oxide reduction predominated in sediment communities. These results indicate that ecological differentiation within thermal spring habitats is common across a range of spring geochemistry and is influenced by the availability of dissolved nutrients and minerals that can be used in metabolism. PMID:27306555

  12. Directed Evolution of Metabolic Pathways in Microbial Populations. I. Modification of the Acid Phosphatase Ph Optimum in S. CEREVISIAE

    PubMed Central

    Francis, J. C.; Hansche, P. E.

    1972-01-01

    An experimental system for directing the evolution of enzymes and metabolic pathways in microbial populations is proposed and an initial test of its power is provided.—The test involved an attempt to genetically enhance certain functional properties of the enzyme acid phosphatase in S. cerevisiae by constructing an environment in which the functional changes desired would be "adaptive". Naturally occurring mutations in a population of 109 cells were automatically and continuously screened, over 1,000 generations, for their effect on the efficiency (Km) and activity of acid phosphatase at pH 6, and for their effect on the efficiency of orthophosphate metabolism.—The first adaptation observed, M1, was due to a single mutational event that effected a 30% increase in the efficiency of orthophosphate metabolism. The second, M2, effected an adaptive shift in the pH optimum of acid phosphatase and an increase in its activity over a wide range of pH values (an increment of 60% at pH 6). M2 was shown to result from a single mutational event in the region of the acid phosphatase structural gene. The third, M3, effected cell clumping, an adaptation to the culture apparatus that had no effect on phosphate metabolism.—The power of this system for directing the evolution of enzymes and of metabolic pathways is discussed in terms of the kinetic properties of the experimental system and in terms of the results obtained. PMID:4552227

  13. Microbial population dynamics in response to bioaugmentation in a constructed wetland system under 10°C.

    PubMed

    Zhao, Xinyue; Yang, Jixian; Bai, Shunwen; Ma, Fang; Wang, Li

    2016-04-01

    Compound microbial inocula were enriched and applied to a pilot-scale constructed wetland system to investigate their bioaugmentation effect on nitrogen removal under cold temperature (10°C). The results showed a 10% higher removal efficiency of ammonia and total nitrogen compared to a control (unbioaugmented) group. The microbial community structures before and after the bioaugmentation were analyzed through high throughput sequencing using Miseq Illumina platform. A variation of species richness and community equitability was observed in both systems. It is demonstrated that, based on the response of both the performance and microbial community, bioaugmentation using compound microbial inocula can fine tune the bacterial population and enhance the nitrogen removal efficiency of a constructed wetland system. PMID:26826956

  14. Comparative effects of Aroclor 1254 (polychlorinated biphenyls) and phenanthrene on glucose uptake by freshwater microbial populations.

    PubMed Central

    Sayler, G S; Lund, L C; Shiaris, M P; Sherrill, T W; Perkins, R E

    1979-01-01

    The effects of polychlorinated biphenyl (PCB) and phenanthrene stress on glucose uptake by natural microbial populations were examined by the heterotrophic potential technique. Temporal and spatial distributions in glucose uptake velocities were examined for natural samples as well as PCB- and phenanthrene-stressed samples. Statistical analysis indicated significant variability among the various samples. It was demonstrated that the environmental variables contributed significantly to the variability in uptake kinetics. Although general trends indicated a PCB-induced stimulation in uptake velocities, these trends were in part masked by sample variability. Data analysis indicated no statistically significant PCB or phenanthrene effect on either total glucose uptake velocities or the proportion of 14CO2 evolved, as compared to natural unstressed samples. PMID:114110

  15. Microbial population dynamics during sludge granulation in an A/O/A sequencing batch reactor.

    PubMed

    He, Qiulai; Zhou, Jun; Wang, Hongyu; Zhang, Jing; Wei, Li

    2016-08-01

    The evolution of the bacterial population during formation of denitrifying phosphorus removal granular sludge was investigated using high-throughput pyrosequencing. As a result, mature granules with a compact structure were obtained in an anaerobic/aerobic/anoxic (A/O/A) sequencing batch reactor under an organic loading rate as low as 0.3kg COD/(m(3)·d). Rod-shaped microbes were observed to cover with the outer surface of granules. Besides, reliable COD and simultaneous nitrogen and phosphorus removal efficiencies were achieved over the whole operation period. MiSeq pyrosequencing analysis illustrated that both the microbial diversity and richness increased sharply during the granulation process, whereas they stayed stable after the presence of granules. Some microorganisms seemed to contribute to the formation of granules, and some were identified as functional bacterial groups responsible for constructing the biological reactor. PMID:27115745

  16. Survey of microbial populations within Lake Michigan nearshore waters at two Chicago public beaches.

    PubMed

    Malki, Kema; Bruder, Katherine; Putonti, Catherine

    2015-12-01

    Lake Michigan is a critical resource for the residents of Chicago, providing drinking water to its 9+ million area residents. Along Chicago׳s 26 miles of public beaches the populous urban environment and this freshwater environment meet. While city-led monitoring initiatives investigate pathogenic bacteria in these nearshore waters, very little is known about other microbial species present. We collected surface water samples from two Chicago public beaches - Montrose Beach and 57th Street Beach - every ten days from June 5 through August 4, 2013 as well as once in early Fall (October 4, 2013). Sixteen bacterial communities in total were surveyed through targeted sequencing of the V4 16S rRNA gene. Taxa were identified using Mothur. Raw sequence data is available via NCBI׳s SRA database (part of BioProject PRJNA245802). OTU calls for each read are also available at our online repository: www.lakemichiganmicrobes.com/bacteria/. PMID:26958608

  17. Microbial fuel cells with highly active aerobic biocathodes

    NASA Astrophysics Data System (ADS)

    Milner, Edward M.; Popescu, Dorin; Curtis, Tom; Head, Ian M.; Scott, Keith; Yu, Eileen H.

    2016-08-01

    Microbial fuel cells (MFCs), which convert organic waste to electricity, could be used to make the wastewater infrastructure more energy efficient and sustainable. However, platinum and other non-platinum chemical catalysts used for the oxygen reduction reaction (ORR) at the cathode of MFCs are unsustainable due to their high cost and long-term degradation. Aerobic biocathodes, which use microorganisms as the biocatalysts for cathode ORR, are a good alternative to chemical catalysts. In the current work, high-performing aerobic biocathodes with an onset potential for the ORR of +0.4 V vs. Ag/AgCl were enriched from activated sludge in electrochemical half-cells poised at -0.1 and + 0.2 V vs. Ag/AgCl. Gammaproteobacteria, distantly related to any known cultivated gammaproteobacterial lineage, were identified as dominant in these working electrode biofilms (23.3-44.3% of reads in 16S rRNA gene Ion Torrent libraries), and were in very low abundance in non-polarised control working electrode biofilms (0.5-0.7%). These Gammaproteobacteria were therefore most likely responsible for the high activity of biologically catalysed ORR. In MFC tests, a high-performing aerobic biocathode increased peak power 9-fold from 7 to 62 μW cm-2 in comparison to an unmodified carbon cathode, which was similar to peak power with a platinum-doped cathode at 70 μW cm-2.

  18. GEOELECTRICAL EVIDENCE OF MICROBIAL DEGRADATION OF DIESEL CONTAMINATED SEDIMENTS

    EPA Science Inventory

    The alteration of physical properties by microbial activity in petroleum contaminated sediments was investigated using geophysical techniques in laboratory column experiments. Microbial population growth was determined by the Most Probable Number technique (MPN), community dynami...

  19. Limited recovery of soil microbial activity after transient exposure to gasoline vapors.

    PubMed

    Modrzyński, Jakub J; Christensen, Jan H; Mayer, Philipp; Brandt, Kristian K

    2016-09-01

    During gasoline spills complex mixtures of toxic volatile organic compounds (VOCs) are released to terrestrial environments. Gasoline VOCs exert baseline toxicity (narcosis) and may thus broadly affect soil biota. We assessed the functional resilience (i.e. resistance and recovery of microbial functions) in soil microbial communities transiently exposed to gasoline vapors by passive dosing via headspace for 40 days followed by a recovery phase of 84 days. Chemical exposure was characterized with GC-MS, whereas microbial activity was monitored as soil respiration (CO2 release) and soil bacterial growth ([(3)H]leucine incorporation). Microbial activity was strongly stimulated and inhibited at low and high exposure levels, respectively. Microbial growth efficiency decreased with increasing exposure, but rebounded during the recovery phase for low-dose treatments. Although benzene, toluene, ethylbenzene and xylene (BTEX) concentrations decreased by 83-97% during the recovery phase, microbial activity in high-dose treatments did not recover and numbers of viable bacteria were 3-4 orders of magnitude lower than in control soil. Re-inoculation with active soil microorganisms failed to restore microbial activity indicating residual soil toxicity, which could not be attributed to BTEX, but rather to mixture toxicity of more persistent gasoline constituents or degradation products. Our results indicate a limited potential for functional recovery of soil microbial communities after transient exposure to high, but environmentally relevant, levels of gasoline VOCs which therefore may compromise ecosystem services provided by microorganisms even after extensive soil VOC dissipation. PMID:27376993

  20. Effect of plants containing secondary compounds with palm oil on feed intake, digestibility, microbial protein synthesis and microbial population in dairy cows.

    PubMed

    Anantasook, N; Wanapat, M; Cherdthong, A; Gunun, P

    2013-06-01

    The objective of this study was to determine the effect of rain tree pod meal with palm oil supplementation on feed intake, digestibility, microbial protein synthesis and microbial populations in dairy cows. Four, multiparous early-lactation Holstein-Friesian crossbred (75%) lactating dairy cows with an initial body weight (BW) of 405±40 kg and 36±8 DIM were randomly assigned to receive dietary treatments according to a 4×4 Latin square design. The four dietary treatments were un-supplementation (control), supplementation with rain tree pod meal (RPM) at 60 g/kg, supplementation with palm oil (PO) at 20 g/kg, and supplementation with RPM at 60 g/kg and PO at 20 g/kg (RPO), of total dry matter intake. The cows were offered concentrates, at a ratio of concentrate to milk production of 1:2, and chopped 30 g/kg of urea treated rice straw was fed ad libitum. The RPM contained condensed tannins and crude saponins at 88 and 141 g/kg of DM, respectively. It was found that supplementation with RPM and/or PO to dairy cows diets did not show negative effects on feed intake and ruminal pH and BUN at any times of sampling (p>0.05). However, RPM supplementation resulted in lower crude protein digestibility, NH3-N concentration and number of proteolytic bacteria. It resulted in greater allantoin absorption and microbial crude protein (p<0.05). In addition, dairy cows showed a higher efficiency of microbial N supply (EMNS) in both RPM and RPO treatments. Moreover, NDF digestibility and cellulolytic bacteria numbers were highest in RPO supplementation (p<0.05) while, supplementation with RPM and/or PO decreased the protozoa population in dairy cows. Based on this study, supplementation with RPM and/or PO in diets could improve fiber digestibility, microbial protein synthesis in terms of quantity and efficiency and microbial populations in dairy cows. PMID:25049855

  1. Effect of Plants Containing Secondary Compounds with Palm Oil on Feed Intake, Digestibility, Microbial Protein Synthesis and Microbial Population in Dairy Cows

    PubMed Central

    Anantasook, N.; Wanapat, M.; Cherdthong, A.; Gunun, P.

    2013-01-01

    The objective of this study was to determine the effect of rain tree pod meal with palm oil supplementation on feed intake, digestibility, microbial protein synthesis and microbial populations in dairy cows. Four, multiparous early-lactation Holstein-Friesian crossbred (75%) lactating dairy cows with an initial body weight (BW) of 405±40 kg and 36±8 DIM were randomly assigned to receive dietary treatments according to a 4×4 Latin square design. The four dietary treatments were un-supplementation (control), supplementation with rain tree pod meal (RPM) at 60 g/kg, supplementation with palm oil (PO) at 20 g/kg, and supplementation with RPM at 60 g/kg and PO at 20 g/kg (RPO), of total dry matter intake. The cows were offered concentrates, at a ratio of concentrate to milk production of 1:2, and chopped 30 g/kg of urea treated rice straw was fed ad libitum. The RPM contained condensed tannins and crude saponins at 88 and 141 g/kg of DM, respectively. It was found that supplementation with RPM and/or PO to dairy cows diets did not show negative effects on feed intake and ruminal pH and BUN at any times of sampling (p>0.05). However, RPM supplementation resulted in lower crude protein digestibility, NH3-N concentration and number of proteolytic bacteria. It resulted in greater allantoin absorption and microbial crude protein (p<0.05). In addition, dairy cows showed a higher efficiency of microbial N supply (EMNS) in both RPM and RPO treatments. Moreover, NDF digestibility and cellulolytic bacteria numbers were highest in RPO supplementation (p<0.05) while, supplementation with RPM and/or PO decreased the protozoa population in dairy cows. Based on this study, supplementation with RPM and/or PO in diets could improve fiber digestibility, microbial protein synthesis in terms of quantity and efficiency and microbial populations in dairy cows. PMID:25049855

  2. Microbial Populations Associated with Phosphate-Mediated Vadose Zone Sequestration of Strontium and Uranium

    NASA Astrophysics Data System (ADS)

    Wu, C. H.; Chou, J.; Fujita, Y.; Bill, M.; Brodie, E. L.; Andersen, G. L.; Hazen, T. C.; Conrad, M. S.

    2007-12-01

    Significant quantities of metals and radionuclides are contained in thick unsaturated zones at several contaminated sites in the western US. In many cases, this contamination has migrated to underlying groundwater, sometimes decades after being released into the subsurface. Because of the prohibitive costs associated with physically removing the contamination, an attractive remedy to this problem is to develop methods for long-term in situ stabilization of the contamination in the vadose zone. Our research focuses on developing a method of introducing gaseous compounds to stimulate precipitation of stable phosphate mineral phases in the vadose zone to immobilize soluble contaminants thus minimizing further transport to groundwater. Preliminary studies have demonstrated that biological precipitation of phosphate minerals can be stimulated under unsaturated conditions by injection of triethyl phosphate (TEP) gas. Microorganisms hydrolyze TEP, releasing inorganic phosphate, catalyzing the precipitation of metals and radionuclide-containing phosphate minerals. Our initial results demonstrate that a mixed culture of aerobic microorganisms from vadose zone sediments, enriched with TEP, produce significantly higher concentrations of inorganic phosphate than the no TEP control. A high-density microarray (PhyloChip) capable of detecting up to 9,000 prokaryotic taxa will be used to identify the microbial community composition of the enriched culture. In addition, the metabolically active organisms will be investigated through extraction and hybridization of ribosomal RNA. Organisms capable of hydrolyzing TEP to inorganic phosphate will be further characterized to determine the requirements for aerobic microbially-mediated radionuclide immobilization. The chemical and isotopic compositions of the reactants and products will be measured to enable in situ monitoring of microbial TEP utilization. The result of these studies will be the basis for unsaturated column experiments

  3. RELATIONSHIPS BETWEEN CULTURABLE SOIL MICROBIAL POPULATIONS AND GROSS NITROGEN TRANSFORMATION PROCESSES IN A CLAY LOAM SOIL ACROSS ECOSYSTEMS

    EPA Science Inventory

    The size and quality of soil organic matter (SOM) pool can vary between ecosystems and can affect many soil properties. The objective of this study was to examine the relationship between gross N transformation rates and microbial populations and to investigate the role that SOM...

  4. Microbial diversity and activity in seafloor brine lake sediments (Alaminos Canyon block 601, Gulf of Mexico).

    PubMed

    Crespo-Medina, M; Bowles, M W; Samarkin, V A; Hunter, K S; Joye, S B

    2016-09-01

    The microbial communities thriving in deep-sea brines are sustained largely by energy rich substrates supplied through active seepage. Geochemical, microbial activity, and microbial community composition data from different habitats at a Gulf of Mexico brine lake in Alaminos Canyon revealed habitat-linked variability in geochemistry that in turn drove patterns in microbial community composition and activity. The bottom of the brine lake was the most geochemically extreme (highest salinity and nutrient concentrations) habitat and its microbial community exhibited the highest diversity and richness indices. The habitat at the upper halocline of the lake hosted the highest rates of sulfate reduction and methane oxidation, and the largest inventories of dissolved inorganic carbon, particulate organic carbon, and hydrogen sulfide. Statistical analyses indicated a significant positive correlation between the bacterial and archaeal diversity in the bottom brine sample and NH4+ inventories. Other environmental factors with positive correlation with microbial diversity indices were DOC, H2 S, and DIC concentrations. The geochemical regime of different sites within this deep seafloor extreme environment exerts a clear selective force on microbial communities and on patterns of microbial activity. PMID:27444236

  5. Contrasting effects of biochar versus manure on soil microbial communities and enzyme activities in an Aridisol

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Biochar has been shown to increase microbial activity, alter microbial community structure, and increase soil fertility in arid and semi-arid soils, but at relatively high rates that may be impractical for large-scale field studies. This contrasts with organic amendments such as manure, which can be...

  6. Periphytic photosynthetic stimulation of extracellular enzyme activity in aquatic microbial communities associated with decaying typha litter.

    PubMed

    Francoeur, Steven N; Schaecher, Mark; Neely, Robert K; Kuehn, Kevin A

    2006-11-01

    We examined the effect of light on extracellular enzyme activities of periphytic/endogenous microbial assemblages associated with decomposing litter of an emergent macrophyte Typha angustifolia within a small inland wetland in southeastern Michigan. Standing-dead Typha leaf litter was collected, placed into floating wire mesh litter baskets, and submerged in a wetland pool. Enzyme saturation assays were conducted on three occasions following litter submergence (days 9, 28, and 44) to generate saturation curves for the individual enzymes tested and to examine potential differences in enzyme saturation kinetics during microbial colonization and development. Experimental light manipulations were conducted on two occasions during microbial development (days 10 and 29). Short-term (30 min) light exposure significantly increased extracellular beta-glucosidase activity of litter-associated microbial communities. Activities of beta-xylosidase and leucine-aminopeptidase were not stimulated, and stimulation of phosphatase activity was variable. The exact mechanism for increased enzyme activity remains unknown, but it may have been increased pH arising from periphytic algal photosynthesis. These results suggest that extracellular enzyme activity in microbial communities colonizing natural organic substrata may be influenced by light/photosynthesis, as has previously been demonstrated for periphyton communities grown on artificial, inert substrata. Thus, light/photosynthetic mediated stimulation of extracellular enzyme activities may be a common occurrence in microbial communities associated with natural decaying plant litter in wetlands and might engender diurnal patterns in other microbial decay processes (e.g., production, organic matter decomposition, and mineralization). PMID:17082997

  7. Stellar populations in Active Galactic Nuclei III

    NASA Astrophysics Data System (ADS)

    Boisson, C.; Joly, M.; Pelat, D.; Ward, M. J.

    2004-12-01

    In this paper we apply the stellar population synthesis method previously described in Boisson et al. (\\cite{Boisson2000}) to five more AGN. The analysis of these new data strengthen our previous conclusions: i) homogeneity of the stellar population within a class of nuclear activity regardless of the morphological type of the host galaxy; ii) populations within the nuclear regions of LINERs and Seyfert 2s are different: LINERs have a very old metal-rich population while in the Seyfert 2s a contribution of a weak burst of star formation is observed together with the old high metallicity component; iii) in the circum-nuclar region (200 pc ≤D≤1 kpc) of all the active galaxies in our sample, except for NGC 2992, we detect an old burst of star formation (0.2-1 Gyr),which is contrary to what is observed in normal galaxies. We note that the broad OIλ8446 Å emission line detected in the spectrum of the nucleus of NGC 2992 confirms its classification as a Seyfert 1. Based on observations collected at the New Technology Telescope of the European Southern Observatory, La Silla, Chile.

  8. Monitoring microbial populations of sulfate-reducing bacteria using an impedimetric immunosensor based on agglutination assay.

    PubMed

    Wan, Yi; Zhang, Dun; Hou, Baorong

    2009-11-15

    An impedimetric immunosensor was fabricated for rapid and non-labeled detection of sulfate-reducing bacteria, Desulforibrio caledoiensis (SRB) by immobilizing lectin-Concanavalin A using an agglutination assay. The immobilization of lectin was conducted using amine coupling on the surface of a gold (Au) electrode assembled with 11-Mercaptoundecanoic acid. Electrochemical impedance spectroscopy (EIS) was used to verify the stepwise assembly of the sensor system. The work conditions of the impedimetric immunosensor, such as pH of the buffer solutions and the incubation time of lectin, were optimized. Faradic impedance spectra for charge transfer for the redox probe Fe(CN)(6)(3-/4-)were measured to determine SRB concentrations. The diameter of the Nyquist diagram that is equal to the charge-transfer resistance (R(ct)) increased with increasing SRB concentration. A linear relationship between R(ct) and SRB concentration was obtained in SRB concentration range of 1.8 to 1.8 x 10(7)cfu/ml. The variation of the SRB population during the growth process was also monitored using the impedimetric immunosensor. This approach has great potential for simple, low-cost, and time-saving monitoring of microbial populations. PMID:19782217

  9. Assessment of partial nitrification reactor performance through microbial population shift using quinone profile, FISH and SEM.

    PubMed

    Sinha, B; Annachhatre, A P

    2007-12-01

    In engineered systems, biological nitrogen removal through partial nitrification to nitrite is of great interest. Accordingly, effect of operating parameters such as pH, DO and temperature on the accumulation of ammonia-oxidizers was investigated. pH of 8, DO of 0.3-0.5mg/l and temperature of 35 degrees C yielded a ratio of 0.9-1.5 of NO(2)N:NH(4)N in the effluent suitable as a feed for Anammox reactor. Microbial population shift during start-up was assessed using quinone profile, SEM and FISH. UQ-8 in the biomass, which is the predominant quinone in ammonia-oxidizers, increased from 24.8% on Day 1 to 61.2% on Day 136. Fluorescence in situ hybridization analysis in the reactor showed that ammonia-oxidizing bacteria gradually outcompeted other bacteria and was the dominant population. The morphology and inner structure of the granular sludge was observed using SEM and the photographs indicated that the aerobic granular sludge showed a shift towards spherical and small rod-shaped clusters. PMID:17257833

  10. Microbial mediators of carbon fate in thawing permafrost: connecting microbial activity to geochemistry across an in situ thaw gradient

    NASA Astrophysics Data System (ADS)

    Kim, E.; Mondav, R.; Woodcroft, B. J.; Hodgkins, S. B.; McCalley, C. K.; Wehr, R.; Logan, T.; VerBerkmoes, N. C.; Crill, P. M.; Chanton, J.; Saleska, S. R.; Rich, V. I.; Tyson, G. W.

    2012-12-01

    Permafrost holds approximately one third of global soil carbon in a relatively unavailable form. Climate change is predicted to virtually eliminate permafrost by the end of the century. The fate of the stored carbon will be driven by local geohydrology and mediated by microbial carbon transformations. Predicting thaw-induced feedbacks to climate change requires improving our understanding of concomitant changes in microbial activity, particularly in CO2 fixation, organic matter degradation, and CH4 cycling. Our team is using diverse geochemical and molecular measurements to track changes in carbon cycling and microbial communities across a natural permafrost thaw gradient. The gradient habitats are highly instrumented for ecological, hydrologic, and biogeochemical monitoring, and the thaw progression has been documented over decades. Permafrost thaw has caused slumping ground level and progressive changes in hydrology and plant composition, culminating in sedge-dominated fen wetland. Although this endpoint habitat supports higher plant productivity, there is a net increase in radiative forcing due to high methane emissions. This natural laboratory permits the examination of in situ changes in microbial composition and activity across thaw-induced habitat change. Specifically, taxonomic and metabolic profiling (16S rRNA gene amplicon, metagenomic and metaproteomic sequencing) is linking microbial metabolisms to synoptic geochemistry. Community data have revealed the presence of a novel highly active methanogen from the euryarchaeal lineage Rice Cluster-II. The abundance and distribution of RC-II across the thaw gradient habitats correlate to methane emission. The 2.1Mb RC-II genome (in 117 contigs, median 47kb, longest 135kb) was assembled from metagenomic data. The genome suggests the ability to perform hydrogenotrophic methanogenesis. To link resident microbes to active carbon cycling, we determined in situ community global protein expression profiles (i

  11. Microbial population dynamics and changes in main nutrients during the acidification process of pig manures.

    PubMed

    Zhang, Dongdong; Yuan, Xufeng; Guo, Peng; Suo, Yali; Wang, Xiaofen; Wang, Weidong; Cui, Zongjun

    2011-01-01

    This study evaluated the impact of pig manure acidification on anaerobic treatment and composition of the fecal microbial community. According to the different chemical oxygen demand (COD) in the anaerobic treatment processes, pig manure was diluted 4 times (x4), 16 times (x16), or 64 times (x64) and subjected to acidification. During the acidification process, pH, soluble chemical oxygen demand (SCOD), volatile fatty acids (VFAs), nitrogen (N), phosphorus (P) and potassium (K) were determined along with microbial population dynamics. The pH of the three dilutions first declined, and then slowly increased. The total VFAs of x4 and x16 dilutions peaked on day 15 and 20, respectively. The content of acetic acid, propanoic acid, butanoic acid and valeric acid of the x4 dilution were 23.6, 11.4, 8.8 and 0.6 g/L respectively, and that of the x16 dilution was 5.6, 2.3, 0.9 and 0.2 g/L respectively. Only acetic acid was detected in the x64 dilution, and its level peaked on day 10. The results showed that the liquid pig manure was more suitable to enter the anaerobic methanogenic bioreactors after two weeks of acidification. During the acidification process, total P concentration increased during the first ten days, then dropped sharply, and rose again to a relatively high final concentration, while total N concentration rose initially and then declined. Based on the analysis of denaturing gradient gel electrophoresis (DGGE) and 16S rRNA gene clone library, we concluded that the acidification process reduced the number of pathogenic bacteria species in pig manure. PMID:21520820

  12. Soil Microbial Activity Provides Insight to Carbon Cycling in Shrub Ecotones of Sub-Arctic Sweden

    NASA Astrophysics Data System (ADS)

    Marek, E.; Kashi, N. N.; Chen, J.; Hobbie, E. A.; Schwan, M. R.; Varner, R. K.

    2015-12-01

    Shrubs are expanding in Arctic and sub-Arctic regions due to rising atmospheric temperatures. Microbial activity increases as growing temperatures cause permafrost warming and subsequent thaw, leading to a greater resource of soil nutrients enabling shrub growth. Increased carbon inputs from shrubs is predicted to result in faster carbon turnover by microbial decomposition. Further understanding of microbial activity underneath shrubs could uncover how microbes and soil processes interact to promote shrub expansion and carbon cycling. To address how higher soil carbon input from shrubs influences decomposition, soil samples were taken across a heath, shrub, and forest ecotone gradient at two sites near Abikso, Sweden. Samples were analyzed for soluble carbon and nitrogen, microbial abundance, and microbial activity of chitinase, glucosidase, and phosphatase to reflect organic matter decomposition and availability of nitrogen, carbon, and phosphate respectively. Chitinase activity positively correlated with shrub cover, suggesting microbial demands for nitrogen increase with higher shrub cover. Glucosidase activity negatively correlated with shrub cover and soluble carbon, suggesting decreased microbial demand for carbon as shrub cover and carbon stores increase. Lower glucosidase activity in areas with high carbon input from shrubs implies that microbes are decomposing carbon less readily than carbon is being put into the soil. Increasing soil carbon stores in shrub covered areas can lead to shrubs becoming a net carbon sink and a negative feedback to changing climate.

  13. Assessing microbial activities in metal contaminated agricultural volcanic soils - An integrative approach.

    PubMed

    Parelho, C; Rodrigues, A S; Barreto, M C; Ferreira, N G C; Garcia, P

    2016-07-01

    Volcanic soils are unique naturally fertile resources, extensively used for agricultural purposes and with particular physicochemical properties that may result in accumulation of toxic substances, such as trace metals. Trace metal contaminated soils have significant effects on soil microbial activities and hence on soil quality. The aim of this study is to determine the soil microbial responses to metal contamination in volcanic soils under different agricultural land use practices (conventional, traditional and organic), based on a three-tier approach: Tier 1 - assess soil microbial activities, Tier 2 - link the microbial activity to soil trace metal contamination and, Tier 3 - integrate the microbial activity in an effect-based soil index (Integrative Biological Response) to score soil health status in metal contaminated agricultural soils. Our results showed that microbial biomass C levels and soil enzymes activities were decreased in all agricultural soils. Dehydrogenase and β-glucosidase activities, soil basal respiration and microbial biomass C were the most sensitive responses to trace metal soil contamination. The Integrative Biological Response value indicated that soil health was ranked as: organic>traditional>conventional, highlighting the importance of integrative biomarker-based strategies for the development of the trace metal "footprint" in Andosols. PMID:27057992

  14. Microbial activities and phosphorus cycling: An application of oxygen isotope ratios in phosphate

    NASA Astrophysics Data System (ADS)

    Stout, Lisa M.; Joshi, Sunendra R.; Kana, Todd M.; Jaisi, Deb P.

    2014-08-01

    Microorganisms carry out biochemical transformations of nutrients that make up their cells. Therefore, understanding how these nutrients are transformed or cycled in natural environments requires knowledge of microbial activity. Commonly used indicators for microbial activity typically include determining microbial respiration by O2/CO2 measurements, cell counts, and measurement of enzyme activities. However, coupled studies on nutrient cycling and microbial activity are not given enough emphasis. Here we apply phosphate oxygen isotope ratios (δ18OP) as a tool for measurement of microbial activity and compare the rate of isotope exchange with methods of measuring microbial activities that are more commonly applied in environmental studies including respiration, dehydrogenase activity, alkaline phosphatase activity, and cell counts. Our results show that different bacteria may have different strategies for P uptake, storage and release, their respiration and consequently expression of DHA and APase activities, but in general the trend of their enzyme activities are comparable. Phosphate δ18OP values correlated well with these other parameters used to measure microbial activity with the strongest linear relationships between δ18OP and CO2 evolution (r = -0.99). Even though the rate of isotope exchange for each microorganism used in this study is different, the rate per unit CO2 respiration showed one general trend, where δ18OP values move towards equilibrium while CO2 is generated. While this suggests that P cycling among microorganisms used in this study can be generalized, further research is needed to determine whether the microorganism-specific isotope exchange trend may occur in natural environments. In summary, phosphate oxygen isotope measurements may offer an alternative for use as a tracer to measure microbial activity in soils, sediments, and many other natural environments.

  15. Effect of altitude and season on microbial activity, abundance and community structure in Alpine forest soils.

    PubMed

    Siles, José A; Cajthaml, Tomas; Minerbi, Stefano; Margesin, Rosa

    2016-03-01

    In the current context of climate change, the study of microbial communities along altitudinal gradients is especially useful. Only few studies considered altitude and season at the same time. We characterized four forest sites located in the Italian Alps, along an altitude gradient (545-2000 m a.s.l.), to evaluate the effect of altitude in spring and autumn on soil microbial properties. Each site in each season was characterized with regard to soil temperature, physicochemical properties, microbial activities (respiration, enzymes), community level physiological profiles (CLPP), microbial abundance and community structure (PLFA). Increased levels of soil organic matter (SOM) and nutrients were found at higher altitudes and in autumn, resulting in a significant increase of (soil dry-mass related) microbial activities and abundance at higher altitudes. Significant site- and season-specific effects were found for enzyme production. The significant interaction of the factors site and incubation temperature for soil microbial activities indicated differences in microbial communities and their responses to temperature among sites. CLPP revealed site-specific effects. Microbial community structure was influenced by altitudinal, seasonal and/or site-specific effects. Correlations demonstrated that altitude, and not season, was the main factor determining the changes in abiotic and biotic characteristics at the sites investigated. PMID:26787774

  16. Microbial and enzymatic activity of soil contaminated with azoxystrobin.

    PubMed

    Baćmaga, Małgorzata; Kucharski, Jan; Wyszkowska, Jadwiga

    2015-10-01

    The use of fungicides in crop protection still effectively eliminates fungal pathogens of plants. However, fungicides may dissipate to various elements of the environment and cause irreversible changes. Considering this problem, the aim of the presented study was to evaluate changes in soil biological activity in response to contamination with azoxystrobin. The study was carried out in the laboratory on samples of sandy loam with a pH of 7.0 in 1 Mol KCl dm(-3). Soil samples were treated with azoxystrobin in one of four doses: 0.075 (dose recommended by the manufacturer), 2.250, 11.25 and 22.50 mg kg(-1) soil DM (dry matter of soil). The control soil sample did not contain fungicide. Bacteria were identified based on 16S rRNA gene sequencing, and fungi were identified by internal transcribed spacer (ITS) region sequencing. The study revealed that increased doses of azoxystrobin inhibited the growth of organotrophic bacteria, actinomycetes and fungi. The fungicide also caused changes in microbial biodiversity. The lowest values of the colony development (CD) index were recorded for fungi and the ecophysiological (EP) index for organotrophic bacteria. Azoxystrobin had an inhibitory effect on the activity of dehydrogenases, catalase, urease, acid phosphatase and alkaline phosphatase. Dehydrogenases were found to be most resistant to the effects of the fungicide, while alkaline phosphatase in the soil recovered the balance in the shortest time. Four species of bacteria from the genus Bacillus and two species of fungi from the genus Aphanoascus were isolated from the soil contaminated with the highest dose of azoxystrobin (22.50 mg kg(-1)). PMID:26343782

  17. Comparisons of ruminal fermentation characteristics and microbial populations in bison and cattle.

    PubMed Central

    Towne, G; Nagaraja, T G; Cochran, R C; Harmon, D L; Owensby, C E; Kaufman, D W

    1988-01-01

    Ruminal microbial populations, fermentation characteristics, digestibility, and liquid flow rates in two ruminally cannulated bison and two ruminally cannulated Hereford steers fed a prairie hay diet were compared. No significant differences in anaerobic bacterial counts, volatile fatty acid concentrations, or ruminal pHs were evident between bison and cattle. Also, no significant differences in neutral detergent fiber digestibility, indigestible fiber retention time, or intake were detected between bison and cattle, although cattle had higher levels (P less than 0.08) of ruminal dry matter and indigestible fiber than bison. Bison had a smaller (P = .02) ruminoreticular volume, faster liquid dilution rates, and faster liquid turnover times than cattle. The average ruminal ammonia nitrogen concentration was higher (P = 0.02) in bison (1.17 mg/dl) than in cattle (0.79 mg/dl). Total ciliate protozoal counts and cell volume were greater (P = 0.07) in bison (32.8 x 10(4)/g and 407.1 x 10(-4) ml/g, respectively) than in cattle (15.7 x 10(4)/g and 162.2 x 10(-4) ml/g, respectively). Bison harbored higher (P less than 0.02) numbers of Dasytricha spp., Eudiplodinium maggii, Eudiplodinium bursa, and Epidinium spp. than cattle and possessed a type B protozoan population. The cattle possessed a mixed type A-type B population that was characterized by Ophryoscolex spp. and Polyplastron spp. in association with low concentrations of Epidinium spp. and Eudiplodinium maggii. PMID:3272131

  18. Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses.

    PubMed

    Ferreira, Ari J S; Siam, Rania; Setubal, João C; Moustafa, Ahmed; Sayed, Ahmed; Chambergo, Felipe S; Dawe, Adam S; Ghazy, Mohamed A; Sharaf, Hazem; Ouf, Amged; Alam, Intikhab; Abdel-Haleem, Alyaa M; Lehvaslaiho, Heikki; Ramadan, Eman; Antunes, André; Stingl, Ulrich; Archer, John A C; Jankovic, Boris R; Sogin, Mitchell; Bajic, Vladimir B; El-Dorry, Hamza

    2014-01-01

    Metagenomics-based functional profiling analysis is an effective means of gaining deeper insight into the composition of marine microbial populations and developing a better understanding of the interplay between the functional genome content of microbial communities and abiotic factors. Here we present a comprehensive analysis of 24 datasets covering surface and depth-related environments at 11 sites around the world's oceans. The complete datasets comprises approximately 12 million sequences, totaling 5,358 Mb. Based on profiling patterns of Clusters of Orthologous Groups (COGs) of proteins, a core set of reference photic and aphotic depth-related COGs, and a collection of COGs that are associated with extreme oxygen limitation were defined. Their inferred functions were utilized as indicators to characterize the distribution of light- and oxygen-related biological activities in marine environments. The results reveal that, while light level in the water column is a major determinant of phenotypic adaptation in marine microorganisms, oxygen concentration in the aphotic zone has a significant impact only in extremely hypoxic waters. Phylogenetic profiling of the reference photic/aphotic gene sets revealed a greater variety of source organisms in the aphotic zone, although the majority of individual photic and aphotic depth-related COGs are assigned to the same taxa across the different sites. This increase in phylogenetic and functional diversity of the core aphotic related COGs most probably reflects selection for the utilization of a broad range of alternate energy sources in the absence of light. PMID:24921648

  19. Core Microbial Functional Activities in Ocean Environments Revealed by Global Metagenomic Profiling Analyses

    PubMed Central

    Ferreira, Ari J. S.; Siam, Rania; Setubal, João C.; Moustafa, Ahmed; Sayed, Ahmed; Chambergo, Felipe S.; Dawe, Adam S.; Ghazy, Mohamed A.; Sharaf, Hazem; Ouf, Amged; Alam, Intikhab; Abdel-Haleem, Alyaa M.; Lehvaslaiho, Heikki; Ramadan, Eman; Antunes, André; Stingl, Ulrich; Archer, John A. C.; Jankovic, Boris R.; Sogin, Mitchell; Bajic, Vladimir B.; El-Dorry, Hamza

    2014-01-01

    Metagenomics-based functional profiling analysis is an effective means of gaining deeper insight into the composition of marine microbial populations and developing a better understanding of the interplay between the functional genome content of microbial communities and abiotic factors. Here we present a comprehensive analysis of 24 datasets covering surface and depth-related environments at 11 sites around the world's oceans. The complete datasets comprises approximately 12 million sequences, totaling 5,358 Mb. Based on profiling patterns of Clusters of Orthologous Groups (COGs) of proteins, a core set of reference photic and aphotic depth-related COGs, and a collection of COGs that are associated with extreme oxygen limitation were defined. Their inferred functions were utilized as indicators to characterize the distribution of light- and oxygen-related biological activities in marine environments. The results reveal that, while light level in the water column is a major determinant of phenotypic adaptation in marine microorganisms, oxygen concentration in the aphotic zone has a significant impact only in extremely hypoxic waters. Phylogenetic profiling of the reference photic/aphotic gene sets revealed a greater variety of source organisms in the aphotic zone, although the majority of individual photic and aphotic depth-related COGs are assigned to the same taxa across the different sites. This increase in phylogenetic and functional diversity of the core aphotic related COGs most probably reflects selection for the utilization of a broad range of alternate energy sources in the absence of light. PMID:24921648

  20. Effect of sulfate and lactate loading rates on the respiration process and microbial population changes measured by ecological indices.

