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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. Evaluating digestion efficiency in full-scale anaerobic digesters by identifying active microbial populations through the lens of microbial activity

    NASA Astrophysics Data System (ADS)

    Mei, Ran; Narihiro, Takashi; Nobu, Masaru K.; Kuroda, Kyohei; Liu, Wen-Tso

    2016-09-01

    Anaerobic digestion is a common technology to biologically stabilize wasted solids produced in municipal wastewater treatment. Its efficiency is usually evaluated by calculating the reduction in volatile solids, which assumes no biomass growth associated with digestion. To determine whether this assumption is valid and further evaluate digestion efficiency, this study sampled 35 digester sludge from different reactors at multiple time points together with the feed biomass in a full-scale water reclamation plant at Chicago, Illinois. The microbial communities were characterized using Illumina sequencing technology based on 16S rRNA and 16S rRNA gene (rDNA). 74 core microbial populations were identified and represented 58.7% of the entire digester community. Among them, active populations were first identified using the ratio of 16S rRNA and 16S rDNA (rRNA/rDNA) for individual populations, but this approach failed to generate consistent results. Subsequently, a recently proposed mass balance model was applied to calculate the specific growth rate (μ), and this approach successfully identified active microbial populations in digester (positive μ) that could play important roles than those with negative μ. It was further estimated that 82% of microbial populations in the feed sludge were digested in comparison with less than 50% calculated using current equations.

  3. Evaluating digestion efficiency in full-scale anaerobic digesters by identifying active microbial populations through the lens of microbial activity

    PubMed Central

    Mei, Ran; Narihiro, Takashi; Nobu, Masaru K.; Kuroda, Kyohei; Liu, Wen-Tso

    2016-01-01

    Anaerobic digestion is a common technology to biologically stabilize wasted solids produced in municipal wastewater treatment. Its efficiency is usually evaluated by calculating the reduction in volatile solids, which assumes no biomass growth associated with digestion. To determine whether this assumption is valid and further evaluate digestion efficiency, this study sampled 35 digester sludge from different reactors at multiple time points together with the feed biomass in a full-scale water reclamation plant at Chicago, Illinois. The microbial communities were characterized using Illumina sequencing technology based on 16S rRNA and 16S rRNA gene (rDNA). 74 core microbial populations were identified and represented 58.7% of the entire digester community. Among them, active populations were first identified using the ratio of 16S rRNA and 16S rDNA (rRNA/rDNA) for individual populations, but this approach failed to generate consistent results. Subsequently, a recently proposed mass balance model was applied to calculate the specific growth rate (μ), and this approach successfully identified active microbial populations in digester (positive μ) that could play important roles than those with negative μ. It was further estimated that 82% of microbial populations in the feed sludge were digested in comparison with less than 50% calculated using current equations. PMID:27666090

  4. Influence of combined pollution of antimony and arsenic on culturable soil microbial populations and enzyme activities.

    PubMed

    Wang, Qiongshan; He, Mengchang; Wang, Ying

    2011-01-01

    The effects of both combined and single pollution of antimony (Sb) and arsenic (As) in different concentrations on culturable soil microbial populations and enzyme activities were studied under laboratory conditions. Joint effects of both Sb and As were different from that of Sb or As alone. The inhibition rate of culturable soil microbial populations under Sb and As pollution followed the order: bacterial > fungi > actinomycetes. There existed antagonistic inhibiting effect on urease and acid phophatase and synergistic inhibiting effect on protease under the combined pollution of Sb (III) and As (III). Only urease appeared to be the most sensitive indicator under Sb (V) and As (V) pollution, and there existed antagonistic inhibiting effect on acid phophatase and synergistic inhibiting effect on urease and protease under Sb (V) and As (V) combined pollution at most time. In this study, we also confirmed that the trivalent states of Sb and As were more toxic to all the microbes tested and more inhibitory on microbial enzyme activities then their pentavalent counterparts. The results also suggest that not only the application rate of the two metalloids but also the chemical form of metalloids should be considered while assessing the effect of metalloid on culturable microbial populations and enzyme activities. Urease and acid phosphatase can be used as potential biomarkers to evaluate the intensity of Sb (III) and As (III) stress.

  5. 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.

  6. 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

  7. Prokaryotic diversity and metabolically active microbial populations in sediments from an active mud volcano in the Gulf of Mexico.

    PubMed

    Martinez, Robert J; Mills, Heath J; Story, Sandra; Sobecky, Patricia A

    2006-10-01

    In this study, ribosomes and genomic DNA were extracted from three sediment depths (0-2, 6-8 and 10-12 cm) to determine the vertical changes in the microbial community composition and identify metabolically active microbial populations in sediments obtained from an active seafloor mud volcano site in the northern Gulf of Mexico. Domain-specific Bacteria and Archaea 16S polymerase chain reaction primers were used to amplify 16S rDNA gene sequences from extracted DNA. Complementary 16S ribosomal DNA (crDNA) was obtained from rRNA extracted from each sediment depth that had been subjected to reverse transcription polymerase chain reaction amplification. Twelve different 16S clone libraries, representing the three sediment depths, were constructed and a total of 154 rDNA (DNA-derived) and 142 crDNA (RNA-derived) Bacteria clones and 134 rDNA and 146 crDNA Archaea clones obtained. Analyses of the 576 clones revealed distinct differences in the composition and patterns of metabolically active microbial phylotypes relative to sediment depth. For example, epsilon-Proteobacteria rDNA clones dominated the 0-2 cm clone library whereas gamma-Proteobacteria dominated the 0-2 cm crDNA library suggesting gamma to be among the most active in situ populations detected at 0-2 cm. Some microbial lineages, although detected at a frequency as high as 9% or greater in the total DNA library (i.e. Actinobacteria, alpha-Proteobacteria), were markedly absent from the RNA-derived libraries suggesting a lack of in situ activity at any depth in the mud volcano sediments. This study is one of the first to report the composition of the microbial assemblages and physiologically active members of archaeal and bacterial populations extant in a Gulf of Mexico submarine mud volcano. PMID:16958759

  8. 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

  9. 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

  10. 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

  11. Effects of butachlor on microbial populations and enzyme activities in paddy soil.

    PubMed

    Min, H; Ye, Y F; Chen, Z Y; Wu, W X; Yufeng, D

    2001-09-01

    This paper reports the influences of the herbicide butachlor (n-butoxymethlchloro -2', 6'-diethylacetnilide) on microbial populations, respiration, nitrogen fixation and nitrification, and on the activities of dehydrogenase and hydrogen peroxidase in paddy soil. The results showed that the number of actinomycetes declined significantly after the application of butachlor at different concentrations ranging from 5.5 microg g(-1) to 22.0 microg g(-1) dried soil, while that of bacteria and fungi increased. Fungi were easily affected by butachlor compared to the bacteria. The growth of fungi was retarded by butachlor at higher concentrations. Butachlor however, stimulated the growth of anaerobic hydrolytic fermentative bacteria, sulfate-reducing bacteria (SRB) and denitrifying bacteria. The increased concentration of butachlor applied resulted in the higher number of SRB. Butachlor inhibited the growth of hydrogen-producing acetogenic bacteria. The effect of butachlor varied on methane-producing bacteria (MPB) at different concentrations. Butachlor at the concentration of 1.0 microg g(-1) dried soil or less than this concentration accelerated the growth of MPB, while at 22.0 microg g(-1) dried soil showed an inhibition. Butachlor enhanced the activity of dehydrogenase at increasing concentrations. The soil dehydrogenase showed the highest activity on the 16th day after application of 22.0 microg g(-1) dried soil of butachlor. The hydrogen peroxidase could be stimulated by butachlor. The soil respiration was depressed during the period from several days to more than 20 days, depending on concentrations of butachlor applied. Both the nitrogen fixation and nitrification were stimulated in the beginning but reduced greatly afterwards in paddy soil.

  12. Microbial populations in contaminant plumes

    USGS Publications Warehouse

    Haack, S.K.; Bekins, B.A.

    2000-01-01

    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.

  13. Effects of fomesafen on soil enzyme activity, microbial population, and bacterial community composition.

    PubMed

    Zhang, Qingming; Zhu, Lusheng; Wang, Jun; Xie, Hui; Wang, Jinhua; Wang, Fenghua; Sun, Fengxia

    2014-05-01

    Fomesafen is a diphenyl ether herbicide that has an important role in the removal of broadleaf weeds in bean and fruit tree fields. However, very little information is known about the effects of this herbicide on soil microbial community structure and activities. In the present study, laboratory experiments were conducted to examine the effects of different concentrations of fomesafen (0, 10, 100, and 500 μg/kg) on microbial community structure and activities during an exposure period of 60 days, using soil enzyme assays, plate counting, and denaturing gradient gel electrophoresis (DGGE). The results of enzymatic activity experiments showed that fomesafen had different stimulating effects on the activities of acid phosphatase, alkaline phosphatase, and dehydrogenase, with dehydrogenase being most sensitive to fomesafen. On the tenth day, urease activity was inhibited significantly after treatment of different concentrations of fomesafen; this inhibiting effect then gradually disappeared and returned to the control level after 30 days. Plate counting experiments indicated that the number of bacteria and actinomycetes increased in fomesafen-spiked soil relative to the control after 30 days of incubation, while fungal number decreased significantly after only 10 days. The DGGE results revealed that the bacterial community varied in response to the addition of fomesafen, and the intensity of these six bands was greater on day 10. Sequencing and phylogenetic analyses indicated that the six excised DGGE bands were closely related to Emticicia, Bacillus, and uncultured bacteria. After 10 days, the bacterial community exhibited no obvious change compared with the control. Throughout the experiment, we concluded that 0-500 μg/kg of fomesafen could not produce significant toxic effects on soil microbial community structure and activities.

  14. Effect of untreated sewage effluent irrigation on heavy metal content, microbial population and enzymatic activities of soils in Aligarh.

    PubMed

    Bansal, O P; Singh, Gajraj; Katiyar, Pragati

    2014-07-01

    The study pertains to the impact of domestic and industrial sewage water irrigation on the chemical, biological and enzymatic activities in alluvial soils of Aligarh District. Results showed that soil enzymatic [dehydogenase (DHA), acid and alkaline phosphatase, urease and catalase] activities in the soils increased up to 14 days of incubation and thereafter inhibited significantly. The enzymatic activity were in the order sewage effluent > partial sewage effluent > ground water irrigated soils. Increase in soil enzymatic activities up to 2nd week of incubation was due to decomposition of organic matter. Maximum inhibition of enzymatic activities, after 14 days of incubation were found in sewage effluent irrigated soils and minimum in ground water irrigated soils. Similar trend was also seen for microbial population. Soil enzymatic activities and microbial population were significantly and positively correlated with soil organic matter. Results also indicated that the microbial population and enzymatic activities in sewage irrigated soils decreased continually with irrigation period. The average concentration of total heavy metals in sewage irrigated soils and partial sewage irrigated soils increased and was 3 and 2 times higher for Zn; 4.5 and 1.7 times higher for Cu; 3.8 and 2.4 times higher for Cr; 5.7 and 3.5 times higher for Pb; 3.5 and 2.2 times higher for Cd and 2.7 and 2.0 times higher for Ni respectively than that of ground water irrigated soils. Results also showed that though total heavy metals concentration increased with period of sewage irrigation but the concentration of diethylene triamine pentaacetic acid (DTPA) extractable heavy metals in partial sewage irrigated and sewage irrigated soils remained almost same, which might be due to deposition of heavy metals in crops grown on the soils.

  15. Metaproteomic survey of six aquatic habitats: discovering the identities of microbial populations active in biogeochemical cycling.

    PubMed

    Hanson, Buck T; Hewson, Ian; Madsen, Eugene L

    2014-04-01

    Our goal is to strengthen the foundations of metaproteomics as a microbial community analysis tool that links the functional identity of actively expressed gene products with host phylogeny. We used shotgun metaproteomics to survey waters in six disparate aquatic habitats (Cayuga Lake, NY; Oneida Lake, NY; Gulf of Maine; Chesapeake Bay, MD; Gulf of Mexico; and the South Pacific). Peptide pools prepared from filter-gathered microbial biomass, analyzed by nano-liquid chromatography-mass spectrometry (MS/MS) generating 9,693 ± 1,073 mass spectra identified 326 ± 107 bacterial proteins per sample. Distribution of proteobacterial (Alpha and Beta) and cyanobacterial (Prochlorococcus and Synechococcus spp.) protein hosts across all six samples was consistent with the previously published biogeography for these microorganisms. Marine samples were enriched in transport proteins (TRAP-type for dicarboxylates and ATP binding cassette (ABC)-type for amino acids and carbohydrates) compared with the freshwater samples. We were able to match in situ expression of many key proteins catalyzing C-, N-, and S-cycle processes with their bacterial hosts across all six habitats. Pelagibacter was identified as the host of ABC-type sugar-, organic polyanion-, and glycine betaine-transport proteins; this extends previously published studies of Pelagibacter's in situ biogeochemical role in marine C- and N-metabolism. Proteins matched to Ruegeria confirmed these organism's role in marine waters oxidizing both carbon monoxide and sulfide. By documenting both processes expressed in situ and the identity of host cells, metaproteomics tested several existing hypotheses about ecophysiological processes and provided fodder for new ones. PMID:24425229

  16. [Effects of bio-mulching on rhizosphere soil microbial population, enzyme activity and tree growth in poplar plantation].