    PubMed

    García-Saucedo, C; Fernández, F J; Cuervo-López, F M; Gómez, J

    2015-01-01

    In a sulfate reducing process, increasing loading rates and sulfide accumulation may induce population changes resulting in decreasing effectiveness of the process. Thus, the relationship between microbial metabolism changes and population dynamics was studied. An upflow anaerobic sludge blanket reactor was operated at different sulfate loading rates (SLR), from 290 to 981 mg SO4-S/L d at a constant carbon/sulfur ratio of 0.75. When the SLR was increased, the total organic carbon and sulfate consumption efficiencies decreased to nearly 30% and 25%, respectively. The acetate and propionate yields increased with increasing SLR and 385±7 mg sulfide-S/L d was reached. The ecological indices, determined by random amplified polymorphic DNA and denaturing gradient gel electrophoresis techniques, diversity and evenness were found to be constant, and similarity coefficient values remained higher than 76%. The results suggest that the microbial population changes were negligible compared with metabolic changes when SLR was increased. The sulfide accumulation did not modify the microbial diversity. The sequencing of 16S rRNA genes showed strains related to sulfate reducing, fermentation, and methanogenesis processes. The results indicated that the decreasing of effectiveness, under the experimental conditions tested, was dependent more on operational parameters than microbial changes. PMID:25607675

  1. Genome-Centric Analysis of Microbial Populations Enriched by Hydraulic Fracture Fluid Additives in a Coal Bed Methane Production Well.

    PubMed

    Robbins, Steven J; Evans, Paul N; Parks, Donovan H; Golding, Suzanne D; Tyson, Gene W

    2016-01-01

    Coal bed methane (CBM) is generated primarily through the microbial degradation of coal. Despite a limited understanding of the microorganisms responsible for this process, there is significant interest in developing methods to stimulate additional methane production from CBM wells. Physical techniques including hydraulic fracture stimulation are commonly applied to CBM wells, however the effects of specific additives contained in hydraulic fracture fluids on native CBM microbial communities are poorly understood. Here, metagenomic sequencing was applied to the formation waters of a hydraulically fractured and several non-fractured CBM production wells to determine the effect of this stimulation technique on the in-situ microbial community. The hydraulically fractured well was dominated by two microbial populations belonging to the class Phycisphaerae (within phylum Planctomycetes) and candidate phylum Aminicenantes. Populations from these phyla were absent or present at extremely low abundance in non-fractured CBM wells. Detailed metabolic reconstruction of near-complete genomes from these populations showed that their high relative abundance in the hydraulically fractured CBM well could be explained by the introduction of additional carbon sources, electron acceptors, and biocides contained in the hydraulic fracture fluid. PMID:27375557

  2. Genome-Centric Analysis of Microbial Populations Enriched by Hydraulic Fracture Fluid Additives in a Coal Bed Methane Production Well

    PubMed Central

    Robbins, Steven J.; Evans, Paul N.; Parks, Donovan H.; Golding, Suzanne D.; Tyson, Gene W.

    2016-01-01

    Coal bed methane (CBM) is generated primarily through the microbial degradation of coal. Despite a limited understanding of the microorganisms responsible for this process, there is significant interest in developing methods to stimulate additional methane production from CBM wells. Physical techniques including hydraulic fracture stimulation are commonly applied to CBM wells, however the effects of specific additives contained in hydraulic fracture fluids on native CBM microbial communities are poorly understood. Here, metagenomic sequencing was applied to the formation waters of a hydraulically fractured and several non-fractured CBM production wells to determine the effect of this stimulation technique on the in-situ microbial community. The hydraulically fractured well was dominated by two microbial populations belonging to the class Phycisphaerae (within phylum Planctomycetes) and candidate phylum Aminicenantes. Populations from these phyla were absent or present at extremely low abundance in non-fractured CBM wells. Detailed metabolic reconstruction of near-complete genomes from these populations showed that their high relative abundance in the hydraulically fractured CBM well could be explained by the introduction of additional carbon sources, electron acceptors, and biocides contained in the hydraulic fracture fluid. PMID:27375557

  3. Microbial Population Analysis of the Salivary Glands of Ticks; A Possible Strategy for the Surveillance of Bacterial Pathogens

    PubMed Central

    Qiu, Yongjin; Nakao, Ryo; Ohnuma, Aiko; Kawamori, Fumihiko; Sugimoto, Chihiro

    2014-01-01

    Ticks are one of the most important blood-sucking vectors for infectious microorganisms in humans and animals. When feeding they inject saliva, containing microbes, into the host to facilitate the uptake of blood. An understanding of the microbial populations within their salivary glands would provide a valuable insight when evaluating the vectorial capacity of ticks. Three tick species (Ixodes ovatus, I. persulcatus and Haemaphysalis flava) were collected in Shizuoka Prefecture of Japan between 2008 and 2011. Each tick was dissected and the salivary glands removed. Bacterial communities in each salivary gland were characterized by 16S amplicon pyrosequencing using a 454 GS-Junior Next Generation Sequencer. The Ribosomal Database Project (RDP) Classifier was used to classify sequence reads at the genus level. The composition of the microbial populations of each tick species were assessed by principal component analysis (PCA) using the Metagenomics RAST (MG-RAST) metagenomic analysis tool. Rickettsia-specific PCR was used for the characterization of rickettsial species. Almost full length of 16S rDNA was amplified in order to characterize unclassified bacterial sequences obtained in I. persulcatus female samples. The numbers of bacterial genera identified for the tick species were 71 (I. ovatus), 127 (I. persulcatus) and 59 (H. flava). Eighteen bacterial genera were commonly detected in all tick species. The predominant bacterial genus observed in all tick species was Coxiella. Spiroplasma was detected in Ixodes, and not in H. flava. PCA revealed that microbial populations in tick salivary glands were different between tick species, indicating that host specificities may play an important role in determining the microbial complement. Four female I. persulcatus samples contained a high abundance of several sequences belonging to Alphaproteobacteria symbionts. This study revealed the microbial populations within the salivary glands of three species of ticks, and the

  4. Diversity, Abundance, and Potential Activity of Nitrifying and Nitrate-Reducing Microbial Assemblages in a Subglacial Ecosystem

    NASA Astrophysics Data System (ADS)

    Skidmore, M. L.; Boyd, E. S.; Lange, R. K.; Mitchell, A. C.; Havig, J. R.; Hamilton, T. L.; Lafreniere, M. J.; Shock, E.; Peters, J.

    2011-12-01

    Ice currently covers 11% of the terrestrial landmass and has covered significantly greater portions of the planet during Earth's history. Significant microbial populations have been documented in all subglacial settings sampled to date. Recent research has demonstrated sizable volumes of subglacial sediment beneath the Antarctic Ice Sheet that are greater than 1km thick in places and where sampled active microbial populations have been documented. Collectively this suggests subglacial microbial populations may impact global biogeochemical cycles on glacial-interglacial timescales, however, nitrogen cycling in subglacial systems is poorly understood. Subglacial sediments sampled from beneath Robertson Glacier, Alberta, Canada harbor a diverse assemblage of potential nitrifiers, nitrate reducers, and diazotrophs, as assessed by amoA, narG, and nifH gene biomarker diversity. Archaeal amoA genes were less abundant and less diverse than bacterial amoA. Nitrification and nitrate reduction were measured in microcosms incubated at 4 degrees Celsius indicating the potential for these processes to occur in situ. Subglacial sediment porewaters and bulk meltwaters have low concentrations of dissolved inorganic and organic nitrogen compounds and a high C/N ratio of dissolved organic matter in sediment porewaters, indicating that the sediment communities are N limited. This may reflect the combined biological activities of organic N mineralization, nitrification, and nitrate reduction. Despite evidence for N limitation and detection of nifH, biological nitrogen fixation was not detected in subglacial sediment microcosm experiments at 4 degrees Celsius. Collectively, our results suggest a role for nitrification and nitrate reduction in sustaining microbial communities in subglacial environments.

  5. Molecular Signatures of Microbial Metabolism in an Actively Growing, Silicified, Microbial Structure from Yellowstone National Park

    NASA Astrophysics Data System (ADS)

    Ferreira, M.; Creveling, J.; Hilburn, I.; Karlsson, E.; Pepe-Ranney, C.; Spear, J.; Dawson, S.; Geobio2008, I.

    2008-12-01

    Silicified structures that exhibit a putative biologic component in their formation permeate the rock record as stromatolites. We have studied a silicified microbial structure from a hot spring in Yellowstone National Park using phenotypic, phylogenetic, and metagenomic analyses to determine microbial carbon metabolic pathways and the phylogenetic affiliations of microbes present in this unique structure. In this multi-faceted approach, dominant physiologies, specifically with regards to anaerobic and aerobic metabolisms, were inferred from 16S rRNA gene sequences and 454 sequencing data from bulk DNA samples of the structure. Carbon utilization as indicated by ECO Biolog plates showed abundant heterotrophy and heterotrophic diversity throughout the microbial structure. Microbes within the structure are able to utilize all tested sources of carbohydrates, lipids/fatty acids, and protein/amino acids as carbon sources. ECO plate testing of the hot spring water yielded considerable less carbohydrate consumption (only 4 out of 13 tested carbohydrates) and similar lipids/fatty acids and protein/amino acids consumption (2 out of 3 and 5 out of 5 tested sources respectively). Full length 16S rRNA gene sequences and metagenomic 454 pyrosequencing of community DNA showed limited diversity among primary producers. From the 16S data, the majority of the autotrophs are inferred to utilize the Calvin cycle for CO2 fixation, followed by 3-hydroxypropionate/4- hydroxybutyrate CO2 fixation. However, an analysis of the metagenomic data compared to the KEGG database does not show genes directly involved with Calvin cycle carbon fixation. Further BLAST searches of our data failed to find significant matches within our 6514 metagenomic sequences to known RuBisCo sequences taken from the NCBI database. This is likely due to a far under-sampled dataset of metagenomic sequences, and the low number (958) that had matches to the KEGG pathways database. Anaerobic versus aerobic physiology

  6. Active Asteroids in the NEO Population

    NASA Astrophysics Data System (ADS)

    Jenniskens, Peter

    2016-01-01

    Some main-belt asteroids evolve into near-Earth objects. They can then experience the same meteoroid-producing phenomena as active asteroids in the main belt. If so, they would produce meteoroid streams, some of which evolve to intersect Earth's orbit and produce meteor showers at Earth. Only few of those are known. Meteoroid streams that move in orbits with Tisserand parameter well in excess of 3 are the Geminids and Daytime Sextantids of the Phaethon complex and the lesser known epsilon Pegasids. The observed activity appears to be related to nearly whole scale disintegrations, rather than dust ejection from volatile outgassing as observed in active comets. There is only a small population of asteroids with a main-belt origin that recently disintegrated into meteoroid streams.

  7. Effect of salinity tolerant PDH45 transgenic rice on physicochemical properties, enzymatic activities and microbial communities of rhizosphere soils

    PubMed Central

    Sahoo, Ranjan Kumar; Tuteja, Narendra

    2013-01-01

    The effect of genetically modified (GM) plants on environment is now major concern worldwide. The plant roots of rhizosphere soil interact with variety of bacteria which could be influenced by the transgene in GM plants. The antibiotic resistance genes in GM plants may be transferred to soil microbes. In this study we have examined the effect of overexpression of salinity tolerant pea DNA helicase 45 (PDH45) gene on microbes and enzymatic activities in the rhizosphere soil of transgenic rice IR64 in presence and absence of salt stress in two different rhizospheric soils (New Delhi and Odisha, India). The diversity of the microbial community and soil enzymes viz., dehydrogenase, alkaline phosphatase, urease and nitrate reductase was assessed. The results revealed that there was no significant effect of transgene expression on rhizosphere soil of the rice plants. The isolated bacteria were phenotyped both in absence and presence of salt and no significant changes were found in their phenotypic characters as well as in their population. Overall, the overexpression of PDH45 in rice did not cause detectable changes in the microbial population, soil enzymatic activities and functional diversity of the rhizosphere soil microbial community. PMID:23733066

  8. Fire Effects on Microbial Enzyme Activities in Larch Forests of the Siberian Arctic

    NASA Astrophysics Data System (ADS)

    Ludwig, S.; Alexander, H. D.; Bulygina, E. B.; Mann, P. J.; Natali, S.

    2012-12-01

    severity 1 d post-fire, but by 8 d post-fire activity was the same in all treatments, indicating complete recovery of the microbial population. Phenol oxidase activity was low in all treatments 1 d post-fire, but by 8 d post-fire, severe plots had substantially increased phenol oxidase activity, likely due to microbial efforts to mitigate phenolic compound toxicity following severe fires. Both DOC and the slope ratio of CDOM absorbance increased with burn severity 1 d post-fire, indicating higher extractability of lighter molecular weight C from severe burns. These results imply that black C created from fires remains as a stable C pool while more labile C is mobilized with increasing burn severity. Our results suggest that the immediate effects of fire severity on microbial communities have the potential to change both nutrient use and the form and concentration of C being processed and mobilized from larch forest ecosystems. These findings highlight the importance of changing fire regimes on soil dynamics with implications for forest re-growth, soil-atmospheric feedbacks, and terrestrial inputs to aquatic ecosystems.

  9. 13C-DEPLETED MICROBIAL LIPIDS INDICATE SEASONAL METHANOTROPHIC ACTIVITY IN SHALLOW ESTUARINE SEDIMENTS

    EPA Science Inventory

    Compound specific isotope analysis was combined with phospholipid fatty acid (PLFA) analysis to identify methanotrophic activity in members of the sedimentary microbial community in the Altamaha and Savannah River estuaries in Georgia. 13C-depleted PLFAs indicate methane utilizat...

  10. CARBON AND NITROGEN ACCUMULATION AND MICROBIAL ACTIVITY IN MOUNT ST. HELENS PYROCLASTIC SUBSTRATES AFTER 25 YEARS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Lupines are important ecosystem engineers, linking above and belowground recovery of Mount St. Helens pyroclastic substrates by increasing soil organic matter and microbial activity and by influencing other biotic processes. Various soil properties were measured in samples collected from locations ...

  11. Microbial enzyme activities of peatland soils in south central Alaska lowlands

    EPA Science Inventory

    Microbial enzyme activities related to carbon and nutrient acquisition were measured on Alaskan peatland soils as indicators of nutrient limitation and biochemical sustainability. Peat decomposition is mediated by microorganisms and enzymes that in turn are limited by various ph...

  12. Metatranscriptomic Analysis of Groundwater Reveals an Active Anammox Bacterial Population

    NASA Astrophysics Data System (ADS)

    Jewell, T. N. M.; Karaoz, U.; Thomas, B. C.; Banfield, J. F.; Brodie, E.; Williams, K. H.; Beller, H. R.

    2014-12-01

    Groundwater is a major natural resource, yet little is known about the contribution of microbial anaerobic ammonium oxidation (anammox) activity to subsurface nitrogen cycling. During anammox, energy is generated as ammonium is oxidized under anaerobic conditions to dinitrogen gas, using nitrite as the final electron acceptor. This process is a global sink for fixed nitrogen. Only a narrow range of monophyletic bacteria within the Planctomycetes carries out anammox, and the full extent of their metabolism, and subsequent impact on nitrogen cycling and microbial community structure, is still unknown. Here, we employ a metatranscriptomic analysis on enriched mRNA to identify the abundance and activity of a population of anammox bacteria within an aquifer at Rifle, CO. Planktonic biomass was collected over a two-month period after injection of up to 1.5 mM nitrate. Illumina-generated sequences were mapped to a phylogenetically binned Rifle metagenome database. We identified transcripts for genes with high protein sequence identities (81-98%) to those of anammox strain KSU-1 and to two of the five anammox bacteria genera, Brocadia and Kuenenia, suggesting an active, if not diverse, anammox population. Many of the most abundant anammox transcripts mapped to a single scaffold, indicative of a single dominant anammox species. Transcripts of the genes necessary for the anammox pathway were present, including an ammonium transporter (amtB), nitrite/formate transporter, nitrite reductase (nirK), and hydrazine oxidoreductase (hzoB). The form of nitrite reductase encoded by anammox is species-dependent, and we only identified nirK, with no evidence of anammox nirS. In addition to the anammox pathway we saw evidence of the anammox bacterial dissimilatory nitrate reduction to ammonium pathway (narH, putative nrfA, and nrfB), which provides an alternate means of generating substrates for anammox from nitrate, rather than relying on an external pool. Transcripts for hydroxylamine

  13. Microbial population index and community structure in saline-alkaline soil using gene targeted metagenomics.

    PubMed

    Keshri, Jitendra; Mishra, Avinash; Jha, Bhavanath

    2013-03-30

    Population indices of bacteria and archaea were investigated from saline-alkaline soil and a possible microbe-environment pattern was established using gene targeted metagenomics. Clone libraries were constructed using 16S rRNA and functional gene(s) involved in carbon fixation (cbbL), nitrogen fixation (nifH), ammonia oxidation (amoA) and sulfur metabolism (apsA). Molecular phylogeny revealed the dominance of Actinobacteria, Firmicutes and Proteobacteria along with archaeal members of Halobacteraceae. The library consisted of novel bacterial (20%) and archaeal (38%) genera showing ≤95% similarity to previously retrieved sequences. Phylogenetic analysis indicated ability of inhabitant to survive in stress condition. The 16S rRNA gene libraries contained novel gene sequences and were distantly homologous with cultured bacteria. Functional gene libraries were found unique and most of the clones were distantly related to Proteobacteria, while clones of nifH gene library also showed homology with Cyanobacteria and Firmicutes. Quantitative real-time PCR exhibited that bacterial abundance was two orders of magnitude higher than archaeal. The gene(s) quantification indicated the size of the functional guilds harboring relevant key genes. The study provides insights on microbial ecology and different metabolic interactions occurring in saline-alkaline soil, possessing phylogenetically diverse groups of bacteria and archaea, which may be explored further for gene cataloging and metabolic profiling. PMID:23083746

  14. Fermentation and microbial population dynamics during the ensiling of native grass and subsequent exposure to air.

    PubMed

    Zhang, Qing; Wu, Baiyila; Nishino, Naoki; Wang, Xianguo; Yu, Zhu

    2016-03-01

    To study the microbial population and fermentation dynamics of large needlegrass (LN) and Chinese leymus (CL) during ensiling and subsequent exposure to air, silages were sampled and analyzed using culture-based techniques and denaturing gradient gel electrophoresis (DGGE). A total of 112 lactic acid bacteria (LAB) strains were isolated and identified using the 16S rRNA sequencing method. Lactic acid was not detected in the first 20 days in LN silage and the pH decreased to 6.13 after 45 days of ensiling. The temperature of the LN silage increased after approximately 30 h of air exposure and the CL silage showed a slight temperature variation. Enterococcus spp. were mainly present in LN silage. The proportion of Lactobacillus brevis in CL silage increased after exposure to air. LN silage with a higher proportion of Enterococcus spp. and propionic acid concentration did not show higher fermentation quality or aerobic stability than CL silage, which had a higher concentration of acetic acid, butyric acid and increased proportion of L. brevis after exposure to air. PMID:26950516

  15. Particulate DNA in smoker fluids: Evidence for existence of microbial populations in hot hydrothermal systems

    SciTech Connect

    Straube, W.L.; Colwell, R.R. Univ. of Maryland, Baltimore ); Deming, J.W.; Baross, J.A. ); Somerville, C.C. )

    1990-05-01

    As part of an interdisciplinary study of hydrothermal vents on the Endeavour Segment of the Juan de Fuca Ridge, we used the submersible ALVIN to collect 57 fluid samples from 17 different hot vents (smokers and flanges) and their environs for the purpose of extracting particulate DNA. Particulate material concentrated from these samples was lysed enzymatically (enz) and by a combination of enzyme and French press treatment (fp). Concentrations of partially purified DNA recovered from these lysates were determined spectrofluorometrically. Ambient seawater surrounding the vents was found to contain low DNA concentrations, 0.18 to 0.32 ng of DNA per ml, while low-temperature vent samples yielded significantly higher concentrations of 0.37 to 2.12 ng of DNA per ml. Although DNA recovery values from superheated (210 to 345{degree}C) flange samples were not significantly different from ambient seawater values, most of the superheated (174 to 357{degree}C) smoker fluid samples contained particulate DNA in concentrations too high to be attributable to entrained seawater. Detailed sampling at one smoker site demonstrated not only the existence of significant levels of particulate DNA in the superheated smoker fluids but also the presence of an elevated microbial population in the buoyant plume 20 to 100 m above the smoker. These results underscore the heterogeneity of smoker environments within a given hydrothermal vent fluid and indicate that microorganisms exist in some superheated fluids.

  16. Effects of Environmental Factors on Microbial Populations in Brackish Waters off the Southern Coast of Finland

    PubMed Central

    Väätänen, Pentti

    1980-01-01

    The roles played by environmental factors in seasonal changes in microbial populations were investigated in the Tvärminne area, off the southern coast of Finland. Surface-layer samples were collected at 1- or 2-week intervals in 1976-78, and 14 microbiological and 10 environmental parameters were determined. Stepwise multiple regression analysis was used to explain seasonal variation in the microbiological parameters. Separate analyses were made of the data from the open-water and ice-cover periods. In analyses of data from both periods, the environmental factors included accounted for a significant proportion of the variation in the parameters for community respiration (90%) and bacterial spores (80%), and a smaller proportion (60 to 65%) of the variation in total counts of bacteria and plate counts of psychrophiles and yeasts. Lower values (40 to 55%) were obtained for the variation in the other microbiological parameters. The environmental factors with maximal contributions were organic matter, water temperature, chlorophyll a, and salinity, but rainfall and winds also explained part of the variation in some microbiological parameters. In the winter analysis the results differed from those obtained for the other seasons, the variation being governed by parameters indicating freshwater outflows, namely, humic matter, salinity, water temperature (positive regression coefficient), and rainfall (negative regression coefficient). PMID:16345595

  17. Effect of incremental doses of radiation on viability of the microbial population on synthetic operating room gowns

    SciTech Connect

    Whitby, J.L.; Storey, D.G.

    1982-03-01

    A total of 700 25-cm/sup 2/ samples of surgical gown material were exposed to doses of cobalt-60 radiation of 0.0 to 0.6 Mrad in 0.1-Mrad increments. Pour plates were made, and the microbial colonies that arose were enumerated, isolated, and identified as to species. The death rate of the microbial population was calculated, and the mean D/sub 10/ value of 0.269 Mrad was obtained. Analysis showed that the initial population on unirradiated material had been underestimated; when the counts obtained by homogenization of unirradiated material were substituted, a corrected mean D/sub 10/ value of 0.249 Mrad was obtained. The isolates obtained were identified, and 70.7% were found to be Bacillus spp. with 12 different spcies identified, 16.2% were Micrococcus spp. with 6 different species identified, and 8.2% were fungi with 10 different species identified. Calculations were made for appropriate doses of radiation to sterilize gowns with this contaminating microbial population. These calculations gave an estimated dose of radiation of 1.98 to 1.81 Mrad to reduce the observed population to 0.001, a standad where 1 gown in 1,000 might contain a living organism. Comparison of the radiation resistance of this popultion with that of others reported in the literature showed good agreement.

  18. Microbial community changes along the active seepage site of one cold seep in the Red Sea

    PubMed Central

    Cao, Huiluo; Zhang, Weipeng; Wang, Yong; Qian, Pei-Yuan

    2015-01-01

    The active seepage of the marine cold seeps could be a critical process for the exchange of energy between the submerged geosphere and the sea floor environment through organic-rich fluids, potentially even affecting surrounding microbial habitats. However, few studies have investigated the associated microbial community changes. In the present study, 16S rRNA genes were pyrosequenced to decipher changes in the microbial communities from the Thuwal seepage point in the Red Sea to nearby marine sediments in the brine pool, normal marine sediments and water, and benthic microbial mats. An unexpected number of reads from unclassified groups were detected in these habitats; however, the ecological functions of these groups remain unresolved. Furthermore, ammonia-oxidizing archaeal community structures were investigated using the ammonia monooxygenase subunit A (amoA) gene. Analysis of amoA showed that planktonic marine habitats, including seeps and marine water, hosted archaeal ammonia oxidizers that differed from those in microbial mats and marine sediments, suggesting modifications of the ammonia oxidizing archaeal (AOA) communities along the environmental gradient from active seepage sites to peripheral areas. Changes in the microbial community structure of AOA in different habitats (water vs. sediment) potentially correlated with changes in salinity and oxygen concentrations. Overall, the present results revealed for the first time unanticipated novel microbial groups and changes in the ammonia-oxidizing archaea in response to environmental gradients near the active seepages of a cold seep. PMID:26284035

  19. Microbial community changes along the active seepage site of one cold seep in the Red Sea.

    PubMed

    Cao, Huiluo; Zhang, Weipeng; Wang, Yong; Qian, Pei-Yuan

    2015-01-01

    The active seepage of the marine cold seeps could be a critical process for the exchange of energy between the submerged geosphere and the sea floor environment through organic-rich fluids, potentially even affecting surrounding microbial habitats. However, few studies have investigated the associated microbial community changes. In the present study, 16S rRNA genes were pyrosequenced to decipher changes in the microbial communities from the Thuwal seepage point in the Red Sea to nearby marine sediments in the brine pool, normal marine sediments and water, and benthic microbial mats. An unexpected number of reads from unclassified groups were detected in these habitats; however, the ecological functions of these groups remain unresolved. Furthermore, ammonia-oxidizing archaeal community structures were investigated using the ammonia monooxygenase subunit A (amoA) gene. Analysis of amoA showed that planktonic marine habitats, including seeps and marine water, hosted archaeal ammonia oxidizers that differed from those in microbial mats and marine sediments, suggesting modifications of the ammonia oxidizing archaeal (AOA) communities along the environmental gradient from active seepage sites to peripheral areas. Changes in the microbial community structure of AOA in different habitats (water vs. sediment) potentially correlated with changes in salinity and oxygen concentrations. Overall, the present results revealed for the first time unanticipated novel microbial groups and changes in the ammonia-oxidizing archaea in response to environmental gradients near the active seepages of a cold seep. PMID:26284035

  20. Spatial Variations of Soil Microbial Activities in Saline Groundwater-Irrigated Soil Ecosystem

    NASA Astrophysics Data System (ADS)

    Chen, Li-Juan; Feng, Qi; Li, Chang-Sheng; Song, You-Xi; Liu, Wei; Si, Jian-Hua; Zhang, Bao-Gui

    2016-05-01

    Spatial variations of soil microbial activities and its relationship with environmental factors are very important for estimating regional soil ecosystem function. Based on field samplings in a typical saline groundwater-irrigated region, spatial variations of soil microbial metabolic activities were investigated. Combined with groundwater quality analysis, the relationship between microbial activities and water salinity was also studied. The results demonstrated that moderate spatial heterogeneity of soil microbial activities presented under the total dissolved solids (TDS) of groundwater ranging from 0.23 to 12.24 g L-1. Groundwater salinity and microbial activities had almost opposite distribution characteristics: slight saline water was mainly distributed in west Baqu and south Quanshan, while severe saline and briny water were dominant in east Baqu and west Huqu; however, total AWCD was higher in the east-center and southwest of Baqu and east Huqu, while it was lower in east Baqu and northwest Huqu. The results of correlation analyses demonstrated that high-salinity groundwater irrigation had significantly adverse effects on soil microbial activities. Major ions Ca2+, Mg2+, Cl_, and SO4 2- in groundwater decisively influenced the results. Three carbon sources, carbohydrates, amines, and phenols, which had minor utilization rates in all irrigation districts, were extremely significantly affected by high-salinity groundwater irrigation. The results presented here offer an approach for diagnosing regional soil ecosystem function changes under saline water irrigation.

  1. Spatial Variations of Soil Microbial Activities in Saline Groundwater-Irrigated Soil Ecosystem.

    PubMed

    Chen, Li-Juan; Feng, Qi; Li, Chang-Sheng; Song, You-Xi; Liu, Wei; Si, Jian-Hua; Zhang, Bao-Gui

    2016-05-01

    Spatial variations of soil microbial activities and its relationship with environmental factors are very important for estimating regional soil ecosystem function. Based on field samplings in a typical saline groundwater-irrigated region, spatial variations of soil microbial metabolic activities were investigated. Combined with groundwater quality analysis, the relationship between microbial activities and water salinity was also studied. The results demonstrated that moderate spatial heterogeneity of soil microbial activities presented under the total dissolved solids (TDS) of groundwater ranging from 0.23 to 12.24 g L(-1). Groundwater salinity and microbial activities had almost opposite distribution characteristics: slight saline water was mainly distributed in west Baqu and south Quanshan, while severe saline and briny water were dominant in east Baqu and west Huqu; however, total AWCD was higher in the east-center and southwest of Baqu and east Huqu, while it was lower in east Baqu and northwest Huqu. The results of correlation analyses demonstrated that high-salinity groundwater irrigation had significantly adverse effects on soil microbial activities. Major ions Ca(2+), Mg(2+), Cl(_), and SO4 (2-) in groundwater decisively influenced the results. Three carbon sources, carbohydrates, amines, and phenols, which had minor utilization rates in all irrigation districts, were extremely significantly affected by high-salinity groundwater irrigation. The results presented here offer an approach for diagnosing regional soil ecosystem function changes under saline water irrigation. PMID:26872886

  2. Seasonal and Diel Variability in Dissolved DNA and in Microbial Biomass and Activity in a Subtropical Estuary

    PubMed Central

    Paul, John H.; DeFlaun, Mary F.; Jeffrey, Wade H.; David, Andrew W.

    1988-01-01

    Dissolved DNA and microbial biomass and activity parameters were measured over a 15-month period at three stations along a salinity gradient in Tampa Bay, Fla. Dissolved DNA showed seasonal variation, with minimal values in December and January and maximal values in summer months (July and August). This pattern of seasonal variation followed that of particulate DNA and water temperature and did not correlate with bacterioplankton (direct counts and [3H]thymidine incorporation) or phytoplankton (chlorophyll a and 14CO2 fixation) biomass and activity. Microautotrophic populations showed maxima in the spring and fall, whereas microheterotrophic activity was greatest in late summer (September). Both autotrophic and heterotrophic microbial activity was greatest at the high estuarine (low salinity) station and lowest at the mouth of the bay (high salinity station), irrespective of season. Dissolved DNA carbon and phosphorus constituted 0.11 ± 0.05% of the dissolved organic carbon and 6.6 ± 6.5% of the dissolved organic phosphorus, respectively. Strong diel periodicity was noted in dissolved DNA and in microbial activity in Bayboro Harbor during the dry season. A noon maximum in primary productivity was followed by an 8 p.m. maximum in heterotrophic activity and a midnight maximum in dissolved DNA. This diel periodicity was less pronounced in the wet season, when microbial parameters were strongly influenced by episodic inputs of freshwater. These results suggest that seasonal and diel production of dissolved DNA is driven by primary production, either through direct DNA release by phytoplankton, or more likely, through growth of bacterioplankton on phytoplankton exudates, followed by excretion and lysis. PMID:16347583

  3. Promoting Uranium Immobilization by the Activities of Microbial Phosphatases

    SciTech Connect

    Robert J. Martinez; Melanie J. Beazley; Samuel M. Webb; Martial Taillefert; and Patricia A. Sobecky

    2007-04-19

    The overall objective of this project is to examine the activity of nonspecific phosphohydrolases present in naturally occurring subsurface microorganisms for the purpose of promoting the immobilization of radionuclides through the production of uranium [U(VI)] phosphate precipitates. Specifically, we hypothesize that the precipitation of U(VI) phosphate minerals may be promoted through the microbial release and/or accumulation of PO4 3- as a means to detoxify radionuclides and heavy metals. An experimental approach was designed to determine the extent of phosphatase activity in bacteria previously isolated from contaminated subsurface soils collected at the ERSP Field Research Center (FRC) in Oak Ridge, TN. Screening of 135 metal resistant isolates for phosphatase activity indicated the majority (75 of 135) exhibited a phosphatase-positive phenotype. During this phase of the project, a PCR based approach has also been designed to assay FRC isolates for the presence of one or more classes of the characterized non-specific acid phophastase (NSAP) genes likely to be involved in promoting U(VI) precipitation. Testing of a subset of Pb resistant (Pbr) Arthrobacter, Bacillus and Rahnella strains indicated 4 of the 9 Pbr isolates exhibited phosphatase phenotypes suggestive of the ability to bioprecipitate U(VI). Two FRC strains, a Rahnella sp. strain Y9602 and a Bacillus sp. strain Y9-2, were further characterized. The Rahnella sp. exhibited enhanced phosphatase activity relative to the Bacillus sp. Whole-cell enzyme assays identified a pH optimum of 5.5, and inorganic phosphate accumulated in pH 5.5 synthetic groundwater (designed to mimic FRC conditions) incubations of both strains in the presence of a model organophosphorus substrate provided as the sole C and P source. Kinetic experiments showed that these two organisms can grow in the presence of 200 μM dissolved uranium and that Rahnella is much more efficient in precipitating U(VI) than Bacillus sp. The

  4. Arabinoxylan‐oligosaccharides (AXOS) affect the protein/carbohydrate fermentation balance and microbial population dynamics of the Simulator of Human Intestinal Microbial Ecosystem

    PubMed Central

    Sanchez, J. I.; Marzorati, M.; Grootaert, C.; Baran, M.; Van Craeyveld, V.; Courtin, C. M.; Broekaert, W. F.; Delcour, J. A.; Verstraete, W.; Van de Wiele, T.

    2009-01-01

    Summary Arabinoxylan‐oligosaccharides (AXOS) are a recently newly discovered class of candidate prebiotics as – depending on their structure – they are fermented in different regions of gastrointestinal tract. This can have an impact on the protein/carbohydrate fermentation balance in the large intestine and, thus, affect the generation of potentially toxic metabolites in the colon originating from proteolytic activity. In this study, we screened different AXOS preparations for their impact on the in vitro intestinal fermentation activity and microbial community structure. Short‐term fermentation experiments with AXOS with an average degree of polymerization (avDP) of 29 allowed part of the oligosaccharides to reach the distal colon, and decreased the concentration of proteolytic markers, whereas AXOS with lower avDP were primarily fermented in the proximal colon. Additionally, prolonged supplementation of AXOS with avDP 29 to the Simulator of Human Intestinal Microbial Ecosystem (SHIME) reactor decreased levels of the toxic proteolytic markers phenol and p‐cresol in the two distal colon compartments and increased concentrations of beneficial short‐chain fatty acids (SCFA) in all colon vessels (25–48%). Denaturant gradient gel electrophoresis (DGGE) analysis indicated that AXOS supplementation only slightly modified the total microbial community, implying that the observed effects on fermentation markers are mainly caused by changes in fermentation activity. Finally, specific quantitative PCR (qPCR) analysis showed that AXOS supplementation significantly increased the amount of health‐promoting lactobacilli as well as of Bacteroides–Prevotella and Clostridium coccoides–Eubacterium rectale groups. These data allow concluding that AXOS are promising candidates to modulate the microbial metabolism in the distal colon. PMID:21261885

  5. Microbial dechlorination of historically present and freshly spiked chlorinated dioxins and diversity of dioxin-dechlorinating populations.

    PubMed Central

    Barkovskii, A L; Adriaens, P

    1996-01-01

    The ability of a microbial consortium eluted from dioxin-contaminated Passaic River sediments to dechlorinate polychlorinated dibenzo-p-dioxins (PCDDs) was investigated under methanogenic conditions. Aged 2,3,7,8-tetraCDD, which had partitioned into the microbial consortium from sediments, was stoichiometrically converted to tri- and monoCDD congeners. During dechlorination, dominant microbial activity within the consortium shifted from methanogenic to nonmethanogenic activity. Freshly spiked octaCDD was converted to hepta-, hexa-, penta-, tetra-, tri-, di-, and monochlorinated isomers, but the reaction stoichiometry was not determined. No methanogenic activity was observed, and the maximum yield of protein coincided with the production of less-chlorinated DD congeners. Two distinct pathways of dechlorination were observed: the peri-dechlorination pathway of 2,3,7,8-substituted hepta- to pentaCDDs, resulting in the production of 2,3,7,8-tetraCDD, and the peri-lateral dechlorination pathway of non-2,3,7,8-substituted congeners. Direct evidence of further lateral dechlorination of 2,3,7,8-tetraCDD was obtained from the historically contaminated incubations; no isomer-specific identification of triCDDs in spiked incubations was determined. Pasteurized cells exhibited no peri-dechlorination pathway, and triCDDs were the least-chlorinated congeners produced in these treatments. These results demonstrate that (i) both freshly spiked and aged PCDDs are available to microbial reductive dechlorination, (ii) the peri and triCDD dechlorinations are attributed to activities of nonmethanogenic, non-spore-forming microbial subpopulations, and (iii) the 2,3,7,8-residue patterns in historically contaminated sediments are likely affected by microbial activity. PMID:8953727

  6. Identification of vaginal fluid, saliva, and feces using microbial signatures in a Han Chinese population.

    PubMed

    Zou, Kai-Nan; Ren, Li-Jie; Ping, Yuan; Ma, Ke; Li, Hui; Cao, Yu; Zhou, Huai-Gu; Wei, Yi-Liang

    2016-10-01

    In recent years, forensic scientists have focused on the discrimination of body fluids using microbial signatures. In this study, we performed PCR-based detection of microbial signatures of vaginal fluid, saliva, and feces in a Han Chinese population. We investigated the 16S rRNA genes of Lactobacillus crispatus, Lactobacillus gasseri, Lactobacillus jensenii, Lactobacillus iners, and Atopobium vaginae in vaginal fluid, the 16S rRNA and the glucosyltransferase enzyme genes of Streptococcus salivarius and Streptococcus mutans in saliva, and the 16S rRNA genes of Enterococcus species, the RNA polymerase β-subunit gene of Bacteroides uniformis and Bacteroides vulgatus, and the α-1-6 mannanase gene of Bacteroides thetaiotaomicron in feces. As a result, the detection proportions of L. crispatus, L. gasseri, L. jensenii, L. iners, and A. vaginae were 15/16, 5/16, 8/16, 14/16, and 3/16 in 16 vaginal fluid donors, respectively. L. crispatus and L. jensenii were specifically detected in vaginal fluid; L. gasseri, L. iners, and A. vaginae were also detected in non-vaginal fluid. S. salivarius and S. mutans were not specifically detected in saliva. The detection proportions of Enterococcus species, B. uniformis, B. vulgatus, and B. thetaiotaomicron in 16 feces samples were 16/16, 12/16, 15/16, and 11/16, respectively. B. uniformis and B. thetaiotaomicron were specifically detected in feces. In addition, DNA samples prepared for the identification of body fluid can also be used for individual identification by short tandem repeat typing. The mean detection sensitivities of L. crispatus and L. jensenii were 0.362 and 0.249 pg/uL, respectively. In conclusion, L. crispatus, L. jensenii, B. uniformis, and B. thetaiotaomicron can be used as effective markers for forensic identification of vaginal fluid and feces. PMID:27570236

  7. Microbial dynamics and enzyme activities in tropical Andosols depending on land use and nutrient inputs

    NASA Astrophysics Data System (ADS)

    Mganga, Kevin; Razavi, Bahar; Kuzyakov, Yakov

    2015-04-01

    Microbial decomposition of soil organic matter is mediated by enzymes and is a key source of terrestrial CO2 emissions. Microbial and enzyme activities are necessary to understand soil biochemical functioning and identify changes in soil quality. However, little is known about land use and nutrients availability effects on enzyme activities and microbial processes, especially in tropical soils of Africa. This study was conducted to examine how microbial and enzyme activities differ between different land uses and nutrient availability. As Andosols of Mt. Kilimanjaro are limited by nutrient concentrations, we hypothesize that N and P additions will stimulate enzyme activity. N and P were added to soil samples (0-20 cm) representing common land use types in East Africa: (1) savannah, (2) maize fields, (3) lower montane forest, (4) coffee plantation, (5) grasslands and (6) traditional Chagga homegardens. Total CO2 efflux from soil, microbial biomass and activities of β-glucosidase, cellobiohydrolase, chitinase and phosphatase involved in C, N and P cycling, respectively was monitored for 60 days. Total CO2 production, microbial biomass and enzyme activities varied in the order forest soils > grassland soils > arable soils. Increased β-glucosidase and cellobiohydrolase activities after N addition of grassland soils suggest that microorganisms increased N uptake and utilization to produce C-acquiring enzymes. Low N concentration in all soils inhibited chitinase activity. Depending on land use, N and P addition had an inhibitory or neutral effect on phosphatase activity. We attribute this to the high P retention of Andosols and low impact of N and P on the labile P fractions. Enhanced CO2 production after P addition suggests that increased P availability could stimulate soil organic matter biodegradation in Andosols. In conclusion, land use and nutrients influenced soil enzyme activities and microbial dynamics and demonstrated the decline in soil quality after landuse

  8. Production of microbial glycolipid biosurfactants and their antimicrobial activity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microbial glycolipids produced by bacteria or yeast as secondary metabolites, such as sophorolipids (SLs), rhamnolipids (RLs) and mannosylerythritol lipids (MELs) are “green” biosurfactants desirable in a bioeconomy. High cost of production is a major hurdle toward widespread commercial use of bios...

  9. Effects of Momordica charantia Saponins on In vitro Ruminal Fermentation and Microbial Population.

    PubMed

    Kang, Jinhe; Zeng, Bo; Tang, Shaoxun; Wang, Min; Han, Xuefeng; Zhou, Chuanshe; Yan, Qiongxian; He, Zhixiong; Liu, Jinfu; Tan, Zhiliang

    2016-04-01

    This study was conducted to investigate the effects of Momordica charantia saponin (MCS) on ruminal fermentation of maize stover and abundance of selected microbial populations in vitro. Five levels of MCS supplements (0, 0.01, 0.06, 0.30, 0.60 mg/mL) were tested. The pH, NH3-N, and volatile fatty acid were measured at 6, 24, 48 h of in vitro mixed incubation fluids, whilst the selected microbial populations were determined at 6 and 24 h. The high dose of MCS increased the initial fractional rate of degradation at t-value = 0 (FRD0) and the fractional rate of gas production (k), but decreased the theoretical maximum of gas production (V F) and the half-life (t0.5) compared with the control. The NH3-N concentration reached the lowest concentration with 0.01 mg MCS/mL at 6 h. The MSC inclusion increased (p<0.001) the molar proportion of butyrate, isovalerate at 24 h and 48 h, and the molar proportion of acetate at 24 h, but then decreased (p<0.05) them at 48 h. The molar proportion of valerate was increased (p<0.05) at 24 h. The acetate to propionate ratio (A/P; linear, p<0.01) was increased at 24 h, but reached the least value at the level of 0.30 mg/mL MCS. The MCS inclusion decreased (p<0.05) the molar proportion of propionate at 24 h and then increased it at 48 h. The concentration of total volatile fatty acid was decreased (p<0.001) at 24 h, but reached the greatest concentration at the level of 0.01 mg/mL and the least concentration at the level of 0.60 mg/mL. The relative abundance of Ruminococcus albus was increased at 6 h and 24 h, and the relative abundance of Fibrobacter succinogenes was the lowest (p<0.05) at 0.60 mg/mL at 6 h and 24 h. The relative abundance of Butyrivibrio fibrisolvens and fungus reached the greatest value (p<0.05) at low doses of MCS inclusion and the least value (p<0.05) at 0.60 mg/mL at 24 h. The present results demonstrates that a high level of MCS quickly inhibits in vitro fermentation of maize stover, while MCS at low doses has

  10. Effects of Momordica charantia Saponins on In vitro Ruminal Fermentation and Microbial Population

    PubMed Central

    Kang, Jinhe; Zeng, Bo; Tang, Shaoxun; Wang, Min; Han, Xuefeng; Zhou, Chuanshe; Yan, Qiongxian; He, Zhixiong; Liu, Jinfu; Tan, Zhiliang

    2016-01-01

    This study was conducted to investigate the effects of Momordica charantia saponin (MCS) on ruminal fermentation of maize stover and abundance of selected microbial populations in vitro. Five levels of MCS supplements (0, 0.01, 0.06, 0.30, 0.60 mg/mL) were tested. The pH, NH3-N, and volatile fatty acid were measured at 6, 24, 48 h of in vitro mixed incubation fluids, whilst the selected microbial populations were determined at 6 and 24 h. The high dose of MCS increased the initial fractional rate of degradation at t-value = 0 (FRD0) and the fractional rate of gas production (k), but decreased the theoretical maximum of gas production (VF) and the half-life (t0.5) compared with the control. The NH3-N concentration reached the lowest concentration with 0.01 mg MCS/mL at 6 h. The MSC inclusion increased (p<0.001) the molar proportion of butyrate, isovalerate at 24 h and 48 h, and the molar proportion of acetate at 24 h, but then decreased (p<0.05) them at 48 h. The molar proportion of valerate was increased (p<0.05) at 24 h. The acetate to propionate ratio (A/P; linear, p<0.01) was increased at 24 h, but reached the least value at the level of 0.30 mg/mL MCS. The MCS inclusion decreased (p<0.05) the molar proportion of propionate at 24 h and then increased it at 48 h. The concentration of total volatile fatty acid was decreased (p<0.001) at 24 h, but reached the greatest concentration at the level of 0.01 mg/mL and the least concentration at the level of 0.60 mg/mL. The relative abundance of Ruminococcus albus was increased at 6 h and 24 h, and the relative abundance of Fibrobacter succinogenes was the lowest (p<0.05) at 0.60 mg/mL at 6 h and 24 h. The relative abundance of Butyrivibrio fibrisolvens and fungus reached the greatest value (p<0.05) at low doses of MCS inclusion and the least value (p<0.05) at 0.60 mg/mL at 24 h. The present results demonstrates that a high level of MCS quickly inhibits in vitro fermentation of maize stover, while MCS at low doses has the

  11. Active Marine Subsurface Bacterial Population Composition in Low Organic Carbon Environments from IODP Expedition 320

    NASA Astrophysics Data System (ADS)

    Shepard, A.; Reese, B. K.; Mills, H. J.; IODP Expedition 320 Shipboard Science Party

    2011-12-01

    The marine subsurface environment contains abundant and active microorganisms. These microbial populations are considered integral players in the marine subsurface biogeochemical system with significance in global geochemical cycles and reservoirs. However, variations in microbial community structure, activity and function associated with the wide-ranging sedimentary and geochemical environments found globally have not been fully resolved. Integrated Ocean Drilling Program Expedition 320 recovered sediments from site U1332. Two sampling depths were selected for analysis that spanned differing lithological units in the sediment core. Sediments were composed of mostly clay with zeolite minerals at 8 meters below sea floor (mbsf). At 27 mbsf, sediments were composed of alternating clayey radiolarian ooze and nannofossil ooze. The concentration of SO42- had little variability throughout the core and the concentration of Fe2+ remained close to, or below, detection limits (0.4 μM). Total organic carbon content ranged from a low of 0.03 wt% to a high of 0.07 wt% between 6 and 30 mbsf providing an opportunity to evaluate marine subsurface microbial communities under extreme electron donor limiting conditions. The metabolically active fraction of the bacterial population was isolated by the extraction and amplification of 16S ribosomal RNA. Pyrosequencing of 16S rRNA transcripts and subsequent bioinformatic analyses provided a robust data set (15,931 total classified sequences) to characterize the community at a high resolution. As observed in other subsurface environments, the overall diversity of active bacterial populations decreased with depth. The population shifted from a diverse but evenly distributed community at approximately 8 mbsf to a Firmicutes dominated population at 27 mbsf (80% of sequences). A total of 95% of the sequences at 27 mbsf were grouped into three genera: Lactobacillus (phylum Firmicutes) at 80% of the total sequences, Marinobacter (phylum

  12. Effects of plastic film residues on occurrence of phthalates and microbial activity in soils.

    PubMed

    Wang, Jun; Lv, Shenghong; Zhang, Manyun; Chen, Gangcai; Zhu, Tongbin; Zhang, Shen; Teng, Ying; Christie, Peter; Luo, Yongming

    2016-05-01

    Plastic film mulching has played an important role in Chinese agriculture, especially in vegetable production, but large amounts of film residues can accumulate in the soil. The present study investigated the effects of plastic film residues on the occurrence of soil PAEs and microbial activities using a batch pot experiment. PAE concentrations increased with increasing plastic film residues but the soil microbial carbon and nitrogen, enzyme activities and microbial diversity decreased significantly. At the end of the experiment the PAE concentrations were 0-2.02 mg kg(-1) in the different treatments. Soil microbial C and N, enzyme activities, AWCD value, and Shannon-Weaver and Simpson indices declined by about 28.9-76.2%, 14.9-59.0%, 4.9-22.7%, 23.0-42.0% and 1.8-18.7%, respectively. Soil microbial activity was positively correlated with soil PAE concentration, and soil PAE concentrations were impacted by plastic color and residue volume. Correlations among, and molecular mechanisms of, plastic film residues, PAE occurrence and microbial activity require further study. PMID:26938679

  13. Quantitative analysis of ruminal methanogenic microbial populations in beef cattle divergent in phenotypic residual feed intake (RFI) offered contrasting diets

    PubMed Central

    2014-01-01

    Background Methane (CH4) emissions in cattle are an undesirable end product of rumen methanogenic fermentative activity as they are associated not only with negative environmental impacts but also with reduced host feed efficiency. The aim of this study was to quantify total and specific rumen microbial methanogenic populations in beef cattle divergently selected for residual feed intake (RFI) while offered (i) a low energy high forage (HF) diet followed by (ii) a high energy low forage (LF) diet. Ruminal fluid was collected from 14 high (H) and 14 low (L) RFI animals across both dietary periods. Quantitative real time PCR (qRT-PCR) analysis was conducted to quantify the abundance of total and specific rumen methanogenic microbes. Spearman correlation analysis was used to investigate the association between the relative abundance of methanogens and animal performance, rumen fermentation variables and diet digestibility. Results Abundance of methanogens, did not differ between RFI phenotypes. However, relative abundance of total and specific methanogen species was affected (P < 0.05) by diet type, with greater abundance observed while animals were offered the LF compared to the HF diet. Conclusions These findings suggest that differences in abundance of specific rumen methanogen species may not contribute to variation in CH4 emissions between efficient and inefficient animals, however dietary manipulation can influence the abundance of total and specific methanogen species. PMID:25276350

  14. Environmental parameters controlling microbial activities in terrestrial subsurface environments

    SciTech Connect

    Kieft, T.L.

    1990-01-01

    This project was begun in July 1988 as part of Phase I of the Deep Microbiology Subprogram. At this time, the Subprogram was preparing for sampling near the Savannah River Site (SRS) from what was being termed the Investigator's Hole.'' This was the fourth hole drilled for sampling in the coastal plain sediments at a site near the SRS. Since there was a possibility of sampling from the saline Triassic basin in the deeper regions in this fourth hole, there was particular interest in quantifying halotolerant microorganisms from these samples and in determining the responses of subsurface microbes to a range of soft concentrations. Further interest in the soft tolerances of microbes from these coastal sediments arose from the fact that all of these sediments were deposited under marine conditions. It was also anticipated that samples would be available from the shallow unsaturated (vadose) zone at this site, so there was interest in quantifying microbial responses to matric water potential as well as solute water potential. The initial objectives of this research project were to: characterize microbial communities in a saline aquifer; determine the potential for microbial metabolism of selected organic compounds in a saline aquifers; characterize microbial communities in unsaturated subsurface materials (vadose zones); and determine the potential for microbial metabolism of selected organic compounds in unsaturated subsurface materials (vadose zones). Samples were collected from the borehole during a period extending from August to October 1988. A total of nine samples were express shipped to New Mexico Tech for analyses. These were all saturated zone samples from six different geological formations. Water contents and water potentials were measured at the time of sample arrival.

  15. Microbial activity promotes carbon storage in temperate soils

    NASA Astrophysics Data System (ADS)

    Lange, Markus; Eisenhauer, Nico; Sierra, Carlos; Gleixner, Gerd

    2014-05-01

    Soils are one of the most important carbon sink and sources. Soils contain up to 3/4 of all terrestrial carbon. Beside physical aspects of soil properties (e.g. soil moisture and texture) plants play an important role in carbon sequestration. The positive effect of plant diversity on carbon storage is already known, though the underlying mechanisms remain still unclear. In the frame of the Jena Experiment, a long term biodiversity experiment, we are able to identify these processes. Nine years after an land use change from an arable field to managed grassland the mean soil carbon concentrations increased towards the concentrations of permanent meadows. The increase was positively linked to a plant diversity gradient. High diverse plant communities produce more biomass, which in turn results in higher amounts of litter inputs. The plant litter is transferred to the soil organic matter by the soil microbial community. However, higher plant diversity also causes changes in micro-climatic condition. For instance, more diverse plant communities have a more dense vegetation structure, which reduced the evaporation of soils surface and thus, increases soil moisture in the top layer. Higher inputs and higher soil moisture lead to an enlarged respiration of the soil microbial community. Most interestingly, the carbon storage in the Jena Experiment was much more related to microbial respiration than to plant root inputs. Moreover, using radiocarbon, we found a significant younger carbon age in soils of more diverse plant communities than in soils of lower diversity, indicating that more fresh carbon is integrated into the carbon pool. Putting these findings together, we could show, that the positive link between plant diversity and carbon storage is due to a higher microbial decomposition of plant litter, pointing out that carbon storage in soils is a function of the microbial community.

  16. Distribution and Composition of Microbial Populations in a Landfill Leachate Contaminated Aquifer (Grindsted, Denmark).

    PubMed

    Ludvigsen; Albrechtsen; Ringelberg; Ekelund; Christensen

    1999-04-01

    > Abstract To investigate whether landfill leachates affected the microbial biomass and/or community composition of the extant microbiota, 37 samples were collected along a 305-m transect of a shallow landfill-leachate polluted aquifer. The samples were analyzed for total numbers of bacteria by use of the acridine orange direct count method (AODC). Numbers of dominant, specific groups of bacteria and total numbers of protozoa were measured by use of the most probable number method (MPN). Viable biomass estimates were obtained from measures of ATP and ester-linked phospholipid fatty acid (PLFA) concentrations. The estimated numbers of total bacteria by direct counts were relatively constant throughout the aquifer, ranging from a low of 4.8 x 10(6) cells/g dry weight (dw) to a high of 5.3 x 10(7) cells/g dw. Viable biomass estimates based on PLFA concentrations were one to three orders of magnitude lower with the greatest concentrations (up to 4 x 10(5) cells/g dw) occurring at the border of the landfill and in samples collected from thin lenses of clay and silt with sand streaks. Cell number estimates based on ATP concentrations were also found to be lower than the direct count measurements (<2.2 x 10(6) cells/g dw), and with the greatest concentrations close to the landfill. Methanogens (Archaea) and reducers of sulfate, iron, manganese, and nitrate were all observed in the aquifer. Methanogens were found to be restricted to the most polluted and reduced part of the aquifer at a maximum cell number of 5.4 x 10(4) cells/g dw. Populations of sulfate reducers decreased with an increase in horizontal distance from the landfill ranging from a high of 9.0 x 10(3) cells/g dw to a low of 6 cells/g dw. Iron, manganese, and nitrate reducers were detected throughout the leachate plume all at maximum cell numbers of 10(6) cells/g dw. Changes in PLFA profiles indicated that a shift in microbial community composition occurred with increasing horizontal distance from the landfill

  17. Population density and total biomass of microbial communities in chestnut soils and solonetzes of the dry steppe zone in the Lower Volga region

    NASA Astrophysics Data System (ADS)

    Kashirskaya, N. N.; Khomutova, T. E.; Chernysheva, E. V.; El'tsov, M. V.; Demkin, V. A.

    2015-03-01

    The population density and total biomass of microbial communities were determined in chestnut soils and solonetzes of the dry steppe zone in the Lower Volga region with the use of the methods of sequential fractionation of the soil and direct counting. The mean weighted values of the population density of the microbial communities in the soil profiles (A1 + B1 + B2 horizons) in the studied soils varied within 3.8-8.0 × 1011 cells/g of soil. The total microbial biomass in the soils of the Privolzhskaya Upland reached 0.9-2.4 mg C/g of soil; in the soils of the Ergeni Upland, it was 20 to 75% lower. The microbial cells in the soils of the Privolzhskaya Upland were larger than those in the soils of the Ergeni Upland. Sequential fractionation of the soil prior to direct counting contributed to the more complete assessment of the population density of the microbial communities.

  18. Comparison of fermentation of diets of variable composition and microbial populations in the rumen of sheep and Rusitec fermenters. I. Digestibility, fermentation parameters, and microbial growth.

    PubMed

    Martínez, M E; Ranilla, M J; Tejido, M L; Ramos, S; Carro, M D

    2010-08-01

    Four ruminally and duodenally cannulated sheep and 8 Rusitec fermenters were used to determine the effects of forage to concentrate (F:C) ratio and type of forage in the diet on ruminal fermentation and microbial protein synthesis. The purpose of the study was to assess how closely fermenters can mimic the dietary differences found in vivo. The 4 experimental diets contained F:C ratios of 70:30 or 30:70 with either alfalfa hay or grass hay as the forage. Microbial growth was determined in both systems using (15)N as a microbial marker. Rusitec fermenters detected differences between diets similar to those observed in sheep by changing F:C ratio on pH; neutral detergent fiber digestibility; total volatile fatty acid concentrations; molar proportions of acetate, propionate, butyrate, isovalerate, and caproate; and amylase activity. In contrast, Rusitec fermenters did not reproduce the dietary differences found in sheep for NH(3)-N and lactate concentrations, dry matter (DM) digestibility, proportions of isobutyrate and valerate, carboxymethylcellulase and xylanase activities, and microbial growth and its efficiency. Regarding the effect of the type of forage in the diet, Rusitec fermenters detected differences between diets similar to those found in sheep for most determined parameters, with the exception of pH, DM digestibility, butyrate proportion, and carboxymethylcellulase activity. Minimum pH and maximal volatile fatty acid concentrations were reached at 2h and at 6 to 8h postfeeding in sheep and fermenters, respectively, indicating that feed fermentation was slower in fermenters compared with that in sheep. There were differences between systems in the magnitude of most determined parameters. In general, fermenters showed lower lactate concentrations, neutral detergent fiber digestibility, acetate:propionate ratios, and enzymatic activities. On the contrary, fermenters showed greater NH(3)-N concentrations, DM digestibility, and proportions of propionate

  19. Microbial diversity and activity are increased by compost amendment of metal-contaminated soil.

    PubMed

    Farrell, Mark; Griffith, Gareth W; Hobbs, Phil J; Perkins, William T; Jones, Davey L

    2010-01-01

    Unlike organic pollutants, heavy metals cannot be degraded and can constitute a persistent environmental hazard. Here, we investigated the success of different remediation strategies in promoting microbial diversity and function with depth in an acidic soil heavily contaminated with Cu, Pb and Zn. Remediation involved the incorporation of either a high- or a low-quality compost or inorganic fertilizer into the topsoil and monitoring of microbial activity and diversity with soil depth over a 4-month period. While changes in topsoil microbial activity were expected, the possible effects on the subsurface microbial community due to the downward movement of metals, nutrients and/or soluble organic matter have not been examined previously. The results showed that both compost additions, especially the low-quality compost, resulted in significantly increased bacterial and fungal diversity (as assessed by terminal restriction fragment length polymorphism) and activity compared with the inorganic and control treatments in the topsoil. Although phospholipid fatty acid profiling indicated that compost addition had promoted enhanced microbial diversity in the subsoil, no concomitant increase in subsoil microbial activity was observed, suggesting that amelioration of the heavy metals remained localized in the topsoil. We conclude that although composts can successfully immobilize heavy metals and promote ecosystem diversity/function, surface incorporation had little remedial effect below the surface layer over the course of our short-term trial. PMID:19845764

  20. Physical and Chemical Correlates of Microbial Activity and Biomass in Composting Municipal Sewage Sludge

    PubMed Central

    McKinley, Vicky L.; Vestal, J. Robie

    1985-01-01

    Various physical and chemical parameters were monitored to evaluate their influence on the microbial communities present in composting municipal sewage sludge. Temperature, moisture content, depth, pH, protein content, total nitrogen, total carbon, lipid phosphate biomass, and the rates of microbial incorporation of substrates into lipids were measured at several times throughout the 17- to 19-day composting runs. Temperature was found to have the most consistent and dramatic effect on microbial activity and biomass. When temperatures exceeded 55 to 60°C, microbial activity fell dramatically, usually by more than 1 order of magnitude. Microbial activity was generally greatest in samples taken from the 35 to 50°C areas of the composting piles. Changes in the composition of the compost over time included increased pH, increased protein content, and decreased total organic content. The changes in these parameters appeared to reflect the microbial activity and biomass present. The results of this study indicate that the rate of composting may best be optimized by controlling the composting temperatures, provided that the other parameters fall within reasonable limits in the starting material. PMID:16346940

  1. Effects of Flavonoid-rich Plant Extracts on In vitro Ruminal Methanogenesis, Microbial Populations and Fermentation Characteristics.

    PubMed

    Kim, Eun T; Guan, Le Luo; Lee, Shin J; Lee, Sang M; Lee, Sang S; Lee, Il D; Lee, Su K; Lee, Sung S

    2015-04-01

    The objective of this study was to evaluate the in vitro effects of flavonoid-rich plant extracts (PE) on ruminal fermentation characteristics and methane emission by studying their effectiveness for methanogenesis in the rumen. A fistulated Holstein cow was used as a donor of rumen fluid. The PE (Punica granatum, Betula schmidtii, Ginkgo biloba, Camellia japonica, and Cudrania tricuspidata) known to have high concentrations of flavonoid were added to an in vitro fermentation incubated with rumen fluid. Total gas production and microbial growth with all PE was higher than that of the control at 24 h incubation, while the methane emission was significantly lower (p<0.05) than that of the control. The decrease in methane accumulation relative to the control was 47.6%, 39.6%, 46.7%, 47.9%, and 48.8% for Punica, Betula, Ginkgo, Camellia, and Cudrania treatments, respectively. Ciliate populations were reduced by more than 60% in flavonoid-rich PE treatments. The Fibrobacter succinogenes diversity in all added flavonoid-rich PE was shown to increase, while the Ruminoccocus albus and R. flavefaciens populations in all PE decreased as compared with the control. In particular, the F. succinogenes community with the addition of Birch extract increased to a greater extent than that of others. In conclusion, the results of this study showed that flavonoid-rich PE decreased ruminal methane emission without adversely affecting ruminal fermentation characteristics in vitro in 24 h incubation time, suggesting that the flavonoid-rich PE have potential possibility as bio-active regulator for ruminants. PMID:25656200

  2. Effects of Flavonoid-rich Plant Extracts on In vitro Ruminal Methanogenesis, Microbial Populations and Fermentation Characteristics

    PubMed Central

    Kim, Eun T.; Guan, Le Luo; Lee, Shin J.; Lee, Sang M.; Lee, Sang S.; Lee, Il D.; Lee, Su K.; Lee, Sung S.

    2015-01-01

    The objective of this study was to evaluate the in vitro effects of flavonoid-rich plant extracts (PE) on ruminal fermentation characteristics and methane emission by studying their effectiveness for methanogenesis in the rumen. A fistulated Holstein cow was used as a donor of rumen fluid. The PE (Punica granatum, Betula schmidtii, Ginkgo biloba, Camellia japonica, and Cudrania tricuspidata) known to have high concentrations of flavonoid were added to an in vitro fermentation incubated with rumen fluid. Total gas production and microbial growth with all PE was higher than that of the control at 24 h incubation, while the methane emission was significantly lower (p<0.05) than that of the control. The decrease in methane accumulation relative to the control was 47.6%, 39.6%, 46.7%, 47.9%, and 48.8% for Punica, Betula, Ginkgo, Camellia, and Cudrania treatments, respectively. Ciliate populations were reduced by more than 60% in flavonoid-rich PE treatments. The Fibrobacter succinogenes diversity in all added flavonoid-rich PE was shown to increase, while the Ruminoccocus albus and R. flavefaciens populations in all PE decreased as compared with the control. In particular, the F. succinogenes community with the addition of Birch extract increased to a greater extent than that of others. In conclusion, the results of this study showed that flavonoid-rich PE decreased ruminal methane emission without adversely affecting ruminal fermentation characteristics in vitro in 24 h incubation time, suggesting that the flavonoid-rich PE have potential possibility as bio-active regulator for ruminants. PMID:25656200

  3. Metaproteomics: extracting and mining proteome information to characterize metabolic activities in microbial communities

    SciTech Connect

    Abraham, Paul E; Giannone, Richard J; Xiong, Weili; Hettich, Robert {Bob} L

    2014-01-01

    Contemporary microbial ecology studies usually employ one or more omics approaches to investigate the structure and function of microbial communities. Among these, metaproteomics aims to characterize the metabolic activities of the microbial membership, providing a direct link between the genetic potential and functional metabolism. The successful deployment of metaproteomics research depends on the integration of high-quality experimental and bioinformatic techniques for uncovering the metabolic activities of a microbial community in a way that is complementary to other meta-omic approaches. The essential, quality-defining informatics steps in metaproteomics investigations are: (1) construction of the metagenome, (2) functional annotation of predicted protein-coding genes, (3) protein database searching, (4) protein inference, and (5) extraction of metabolic information. In this article, we provide an overview of current bioinformatic approaches and software implementations in metaproteome studies in order to highlight the key considerations needed for successful implementation of this powerful community-biology tool.

  4. Metaproteomics: extracting and mining proteome information to characterize metabolic activities in microbial communities.

    PubMed

    Abraham, Paul E; Giannone, Richard J; Xiong, Weili; Hettich, Robert L

    2014-01-01

    Contemporary microbial ecology studies usually employ one or more "omics" approaches to investigate the structure and function of microbial communities. Among these, metaproteomics aims to characterize the metabolic activities of the microbial membership, providing a direct link between the genetic potential and functional metabolism. The successful deployment of metaproteomics research depends on the integration of high-quality experimental and bioinformatic techniques for uncovering the metabolic activities of a microbial community in a way that is complementary to other "meta-omic" approaches. The essential, quality-defining informatics steps in metaproteomics investigations are: (1) construction of the metagenome, (2) functional annotation of predicted protein-coding genes, (3) protein database searching, (4) protein inference, and (5) extraction of metabolic information. In this article, we provide an overview of current bioinformatic approaches and software implementations in metaproteome studies in order to highlight the key considerations needed for successful implementation of this powerful community-biology tool. PMID:24939130

  5. Combination of sodium chlorite and calcium propionate reduces enzymatic browning and microbial population of fresh-cut ‘Granny Smith’ apples

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Tissue browning and microbial growth are the main concerns associated with fresh-cut apples. In this study, effects of sodium chlorite (SC) and calcium propionate (CP), individually and combined, on quality and microbial population of apple slices were investigated. ‘Granny Smith’ apple slices, dipp...

  6. Soil Enzyme Activities, Microbial Communities and Carbon and Nitrogen Availability in Organic Agroecosystems Across an Intensively-Managed Agricultural Landscape

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Variability in the activity and composition of soil microbial communities may have important implications for the suite of microbially-derived ecosystem functions upon which agricultural systems rely, particularly organic agriculture. An on-farm approach was used to investigate microbial communitie...

  7. Ecology, Microbial

    SciTech Connect

    Konopka, Allan

    2009-03-19

    Microbial ecology is a relatively young discipline within the field of microbiology. Its modern history spans just the past 60 years, and the field is defined by its emphasis on understanding the interactions of microbes with their environment, rather than their behavior under artificial laboratory conditions. Because microbes are ubiquitous, microbial ecologists study a broad diversity of habitats that range from aquatic to terrestrial to plant- or animal-associated. This has made it a challenge to identify unifying principles within the field. One approach is to recognize that although the activity of microbes in nature have effects at the macroscale, they interact with their physical, chemical and biological milieu at a scale of micrometers. At this scale, several different microbial ecosystems can be defined, based upon association with particles, the presence of environmental gradients and the continuous availability of water. Principles applicable to microbial ecology reflect not only their population ecology and physiological ecology, but also their broad versatility and quantitative importance in the biosphere as biogeochemical catalysts and capacity for rapid physiological and evolutionary responses.

  8. Ecology, Microbial

    SciTech Connect

    Konopka, Allan

    2009-05-15

    Microbial ecology is a relatively young discipline within the field of microbiology. Its modern history spans just the past 60 years, and the field is defined by its emphasis on understanding the interactions of microbes with their environment, rather than their behavior under artificial laboratory conditions. Because microbes are ubiquitous, microbial ecologists study a broad diversity of habitats that range from aquatic to terrestrial to plant- or animal-associated. This has made it a challenge to identify unifying principles within the field. One approach is to recognize that although the activity of microbes in nature have effects at the macroscale, they interact with their physical, chemical and biological milieu at a scale of micrometers. At this scale, several different microbial ecosystems can be defined, based upon association with particles, the presence of environmental gradients and the continuous availability of water. Principles applicable to microbial ecology reflect not only their population ecology and physiological ecology, but also their broad versatility and quantitative importance in the biosphere as biogeochemical catalysts and capacity for rapid physiological and evolutionary responses.

  9. Electricity generation from cattle dung using microbial fuel cell technology during anaerobic acidogenesis and the development of microbial populations.

    PubMed

    Zhao, Guang; Ma, Fang; Wei, Li; Chua, Hong; Chang, Chein-Chi; Zhang, Xiao-Jun

    2012-09-01

    A microbial fuel cell (MFC) was constructed to investigate the possible generation of electricity using cattle dung as a substrate. After 30 days of operation, stable electricity was generated, and the maximum volumetric power density was 0.220 W/m(3). The total chemical oxygen demand (TCOD) removal and coulombic efficiency (CE) of the MFC reached 73.9±1.8% and 2.79±0.6%, respectively, after 120 days of operation. Acetate was the main metabolite in the anolyte, and other volatile fatty acids (VFAs) (propionate and butyrate) were present in minor amounts. The PCR-DGGE analysis indicated that the following five groups of microbes were present: Proteobacteria, Bacteroides, Chloroflexi, Actinobacteria and Firmicutes. Proteobacteria and Firmicutes were the dominant phyla in the sample; specifically, 36.3% and 24.2% of the sequences obtained were Proteobacteria and Firmicutes, respectively. Clostridium sp., Pseudomonas luteola and Ochrobactrum pseudogrignonense were the most dominant groups during the electricity generation process. The diversity of archaea dramatically decreased after 20 days of operation. The detected archaea were hydrogenotrophic methanogens, and the Methanobacterium genus disappeared during the periods of stable electricity generation via acidogenesis. PMID:22595839

  10. Particulate DNA in Smoker Fluids: Evidence for Existence of Microbial Populations in Hot Hydrothermal Systems

    PubMed Central

    Straube, W. L.; Deming, J. W.; Somerville, C. C.; Colwell, R. R.; Baross, J. A.

    1990-01-01

    As part of an interdisciplinary study of hydrothermal vents on the Endeavour Segment of the Juan de Fuca Ridge, we used the submersible ALVIN to collect 57 fluid samples in titanium syringes and Go Flo Niskin bottles from 17 different hot vents (smokers and flanges) and their environs for the purpose of extracting particulate DNA. The relative purity of the vent fluids collected was determined by Mg content as an indicator of seawater entrainment. Particulate material concentrated from these samples was lysed enzymatically (enz) and by a combination of enzyme and French press treatment (fp). Concentrations of partially purified DNA recovered from these lysates were determined spectrofluorometrically by using the dye Hoechst 33258. Ambient seawater surrounding the vents was found to contain low DNA concentrations, 0.18 to 0.32 ng of DNA per ml (n = 4; meanenz = 0.23 ± 0.05; meanfp = 0.26 ± 0.05), while low-temperature vent samples yielded significantly higher concentrations of 0.37 to 2.12 ng of DNA per ml (n = 4; meanenz = 0.97 ± 0.68; meanfp = 1.05 ± 0.54). Although DNA recovery values from superheated (210 to 345°C) flange samples (meanenz = 0.14 ± 0.10; meanfp = 0.12 ± 0.14) were not significantly different from ambient seawater values, most of the superheated (174 to 357°C) smoker fluid samples contained particulate DNA in concentrations too high to be attributable to entrained seawater. Detailed sampling at one smoker site demonstrated not only the existence of significant levels of particulate DNA in the superheated smoker fluids but also the presence of an elevated microbial population in the buoyant plume 20 to 100 m above the smoker. These results underscore the heterogeneity of smoker environments within a given hydrothermal vent field and indicate that microorganisms exist in some superheated fluids. PMID:16348193

  11. Particulate DNA in smoker fluids: evidence for existence of microbial populations in hot hydrothermal systems.

    PubMed

    Straube, W L; Deming, J W; Somerville, C C; Colwell, R R; Baross, J A

    1990-05-01

    As part of an interdisciplinary study of hydrothermal vents on the Endeavour Segment of the Juan de Fuca Ridge, we used the submersible ALVIN to collect 57 fluid samples in titanium syringes and Go Flo Niskin bottles from 17 different hot vents (smokers and flanges) and their environs for the purpose of extracting particulate DNA. The relative purity of the vent fluids collected was determined by Mg content as an indicator of seawater entrainment. Particulate material concentrated from these samples was lysed enzymatically (enz) and by a combination of enzyme and French press treatment (fp). Concentrations of partially purified DNA recovered from these lysates were determined spectrofluorometrically by using the dye Hoechst 33258. Ambient seawater surrounding the vents was found to contain low DNA concentrations, 0.18 to 0.32 ng of DNA per ml (n = 4; mean(enz) = 0.23 +/- 0.05; mean(fp) = 0.26 +/- 0.05), while low-temperature vent samples yielded significantly higher concentrations of 0.37 to 2.12 ng of DNA per ml (n = 4; mean(enz) = 0.97 +/- 0.68; mean(fp) = 1.05 +/- 0.54). Although DNA recovery values from superheated (210 to 345 degrees C) flange samples (mean(enz) = 0.14 +/- 0.10; mean(fp) = 0.12 +/- 0.14) were not significantly different from ambient seawater values, most of the superheated (174 to 357 degrees C) smoker fluid samples contained particulate DNA in concentrations too high to be attributable to entrained seawater. Detailed sampling at one smoker site demonstrated not only the existence of significant levels of particulate DNA in the superheated smoker fluids but also the presence of an elevated microbial population in the buoyant plume 20 to 100 m above the smoker. These results underscore the heterogeneity of smoker environments within a given hydrothermal vent field and indicate that microorganisms exist in some superheated fluids. PMID:16348193

  12. Biomineral formation as a biosignature for microbial activities Precambrian cherts

    NASA Astrophysics Data System (ADS)

    Rincón Tomás, Blanca; Mühlen, Dominik; Hoppert, Michael; Reitner, Joachim

    2015-04-01

    In recent anoxic sediments manganese(II)carbonate minerals (e.g., rhodochrosite, kutnohorite) derive mainly from the reduction of manganese(IV) compounds by microbial anaerobic respiration. Small particles of rhodochrosite in stromatolite-like features in the Dresser chert Fm (Pilbara supergroup, W-Australia), associated with small flakes of kerogen, account for biogenic formation of the mineral in this early Archaean setting. Contrastingly, the formation of huge manganese-rich (carbonate) deposits requires effective manganese redox cycling, also conducted by various microbial processes, mainly requiring conditions of the early and late Proterozoic (Kirschvink et al., 2000; Nealson and Saffrani 1994). However, putative anaerobic pathways like microbial nitrate-dependent manganese oxidation (Hulth et al., 1999), anoxygenic photosynthesis (Johnson et al., 2013) and oxidation in UV light may facilitate manganese cycling even in a reducing atmosphere. Thus manganese redox cycling might have been possible even before the onset of oxygenic photosynthesis. Hence, there are several ways how manganese carbonates could have been formed biogenically and deposited in Precambrian sediments. Thus, the minerals may be suitable biosignatures for microbial redox processes in many respects. The hyperthermophilic archaeon Pyrobaculum islandicum produces rhodochrosite during growth on hydrogen and organic compounds and may be a putative model organism for the reduction of Mn(IV). References Hulth S, Aller RC, Gilbert F. (1999) Geochim Cosmochim Acta, 63, 49-66. Johnson JE, Webb SM, Thomas K, Ono S, Kirschvink JL, Fischer WW. (2013) Proc Natl Acad Sci USA, 110, 11238-11243. Kirschvink JL, Gaidos EJ, Bertani LE, Beukes NJ, Gutzmer J, Maepa LN, Steinberger LE. (2000) Proc Natl Acad Sci USA, 97, 1400-1405. Nealson KH, Saffarini D. (1994). Annu Rev Microbiol, 48, 311-343.

  13. Persistently Active Microbial Molecules Prolong Innate Immune Tolerance In Vivo

    PubMed Central

    Lu, Mingfang; Varley, Alan W.; Munford, Robert S.