    PubMed

    Liu, Jiu-Jun; Fang, Sheng-Zuo; Xie, Bao-Dong; Hao, Juan-Juan

    2008-06-01

    Coriaria nepalensis, Pteridium aquilinum var. latiuscukum, Imperata cylindrical var. major, and Quercus fabric were used as mulching materials to study their effects on the rhizosphere soil microbial population and enzyme activity and the tree growth in poplar plantation. The results showed that after mulching with test materials, the populations of both bacteria and fungi in rhizosphere soil were more than those of the control. Of the mulching materials, I. cylindrical and Q. fabric had the best effect, with the numbers of bacteria and fungi being 23.56 and 1.43 times higher than the control, respectively. The bacterial and fungal populations in rhizosphere soil increased with increasing mulching amount. When the mulching amount was 7.5 kg m(-2), the numbers of bacteria and fungi in rhizosphere soil were 0.5 and 5.14 times higher than the control, respectively. Under bio-mulching, the bacterial and fungal populations in rhizosphere soil had a similar annual variation trend, which was accorded with the annual fluctuation of soil temperature and got to the maximum in July and the minimum in December. The urease and phosphatase activities in rhizosphere soil also increased with increasing mulching amount. As for the effects of different mulching materials on the enzyme activities, they were in the order of C. nepalensis > P. aquilinum > I. cylindrical > Q. fabric. The annual variation of urease and phosphatase activities in rhizosphere soil was similar to that of bacterial and fungal populations, being the highest in July and the lowest in December. Bio-mulching promoted the tree height, DBH, and biomass of poplar trees significantly.

  17. 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

  18. 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.

  19. Microbial diversity--insights from population genetics.

    PubMed

    Mes, Ted H M

    2008-01-01

    Although many environmental microbial populations are large and genetically diverse, both the level of diversity and the extent to which it is ecologically relevant remain enigmatic. Because the effective (or long-term) population size, N(e), is one of the parameters that determines population genetic diversity, tests and simulations that assume selectively neutral mutations may help to identify the processes that have shaped microbial diversity. Using ecologically important genes, tests of selective neutrality suggest that adaptive as well as non-adaptive types of selection act and that departure from neutrality may be widespread or restricted to small groups of genotypes. Population genetic simulations using population sizes between 10(3) and 10(7) suggest extremely high levels of microbial diversity in environments that sustain large populations. However, census and effective population sizes may differ considerably, and because we know nothing of the evolutionary history of environmental microbial populations, we also have no idea what N(e) of environmental populations is. On the one hand, this reflects our ignorance of the microbial world. On the other hand, the tests and simulations illustrate interactions between microbial diversity and microbial population genetics that should inform our thinking in microbial ecology. Because of the different views on microbial diversity across these disciplines, such interactions are crucial if we are to understand the role of genes in microbial communities.

  20. 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

  1. Microbial populations and decomposition activity in three subsurface flow constructed wetlands

    SciTech Connect

    Hatano, K.; Trettin, C.C.; House, C.H.; Wollum, A.G. II

    1991-12-31

    Metabolic activity of microorganisms is the primary mechanism for organic matter degradation in constructed wetlands. However, the occurrence and abundance of different types of microorganisms responsible for degradation reactions has not been widely studied. The objective of this paper is to characterize the distribution and abundance of microorganisms in three constructed wetlands and evaluate their potent decomposition activity.

  2. Microbial populations and decomposition activity in three subsurface flow constructed wetlands

    SciTech Connect

    Hatano, K.; Trettin, C.C.; House, C.H.; Wollum, A.G. II )

    1991-01-01

    Metabolic activity of microorganisms is the primary mechanism for organic matter degradation in constructed wetlands. However, the occurrence and abundance of different types of microorganisms responsible for degradation reactions has not been widely studied. The objective of this paper is to characterize the distribution and abundance of microorganisms in three constructed wetlands and evaluate their potent decomposition activity.

  3. 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.

  4. Microbial activity in weathering columns.

    PubMed

    García, C; Ballester, A; González, F; Blázquez, M L

    2007-03-22

    The aim of the present work was to evaluate the metabolic activity of the microbial population associated with a pyritic tailing after a column-weathering test. For this purpose, a column 150cm high and 15cm diameter was used. The solid was a tailing with 63.4% pyrite and with minor amounts of Cu, Pb and Zn sulfides (1.4, 0.5 and 0.8%, respectively). The column model was the habitual one for weathering tests: distilled water was added at the top of the column; the water flowed down through tailings and finally was collected at the bottom for chemical and microbiological analysis. Weathering was maintained for 36 weeks. The results showed a significant presence of microbial life that was distributed selectively over the column: sulfur- and iron-oxidizing aerobic bacteria were in the more oxygenated zone; anaerobic sulfur-reducing bacteria were isolated from the samples taken from the anoxic part of the column. Activity testing showed that (oxidizing and reducing) bacteria populations were active at the end of the weathering test. The quality of the water draining from the column was thus the final product of biological oxidation and reduction promoted by the bacteria consortia.

  5. Undecompressed microbial populations from the deep sea.

    PubMed Central

    Jannasch, H J; Wirsen, C O; Taylor, C D

    1976-01-01

    Metabolic transformations of glutamate and Casamino Acids by natural microbial populations collected from deep waters (1,600 to 3,100 m) were studied in decompressed and undecompressed samples. Pressure-retaining sampling/incubation vessels and appropriate subsampling/incubation vessels and appropriate subsampling techniques permitted time course experiments. In all cases the metabolic activity in undecompressed samples was lower than it was when incubated at 1 atm. Surface water controls showed a reduced activity upon compression. The processes involving substrate incorporation into cell material were more pressure sensitive than was respiration. The low utilization of substrates, previously found by in situ incubations for up to 12 months, was confirmed and demonstrated to consist of an initial phase of activity, in the range of 5 to 60 times lower than the controls, followed by a stationary phase of virtually no substrate utilization. No barophilic growth response (higher rates at elevated pressure than at 1 atm) was recorded; all populations observed exhibition various degrees of barotolerance. Images PMID:791117

  6. 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...

  7. Impact of fungicide mancozeb at different application rates on soil microbial populations, soil biological processes, and enzyme activities in soil.

    PubMed

    Walia, Abhishek; 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

  8. 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

  9. Septic tank additive impacts on microbial populations.

    PubMed

    Pradhan, S; Hoover, M T; Clark, G H; Gumpertz, M; Wollum, A G; Cobb, C; Strock, J

    2008-01-01

    Environmental health specialists, other onsite wastewater professionals, scientists, and homeowners have questioned the effectiveness of septic tank additives. This paper describes an independent, third-party, field scale, research study of the effects of three liquid bacterial septic tank additives and a control (no additive) on septic tank microbial populations. Microbial populations were measured quarterly in a field study for 12 months in 48 full-size, functioning septic tanks. Bacterial populations in the 48 septic tanks were statistically analyzed with a mixed linear model. Additive effects were assessed for three septic tank maintenance levels (low, intermediate, and high). Dunnett's t-test for tank bacteria (alpha = .05) indicated that none of the treatments were significantly different, overall, from the control at the statistical level tested. In addition, the additives had no significant effects on septic tank bacterial populations at any of the septic tank maintenance levels. Additional controlled, field-based research iswarranted, however, to address additional additives and experimental conditions.

  10. 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.

  11. 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

  12. 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

  13. Microbial activity in soils following steam treatment.

    PubMed

    Richardson, Ruth E; James, C Andrew; Bhupathiraju, Vishvesh K; Alvarez-Cohen, Lisa

    2002-01-01

    Steam enhanced extraction (SEE) is an aquifer remediation technique that can be effective at removing the bulk of non-aqueous phase liquid (NAPL) contamination from the subsurface, particularly highly volatile contaminants. However, low volatility compounds such as polynuclear aromatic hydrocarbons (PAHs) are less efficiently removed by this process. This research evaluated the effects of steam injection on soil microbial activity, community structure, and the potential for biodegradation of contaminants following steam treatment. Three different soils were evaluated: a laboratory-prepared microbially-enriched soil, soil from a creosote contaminated field site, and soil from a chlorinated solvent and waste oil contaminated field site. Results from field-scale steaming are also presented. Microbial activity before and after steam treatment was evaluated using direct epifluorescent microscopy (DEM) using the respiratory activity dye 5-cyano-2,3, ditolyl tetrazolium chloride (CTC) in conjunction with the fluorochrome 5-(4,6-dichlorotriazinyl) aminofluorescein (DTAF) to yield a quantitative assessment of active and total microbial numbers. DEM results indicate that steamed soils that were analyzed while still hot exhibited microbial activity levels that were below detection. However, soil samples that were slowly cooled, more closely reflecting the conditions of applied SEE, exhibited microbial activity levels that were comparable to presteamed soils. Samples from a field-site where steam was applied continuously for 6 weeks also showed high levels of microbial activity following cooling. The metabolic capabilities of the steamed communities were investigated by measuring cell growth in enrichment cultures on various substrates. These studies provided evidence that organisms capable of biodegradation were among the mesophilic populations that survived steam treatment. Fluorescent in situ hybridization (FISH) analysis of the soils with domain-level rRNA probes suggest

  14. The influence of mineral fertilizer combined with a nitrification inhibitor on microbial populations and activities in calcareous Uzbekistanian soil under cotton cultivation.

    PubMed

    Egamberdiyeva, D; Mamiev, M; Poberejskaya, S K

    2001-10-30

    Application of fertilizers combined with nitrification inhibitors affects soil microbial biomass and activity. The objective of this research was to determine the effects of fertilizer application combined with the nitrification inhibitor potassium oxalate (PO) on soil microbial population and activities in nitrogen-poor soil under cotton cultivation in Uzbekistan. Fertilizer treatments were N as urea, P as ammophos, and K as potassium chloride. The nitrification inhibitor PO was added to urea and ammophos at the rate of 2%. Three treatments--N200 P140 K60 (T1), N200 PO P140 K60 (T2), and N200 P140 PO K60 (T3) mg kg(-1) soil--were applied for this study. The control (C) was without fertilizer and PO. The populations of oligotrophic bacteria, ammonifying bacteria, nitrifying bacteria, denitrifying bacteria, mineral assimilating bacteria, oligonitrophilic bacteria, and bacteria group Azotobacter were determined by the most probable number method. The treatments T2 and T3 increased the number of oligonitrophilic bacteria and utilization mineral forms of nitrogen on the background of reducing number of ammonifying bacteria. T2 and T3 also decreased the number of nitrifying bacteria, denitrifying bacteria, and net nitrification. In conclusion, our experiments showed that PO combined with mineral fertilizer is one of the most promising compounds for inhibiting nitrification rate, which was reflected in the increased availability and efficiency of fertilizer nitrogen to the cotton plants. PO combined with mineral fertilizer has no negative effects on nitrogen-fixing bacteria Azotobacter and oligo-nitrophilic bacteria.

  15. Minimal models of growth and decline of microbial populations.

    PubMed

    Juška, Alfonsas

    2011-01-21

    Dynamics of growth and decline of microbial populations were analysed and respective models were developed in this investigation. Analysis of the dynamics was based on general considerations concerning the main properties of microorganisms and their interactions with the environment which was supposed to be affected by the activity of the population. Those considerations were expressed mathematically by differential equations or systems of the equations containing minimal sets of parameters characterizing those properties. It has been found that: (1) the factors leading to the decline of the population have to be considered separately, namely, accumulation of metabolites (toxins) in the medium and the exhaustion of resources; the latter have to be separated again into renewable ('building materials') and non-renewable (sources of energy); (2) decline of the population is caused by the exhaustion of sources of energy but no decline is predicted by the model because of the exhaustion of renewable resources; (3) the model determined by the accumulation of metabolites (toxins) in the medium does not suggest the existence of a separate 'stationary phase'; (4) in the model determined by the exhaustion of energy resources the 'stationary' and 'decline' phases are quite discernible; and (5) there is no symmetry in microbial population dynamics, the decline being slower than the rise. Mathematical models are expected to be useful in getting insight into the process of control of the dynamics of microbial populations. The models are in agreement with the experimental data. PMID:21036180

  16. CRISPR-induced distributed immunity in microbial populations.

    PubMed

    Childs, Lauren M; England, Whitney E; 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.

  17. 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

  18. 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

  19. 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.

  20. Effect of the tropical grass Brachiaria brizantha (Hochst. ex A. Rich.) Stapf on microbial population and activity in petroleum-contaminated soil.

    PubMed

    Merkl, Nicole; Schultze-Kraft, Rainer; Arias, Marianela

    2006-01-01

    The effect of the tropical pasture grass Brachiaria brizantha on numbers of bacteria, fungi and degraders of alkanes, aromatics, cycloalkanes and crude oil in petroleum hydrocarbon contaminated and uncontaminated savannah soil was evaluated. Substrate induced soil respiration and soil pH were compared between planted and unplanted soil. B. brizantha had a mostly increasing effect on microbial numbers. As an exception, growth of bacteria was not or negatively affected. Microbial respiration and pH were always lower in planted than in unplanted soil. Low pH may result from enhanced oil degradation in planted soil leading to an accumulation of organic acids. A comparable stimulation of crude oil degraders and fungi in planted soil points to the importance of fungi. Since they tolerate lower pH values than bacteria, they are considered to play a central role in oil degradation. Given that the enhancement of crude oil degradation under the influence of B. brizantha could not clearly be correlated to microbial numbers and activity, other factors like oxygen availability, plant enzymes and synergistic degradation by microbial consortia have to be considered.

  1. 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)

  2. Soil ventilation: Effects on microbial populations in gasoline-contaminated subsurface soils

    SciTech Connect

    Hickey, W.J.