    2013-01-01

    Measures that bolster the resolution phase of infectious diseases may offer new opportunities for improving outcome. Here we show that inactivation of microbial lipopolysaccharides (LPS) can be required for animals to recover from the innate immune tolerance that follows exposure to Gram-negative bacteria. When wildtype mice are exposed to small parenteral doses of LPS or Gram-negative bacteria, their macrophages become reprogrammed (tolerant) for a few days before they resume normal function. Mice that are unable to inactivate LPS, in contrast, remain tolerant for several months; during this time they respond sluggishly to Gram-negative bacterial challenge, with high mortality. We show here that prolonged macrophage reprogramming is maintained in vivo by the persistence of stimulatory LPS molecules within the cells' in vivo environment, where naïve cells can acquire LPS via cell-cell contact or from the extracellular fluid. The findings provide strong evidence that inactivation of a stimulatory microbial molecule can be required for animals to regain immune homeostasis following parenteral exposure to bacteria. Measures that disable microbial molecules might enhance resolution of tissue inflammation and help restore innate defenses in individuals recovering from many different infectious diseases. PMID:23675296

  14. On the use of antibiotics to reduce rhizoplane microbial populations in root physiology and ecology investigations.

    PubMed

    Smart, D R; Ferro, A; Ritchie, K; Bugbee, B G

    1995-01-01

    No straightforward method exists for separating the proportion of ion exchange and respiration due to rhizoplane microbial organisms from that of root ion exchange and respiration. We examined several antibiotics that might be used for the temporary elimination of rhizoplane bacteria from hydroponically grown wheat roots (Triticum aestivum cv. Veery 10). Each antibiotic was tested for herbicidal activity and plate counts were used to enumerate bacteria and evaluate antibiotic kinetics. Only lactam antibiotics (penicillins and cephalosporins) did not reduce wheat growth rates. Aminoglycosides, the pyrimidine trimethoprim, colistin and rifampicin reduced growth rates substantially. Antibiotics acted slowly, with maximum reductions in rhizoplane bacteria occurring after more than 48 h of exposure. Combinations of nonphytotoxic antibiotics reduced platable rhizoplane bacteria by as much as 98%; however, this was generally a reduction from about 10(9) to 10(6) colony forming units per gram of dry root mass, so that many viable bacteria remained on root surfaces. We present evidence which suggests that insufficient bacterial biomass exists on root surfaces of nonstressed plants grown under well-aerated conditions to quantitatively interfere with root nitrogen absorption measurements. PMID:11540615

  15. On the use of antibiotics to reduce rhizoplane microbial populations in root physiology and ecology investigations

    NASA Technical Reports Server (NTRS)

    Smart, D. R.; Ferro, A.; Ritchie, K.; Bugbee, B. G.

    1995-01-01

    No straightforward method exists for separating the proportion of ion exchange and respiration due to rhizoplane microbial organisms from that of root ion exchange and respiration. We examined several antibiotics that might be used for the temporary elimination of rhizoplane bacteria from hydroponically grown wheat roots (Triticum aestivum cv. Veery 10). Each antibiotic was tested for herbicidal activity and plate counts were used to enumerate bacteria and evaluate antibiotic kinetics. Only lactam antibiotics (penicillins and cephalosporins) did not reduce wheat growth rates. Aminoglycosides, the pyrimidine trimethoprim, colistin and rifampicin reduced growth rates substantially. Antibiotics acted slowly, with maximum reductions in rhizoplane bacteria occurring after more than 48 h of exposure. Combinations of nonphytotoxic antibiotics reduced platable rhizoplane bacteria by as much as 98%; however, this was generally a reduction from about 10(9) to 10(6) colony forming units per gram of dry root mass, so that many viable bacteria remained on root surfaces. We present evidence which suggests that insufficient bacterial biomass exists on root surfaces of nonstressed plants grown under well-aerated conditions to quantitatively interfere with root nitrogen absorption measurements.

  16. Microbial activity in forest soil reflects the changes in ecosystem properties between summer and winter.

    PubMed

    Žifčáková, Lucia; Větrovský, Tomáš; Howe, Adina; Baldrian, Petr

    2016-01-01

    Understanding the ecology of coniferous forests is very important because these environments represent globally largest carbon sinks. Metatranscriptomics, microbial community and enzyme analyses were combined to describe the detailed role of microbial taxa in the functioning of the Picea abies-dominated coniferous forest soil in two contrasting seasons. These seasons were the summer, representing the peak of plant photosynthetic activity, and late winter, after an extended period with no photosynthate input. The results show that microbial communities were characterized by a high activity of fungi especially in litter where their contribution to microbial transcription was over 50%. Differences in abundance between summer and winter were recorded for 26-33% of bacterial genera and < 15% of fungal genera, but the transcript profiles of fungi, archaea and most bacterial phyla were significantly different among seasons. Further, the seasonal differences were larger in soil than in litter. Most importantly, fungal contribution to total microbial transcription in soil decreased from 33% in summer to 16% in winter. In particular, the activity of the abundant ectomycorrhizal fungi was reduced in winter, which indicates that plant photosynthetic production was likely one of the major drivers of changes in the functioning of microbial communities in this coniferous forest. PMID:26286355

  17. Combination of sodium chlorite and calcium propionate reduces enzymatic browning and microbial population of fresh-cut "Granny Smith" apples.

    PubMed

    Guan, Wenqiang; Fan, Xuetong

    2010-03-01

    Tissue browning and microbial growth are the main concerns associated with fresh-cut apples. In this study, effects of sodium chlorite (SC) and calcium propionate (CP), individually and combined, on quality and microbial population of apple slices were investigated. "Granny Smith" apple slices, dipped for 5 min in CP solutions at 0%, 0.5%, 1%, and 2% (w/v) either alone or in combination with 0.05% (w/v) SC, were stored at 3 and 10 degrees C for up to 14 d. Color, firmness, and microflora population were measured at 1, 7, and 14 d of storage. Results showed that CP alone had no significant effect on the browning of cut apples. Even though SC significantly inhibited tissue browning initially, the apple slices turned brown during storage at 10 degrees C. The combination of CP and SC was able to inhibit apple browning during storage. Samples treated with the combination of SC with CP did not show any detectable yeast and mold growth during the entire storage period at 3 degrees C. At 10 degrees C, yeast and mold count increased on apple slices during storage while CP reduced the increase. However, high concentrations of CP reduced the efficacy of SC in inactivating E. coli inoculated on apples. Overall, our results suggested that combination of SC with 0.5% and 1% CP could be used to inhibit tissue browning and maintain firmness while reducing microbial population. Practical Application: Apple slices, which contain antioxidants and other nutrient components, have emerged as popular snacks in food service establishments, school lunch programs, and for family consumption. However, the further growth of the industry is limited by product quality deterioration caused by tissue browning, short shelf-life due to microbial growth, and possible contamination with human pathogens during processing. Therefore, this study was conducted to develop treatments to reduce microbial population and tissue browning of "Granny Smith" apple slices. Results showed that an antimicrobial

  18. Quantifying microbial activity in deep subsurface sediments using a tritium based hydrognease enzyme assay

    NASA Astrophysics Data System (ADS)

    Adhikari, R.; Nickel, J.; Kallmeyer, J.

    2012-12-01

    Microbial life is widespread in Earth's subsurface and estimated to represent a significant fraction of Earth's total living biomass. However, very little is known about subsurface microbial activity and its fundamental role in biogeochemical cycles of carbon and other biologically important elements. Hydrogen is one of the most important elements in subsurface anaerobic microbial metabolism. Heterotrophic and chemoautotrophic microorganisms use hydrogen in their metabolic pathways. They either consume or produce protons for ATP synthesis. Hydrogenase (H2ase) is a ubiquitous intracellular enzyme that catalyzes the interconversion of molecular hydrogen and/or water into protons and electrons. The protons are used for the synthesis of ATP, thereby coupling energy generating metabolic processes to electron acceptors such as CO2 or sulfate. H2ase enzyme targets a key metabolic compound in cellular metabolism therefore the assay can be used as a measure for total microbial activity without the need to identify any specific metabolic process. Using the highly sensitive tritium assay we measured H2ase enzyme activity in the organic-rich sediments of Lake Van, a saline, alkaline lake in eastern Turkey, in marine sediments of the Barents Sea and in deep subseafloor sediments from the Nankai Trough. H2ase activity could be quantified at all depths of all sites but the activity distribution varied widely with depth and between sites. At the Lake Van sites H2ase activity ranged from ca. 20 mmol H2 cm-3d-1 close to the sediment-water interface to 0.5 mmol H2 cm-3d-1 at a depth of 0.8 m. In samples from the Barents Sea H2ase activity ranged between 0.1 to 2.5 mmol H2 cm-3d-1 down to a depth of 1.60 m. At all sites the sulfate reduction rate profile followed the upper part of the H2ase activity profile until sulfate reduction reached the minimum detection limit (ca. 10 pmol cm-3d-1). H2ase activity could still be quantified after the decline of sulfate reduction, indicating that

  19. The elevational pattern of microbial community and enzyme activity along the northern slop of Changbai Mountain

    NASA Astrophysics Data System (ADS)

    Xu, Zhiwei; Yu, Guirui; Zhang, Xinyu; Ge, Jianpin; He, Nianpeng; Wang, Qiufeng; Wang, Dan

    2014-05-01

    we present a comprehensive analysis of soil microbial community structure, enzyme activities and their role in soil organic matter mineralization along six elevations representing five typical vegetation types from forest to alpine tundra in Changbai Mountain, China. The results showed that the microbial PLFAs presented hump-shaped patterns along the elevation with the total microbial PLFAs highest in Ermans birch forest soil. The fungi to bacteria and gram positive to negative bacteria ratios increased along the elevation with the lowest values in Broad leaved forest and Dark-coniferous spruce-fir forest soil, respectively. The soil microbial community structures showed a biogeography distribution pattern in vertical direction with microbial community structures in Broad leaved forest and Mixed coniferous broad leaved forest different from other four sites. The soil enzyme activities in Broad leaved forest and Mixed coniferous broad leaved forest were significantly higher than in other four elevations. Principal component analysis (PCA) revealed substantial differences in soil microbial community composition among study sites, appeared to be driven primarily by MAT, MAP, soil temperature and content of silt & clay on the first principal component (PC1) which accounted for 87.1 % of the total sample variance. However, soil nutrients mainly responsible for the variation of soil enzyme activities. The soil organic matter mineralization rates tended to be highest in Ermans birch forest site and lowest in Dark-coniferous spruce-fir forest site and showed positive relationship with total microbial, bacterial and actinomycetes PLFAs. These findings could be used to facilitate interpretation of soil microbial community and ecological function in latitude forests ecosystem especially in volcanic forest ecosystem.

  20. Charcoal produced by prescribed fire increases dissolved organic carbon and soil microbial activity

    NASA Astrophysics Data System (ADS)

    Poon, Cheryl; Jenkins, Meaghan; Bell, Tina; Adams, Mark

    2014-05-01

    In Australian forests fire is an important driver of carbon (C) storage. When biomass C is combusted it is transformed into vegetation residue (charcoal) and deposited in varying amounts and forms onto soil surfaces. The C content of charcoal is high but is largely in a chemically stable form of C, which is highly resistance to microbial decomposition. We conducted two laboratory incubations to examine the influence of charcoal on soil microbial activity as indicated by microbial respiration. Seven sites were chosen in mixed species eucalypt forest in Victoria, Australia. Soil was sampled prior to burning to minimise the effects of heating or addition of charcoal during the prescribed burn. Charcoal samples were collected from each site after the burn, homogenised and divided into two size fractions. Prior to incubation, soils were amended with the two size fractions (<1 and 1-4.75 mm) and at two rates of amount (2.5 and 5% by soil dry weight). Charcoal-amended soils were incubated in the laboratory for 86 d, microbial respiration was measured nine times at day 1, 3, 8, 15, 23, 30, 45, 59 and 86 d. We found that addition of charcoal resulted in faster rates of microbial respiration compared to unamended soil. Fastest rates of microbial respiration in all four treatments were measured 1 d after addition of charcoal (up to 12 times greater than unamended soil). From 3 to 8 d, respiration rates in all four treatments decreased and only treatments with greater charcoal addition (5%) remained significantly faster than unamended soil. From 15 d to 86 d, all treatments had respiration rates similar to unamended soil. Overall, adding greater amount of charcoal (5%) resulted in a larger cumulative amount of CO2 released over the incubation period when compared to unamended soil. The second laboratory incubation focused on the initial changes in soil nutrient and microbial respiration after addition of charcoal over a 72 h period. Charcoal (<2 mm) was added at rate of 5% to

  1. EFFECT OF BIOSOLARISATION ON THE MICROBIAL POPULATIONS OF SUBSTRATES INFESTED WITH FUSARIUM OXYSPORUM BY PCR-DGGE.

    PubMed

    Pugliese, M; Ferrocino, I; Gilardi, G; Gullino, M L; Garibaldi, A

    2015-01-01

    Biosolarisation consists of combining solarisation and organic matter application for controlling soilborne pathogens. The effects of this control strategy on the microbial community is almost unknown and needs to be investigated with molecular tools. The aim of the research was to investigate how biosolarisation can affect the structure of the microbial populations evaluated by a culture independent method using DGGE of PCR-amplified 18S-ITS genes-coding fragments from DNA extracted directly from infested substrate. Substrate samples were artificially infested with Fusarium oxysporum f. sp. conglutinans (FOC) and F. oxysporum f.sp. basilici (FOB) in order to evaluate the shift in fungal population by using culture independent methods. Solarisation was carried out with transparent polyethylene film during the summer period in a greenhouse located in Northern Italy, in combination or not with Brassica carinata defatted seed meals and/or compost. Biosolarisation treatment was carried out in a growth chamber by heating the substrate for 7 and 14 days at optimal (55-52 degrees C for 6 h, 50-48 degrees C for 8 h and 47-45 degrees C for 10 h/day) and sub-optimal (50-48 degrees C for 20 h, 45-43 degrees C for 8 h and 40-38 degrees C for 10 h/day) temperatures. Plate counts and polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) analyses were performed to evaluate the effect of biosolarisation on the microbial population. The abundance of FOC and FOB was reduced as a consequence of biosolarisation, while bacterial populations were higher compared to control samples during the experiment. PCR-DGGE fingerprints of the ascomycete community obtained from DNA directly extracted from infested substrate samples showed that the use of organic amendments increased the similarity of the fungal populations. PMID:27141761

  2. Analytical applications of microbial fuel cells. Part II: Toxicity, microbial activity and quantification, single analyte detection and other uses.

    PubMed

    Abrevaya, Ximena C; Sacco, Natalia J; Bonetto, Maria C; Hilding-Ohlsson, Astrid; Cortón, Eduardo

    2015-01-15

    Microbial fuel cells were rediscovered twenty years ago and now are a very active research area. The reasons behind this new activity are the relatively recent discovery of electrogenic or electroactive bacteria and the vision of two important practical applications, as wastewater treatment coupled with clean energy production and power supply systems for isolated low-power sensor devices. Although some analytical applications of MFCs were proposed earlier (as biochemical oxygen demand sensing) only lately a myriad of new uses of this technology are being presented by research groups around the world, which combine both biological-microbiological and electroanalytical expertises. This is the second part of a review of MFC applications in the area of analytical sciences. In Part I a general introduction to biological-based analytical methods including bioassays, biosensors, MFCs design, operating principles, as well as, perhaps the main and earlier presented application, the use as a BOD sensor was reviewed. In Part II, other proposed uses are presented and discussed. As other microbially based analytical systems, MFCs are satisfactory systems to measure and integrate complex parameters that are difficult or impossible to measure otherwise, such as water toxicity (where the toxic effect to aquatic organisms needed to be integrated). We explore here the methods proposed to measure toxicity, microbial metabolism, and, being of special interest to space exploration, life sensors. Also, some methods with higher specificity, proposed to detect a single analyte, are presented. Different possibilities to increase selectivity and sensitivity, by using molecular biology or other modern techniques are also discussed here. PMID:24906984

  3. Vadose zone microbial community structure and activity in metal/radionuclide contaminated sediments. Final technical report

    SciTech Connect

    Balkwill, David L.

    2002-08-17

    This final technical report describes the research carried out during the final two months of the no-cost extension ending 11/14/01. The primary goals of the project were (1) to determine the potential for transformation of Cr(VI) (oxidized, mobile) to Cr(III) (reduced, immobile) under unsaturated conditions as a function of different levels and combinations of (a) chromium, (b) nitrate (co-disposed with Cr), and (c) molasses (inexpensive bioremediation substrate), and (2) to determine population structure and activity in experimental treatments by characterization of the microbial community by signature biomarker analysis and by RT-PCR and terminal restriction fragment length polymorphism (T-RFLP) and 16S ribosomal RNA genes. It was determined early in the one-year no-cost extension period that the T-RFLP approach was problematic in regard to providing information on the identities of microorganisms in the samples examined. As a result, it could not provide the detailed information on microbial community structure that was needed to assess the effects of treatments with chromium, nitrate, and/or molasses. Therefore, we decided to obtain the desired information by amplifying (using TR-PCR, with the same primers used for T-RFLP) and cloning 16S rRNA gene sequences from the same RNA extracts that were used for T-RFLP analysis. We also decided to use a restriction enzyme digest procedure (fingerprinting procedure) to place the clones into types. The primary focus of the research carried out during this report period was twofold: (a) to complete the sequencing of the clones, and (b) to analyze the clone sequences phylogenetically in order to determine the relatedness of the bacteria detected in the samples to each other and to previously described genera and species.

  4. Monitoring the Perturbation of Soil and Groundwater Microbial Communities Due to Pig Production Activities

    PubMed Central

    Hong, Pei-Ying; Yannarell, Anthony C.; Dai, Qinghua; Ekizoglu, Melike

    2013-01-01

    This study aimed to determine if biotic contaminants originating from pig production farms are disseminated into soil and groundwater microbial communities. A spatial and temporal sampling of soil and groundwater in proximity to pig production farms was conducted, and quantitative PCR (Q-PCR) was utilized to determine the abundances of tetracycline resistance genes (i.e., tetQ and tetZ) and integrase genes (i.e., intI1 and intI2). We observed that the abundances of tetZ, tetQ, intI1, and intI2 in the soils increased at least 6-fold after manure application, and their abundances remained elevated above the background for up to 16 months. Q-PCR further determined total abundances of up to 5.88 × 109 copies/ng DNA for tetZ, tetQ, intI1, and intI2 in some of the groundwater wells that were situated next to the manure lagoon and in the facility well used to supply water for one of the farms. We further utilized 16S rRNA-based pyrosequencing to assess the microbial communities, and our comparative analyses suggest that most of the soil samples collected before and after manure application did not change significantly, sharing a high Bray-Curtis similarity of 78.5%. In contrast, an increase in Bacteroidetes and sulfur-oxidizing bacterial populations was observed in the groundwaters collected from lagoon-associated groundwater wells. Genera associated with opportunistic human and animal pathogens, such as Acinetobacter, Arcobacter, Yersinia, and Coxiella, were detected in some of the manure-treated soils and affected groundwater wells. Feces-associated bacteria such as Streptococcus, Erysipelothrix, and Bacteroides were detected in the manure, soil, and groundwater ecosystems, suggesting a perturbation of the soil and groundwater environments by invader species from pig production activities. PMID:23396341

  5. Interactions between properties of amended strip mine spoils and microbial activities

    SciTech Connect

    Utsalo, S.J.

    1981-01-01

    Properties of strip mine spoils before and after amendment with varying levels of carbon and nitrogen sources are characterized and compared with properties of similarly amended garden soil samples. Changes in spoils as reflected in the stimulation of microbial populations, rate of nitrate formation, the turnover of microbial biomass and the growth yields of white clover and rye grass are evaluated. Limed spoils and garden soils were fertilized and incubated at 25/sup 0/C following amendments with organic substrates. Changes in parameters related to soil fertility status were analyzed on a weekly basis. The possible identity and the toxic effects on white clover and a Rhizobium of acidity factors present in strip mine spoils were evaluated using soil experiments and pure culture studies in artificial culture media. The results indicate that acid spoils contain low numbers of viable microorganisms which readily respond to soil amendment with substrates. No nitrification occurs in acid spoils but liming and inoculation with compost infusion stimulate active nitrification. Aluminum, manganese and acidity appear to be important factors which inhibit the survival of plants and microbes in spoils. Adequate liming improves rhizobial survival and growth and nodulation of white clover in spoils. Acidity factors have greater impact on Rhizobium than on the white clover host under nutritionally independent conditions. Increase in inoculum size enhances nodulation and growth of clover at low aluminum levels. Reducing the time of exposure of rhizobia to acidity factors outside the symbiotic host does not appear to enhance the growth yield of clover under symbiotic conditions. Molds appear to contribute more to the increased aggregate stability observed in amended soils than bacteria and actinomycetes.

  6. Impaired leaf litter processing in acidified streams : learning from microbial enzyme activities.

    PubMed

    Clivot, Hugues; Danger, Michael; Pagnout, Christophe; Wagner, Philippe; Rousselle, Philippe; Poupin, Pascal; Guérold, François

    2013-01-01

    Anthropogenic acidification in headwater streams is known to affect microbial assemblages involved in leaf litter breakdown. Far less is known about its potential effects on microbial enzyme activities. To assess the effects of acidification on microbial activities associated with decaying leaves, a 70-day litter bag experiment was conducted in headwater streams at six sites across an acidification gradient. The results revealed that microbial leaf decomposition was strongly and negatively correlated with total Al concentrations (r = -0.99, p < 0.001) and positively correlated with Ca(2+) concentrations (r = 0.94, p = 0.005) and pH (r = 0.93, p = 0.008). Denaturing gradient gel electrophoresis analyses showed that microbial assemblages differed between non-impacted and impacted sites, whereas fungal biomass associated with decaying leaves was unaffected. The nutrient content of leaf detritus and ecoenzymatic activities of carbon (C), nitrogen (N) and phosphorus (P) acquisition revealed that N acquisition was unaltered, while P acquisition was significantly reduced across the acidification gradient. The P content of leaf litter was negatively correlated with total Al concentrations (r = -0.94, p < 0.01) and positively correlated with decomposition rates (r = 0.95, p < 0.01). This potential P limitation of microbial decomposers in impacted sites was confirmed by the particularly high turnover activity for phosphatase and imbalanced ratios between the ecoenzymatic activities of C and P acquisition. The toxic form of Al has well-known direct effects on aquatic biota under acidic conditions, but in this study, Al was found to also potentially affect microbially mediated leaf processing by interfering with the P cycle. These effects may in turn have repercussions on higher trophic levels and whole ecosystem functioning. PMID:22903164

  7. Soil Microbial Biomass, Basal Respiration and Enzyme Activity of Main Forest Types in the Qinling Mountains

    PubMed Central

    Cheng, Fei; Peng, Xiaobang; Zhao, Peng; Yuan, Jie; Zhong, Chonggao; Cheng, Yalong; Cui, Cui; Zhang, Shuoxin

    2013-01-01

    Different forest types exert essential impacts on soil physical-chemical characteristics by dominant tree species producing diverse litters and root exudates, thereby further regulating size and activity of soil microbial communities. However, the study accuracy is usually restricted by differences in climate, soil type and forest age. Our objective is to precisely quantify soil microbial biomass, basal respiration and enzyme activity of five natural secondary forest (NSF) types with the same stand age and soil type in a small climate region and to evaluate relationship between soil microbial and physical-chemical characters. We determined soil physical-chemical indices and used the chloroform fumigation-extraction method, alkali absorption method and titration or colorimetry to obtain the microbial data. Our results showed that soil physical-chemical characters remarkably differed among the NSFs. Microbial biomass carbon (Cmic) was the highest in wilson spruce soils, while microbial biomass nitrogen (Nmic) was the highest in sharptooth oak soils. Moreover, the highest basal respiration was found in the spruce soils, but mixed, Chinese pine and spruce stands exhibited a higher soil qCO2. The spruce soils had the highest Cmic/Nmic ratio, the greatest Nmic/TN and Cmic/Corg ratios were found in the oak soils. Additionally, the spruce soils had the maximum invertase activity and the minimum urease and catalase activities, but the maximum urease and catalase activities were found in the mixed stand. The Pearson correlation and principle component analyses revealed that the soils of spruce and oak stands obviously discriminated from other NSFs, whereas the others were similar. This suggested that the forest types affected soil microbial properties significantly due to differences in soil physical-chemical features. PMID:23840671

  8. Soil microbial biomass, basal respiration and enzyme activity of main forest types in the Qinling Mountains.

    PubMed

    Cheng, Fei; Peng, Xiaobang; Zhao, Peng; Yuan, Jie; Zhong, Chonggao; Cheng, Yalong; Cui, Cui; Zhang, Shuoxin

    2013-01-01

    Different forest types exert essential impacts on soil physical-chemical characteristics by dominant tree species producing diverse litters and root exudates, thereby further regulating size and activity of soil microbial communities. However, the study accuracy is usually restricted by differences in climate, soil type and forest age. Our objective is to precisely quantify soil microbial biomass, basal respiration and enzyme activity of five natural secondary forest (NSF) types with the same stand age and soil type in a small climate region and to evaluate relationship between soil microbial and physical-chemical characters. We determined soil physical-chemical indices and used the chloroform fumigation-extraction method, alkali absorption method and titration or colorimetry to obtain the microbial data. Our results showed that soil physical-chemical characters remarkably differed among the NSFs. Microbial biomass carbon (Cmic) was the highest in wilson spruce soils, while microbial biomass nitrogen (Nmic) was the highest in sharptooth oak soils. Moreover, the highest basal respiration was found in the spruce soils, but mixed, Chinese pine and spruce stands exhibited a higher soil qCO2. The spruce soils had the highest Cmic/Nmic ratio, the greatest Nmic/TN and Cmic/Corg ratios were found in the oak soils. Additionally, the spruce soils had the maximum invertase activity and the minimum urease and catalase activities, but the maximum urease and catalase activities were found in the mixed stand. The Pearson correlation and principle component analyses revealed that the soils of spruce and oak stands obviously discriminated from other NSFs, whereas the others were similar. This suggested that the forest types affected soil microbial properties significantly due to differences in soil physical-chemical features. PMID:23840671

  9. Organic Amendments to Avocado Crops Induce Suppressiveness and Influence the Composition and Activity of Soil Microbial Communities

    PubMed Central

    Bonilla, Nuria; Vida, Carmen; Martínez-Alonso, Maira; Landa, Blanca B.; Gaju, Nuria; Cazorla, Francisco M.

    2015-01-01

    One of the main avocado diseases in southern Spain is white root rot caused by the fungus Rosellinia necatrix Prill. The use of organic soil amendments to enhance the suppressiveness of natural soil is an inviting approach that has successfully controlled other soilborne pathogens. This study tested the suppressive capacity of different organic amendments against R. necatrix and analyzed their effects on soil microbial communities and enzymatic activities. Two-year-old avocado trees were grown in soil treated with composted organic amendments and then used for inoculation assays. All of the organic treatments reduced disease development in comparison to unamended control soil, especially yard waste (YW) and almond shells (AS). The YW had a strong effect on microbial communities in bulk soil and produced larger population levels and diversity, higher hydrolytic activity and strong changes in the bacterial community composition of bulk soil, suggesting a mechanism of general suppression. Amendment with AS induced more subtle changes in bacterial community composition and specific enzymatic activities, with the strongest effects observed in the rhizosphere. Even if the effect was not strong, the changes caused by AS in bulk soil microbiota were related to the direct inhibition of R. necatrix by this amendment, most likely being connected to specific populations able to recolonize conducive soil after pasteurization. All of the organic amendments assayed in this study were able to suppress white root rot, although their suppressiveness appears to be mediated differentially. PMID:25769825

  10. Organic amendments to avocado crops induce suppressiveness and influence the composition and activity of soil microbial communities.

    PubMed

    Bonilla, Nuria; Vida, Carmen; Martínez-Alonso, Maira; Landa, Blanca B; Gaju, Nuria; Cazorla, Francisco M; de Vicente, Antonio

    2015-05-15

    One of the main avocado diseases in southern Spain is white root rot caused by the fungus Rosellinia necatrix Prill. The use of organic soil amendments to enhance the suppressiveness of natural soil is an inviting approach that has successfully controlled other soilborne pathogens. This study tested the suppressive capacity of different organic amendments against R. necatrix and analyzed their effects on soil microbial communities and enzymatic activities. Two-year-old avocado trees were grown in soil treated with composted organic amendments and then used for inoculation assays. All of the organic treatments reduced disease development in comparison to unamended control soil, especially yard waste (YW) and almond shells (AS). The YW had a strong effect on microbial communities in bulk soil and produced larger population levels and diversity, higher hydrolytic activity and strong changes in the bacterial community composition of bulk soil, suggesting a mechanism of general suppression. Amendment with AS induced more subtle changes in bacterial community composition and specific enzymatic activities, with the strongest effects observed in the rhizosphere. Even if the effect was not strong, the changes caused by AS in bulk soil microbiota were related to the direct inhibition of R. necatrix by this amendment, most likely being connected to specific populations able to recolonize conducive soil after pasteurization. All of the organic amendments assayed in this study were able to suppress white root rot, although their suppressiveness appears to be mediated differentially. PMID:25769825

  11. Microbial metagenomes from three aquifers in the Fennoscandian shield terrestrial deep biosphere reveal metabolic partitioning among populations.

    PubMed

    Wu, Xiaofen; Holmfeldt, Karin; Hubalek, Valerie; Lundin, Daniel; Åström, Mats; Bertilsson, Stefan; Dopson, Mark

    2016-05-01

    Microorganisms in the terrestrial deep biosphere host up to 20% of the earth's biomass and are suggested to be sustained by the gases hydrogen and carbon dioxide. A metagenome analysis of three deep subsurface water types of contrasting age (from <20 to several thousand years) and depth (171 to 448 m) revealed phylogenetically distinct microbial community subsets that either passed or were retained by a 0.22 μm filter. Such cells of <0.22 μm would have been overlooked in previous studies relying on membrane capture. Metagenomes from the three water types were used for reconstruction of 69 distinct microbial genomes, each with >86% coverage. The populations were dominated by Proteobacteria, Candidate divisions, unclassified archaea and unclassified bacteria. The estimated genome sizes of the <0.22 μm populations were generally smaller than their phylogenetically closest relatives, suggesting that small dimensions along with a reduced genome size may be adaptations to oligotrophy. Shallow 'modern marine' water showed community members with a predominantly heterotrophic lifestyle. In contrast, the deeper, 'old saline' water adhered more closely to the current paradigm of a hydrogen-driven deep biosphere. The data were finally used to create a combined metabolic model of the deep terrestrial biosphere microbial community. PMID:26484735

  12. Geophysical Signatures of Microbial Activity at Hydrocarbon Contaminated Sites: A Review

    NASA Astrophysics Data System (ADS)

    Atekwana, Estella A.; Atekwana, Eliot A.

    2010-03-01

    Microorganisms participate in a variety of geologic processes that alter the chemical and physical properties of their environment. Understanding the geophysical signatures of microbial activity in the environment has resulted in the development of a new sub-discipline in geophysics called “biogeophysics”. This review focuses primarily on literature pertaining to biogeophysical signatures of sites contaminated by light non-aqueous phase liquids (LNAPL), as these sites provide ideal laboratories for investigating microbial-geophysical relationships. We discuss the spatial distribution and partitioning of LNAPL into different phases because the physical, chemical, and biological alteration of LNAPL and the subsequent impact to the contaminated environment is in large part due to its distribution. We examine the geophysical responses at contaminated sites over short time frames of weeks to several years when the alteration of the LNAPL by microbial activity has not occurred to a significant extent, and over the long-term of several years to decades, when significant microbial degradation of the LNAPL has occurred. A review of the literature suggests that microbial processes profoundly alter the contaminated environment causing marked changes in the petrophysical properties, mineralogy, solute concentration of pore fluids, and temperature. A variety of geophysical techniques such as electrical resistivity, induced polarization, electromagnetic induction, ground penetrating radar, and self potential are capable of defining the contaminated zones because of the new physical properties imparted by microbial processes. The changes in the physical properties of the contaminated environment vary spatially because microbial processes are controlled by the spatial distribution of the contaminant. Geophysical studies must consider the spatial variations in the physical properties during survey design, data analysis, and interpretation. Geophysical data interpretation from

  13. Spatial variability of microbial activity and substrate utilization patterns in top- and subsoils under European beech

    NASA Astrophysics Data System (ADS)

    Niebuhr, Jana; Heinze, Stefanie; Mikutta, Robert; Mueller, Carsten W.; Preusser, Sebastian; Marschner, Bernd

    2014-05-01

    The role of subsoils in the global carbon cycle is poorly understood and probably underestimated. This is due to an incomplete understanding of processes and mechanisms that influence carbon storage and decomposition in deeper soil horizons. Microbial communities play an important role in these processes, as their presence, structure and function are crucial for the decomposition and/or stabilization of organic compounds. In this study, carried out in a European beech (Fagus sylvatica L.) forest on a podzolic Cambisol near Hannover, the spatial variability of microbial activity and substrate utilization patterns were investigated in the subsoil. For this purpose, samples were taken from regular grids at dm distances in three soil profiles of 1.85 m depth and 3.15 m length, totaling 192 soil samples. Activities of 9 extracellular enzymes of the C-, S-, P- and N-cycle were determined with a multi-substrate enzymatic assay and for substrate utilization patterns the MicroRespTM method was applied. The results showed a strong decline of microbial activity from topsoil to subsoil. Enzyme activities varied greatly at the dm scale. The correlation of the variability of both microbial activity and substrate utilization patterns with depth and soil parameters such as pH, soil water content, total and dissolved organic carbon was tested with a principal component analysis. Existing dependencies of the variabilities on these parameters help to verify the hypotheses that microbial activity is spatially highly variable in the subsoil and this variability is due to the existence of certain hot spots of substrate availability and that outside these 'hot spots' the microbial activity and thus the decomposition of SOM are mainly limited by substrate availability.

  14. Senescent leaf exudate increases mosquito survival and microbial activity

    PubMed Central

    PELZ-STELINSKI, K. S.; WALKER, E. D.; KAUFMAN, M. G.

    2010-01-01

    We conducted experiments to evaluate the effects of soluble components in senescent leaf material on the growth and development of the eastern tree hole mosquito, Aedes triseriatus (Say). Oak leaves that were either leached for three days to remove the labile nutrient fraction, or were not leached, served as basal nutrient inputs in each experiment. Mosquito performance in microcosms containing leachate only was significantly worse compared with microcosms containing leaf material in combination with either leachate or water, indicating the importance of leaf substrates to mosquito production. Adult mosquito biomass, emergence, and development time were significantly higher in microcosms containing unleached leaves compared with leached leaf material. Additions of leachate to leached leaf treatments enhanced adult production, but not to the level observed in unleached leaf treatments. Filtered and unfiltered leachate added substantial nitrogen and phosphorus to microcosms and significantly affected mosquito growth responses. Bacterial productivity and abundance were also significantly affected by leachate additions and filtering. Taken together, these results suggest that while leaves decline with respect to nutritional value during decomposition, they remain important components of the habitat as substrates for microbial growth and mosquito feeding, particularly when nutrients (here, leachate) enter the system. Our results also illustrate the importance of soluble leaf material, which enhances mosquito production through effects on microbial community dynamics. PMID:21113430

  15. Minimum Energy Requirements for Sustained Microbial Activity in Anoxic Sediments

    NASA Technical Reports Server (NTRS)

    Hoehler, Tori M.; Alperin, Marc J.; Albert, Daniel B.; Martens, Christoper S.; DeVincenzi, Donald L. (Technical Monitor)

    2000-01-01

    Currently understood mechanisms of biochemical energy conservation dictate that, in order to be biologically useful, energy must be available to organisms in "quanta" equal to, at minimum one-third to one-fifth of the energy required to synthesize ATP in vivo. The existence of this biological energy quantum means that a significant fraction of the chemical amp on Earth cannot be used to drive biological productivity, and places a fundamental thermodynamic constraint on the origins, evolution, and distribution of life. We examined the energy requirements of intact microbial assemblages in anoxic sediments from Cape Lookout Bight, NC, USA, using dissolved hydrogen concentrations as a non-invasive probe. In this system, the thermodynamics of metabolic processes occurring inside microbial cells is reflected quantitatively by H2 concentrations measured outside those cells. We find that methanogenic archaea are supported by energy yields as small as 10 kJ per mol, about half the quantity calculated from studies of microorganisms in culture. This finding implies that a significantly broader range of geologic and chemical niches might be exploited by microorganisms than would otherwise be expected.

  16. Microbial Diversity Analysis of the Bacterial and Archaeal Population in Present Day Stromatolites

    NASA Technical Reports Server (NTRS)

    Ortega, Maya C.

    2011-01-01

    Stromatolites are layered sedimentary structures resulting from microbial mat communities that remove carbon dioxide from their environment and biomineralize it as calcium carbonate. Although prevalent in the fossil record, stromatolites are rare in the modem world and are only found in a few locations including Highbome Cay in the Bahamas. The stromatolites found at this shallow marine site are analogs to ancient microbial mat ecosystems abundant in the Precambrian period on ancient Earth. To understand how stromatolites form and develop, it is important to identify what microorganisms are present in these mats, and how these microbes contribute to geological structure. These results will provide insight into the molecular and geochemical processes of microbial communities that prevailed on ancient Earth. Since stromatolites are formed by lithifying microbial mats that are able to mineralize calcium carbonate, understanding the biological mechanisms involved may lead to the development of carbon sequestration technologies that will be applicable in human spaceflight, as well as improve our understanding of global climate and its sustainability. The objective of my project was to analyze the archaeal and bacterial dIversity in stromatolites from Highborn Cay in the Bahamas. The first step in studying the molecular processes that the microorganisms carry out is to ascertain the microbial complexity within the mats, which includes identifying and estimating the numbers of different microbes that comprise these mats.

  17. Interactions between Snow Chemistry, Mercury Inputs and Microbial Population Dynamics in an Arctic Snowpack

    PubMed Central

    Larose, Catherine; Prestat, Emmanuel; Cecillon, Sébastien; Berger, Sibel; Malandain, Cédric; Lyon, Delina; Ferrari, Christophe; Schneider, Dominique; Dommergue, Aurélien; Vogel, Timothy M.

    2013-01-01

    We investigated the interactions between snowpack chemistry, mercury (Hg) contamination and microbial community structure and function in Arctic snow. Snowpack chemistry (inorganic and organic ions) including mercury (Hg) speciation was studied in samples collected during a two-month field study in a high Arctic site, Svalbard, Norway (79°N). Shifts in microbial community structure were determined by using a 16S rRNA gene phylogenetic microarray. We linked snowpack and meltwater chemistry to changes in microbial community structure by using co-inertia analyses (CIA) and explored changes in community function due to Hg contamination by q-PCR quantification of Hg-resistance genes in metagenomic samples. Based on the CIA, chemical and microbial data were linked (p = 0.006) with bioavailable Hg (BioHg) and methylmercury (MeHg) contributing significantly to the ordination of samples. Mercury was shown to influence community function with increases in merA gene copy numbers at low BioHg levels. Our results show that snowpacks can be considered as dynamic habitats with microbial and chemical components responding rapidly to environmental changes. PMID:24282515

  18. Effect of membrane bioreactor configurations on sludge structure and microbial activity.

    PubMed

    Clouzot, L; Roche, N; Marrot, B

    2011-01-01

    The aim of this paper was to determine the effect of two different membrane bioreactor (MBR) configurations (external/immersed) on sludge structure and microbial activity. Sludge structure was deduced from rheological measurements. The high shear stress induced by the recirculation pump in the external MBR was shown to result in decreasing viscosity due to activated sludge (AS) deflocculation. Besides, soluble microbial products (SMP) release was higher in the external MBR (5 mgCOD gMLVSS(-1)) than in the immersed configuration (2 mgCOD gMLVSS(-1)). Microbial activity was followed from respirometry tests by focusing on the distinction between heterotrophs and autotrophs. An easier autotrophic microbe development was then observed in the immersed MBR compared to the external one. However, the external MBR was shown to allow better heterotrophic microbe development. PMID:20947340

  19. Assessment of Anaerobic Metabolic Activity and Microbial Diversity in a Petroleum-Contaminated Aquifer Using Push-Pull Tests in Combination With Molecular Tools and Stable Isotopes

    NASA Astrophysics Data System (ADS)

    Schroth, M. H.; Kleikemper, J.; Pombo, S. A.; Zeyer, J.

    2002-12-01

    In the past, studies on microbial communities in natural environments have typically focused on either their structure or on their metabolic function. However, linking structure and function is important for understanding microbial community dynamics, in particular in contaminated environments. We will present results of a novel combination of a hydrogeological field method (push-pull tests) with molecular tools and stable isotope analysis, which was employed to quantify anaerobic activities and associated microbial diversity in a petroleum-contaminated aquifer in Studen, Switzerland. Push-pull tests consisted of the injection of test solution containing a conservative tracer and reactants (electron acceptors, 13C-labeled carbon sources) into the aquifer anoxic zone. Following an incubation period, the test solution/groundwater mixture was extracted from the same location. Metabolic activities were computed from solute concentrations measured during extraction. Simultaneously, microbial diversity in sediment and groundwater was characterized by using fluorescence in situ hybridization (FISH), denaturing gradient gel electrophoresis (DGGE), as well as phospholipids fatty acid (PLFA) analysis in combination with 13C isotopic measurements. Results from DGGE analyses provided information on the general community structure before, during and after the tests, while FISH yielded information on active populations. Moreover, using 13C-labeling of microbial PLFA we were able to directly link carbon source assimilation in an aquifer to indigenous microorganisms while providing quantitative information on respective carbon source consumption.

  20. Contrasting effects of biochar versus manure on soil microbial communities and enzyme activities in an Aridisol.

    PubMed

    Elzobair, Khalid A; Stromberger, Mary E; Ippolito, James A; Lentz, Rodrick D

    2016-01-01

    Biochar can increase microbial activity, alter microbial community structure, and increase soil fertility in arid and semi-arid soils, but at relatively high rates that may be impractical for large-scale field studies. This contrasts with organic amendments such as manure, which can be abundant and inexpensive if locally available, and thus can be applied to fields at greater rates than biochar. In a field study comparing biochar and manure, a fast pyrolysis hardwood biochar (22.4 Mg ha(-1)), dairy manure (42 Mg ha(-1) dry wt), a combination of biochar and manure at the aforementioned rates, or no amendment (control) was applied to an Aridisol (n=3) in fall 2008. Plots were annually cropped to corn (Zea maize L.). Surface soils (0-30 cm) were sampled directly under corn plants in late June 2009 and early August 2012, and assayed for microbial community fatty acid methyl ester (FAME) profiles and six extracellular enzyme activities involved in soil C, N, and P cycling. Arbuscular mycorrhizal (AM) fungal colonization was assayed in corn roots in 2012. Biochar had no effect on microbial biomass, community structure, extracellular enzyme activities, or AM fungi root colonization of corn. In the short-term, manure amendment increased microbial biomass, altered microbial community structure, and significantly reduced the relative concentration of the AM fungal biomass in soil. Manure also reduced the percent root colonization of corn by AM fungi in the longer-term. Thus, biochar and manure had contrasting short-term effects on soil microbial communities, perhaps because of the relatively low application rate of biochar. PMID:26138708

  1. Microbial population dynamics in response to increasing loadings of pre-hydrolyzed pig manure in an expanded granular sludge bed.

    PubMed

    Wang, Haoyu; Tao, Yu; Gao, Dawen; Liu, Gang; Chen, Chunhong; Ren, Nanqi; van Lier, Jules B; de Kreuk, Merle

    2015-12-15

    In recent years, pig manure (PM) has been regarded as a valuable substrate for energy and resource recovery via bioprocesses such as anaerobic digestion (AD), however, the efficiency of digesting raw PM is limited by the presence of refractory compounds. In this study, we applied a series of pretreatment on raw PM, consisting of subsequent thermochemical pretreatment, enzymatic hydrolysis, tyndallization and filtration. The liquid PM hydrolysates were fed to an expanded granular sludge bed (EGSB) for the production of biogas. The general performance and population dynamics of the EGSB reactor were assessed during an extended operational period of 339 days. An efficient and stable digestion process was achieved under high organic loading rates (OLRs) up to 21 kg-COD/(m(3)·d), agreeing with a sludge loading rate of 0.75 kg-COD/(kg-VSS·d), 1600 mg-NH4(+)-N/L and 17 mg/L of free ammonia nitrogen. The tyndallization decreased the total amount of active cells from 1 × 10(8) to 1 × 10(2) CFU/ml. Hence, bio-augmentation with pigs' intestinal microbiota was absent and the community dynamics were mainly credited to the composition of the substrate (i.e. PM hydrolysates) and the environmental conditions inside the reactor. The results showed the influence of both the seed community and the imposed loading rates on the evolutionary trajectory of the EGSB microbial community. Four bacterial genera (Clostridium, Cytophaga, Bacillus and Bacteroides) and two methanogenic genera (Methanosaeta and Methanobacterium) dominated the communities. An obvious shift from aceticlastic Methanosaeta to hydrogenotrophic Methanobacterium appeared when the OLR was increased to over 10 kg-COD/(m(3)·d). PMID:26378729

  2. Effects of soil type and farm management on soil ecological functional genes and microbial activities.

    PubMed

    Reeve, Jennifer R; Schadt, Christopher W; Carpenter-Boggs, Lynne; Kang, Sanghoon; Zhou, Jizhong; Reganold, John P

    2010-09-01

    Relationships between soil microbial diversity and soil function are the subject of much debate. Process-level analyses have shown that microbial function varies with soil type and responds to soil management. However, such measurements cannot determine the role of community structure and diversity in soil function. The goal of this study was to investigate the role of gene frequency and diversity, measured by microarray analysis, on soil processes. The study was conducted in an agro-ecosystem characterized by contrasting management practices and soil types. Eight pairs of adjacent commercial organic and conventional strawberry fields were matched for soil type, strawberry variety, and all other environmental conditions. Soil physical, chemical and biological analyses were conducted including functional gene microarrays (FGA). Soil physical and chemical characteristics were primarily determined by soil textural type (coarse vs fine-textured), but biological and FGA measures were more influenced by management (organic vs conventional). Organically managed soils consistently showed greater functional activity as well as FGA signal intensity (SI) and diversity. Overall FGA SI and diversity were correlated to total soil microbial biomass. Functional gene group SI and/or diversity were correlated to related soil chemical and biological measures such as microbial biomass, cellulose, dehydrogenase, ammonium and sulfur. Management was the dominant determinant of soil biology as measured by microbial gene frequency and diversity, which paralleled measured microbial processes. PMID:20376100

  3. Effects of soil type and farm management on soil ecological functional genes and microbial activities

    SciTech Connect

    Reeve, Jennifer; Schadt, Christopher Warren; Carpenter-Boggs, Lynne; Kang, S.; Zhou, Jizhong; Reganold, John P.

    2010-01-01

    Relationships between soil microbial diversity and soil function are the subject of much debate. Process-level analyses have shown that microbial function varies with soil type and responds to soil management. However, such measurements cannot determine the role of community structure and diversity in soil function. The goal of this study was to investigate the role of gene frequency and diversity, measured by microarray analysis, on soil processes. The study was conducted in an agro-ecosystem characterized by contrasting management practices and soil types. Eight pairs of adjacent commercial organic and conventional strawberry fields were matched for soil type, strawberry variety, and all other environmental conditions. Soil physical, chemical and biological analyses were conducted including functional gene microarrays (FGA). Soil physical and chemical characteristics were primarily determined by soil textural type (coarse vs fine-textured), but biological and FGA measures were more influenced by management (organic vs conventional). Organically managed soils consistently showed greater functional activity as well as FGA signal intensity (SI) and diversity. Overall FGA SI and diversity were correlated to total soil microbial biomass. Functional gene group SI and/or diversity were correlated to related soil chemical and biological measures such as microbial biomass, cellulose, dehydrogenase, ammonium and sulfur. Management was the dominant determinant of soil biology as measured by microbial gene frequency and diversity, which paralleled measured microbial processes.

  4. Extracellular polymeric substances, microbial activity and microbial community of biofilm and suspended sludge at different divalent cadmium concentrations.

    PubMed

    Wang, Zichao; Gao, Mengchun; Wei, Junfeng; Ma, Kedong; Zhang, Jing; Yang, Yusuo; Yu, Shuping

    2016-04-01

    The differences between biofilm and suspended sludge (S-sludge) in extracellular polymeric substances (EPS), microbial activity, and microbial community in an anoxic-aerobic sequencing batch biofilm reactor (SBBR) at different concentrations of divalent cadmium (Cd(II)) were investigated. As the increase of Cd(II) concentration from 0 to 50mgL(-1), the specific ammonium oxidation rate (SAOR), specific nitrite oxidation rate (SNOR), and specific nitrate reduction rate (SNRR) of biofilm decreased from 4.85, 5.22 and 45mgNg(-1) VSSh(-1) to 1.54, 2.38 and 26mgNg(-1)VSSh(-1), respectively, and the SAOR, SNOR and SNRR of S-sludge decreased from 4.80, 5.02 and 34mgNg(-1)VSSh(-1) to 1.46, 2.20 and 17mgNg(-1)VSSh(-1), respectively. Biofilm had higher protein (PN) content in EPS than S-sludge. Contrast to S-sludge, biofilm could provide Nitrobacter vulgaris, beta proteobacterium INBAF015, and Pseudoxanthomonas mexicana with the favorable conditions of growth and reproduction. PMID:26829529

  5. Effect of a microbiota activator on accumulated ammonium and microbial community structure in a pilot-scale membrane bioreactor.

    PubMed

    Sato, Yuya; Hori, Tomoyuki; Navarro, Ronald R; Ronald, Navarro R; Habe, Hiroshi; Ogata, Atsushi

    2015-01-01

    Microbiota activators (MAs) have been used to improve the reactor performances of biological wastewater treatment processes. In this study, to remove ammonium (NH4(+)) accumulated during the pre-operation of a pilot-scale membrane bioreactor (MBR) under high-organic-loading conditions, an MA was added to the MBR system and the resulting changes in reactor performances and microbial communities were monitored for 12 days. The NH4(+) concentrations in the sludge and effluent decreased (from 427 to 246 mg/L in the sludge (days 1-9)), and mixed liquor suspended solid increased (from 6,793 to 11,283 mg/L (days 1-12)) after the addition of MA. High-throughput Illumina sequencing of 16S rRNA genes revealed that the microbial community structure changed along with the NH4(+) removal resulting from the MA addition. In particular, the relative abundance of an Acidovorax-related operational taxonomic unit (OTU) increased significantly, accounting for approximately 50% of the total microbial population at day 11. In contrast, the ammonia-oxidizing bacteria and archaea showed low abundances (<0.05%), and no anaerobic ammonia oxidizers were detected. These results suggested that the Acidovorax-related OTU was mainly involved in the NH4(+) removal in the MBR, probably due to its ammonia-assimilating metabolism. PMID:26377133

  6. Experimental evidence that microbial activity lowers the albedo of glacier surfaces: the cryoconite casserole experiment.

    NASA Astrophysics Data System (ADS)

    Musilova, M.; Tranter, M.; Takeuchi, N.; Anesio, A. M.

    2014-12-01

    Darkened glacier and ice sheet surfaces have lower albedos, absorb more solar radiation and consequently melt more rapidly. The increase in glacier surface darkening is an important positive feedback to warming global temperatures, leading to ever growing world-wide ice mass loss. Most studies focus primarily on glacial albedo darkening caused by the physical properties of snow and ice surfaces, and the deposition of dark impurities on glaciers. To date, however, the important effects of biological activity have not been included in most albedo reduction models. This study provides the first experimental evidence that microbial activity can significantly decrease the albedo of glacier surfaces. An original laboratory experiment, the cryoconite casserole, was designed to test the microbial darkening of glacier surface debris (cryoconite) under simulated Greenlandic summer conditions. It was found that minor fertilisation of the cryoconite (at nutrient concentrations typical of glacial ice melt) stimulated extensive microbial activity. Microbes intensified their organic carbon fixation and even mined phosphorous out of the glacier surface sediment. Furthermore, the microbial organic carbon production, accumulation and transformation caused the glacial debris to darken further by 17.3% reflectivity (albedo analogue). These experiments are consistent with the hypothesis that enhanced fertilisation by anthropogenic inputs results in substantial amounts of organic carbon fixation, debris darkening and ultimately to a considerable decrease in the ice albedo of glacier surfaces on global scales. The sizeable amounts of microbially produced glacier surface organic matter and nutrients can thus be a vital source of bioavailable nutrients for subglacial and downstream environments.

  7. Humic fractions of forest, pasture and maize crop soils resulting from microbial activity.

    PubMed

    Tavares, Rose Luiza Moraes; Nahas, Ely

    2014-01-01

    Humic substances result from the degradation of biopolymers of organic residues in the soil due to microbial activity. The objective of this study was to evaluate the influence of three different ecosystems: forest, pasture and maize crop on the formation of soil humic substances relating to their biological and chemical attributes. Microbial biomass carbon (MBC), microbial respiratory activity, nitrification potential, total organic carbon, soluble carbon, humic and fulvic acid fractions and the rate and degree of humification were determined. Organic carbon and soluble carbon contents decreased in the order: forest > pasture > maize; humic and fulvic acids decreased in the order forest > pasture = maize. The MBC and respiratory activity were not influenced by the ecosystems; however, the nitrification potential was higher in the forest than in other soils. The rate and degree of humification were higher in maize soil indicating greater humification of organic matter in this system. All attributes studied decreased significantly with increasing soil depth, with the exception of the rate and degree of humification. Significant and positive correlations were found between humic and fulvic acids contents with MBC, microbial respiration and nitrification potential, suggesting the microbial influence on the differential formation of humic substances of the different ecosystems. PMID:25477932

  8. Humic fractions of forest, pasture and maize crop soils resulting from microbial activity

    PubMed Central

    Tavares, Rose Luiza Moraes; Nahas, Ely

    2014-01-01

    Humic substances result from the degradation of biopolymers of organic residues in the soil due to microbial activity. The objective of this study was to evaluate the influence of three different ecosystems: forest, pasture and maize crop on the formation of soil humic substances relating to their biological and chemical attributes. Microbial biomass carbon (MBC), microbial respiratory activity, nitrification potential, total organic carbon, soluble carbon, humic and fulvic acid fractions and the rate and degree of humification were determined. Organic carbon and soluble carbon contents decreased in the order: forest > pasture > maize; humic and fulvic acids decreased in the order forest > pasture=maize. The MBC and respiratory activity were not influenced by the ecosystems; however, the nitrification potential was higher in the forest than in other soils. The rate and degree of humification were higher in maize soil indicating greater humification of organic matter in this system. All attributes studied decreased significantly with increasing soil depth, with the exception of the rate and degree of humification. Significant and positive correlations were found between humic and fulvic acids contents with MBC, microbial respiration and nitrification potential, suggesting the microbial influence on the differential formation of humic substances of the different ecosystems. PMID:25477932

  9. Carbonate Precipitation through Microbial Activities in Natural Environment, and Their Potential in Biotechnology: A Review

    PubMed Central

    Zhu, Tingting; Dittrich, Maria

    2016-01-01

    Calcium carbonate represents a large portion of carbon reservoir and is used commercially for a variety of applications. Microbial carbonate precipitation, a by-product of microbial activities, plays an important metal coprecipitation and cementation role in natural systems. This natural process occurring in various geological settings can be mimicked and used for a number of biotechnologies, such as metal remediation, carbon sequestration, enhanced oil recovery, and construction restoration. In this study, different metabolic activities leading to calcium carbonate precipitation, their native environment, and potential applications and challenges are reviewed. PMID:26835451

  10. Carbonate Precipitation through Microbial Activities in Natural Environment, and Their Potential in Biotechnology: A Review.

    PubMed

    Zhu, Tingting; Dittrich, Maria

    2016-01-01

    Calcium carbonate represents a large portion of carbon reservoir and is used commercially for a variety of applications. Microbial carbonate precipitation, a by-product of microbial activities, plays an important metal coprecipitation and cementation role in natural systems. This natural process occurring in various geological settings can be mimicked and used for a number of biotechnologies, such as metal remediation, carbon sequestration, enhanced oil recovery, and construction restoration. In this study, different metabolic activities leading to calcium carbonate precipitation, their native environment, and potential applications and challenges are reviewed. PMID:26835451

  11. Arctic Gypsum Endoliths: a biogeochemical characterization of a viable and active microbial community

    NASA Astrophysics Data System (ADS)

    Ziolkowski, L. A.; Mykytczuk, N. C. S.; Omelon, C. R.; Johnson, H.; Whyte, L. G.; Slater, G. F.

    2013-02-01

    evidence of microbial-mineral interaction, an alternative hypothesis is that the soluble and friable nature of the gypsum and harsh conditions lead to elevated erosion rates, limiting microbial residence times in this habitat. Regardless, this endolithic community represents a microbial system that does not rely on a nutrient pool from the host gypsum cap rock, instead receiving these elements from allochthonous debris to maintain a more diverse and active community than might have been predicted in the polar desert of the Canadian high Arctic.

  12. Submersible microbial fuel cell sensor for monitoring microbial activity and BOD in groundwater: focusing on impact of anodic biofilm on sensor applicability.

    PubMed

    Zhang, Yifeng; Angelidaki, Irini

    2011-10-01

    A sensor, based on a submersible microbial fuel cell (SUMFC), was developed for in situ monitoring of microbial activity and biochemical oxygen demand (BOD) in groundwater. Presence or absence of a biofilm on the anode was a decisive factor for the applicability of the sensor. Fresh anode was required for application of the sensor for microbial activity measurement, while biofilm-colonized anode was needed for utilizing the sensor for BOD content measurement. The current density of SUMFC sensor equipped with a biofilm-colonized anode showed linear relationship with BOD content, to up to 250 mg/L (∼233 ± 1 mA/m(2)), with a response time of <0.67 h. This sensor could, however, not measure microbial activity, as indicated by the indifferent current produced at varying active microorganisms concentration, which was expressed as microbial adenosine-triphosphate (ATP) concentration. On the contrary, the current density (0.6 ± 0.1 to 12.4 ± 0.1 mA/m(2)) of the SUMFC sensor equipped with a fresh anode showed linear relationship, with active microorganism concentrations from 0 to 6.52 nmol-ATP/L, while no correlation between the current and BOD was observed. It was found that temperature, pH, conductivity, and inorganic solid content were significantly affecting the sensitivity of the sensor. Lastly, the sensor was tested with real contaminated groundwater, where the microbial activity and BOD content could be detected in <3.1 h. The microbial activity and BOD concentration measured by SUMFC sensor fitted well with the one measured by the standard methods, with deviations ranging from 15% to 22% and 6% to 16%, respectively. The SUMFC sensor provides a new way for in situ and quantitative monitoring contaminants content and biological activity during bioremediation process in variety of anoxic aquifers. PMID:21557205

  13. Hydrogeology, Chemical and Microbial Activity Measurement Through Deep Permafrost

    USGS Publications Warehouse

    Stotler, R.L.; Frape, S.K.; Freifeld, B.M.; Holden, B.; Onstott, T.C.; Ruskeeniemi, T.; Chan, E.

    2011-01-01

    Little is known about hydrogeochemical conditions beneath thick permafrost, particularly in fractured crystalline rock, due to difficulty in accessing this environment. The purpose of this investigation was to develop methods to obtain physical, chemical, and microbial information about the subpermafrost environment from a surface-drilled borehole. Using a U-tube, gas and water samples were collected, along with temperature, pressure, and hydraulic conductivity measurements, 420 m below ground surface, within a 535 m long, angled borehole at High Lake, Nunavut, Canada, in an area with 460-m-thick permafrost. Piezometric head was well above the base of the permafrost, near land surface. Initial water samples were contaminated with drill fluid, with later samples <40% drill fluid. The salinity of the non-drill fluid component was <20,000 mg/L, had a Ca/Na ratio above 1, with ??18O values ???5??? lower than the local surface water. The fluid isotopic composition was affected by the permafrost-formation process. Nonbacteriogenic CH4 was present and the sample location was within methane hydrate stability field. Sampling lines froze before uncontaminated samples from the subpermafrost environment could be obtained, yet the available time to obtain water samples was extended compared to previous studies. Temperature measurements collected from a distributed temperature sensor indicated that this issue can be overcome easily in the future. The lack of methanogenic CH4 is consistent with the high sulfate concentrations observed in cores. The combined surface-drilled borehole/U-tube approach can provide a large amount of physical, chemical, and microbial data from the subpermafrost environment with few, controllable, sources of contamination. ?? 2010 The Author(s). Journal compilation ?? 2010 National Ground Water Association.

  14. Hydrogeology, chemical and microbial activity measurement through deep permafrost

    SciTech Connect

    Stotler, R.L.; Frape, S.K.; Freifeld, B.M.; Holden, B.; Onstott, T.C.; Ruskeeniemi, T.; Chan, E.

    2010-04-01

    Little is known about hydrogeochemical conditions beneath thick permafrost, particularly in fractured crystalline rock, due to difficulty in accessing this environment. The purpose of this investigation was to develop methods to obtain physical, chemical, and microbial information about the subpermafrost environment from a surface-drilled borehole. Using a U-tube, gas and water samples were collected, along with temperature, pressure, and hydraulic conductivity measurements, 420 m below ground surface, within a 535 m long, angled borehole at High Lake, Nunavut, Canada, in an area with 460-m-thick permafrost. Piezometric head was well above the base of the permafrost, near land surface. Initial water samples were contaminated with drill fluid, with later samples <40% drill fluid. The salinity of the non-drill fluid component was <20,000 mg/L, had a Ca/Na ratio above 1, with {delta}{sup 18}O values {approx}5{per_thousand} lower than the local surface water. The fluid isotopic composition was affected by the permafrost-formation process. Nonbacteriogenic CH{sub 4} was present and the sample location was within methane hydrate stability field. Sampling lines froze before uncontaminated samples from the subpermafrost environment could be obtained, yet the available time to obtain water samples was extended compared to previous studies. Temperature measurements collected from a distributed temperature sensor indicated that this issue can be overcome easily in the future. The lack of methanogenic CH{sub 4} is consistent with the high sulfate concentrations observed in cores. The combined surface-drilled borehole/U-tube approach can provide a large amount of physical, chemical, and microbial data from the subpermafrost environment with few, controllable, sources of contamination.

  15. Phenol- and Toluene-Degrading Microbial Populations from an Aquifer in Which Successful Trichloroethene Cometabolism Occurred

    PubMed Central

    Fries, M. R.; Forney, L. J.; Tiedje, J. M.

    1997-01-01

    - and toluene-stimulated TCE removal that occurred during the field assessment of this remediation process. This suggests that naturally occurring communities of only moderate TCE-cooxidizing ability may support successful TCE bioremediation as long as the phenol or toluene present is not limiting. This activity, however, may not be sustainable for the long term, because TCE-inactive populations that consumed toluene at rates equal to that of the best TCE degraders were present and hence would be expected to eventually dominate the community. PMID:16535577

  16. Comparison of methods for measuring soil microbial activity using cotton strips and a respirometer.

    PubMed

    Nachimuthu, Gunasekhar; King, Kathleen; Kristiansen, Paul; Lockwood, Peter; Guppy, Chris

    2007-05-01

    In order to develop a method of measuring the level of microbial activity in soil that is suitable for use by farmers, land managers, and other non-scientists, a simple method for determining soil microbial activity was evaluated and compared with two standard techniques. Soils sampled from vegetable farms in south east Queensland were incubated in the laboratory under controlled moisture and temperature conditions. Three methods were used to measure soil microbial activity, a respirometry method and two methods using the cotton strip assay (CSA) technique (image analysis and tensometer). The standard CSA method measured loss of tensile strength over a 35 day incubation period of buried cotton strips using a tensometer. The new CSA technique measured the intensity of staining by microbes using a flatbed scanner to create an image of the cotton strip whose staining percentage was determined using Photoshop software. The respirometry method used the substrate induced respiration rate (SIR) to determine microbial biomass in the soil at day 12 of incubation. The strong correlation between the image analysis method and the tensometer method (r(2)=0.81), a technique used by scientific researchers, suggests that the image analysis method could be used to monitor aspects of soil biological health by general community land-care groups and farmers. The image analysis method uses equipment which is readily available and, while not strongly correlated with more precise measurements of soil biological activity such as microbial biomass (r(2)=0.26), it can detect gross trends in biological health in a soil monitoring program. The CSA method using image analysis was the cheapest technique to measure soil microbial activity. CSA using image analysis can be a valuable tool in conjunction with other simple indicators of soil physical and chemical health such as slaking and pH to monitor soil amelioration or rehabilitation programs. PMID:17376552

  17. Sub-soil microbial activity under rotational cotton crops in Australia

    NASA Astrophysics Data System (ADS)

    Polain, Katherine; Knox, Oliver; Wilson, Brian; Pereg, Lily

    2016-04-01

    Soil microbial communities contribute significantly to soil organic matter formation, stabilisation and destabilisation, through nutrient cycling and biodegradation. The majority of soil microbial research examines the processes occurring in the top 0 cm to 30 cm of the soil, where organic nutrients are easily accessible. In soils such as Vertosols, the high clay content causes swelling and cracking. When soil cracking is coupled with rain or an irrigation event, a flush of organic nutrients can move down the soil profile, becoming available for subsoil microbial community use and potentially making a significant contribution to nutrient cycling and biodegradation in soils. At present, the mechanisms and rates of soil nutrient turnover (such as carbon and nitrogen) at depth under cotton rotations are mostly speculative and the process-response relationships remain unclear, although they are undoubtedly underpinned by microbial activity. Our research aims to determine the contribution and role of soil microbiota to the accumulation, cycling and mineralisation of carbon and nitrogen through the whole root profile under continuous cotton (Gossypium hirsutum) and cotton-maize rotations in regional New South Wales, Australia. Through seasonal work, we have established both baseline and potential microbial activity rates from 0 cm to 100 cm down the Vertosol profile, using respiration and colourimetric methods. Further whole soil profile analyses will include determination of microbial biomass and isotopic carbon signatures using phospholipid fatty acid (PLFA) methodology, identification of microbial communities (sequencing) and novel experiments to investigate potential rates of nitrogen mineralisation and quantification of associated genes. Our preliminary observations and the hypotheses tested in this three-year study will be presented.

  18. Microbial catabolic activities are naturally selected by metabolic energy harvest rate.

    PubMed

    González-Cabaleiro, Rebeca; Ofiţeru, Irina D; Lema, Juan M; Rodríguez, Jorge

    2015-12-01

    The fundamental trade-off between yield and rate of energy harvest per unit of substrate has been largely discussed as a main characteristic for microbial established cooperation or competition. In this study, this point is addressed by developing a generalized model that simulates competition between existing and not experimentally reported microbial catabolic activities defined only based on well-known biochemical pathways. No specific microbial physiological adaptations are considered, growth yield is calculated coupled to catabolism energetics and a common maximum biomass-specific catabolism rate (expressed as electron transfer rate) is assumed for all microbial groups. Under this approach, successful microbial metabolisms are predicted in line with experimental observations under the hypothesis of maximum energy harvest rate. Two microbial ecosystems, typically found in wastewater treatment plants, are simulated, namely: (i) the anaerobic fermentation of glucose and (ii) the oxidation and reduction of nitrogen under aerobic autotrophic (nitrification) and anoxic heterotrophic and autotrophic (denitrification) conditions. The experimentally observed cross feeding in glucose fermentation, through multiple intermediate fermentation pathways, towards ultimately methane and carbon dioxide is predicted. Analogously, two-stage nitrification (by ammonium and nitrite oxidizers) is predicted as prevailing over nitrification in one stage. Conversely, denitrification is predicted in one stage (by denitrifiers) as well as anammox (anaerobic ammonium oxidation). The model results suggest that these observations are a direct consequence of the different energy yields per electron transferred at the different steps of the pathways. Overall, our results theoretically support the hypothesis that successful microbial catabolic activities are selected by an overall maximum energy harvest rate. PMID:26161636

  19. Analyses of microbial populations and antibiotic resistance present in stored swine manure from underground storage pits

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Antimicrobial compounds have been commonly used as feed additives for domestic animals to reduce infection and promote growth. Recent concerns have suggested such feeding practices may result in increased microbial resistance to antibiotics, which can have an impact on human health. While many inves...

  20. Cow Teat Skin, a Potential Source of Diverse Microbial Populations for Cheese Production

    PubMed Central

    Gagne, Geneviève; Bornes, Stéphanie; Monsallier, Françoise; Veisseire, Philippe; Delbès-Paus, Céline; Montel, Marie-Christine

    2012-01-01

    The diversity of the microbial community on cow teat skin was evaluated using a culture-dependent method based on the use of different dairy-specific media, followed by the identification of isolates by 16S rRNA gene sequencing. This was combined with a direct molecular approach by cloning and 16S rRNA gene sequencing. This study highlighted the large diversity of the bacterial community that may be found on teat skin, where 79.8% of clones corresponded to various unidentified species as well as 66 identified species, mainly belonging to those commonly found in raw milk (Enterococcus, Pediococcus, Enterobacter, Pantoea, Aerococcus, and Staphylococcus). Several of them, such as nonstarter lactic acid bacteria (NSLAB), Staphylococcus, and Actinobacteria, may contribute to the development of the sensory characteristics of cheese during ripening. Therefore, teat skin could be an interesting source or vector of biodiversity for milk. Variations of microbial counts and diversity between the farms studied have been observed. Moreover, Staphylococcus auricularis, Staphylococcus devriesei, Staphylococcus arlettae, Streptococcus bovis, Streptococcus equinus, Clavibacter michiganensis, Coprococcus catus, or Arthrobacter gandavensis commensal bacteria of teat skin and teat canal, as well as human skin, are not common in milk, suggesting that there is a breakdown of microbial flow from animal to milk. It would then be interesting to thoroughly study this microbial flow from teat to milk. PMID:22081572

  1. Differential Incorporation of Carbon Substrates among Microbial Populations Identified by Field-Based, DNA Stable-Isotope Probing in South China Sea

    PubMed Central

    Xie, Xiabing; Jiao, Nianzhi

    2016-01-01

    To determine the adapted microbial populations to variant dissolved organic carbon (DOC) sources in the marine environment and improve the understanding of the interaction between microorganisms and marine DOC pool, field-based incubation experiments were carried out using supplemental 13C-labeled typical substrates D-glucose and D-glucosamine (D-Glc and D-GlcN, respectively), which are two important components in marine DOC pool in the South China Sea. 13C- and 12C-DNA were then fractionated by ultracentrifugation and the microbial community was analyzed by terminal-restriction fragment length polymorphism and 454 pyrosequencing of 16S rRNA gene. 12C-DNA-based communities showed relatively high similarities with their corresponding in situ communities, and their bacterial diversities were generally higher than 13C-DNA-based counterparts. Distinct differences in community composition were found between 13C- and 12C-DNA-based communities and between two substrate-supplemented 13C-DNA-based communities; these differences distinctly varied with depth and site. In most cases, there were more genera with relative abundances of >0.1% in D-Glc-incorporating communities than in D-GlcN-incorporating communities. The Roseobacter clade was one of the prominent actively substrate-incorporating bacterial populations in all 13C-DNA-based communities. Vibrio was another prominent actively D-GlcN-incorporating bacterial population in most incubations. However notably, different OTUs dominated this clade or genus in different treatments at different depths. Altogether, these results suggested that there were taxa-specific differences in DOC assimilations and, moreover, their differences varied among the typical water masses, which could have been caused by the variant compositions of original bacterial communities from different hydrological environments. This implies that ecologically, the levels of labile or recalcitrance of DOC can be maintained only in a specific environmental

  2. Earthworms facilitate the stabilization of pelletized dewatered sludge through shaping microbial biomass and activity and community.

    PubMed

    Fu, Xiaoyong; Cui, Guangyu; Huang, Kui; Chen, Xuemin; Li, Fusheng; Zhang, Xiaoyu; Li, Fei

    2016-03-01

    In this study, the effect of earthworms on microbial features during vermicomposting of pelletized dewatered sludge (PDS) was investigated through comparing two degradation systems with and without earthworm E isenia fetida involvement. After 60 days of experimentation, a relatively stable product with low organic matter and high nitrate and phosphorous was harvested when the earthworms were involved. During the process, earthworms could enhance microbial activity and biomass at the initial stage and thus accelerating the rapid decomposition of PDS. The end products of vermicomposting allowed the lower values of bacterial and eukaryotic densities comparison with those of no earthworm addition. In addition, the presence of earthworms modified the bacterial and fungal diversity, making the disappearances of some pathogens and specific decomposing bacteria of recalcitrant substrates in the vermicomposting process. This study evidences that earthworms can facilitate the stabilization of PDS through modifying microbial activity and number and community during vermicomposting. PMID:26514568

  3. Microbial community analysis during continuous fermentation of thermally hydrolysed waste activated sludge.

    PubMed

    Cirne, D G; Bond, P; Pratt, S; Lant, P; Batstone, D J

    2012-01-01

    Acidogenic fermentation of thermally hydrolysed waste activated sludge was carried out at laboratory scale in two reactors operated under different hydraulic retention times (HRT). Process performance was assessed in terms of volatile fatty acid (VFA) composition and yield. The diversity of the microbial population was investigated by constructing a 16S rRNA gene library and subsequent phylogenetic analysis of clones. Fluorescence in situ hybridization (FISH) was used to assess the relative abundance of different bacterial groups. Bacteroidetes and Firmicutes were the dominant taxonomic groups representing 93% of the total sequences obtained in the reactor with 4 d HRT. A similar VFA yield (0.4-0.5 g VFA(COD) g SCOD(-1)) was obtained for the HRTs tested (1-4 d), indicating that extended retention times were not useful. Within Firmicutes, Clostridia was the major group detected in the clone sequences. These had close affiliation to Sporanaerobacter acetigenes, suggesting organisms of this group were important for hydrolysis of the protein fraction of the substrate. However, FISH analysis failed to detect the major portion of the bacteria, and this is most likely due to the lack of appropriate probes. This work emphasizes the diversity of fermentative communities, and indicates that more work is needed to identify and detect the important members. PMID:22173402

  4. Microbial populations identified by fluorescence in situ hybridization in a constructed wetland treating acid coal mine drainage

    SciTech Connect

    Nicomrat, D.; Dick, W.A.; Tuovinen, O.H.

    2006-07-15

    Microorganisms are an integral part of the biogeochemical processes in wetlands, yet microbial communities in sediments within constructed wetlands receiving acid mine drainage (AMD) are only poorly understood. The purpose of this study was to characterize the microbial diversity and abundance in a wetland receiving AMD using fluorescence in situ hybridization (FISH) analysis. Seasonal samples of oxic surface sediments, comprised of Fe(III) precipitates, were collected from two treatment cells of the constructed wetland system. The pH of the bulk samples ranged between pH 2.1 and 3.9. Viable counts of acidophilic Fe and S oxidizers and heterotrophs were determined with a most probable number (MPN) method. The MPN counts were only a fraction of the corresponding FISH counts. The sediment samples contained microorganisms in the Bacteria (including the subgroups of acidophilic Fe- and S-oxidizing bacteria and Acidiphilium spp.) and Eukarya domains. Archaea were present in the sediment surface samples at < 0.01% of the total microbial community. The most numerous bacterial species in this wetland system was Acidithiobacillus ferrooxidans, comprising up to 37% of the bacterial population. Acidithiobacillus thiooxidans was also abundant.

  5. Oil Biodegradation and Oil-Degrading Microbial Populations in Marsh Sediments Impacted by Oil from the Deepwater Horizon Well Blowout.

    PubMed

    Atlas, Ronald M; Stoeckel, Donald M; Faith, Seth A; Minard-Smith, Angela; Thorn, Jonathan R; Benotti, Mark J

    2015-07-21

    To study hydrocarbon biodegradation in marsh sediments impacted by Macondo oil from the Deepwater Horizon well blowout, we collected sediment cores 18-36 months after the accident at the marshes in Bay Jimmy (Upper Barataria Bay), Louisiana, United States. The highest concentrations of oil were found in the top 2 cm of sediment nearest the waterline at the shorelines known to have been heavily oiled. Although petroleum hydrocarbons were detectable, Macondo oil could not be identified below 8 cm in 19 of the 20 surveyed sites. At the one site where oil was detected below 8 cm, concentrations were low. Residual Macondo oil was already highly weathered at the start of the study, and the concentrations of individual saturated hydrocarbons and polycyclic aromatic hydrocarbons continued to decrease over the course of the study due to biodegradation. Desulfococcus oleovorans, Marinobacter hydrocarbonoclasticus, Mycobacterium vanbaalenii, and related mycobacteria were the most abundant oil-degrading microorganisms detected in the top 2 cm at the oiled sites. Relative populations of these taxa declined as oil concentrations declined. The diversity of the microbial community was low at heavily oiled sites compared to that of the unoiled reference sites. As oil concentrations decreased over time, microbial diversity increased and approached the diversity levels of the reference sites. These trends show that the oil continues to be biodegraded, and microbial diversity continues to increase, indicating ongoing overall ecological recovery. PMID:26091189

  6. [Effects of Different Altitudes on Soil Microbial PLFA and Enzyme Activity in Two Kinds of Forests].