    1995-07-01

    Short- and long-term effects of vapor extraction (VE) in an unsaturated subsurface soil and in situ biodegradation of gasoline were evaluated in a field study. Subsurface temperature, moisture, solid- and gas-phase contaminant levels, atmospheric gases, nutrient levels, and microbial population densities were measured during and after soil VE for 462 d. Microbial activity, based on in situ O{sub 2} consumption rates, measured 7 d after VE started averaged 3.8% O{sub 2} d{sup -1}; by Day 62 these rates dropped to 0.2% O{sub 2} d{sup -1}. Soil VE was stopped on Day 180 and about 70 d elapsed before renewed, low-level (0.05% O{sub 2} d{sup -1}) activity was detectable. Following a second round of VE, average O{sub 2} consumption rates increased to 0.11% O{sub 2} d{sup -1}. Microbial population densities did not consistently reflect activity changes measured by O{sub 2} consumption. Activity increases in the latter part of the study were not adequately accounted for by changes in subsurface moisture levels, temperature, or contaminant vapor concentrations. At the study`s completion, 400 kg of gasoline was volatilized from the soil and another 139 kg estimated to be biodegraded in situ. A two-phase process is proposed to account for the effects of VE on microbial activity. The initial phase is characterized by declining microbial activity levels in response to substrate reduction. Microbial activity slowly increases as a result of interactions between gasoline vapor concentrations and possibly changes in degradative activities of the microbial population. More work is needed to identify the gasoline constituents serving as substrates for microbial populations before and after ventilation. 31 refs., 8 figs., 5 tabs.

  3. Microbial ecology on the microcosm level: Activity and population dynamics of methanotrophic bacteria during early succession in a flooded rice field soil

    NASA Astrophysics Data System (ADS)

    Krause, S.; Frenzel, P.

    2009-04-01

    Methane oxidizing bacteria (methanotrophs) play an important role in natural wetlands and rice fields preventing large amounts of methane from escaping into the atmosphere. The occurrence of both type I and type II methanotrophs in the soil surface layer has been demonstrated in many studies. However, there is no profound understanding which of them are responsible for the oxidizing activity and how they differ ecologically. Hence, a gradient microcosm system was applied simulating oxic-anoxic interfaces of water saturated soils to unravel population dynamics in early succession of methanotrophs in a flooded rice paddy. Additionally, environmental parameters were analyzed to link environment, populations, and their specific activity. We measured pmoA-based (particulate methane monooxygenase) terminal restriction fragment length polymorphism (T-RFLP) profiles both on transcription and population level. DNA T-RFLP patterns showed no major differences in the methanotrophic community structure remaining relatively constant over time. In contrast the active methanotrophic community structure as detected by pmoA mRNA T-RFLP analysis clearly demonstrated a distinct pattern from DNA T-RFLP profiles. While type II represented the most prominent group on the population level it seems to play a minor role on the transcription level. Furthermore there were no clear implications towards a link between soil parameters (e.g. NH4+ concentration) and methanotrophic community structure.

  4. 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.

  5. 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)

  6. 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.

  7. 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.

  8. Evaluation of DNA extraction methods of rumen microbial populations.

    PubMed

    Villegas-Rivera, Gabriela; Vargas-Cabrera, Yevani; González-Silva, Napoleón; Aguilera-García, Florentino; Gutiérrez-Vázquez, Ernestina; Bravo-Patiño, Alejandro; Cajero-Juárez, Marcos; Baizabal-Aguirre, Víctor Manuel; Valdez-Alarcón, Juan José

    2013-02-01

    The dynamism of microbial populations in the rumen has been studied with molecular methods that analyze single nucleotide polymorphisms of ribosomal RNA gene fragments (rDNA). Therefore DNA of good quality is needed for this kind of analysis. In this work we report the evaluation of four DNA extraction protocols (mechanical lysis or chemical lysis with CTAB, ethylxanthogenate or DNAzol(®)) from ruminal fluid. The suitability of two of these protocols (mechanical lysis and DNAzol(®)) was tested on single-strand conformation polymorphism (SSCP) of rDNA of rumen microbial populations. DNAzol(®) was a simple method that rendered good integrity, yield and purity. With this method, subtle changes in protozoan populations were detected in young bulls fed with slightly different formulations of a supplement of multinutritional blocks of molasses and urea. Sequences related to Eudiplodinium maggi and a non-cultured Entodiniomorphid similar to Entodinium caudatum, were related to major fluctuating populations in an SSCP assay.

  9. 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...

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. Effect of surgical scrub on microbial population under the fingernails.

    PubMed

    Gross, A; Cutright, D E; D'Alessandro, S M

    1979-09-01

    The effectiveness of two methods of presurgical hand preparation, the 10 minute routine scrub and the 90 second Hydroscrub, in reducing microbial numbers under the fingernails was determined. Bacteriologic cultures of 162 subungual areas of nine subjects revealed prescrub microbial counts of up to 1.9 X 10(5) colony-forming units per area. After the surgical scrub, bacterial concentrations were reduced to a different degree among the persons tested. The mean values of 3.0 X 10(3) to 7.8 X 10(3) colony-forming units immediately after scrub indicated that neither of the two methods tested reduced the microbial population under the fingernails of most persons to acceptable levels. The finding of high postscrub microbial counts under the fingernails is of particular interest and significance in view of the relatively low counts on the fingertips. On the basis of the results of this study, we conclude that degerming of the areas under the fingernails by present methods is not satisfactory. The implication of these findings is discussed.

  16. 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.

  17. 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

  18. 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.

  19. 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.

  20. 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

  1. 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.

  2. 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.

  3. Management and control of microbial populations: development in LSS of missions of different durations

    NASA Astrophysics Data System (ADS)

    Somova, L. A.

    The problem of interaction between man and microorganisms in closed habitats is an inalienable 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 LSS into three groups: useful, neutral and harmful. The tasks, for human beings for optimal coexistence with micro habitants 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 biological recycling. In these systems, microbial populations should be the most useful and active agents. Some problems of microbial populations control and management are discussed in the paper.

  4. 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

  5. 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.

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. 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".

  12. Influence of interfaces on microbial activity.

    PubMed Central

    van Loosdrecht, M C; Lyklema, J; Norde, W; Zehnder, A J

    1990-01-01

    Bacterial adhesion in natural and artificial systems has been critically reviewed to investigate the influences exerted by the presence of interfaces. Numerous investigations have demonstrated that, in the presence of a solid phase, the activity of bacterial cultures is changed. Reviewing relevant literature, two problems were encountered. One is of an experimental nature. Due to lack of similarity in experimental conditions, disparate experiments often cannot be compared; their results may even appear conflicting. The other problem is of an interpretational nature: several hypothetical theories exist which try to explain the effect of surfaces on microbial activity. These theories often confuse changes in the medium and limitations in mass transfer which are due to the presence of solid surfaces (indirect influences) with changes in cell properties (direct influences). Whenever a surface is reported to influence the metabolism of bacteria, the action is found almost exclusively to be due to changes in the medium or environment and is therefore indirect. Based on data reported in the literature, and by using thermodynamic and kinetic considerations, it is concluded that so far neither experimental nor theoretical evidence exists for a direct influence of interfaces on microbial activity. PMID:2181260

  13. Activity assessment of microbial fibrinolytic enzymes.

    PubMed

    Kotb, Essam

    2013-08-01

    Conversion of fibrinogen to fibrin inside blood vessels results in thrombosis, leading to myocardial infarction and other cardiovascular diseases. In general, there are four therapy options: surgical operation, intake of antiplatelets, anticoagulants, or fibrinolytic enzymes. Microbial fibrinolytic enzymes have attracted much more attention than typical thrombolytic agents because of the expensive prices and the side effects of the latter. The fibrinolytic enzymes were successively discovered from different microorganisms, the most important among which is the genus Bacillus. Microbial fibrinolytic enzymes, especially those from food-grade microorganisms, have the potential to be developed as functional food additives and drugs to prevent or cure thrombosis and other related diseases. There are several assay methods for these enzymes; this may due to the insolubility of substrate, fibrin. Existing assay methods can be divided into three major groups. The first group consists of assay of fibrinolytic activity with natural proteins as substrates, e.g., fibrin plate methods. The second and third groups of assays are suitable for kinetic studies and are based on the determination of hydrolysis of synthetic peptide esters. This review will deal primarily with the microorganisms that have been reported in literature to produce fibrinolytic enzymes and the first review discussing the methods used to assay the fibrinolytic activity.

  14. 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

  15. 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...

  16. 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

  17. Modeling the impact of the indigenous microbial population on the maximum population density of Salmonella on alfalfa.

    PubMed

    Rijgersberg, Hajo; Franz, Eelco; Nierop Groot, Masja; Tromp, Seth-Oscar

    2013-07-01

    Within a microbial risk assessment framework, modeling the maximum population density (MPD) of a pathogenic microorganism is important but often not considered. This paper describes a model predicting the MPD of Salmonella on alfalfa as a function of the initial contamination level, the total count of the indigenous microbial population, the maximum pathogen growth rate and the maximum population density of the indigenous microbial population. The model is parameterized by experimental data describing growth of Salmonella on sprouting alfalfa seeds at inoculum size, native microbial load and Pseudomonas fluorescens 2-79. The obtained model fits well to the experimental data, with standard errors less than ten percent of the fitted average values. The results show that the MPD of Salmonella is not only dictated by performance characteristics of Salmonella but depends on the characteristics of the indigenous microbial population like total number of cells and its growth rate. The model can improve the predictions of microbiological growth in quantitative microbial risk assessments. Using this model, the effects of preventive measures to reduce pathogenic load and a concurrent effect on the background population can be better evaluated. If competing microorganisms are more sensitive to a particular decontamination method, a pathogenic microorganism may grow faster and reach a higher level. More knowledge regarding the effect of the indigenous microbial population (size, diversity, composition) of food products on pathogen dynamics is needed in order to make adequate predictions of pathogen dynamics on various food products.

  18. 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

  19. 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

  20. 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

  1. 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.

  2. 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

  3. Microbial biomass and activity in subsurface sediments from Vejen, Denmark.

    PubMed

    Albrechtsen, H J; Winding, A

    1992-05-01

    Subsurface sediment samples were collected from 4 to 31 m below landsurface in glacio-fluvial sediments from the Quaternary period. The samples were described in terms of pH, electrical conductivity, chloride concentration, organic matter content, and grain size distribution. Viable counts of bacteria varied from 0.5 to 1,203 x 103 colony forming units/g dry weight (gdw); total numbers of bacteria acridine orange direct counts (AODC) varied from 1.7 to 147 × 10(7) cells/gdw; growth rates (incorporation of [(3)H]-thymidine) varied from 1.4 to 60.7 × 10(4) cells/(gdw · day); and rate constants for mineralization of (14)C-labelled compounds varied from 0.2 to 2.3 × 10(-3) ml/(dpm · day) for acetate, and from 0 to 2.0 × 10(-3) ml/(dpm · day) for phenol. Sediment texture influenced the total number of bacteria and potential for mineralization; with increasing content of clay and silt and decreasing content of sand, AODC increased and the mineralization rate declined. Intrinsic permeability calculated from grain size correlated positively with mineralization rate for acetate. Statistical correlation analysis showed high correlations between some of the abiotic parameters, but it was not possible to point out a single abiotic parameter that could explain the variation of size and activity of the microbial population. The microbial data obtained in these geologically young sediments were compared to literature data from older sediments, and this comparison showed that age and type of geological formation might be important for the size and activity of the microbial populations. PMID:24192937

  4. Enumeration of microbial populations in radioactive environments by epifluorescence microscopy

    SciTech Connect

    Pansoy-Hjelvik, M.E.; Strietelmeier, B.A.; Paffett, M.T.

    1997-01-01

    Epifluorescence microscopy was utilized to enumerate halophilic bacterial populations in two studies involving inoculated, actual waste/brine mixtures and pure brine solutions. The studies include an initial set of experiments designed to elucidate potential transformations of actinide-containing wastes under salt-repository conditions, including microbially mediated changes. The first study included periodic enumeration of bacterial populations of a mixed inoculum initially added to a collection of test containers. The contents of the test containers are the different types of actual radioactive waste that could potentially be stored in nuclear waste repositories in a salt environment. The transuranic waste was generated from materials used in actinide laboratory research. The results show that cell numbers decreased with time. Sorption of the bacteria to solid surfaces in the test system is discussed as a possible mechanism for the decrease in cell numbers. The second study was designed to determine radiological and/or chemical effects of {sup 239}Pu, {sup 243}Am, {sup 237}Np, {sup 232}Th and {sup 238}U on the growth of pure and mixed anaerobic, denitrifying bacterial cultures in brine media. Pu, Am, and Np isotopes at concentrations of {le}1x10{sup -6} M , {le}5x10{sup -6} M and {le}5x10{sup -4}M respectively, and Th and U isotopes {le}4x10{sup -3}M were tested in these media. The results indicate that high concentrations of certain actinides affected both the bacterial growth rate and morphology. However, relatively minor effects from Am were observed at all tested concentrations with the pure culture.

  5. Enumeration of Microbial Populations in Radioactive Environments by Epifluorescence Microscopy

    SciTech Connect

    Pansoy-Hjelvik, M.E.A.; Strietelmeierr, B.A.; Paffett, M.T.; Kitten, S.M.; Leonard, P.A.; Dunn, M.; Gillow, J.B.; Dodge, C.J.; Villarreal, R.; Triay, I.; Francis, A.J.