    PubMed

    Zeng, Qing-ping; He, Bing-hui; Mao, Qiao-zhi; Wu, Yao-peng; Huang, Qi; Li, Yuan

    2015-12-01

    The soil microbial community is an important part in soil ecosystem, and it is sensitive to the ecological environment. Phospholipid-derived fatty acids ( PLFA ) analysis was used to examine variations in soil microbial community diversity and its influencing factors. The results showed that: there existed 48 PLFAs that were significant in the soil samples from six altitudes. The PLFAs of six altitudes with the highest contents were i16:0, 10Me17:0, 10Me18:0 TBSA. The citrus forest exhibited richer soil PLFAs distribution both in type and amount than those in masson pine. The microbial activity and functional diversity of masson pine were increased with increasing altitudes, and citrus forest gradually decreased, the PLFA content of different microbial groups in each altitude were significantly different. The richness index, Shannon-Wiener index and Pielou evenness index of masson pine in low elevation were holistically higher than those in high elevation. However, the highest richness index of citrus forest was in low altitude, the highest Shannon-Wiener index and Pielou evenness index were in high altitude. The PLFAs content of different microbial groups were closely correlated to the soil enzyme activities and environmental factors. The PLFAs of bacteria, actinomycetes, G⁻ (Gram- positive), G⁺ (Gram-negative) were positively correlated with Ure(urease) , Ive(invertase) , CAT( catalase activity) and forest type, the PLFAs of fungi was significantly correlated with Ure, Ive, CAT, the PLFAs of bacteria, fungi, actinomycetes, G⁻ , G⁺ were significantly negatively or less correlated with elevation. Ure, Ive, CAT, forest type and elevation are the pivotal factors controlling the soil microbial biomass and activities. PMID:27012007

  7. Microbial Diversity of a Brazilian Coastal Region Influenced by an Upwelling System and Anthropogenic Activity

    PubMed Central

    Cury, Juliano C.; Araujo, Fabio V.; Coelho-Souza, Sergio A.; Peixoto, Raquel S.; Oliveira, Joana A. L.; Santos, Henrique F.; Dávila, Alberto M. R.; Rosado, Alexandre S.

    2011-01-01

    Background Upwelling systems are characterised by an intense primary biomass production in the surface (warmest) water after the outcrop of the bottom (coldest) water, which is rich in nutrients. Although it is known that the microbial assemblage plays an important role in the food chain of marine systems and that the upwelling systems that occur in southwest Brazil drive the complex dynamics of the food chain, little is known about the microbial composition present in this region. Methodology/Principal Findings We carried out a molecular survey based on SSU rRNA gene from the three domains of the phylogenetic tree of life present in a tropical upwelling region (Arraial do Cabo, Rio de Janeiro, Brazil). The aim was to analyse the horizontal and vertical variations of the microbial composition in two geographically close areas influenced by anthropogenic activity (sewage disposal/port activity) and upwelling phenomena, respectively. A lower estimated diversity of microorganisms of the three domains of the phylogenetic tree of life was found in the water of the area influenced by anthropogenic activity compared to the area influenced by upwelling phenomena. We observed a heterogenic distribution of the relative abundance of taxonomic groups, especially in the Archaea and Eukarya domains. The bacterial community was dominated by Proteobacteria, Cyanobacteria and Bacteroidetes phyla, whereas the microeukaryotic community was dominated by Metazoa, Fungi, Alveolata and Stramenopile. The estimated archaeal diversity was the lowest of the three domains and was dominated by uncharacterised marine Crenarchaeota that were most closely related to Marine Group I. Conclusions/Significance The variety of conditions and the presence of different microbial assemblages indicated that the area of Arraial do Cabo can be used as a model for detailed studies that contemplate the correlation between pollution-indicating parameters and the depletion of microbial diversity in areas close

  8. Among-Population Variation in Microbial Community Structure in the Floral Nectar of the Bee-Pollinated Forest Herb Pulmonaria officinalis L

    PubMed Central

    Jacquemyn, Hans; Lenaerts, Marijke; Brys, Rein; Willems, Kris; Honnay, Olivier; Lievens, Bart

    2013-01-01

    Background Microbial communities in floral nectar have been shown to be characterized by low levels of species diversity, yet little is known about among-plant population variation in microbial community composition. Methodology/Principal Findings We investigated the microbial community structure (yeasts and bacteria) in floral nectar of ten fragmented populations of the bee-pollinated forest herb Pulmonaria officinalis. We also explored possible relationships between plant population size and microbial diversity in nectar, and related microbial community composition to the distance separating plant populations. Culturable bacteria and yeasts occurring in the floral nectar of a total of 100 plant individuals were isolated and identified by partially sequencing the 16S rRNA gene and D1/D2 domains of the 26S rRNA gene, respectively. A total of 9 and 11 yeast and 28 and 39 bacterial OTUs was found, taking into account a 3% (OTU0.03) and 1% sequence dissimilarity cut-off (OTU0.01). OTU richness at the plant population level (i.e. the number of OTUs per population) was low for yeasts (mean: 1.7, range: 0–4 OTUs0.01/0.03 per population), whereas on average 6.9 (range: 2–13) OTUs0.03 and 7.9 (range 2–16) OTUs0.01 per population were found for bacteria. Both for yeasts and bacteria, OTU richness was not significantly related to plant population size. Similarity in community composition among populations was low (average Jaccard index: 0.14), and did not decline with increasing distance between populations. Conclusions/Significance We found low similarity in microbial community structure among populations, suggesting that the assembly of nectar microbiota is to a large extent context-dependent. Although the precise factors that affect variation in microbial community structure in floral nectar require further study, our results indicate that both local and regional processes may contribute to among-population variation in microbial community structure in nectar. PMID

  9. Comparison of microbial communities of activated sludge and membrane biofilm in 10 full-scale membrane bioreactors.

    PubMed

    Jo, Sung Jun; Kwon, Hyeokpil; Jeong, So-Yeon; Lee, Chung-Hak; Kim, Tae Gwan

    2016-09-15

    Operation of membrane bioreactors (MBRs) for wastewater treatment is hampered by the membrane biofouling resulting from microbial activities. However, the knowledge of the microbial ecology of both biofilm and activated sludge in MBRs has not been sufficient. In this study, we scrutinized microbial communities of biofilm and activated sludge from 10 full-scale MBR plants. Overall, Flavobacterium, Dechloromonas and Nitrospira were abundant in order of abundance in biofilm, whereas Dechloromonas, Flavobacterium and Haliscomenobacter in activated sludge. Community structure was analyzed in either biofilm or activated sludge. Among MBRs, as expected, not only diversity of microbial community but also its composition was different from one another (p < 0.05). Between the biofilm and activated sludge, community composition made significant difference, but its diversity measures (i.e., alpha diversity, e.g., richness, diversity and evenness) did not (p > 0.05). Effects of ten environmental factors on community change were investigated using Spearman correlation. MLSS, HRT, F/M ratio and SADm explained the variation of microbial composition in the biofilm, whereas only MLSS did in the activated sludge. Microbial networks were constructed with the 10 environmental factors. The network results revealed that there were different topological characteristics between the biofilm and activated sludge networks, in which each of the 4 factors had different associations with microbial nodes. These results indicated that the different microbial associations were responsible for the variation of community composition between the biofilm and activated sludge. PMID:27262549

  10. Enhancement and inhibition of microbial activity in hydrocarbon- contaminated arctic soils: Implications for nutrient-amended bioremediation

    USGS Publications Warehouse

    Braddock, J.F.; Ruth, M.L.; Catterall, P.H.; Walworth, J.L.; McCarthy, K.A.

    1997-01-01

    Bioremediation is being used or proposed as a treatment option at many hydrocarbon-contaminated sites. One such site is a former bulk-fuel storage facility near Barrow, AK, where contamination persists after approximately 380 m3 of JP-5 was spilled in 1970. The soil at the site is primarily coarse sand with low organic carbon (<1%) end low moisture (1-3%) contents. We examined the effects of nutrient additions on microorganisms in contaminated soil from this site in laboratory microcosms and in mesocosms incubated for 6 weeks in the field. Nitrogen was the major limiting nutrient in this system, but microbial populations and activity were maximally enhanced by additions of both nitrogen and phosphorus. When nutrients were added to soil in the field at three levels of N:P (100:45, 200:90, and 300:135 mg/kg soil), the greatest stimulation in microbial activity occurred at the lowest, rather than the highest, level of nutrient addition. The total soil-water potentials ranged from -2 to -15 bar with increasing levels of fertilizer. Semivolatile hydrocarbon concentrations declined significantly only in the soils treated at the low fertilizer level. These results indicate that an understanding of nutrient effects at a specific site is essential for successful bioremediation.Bioremediation is being used or proposed as a treatment option at many hydrocarbon-contaminated sites. One such site is a former bulk-fuel storage facility near Barrow, AK, where contamination persists after approximately 380 m3 of JP-5 was spilled in 1970. The soil at the site is primarily coarse sand with low organic carbon (<1%) and low moisture (1-3%) contents. We examined the effects of nutrient additions on microorganisms in contaminated soil from this site in laboratory microcosms and in mesocosms incubated for 6 weeks in the field. Nitrogen was the major limiting nutrient in this system, but microbial populations and activity were maximally enhanced by additions of both nitrogen and phosphorus

  11. Effect of cassava mill effluent on biological activity of soil microbial community.

    PubMed

    Igbinosa, Etinosa O

    2015-07-01

    This study assessed the effect of cassava effluent on soil microbiological characteristics and enzymatic activities were investigated in soil samples. Soil properties and heavy metal concentrations were evaluated using standard soil analytical and spectroscopic methods, respectively. The microbiological parameters measured include microbial biomass carbon, basal soil respiration, catalase, urease, dehydrogenase activities and number of culturable aerobic bacteria, fungi and actinomycetes. The pH and temperature regime vary significantly (p < 0.05) throughout the study period. All other physicochemical parameters studied were significantly different (p < 0.05) higher than the control site. Soil organic carbon content gave significant positive correlations with microbial biomass carbon, basal soil respiration, catalase activity and dehydrogenase activity (r = 0.450, 0.461, 0.574 and 0.591 at p < 0.01), respectively. The quantitative analysis of soil microbial density demonstrates a marked decrease in total culturable numbers of the different microbial groups of the polluted soil samples. Soil contamination decreased catalase, urease and dehydrogenase activities. The findings revealed that soil enzymes can be used as indices of soil contamination and bio-indicator of soil quality. PMID:26055654

  12. Effect of land use on microbial biomass and enzyme activities in tropical soil

    NASA Astrophysics Data System (ADS)

    Maharjan, Menuka; Sanaullah, Muhammad; Kuzyakov, Yakov

    2016-04-01

    Land use change especially from forest to intensive agriculture for sustaining livelihood causing severe consequence on soil quality. Soil microbial biomass and enzyme activities are very sensitive to change in environment. The objective was to assess effects of three land uses i.e. forest, organic and conventional farming on microbial biomass C and N and enzymes involved in C-cycle (β-glucosidase), N-cycle (leucine-aminopeptidase), P-cycle (Phosphatase) and S-cycle (Sulphatase) at different depth (0-100 cm with 10 cm in interval) of soil in Chitwan, Nepal. The result showed that both carbon and nitrogen content (%) was significantly higher in organic farming than conventional farming and forest. However, the trend decreased in lower depth. Significantly high microbial biomass C and N (μg C and N g-1 soil) were found in organic farming than conventional farming and forest at 0-10 cm but the trend was inconsistent in lower depth. β-glucosidase, leucine-aminopeptidase and sulphatase (nmol g-1 soil) activities were higher in organic and conventional farming compared to forest at 0-20 cm. Phosphatase activity was higher in conventional farming than forest and organic farming at 0-20cm. The activities were inconsistent below 20 cm. Application of farmyard manure and organic matter from the vegetation contributes the higher microbial biomass and enzyme activities in organic farming.

  13. Directed Evolution of Metabolic Pathways in Microbial Populations II. a Repeatable Adaptation in SACCHAROMYCES CEREVISIAE

    PubMed Central

    Francis, J. C.; Hansche, P. E.

    1973-01-01

    A selection experiment was conducted for approximately 1,000 generations in a chemostat population of 109 cells of the haploid yeast, S. cerevisiae. The experiment was designed to enhance genetically the rate at which the external enzyme acid phosphatase catalyzed the hydrolysis of very low concentrations of β-glycerophosphate at an unfavorably high pH. The observed genetic adaptation in this experiment consisted of a mutation (ACP-2) in the acid phosphatase structural gene which effected a shift in the pH optimum of the enzyme and incremented its activity. The effects of ACP-2 and a similar mutation, ACP-1, on acid phosphatase substrate specificity are also reported. PMID:17248616

  14. Alteration of rare earth element distribution as a result of microbial activity and empirical methane injection

    NASA Astrophysics Data System (ADS)

    Castillo, D. J.; Davies, N. W.; Thurber, A. R.; Haley, B. A.; Colwell, F. S.

    2014-12-01

    As a result of warming, methane is being released into the marine environment in areas that have not historically experienced methane input. While methane is a potent greenhouse gas, microbial oxidation of methane within the sediment greatly limits the role of marine methane sources on atmospheric forcing. However, in these areas of new methane release, consumption of methane prior to its release into the atmosphere is a result of the response of the microbial community to this new input of methane. Further, rare earth elements (REEs) are not currently thought to be involved with microbial activity, but this assumption has not been rigorously tested. Here we test that: (1) microbial communities will rapidly respond to the onset of methane emission, and (2) the microbial response to this methane input will impact the distribution of REEs within the sediment. Undisturbed cores sampled from a tidal flat at Yaquina Bay, OR, were brought back to a lab and injected with anoxic seawater (as a control) or anoxic sea water saturated with methane gas for a total of 2 weeks. Aerobic methanotrophs proliferated over this short time period, becoming an abundant member of the microbial community as identified using fatty acid biomarkers. Excitingly, the experimental injection of methane also shifted the distribution of REEs within the sediment, a trend that appeared to follow the microbial response and that was different from the control cores. Further, the lightest REEs appeared to be used more than the heavier ones, supporting that the REEs are being actively used by the microbes. While we focused on identifying the response of those microbes responsible in methane-cycling, we also identified how the entire microbial community shifts as a result of methane input, and correlating with shifts in REE distribution. Here we have empirically demonstrated the rapid response of methanotrophs to the onset of methane emission and that REE distribution within the sediment is likely

  15. Microbial life in cold, hydrologically active oceanic crustal fluids

    NASA Astrophysics Data System (ADS)

    Meyer, J. L.; Jaekel, U.; Girguis, P. R.; Glazer, B. T.; Huber, J. A.

    2012-12-01

    It is estimated that at least half of Earth's microbial biomass is found in the deep subsurface, yet very little is known about the diversity and functional roles of these microbial communities due to the limited accessibility of subseafloor samples. Ocean crustal fluids, which may have a profound impact on global nutrient cycles given the large volumes of water moving through the crustal aquifer, are particularly difficult to sample. Access to uncontaminated ocean crustal fluids is possible with CORK (Circulation Obviation Retrofit Kit) observatories, installed through the Integrated Ocean Drilling Program (IODP). Here we present the first microbiological characterization of the formation fluids from cold, oxygenated igneous crust at North Pond on the western flank of the Mid Atlantic Ridge. Fluids were collected from two CORKs installed at IODP boreholes 1382A and 1383C and include fluids from three different depth horizons within oceanic crust. Collection of borehole fluids was monitored in situ using an oxygen optode and solid-state voltammetric electrodes. In addition, discrete samples were analyzed on deck using a comparable lab-based system as well as a membrane-inlet mass spectrometer to quantify all dissolved volatiles up to 200 daltons. The instruments were operated in parallel and both in situ and shipboard geochemical measurements point to a highly oxidized fluid, revealing an apparent slight depletion of oxygen in subsurface fluids (~215μM) relative to bottom seawater (~245μM). We were unable to detect reduced hydrocarbons, e.g. methane. Cell counts indicated the presence of roughly 2 x 10^4 cells per ml in all fluid samples, and DNA was extracted and amplified for the identification of both bacterial and archaeal community members. The utilization of ammonia, nitrate, dissolved inorganic carbon, and acetate was measured using stable isotopes, and oxygen consumption was monitored to provide an estimate of the rate of respiration per cell per day

  16. Stratified Microbial Structure and Activity in Sulfide- and Methane-Producing Anaerobic Sewer Biofilms

    PubMed Central

    Sun, Jing; Hu, Shihu; Sharma, Keshab Raj; Ni, Bing-Jie

    2014-01-01

    Simultaneous production of sulfide and methane by anaerobic sewer biofilms has recently been observed, suggesting that sulfate-reducing bacteria (SRB) and methanogenic archaea (MA), microorganisms known to compete for the same substrates, can coexist in this environment. This study investigated the community structures and activities of SRB and MA in anaerobic sewer biofilms (average thickness of 800 μm) using a combination of microelectrode measurements, molecular techniques, and mathematical modeling. It was seen that sulfide was mainly produced in the outer layer of the biofilm, between the depths of 0 and 300 μm, which is in good agreement with the distribution of SRB population as revealed by cryosection-fluorescence in situ hybridization (FISH). SRB had a higher relative abundance of 20% on the surface layer, which decreased gradually to below 3% at a depth of 400 μm. In contrast, MA mainly inhabited the inner layer of the biofilm. Their relative abundances increased from 10% to 75% at depths of 200 μm and 700 μm, respectively, from the biofilm surface layer. High-throughput pyrosequencing of 16S rRNA amplicons showed that SRB in the biofilm were mainly affiliated with five genera, Desulfobulbus, Desulfomicrobium, Desulfovibrio, Desulfatiferula, and Desulforegula, while about 90% of the MA population belonged to the genus Methanosaeta. The spatial organizations of SRB and MA revealed by pyrosequencing were consistent with the FISH results. A biofilm model was constructed to simulate the SRB and MA distributions in the anaerobic sewer biofilm. The good fit between model predictions and the experimental data indicate that the coexistence and spatial structure of SRB and MA in the biofilm resulted from the microbial types and their metabolic transformations and interactions with substrates. PMID:25192994

  17. Arctic gypsum endoliths: a biogeochemical characterization of a viable and active microbial community

    NASA Astrophysics Data System (ADS)

    Ziolkowski, L. A.; Mykytczuk, N. C. S.; Omelon, C. R.; Johnson, H.; Whyte, L. G.; Slater, G. F.

    2013-11-01

    , which contrasts with other endolithic habitats. While it is possible that these communities turn over carbon quickly and leave little evidence of microbe-mineral interaction, an alternative hypothesis is that the soluble and friable nature of gypsum and harsh conditions lead to elevated erosion rates, limiting microbial residence times in this habitat. Regardless, this endolithic community represents a microbial system that does not rely on a nutrient pool from the host gypsum cap rock, instead receiving these elements from allochthonous debris to maintain a more diverse and active community than might have been predicted in the polar desert of the Canadian high Arctic.

  18. Effects of Environmental Toxicants on Metabolic Activity of Natural Microbial Communities

    PubMed Central

    Barnhart, Carole L. H.; Vestal, J. Robie

    1983-01-01

    Two methods of measuring microbial activity were used to study the effects of toxicants on natural microbial communities. The methods were compared for suitability for toxicity testing, sensitivity, and adaptability to field applications. This study included measurements of the incorporation of 14C-labeled acetate into microbial lipids and microbial glucosidase activity. Activities were measured per unit biomass, determined as lipid phosphate. The effects of various organic and inorganic toxicants on various natural microbial communities were studied. Both methods were useful in detecting toxicity, and their comparative sensitivities varied with the system studied. In one system, the methods showed approximately the same sensitivities in testing the effects of metals, but the acetate incorporation method was more sensitive in detecting the toxicity of organic compounds. The incorporation method was used to study the effects of a point source of pollution on the microbiota of a receiving stream. Toxic doses were found to be two orders of magnitude higher in sediments than in water taken from the same site, indicating chelation or adsorption of the toxicant by the sediment. The microbiota taken from below a point source outfall was 2 to 100 times more resistant to the toxicants tested than was that taken from above the outfall. Downstream filtrates in most cases had an inhibitory effect on the natural microbiota taken from above the pollution source. The microbial methods were compared with commonly used bioassay methods, using higher organisms, and were found to be similar in ability to detect comparative toxicities of compounds, but were less sensitive than methods which use standard media because of the influences of environmental factors. PMID:16346432

  19. Microbial Functional Diversity, Biomass and Activity as Affected by Soil Surface Mulching in a Semiarid Farmland

    PubMed Central

    Shen, Yufang; Chen, Yingying; Li, Shiqing

    2016-01-01

    Mulching is widely used to increase crop yield in semiarid regions in northwestern China, but little is known about the effect of different mulching systems on the microbial properties of the soil, which play an important role in agroecosystemic functioning and nutrient cycling. Based on a 4-year spring maize (Zea mays L.) field experiment at Changwu Agricultural and Ecological Experimental Station, Shaanxi, we evaluated the responses of soil microbial activity and crop to various management systems. The treatments were NMC (no mulching with inorganic N fertilizer), GMC (gravel mulching with inorganic N fertilizer), FMC (plastic-film mulching with inorganic N fertilizer) and FMO (plastic-film mulching with inorganic N fertilizer and organic manure addition). The results showed that the FMO soil had the highest contents of microbial biomass carbon and nitrogen, dehydrogenase activity, microbial activity and Shannon diversity index. The relative use of carbohydrates and amino acids by microbes was highest in the FMO soil, whereas the relative use of polymers, phenolic compounds and amines was highest in the soil in the NMC soil. Compared with the NMC, an increased but no significant trend of biomass production and nitrogen accumulation was observed under the GMC treatment. The FMC and FMO led a greater increase in biomass production than GMC and NMC. Compare with the NMC treatment, FMC increased grain yield, maize biomass and nitrogen accumulation by 62.2, 62.9 and 86.2%, but no significant difference was found between the FMO and FMC treatments. Some soil biological properties, i.e. microbial biomass carbon, microbial biomass nitrogen, being sensitive to the mulching and organic fertilizer, were significant correlated with yield and nitrogen availability. Film mulching over gravel mulching can serve as an effective measure for crop production and nutrient cycling, and plus organic fertilization additions may thus have improvements in the biological quality of the

  20. Microbial Functional Diversity, Biomass and Activity as Affected by Soil Surface Mulching in a Semiarid Farmland.

    PubMed

    Shen, Yufang; Chen, Yingying; Li, Shiqing

    2016-01-01

    Mulching is widely used to increase crop yield in semiarid regions in northwestern China, but little is known about the effect of different mulching systems on the microbial properties of the soil, which play an important role in agroecosystemic functioning and nutrient cycling. Based on a 4-year spring maize (Zea mays L.) field experiment at Changwu Agricultural and Ecological Experimental Station, Shaanxi, we evaluated the responses of soil microbial activity and crop to various management systems. The treatments were NMC (no mulching with inorganic N fertilizer), GMC (gravel mulching with inorganic N fertilizer), FMC (plastic-film mulching with inorganic N fertilizer) and FMO (plastic-film mulching with inorganic N fertilizer and organic manure addition). The results showed that the FMO soil had the highest contents of microbial biomass carbon and nitrogen, dehydrogenase activity, microbial activity and Shannon diversity index. The relative use of carbohydrates and amino acids by microbes was highest in the FMO soil, whereas the relative use of polymers, phenolic compounds and amines was highest in the soil in the NMC soil. Compared with the NMC, an increased but no significant trend of biomass production and nitrogen accumulation was observed under the GMC treatment. The FMC and FMO led a greater increase in biomass production than GMC and NMC. Compare with the NMC treatment, FMC increased grain yield, maize biomass and nitrogen accumulation by 62.2, 62.9 and 86.2%, but no significant difference was found between the FMO and FMC treatments. Some soil biological properties, i.e. microbial biomass carbon, microbial biomass nitrogen, being sensitive to the mulching and organic fertilizer, were significant correlated with yield and nitrogen availability. Film mulching over gravel mulching can serve as an effective measure for crop production and nutrient cycling, and plus organic fertilization additions may thus have improvements in the biological quality of the

  1. Soil microbial activity and structure in mineralized terranes of the Western US

    NASA Astrophysics Data System (ADS)

    Blecker, S. W.; Stillings, L. L.; Decrappeo, N.; Ippolito, J.

    2009-12-01

    Mineralized terranes (areas enriched in metal-bearing minerals) occur throughout the Western US, and are characterized by highly variable soil trace metal concentrations across small spatial scales. Assuming that non-lithologic (extrinsic) soil forming factors are relatively constant between mineralized and unmineralized zones, these mineralized areas allowed us to evaluate the effect of lithology on soil microbial activity. We established the following study sites: 1) sage-grassland on a Mo/Cu deposit (Battle Mountain, NV); 2) pine-chaparral on Ni/Cr bearing rocks (Chinese Camp, CA); and 3) two pine woodland sites on acid-sulfate altered rocks (Reno, NV; Bridgeport, CA). Microbial, physical and chemical measurements were performed on soils from undisturbed mineralized areas and adjacent unmineralized areas to determine baseline conditions for comparison to sites disturbed by mining. A host of abiotic soil parameters, along with bioavailable (diethylenetriaminepentaacetic acid (DTPA)-extractable) and total metals, were measured to examine their correlation with the following measures of microbial activity: enzyme assays (arylsulfatase, phosphatase, fluorescein diacetate hydrolysis), C/N mineralization potential, C substrate utilization (Biolog Ecoplate), and microbial biomass and community structure (phospholipid fatty acid analysis). Within the Battle Mountain study area, both microbial activity and structure were statistically similar between mineralized and unmineralized soils. Nutrient and metal concentrations were also similar; the only differences being higher Cu and lower P in the mineralized soils. Within the Chinese Camp study area, soil organic carbon and total nitrogen concentrations were similar between the serpentine (Ni/Cr bearing) and adjacent andesite soils, while differences were noted for other nutrients (S, P, Ca, Mg). For the serpentine soils, Co, Fe, Mn, and Ni showed the strongest correlations with microbial activity, where Cr, Mn showed the

  2. Reconstructing ecosystem functions of the active microbial community of the Baltic Sea oxygen depleted sediments.

    PubMed

    Thureborn, Petter; Franzetti, Andrea; Lundin, Daniel; Sjöling, Sara

    2016-01-01

    Baltic Sea deep water and sediments hold one of the largest anthropogenically induced hypoxic areas in the world. High nutrient input and low water exchange result in eutrophication and oxygen depletion below the halocline. As a consequence at Landsort Deep, the deepest point of the Baltic Sea, anoxia in the sediments has been a persistent condition over the past decades. Given that microbial communities are drivers of essential ecosystem functions we investigated the microbial community metabolisms and functions of oxygen depleted Landsort Deep sediments by metatranscriptomics. Results show substantial expression of genes involved in protein metabolism demonstrating that the Landsort Deep sediment microbial community is active. Identified expressed gene suites of metabolic pathways with importance for carbon transformation including fermentation, dissimilatory sulphate reduction and methanogenesis were identified. The presence of transcripts for these metabolic processes suggests a potential for heterotrophic-autotrophic community synergism and indicates active mineralisation of the organic matter deposited at the sediment as a consequence of the eutrophication process. Furthermore, cyanobacteria, probably deposited from the water column, are transcriptionally active in the anoxic sediment at this depth. Results also reveal high abundance of transcripts encoding integron integrases. These results provide insight into the activity of the microbial community of the anoxic sediment at the deepest point of the Baltic Sea and its possible role in ecosystem functioning. PMID:26823996

  3. INFLUENCE OF DEEP OCEAN SEWAGE OUTFALLS ON THE MICROBIAL ACTIVITY OF THE SURROUNDING SEDIMENT

    EPA Science Inventory

    The microbial activity near two deep ocean sewage outfalls off the coast of the island of Oahu, HI, was characterized. Water samples and sediment samples to a depth of 4.5 cm were analyzed from an area of approximately 4.5 x 10000 sq m surrounding the outfalls. Although the efflu...

  4. Microbial respiration and extracellular enzyme activity in sediments from the Gulf of Mexico hypoxic zone

    EPA Science Inventory

    This study explores the relationship between sediment chemistry (TC, TN, TP) and microbial respiration (DHA) and extracellular enzyme activity (EEA) across the Gulf of Mexico (GOM) hypoxic zone. TC, TN, and TP were all positively correlated with each other (r=0.19-0.68). DHA was ...

  5. Imidazolium tagged acridines: Synthesis, characterization and applications in DNA binding and anti-microbial activities

    NASA Astrophysics Data System (ADS)

    Raju, Gembali; Vishwanath, S.; Prasad, Archana; Patel, Basant K.; Prabusankar, Ganesan

    2016-03-01

    New water soluble 4,5-bis imidazolium tagged acridines have been synthesized and structurally characterized by multinuclear NMR and single crystal X-ray diffraction techniques. The DNA binding and anti-microbial activities of these acridine derivatives were investigated by fluorescence and far-UV circular dichroism studies.

  6. Soil microbial communities and activities under different orchard floor management systems in Oregan Sweet Cherry Orchards

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Although the importance of microorganisms in nutrient cycling and productivity is well recognized in annual cropping systems, specific information regarding the size, composition and activity of soil microbes in orchard systems is lacking. This study assessed the soil microbial community structure (...

  7. Soil Microbial Communities and Activities Under Different Orchard Floor Management Systems in Oregon Sweet Cherry Orchards

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Although the importance of microorganisms in nutrient cycling and productivity is well recognized in annual cropping systems, specific information regarding the size, composition and activity of soil microbes in orchard systems is lacking. This study assessed the soil microbial community structure (...

  8. Reconstructing ecosystem functions of the active microbial community of the Baltic Sea oxygen depleted sediments

    PubMed Central

    Franzetti, Andrea; Lundin, Daniel; Sjöling, Sara

    2016-01-01

    Baltic Sea deep water and sediments hold one of the largest anthropogenically induced hypoxic areas in the world. High nutrient input and low water exchange result in eutrophication and oxygen depletion below the halocline. As a consequence at Landsort Deep, the deepest point of the Baltic Sea, anoxia in the sediments has been a persistent condition over the past decades. Given that microbial communities are drivers of essential ecosystem functions we investigated the microbial community metabolisms and functions of oxygen depleted Landsort Deep sediments by metatranscriptomics. Results show substantial expression of genes involved in protein metabolism demonstrating that the Landsort Deep sediment microbial community is active. Identified expressed gene suites of metabolic pathways with importance for carbon transformation including fermentation, dissimilatory sulphate reduction and methanogenesis were identified. The presence of transcripts for these metabolic processes suggests a potential for heterotrophic-autotrophic community synergism and indicates active mineralisation of the organic matter deposited at the sediment as a consequence of the eutrophication process. Furthermore, cyanobacteria, probably deposited from the water column, are transcriptionally active in the anoxic sediment at this depth. Results also reveal high abundance of transcripts encoding integron integrases. These results provide insight into the activity of the microbial community of the anoxic sediment at the deepest point of the Baltic Sea and its possible role in ecosystem functioning. PMID:26823996

  9. Arid soil microbial enzymatic activity profile as affected by geographical location and soil degradation status

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Evaluating soil health is critical for any successful remediation effort. Arid lands, with their minimal carbon and water contents, low nutritional status and restricted, seasonal microbial activity pose specific challenges to soil health restoration and by extension, restoration of ecosystem repr...

  10. Effect of Municipal Wastewater as a Wetland Water Source on Soil Microbial Activity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microbial activity, as determined by CO2 evolution, was compared between two soils irrigated with either municipal wastewater effluent or Missouri River water. Irrigation of soils was conducted in greenhouse microcosms with irrigation timing and quantity designed to simulate wetland moist-soil mana...

  11. A Qualitative Experiment to Analyze Microbial Activity in Topsoil Using Paper and a Handmade Reflection Photometer

    ERIC Educational Resources Information Center

    Agbeko, Julius Kofi; Kita, Masakazu

    2007-01-01

    This article describes a novel, hands-on method to qualitatively determine the extent of microbial activity in topsoil using ordinary blank paper. Appropriate and scalable for the high school and college level, these experiments expose students to some of the challenges facing environmental researchers and also contribute to curriculum development…

  12. MICROBIAL ACTIVITY IN SUBSURFACE SAMPLES BEFORE AND DURING NITRATE-ENHANCED BIOREMEDIATION

    EPA Science Inventory

    A study was conducted to determine the microbial activity of a site contaminated with JP-4 jet fuel, before and during nitrate-enhanced bioremediation. amples at three depths from six different locations were collected aseptically under anaerobic conditions before and during trea...

  13. Involvement of microbial populations during the composting of olive mill wastewater sludge.

    PubMed

    Abid, N; Chamkha, M; Godon, J J; Sayadi, S

    2007-07-01

    Olive mill waste water sludge obtained by the electro-Fenton oxidation of olive mill waste water was composted in a bench scale reactor. The evolution of microbial species within the composter was investigated using a respirometric test and by means of both cultivation-dependent and independent approaches (Polymerase Chain Reaction-Single Strand Conformation Polymorphism, PCR SSCP). During the period of high respiration rate (7-24 days), cultivation method showed that thermophilic bacteria as well as actinomycetes dominated over eumycetes. During the composting process, the PCR-SSCP method showed a higher diversity of the bacterial community than the eukaryotic one. After 60 days of composting, the compost exhibited a microbial stability and a clear absence of phytotoxicity. PMID:17674648

  14. Effects of slow-release urea fertilizers on urease activity, microbial biomass, and nematode communities in an aquic brown soil.

    PubMed

    Jiao, Xiaoguang; Liang, Wenju; Chen, Lijun; Zhang, Haijun; Li, Qi; Wang, Peng; Wen, Dazhong

    2005-05-01

    A field experiment was carried out at the Shenyang Experimental Station of Ecology (CAS) in order to study the effects of slow-release urea fertilizers high polymer-coated urea (SRU1), SRU1 mixed with dicyandiamide DCD (SRU2), and SRU1 mixed with calcium carbide CaC2 (SRU3) on urease activity, microbial biomass C and N, and nematode communities in an aquic brown soil during the maize growth period. The results demonstrated that the application of slow-release urea fertilizers inhibits soil urease activity and increases the soil NH4+-N content. Soil available N increment could promote its immobilization by microorganisms. Determination of soil microbial biomass N indicated that a combined application of coated urea and nitrification inhibitors increased the soil active N pool. The population of predators/omnivores indicated that treatment with SRU2 could provide enough soil NH4+-N to promote maize growth and increased the food resource for the soil fauna compared with the other treatments. PMID:16089326

  15. Zinc, cadmium and lead accumulation and characteristics of rhizosphere microbial population associated with hyperaccumulator Sedum alfredii Hance under natural conditions.

    PubMed

    Long, Xin-Xian; Zhang, Yu-Gang; Jun, Dai; Zhou, Qixing

    2009-04-01

    A field survey was conducted to study the characteristics of zinc, cadmium, and lead accumulation and rhizosphere microbial population associated with hyperaccumulator Sedum alfredii Hance growing natively on an old lead/zinc mining site. We found significant hyperaccumulation of zinc and cadmium in field samples of S. alfredii, with maximal shoot concentrations of 9.10-19.61 g kg(-1) zinc and 0.12-1.23 g kg(-1) cadmium, shoot/root ratios ranging from 1.75 to 3.19 (average 2.54) for zinc, 3.36 to 4.43 (average 3.85) for cadmium, shoot bioaccumulation factors of zinc and cadmium being 1.46-4.84 and 7.35-17.41, respectively. While most of lead was retained in roots, thus indicating exclusion as a tolerance strategy for lead. Compared to the non-rhizosphere soil, organic matter and total nitrogen and phosphorus content, CEC and water extractable zinc, cadmium, and lead concentration were significantly higher, but pH was smaller in rhizosphere soil. The rhizosphere soil of S. alfredii harbored a wide variety of microorganism. In general, significantly higher numbers of culturable bacteria, actinomycetes, and fungi were found in the rhizosphere compared to bulk soil, confirming the stimulatory effect of the S. alfredii rhizosphere on microbial growth and proliferation. Analyses of BIOLOG data also showed that the growth of S. alfredii resulted in observable changes in BIOLOG metabolic profiles, utilization ability of different carbon substrates of microbial communities in the rhizosphere soil were also higher than the non-rhizosphere, confirming a functional effect of the rhizosphere of S. alfredii on bacterial population. PMID:19183820

  16. Microbial populations identified by fluorescence in situ hybridization in a constructed wetland treating acid coal mine drainage.

    PubMed

    Nicomrat, Duongruitai; Dick, Warren A; Tuovinen, Olli H

    2006-01-01

    Microorganisms are an integral part of the biogeochemical processes in wetlands, yet microbial communities in sediments within constructed wetlands receiving acid mine drainage (AMD) are only poorly understood. The purpose of this study was to characterize the microbial diversity and abundance in a wetland receiving AMD using fluorescence in situ hybridization (FISH) analysis. Seasonal samples of oxic surface sediments, comprised of Fe(III) precipitates, were collected from two treatment cells of the constructed wetland system. The pH of the bulk samples ranged between pH 2.1 and 3.9. Viable counts of acidophilic Fe and S oxidizers and heterotrophs were determined with a most probable number (MPN) method. The MPN counts were only a fraction of the corresponding FISH counts. The sediment samples contained microorganisms in the Bacteria (including the subgroups of acidophilic Fe- and S-oxidizing bacteria and Acidiphilium spp.) and Eukarya domains. Archaea were present in the sediment surface samples at < 0.01% of the total microbial community. The most numerous bacterial species in this wetland system was Acidithiobacillus ferrooxidans, comprising up to 37% of the bacterial population. Acidithiobacillus thiooxidans was also abundant. Heterotrophs in the Acidiphilium genus totaled 20% of the bacterial population. Leptospirillum ferrooxidans was below the level of detection in the bacterial community. The results from the FISH technique from this field study are consistent with results from other experiments involving enumeration by most probable number, dot-blot hybridization, and denaturing gradient gel electrophoresis analyses and with the geochemistry of the site. PMID:16825452

  17. Using dispersants after oil spills: impacts on the composition and activity of microbial communities.

    PubMed

    Kleindienst, Sara; Paul, John H; Joye, Samantha B

    2015-06-01

    Dispersants are globally and routinely applied as an emergency response to oil spills in marine ecosystems with the goal of chemically enhancing the dissolution of oil into water, which is assumed to stimulate microbially mediated oil biodegradation. However, little is known about how dispersants affect the composition of microbial communities or their biodegradation activities. The published findings are controversial, probably owing to variations in laboratory methods, the selected model organisms and the chemistry of different dispersant-oil mixtures. Here, we argue that an in-depth assessment of the impacts of dispersants on microorganisms is needed to evaluate the planning and use of dispersants during future responses to oil spills. PMID:25944491

  18. Potential Health Hazards from Microbial Aerosols in Densely Populated Urban Regions

    PubMed Central

    Cronholm, Lois S.