    1996-12-02

    Epifluorescence microscopy was utilized to enumerate halophilic bacterial populations in two studies involving inoculated, actual radioactive waste/brine mixtures and pure brine solutions. The studies include an initial set of experiments designed to elucidate potential transformations of actinide-containing wastes under salt-repository conditions, including microbially mediated changes. The first study included periodic enumeration of bacterial populations of a mixed inoculum initially added to a collection of test containers. The contents of the test containers are the different types of actual radioactive waste that could potentially be stored in nuclear waste repositories in a salt environment. The transuranic waste was generated from materials used in actinide laboratory research. The results show that cell numbers decreased with time. Sorption of the bacteria to solid surfaces in the test system is discussed as a possible mechanism for the decrease in cell numbers. The second study was designed to determine radiological and/or chemical effects of {sup 239}Pu, {sup 243}Am, {sup 237}Np, {sup 232}Th and {sup 238}U on the growth of pure and mixed anaerobic, denitrifying bacterial cultures in brine media. Pu, Am, and Np isotopes at concentrations of <=1 x 10{sup {minus}5}M, <=5 x 10{sup {minus}6}M and <=5 x 10{sup {minus}4}M respectively, and Th and U isotopes <=4 x 10{sup {minus}3}M were tested in these media. The results indicate that high actinide concentration affected both the bacterial growth rate and morphology. However, relatively minor effects from Am were observed at all tested concentrations with the pure culture.

  6. 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

  7. New methods for analysis of spatial distribution and coaggregation of microbial populations in complex biofilms.

    PubMed

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

    2013-10-01

    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.

  8. Microbial biomass, activity and community composition in constructed wetlands.

    PubMed

    Truu, Marika; Juhanson, Jaanis; Truu, Jaak

    2009-06-15

    The aim of the current article is to give an overview about microbial communities and their functioning but also about factors affecting microbial activity in the three most common types (surface flow and two types of sub-surface flow) of constructed wetlands. The paper reviews the community composition and structural diversity of the microbial biomass, analyzing different aspects of microbial activity with respect to wastewater properties, specific wetland type, and environmental parameters. A brief introduction about the application of different novel molecular techniques for the assessment of microbial communities in constructed wetlands is also given. Microbially mediated processes in constructed wetlands are mainly dependent on hydraulic conditions, wastewater properties, including substrate and nutrient quality and availability, filter material or soil type, plants, and different environmental factors. Microbial biomass is within similar ranges in both horizontal and vertical subsurface flow and surface flow constructed wetlands. Stratification of the biomass but also a stratified structural pattern of the bacterial community can be seen in subsurface flow systems. Microbial biomass C/N ratio is higher in horizontal flow systems compared to vertical flow systems, indicating the structural differences in microbial communities between those two constructed wetland types. The total activity of the microbial community is in the same range, but heterotrophic growth is higher in the subsurface (vertical flow) system compared to the surface flow systems. Available species-specific data about microbial communities in different types of wetlands is scarce and therefore it is impossible make any general conclusions about the dynamics of microbial community structure in wetlands, its relationship to removal processes and operational parameters.

  9. Molecular characterization of microbial populations in groundwater sources and sand filters for drinking water production.

    PubMed

    de Vet, W W J M; Dinkla, I J T; Muyzer, G; Rietveld, L C; van Loosdrecht, M C M

    2009-01-01

    In full-scale drinking water production from groundwater, subsurface aeration is an effective means of enhancing the often troublesome process of nitrification. Until now the exact mechanism, however, has been unknown. By studying the microbial population we can improve the understanding of this process. Denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA gene fragments of bacteria, archaea and ammonia-oxidizing bacteria was used to characterize the microbial populations in raw groundwater and trickling filters of an active nitrifying surface aerated system and an inactive non-surface aerated system. Only in the active filter were nitrifying microorganisms found above the detection limit of the method. In ammonia oxidation in this groundwater filter both bacteria and archaea played a role, while members belonging to the genus Nitrospira were the only nitrite-oxidizing species found. The subsurface aerated groundwater did not contain any of the nitrifying organisms active in the filter above the detection limit, but did contain Gallionella species that might play a major role in iron oxidation in the filter.

  10. Measurement of microbial biomass and activity in landfill soils.

    SciTech Connect

    Bogner, J. E.; Miller, R. M.; Spokas, K.; Environmental Research

    1995-01-01

    Two complementary techniques, which have been widely used to provide a general measure of microbial biomass or microbial activity in natural soils, were evaluated for their applicability to soils from the Mallard North and Mallard Lake Landfills, DuPage County, Illinois, U.S.A. Included were: (1) a potassium sulphate extraction technique with quantification of organic carbon for measurement of microbial biomass; and (2) an arginine ammonification technique for microbial activity. Four profiles consisting of replaced soils were sampled for this study; units included topsoil (mixed mollisol A and B horizons), compacted clay cover (local calcareous Wisconsinan age glacial till), and mixed soil/refuse samples. Internally consistent results across the four profiles and good correlations with other independent indicators of microbial activity (moisture, organic matter content, nitrogen, and phosphorus) suggest that, even though these techniques were developed mainly for natural mineral soils, they are also applicable to disturbed landfill soils.

  11. 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

  12. Contribution of wheat endogenous and wheat kernel associated microbial endoxylanases to changes in the arabinoxylan population during breadmaking.

    PubMed

    Dornez, Emmie; Cuyvers, Sven; Gebruers, Kurt; Delcour, Jan A; Courtin, Christophe M

    2008-03-26

    Wheat kernel associated endoxylanases consist of a majority of microbial endoxylanases and a minority of endogenous endoxylanases. At least part of these enzymes can be expected to end up in wheat flour upon milling. In this study, the contribution of both types of these endoxylanases to changes in the arabinoxylan (AX) population during wheat flour breadmaking was assessed. To this end, wheat flour produced from two wheat varieties with different endoxylanase activity levels, both before and after sodium hypochlorite surface treatment of the wheat kernels, was used in a straight dough breadmaking procedure. Monitoring of the AX population during the breadmaking process showed that changes in AX are to a large extent caused by endogenous endoxylanases, whereas the contribution of microbial endoxylanases to these changes was generally very low. The latter points to a limited contamination of wheat flour with microbial enzymes during milling or to an extensive inactivation of these wheat flour associated microbial endoxylanases by endoxylanase inhibitors, present in wheat flour. When all wheat kernel associated microbial endoxylanases were first washed from the kernels and then added to the bread recipe, they drastically affected the AX population, suggesting that they can have a large impact on whole meal breadmaking.

  13. 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.

  14. 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

  15. [Characteristics of soil microbial populations in depressions between karst hills under different land use patterns].

    PubMed

    Song, Min; Zou, Dong-Sheng; Du, Hu; Peng, Wan-Xia; Zeng, Fu-Ping; Tan, Qiu-Jin; Fan, Fu-Jing

    2013-09-01

    Based on the investigation and analysis of six soil microbial indices, eight soil conventional nutrient indices, six soil mineral nutrient indices, and 15 vegetation indices in the farmland, grassland, scrub, forest plantation, secondary forest, and primary forest in the depressions between karst hills, this paper analyzed the main soil microbial populations, soil microbial biomass carbon (MBC), nitrogen (MBN), and phosphorus (MBP) and their fractal characteristics, and the relationships of the soil microbes with vegetation, soil nutrients, and soil mineral components under different land use patterns. The soil microbial populations differed in their quantity and composition under different land use patterns. Primary forest and farmland had the highest quantity of soil microbial populations, while forest plantation had the lowest one. The three forests had a higher proportion of soil bacteria, the farmland, grassland, and scrub had a higher proportion of actinomycetes, and all the six land use patterns had a low proportion of soil fungi. Under the six land use patterns, the soil MBC, MBN, and MBP were all high, with the maximum in primary forest. There was a good fractal relationship between the soil MBC and microbial populations, but no fractal relationships between the soil MBN and MBP and the microbial populations. Significant relationships were observed between the soil microbes and the vegetation, soil nutrients, and soil mineral components, and the soil MBC had the closest relationships with the Shannon index of tree layer and the soil total nitrogen, Fe2O3, and CaO contents.

  16. 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

  17. Evaluation of microbial activity for long-term performance assessments of deep geologic nuclear waste repositories.

    SciTech Connect

    Francis, Arokiasamy J.; Wang, Yifeng

    2005-06-01

    Microorganisms are ubiquitous in subsurface environments and play a major role in the biogeochemical recycling of various elements. In this paper, we have developed a general approach for a systematic evaluation of microbial impact on the long-term performance of the repository. We have demonstrated that data on microbial population alone are not sufficient for the evaluation of microbial impact on repository performance and a sensible approach for such evaluation must be based on the consideration of environmental constraints on microbial reaction pathways. We have applied our approach to both the Yucca Mountain (YM) repository and the Waste Isolation Pilot Plant (WIPP). We have demonstrated that the effect of microbial activity on the near-field chemistry in the Yucca Mountain repository is negligible because of limited nutrient supply and harsh environmental conditions created by waste emplacement. Whereas for the WIPP, we have shown that, due to the presence of a large quantity of organic materials and nutrients in the wastes, a significant microbial activity can potentially be stimulated and its impact on repository performance can be evaluated with carefully designed incubation experiments coupled with performance assessment calculations. The impact of microbial gas generation on disposal room chemistry in the WIPP can be mitigated by introducing MgO as a backfill material.

  18. 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.

  19. Active microbial soil communities in different agricultural managements

    NASA Astrophysics Data System (ADS)

    Landi, S.; Pastorelli, R.

    2009-04-01

    We studied the composition of active eubacterial microflora by RNA extraction from soil (bulk and rhizosphere) under different environmental impact managements, in a hilly basin in Gallura (Sardinia). We contrasted grassy vineyard, in which the soil had been in continuous contact with plant roots for a long period of time, with traditional tilled vineyard. Moreover, we examined permanent grassland, in which plants had been present for some years, with temporary grassland, in which varying plants had been present only during the respective growing seasons. Molecular analysis of total population was carried out by electrophoretic separation by Denaturing Gradient Gel Electrophoresis (DGGE) of amplified cDNA fragments obtained from 16S rRNA. In vineyards UPGMA (Unweighted Pair Group Mathematical Average) analysis made up separate clusters depending on soil management. In spring both clusters showed similarity over 70%, while in autumn the similarity increased, 84% and 90% for grassy and conventional tilled vineyard respectively. Permanent and temporary grassland joined in a single cluster in spring, while in autumn a partial separation was evidenced. The grassy vineyard, permanent and temporary grassland showed higher richness and diversity Shannon-Weiner index values than vineyard with conventional tillage although no significant. In conclusion the expected effect of the rhizosphere was visible: the grass cover influenced positively the diversity of active microbial population.

  20. 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

  1. 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

  2. Nutrient Limitation and Adaptation of Microbial Populations to Chemical Transformations

    PubMed Central

    Lewis, David L.; Kollig, Heinz P.; Hodson, Robert E.

    1986-01-01

    Using field-collected periphyton and bacterial isolates, we determined adaptation lag periods for microbial transformation of p-cresol. Lag periods were longer for periphyton samples collected from field sites that were low in dissolved inorganic nitrogen and phosphorus. Moreover, lag periods decreased in samples amended with N or P. Our data suggest that adaptation lag periods for microbial transformation of low concentrations of chemicals may correlate with limiting nutrient concentrations, and this correlation may provide a basis for predictive mathematical modeling of lag periods. PMID:16347021

  3. Diets of differentially processed wheat alter ruminal fermentation parameters and microbial populations in beef cattle.

    PubMed

    Jiang, S Z; Yang, Z B; Yang, W R; Li, Z; Zhang, C Y; Liu, X M; Wan, F C

    2015-11-01

    The influences of differently processed wheat products on rumen fermentation, microbial populations, and serum biochemistry profiles in beef cattle were studied. Four ruminally cannulated Limousin × Luxi beef cattle (400 ± 10 kg) were used in the experiment with a 4 × 4 Latin square design. The experimental diets contained (on a DM basis) 60% corn silage as a forage source and 40% concentrate with 4 differently processed wheat products (extruded, pulverized, crushed, and rolled wheat). Concentrations of ruminal NH-N and microbial protein (MCP) in cattle fed crushed and rolled wheat were greater ( < 0.05) than the corresponding values in cattle fed pulverized and extruded wheat. Ruminal concentrations of total VFA and acetate and the ratio of acetate to propionate decreased ( < 0.05) with increased geometric mean particle size (geometric mean diameter) of processed wheat, except for extruded wheat; cattle fed extruded wheat had the lowest concentrations of total VFA and acetate among all treatments. The relative abundance of , , ciliated protozoa, and was lower in cattle fed the pulverized wheat diet than in the other 3 diets ( < 0.05), whereas the relative abundance of was decreased in cattle fed extruded wheat compared with cattle fed crushed and rolled wheat ( < 0.05). No treatment effect was obtained for serum enzyme activity and protein concentration ( > 0.05). Our findings suggest that the method of wheat processing could have a significant effect on ruminal fermentation parameters and microbial populations in beef cattle and that crushed and rolled processing is better in terms of ruminal NH-N and MCP content, acetate-to-propionate ratio, and relative abundance of rumen microorganisms.

  4. 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.

  5. 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

  6. 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...

  7. 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

  8. 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

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. Response to high-pressure, low-temperature treatment in vegetables: determination of survival rates of microbial populations using flow cytometry and detection of peroxidase activity using confocal microscopy.

    PubMed

    Arroyo, G; Sanz, P D; Préstamo, G

    1999-03-01

    Application of high hydrostatic pressure (200, 300, 350 and 400 MPa) at 5 degrees C for 30 min to different micro-organisms, including Gram-positive and Gram-negative bacteria, moulds and yeasts, proved to be more effective in inactivating these organisms than treatments at 20 degrees C for 10 min and at 10 degrees C for 20 min. Moulds, yeasts, Gram-negative bacteria and Listeria monocytogenes were most sensitive, and their populations were completely inactivated at pressures between 300 and 350 MPa. The same conditions of pressure, temperature, and time were applied to different vegetables (lettuce, tomato, asparagus, spinach, cauliflower and onion), achieving reductions of from 2-4 log units in both viable mesophiles and moulds and yeasts at pressures of between 300 and 400 MPa. Sensory characteristics were unaltered, especially in asparagus, onion, tomato and cauliflower, though slight browning was observed in cauliflower at 350 MPa. Flow cytometry was applied to certain of the microbial populations used in the above experiment before and after the pressurization treatment. The results were indicative of differing percentage survival rates depending on micro-organism type, with higher survival rates for Gram-positive bacteria, except L. monocytogenes, than in the other test micro-organisms. Growth of survivors was undetectable using the plate count method, suggesting that micro-organisms suffering from pressure stress were metabolically inactive though alive. The pressurization treatments did not inactivate the peroxidase responsible for browning in vegetables. Confocal microscopic examination of epidermal tissue from onion showed that the enzyme had been displaced to the cell interior. Use of low temperatures and moderately long pressurization times yielded improved inactivation of micro-organisms and better sensorial characteristics of the vegetables, and should lower industrial costs.

  15. 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.

  16. The role of microbial populations in the containment of aromatic hydrocarbons in the subsurface.

    PubMed

    Franzmann, P D; Robertson, W J; Zappia, L R; Davis, G B

    2002-01-01

    A survey of soil gases associated with gasoline stations on the Swan Coastal Plain of Western Australia has shown that 20% leak detectable amounts of petroleum. The fates of volatile hydrocarbons in the vadose zone at one contaminated site, and dissolved hydrocarbons in groundwater at another site were followed in a number of studies which are herein reviewed. Geochemical evidence from a plume of hydrocarbon-contaminated groundwater has shown that sulfate reduction rapidly developed as the terminal electron accepting process. Toluene degradation but not benzene degradation was linked to sulfate reduction. The sulfate-reducing bacteria isolated from the plume represented a new species, Desulfosporosinus meridiei. Strains of the species do not mineralise 14C-toluene in pure culture. The addition of large numbers of cells and sulfate to microcosms did stimulate toluene mineralisation but not benzene mineralisation. Attempts to follow populations of sulfate-reducing bacteria by phospholipid signatures, or Desulfosporosinus meridiei by FISH in the plume were unsuccessful, but fluorescently-labeled polyclonal antibodies were successfully used. In the vadose zone at a different site, volatile hydrocarbons were consumed in the top 0.5 m of the soil profile. The fastest measured rate of mineralisation of 14C-benzene in soils collected from the most active zone (6.5 mg kg(-1) day(-1)) could account for the majority of the flux of hydrocarbon vapourtowards the surface. The studies concluded that intrinsic remediation by subsurface microbial populations in groundwater on the Swan Coastal Plain can control transport of aromatic hydrocarbon contamination, except for the transport of benzene in groundwater. In the vadose zone, intrinsic remediation by the microbial populations in the soil profile can contain the transport of aromatic hydrocarbons, provided the physical transport of gases, in particular oxygen from the atmosphere, is not impeded by structures.

  17. 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

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

    PubMed

    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

  19. 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.

  20. The antimicrobial activity of embalming chemicals and topical disinfectants on the microbial flora of human remains.

    PubMed

    Burke, P A; Sheffner, A L

    1976-10-01

    The antimicrobial activity of embalming chemicals an topical disinfectants was evaluated to determine the degree of disinfection achieved during the embalming of human remains. The administration of arterial and cavity embalming chemicals resulted in a 99% reduction of the postmortem microbial population after 2 hours of contact. This level of disinfection was maintained for the 24 hours test period. Topical disinfection of the body orifices was also observed. Therefore, it is probable that present embalming practices reduce the hazard from transmission of potentially infectious microbial agents within the immediate environment of embalmed human remains.

  1. 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.

  2. 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

  3. 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.

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. Influence of Deep Ocean Sewage Outfalls on the Microbial Activity of the Surrounding Sediment

    PubMed Central

    Novitsky, James A.; Karl, David M.

    1985-01-01

    The microbial activity near two deep ocean sewage outfalls off the coast of the island of Oahu, Hawaii, was characterized. Water samples and sediment samples to a depth of 4.5 cm were analyzed from an area of approximately 4.5 × 104 m2 surrounding the outfalls. Although the effluent water at both sites exhibited heterotrophic activity that was 2 orders of magnitude greater than water from a control site, ambient water samples taken within 1 m of the discharge ports exhibited activity only twice that of the control water. The heterotrophic activity of the outfall sediment was only elevated above that of the control site for surface samples collected within 10 m of the outfall. Likewise, the rates of microbial nucleic acid synthesis and carbon production in the sediment were only elevated immediately adjacent to the outfalls. Total microbial biomass, as determined by the ATP content of the sediment, varied spatially but was generally elevated at the outfall sites. The specific growth rates calculated for the sediment microbial populations, however, were not greater at the outfall sites. At one site the rocks surrounding the diffuser pipe were covered with copious amounts of slime that appeared to be composed entirely of microbial cells and filaments. This microbial mat was extremely active with respect to heterotrophic activity and biomass production. Overall, it appears that the impact of the sewage discharge on the ambient seawater microbiota is slight and that the effect on the sediment microbiota is confined to an area immediately adjacent to the diffuser ports. In the sand itself, the effect is limited to the upper 2 cm at most. PMID:16346944

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

    PubMed

    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.

  10. 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

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

    PubMed

    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

  12. A reexamination of integrated population activities.

    PubMed

    Files, L A

    1982-10-01

    The term integrated population activities came into style at the World Population Conference at Bucharest in 1974, where it was used to refer to national planning that recognizes the integral role of population in development, the use of socioeconomic change to solve a nation's population problem, or the implementation of population activities along with health or agricultural projects. In this paper, Laurel Files calls for a more precise definition of the word integrated and the use of different terminology for other types of coordinating activities. She argues that integrated is meaningful only when it refers to planning or implementation of population activities by several ministries, or to the combination of population activities with related services. Beyond restricting the definition, Files calls into question the habit of appending integrated onto population activities as a kind of halo. "Unintegrated" family planning does not deserve a pejorative connotation, for in some situations it may be more effective than integrated family planning.

  13. 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.

  14. Microbial life in frozen boreal soils-environmental constraints on catabolic and anabolic activity

    NASA Astrophysics Data System (ADS)

    Oquist, M. G.; Sparrman, T.; Haei, M.; Segura, J.; Schleucher, J.; Nilsson, M. B.

    2013-12-01

    Microbial activity in frozen soils has recently gained increasing attention and the fact that soil microorganisms can perform significant metabolic activity at temperatures below freezing is apparent. However, to what extent microbial activity is constrained by the environmental conditions prevailing in a frozen soil matrix is still very uncertain. This presentation will address how the fundamental environmental factors of temperature, liquid water availability and substrate availability combine to regulate rates of catabolic and anabolic microbial processes in frozen soils. The presented results are gained from investigations of the surface layers of boreal forest soils with 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. In turn, the capacity for a specific soil to retain liquid water at sub-zero temperatures is controlled by the structural composition of the soil, and especially the soil organic matter is of integral importance. 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. 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

  15. Response of soil microbial activity and biodiversity in soils polluted with different concentrations of cypermethrin insecticide.

    PubMed

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

    2015-07-01

    We performed a laboratory study into the effect of cypermethrin insecticide applied to different concentrations on biological properties in two soils [Typic Xerofluvent (soil A) and Xerollic Calciorthid (soil B)]. Two kg of each soil were polluted with cypermethrin at a rate of 60, 300, 600, and 1,200 g ha(-1) (C1, C2, C3, and C4 treatments). A nonpolluted soil was used as a control (C0 treatment). For all treatments and each experimental soil, soil dehydrogenase, urease, β-glucosidase, phosphatase, and arylsulphatase activities and soil microbial community were analysed by phospholipid fatty acids, which were measured at six incubation times (3, 7, 15, 30, 60, and 90 days). The behavior of the enzymatic activities and microbial population were dependent on the dose of insecticide applied to the soil. Compared with the C0 treatment, in soil A, the maximum inhibition of the enzymatic activities was at 15, 30, 45, and 90 days for the C1, C2, C3, and C4 treatments, respectively. However, in soil B, the maximum inhibition occurred at 7, 15, 30, and 45 days for the C1, C2, C3, and C4 treatments, respectively. These results suggest that the cypermethrin insecticide caused a negative effect on soil enzymatic activities and microbial diversity. This negative impact was greater when a greater dose of insecticide was used; this impact was also greater in soil with lower organic matter content. For both soils, and from these respective days onward, the enzymatic activities and microbial populations progressively increased by the end of the experimental period. This is possibly due to the fact that the insecticide or its breakdown products and killed microbial cells, subsequently killed by the insecticide, are being used as a source of energy or as a carbon source for the surviving microorganisms for cell proliferation.

  16. Identification of microbial populations driving biopolymer degradation in acidic peatlands by metatranscriptomic analysis.

    PubMed

    Ivanova, Anastasia A; Wegner, Carl-Eric; Kim, Yongkyu; Liesack, Werner; Dedysh, Svetlana N

    2016-10-01

    Northern peatlands play a crucial role in the global carbon balance, serving as a persistent sink for atmospheric CO2 and a global carbon store. Their most extensive type, Sphagnum-dominated acidic peatlands, is inhabited by microorganisms with poorly understood degradation capabilities. Here, we applied a combination of barcoded pyrosequencing of SSU rRNA genes and Illumina RNA-Seq of total RNA (metatranscriptomics) to identify microbial populations and enzymes involved in degrading the major components of Sphagnum-derived litter and exoskeletons of peat-inhabiting arthropods: cellulose, xylan, pectin and chitin. Biopolymer addition to peat induced a threefold to fivefold increase in bacterial cell numbers. Functional community profiles of assembled mRNA differed between experimental treatments. In particular, pectin and xylan triggered increased transcript abundance of genes involved in energy metabolism and central carbon metabolism, such as glycolysis and TCA cycle. Concurrently, the substrate-induced activity of bacteria on these two biopolymers stimulated grazing of peat-inhabiting protozoa. Alveolata (ciliates) was the most responsive protozoa group as confirmed by analysis of both SSU rRNA genes and SSU rRNA. A stimulation of alphaproteobacterial methanotrophs on pectin was consistently shown by rRNA and mRNA data. Most likely, their significant enrichment was due to the utilization of methanol released during the degradation of pectin. Analysis of SSU rRNA and total mRNA revealed a specific response of Acidobacteria and Actinobacteria to chitin and pectin, respectively. Relatives of Telmatobacter bradus were most responsive among the Acidobacteria, while the actinobacterial response was primarily affiliated with Frankiales and Propionibacteriales. The expression of a wide repertoire of carbohydrate-active enzymes (CAZymes) corresponded well to the detection of a highly diverse peat-inhabiting microbial community, which is dominated by yet uncultivated

  17. Identification of microbial populations driving biopolymer degradation in acidic peatlands by metatranscriptomic analysis.

    PubMed

    Ivanova, Anastasia A; Wegner, Carl-Eric; Kim, Yongkyu; Liesack, Werner; Dedysh, Svetlana N

    2016-10-01

    Northern peatlands play a crucial role in the global carbon balance, serving as a persistent sink for atmospheric CO2 and a global carbon store. Their most extensive type, Sphagnum-dominated acidic peatlands, is inhabited by microorganisms with poorly understood degradation capabilities. Here, we applied a combination of barcoded pyrosequencing of SSU rRNA genes and Illumina RNA-Seq of total RNA (metatranscriptomics) to identify microbial populations and enzymes involved in degrading the major components of Sphagnum-derived litter and exoskeletons of peat-inhabiting arthropods: cellulose, xylan, pectin and chitin. Biopolymer addition to peat induced a threefold to fivefold increase in bacterial cell numbers. Functional community profiles of assembled mRNA differed between experimental treatments. In particular, pectin and xylan triggered increased transcript abundance of genes involved in energy metabolism and central carbon metabolism, such as glycolysis and TCA cycle. Concurrently, the substrate-induced activity of bacteria on these two biopolymers stimulated grazing of peat-inhabiting protozoa. Alveolata (ciliates) was the most responsive protozoa group as confirmed by analysis of both SSU rRNA genes and SSU rRNA. A stimulation of alphaproteobacterial methanotrophs on pectin was consistently shown by rRNA and mRNA data. Most likely, their significant enrichment was due to the utilization of methanol released during the degradation of pectin. Analysis of SSU rRNA and total mRNA revealed a specific response of Acidobacteria and Actinobacteria to chitin and pectin, respectively. Relatives of Telmatobacter bradus were most responsive among the Acidobacteria, while the actinobacterial response was primarily affiliated with Frankiales and Propionibacteriales. The expression of a wide repertoire of carbohydrate-active enzymes (CAZymes) corresponded well to the detection of a highly diverse peat-inhabiting microbial community, which is dominated by yet uncultivated

  18. 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...