    1980-01-01

    Aerosolized bacteria were recovered up to 930 m downwind of three sewage treatment plants in Jefferson County, Ky. This distance includes homes in the proximity of several hundred such plants in that county. Bacterial counts were elevated on foliage near activated sludge tanks; although these counts decreased rapidly, at 48 h after exposure they were significantly higher than the counts on unexposed leaves. The 50% lethal dose of aerosolized Klebsiella pneumoniae was comparable to the 50% lethal dose of a virulent clinical isolate, and enteric bacteria were recovered from the respiratory organs of mice after forced inhalation adjacent to an aerated sludge tank. The coliform density in the effluents of the plants tested was inversely related to the airborne bacterial load at those plants. This relationship was attributed to the correlation between effluent quality and extent of aeration of activated sludge. Wind direction and distance influenced the airborne counts, but the extreme variation in counts indicates that it is not possible to predict emission rates accurately in an open ecosystem. Airborne enteric bacteria also were isolated near a decorative fountain used by humans for wading. The discovery of these sources of aerosolized microorganisms from polluted waters in densely populated areas suggests that a potential health hazard may be created by the increased probability of inhaling and ingesting microorganisms of fecal origin. Images PMID:6986851

  19. The Influence of Age and Gender on Skin-Associated Microbial Communities in Urban and Rural Human Populations

    PubMed Central

    Ying, Shi; Zeng, Dan-Ning; Chi, Liang; Tan, Yuan; Galzote, Carlos; Cardona, Cesar; Lax, Simon; Gilbert, Jack; Quan, Zhe-Xue

    2015-01-01

    Differences in the bacterial community structure associated with 7 skin sites in 71 healthy people over five days showed significant correlations with age, gender, physical skin parameters, and whether participants lived in urban or rural locations in the same city. While body site explained the majority of the variance in bacterial community structure, the composition of the skin-associated bacterial communities were predominantly influenced by whether the participants were living in an urban or rural environment, with a significantly greater relative abundance of Trabulsiella in urban populations. Adults maintained greater overall microbial diversity than adolescents or the elderly, while the intragroup variation among the elderly and rural populations was significantly greater. Skin-associated bacterial community structure and composition could predict whether a sample came from an urban or a rural resident ~5x greater than random. PMID:26510185

  20. Turnover of microbial lipids in the deep biosphere and growth of benthic archaeal populations

    NASA Astrophysics Data System (ADS)

    Xie, Sitan; Lipp, Julius S.; Wegener, Gunter; Ferdelman, Timothy G.; Hinrichs, Kai-Uwe

    2013-04-01

    Deep subseafloor sediments host a microbial biosphere with unknown impact on global biogeochemical cycles. This study tests previous evidence based on microbial intact polar lipids (IPLs) as proxies of live biomass, suggesting that Archaea dominate the marine sedimentary biosphere. We devised a sensitive radiotracer assay to measure the decay rate of ([14C]glucosyl)-diphytanylglyceroldiether (GlcDGD) as an analog of archaeal IPLs in continental margin sediments. The degradation kinetics were incorporated in model simulations that constrained the fossil fraction of subseafloor IPLs and rates of archaeal turnover. Simulating the top 1 km in a generic continental margin sediment column, we estimated degradation rate constants of GlcDGD being one to two orders of magnitude lower than those of bacterial IPLs, with half-lives of GlcDGD increasing with depth to 310 ky. Given estimated microbial community turnover times of 1.6-73 ky in sediments deeper than 1 m, 50-96% of archaeal IPLs represent fossil signals. Consequently, previous lipid-based estimates of global subseafloor biomass probably are too high, and the widely observed dominance of archaeal IPLs does not rule out a deep biosphere dominated by Bacteria. Reverse modeling of existing concentration profiles suggest that archaeal IPL synthesis rates decline from around 1,000 pgṡmL-1 sedimentṡy-1 at the surface to 0.2 pgṡmL-1ṡy-1 at 1 km depth, equivalent to production of 7 × 105 to 140 archaeal cellsṡmL-1 sedimentṡy-1, respectively. These constraints on microbial growth are an important step toward understanding the relationship between the deep biosphere and the carbon cycle.

  1. Turnover of microbial lipids in the deep biosphere and growth of benthic archaeal populations

    PubMed Central

    Xie, Sitan; Lipp, Julius S.; Wegener, Gunter; Ferdelman, Timothy G.; Hinrichs, Kai-Uwe

    2013-01-01

    Deep subseafloor sediments host a microbial biosphere with unknown impact on global biogeochemical cycles. This study tests previous evidence based on microbial intact polar lipids (IPLs) as proxies of live biomass, suggesting that Archaea dominate the marine sedimentary biosphere. We devised a sensitive radiotracer assay to measure the decay rate of ([14C]glucosyl)-diphytanylglyceroldiether (GlcDGD) as an analog of archaeal IPLs in continental margin sediments. The degradation kinetics were incorporated in model simulations that constrained the fossil fraction of subseafloor IPLs and rates of archaeal turnover. Simulating the top 1 km in a generic continental margin sediment column, we estimated degradation rate constants of GlcDGD being one to two orders of magnitude lower than those of bacterial IPLs, with half-lives of GlcDGD increasing with depth to 310 ky. Given estimated microbial community turnover times of 1.6–73 ky in sediments deeper than 1 m, 50–96% of archaeal IPLs represent fossil signals. Consequently, previous lipid-based estimates of global subseafloor biomass probably are too high, and the widely observed dominance of archaeal IPLs does not rule out a deep biosphere dominated by Bacteria. Reverse modeling of existing concentration profiles suggest that archaeal IPL synthesis rates decline from around 1,000 pg⋅mL−1 sediment⋅y−1 at the surface to 0.2 pg⋅mL−1⋅y−1 at 1 km depth, equivalent to production of 7 × 105 to 140 archaeal cells⋅mL−1 sediment⋅y−1, respectively. These constraints on microbial growth are an important step toward understanding the relationship between the deep biosphere and the carbon cycle. PMID:23530229

  2. Enhancement of the sweep efficiency of waterflooding operations by the in-situ microbial population of petroleum reservoirs

    SciTech Connect

    Brown, L.R.; Vadie, A.A.; Stephens, J.O.; Azadpour, A.

    1995-12-31

    Live cores were obtained from five reservoirs using special precautions to prevent contamination by exogenous microorganisms and minimize exposure to oxygen. The depths from which the cores were obtained ranged from 2,705 ft to 6,568 ft. Core plugs were cut radially from live cores, encased in heat-shrink plastic tubes, placed in core holders, and fitted with inlets and outlets. Nutrient additions stimulated the in-situ microbial population to increase, dissolve stratal material, produce gases, and release oil. Reduction in flow through the core plugs was observed in some cases, while in other cases flow was increased, probably due to the dissolution of carbonates in the formation. A field demonstration of the ability of the in-situ microbial population to increase oil recovery by blocking the more permeable zones of the reservoir is currently underway. This demonstration is being conducted in the North Blowhorn Creek Unit situated in Lamar County, Alabama. Live cores were obtained from a newly drilled well in the field and tested as described above. The field project involves four test patterns each including one injector, four to five producers, and a comparable control injector with its four to five producers. Nutrient injection in the field began November 1994.

  3. Segregated flux balance analysis constrained by population structure/function data: the case of PHA production by mixed microbial cultures.

    PubMed

    Pardelha, F; Albuquerque, M G E; Carvalho, G; Reis, M A M; Dias, J M L; Oliveira, R

    2013-08-01

    In this study we developed a segregated flux balance analysis (FBA) method to calculate metabolic flux distributions of the individual populations present in a mixed microbial culture (MMC). Population specific flux data constraints were derived from the raw data typically obtained by the fluorescence in situ hybridization (FISH) and microautoradiography (MAR)-FISH techniques. This method was applied to study the metabolic heterogeneity of a MMC that produces polyhydroxyalkanoates (PHA) from fermented sugar cane molasses. Three populations were identified by FISH, namely Paracoccus sp., Thauera sp., and Azoarcus sp. The segregated FBA method predicts a flux distribution for each of the identified populations. The method is shown to predict with high accuracy the average PHA storage flux and the respective monomeric composition for 16 independent experiments. Moreover, flux predictions by segregated FBA were slightly better than those obtained by nonsegregated FBA, and also highly concordant with metabolic flux analysis (MFA) estimated fluxes. The segregated FBA method can be of high value to assess metabolic heterogeneity in MMC systems and to derive more efficient eco-engineering strategies. For the case of PHA-producing MMC considered in this work, it becomes apparent that the PHA average monomeric composition might be controlled not only by the volatile fatty acids (VFA) feeding profile but also by the population composition present in the MMC. PMID:23475571

  4. [Microbial composition of the activated sludges of the Moscow wastewater treatment plants].

    PubMed

    Kallistova, A Iu; Pimenov, N V; Kozlov, M N; Nikolaev, Iu A; Dorofeev, A G; Aseeva, V G; Grachev, V A; Men'ko, E V; Berestovskaia, Iu Iu; Nozhevnikova, A N; Kevbrina, M V

    2014-01-01

    The contribution of the major technologically important microbial groups (ammonium- and nitrite-oxidizing, phosphate-accumulating, foam-inducing, and anammox bacteria, as well as planctomycetes and methanogenic archaea) was characterized for the aeration tanks of the Moscow wastewater treatment facilities. FISH investigation revealed that aerobic sludges were eubacterial communities; the metabolically active archaea contributed insignificantly. Stage II nitrifying microorganisms and planctomycetes were significant constituents of the bacterial component of activated sludge, with Nitrobacter spp. being the dominant nitrifier. No metabolically active anammox bacteria were revealed in the sludge from aeration tanks. The sludge from the aeration tanks using different wastewater treatment technologies were found to differ in characteristics. Abundance of the nitrifying and phosphate-accumulating bacteria in the sludges generally correlated with microbial activity, in microcosms and with efficiency of nitrogen and phosphorus removal from wastewater. The highest microbial numbers and activity were found in the sludges of the tanks operating according to the technologies developed in the universities of Hanover and Cape Town. The activated sludge from the Novokur yanovo facilities, where abundant growth of filamentous bacteria resulted in foam formation, exhibited the lowest activity The group of foaming bacteria included Gordonia spp. and Acinetobacter spp., utilizing petroleum and motor oils, Sphaerotilus spp. utilizing unsaturated fatty acids, and Candidatus 'Microthrix parvicella'. Thus, the data on abundance and composition of metabolically active microorganisms obtained by FISH may be used for the technological control of wastewater treatment. PMID:25844473

  5. Impacts of Activated Carbon Amendment on Hg Methylation, Demethylation and Microbial Activity in Marsh Soils

    NASA Astrophysics Data System (ADS)

    Gilmour, C. C.; Ghosh, U.; Santillan, E. F. U.; Soren, A.; Bell, J. T.; Butera, D.; McBurney, A. W.; Brown, S.; Henry, E.; Vlassopoulos, D.

    2015-12-01

    In-situ sorbent amendments are a low-impact approach for remediation of contaminants in sediments, particular in habitats like wetlands that provide important ecosystem services. Laboratory microcosm trials (Gilmour et al. 2013) and early field trials show that activated carbon (AC) can effectively increase partitioning of both inorganic Hg and methylmercury to the solid phase. Sediment-water partitioning can serve as a proxy for Hg and MeHg bioavailability in soils. One consideration in using AC in remediation is its potential impact on organisms. For mercury, a critical consideration is the potential impact on net MeHg accumulation and bioavailability. In this study, we specifically evaluated the impact of AC on rates of methylmercury production and degradation, and on overall microbial activity, in 4 different Hg-contaminated salt marsh soils. The study was done over 28 days in anaerobic, sulfate-reducing slurries. A double label of enriched mercury isotopes (Me199Hg and inorganic 201Hg) was used to separately follow de novo Me201Hg production and Me199Hg degradation. AC amendments decreased both methylation and demethylation rate constants relative to un-amended controls, but the impact on demethylation was stronger. The addition of 5% (dry weight) regenerated AC to soil slurries drove demethylation rate constants to nearly zero; i.e. MeHg sorption to AC almost totally blocked its degradation. The net impact was increased solid phase MeHg concentrations in some of the soil slurries with the highest methylation rate constants. However, the net impact of AC amendments was to increase MeHg (and inorganic Hg) partitioning to the soil phase and decrease concentrations in the aqueous phase. AC significantly decreased aqueous phase inorganic Hg and MeHg concentrations after 28 days. Overall, the efficacy of AC in reducing aqueous MeHg was highest in the soils with the highest MeHg concentrations. The AC addition did not significantly impact microbial activity, as

  6. Comparison of microbial activity in anaerobic and microaerobic digesters.

    PubMed

    Jenicek, P; Celis, C A; Koubova, J; Pokorna, D

    2011-01-01

    Microaerobic alternative of anaerobic digestion offers many advantages especially when sulfide concentration in the digester is high. For better understanding of the microaerobic technology more detailed characterization of biomass activity is needed. Two equal digesters were operated under the same condition except of microaeration in one of them. During long term operation of anaerobic and microaerobic digesters the sludge quality and the biomass activity was monitored. The activity of sulfide oxidizing bacteria of microaerobic biomass was significantly higher in comparison with anaerobic biomass. The activity of sulfate reducing bacteria was comparable. The activity of methanogenic bacteria activity depended on sulfide concentration more than on microaeration. The extent of foaming problems was lower in the microaerobic than in the anaerobic digester. PMID:21977645

  7. Metaproteogenomics reveals the soil microbial communities active in nutrient cycling processes under different tree species

    NASA Astrophysics Data System (ADS)

    Keiblinger, Katharina Maria; Masse, Jacynthe; Zühlke, Daniela; Riedel, Katharina; Zechmeister-Boltenstern, Sophie; Prescott, Cindy E.; Grayston, Sue

    2016-04-01

    Tree species exert strong effects on microbial communities in litter and soil and may alter rates of soil processes fundamental to nutrient cycling and carbon fluxes (Prescott and Grayston 2013). However, the influence of tree species on decomposition processes are still contradictory and poorly understood. An understanding of the mechanisms underlying plant influences on soil processes is important for our ability to predict ecosystem response to altered global/environmental conditions. In order to link microbial community structure and function to forest-floor nutrient cycling processes, we sampled forest floors under western redcedar (Thuja plicata), Douglas-fir (Pseudotsuga menziesii) and Sitka spruce (Picea sitchensis) grown in nutrient-poor sites in common garden experiments on Vancouver island (Canada). We measured forest-floor total N, total C, initial NH4+ and NO3‑ concentrations, DOC, Cmic and Nmic. Gross rates of ammonification and NH4+ consumption were measured using the 15N pool-dilution method. Organic carbon quality was assessed through FTIR analyses. Microbial community structure was analysed by a metaproteogenomic approach using 16S and ITS amplification and sequencing with MiSeq platform. Proteins were extracted and peptides characterized via LC-MS/MS on a Velos Orbitrap to assess the active microbial community. Different microbial communities were active under the three tree species and variation in process rates were observed and will be discussed. This research provides new insights on microbial processes during organic matter decomposition. The metaproteogenomic approach enables us to investigate these changes with respect to possible effects on soil C-storage at even finer taxonomic resolution.

  8. Effects of petroleum contamination on soil microbial numbers, metabolic activity and urease activity.

    PubMed

    Guo, Huan; Yao, Jun; Cai, Minmin; Qian, Yiguang; Guo, Yue; Richnow, Hans H; Blake, Ruth E; Doni, Serena; Ceccanti, Brunello

    2012-06-01

    The influence of petroleum contamination on soil microbial activities was investigated in 13 soil samples from sites around an injection water well (Iw-1, 2, 3, 4) (total petroleum hydrocarbons (TPH): 7.5-78 mg kg(-1)), an oil production well (Op-1, 2, 3, 4, 5) (TPH: 149-1110 mg kg(-1)), and an oil spill accident well (Os-1, 2, 3, 4) (TPH: 4500-34600 mg kg(-1)). The growth rate constant (μ) of glucose stimulated organisms, determined by microcalorimetry, was higher in Iw soil samples than in Op and Os samples. Total cultivable bacteria and fungi and urease activity also decreased with increasing concentration of TPH. Total heat produced demonstrated that TPH at concentrations less than about 1 g kg(-1) soil stimulated anaerobic respiration. A positive correlation between TPH and soil organic matter (OM) and stimulation of fungi-bacteria-urease at low TPH doses suggested that TPH is bound to soil OM and slowly metabolized in Iw soils during OM consumption. These methods can be used to evaluate the potential of polluted soils to carry out self-bioremediation by metabolizing TPH. PMID:22336736

  9. Soil microbial activities beneath Stipa tenacissima L. and in surrounding bare soil

    NASA Astrophysics Data System (ADS)

    Novosadová, I.; Ruiz Sinoga, J. D.; Záhora, J.; Fišerová, H.

    2010-05-01

    Open steppes dominated by Stipa tenacissima L. constitute one of the most representative ecosystems of the semi-arid zones of Eastern Mediterranean Basin (Iberian Peninsula, North of Africa). These steppes show a higher degree of variability in composition and structure. Ecosystem functioning is strongly related to the spatial pattern of grass tussocks. Soils beneath S. tenacissima grass show higher fertility and improved microclimatic conditions, favouring the formation of "resource islands" (Maestre et al., 2007). On the other hand in "resource islands" and in surrounding bare soil exists the belowground zone of influence. The competition for water and resources between plants and microorganisms is strong and mediated trough an enormous variety of exudates and resource depletion intended to regulate soil microbial communities in the rhizosphere, control herbivory, encourage beneficial symbioses, and change chemical and physical properties in soil (Pugnaire et Armas, 2008). Secondary compounds and allelopathy restrict other species growth and contribute to patchy plant distribution. Active root segregation affects not only neighbourś growth but also soil microbial activities. The objective of this study was to assess the effect of Stipa tenacissima on the key soil microbial activities under controlled incubation conditions (basal and potential respiration; net nitrogen mineralization). The experimental plots were located in the province Almería in Sierra de los Filabres Mountains near the village Gérgal (southeast Spain) in the small catchment which is situated between 1090 - 1165 m a.s.l. The area with extent of 82 000 m2 is affected by soil degradation. The climate is semiarid Mediterranean. The mean annual rainfall is of about 240 mm mostly concentrated in autumn and spring. The mean annual temperature is 13.9° C. The studied soil has a loam to sandy clay texture and is classified as Lithosol (FAO-ISRIC and ISSS, 1998). The vegetation of these areas is an

  10. Cold active microbial lipases: some hot issues and recent developments.

    PubMed

    Joseph, Babu; Ramteke, Pramod W; Thomas, George

    2008-01-01

    Lipases are glycerol ester hydrolases that catalyze the hydrolysis of triglycerides to free fatty acids and glycerol. Lipases catalyze esterification, interesterification, acidolysis, alcoholysis and aminolysis in addition to the hydrolytic activity on triglycerides. The temperature stability of lipases has regarded as the most important characteristic for use in industry. Psychrophilic lipases have lately attracted attention because of their increasing use in the organic synthesis of chiral intermediates due to their low optimum temperature and high activity at very low temperatures, which are favorable properties for the production of relatively frail compounds. In addition, these enzymes have an advantage under low water conditions due to their inherent greater flexibility, wherein the activity of mesophilic and thermophilic enzymes are severely impaired by an excess of rigidity. Cold-adapted microorganisms are potential source of cold-active lipases and they have been isolated from cold regions and studied. Compared to other lipases, relatively smaller numbers of cold active bacterial lipases were well studied. Lipases isolated from different sources have a wide range of properties depending on their sources with respect to positional specificity, fatty acid specificity, thermostability, pH optimum, etc. Use of industrial enzymes allows the technologist to develop processes that closely approach the gentle, efficient processes in nature. Some of these processes using cold active lipase from C. antarctica have been patented by pharmaceutical, chemical and food industries. Cold active lipases cover a broad spectrum of biotechnological applications like additives in detergents, additives in food industries, environmental bioremediations, biotransformation, molecular biology applications and heterologous gene expression in psychrophilic hosts to prevent formation of inclusion bodies. Cold active enzymes from psychrotrophic microorganisms showing high catalytic

  11. Microbial Activity and Volatile Fluxes in Seafloor Hydrothermal Systems

    NASA Astrophysics Data System (ADS)

    Corrigan, R. S.; Lowell, R. P.

    2013-12-01

    Understanding geographically and biologically the production or utilization of volatile chemical species such as CO2, CH4, and H2 is crucial not only for understanding hydrothermal processes but also for understanding life processes in the oceanic crust. To estimate the microbial effect on the transport of these volatiles, we consider a double-loop single pass model as shown in Figure 1 to estimate the mass fluxes shown. We then use a simple mixing formulation: C4Q4 = C3 (Q1 -Q3)+ C2Q2, where C2 is the concentration of the chemical in seawater, C3 is the average concentration of the chemical in high temperature focused flow, C4 is the expected concentration of the chemical as a result of mixing, and the relevant mass flows are as shown in Figure 1. Finally, we compare the calculated values of CO2, CH4, and H2 in diffuse flow fluids to those observed. The required data are available for both the Main Endeavour Field on the Juan de Fuca Ridge and the East Pacific Rise 9°50' N systems. In both cases we find that, although individual diffuse flow sites have observed concentrations of some elements that are greater than average, the average concentration of these volatiles is smaller in all cases than the concentration that would be expected from simple mixing. This indicates that subsurface microbes are net utilizers of these chemical constituents at the Main Endeavour Field and at EPR 9°50' N on the vent field scale. Figure 1. Schematic of a 'double-loop' single-pass model above a convecting, crystallizing, replenished AMC (not to scale). Heat transfer from the vigorously convecting, cooling, and replenished AMC across the conductive boundary layer δ drives the overlying hydrothermal system. The deep circulation represented by mass flux Q1 and black smoker temperature T3 induces shallow circulation noted by Q2. Some black smoker fluid mixes with seawater resulting in diffuse discharge Q4, T4, while the direct black smoker mass flux with temperature T3 is reduced

  12. Tracking heavy water (D2O) incorporation for identifying and sorting active microbial cells

    PubMed Central

    Berry, David; Mader, Esther; Lee, Tae Kwon; Woebken, Dagmar; Wang, Yun; Zhu, Di; Palatinszky, Marton; Schintlmeister, Arno; Schmid, Markus C.; Hanson, Buck T.; Shterzer, Naama; Mizrahi, Itzhak; Rauch, Isabella; Decker, Thomas; Bocklitz, Thomas; Popp, Jürgen; Gibson, Christopher M.; Fowler, Patrick W.; Huang, Wei E.; Wagner, Michael

    2015-01-01

    Microbial communities are essential to the function of virtually all ecosystems and eukaryotes, including humans. However, it is still a major challenge to identify microbial cells active under natural conditions in complex systems. In this study, we developed a new method to identify and sort active microbes on the single-cell level in complex samples using stable isotope probing with heavy water (D2O) combined with Raman microspectroscopy. Incorporation of D2O-derived D into the biomass of autotrophic and heterotrophic bacteria and archaea could be unambiguously detected via C-D signature peaks in single-cell Raman spectra, and the obtained labeling pattern was confirmed by nanoscale-resolution secondary ion MS. In fast-growing Escherichia coli cells, label detection was already possible after 20 min. For functional analyses of microbial communities, the detection of D incorporation from D2O in individual microbial cells via Raman microspectroscopy can be directly combined with FISH for the identification of active microbes. Applying this approach to mouse cecal microbiota revealed that the host-compound foragers Akkermansia muciniphila and Bacteroides acidifaciens exhibited distinctive response patterns to amendments of mucin and sugars. By Raman-based cell sorting of active (deuterated) cells with optical tweezers and subsequent multiple displacement amplification and DNA sequencing, novel cecal microbes stimulated by mucin and/or glucosamine were identified, demonstrating the potential of the nondestructive D2O-Raman approach for targeted sorting of microbial cells with defined functional properties for single-cell genomics. PMID:25550518

  13. Tracking heavy water (D2O) incorporation for identifying and sorting active microbial cells.

    PubMed

    Berry, David; Mader, Esther; Lee, Tae Kwon; Woebken, Dagmar; Wang, Yun; Zhu, Di; Palatinszky, Marton; Schintlmeister, Arno; Schmid, Markus C; Hanson, Buck T; Shterzer, Naama; Mizrahi, Itzhak; Rauch, Isabella; Decker, Thomas; Bocklitz, Thomas; Popp, Jürgen; Gibson, Christopher M; Fowler, Patrick W; Huang, Wei E; Wagner, Michael

    2015-01-13

    Microbial communities are essential to the function of virtually all ecosystems and eukaryotes, including humans. However, it is still a major challenge to identify microbial cells active under natural conditions in complex systems. In this study, we developed a new method to identify and sort active microbes on the single-cell level in complex samples using stable isotope probing with heavy water (D2O) combined with Raman microspectroscopy. Incorporation of D2O-derived D into the biomass of autotrophic and heterotrophic bacteria and archaea could be unambiguously detected via C-D signature peaks in single-cell Raman spectra, and the obtained labeling pattern was confirmed by nanoscale-resolution secondary ion MS. In fast-growing Escherichia coli cells, label detection was already possible after 20 min. For functional analyses of microbial communities, the detection of D incorporation from D2O in individual microbial cells via Raman microspectroscopy can be directly combined with FISH for the identification of active microbes. Applying this approach to mouse cecal microbiota revealed that the host-compound foragers Akkermansia muciniphila and Bacteroides acidifaciens exhibited distinctive response patterns to amendments of mucin and sugars. By Raman-based cell sorting of active (deuterated) cells with optical tweezers and subsequent multiple displacement amplification and DNA sequencing, novel cecal microbes stimulated by mucin and/or glucosamine were identified, demonstrating the potential of the nondestructive D2O-Raman approach for targeted sorting of microbial cells with defined functional properties for single-cell genomics. PMID:25550518

  14. Effects of nutrient enrichment on the decomposition of wood and associated microbial activity in streams

    USGS Publications Warehouse

    Gulis, V.; Rosemond, A.D.; Suberkropp, K.; Weyers, H.S.; Benstead, J.P.

    2004-01-01

    1. We determined the effects of nutrient enrichment on wood decomposition rates and microbial activity during a 3-year study in two headwater streams at Coweeta Hydrologic Laboratory, NC, U.S.A. After a 1-year pretreatment period, one of the streams was continuously enriched with inorganic nutrients (nitrogen and phosphorus) for 2 years while the other stream served as a reference. We determined the effects of enrichment on both wood veneers and sticks, which have similar carbon quality but differ in physical characteristics (e.g. surface area to volume ratios, presence of bark) that potentially affect microbial colonisation and activity. 2. Oak wood veneers (0.5 mm thick) were placed in streams monthly and allowed to decompose for approximately 90 days. Nutrient addition stimulated ash-free dry mass loss and increased mean nitrogen content, fungal biomass and microbial respiration on veneers in the treatment stream compared with the reference. The magnitude of the response to enrichment was great, with mass loss 6.1 times, and per cent N, fungal biomass and microbial respiration approximately four times greater in the treatment versus reference stream. 3. Decomposition rate and nitrogen content of maple sticks (ca. 1-2 cm diameter) also increased; however, the effect was less pronounced than for veneers. Wood response overall was greater than that determined for leaves in a comparable study, supporting the hypothesis that response to enrichment may be greater for lower quality organic matter (high C:N) than for higher quality (low C:N) substrates. 4. Our results show that moderate nutrient enrichment can profoundly affect decomposition rate and microbial activity on wood in streams. Thus, the timing and availability of wood that provides retention, structure, attachment sites and food in stream ecosystems may be affected by nutrient concentrations raised by human activities.

  15. Catalytic activity of baker's yeast in a mediatorless microbial fuel cell.

    PubMed

    Sayed, Enas Taha; Tsujiguchi, Takuya; Nakagawa, Nobuyoshi

    2012-08-01

    The catalytic activity of baker's yeast, Saccharomyces cerevisiae, as a biocatalyst was investigated in a mediatorless microbial fuel cell. The yeast cells that adhered on the anode surface were the active biocatalyst for glucose oxidation in a mediatorless biofuel cell, suggesting that the electron transfer took place through the surface confined species. The species in the anolyte solution including the dispersed yeast cells did not take a part in the electron transfer and thus in the power generation. PMID:22357359

  16. Effect of different preservative treatments on the microbial population of Nigerian orange juice.

    PubMed

    Sodeko, O O; Izuagbe, Y S; Ukhun, M E

    1987-01-01

    The effect of different preservative treatments on the microbial load of Nigerian orange juice was studied over a period of 1 month. Results obtained indicated that pasteurization at 60 degrees and 80 degrees C for 20 to 40 min, freezing at -5 degrees C, and addition of sodium benzoate at a concentration of 0.1 to 0.4% (w/v) could form a microbiological basis for the preservation of the juice for 1 month. Leuconostoc mesenteroides, L. paramesenteroides, Streptococcus avium, Lactobacillus plantarum, L. fermentum, L. fructivorans, Klebsiella pneumoniae and Saccharomyces cerevisiae were the micro-organisms isolated from the untreated and treated juice samples. PMID:3316936

  17. Influence of Electron Donor Type and Concentration on Microbial Population Structure During Uranium Reduction and Remobilization

    NASA Astrophysics Data System (ADS)

    Daly, R. A.; Brodie, E. L.; Kim, Y.; Wan, J.; Tokunaga, T.; Desantis, T. Z.; Andersen, G. L.; Hazen, T. C.; Firestone, M. K.

    2007-12-01

    Enhanced reductive precipitation of U(VI) through stimulation of indigenous microorganisms is an attractive, low- cost strategy for in-situ remediation of contaminated groundwaters and sediments. The rate of organic carbon (OC) supply determines not only the amount of electron donor available for bioreduction of U(VI), but also affects the resulting concentration of aqueous (bi)carbonate generated by microbial respiration. Increased (bi)carbonate concentrations drive aqueous U(VI) concentrations to higher levels and make U(IV) oxidation under reducing conditions favorable. We designed a long-term column study to investigate the effects of different OC forms and supply rates on the stability of bioreduced U and on the structure and dynamics of the microbial communities. OC was supplied as acetate or lactate at four different concentrations and columns were sampled at three time points. In the columns receiving high OC supply the time points correspond to a phases of net U-reduction, U(IV) reoxidation and U(VI) remobilization, and stable levels of U mobilization. DNA was extracted from column sediments, 16S rRNA genes were amplified and the communities analyzed using a high-density phylogenetic microarray (PhyloChip). Lactate and acetate supplied at equivalent rates had a similar impact on uranium mobility with higher OC resulting in re-oxidation of U(IV) after an initial period of U(VI) reduction. Similarly, organic carbon (OC) supply rate, not OC form, had the largest impact on microbial community structure. The diversity (richness) of bacterial and archaeal communities increased over time with those receiving lactate having higher initial richness. Known U-reducing bacteria were present in all columns and time points, however the dynamics of these organisms varied with both organic carbon supply rate and form. This data demonstrates that the initial rate of electron donor supply during heavy metal remediation strongly impacts microbial community development

  18. Evaluation of microbial populations, Rhizobium Trifolii, and endomycorrhizal associations in reclamation of surface mine spoils in Texas

    SciTech Connect

    Mott, J.B.

    1984-01-01

    The deficiency of nitrogen and phosphorus in mixed overburden mine spoils has resulted in interest in strategies to minimize fertilizer application. In this study, the abundance of microbial populations, with emphasis on those involved in nitrogen cycle transformations was estimated in variously aged spoils. Two beneficial plant-microbe associations, the clover-Rhizobium trifolii symbiosis and endomycorrhizal associations, were investigated in field and laboratory studies. While most groups of microorganisms regained pre-mining levels in revegetated spoils within 1.5 years after disturbance, algal populations were still reduced ten years after mining. Populations of nitrifying bacteria and asymbiotic nitrogen-fixing bacteria were as high in all spoils as in unmined soil. Indigenous populations of ineffective R. trifolii were present in spoil banks and older revegetated spoil. A laboratory study of survival of three commercial strains of R. trifolii for subterranean clover showed lethal effects of high temperature (45/sup 0/C) especially in moist spoil, and superior survival of strain 162X95. Endomycorrhizal associations, evaluated by assessment of root infection in bermudagrass, reached pre-mining levels by three to seven years after disturbance. Growth chamber studies to investigate the effects of the two symbiotic associations on subterranean clover in mine spoil at different fertility levels indicated that dual infection with Rhizobium and VAM fungi was most beneficial for plant growth, nitrogen fixation, and nitrogen and phosphorus contents.

  19. Population-Sequencing as a Biomarker of Burkholderia mallei and Burkholderia pseudomallei Evolution through Microbial Forensic Analysis

    PubMed Central

    Jakupciak, John P.; Wells, Jeffrey M.; Karalus, Richard J.; Pawlowski, David R.; Lin, Jeffrey S.; Feldman, Andrew B.

    2013-01-01

    Large-scale genomics projects are identifying biomarkers to detect human disease. B. pseudomallei and B. mallei are two closely related select agents that cause melioidosis and glanders. Accurate characterization of metagenomic samples is dependent on accurate measurements of genetic variation between isolates with resolution down to strain level. Often single biomarker sensitivity is augmented by use of multiple or panels of biomarkers. In parallel with single biomarker validation, advances in DNA sequencing enable analysis of entire genomes in a single run: population-sequencing. Potentially, direct sequencing could be used to analyze an entire genome to serve as the biomarker for genome identification. However, genome variation and population diversity complicate use of direct sequencing, as well as differences caused by sample preparation protocols including sequencing artifacts and mistakes. As part of a Department of Homeland Security program in bacterial forensics, we examined how to implement whole genome sequencing (WGS) analysis as a judicially defensible forensic method for attributing microbial sample relatedness; and also to determine the strengths and limitations of whole genome sequence analysis in a forensics context. Herein, we demonstrate use of sequencing to provide genetic characterization of populations: direct sequencing of populations. PMID:24455204

  20. Discovery of New Compounds Active against Plasmodium falciparum by High Throughput Screening of Microbial Natural Products

    PubMed Central

    Pérez-Moreno, Guiomar; Cantizani, Juan; Sánchez-Carrasco, Paula; Ruiz-Pérez, Luis Miguel; Martín, Jesús; el Aouad, Noureddine; Pérez-Victoria, Ignacio; Tormo, José Rubén; González-Menendez, Víctor; González, Ignacio; de Pedro, Nuria; Reyes, Fernando; Genilloud, Olga; Vicente, Francisca; González-Pacanowska, Dolores

    2016-01-01

    Due to the low structural diversity within the set of antimalarial drugs currently available in the clinic and the increasing number of cases of resistance, there is an urgent need to find new compounds with novel modes of action to treat the disease. Microbial natural products are characterized by their large diversity provided in terms of the chemical complexity of the compounds and the novelty of structures. Microbial natural products extracts have been underexplored in the search for new antiparasitic drugs and even more so in the discovery of new antimalarials. Our objective was to find new druggable natural products with antimalarial properties from the MEDINA natural products collection, one of the largest natural product libraries harboring more than 130,000 microbial extracts. In this work, we describe the optimization process and the results of a phenotypic high throughput screen (HTS) based on measurements of Plasmodium lactate dehydrogenase. A subset of more than 20,000 extracts from the MEDINA microbial products collection has been explored, leading to the discovery of 3 new compounds with antimalarial activity. In addition, we report on the novel antiplasmodial activity of 4 previously described natural products. PMID:26735308

  1. Discovery of New Compounds Active against Plasmodium falciparum by High Throughput Screening of Microbial Natural Products.

    PubMed

    Pérez-Moreno, Guiomar; Cantizani, Juan; Sánchez-Carrasco, Paula; Ruiz-Pérez, Luis Miguel; Martín, Jesús; El Aouad, Noureddine; Pérez-Victoria, Ignacio; Tormo, José Rubén; González-Menendez, Víctor; González, Ignacio; de Pedro, Nuria; Reyes, Fernando; Genilloud, Olga; Vicente, Francisca; González-Pacanowska, Dolores

    2016-01-01

    Due to the low structural diversity within the set of antimalarial drugs currently available in the clinic and the increasing number of cases of resistance, there is an urgent need to find new compounds with novel modes of action to treat the disease. Microbial natural products are characterized by their large diversity provided in terms of the chemical complexity of the compounds and the novelty of structures. Microbial natural products extracts have been underexplored in the search for new antiparasitic drugs and even more so in the discovery of new antimalarials. Our objective was to find new druggable natural products with antimalarial properties from the MEDINA natural products collection, one of the largest natural product libraries harboring more than 130,000 microbial extracts. In this work, we describe the optimization process and the results of a phenotypic high throughput screen (HTS) based on measurements of Plasmodium lactate dehydrogenase. A subset of more than 20,000 extracts from the MEDINA microbial products collection has been explored, leading to the discovery of 3 new compounds with antimalarial activity. In addition, we report on the novel antiplasmodial activity of 4 previously described natural products. PMID:26735308

  2. Formation of recent Pb-Ag-Au mineralization by potential sub-surface microbial activity

    NASA Astrophysics Data System (ADS)

    Tornos, Fernando; Velasco, Francisco; Menor-Salván, César; Delgado, Antonio; Slack, John F.; Escobar, Juan Manuel

    2014-08-01

    Las Cruces is a base-metal deposit in the Iberian Pyrite Belt, one of the world’s best-known ore provinces. Here we report the occurrence of major Pb-Ag-Au mineralization resulting from recent sub-surface replacement of supergene oxyhydroxides by carbonate and sulphide minerals. This is probably the largest documented occurrence of recent microbial activity producing an ore assemblage previously unknown in supergene mineralizing environments. The presence of microbial features in the sulphides suggests that these may be the first-described natural bacteriomorphs of galena. The low δ13C values of the carbonate minerals indicate formation by deep anaerobic microbial processes. Sulphur isotope values of sulphides are interpreted here as reflecting microbial reduction in a system impoverished in sulphate. We suggest that biogenic activity has produced around 3.1 × 109 moles of reduced sulphur and 1010 moles of CO2, promoting the formation of ca. 1.19 Mt of carbonates, 114,000 t of galena, 638 t of silver sulphides and 6.5 t of gold.