  19. 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...

  20. 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

  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. 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

  3. 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...

  4. Transport and mixing of microbial population by atmospheric coherent structures

    NASA Astrophysics Data System (ADS)

    Bozorg Magham, A.; Ross, S. D.

    2012-12-01

    Lagrangian coherent structures (LCSs) provide a new means for discussion of spatiotemporal characteristics of the passive transport and mixing of atmospheric pathogen populations, paving the way for new management strategies regarding the spread of infectious diseases affecting plants, domestic animals, and humans, including identification of probable source regions and forecasts of regions at high risk. We report on the relationship of coherent structures to the patchiness of pathogen populations, and the effects of imperfect forecast wind data on the resultant LCSs. Regarding forecasting LCSs, our main contributions are to quantify the accuracy and sensitivity of such predictions with respect to the forecasting parameters. To obtain more reliable atmospheric LCS features, we have incorporated two more concepts. First is the effect of unresolved turbulent motion; this consideration leads to the stochastic finite-time Lyapunov exponent (SFTLE) field and the resultant stochastic LCS. The second concept is ensemble FTLE/LCS forecasting using individual members of the ensemble wind field forecasts.

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

    PubMed

    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).

  6. 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

  7. Rapid evolution of adaptive niche construction in experimental microbial populations.

    PubMed

    Callahan, Benjamin J; Fukami, Tadashi; Fisher, Daniel S

    2014-11-01

    Many species engage in adaptive niche construction: modification of the local environment that increases the modifying organism's competitive fitness. Adaptive niche construction provides an alternative pathway to higher fitness, shaping the environment rather than conforming to it. Yet, experimental evidence for the evolutionary emergence of adaptive niche construction is lacking, leaving its role in evolution uncertain. Here we report a direct observation of the de novo evolution of adaptive niche construction in populations of the bacteria Pseudomonas fluorescens. In a laboratory experiment, we allowed several bacterial populations to adapt to a novel environment and assessed whether niche construction evolved over time. We found that adaptive niche construction emerged rapidly, within approximately 100 generations, and became ubiquitous after approximately 400 generations. The large fitness effect of this niche construction was dominated by the low fitness of evolved strains in the ancestrally modified environment: evolved niche constructors were highly dependent on their specific environmental modifications. Populations were subjected to frequent resetting of environmental conditions and severe reduction of spatial habitat structure, both of which are thought to make adaptive niche construction difficult to evolve. Our finding that adaptive niche construction nevertheless evolved repeatably suggests that it may play a more important role in evolution than generally thought.

  8. 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

  9. Biodegradation of DDT by stimulation of indigenous microbial populations in soil with cosubstrates.

    PubMed

    Ortíz, Irmene; Velasco, Antonio; Le Borgne, Sylvie; Revah, Sergio

    2013-04-01

    Stimulation of native microbial populations in soil by the addition of small amounts of secondary carbon sources (cosubstrates) and its effect on the degradation and theoretical mineralization of DDT [l,l,l-trichloro-2,2-bis(p-chlorophenyl)ethane] and its main metabolites, DDD and DDE, were evaluated. Microbial activity in soil polluted with DDT, DDE and DDD was increased by the presence of phenol, hexane and toluene as cosubstrates. The consumption of DDT was increased from 23 % in a control (without cosubstrate) to 67, 59 and 56 % in the presence of phenol, hexane and toluene, respectively. DDE was completely removed in all cases, and DDD removal was enhanced from 67 % in the control to ~86 % with all substrates tested, except for acetic acid and glucose substrates. In the latter cases, DDD removal was either inhibited or unchanged from the control. The optimal amount of added cosubstrate was observed to be between 0.64 and 2.6 mg C [Formula: see text]. The CO2 produced was higher than the theoretical amount for complete cosubstrate mineralization indicating possible mineralization of DDT and its metabolites. Bacterial communities were evaluated by denaturing gradient gel electrophoresis, which indicated that native soil and the untreated control presented a low bacterial diversity. The detected bacteria were related to soil microorganisms and microorganisms with known biodegradative potential. In the presence of toluene a bacterium related to Azoarcus, a genus that includes species capable of growing at the expense of aromatic compounds such as toluene and halobenzoates under denitrifying conditions, was detected.

  10. 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.

  11. 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.

  12. 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.

  13. Microbial Populations in Extreme Environments: Investigations and Characterizations of the Microbiology and Geochemistry of Galapagos Island Fumaroles

    NASA Astrophysics Data System (ADS)

    Mayhew, L. E.; Childers, S. E.; Geist, D.

    2005-12-01

    The extreme physiochemical conditions, insularity, and wide range in ages of fumaroles of the Galapagos Islands provide an excellent opportunity to explore for novel microorganisms and to study life in extreme environments. This is the first study that measures microbial diversity of Galapagos fumaroles. Forty-seven samples were collected from six distinct fumarole fields on Sierra Negra and Alcedo volcanoes. Vulcan Chico, on Sierra Negra, was activated during the last eruption in 1979. Two of the other fumarole fields on Sierra Negra are associated with a long-lived fault system on the caldera floor and are therefore likely to be significantly older. The fault-associated fumaroles have widespread alteration haloes (up to 100 m in diameter) and thick deposits of native sulfur. The most vigorous of the fumarole fields on Alcedo activated in late 1993 to early 1994. The second fumarole field on Alcedo is associated with a recently extinct geyser and the third is located on a rhyolite vent. A diversity of colors was observed in the substrates at all of the fumarole fields and some may be the result of microbial activity. Collection sites were chosen on the basis of temperature and the variations in the substrate in order to obtain samples from a variety of environments. Temperatures at sample sites range from 25.0 to 178.5° C, and pH from 0 to 6. The material collected varies between sites and includes crystalline sulfur deposits, clay, sandy and rocky soils, and microbial mats. Substrate material is characterized by powder x-ray diffractometry and scanning electron microscopy and gases collected from five of the fumarole fields are being analyzed to test for chemical controls on the microbial populations. Genomic DNA is being extracted from all of the samples. Primers for Bacteria and Archaea are used for PCR amplification of the 16S rRNA gene. To date, 22 of 37 processed samples have amplifiable DNA. Microbial diversity of samples possessing amplifiable DNA is

  14. 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.

  15. 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

  16. Epidemiology. Opposite effects of anthelmintic treatment on microbial infection at individual versus population scales.

    PubMed

    Ezenwa, Vanessa O; Jolles, Anna E

    2015-01-01

    Parasitic worms modulate host immune responses in ways that affect microbial co-infections. For this reason, anthelmintic therapy may be a potent tool for indirectly controlling microbial pathogens. However, the population-level consequences of this type of intervention on co-infecting microbes are unknown. We evaluated the effects of anthelmintic treatment on bovine tuberculosis (BTB) acquisition, mortality after infection, and pathogen fitness in free-ranging African buffalo. We found that treatment had no effect on the probability of BTB infection, but buffalo survival after infection was ninefold higher among treated individuals. These contrasting effects translated into an approximately eightfold increase in the reproductive number of BTB for anthelmintic-treated compared with untreated buffalo. Our results indicate that anthelmintic treatment can enhance the spread of microbial pathogens in some real-world situations.

  17. The microbial population in the air of cultivation facility of oyster mushrooms.

    PubMed

    Chun, Se Chul; Ahn, Yu Na; Khan, Sajid Mohamad; Chung, Il Min; Won, Hyang Yoen; Jhune, Chang Sung; Park, Yool Jin

    2012-12-01

    The microbial population in the air of mushroom cultivation facility was studied to understand the population structure and size depending on the cultivation methods and regions. The air contents of ten farmers' oyster mushroom cultivation facilities in Kyunggi province were sampled. The results indicated that there was no difference in population size depending on the regions of mushroom cultivation. In addition, the population size of bacteria in the growth room was bigger than that of the cooling room and outside of the mushroom house, but the fungal population was similar in size between cultivation stages. With regard to population structure, Pseudomonas and Penicillium species were most frequently isolated from the air of oyster mushroom cultivation facility. PMID:23274995

  18. Factors affecting the microbial populations at full-scale enhanced biological phosphorus removal (EBPR) wastewater treatment plants in The Netherlands.

    PubMed

    López-Vázquez, Carlos M; Hooijmans, Christine M; Brdjanovic, Damir; Gijzen, Huub J; van Loosdrecht, Mark C M

    2008-05-01

    The influence of operating and environmental conditions on the microbial populations of the enhanced biological phosphorus removal (EBPR) process at seven full-scale municipal activated sludge wastewater treatment plants (WWTPs) in The Netherlands was studied. Data from the selected WWTPs concerning process configuration, operating and environmental conditions were compiled. The EBPR activity from each plant was determined by execution of anaerobic-anoxic-aerobic batch tests using fresh activated sludge. Fractions of Accumulibacter as potential phosphorus accumulating organisms (PAO), and Competibacter, Defluviicoccus-related microorganisms and Sphingomonas as potential glycogen accumulating organisms (GAO) were quantified using fluorescence in situ hybridization (FISH). The relationships among plant process configurations, operating parameters, environmental conditions, EBPR activity and microbial populations fractions were evaluated using a statistical approach. A well-defined and operated denitrification stage and a higher mixed liquor pH value in the anaerobic stage were positively correlated with the occurrence of Accumulibacter. A well-defined denitrification stage also stimulated the development of denitrifying PAO (DPAO). A positive correlation was observed between Competibacter fractions and organic matter concentrations in the influent. Nevertheless, Competibacter did not cause a major effect on the EBPR performance. The observed Competibacter fractions were not in the range that would have led to EBPR deterioration. Likely, the low average sewerage temperature (12+/-2 degrees C) limited their proliferation. Defluviicoccus-related microorganisms were seen only in negligible fractions in a few plants (<0.1% as EUB), whereas Sphingomonas were not observed.

  19. Subterranean microbial populations metabolize hydrogen and acetate under in situ conditions in granitic groundwater at 450 m depth in the Äspö Hard Rock Laboratory, Sweden.

    PubMed

    Pedersen, Karsten

    2012-07-01

    Pressure-resistant circulating systems were constructed to enable the investigation of attached and unattached microbial populations under in situ pressure (2.5 MPa), diversity, dissolved gas and chemistry conditions. Three parallel flow cell cabinets were configured to allow observation of the effect on microbial metabolic activity of adding 3 mM hydrogen or 2.4 mM acetate, compared with an untreated control. Hydrogen addition reduced the generation time fourfold to 2 weeks, doubled the sulphide production rate and increased acetate production by approximately 50%. The acetate addition induced acetate consumption. The studied subterranean microbial processes appeared to proceed very slowly in terms of volume and time, although the results suggest that individual cells could be very active. Lytic bacteriophages are hypothesized to have caused this contradictive observation. Phages may consequently significantly reduce the rates of subterranean microbial processes. Furthermore, the results suggest that hydrogen from corroding underground constructions could induce significant local microbial activity and that the low concentrations of hydrogen often observed in pristine subterranean environments may support slow but sustainable microbial activity in deep groundwater.

  20. 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

  1. 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

  2. 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

  3. The tragedy of the commons in microbial populations: insights from theoretical, comparative and experimental studies.

    PubMed

    MacLean, R C

    2008-03-01

    First principles of thermodynamics imply that metabolic pathways are faced with a trade-off between the rate and yield of ATP production. Simple evolutionary models argue that this trade-off generates a fundamental social conflict in microbial populations: average fitness in a population is highest if all individuals exploit common resources efficiently, but individual reproductive rate is maximized by consuming common resources at the highest possible rate, a scenario known as the tragedy of the commons. In this paper, I review studies that have addressed two key questions: What is the evidence that the rate-yield trade-off is an evolutionary constraint on metabolic pathways? And, if so, what determines evolutionary outcome of the conflicts generated by this trade-off? Comparative studies and microbial experiments provide evidence that the rate-yield trade-off is an evolutionary constraint that is driven by thermodynamic constraints that are common to all metabolic pathways and pathway-specific constraints that reflect the evolutionary history of populations. Microbial selection experiments show that the evolutionary consequences of this trade-off depend on both kin selection and biochemical constraints. In well-mixed populations with low relatedness, genotypes with rapid and efficient metabolism can coexist as a result of negative frequency-dependent selection generated by density-dependent biochemical costs of rapid metabolism. Kin selection can promote the maintenance of efficient metabolism in structured populations with high relatedness by ensuring that genotypes with efficient metabolic pathways gain an indirect fitness benefit from their competitive restraint. I conclude by suggesting avenues for future research and by discussing the broader implications of this work for microbial social evolution.

  4. The tragedy of the commons in microbial populations: insights from theoretical, comparative and experimental studies.

    PubMed

    MacLean, R C

    2008-05-01

    First principles of thermodynamics imply that metabolic pathways are faced with a trade-off between the rate and yield of ATP production. Simple evolutionary models argue that this trade-off generates a fundamental social conflict in microbial populations: average fitness in a population is highest if all individuals exploit common resources efficiently, but individual reproductive rate is maximized by consuming common resources at the highest possible rate, a scenario known as the tragedy of the commons. In this paper, I review studies that have addressed two key questions: What is the evidence that the rate-yield trade-off is an evolutionary constraint on metabolic pathways? And, if so, what determines evolutionary outcome of the conflicts generated by this trade-off? Comparative studies and microbial experiments provide evidence that the rate-yield trade-off is an evolutionary constraint that is driven by thermodynamic constraints that are common to all metabolic pathways and pathway-specific constraints that reflect the evolutionary history of populations. Microbial selection experiments show that the evolutionary consequences of this trade-off depend on both kin selection and biochemical constraints. In well-mixed populations with low relatedness, genotypes with rapid and efficient metabolism can coexist as a result of negative frequency-dependent selection generated by density-dependent biochemical costs of rapid metabolism. Kin selection can promote the maintenance of efficient metabolism in structured populations with high relatedness by ensuring that genotypes with efficient metabolic pathways gain an indirect fitness benefit from their competitive restraint. I conclude by suggesting avenues for future research and by discussing the broader implications of this work for microbial social evolution.