  3. Formation of recent Pb-Ag-Au mineralization by potential sub-surface microbial activity.

    PubMed

    Tornos, Fernando; Velasco, Francisco; Menor-Salván, César; Delgado, Antonio; Slack, John F; Escobar, Juan Manuel

    2014-01-01

    Las Cruces is a base-metal deposit in the Iberian Pyrite Belt, one of the world's best-known ore provinces. Here we report the occurrence of major Pb-Ag-Au mineralization resulting from recent sub-surface replacement of supergene oxyhydroxides by carbonate and sulphide minerals. This is probably the largest documented occurrence of recent microbial activity producing an ore assemblage previously unknown in supergene mineralizing environments. The presence of microbial features in the sulphides suggests that these may be the first-described natural bacteriomorphs of galena. The low δ(13)C values of the carbonate minerals indicate formation by deep anaerobic microbial processes. Sulphur isotope values of sulphides are interpreted here as reflecting microbial reduction in a system impoverished in sulphate. We suggest that biogenic activity has produced around 3.1 × 10(9) moles of reduced sulphur and 10(10) moles of CO2, promoting the formation of ca. 1.19 Mt of carbonates, 114,000 t of galena, 638 t of silver sulphides and 6.5 t of gold. PMID:25098677

  4. Benthic microbial abundance and activities in an intensively trawled ecosystem (Thermaikos Gulf, Aegean Sea)

    NASA Astrophysics Data System (ADS)

    Polymenakou, Paraskevi N.; Pusceddu, Antonio; Tselepides, Anastasios; Polychronaki, Thalia; Giannakourou, Antonia; Fiordelmondo, Carla; Hatziyanni, Eleni; Danovaro, Roberto

    2005-12-01

    Abundance of benthic bacteria, heterotrophic nanoflagellates and ciliates, extracellular enzymatic activities, bacterial C production, C mineralisation and sediment community oxygen consumption rates were measured in the Thermaikos Gulf (Northeastern Mediterranean), before (September 2001), and during intense trawling activities (October 2001 and February 2002). The biochemical composition of sedimentary organic matter has revealed that bottom trawling had an effect on the trophic state of Thermaikos Gulf. Changes on the benthic microbial food web were also recorded, during the three sampling seasons. Even though trawling-induced sediment resuspension did not alter significantly the abundance of the microbial components, with the exception of the most impacted station, it determined changes regarding their relative importance. Thus, the ratios of bacterium to nanoflagellates and ciliate to nanoflagellates abundance increased in the trawled stations, causing a sudden increase in bacterial C production, in comparison to the non-trawled station. Four months later, the effects of trawling on the microbial food web were less evident, masked possibly by the drastic decrease in the water temperature. The results of the present work suggest that bottom trawling induces alteration of the sedimentological variables and can be considered as a factor affecting the function of the microbial food web in marine coastal ecosystems. These alterations cause faster mobilisation of organic C buried in the sediment and increase nutrient concentrations and availability in the system, thus inducing an effect that could lead to coastal eutrophication.

  5. Use of Field-Based Stable Isotope Probing To Identify Adapted Populations and Track Carbon Flow through a Phenol-Degrading Soil Microbial Community

    PubMed Central

    DeRito, Christopher M.; Pumphrey, Graham M.; Madsen, Eugene L.

    2005-01-01

    The goal of this field study was to provide insight into three distinct populations of microorganisms involved in in situ metabolism of phenol. Our approach measured 13CO2 respired from [13C]phenol and stable isotope probing (SIP) of soil DNA at an agricultural field site. Traditionally, SIP-based investigations have been subject to the uncertainties posed by carbon cross-feeding. By altering our field-based, substrate-dosing methodologies, experiments were designed to look beyond primary degraders to detect trophically related populations in the food chain. Using gas chromatography-mass spectrometry (GC/MS), it was shown that 13C-labeled biomass, derived from primary phenol degraders in soil, was a suitable growth substrate for other members of the soil microbial community. Next, three dosing regimes were designed to examine active members of the microbial community involved in phenol metabolism in situ: (i) 1 dose of [13C]phenol, (ii) 11 daily doses of unlabeled phenol followed by 1 dose of [13C]phenol, and (iii) 12 daily doses of [13C]phenol. GC/MS analysis demonstrated that prior exposure to phenol boosted 13CO2 evolution by a factor of 10. Furthermore, imaging of 13C-treated soil using secondary ion mass spectrometry (SIMS) verified that individual bacteria incorporated 13C into their biomass. PCR amplification and 16S rRNA gene sequencing of 13C-labeled soil DNA from the 3 dosing regimes revealed three distinct clone libraries: (i) unenriched, primary phenol degraders were most diverse, consisting of α-, β-, and γ-proteobacteria and high-G+C-content gram-positive bacteria, (ii) enriched primary phenol degraders were dominated by members of the genera Kocuria and Staphylococcus, and (iii) trophically related (carbon cross-feeders) were dominated by members of the genus Pseudomonas. These data show that SIP has the potential to document population shifts caused by substrate preexposure and to follow the flow of carbon through terrestrial microbial food

  6. Geochemical and sulfur isotope signatures of microbial activity in acidic and sulfuric hot springs, northern Taiwan

    NASA Astrophysics Data System (ADS)

    Wang, P.; Chen, K.; Cheng, T.; Hsieh, H.; Lin, L.

    2009-12-01

    Acidic and sulfuric hot springs are natural habitats for thermophilic sulfur-utilizing microorganisms. Integration of bioenergetic evaluation, molecular analysis and stable isotopic signatures may be able to exhibit a full view of microbial activity in such an extreme environment. Widely distributed hot springs hosted by the Tatung volcano group in northern Taiwan provide a chance to evaluate the interplay between geochemical variation and microbial metabolism especially for sulfur. Several hot spring ponds varying in sizes and geochemical characteristics were studied to reveal the possible control of fluid compositions on microbial metabolisms, and vice versa. Sulfate, sulfide, elemental sulfur and dissolved organic carbon were available in spring water and sediments in the ponds. Dominant microbial metabolisms inferred from the bioenergetic evaluation were aerobic oxidations of various reduced compounds, including elemental sulfur, pyrite, ferrous iron and organic carbon. Sulfate and sulfur reductions were thermodynamically favorable but provided less energy flux, while sulfur disproportionation was thermodynamically incapable. The analyses of 16S rRNA genes extracted from the spring water and sediments indicated that aerobic oxidation of sulfur, hydrogen or organic carbon and anaerobic elemental sulfur reduction were possible metabolisms. Since the major portion of 16S rRNA sequences were affiliated with unclassified environmental sequences, their potential metabolisms remained obscure. Sulfur isotopic compositions of dissolved sulfate, pyrite and elemental sulfur exhibited significant variations among the different hot spring ponds. Apparently, the microbial effects on the sulfur isotopic signatures were various. A disproportionation reaction of volcanic gas was required to account for high sulfur isotope difference between sulfate and reduced sulfur in the large hot ponds. In contrary, abiotic or microbial oxidation of reduced sulfur might be dominant in the

  7. Geoelectrical measurement and modeling of biogeochemical breakthrough behavior during microbial activity

    USGS Publications Warehouse

    Slater, L.D.; Day-Lewis, F. D.; Ntarlagiannis, D.; O'Brien, M.; Yee, N.

    2009-01-01

    We recorded bulk electrical conductivity (??b) along a soil column during microbially-mediated selenite oxyanion reduction. Effluent fluid electrical conductivity and early time ??b were modeled according to classic advectivedispersive transport of the nutrient medium. However, ??b along the column exhibited strongly bimodal breakthrough which cannot be explained by changes in the electrical conductivity of the pore fluid. We model the anomalous breakthrough by adding a conduction path in parallel with the fluid phase, with a time dependence described by a microbial population-dynamics model. We incorporate a delay time to show that breakthrough curves along the column satisfy the same growth model parameters and offer a possible explanation based on biomass-limited growth that is delayed with distance from influent of the nutrient medium. Although the mechanism causing conductivity enhancement in the presence of biomass is uncertain, our results strongly , suggest that biogeochemical breakthrough curves have been captured in geoelectrical datasets. Copyright 2009 by the American Geophysical Union.

  8. Microbial metabolic activity in soil as measured by dehydrogenase determinations

    NASA Technical Reports Server (NTRS)

    Casida, L. E., Jr.

    1977-01-01

    The dehydrogenase technique for measuring the metabolic activity of microorganisms in soil was modified to use a 6-h, 37 C incubation with either glucose or yeast extract as the electron-donating substrate. The rate of formazan production remained constant during this time interval, and cellular multiplication apparently did not occur. The technique was used to follow changes in the overall metabolic activities of microorganisms in soil undergoing incubation with a limiting concentration of added nutrient. The sequence of events was similar to that obtained by using the Warburg respirometer to measure O2 consumption. However, the major peaks of activity occurred earlier with the respirometer. This possibly is due to the lack of atmospheric CO2 during the O2 consumption measurements.

  9. Impact of demographics on human gut microbial diversity in a US Midwest population

    PubMed Central

    Chen, Jun; Ryu, Euijung; Hathcock, Matthew; Ballman, Karla; Chia, Nicholas; Olson, Janet E

    2016-01-01

    The clinical utility of microbiome biomarkers depends on the reliable and reproducible nature of comparative results. Underappreciation of the variation associated with common demographic, health, and behavioral factors may confound associations of interest and generate false positives. Here, we present the Midwestern Reference Panel (MWRP), a resource for comparative gut microbiome studies conducted in the Midwestern United States. We analyzed the relationships between demographic and health behavior-related factors and the microbiota in this cohort, and estimated their effect sizes. Most variables investigated were associated with the gut microbiota. Specifically, body mass index (BMI), race, sex, and alcohol use were significantly associated with microbial β-diversity (P < 0.05, unweighted UniFrac). BMI, race and alcohol use were also significantly associated with microbial α-diversity (P < 0.05, species richness). Tobacco use showed a trend toward association with the microbiota (P < 0.1, unweighted UniFrac). The effect sizes of the associations, as quantified by adjusted R2 values based on unweighted UniFrac distances, were small (< 1% for all variables), indicating that these factors explain only a small percentage of overall microbiota variability. Nevertheless, the significant associations between these variables and the gut microbiota suggest that they could still be potential confounders in comparative studies and that controlling for these variables in study design, which is the main objective of the MWRP, is important for increasing reproducibility in comparative microbiome studies. PMID:26839739

  10. Using populations of human and microbial genomes for organism detection in metagenomes

    SciTech Connect

    Ames, Sasha K.; Gardner, Shea N.; Marti, Jose Manuel; Slezak, Tom R.; Gokhale, Maya B.; Allen, Jonathan E.

    2015-04-29

    Identifying causative disease agents in human patients from shotgun metagenomic sequencing (SMS) presents a powerful tool to apply when other targeted diagnostics fail. Numerous technical challenges remain, however, before SMS can move beyond the role of research tool. Accurately separating the known and unknown organism content remains difficult, particularly when SMS is applied as a last resort. The true amount of human DNA that remains in a sample after screening against the human reference genome and filtering nonbiological components left from library preparation has previously been underreported. In this study, we create the most comprehensive collection of microbial and reference-free human genetic variation available in a database optimized for efficient metagenomic search by extracting sequences from GenBank and the 1000 Genomes Project. The results reveal new human sequences found in individual Human Microbiome Project (HMP) samples. Individual samples contain up to 95% human sequence, and 4% of the individual HMP samples contain 10% or more human reads. In conclusion, left unidentified, human reads can complicate and slow down further analysis and lead to inaccurately labeled microbial taxa and ultimately lead to privacy concerns as more human genome data is collected.

  11. Using populations of human and microbial genomes for organism detection in metagenomes

    DOE PAGESBeta

    Ames, Sasha K.; Gardner, Shea N.; Marti, Jose Manuel; Slezak, Tom R.; Gokhale, Maya B.; Allen, Jonathan E.

    2015-04-29

    Identifying causative disease agents in human patients from shotgun metagenomic sequencing (SMS) presents a powerful tool to apply when other targeted diagnostics fail. Numerous technical challenges remain, however, before SMS can move beyond the role of research tool. Accurately separating the known and unknown organism content remains difficult, particularly when SMS is applied as a last resort. The true amount of human DNA that remains in a sample after screening against the human reference genome and filtering nonbiological components left from library preparation has previously been underreported. In this study, we create the most comprehensive collection of microbial and reference-freemore » human genetic variation available in a database optimized for efficient metagenomic search by extracting sequences from GenBank and the 1000 Genomes Project. The results reveal new human sequences found in individual Human Microbiome Project (HMP) samples. Individual samples contain up to 95% human sequence, and 4% of the individual HMP samples contain 10% or more human reads. In conclusion, left unidentified, human reads can complicate and slow down further analysis and lead to inaccurately labeled microbial taxa and ultimately lead to privacy concerns as more human genome data is collected.« less

  12. Using populations of human and microbial genomes for organism detection in metagenomes

    PubMed Central

    Ames, Sasha K.; Gardner, Shea N.; Marti, Jose Manuel; Slezak, Tom R.; Gokhale, Maya B.; Allen, Jonathan E.

    2015-01-01

    Identifying causative disease agents in human patients from shotgun metagenomic sequencing (SMS) presents a powerful tool to apply when other targeted diagnostics fail. Numerous technical challenges remain, however, before SMS can move beyond the role of research tool. Accurately separating the known and unknown organism content remains difficult, particularly when SMS is applied as a last resort. The true amount of human DNA that remains in a sample after screening against the human reference genome and filtering nonbiological components left from library preparation has previously been underreported. In this study, we create the most comprehensive collection of microbial and reference-free human genetic variation available in a database optimized for efficient metagenomic search by extracting sequences from GenBank and the 1000 Genomes Project. The results reveal new human sequences found in individual Human Microbiome Project (HMP) samples. Individual samples contain up to 95% human sequence, and 4% of the individual HMP samples contain 10% or more human reads. Left unidentified, human reads can complicate and slow down further analysis and lead to inaccurately labeled microbial taxa and ultimately lead to privacy concerns as more human genome data is collected. PMID:25926546

  13. Production of bioavailable and refractory dissolved organic matter by coastal heterotrophic microbial populations

    NASA Astrophysics Data System (ADS)

    Lønborg, Christian; Álvarez-Salgado, Xosé A.; Davidson, Keith; Miller, Axel E. J.

    2009-05-01

    Production of dissolved organic matter (DOM) by heterotrophic microbial communities isolated from Loch Creran (Scotland) was studied in time course incubations in which cells were re-suspended in artificial seawater amended with variable proportions of glucose, ammonium and phosphate. The incubation experiments demonstrated that microheterotrophs released part of the substrate as new DOM, with a production efficiency of 11 ± 1% for DOC, 18 ± 2% for DON and 17 ± 2% for DOP. Estimating the impact of this production in Loch Creran, showed that from 3 ± 1% (DOC) to 72 ± 16% (DOP) of DOM could originate from the heterotrophic microbial community. The produced DOM (PDOM) was both bioavailable (BDOM) and refractory (RDOM). Bioavailability as assessed by the difference between the maximum and the end DOM concentration, was generally higher than found in natural systems, with DOP (73 ± 15%, average ± SD) more bioavailable than DON (70 ± 15%), and DON than DOC (34 ± 13%). The stoichiometry of PDOM was linked to both nutrient uptake and BDOM ratios. Absorption and fluorescence of DOM increased significantly during the incubation time, indicating that microheterotrophs were also a source of coloured DOM (CDOM) and that they produce both bioavailable protein-like and refractory humic-like fluorophores.

  14. Using populations of human and microbial genomes for organism detection in metagenomes.

    PubMed

    Ames, Sasha K; Gardner, Shea N; Marti, Jose Manuel; Slezak, Tom R; Gokhale, Maya B; Allen, Jonathan E

    2015-07-01

    Identifying causative disease agents in human patients from shotgun metagenomic sequencing (SMS) presents a powerful tool to apply when other targeted diagnostics fail. Numerous technical challenges remain, however, before SMS can move beyond the role of research tool. Accurately separating the known and unknown organism content remains difficult, particularly when SMS is applied as a last resort. The true amount of human DNA that remains in a sample after screening against the human reference genome and filtering nonbiological components left from library preparation has previously been underreported. In this study, we create the most comprehensive collection of microbial and reference-free human genetic variation available in a database optimized for efficient metagenomic search by extracting sequences from GenBank and the 1000 Genomes Project. The results reveal new human sequences found in individual Human Microbiome Project (HMP) samples. Individual samples contain up to 95% human sequence, and 4% of the individual HMP samples contain 10% or more human reads. Left unidentified, human reads can complicate and slow down further analysis and lead to inaccurately labeled microbial taxa and ultimately lead to privacy concerns as more human genome data is collected. PMID:25926546

  15. Progression of natural attenuation processes at a crude oil spill site: II. Controls on spatial distribution of microbial populations

    USGS Publications Warehouse

    Bekins, B.A.; Cozzarelli, I.M.; Godsy, E.M.; Warren, E.; Essaid, H.I.; Tuccillo, M.E.

    2001-01-01

    A multidisciplinary study of a crude-oil contaminated aquifer shows that the distribution of microbial physiologic types is strongly controlled by the aquifer properties and crude oil location. The microbial populations of four physiologic types were analyzed together with permeability, pore-water chemistry, nonaqueous oil content, and extractable sediment iron. Microbial data from three vertical profiles through the anaerobic portion of the contaminated aquifer clearly show areas that have progressed from iron-reduction to methanogenesis. These locations contain lower numbers of iron reducers, and increased numbers of fermenters with detectable methanogens. Methanogenic conditions exist both in the area contaminated by nonaqueous oil and also below the oil where high hydrocarbon concentrations correspond to local increases in aquifer permeability. The results indicate that high contaminant flux either from local dissolution or by advective transport plays a key role in determining which areas first become methanogenic. Other factors besides flux that are important include the sediment Fe(II) content and proximity to the water table. In locations near a seasonally oscillating water table, methanogenic conditions exist only below the lowest typical water table elevation. During 20 years since the oil spill occurred, a laterally continuous methanogenic zone has developed along a narrow horizon extending from the source area to 50-60 m downgradient. A companion paper [J. Contam. Hydrol. 53, 369-386] documents how the growth of the methanogenic zone results in expansion of the aquifer volume contaminated with the highest concentrations of benzene, toluene, ethylbenzene, and xylenes. Copyright ?? 2001 Elsevier Science B.V.

  16. Short-term parasite-infection alters already the biomass, activity and functional diversity of soil microbial communities

    NASA Astrophysics Data System (ADS)

    Li, Jun-Min; Jin, Ze-Xin; Hagedorn, Frank; Li, Mai-He

    2014-11-01

    Native parasitic plants may be used to infect and control invasive plants. We established microcosms with invasive Mikania micrantha and native Coix lacryma-jobi growing in mixture on native soils, with M. micrantha being infected by parasitic Cuscuta campestris at four intensity levels for seven weeks to estimate the top-down effects of plant parasitism on the biomass and functional diversity of soil microbial communities. Parasitism significantly decreased root biomass and altered soil microbial communities. Soil microbial biomass decreased, but soil respiration increased at the two higher infection levels, indicating a strong stimulation of soil microbial metabolic activity (+180%). Moreover, a Biolog assay showed that the infection resulted in a significant change in the functional diversity indices of soil microbial communities. Pearson correlation analysis indicated that microbial biomass declined significantly with decreasing root biomass, particularly of the invasive M. micrantha. Also, the functional diversity indices of soil microbial communities were positively correlated with soil microbial biomass. Therefore, the negative effects on the biomass, activity and functional diversity of soil microbial community by the seven week long plant parasitism was very likely caused by decreased root biomass and root exudation of the invasive M. micrantha.

  17. Soil Rhizosphere Microbial Communities and Enzyme Activities under Organic Farming

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study investigated the activities of ß-glucosidase (C cycling, ß-glucosaminidase (C and N cycling), acid phosphatase (P cycling) and arylsulfatase (S cycling) under lettuce (Lactuca sativa), potato (Solanum Tuberosum), onion (Allium cepa L), broccoli (Brassica oleracea var. botrytis) and Tall f...

  18. MICROBIAL SUCCESSION AND INTESTINAL ENZYME ACTIVITIES IN THE DEVELOPING RAT

    EPA Science Inventory

    The succession of gastrointestinal flora in the developing rat was studied, concomitant with studies of intestinal enzyme activity. Aerobes and anaerobes were identified as members of 4 major bacterial groups, i.e., Lactobacilli spp., Gram positive enterococci, Gram negative rods...

  19. Effects of selected surfactants on soil microbial activity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Surfactants (surface-active agents) facilitate and accentuate the emulsifying, dispersing, spreading, and wetting properties of liquids. Surfactants are used in industry to reduce the surface tension of liquid and to solubilize compounds. For agricultural pest management, surfactants are an import...

  20. Effects of harvester ant (Messor spp.) activity on soil properties and microbial communities in a Negev Desert ecosystem

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Harvester ants (Messor spp.) function as an essential link between aboveground resources and belowground biota such as the microbial community. We examined changes in soil microbial biomass and functional diversity resulting from harvester ant (Messor spp.) activity in the Negev Desert, Israel. Abi...

  1. Microbial and xanthine dehydrogenase inhibitory activity of some flavones.

    PubMed

    Khobragade, C N; Bodade, Ragini G; Shinde, M S; Jaju, Deepa R; Bhosle, R B; Dawane, B S

    2008-06-01

    Xanthine dehydrogenase (XDH) is responsible for the pathological condition called Gout. In the present study different flavones synthesized from chalcone were evaluated in vitro for their inhibitory activity. Inhibitory activity of flavones on XDH was determined in terms of inhibition of uric acid synthesis from Xanthine. The enzymatic activity was found maximum at pH 7.5 and temperature 40 degrees C. The flavones 6-chloro-2-[3-(4-hydroxy-phenyl)-1-phenyl-1-H-pyrazol-4-yl]-chromen-4-one (F(1)) and 6-chloro-7methyl-2-[3-(4-chloro-phenyl)-1-phenyl-1-H-pyrazol-4-yl]-chromen-4-one(F(2)),were noncompetitive and competitive inhibitor with Ki values 1.1 and 0.22 respectively. The flavones (F(1)), (F(2)), 6-chloro-2-[3-(4-chloro-phenyl)-1phenyl-1-H-pyrazol-4-yl]-chromen-4-one(F(3)), 8-bromo-6-chloro-2-[3-(4-chloro-phenyl)-1-phenyl-1-H-pyrazol-4-yl]-chromen-4-one (F(4)), 2-[3-(4-hydroxy-phenyl)-1-phenyl-1-H-pyrazol-4-yl]-chromen-4-one (F(5)) and 6-methyl-2-[3-(4-hydroxy-phenyl)-1-phenyl-1-H-pyrazol-4-yl]-chromen-4-one (F(6)) were also screened for their antimicrobial activity, measured in terms of zone of inhibition. A broad spectrum antifungal activity was obtained against Trichoderma viridae, Candida albicans, Microsporum cannis, Penicillium chrysogenum and Fusarium moniliformae. In case of Aspergillus niger and Aspergillus flavous only spore formation was affected, while antibacterial activity was observed against Staphylococcus aureus, Bacillus subtilis and Serratia marsecens only. The flavones were further analyzed for quantitative structural activity relationship study (QSAR) by using PASS, online software to determine their Pa value. Toxicity and drug relevant properties were revealed by PALLAS software in terms of their molecular weight. Log P values were also studied. The result showed both the F(1) and F(2) flavones as antigout and therefore supports the development of novel drugs for the treatment of gout. PMID:18569337

  2. Biokinetic analyses of adaptation and succession: microbial activity in composting municipal sewage sludge.

    PubMed Central

    McKinley, V L; Vestal, J R

    1984-01-01

    The interactions between temperature and the microbial communities in composting municipal sewage sludge were studied to determine the optimal temperature range for efficient decomposition (stabilization) of the sludge. Information concerning thermophilic successions in such communities was also obtained. Samples were taken from several different temperature areas in a production-scale composting pile throughout the 19-day processing run. Optimum temperatures for microbial activity, determined as the rate of [14C]acetate incorporation into microbial lipids, were determined for each sample. Biomass was determined from the lipid phosphate content of the sample. Maximal activities were generally found in samples coming from lower-temperature areas (25 to 45 degrees C), whereas samples from high temperatures (55 to 74 degrees C) usually had relatively little activity. The temperature giving the optimum activity in samples incubated at a variety of temperatures during the assay tended to increase as the composting time progressed, but never exceeded about 50 degrees C. Many of these temperature response curves were similar in nature to curves reported for purified enzyme systems and pure cultures of bacteria. Comparisons of the apparent energies of activation calculated for different temperature ranges over time also indicated that the overall community was better adapted to higher temperatures during the latter part of the composting run. It was also found that the relationship between the apparent energies of activation and the apparent energies of inactivation (apparent heats of denaturation) consistently changed with sample temperature throughout the composting run, suggesting that the microbial communities from hotter samples were better adapted to high temperatures than those from cooler samples, and vice versa.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:6146292

  3. Primary succession of soil enzyme activity and heterotrophic microbial communities along the chronosequence of Tianshan Mountains No. 1 Glacier, China.

    PubMed

    Zeng, Jun; Wang, Xiao-Xia; Lou, Kai; Eusufzai, Moniruzzaman Khan; Zhang, Tao; Lin, Qing; Shi, Ying-Wu; Yang, Hong-Mei; Li, Zhong-Qing

    2015-02-01

    We investigated the primary successions of soil enzyme activity and heterotrophic microbial communities at the forefields of the Tianshan Mountains No. 1 Glacier by investigating soil microbial processes (microbial biomass and nitrogen mineralization), enzyme activity and community-level physiological profiling. Soils deglaciated between 1959 and 2008 (0, 5, 17, 31 and 44 years) were collected. Soils >1,500 years in age were used as a reference (alpine meadow soils). Soil enzyme activity and carbon-source utilization ability significantly increased with successional time. Amino-acid utilization rates were relatively higher in early, unvegetated soils (0 and 5 years), but carbohydrate utilization was higher in later stages (from 31 years to the reference soil). Discriminant analysis, including data on microbial processes and soil enzyme activities, revealed that newly exposed soils (0-5 years) and older soils (17-44 years) were well-separated from each other and obviously different from the reference soil. Correlation analysis revealed that soil organic carbon, was the primary factor influencing soil enzyme activity and heterotrophic microbial community succession. Redundancy analysis suggested that soil pH and available P were also affect microbial activity to a considerable degree. Our results indicated that glacier foreland soils have continued to develop over 44 years and soils were significantly affected by the geographic location of the glacier and the local topography. Soil enzyme activities and heterotrophic microbial communities were also significantly influenced by these variables. PMID:25472706

  4. Effects of Soil Organic Matter Properties and Microbial Community Composition on Enzyme Activities in Cryoturbated Arctic Soils

    PubMed Central

    Schnecker, Jörg; Wild, Birgit; Hofhansl, Florian; Eloy Alves, Ricardo J.; Bárta, Jiří; Čapek, Petr; Fuchslueger, Lucia; Gentsch, Norman; Gittel, Antje; Guggenberger, Georg; Hofer, Angelika; Kienzl, Sandra; Knoltsch, Anna; Lashchinskiy, Nikolay; Mikutta, Robert; Šantrůčková, Hana; Shibistova, Olga; Takriti, Mounir; Urich, Tim; Weltin, Georg; Richter, Andreas

    2014-01-01

    Enzyme-mediated decomposition of soil organic matter (SOM) is controlled, amongst other factors, by organic matter properties and by the microbial decomposer community present. Since microbial community composition and SOM properties are often interrelated and both change with soil depth, the drivers of enzymatic decomposition are hard to dissect. We investigated soils from three regions in the Siberian Arctic, where carbon rich topsoil material has been incorporated into the subsoil (cryoturbation). We took advantage of this subduction to test if SOM properties shape microbial community composition, and to identify controls of both on enzyme activities. We found that microbial community composition (estimated by phospholipid fatty acid analysis), was similar in cryoturbated material and in surrounding subsoil, although carbon and nitrogen contents were similar in cryoturbated material and topsoils. This suggests that the microbial community in cryoturbated material was not well adapted to SOM properties. We also measured three potential enzyme activities (cellobiohydrolase, leucine-amino-peptidase and phenoloxidase) and used structural equation models (SEMs) to identify direct and indirect drivers of the three enzyme activities. The models included microbial community composition, carbon and nitrogen contents, clay content, water content, and pH. Models for regular horizons, excluding cryoturbated material, showed that all enzyme activities were mainly controlled by carbon or nitrogen. Microbial community composition had no effect. In contrast, models for cryoturbated material showed that enzyme activities were also related to microbial community composition. The additional control of microbial community composition could have restrained enzyme activities and furthermore decomposition in general. The functional decoupling of SOM properties and microbial community composition might thus be one of the reasons for low decomposition rates and the persistence of 400 Gt

  5. Metagenomic analysis of a high carbon dioxide subsurface microbial community populated by chemolithoautotrophs and bacteria and archaea from candidate phyla.

    PubMed

    Emerson, Joanne B; Thomas, Brian C; Alvarez, Walter; Banfield, Jillian F

    2016-06-01

    Research on geologic carbon sequestration raises questions about potential impacts of subsurface microbiota on carbon cycling and biogeochemistry. Subsurface, high-CO2 systems are poorly biologically characterized, partly because of difficulty accessing high-volume, uncontaminated samples. CO2 -driven Crystal Geyser (CG, Utah, USA), an established geologic carbon sequestration analogue, provides high volumes of deep (∼ 200-500 m) subsurface fluids. We explored microbial diversity and metabolic potential in this high-CO2 environment by assembly and analysis of metagenomes recovered from geyser water filtrate. The system is dominated by neutrophilic, iron-oxidizing bacteria, including 'marine' Mariprofundus (Zetaproteobacteria) and 'freshwater' Gallionellales, sulfur-oxidizing Thiomicrospira crunogena and Thiobacillus-like Hydrogenophilales. Near-complete genomes were reconstructed for these bacteria. CG is notably populated by a wide diversity of bacteria and archaea from phyla lacking isolated representatives (candidate phyla) and from as-yet undefined lineages. Many bacteria affiliate with OD1, OP3, OP9, PER, ACD58, WWE3, BD1-5, OP11, TM7 and ZB2. The recovery of nearly 100 genes encoding ribulose-1,5 bisphosphate carboxylase-oxygenase subunit proteins of the Calvin cycle and AMP salvage pathways suggests a strong biological role in high-CO2 subsurface carbon cycling. Overall, we predict microbial impacts on subsurface biogeochemistry via iron, sulfur, and complex carbon oxidation, carbon and nitrogen fixation, fermentation, hydrogen metabolism, and aerobic and anaerobic respiration. PMID:25727367

  6. Detailed Analysis of the Microbial Population in Malaysian Spontaneous Cocoa Pulp Fermentations Reveals a Core and Variable Microbiota

    PubMed Central

    Mathawan, Melissa; Wittocx, Pieter-Jan; Saels, Veerle; Struyf, Nore; Bernaert, Herwig; Vrancken, Gino; Verstrepen, Kevin J.

    2013-01-01

    The fermentation of cocoa pulp is one of the few remaining large-scale spontaneous microbial processes in today's food industry. The microbiota involved in cocoa pulp fermentations is complex and variable, which leads to inconsistent production efficiency and cocoa quality. Despite intensive research in the field, a detailed and comprehensive analysis of the microbiota is still lacking, especially for the expanding Asian production region. Here, we report a large-scale, comprehensive analysis of four spontaneous Malaysian cocoa pulp fermentations across two time points in the harvest season and two fermentation methods. Our results show that the cocoa microbiota consists of a “core” and a “variable” part. The bacterial populations show a remarkable consistency, with only two dominant species, Lactobacillus fermentum and Acetobacter pasteurianus. The fungal diversity is much larger, with four dominant species occurring in all fermentations (“core” yeasts), and a large number of yeasts that only occur in lower numbers and specific fermentations (“variable” yeasts). Despite this diversity, a clear pattern emerges, with early dominance of apiculate yeasts and late dominance of Saccharomyces cerevisiae. Our results provide new insights into the microbial diversity in Malaysian cocoa pulp fermentations and pave the way for the selection of starter cultures to increase efficiency and consistency. PMID:24358116

  7. Milk kefir: composition, microbial cultures, biological activities, and related products

    PubMed Central

    Prado, Maria R.; Blandón, Lina Marcela; Vandenberghe, Luciana P. S.; Rodrigues, Cristine; Castro, Guillermo R.; Thomaz-Soccol, Vanete; Soccol, Carlos R.

    2015-01-01

    In recent years, there has been a strong focus on beneficial foods with probiotic microorganisms and functional organic substances. In this context, there is an increasing interest in the commercial use of kefir, since it can be marketed as a natural beverage that has health promoting bacteria. There are numerous commercially available kefir based-products. Kefir may act as a matrix in the effective delivery of probiotic microorganisms in different types of products. Also, the presence of kefir’s exopolysaccharides, known as kefiran, which has biological activity, certainly adds value to products. Kefiran can also be used separately in other food products and as a coating film for various food and pharmaceutical products. This article aims to update the information about kefir and its microbiological composition, biological activity of the kefir’s microflora and the importance of kefiran as a beneficial health substance. PMID:26579086

  8. Population Activities Fund Agency (PAFA): the journey so far.

    PubMed

    1993-01-01

    Mechanisms are needed funding Nigerian Federal efforts to implement the National Policy on Population for Development, which was approved by the Armed Forces Ruling Council in February, 1988. Subprojects of the Population Activities Fund Agency (PAFA) which were approves are: the integration of family planning (FP) into maternal and child health (MCH) the promotion of Fp through health education, tertiary centers for reproductive health, public enlightenment on population, population/family life education in primary schools, monitoring of National Population Project impact, and integration of population into planning and budgeting. The last obstacle to implementation of PAFA's activities is the signing into law the decree establishing PAFA as a parastatal. The passage is required for continued operations. The national Population for Development policy is unique in providing for quantitative targets, which has attracted the needed financial support of agencies such as the World Bank. As part of the National Population Policy, the National Population Program (NPP) is developing an effective strategy for securing funding and evaluation of subprojects that are designed and implemented b Collaborating Agencies (CAs), both private and public. NPP aims 1) to provide funds for qualified CAs through the Population Activities Fund (PAF) and Agency (PAFA); 2) to monitor PAFA, which manages PAf with the Department of Population Activities, and 3) to stimulate analysis of sociocultural constraints to fertility reduction and international comparisons, and to design innovative interventions through the Population Research Fund (PRF). PAFA funds implementing agencies at all government and nongovernment levels with approaches to population information and services. The goal of PAFA is to realize NPP objectives. The motto is "Towards an improved quality of life for every Nigerian." The mandate is to provide funding for the PAF and NPP, to monitor CAs, to provide assistance to CAs

  9. Brain Microbial Populations in HIV/AIDS: α-Proteobacteria Predominate Independent of Host Immune Status

    PubMed Central

    Branton, William G.; Ellestad, Kristofor K.; Maingat, Ferdinand; Wheatley, B. Matt; Rud, Erling; Warren, René L.; Holt, Robert A.; Surette, Michael G.; Power, Christopher

    2013-01-01

    The brain is assumed to be a sterile organ in the absence of disease although the impact of immune disruption is uncertain in terms of brain microbial diversity or quantity. To investigate microbial diversity and quantity in the brain, the profile of infectious agents was examined in pathologically normal and abnormal brains from persons with HIV/AIDS [HIV] (n = 12), other disease controls [ODC] (n = 14) and in cerebral surgical resections for epilepsy [SURG] (n = 6). Deep sequencing of cerebral white matter-derived RNA from the HIV (n = 4) and ODC (n = 4) patients and SURG (n = 2) groups revealed bacterially-encoded 16 s RNA sequences in all brain specimens with α-proteobacteria representing over 70% of bacterial sequences while the other 30% of bacterial classes varied widely. Bacterial rRNA was detected in white matter glial cells by in situ hybridization and peptidoglycan immunoreactivity was also localized principally in glia in human brains. Analyses of amplified bacterial 16 s rRNA sequences disclosed that Proteobacteria was the principal bacterial phylum in all human brain samples with similar bacterial rRNA quantities in HIV and ODC groups despite increased host neuroimmune responses in the HIV group. Exogenous viruses including bacteriophage and human herpes viruses-4, -5 and -6 were detected variably in autopsied brains from both clinical groups. Brains from SIV- and SHIV-infected macaques displayed a profile of bacterial phyla also dominated by Proteobacteria but bacterial sequences were not detected in experimentally FIV-infected cat or RAG1−/− mouse brains. Intracerebral implantation of human brain homogenates into RAG1−/− mice revealed a preponderance of α-proteobacteria 16 s RNA sequences in the brains of recipient mice at 7 weeks post-implantation, which was abrogated by prior heat-treatment of the brain homogenate. Thus, α-proteobacteria represented the major bacterial component of the primate brain

  10. Microbial Activity in Active and Upper Permafrost Layers in Axel Heiberg Island

    NASA Astrophysics Data System (ADS)

    Vishnivetskaya, T. A.; Allan, J.; Cheng, K.; Chourey, K.; Hettich, R. L.; Layton, A.; Liu, X.; Murphy, J.; Mykytczuk, N. C.; Phelps, T. J.; Pfiffner, S. M.; Saarunya, G.; Stackhouse, B. T.; Whyte, L.; Onstott, T. C.

    2011-12-01

    Data on microbial communities and their metabolic activity in Arctic wetlands and underlying permafrost sediments is lacking. Samples were collected from different depths of a cryosol (D1, D2) and upper permafrost (D3) at the Axel Heiberg Island in July 2009. Upper cryosol has lower H2O but higher C and N content when compared to deeper horizons including upper permafrost layer. Deep cryosol and upper permafrost contained SO42- (155 and 132 ppm) and NO3- (0.12 and 0.10 ppm), respectively. The phylogenetic analyses of the environmental 16S rRNA genes showed the putative SRB were more abundant in permafrost (8%) than in cryosols, D1 (0.2%) and D2 (1.1%). Putative denitrifying bacteria varied along depth with near 0.1% in D1 and a significant increase in D2 (2.7%) and D3 (2.2%). Methanogens were not detected; methanotrophs were present at low levels in D3 (1%). Two sets of microcosms were set up. Firstly, anaerobic microcosms, amended with 10 mM glucose, sulfate or nitrate, were cultivated at varying temperatures (15o, 6o, and 0o C) for 10 months. Metabolic activity was monitored by measuring CO2 and CH4 every 3 months. A total of 89.5% of the D3-originated microcosms showed higher activity in comparison to cryosols in first 3 months. CH4 was not detected in these microcosms, whereas CO2 production was higher at 15o C or with glucose. Metaproteomics analyses of microcosms with higher levels of CO2 production indicated the presence of