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

    PubMed

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

    2015-11-06

    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.

  8. 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

  9. 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

  10. 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

  11. Monitoring microbial populations on wide-body commercial passenger aircraft.

    PubMed

    McKernan, Lauralynn Taylor; Wallingford, Kenneth M; Hein, Misty J; Burge, Harriet; Rogers, Christine A; Herrick, Robert

    2008-03-01

    Although exposure to bacteria has been assessed in cabin air previously, minimal numbers of samples have been collected in-flight. The purpose of this research was to comprehensively characterize bacterial concentrations in the aircraft cabin. Twelve randomly selected flights were sampled on Boeing-767 aircraft, each with a flight duration between 4.5 and 6.5 h. N-6 impactors were used to collect sequential, triplicate air samples in the front and rear of coach class during six sampling intervals throughout each flight: boarding, mid-climb, early cruise, mid-cruise, late cruise and deplaning. Comparison air samples were also collected inside and outside the airport terminals at the origin and destination cities. The MIXED procedure in SAS was used to model the mean and the covariance matrix of the natural log-transformed bacterial concentrations. A total of 513 airborne culturable bacterial samples were collected. During flight (mid-climb and cruise intervals), a model-adjusted geometric mean (GM) of 136 total colony-forming units per cubic meter of air sampled (CFU x m(-3)) and geometric standard deviation of 2.1 were observed. Bacterial concentrations were highest during the boarding (GM 290 CFU x m(-3)) and deplaning (GM 549 CFU x m(-3)) processes. Total bacterial concentrations observed during flight were significantly lower than GMs for boarding and deplaning (P values <0.0001-0.021) in the modeled results. Our findings highlight the fact that aerobiological concentrations can be dynamic and underscore the importance of appropriate sample size and design. The genera analysis indicates that passenger activity and high occupant density contribute to airborne bacterial generation. Overall, our research demonstrates that the bacteria recovered on observed flights were either common skin-surface organisms (primarily gram-positive cocci) or organisms common in dust and outdoor air.

  12. 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.

  13. Microbial protein synthesis, ruminal digestion, microbial populations, and nitrogen balance in sheep fed diets varying in forage-to-concentrate ratio and type of forage.

    PubMed

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

    2009-09-01

    Six ruminally and duodenally cannulated sheep were used in a partially replicated 4 x 4 Latin square to evaluate the effects of 4 diets on microbial synthesis, microbial populations, and ruminal digestion. The experimental diets had forage to concentrate ratios (F:C; DM basis) of 70:30 (HF) or 30:70 (HC) with alfalfa hay (A) or grass hay (G) as forage and were designated as HFA, HCA, HFG, and HCG. The concentrate was based on barley, gluten feed, wheat middlings, soybean meal, palmkern meal, wheat, corn, and mineral-vitamin premix in the proportions of 22, 20, 20, 13, 12, 5, 5, and 3%, respectively (as-is basis). Sheep were fed the diets at a daily rate of 56 g/kg of BW(0.75) to minimize feed selection. High-concentrate diets resulted in greater (P < 0.001) total tract apparent OM digestibility compared with HF diets, but no differences were detected in NDF digestibility. Ruminal digestibility of OM, NDF, and ADF was decreased by increasing the proportion of concentrate, but no differences between forages were detected. Compared with sheep fed HF diets, sheep receiving HC diets had less ruminal pH values and acetate proportions, but greater butyrate proportions. No differences among diets were detected in numbers of cellulolytic bacteria, but protozoa numbers were less (P = 0.004) and total bacteria numbers tended (P = 0.08) to be less for HC diets. Carboxymethylcellulase, xylanase, and amylase activities were greater for HC compared with HF diets, with A diets showing greater (P = 0.008) carboxymethylcellulase activities than G diets. Retained N ranged from 28.7 to 37.9% of N intake and was not affected by F:C (P = 0.62) or the type of forage (P = 0.31). Microbial N synthesis and its efficiency was greater (P < 0.001) for HC diets compared with HF diets. The results indicate that concentrates with low cereal content can be included in the diet of sheep up to 70% of the diet without detrimental effects on ruminal activity, microbial synthesis efficiency, and N

  14. 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

  15. Contribution of microbial activity to carbon chemistry in clouds.

    PubMed

    Vaïtilingom, Mickaël; Amato, Pierre; Sancelme, Martine; Laj, Paolo; Leriche, Maud; Delort, Anne-Marie

    2010-01-01

    The biodegradation of the most abundant atmospheric organic C1 to C4 compounds (formate, acetate, lactate, succinate) by five selected representative microbial strains (three Pseudomonas strains, one Sphingomonas strain, and one yeast strain) isolated from cloud water at the puy de Dôme has been studied. Experiments were first conducted under model conditions and consisted of a pure strain incubated in the presence of a single organic compound. Kinetics showed the ability of the isolates to degrade atmospheric compounds at temperatures representative of low-altitude clouds (5 degrees C and 17 degrees C). Then, to provide data that can be extrapolated to real situations, microcosm experiments were developed. A solution that chemically mimicked the composition of cloud water was used as an incubation medium for microbial strains. Under these conditions, we determined that microbial activity would significantly contribute to the degradation of formate, acetate, and succinate in cloud water at 5 degrees C and 17 degrees C, with lifetimes of 0.4 to 69.1 days. Compared with the reactivity involving free radicals, our results suggest that biological activity drives the oxidation of carbonaceous compounds during the night (90 to 99%), while its contribution accounts for 2 to 37% of the reactivity during the day, competing with photochemistry.

  16. Contribution of microbial activity to virus reduction in saturated soil.

    PubMed

    Nasser, A M; Glozman, R; Nitzan, Y

    2002-05-01

    Application of wastewater to soil may result in the contamination of groundwater and soil with pathogenic microorganisms and other biological and chemical agents. This study was performed to determine the antiviral microbial activity of soil saturated with secondary effluent. Low concentrations (0.05mg/ml) of protease pronase resulted in the inactivation of more than 90% of seeded Cox-A9 virus, whereas Poliovirus type 1, Hepatitis A virus (HAV) and MS2 bacteriophages were found to be insensitive to the enzyme activity. Exposure of Cox A9 virus to P. aeruginosa extracellular enzymes resulted in 99% inactivation of the seeded virus. Hepatitis A virus was found to be as sensitive as the Cox A9 virus, whereas Poliovirus 1 and MS2 were found to be insensitive to P. aeruginosa extracellular enzymatic activity. Furthermore, the time required for 99% reduction (T99) of Cox A9 and MS-2 Bacteriophage, at 15 degrees C, in soil saturated with secondary effluent was found to be 7 and 21 days, respectively. Faster inactivation was observed for MS2 and Cox A9 in soil saturated with secondary effluent incubated at 30 degrees C, T99 of 2 and 0.3 days, respectively. Although the concentration of the total bacterial count in the soil samples increased from 10(3) cfu/g to 10(5) cfu/g after 20 days of incubation at 30 degrees C, the proteolytic activity was below the detection level. The results of this study indicate that the virucidal effect of microbial activity is virus type dependent. Furthermore microbial activity in the soil material can be enhanced by the application of secondary effluent at higher temperature. The results also showed that MS2 bacteriophage can be used to predict viral contamination of soil and groundwater.

  17. Bioenergy feedstock-specific enrichment of microbial populations during high-solids thermophilic deconstruction.

    PubMed

    Reddy, Amitha P; Allgaier, Martin; Singer, Steven W; Hazen, Terry C; Simmons, Blake A; Hugenholtz, Philip; VanderGheynst, Jean S

    2011-09-01

    Thermophilic microbial communities that are active in a high-solids environment offer great potential for the discovery of industrially relevant enzymes that efficiently deconstruct bioenergy feedstocks. In this study, finished green waste compost was used as an inoculum source to enrich microbial communities and associated enzymes that hydrolyze cellulose and hemicellulose during thermophilic high-solids fermentation of the bioenergy feedstocks switchgrass and corn stover. Methods involving the disruption of enzyme and plant cell wall polysaccharide interactions were developed to recover xylanase and endoglucanase activity from deconstructed solids. Xylanase and endoglucanase activity increased by more than a factor of 5, upon four successive enrichments on switchgrass. Overall, the changes for switchgrass were more pronounced than for corn stover; solids reduction between the first and second enrichments increased by a factor of four for switchgrass while solids reduction remained relatively constant for corn stover. Amplicon pyrosequencing analysis of small-subunit ribosomal RNA genes recovered from enriched samples indicated rapid changes in the microbial communities between the first and second enrichment with the simplified communities achieved by the third enrichment. The results demonstrate a successful approach for enrichment of unique microbial communities and enzymes active in a thermophilic high-solids environment.

  18. Sediment biogeochemistry and microbial activity at natural hydrocarbon seeps and at sites impacted by anthropogenic hydrocarbon discharges

    NASA Astrophysics Data System (ADS)

    Joye, S. B.; Sibert, R.; Battles, J.; Fields, L.; Kleindienst, S.; Crespo-Medina, M.; Hunter, K.; Meile, C. D.; Montoya, J. P.

    2013-12-01

    Natural hydrocarbon seeps occur along the seafloor where geologic faults facilitate transfer of deeply sourced fluids enriched in gas, oil, and dissolved organic matter through shallow sediments and into the water column. At natural seeps, microbial populations specialize in hydrocarbon degradation and rates of microbial activity, including sulfate reduction and anaerobic oxidation of methane, can be extremely high. As a result, the biogeochemical signature of sediments near areas of active natural seepage is distinct: high concentrations of metabolic end products, such as dissolved inorganic carbon and hydrogen sulfide, abound, and often, high dissolved inorganic carbon concentrations result in the precipitation of authigenic carbonate minerals. We examined microbial processes and biogeochemical signatures at two natural seeps, Green Canyon 600 and Mississippi Canyon 118. Higher and more frequent seepage loci at the Green Canyon 600 site led to more widespread hotspots of elevated microbial activity and distinct geochemistry. However, rates of microbial activity were comparable at the two sites in areas of active hydrocarbon seepage. The microbial communities at the two sites were surprisingly different. The second group of sites was impacted by anthropogenic hydrocarbon discharges instead of natural seepage. One site, Oceanus 26, lies near the Deepwater Horizon/Macondo wellhead and was impacted by weathered oil sedimentation during the Macondo discharge. The second set of impacted sites, noted as Taylor Energy, lie near a sunken platform and compromised riser, which have together resulted in persistent hydrocarbon discharge to the adjacent oceanic system for more than 6 years. Rates of microbial activity in the upper sediments at Oceanus 26 were depressed relative to activity in the deeper layers, suggesting inhibition by the presence of weathered oil or an microbial community unable to weather the carbon available in the layer. At the Taylor energy site

  19. [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

  20. 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

  1. 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

  2. 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

  3. Microbial Population Dynamics Associated with Crude-Oil Biodegradation in Diverse Soils

    PubMed Central

    Hamamura, Natsuko; Olson, Sarah H.; Ward, David M.; Inskeep, William P.

    2006-01-01

    Soil bacterial population dynamics were examined in several crude-oil-contaminated soils to identify those organisms associated with alkane degradation and to assess patterns in microbial response across disparate soils. Seven soil types obtained from six geographically distinct areas of the United States (Arizona, Oregon, Indiana, Virginia, Oklahoma, and Montana) were used in controlled contamination experiments containing 2% (wt/wt) crude oil spiked with [1-14C]hexadecane. Microbial populations present during hydrocarbon degradation were analyzed using both 16S rRNA gene sequence analysis and by traditional methods for cultivating hydrocarbon-oxidizing bacteria. After a 50-day incubation, all seven soils showed comparable hydrocarbon depletion, where >80% of added crude oil was depleted and approximately 40 to 70% of added [14C]hexadecane was converted to 14CO2. However, the initial rates of hydrocarbon depletion differed up to 10-fold, and preferential utilization of shorter-chain-length n-alkanes relative to longer-chain-length n-alkanes was observed in some soils. Distinct microbial populations developed, concomitant with crude-oil depletion. Phylogenetically diverse bacterial populations were selected across different soils, many of which were identical to hydrocarbon-degrading isolates obtained from the same systems (e.g., Nocardioides albus, Collimonas sp., and Rhodococcus coprophilus). In several cases, soil type was shown to be an important determinant, defining specific microorganisms responding to hydrocarbon contamination. However, similar Rhodococcus erythropolis-like populations were observed in four of the seven soils and were the most common hydrocarbon-degrading organisms identified via cultivation. PMID:16957258

  4. 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.

  5. 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

  6. 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. (

  7. 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

  8. 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.

  9. 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.

  10. Efficacy of gaseous ozone against Salmonella and microbial population on dried oregano.

    PubMed

    Torlak, Emrah; Sert, Durmuş; Ulca, Pelin

    2013-08-01

    Interest in potential food applications of ozone has expanded in recent years in response to consumer demands for green technologies. This study was conducted to evaluate the efficacy of gaseous ozone for the microbial reduction and elimination of Salmonella on dried oregano. Ozone treatment was performed up to 120min under continuous stream of two different constant ozone concentrations (2.8 and 5.3mg/L). Significant (P<0.05) reductions of 2.7 and 1.8 log were observed in aerobic plate counts and yeast and mold counts after ozonation at 2.8mg/L for 120min, respectively. Ozonation performed at 5.3mg/L for 90min yielded a reduction of over 3.2 log in the aerobic plate counts. Initial population of a cocktail of Salmonella serotypes (S. Typhimurium, S. Newport and S. Montevideo) on inoculated oregano determined as 5.8logCFU/g decreased significantly by 2.8 and 3.7 log after ozonation at 2.8 and 5.3mg/L for 120min, respectively. Sensory evaluation results suggested that over the 2 log reduction in the microbial population can be obtained on dried oregano by gaseous ozone treatments with an acceptable taste, flavor and appearance. The results demonstrated that the gaseous ozone treatment is an effective alternative microbial reduction technique for dried oregano.

  11. The active microbial diversity drives ecosystem multifunctionality and is physiologically related to carbon availability in Mediterranean semi-arid soils.

    PubMed

    Bastida, Felipe; Torres, Irene F; Moreno, José L; Baldrian, Petr; Ondoño, Sara; Ruiz-Navarro, Antonio; Hernández, Teresa; Richnow, Hans H; Starke, Robert; García, Carlos; Jehmlich, Nico

    2016-09-01

    Biogeochemical processes and ecosystemic functions are mostly driven by soil microbial communities. However, most methods focus on evaluating the total microbial community and fail to discriminate its active fraction which is linked to soil functionality. Precisely, the activity of the microbial community is strongly limited by the availability of organic carbon (C) in soils under arid and semi-arid climate. Here, we provide a complementary genomic and metaproteomic approach to investigate the relationships between the diversity of the total community, the active diversity and ecosystem functionality across a dissolved organic carbon (DOC) gradient in southeast Spain. DOC correlated with the ecosystem multifunctionality index composed by soil respiration, enzyme activities (urease, alkaline phosphatase and β-glucosidase) and microbial biomass (phospholipid fatty acids, PLFA). This study highlights that the active diversity (determined by metaprotoemics) but not the diversity of the whole microbial community (evaluated by amplicon gene sequencing) is related to the availability of organic C and it is also connected to the ecosystem multifunctionality index. We reveal that DOC shapes the activities of bacterial and fungal populations in Mediterranean semi-arid soils and determines the compartmentalization of functional niches. For instance, Rhizobales thrived at high-DOC sites probably fuelled by metabolism of one-C compounds. Moreover, the analysis of proteins involved in the transport and metabolism of carbohydrates revealed that Ascomycota and Basidiomycota occupied different nutritional niches. The functional mechanisms for niche specialization were not constant across the DOC gradient. PMID:27481114

  12. The active microbial diversity drives ecosystem multifunctionality and is physiologically related to carbon availability in Mediterranean semi-arid soils.

    PubMed

    Bastida, Felipe; Torres, Irene F; Moreno, José L; Baldrian, Petr; Ondoño, Sara; Ruiz-Navarro, Antonio; Hernández, Teresa; Richnow, Hans H; Starke, Robert; García, Carlos; Jehmlich, Nico

    2016-09-01

    Biogeochemical processes and ecosystemic functions are mostly driven by soil microbial communities. However, most methods focus on evaluating the total microbial community and fail to discriminate its active fraction which is linked to soil functionality. Precisely, the activity of the microbial community is strongly limited by the availability of organic carbon (C) in soils under arid and semi-arid climate. Here, we provide a complementary genomic and metaproteomic approach to investigate the relationships between the diversity of the total community, the active diversity and ecosystem functionality across a dissolved organic carbon (DOC) gradient in southeast Spain. DOC correlated with the ecosystem multifunctionality index composed by soil respiration, enzyme activities (urease, alkaline phosphatase and β-glucosidase) and microbial biomass (phospholipid fatty acids, PLFA). This study highlights that the active diversity (determined by metaprotoemics) but not the diversity of the whole microbial community (evaluated by amplicon gene sequencing) is related to the availability of organic C and it is also connected to the ecosystem multifunctionality index. We reveal that DOC shapes the activities of bacterial and fungal populations in Mediterranean semi-arid soils and determines the compartmentalization of functional niches. For instance, Rhizobales thrived at high-DOC sites probably fuelled by metabolism of one-C compounds. Moreover, the analysis of proteins involved in the transport and metabolism of carbohydrates revealed that Ascomycota and Basidiomycota occupied different nutritional niches. The functional mechanisms for niche specialization were not constant across the DOC gradient.

  13. 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

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. 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

  19. 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

  20. 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

  1. 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

  2. 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

  3. 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.

  4. 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.

  5. Seasonal variations in microbial populations and environmental conditions in an extreme acid mine drainage environment.

    PubMed

    Edwards, K J; Gihring, T M; Banfield, J F

    1999-08-01

    Microbial populations, their distributions, and their aquatic environments were studied over a year (1997) at an acid mine drainage (AMD) site at Iron Mountain, Calif. Populations were quantified by fluorescence in situ hybridizations with group-specific probes. Probes were used for the domains Eucarya, Bacteria, and Archaea and the two species most widely studied and implicated for their role in AMD production, Thiobacillus ferrooxidans and Leptospirillum ferrooxidans. Results show that microbial populations, in relative proportions and absolute numbers, vary spatially and seasonally and correlate with geochemical and physical conditions (pH, temperature, conductivity, and rainfall). Bacterial populations were in the highest proportion (>95%) in January. Conversely, archaeal populations were in the highest proportion in July and September ( approximately 50%) and were virtually absent in the winter. Bacterial and archaeal populations correlated with conductivity and rainfall. High concentrations of dissolved solids, as reflected by high conductivity values (up to 125 mS/cm), occurred in the summer and correlated with high archaeal populations and proportionally lower bacterial populations. Eukaryotes were not detected in January, when total microbial cell numbers were lowest (<10(5) cells/ml), but eukaryotes increased at low-pH sites ( approximately 0.5) during the remainder of the year. This correlated with decreasing water temperatures (50 to 30 degrees C; January to November) and increasing numbers of prokaryotes (10(8) to 10(9) cells/ml). T. ferrooxidans was in highest abundance (>30%) at moderate pHs and temperatures ( approximately 2.5 and 20 degrees C) in sites that were peripheral to primary acid-generating sites and lowest (0 to 5%) at low-pH sites (pH approximately 0.5) that were in contact with the ore body. L. ferrooxidans was more widely distributed with respect to geochemical conditions (pH = 0 to 3; 20 to 50 degrees C) but was more abundant at

  6. Effects of butachlor on microbial enzyme activities in paddy soil.

    PubMed

    Min, Hang; Ye, Yang-Fang; Chen, Zhong-Yun; Wu, Wei-Xiang; Du, Yu-Feng

    2002-07-01

    This paper reports the influences of the herbicide butachlor (n-butoxymethl-chloro-2', 6'-diethylacetnilide) on microbial respiration, nitrogen fixation and nitrification, and on the activities of dehydrogenase and hydrogen peroxidase in paddy soil. The results showed that after application of butachlor with concentrations of 5.5 micrograms/g dried soil, 11.0 micrograms/g dried soil and 22.0 micrograms/g dried soil, the application of butachlor enhanced the activity of dehydrogenase at increasing concentrations. The soil dehydrogenase showed the highest activity on the 16th day after application of 22.0 micrograms/g dried soil of butachlor. The hydrogen peroxidase could be stimulated by butachlor. The soil respiration was depressed within a period from several days to more than 20 days, depending on concentrations of butachlor applied. Both the nitrogen fixation and nitrification were stimulated in the beginning but reduced greatly afterwards in paddy soil.

  7. Innate and cytokine-driven signals, rather than microbial antigens, dominate in natural killer T cell activation during microbial infection

    PubMed Central

    Tatituri, Raju V.V.; Watts, Gerald F.M.; Bhowruth, Veemal; Leadbetter, Elizabeth A.; Barton, Nathaniel; Cohen, Nadia R.; Hsu, Fong-Fu; Besra, Gurdyal S.

    2011-01-01

    Invariant natural killer T cells (iNKT cells) are critical for host defense against a variety of microbial pathogens. However, the central question of how iNKT cells are activated by microbes has not been fully explained. The example of adaptive MHC-restricted T cells, studies using synthetic pharmacological α-galactosylceramides, and the recent discovery of microbial iNKT cell ligands have all suggested that recognition of foreign lipid antigens is the main driver for iNKT cell activation during infection. However, when we compared the role of microbial antigens versus innate cytokine-driven mechanisms, we found that iNKT cell interferon-γ production after in vitro stimulation or infection with diverse bacteria overwhelmingly depended on toll-like receptor–driven IL-12. Importantly, activation of iNKT cells in vivo during infection with Sphingomonas yanoikuyae or Streptococcus pneumoniae, pathogens which are known to express iNKT cell antigens and which require iNKT cells for effective protection, also predominantly depended on IL-12. Constitutive expression of high levels of IL-12 receptor by iNKT cells enabled instant IL-12–induced STAT4 activation, demonstrating that among T cells, iNKT cells are uniquely equipped for immediate, cytokine-driven activation. These findings reveal that innate and cytokine-driven signals, rather than cognate microbial antigen, dominate in iNKT cell activation during microbial infections. PMID:21555485

  8. 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

  9. 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

  10. 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

  11. [The influence of Acinetobacter calcoaceticus K-4 surface-active substances on the efficiency of microbial destruction of oil pollutants].

    PubMed

    Pyroh, T P; Antoniuk, S I; Sorokina, A I

    2009-01-01

    The possibility of the use of Acinetobacter calcoaceticus K-4 surface-active substances (SAS) for water purification from oil was shown. The efficiency of oil degradation (2.6 g/l) in the presence of SAS preparations (5-15 %) in the form of postfermentation of cultural liquid or its supernatant was established to be 81-95 %. Intensification of oil destruction was determined by SAS affecting the activity of oil-oxidizing microbial population.

  12. 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

  13. 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

  14. 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.

  15. Pattern and synchrony of gene expression among sympatric marine microbial populations.

    PubMed

    Ottesen, Elizabeth A; Young, Curtis R; Eppley, John M; Ryan, John P; Chavez, Francisco P; Scholin, Christopher A; DeLong, Edward F

    2013-02-01

    Planktonic marine microbes live in dynamic habitats that demand rapid sensing and response to periodic as well as stochastic environmental change. The kinetics, regularity, and specificity of microbial responses in situ, however, are not well-described. We report here simultaneous multitaxon genome-wide transcriptome profiling in a naturally occurring picoplankton community. An in situ robotic sampler using a Lagrangian sampling strategy enabled continuous tracking and repeated sampling of coherent microbial populations over 2 d. Subsequent RNA sequencing analyses yielded genome-wide transcriptome profiles of eukaryotic (Ostreococcus) and bacterial (Synechococcus) photosynthetic picoplankton as well as proteorhodopsin-containing heterotrophs, including Pelagibacter, SAR86-cluster Gammaproteobacteria, and marine Euryarchaea. The photosynthetic picoplankton exhibited strong diel rhythms over thousands of gene transcripts that were remarkably consistent with diel cycling observed in laboratory pure cultures. In contrast, the heterotrophs did not cycle diurnally. Instead, heterotrophic picoplankton populations exhibited cross-species synchronous, tightly regulated, temporally variable patterns of gene expression for many genes, particularly those genes associated with growth and nutrient acquisition. This multitaxon, population-wide gene regulation seemed to reflect sporadic, short-term, reversible responses to high-frequency environmental variability. Although the timing of the environmental responses among different heterotrophic species seemed synchronous, the specific metabolic genes that were expressed varied from taxon to taxon. In aggregate, these results provide insights into the kinetics, diversity, and functional patterns of microbial community response to environmental change. Our results also suggest a means by which complex multispecies metabolic processes could be coordinated, facilitating the regulation of matter and energy processing in a dynamically

  16. Pattern and synchrony of gene expression among sympatric marine microbial populations

    PubMed Central

    Ottesen, Elizabeth A.; Young, Curtis R.; Eppley, John M.; Ryan, John P.; Chavez, Francisco P.; Scholin, Christopher A.; DeLong, Edward F.

    2013-01-01

    Planktonic marine microbes live in dynamic habitats that demand rapid sensing and response to periodic as well as stochastic environmental change. The kinetics, regularity, and specificity of microbial responses in situ, however, are not well-described. We report here simultaneous multitaxon genome-wide transcriptome profiling in a naturally occurring picoplankton community. An in situ robotic sampler using a Lagrangian sampling strategy enabled continuous tracking and repeated sampling of coherent microbial populations over 2 d. Subsequent RNA sequencing analyses yielded genome-wide transcriptome profiles of eukaryotic (Ostreococcus) and bacterial (Synechococcus) photosynthetic picoplankton as well as proteorhodopsin-containing heterotrophs, including Pelagibacter, SAR86-cluster Gammaproteobacteria, and marine Euryarchaea. The photosynthetic picoplankton exhibited strong diel rhythms over thousands of gene transcripts that were remarkably consistent with diel cycling observed in laboratory pure cultures. In contrast, the heterotrophs did not cycle diurnally. Instead, heterotrophic picoplankton populations exhibited cross-species synchronous, tightly regulated, temporally variable patterns of gene expression for many genes, particularly those genes associated with growth and nutrient acquisition. This multitaxon, population-wide gene regulation seemed to reflect sporadic, short-term, reversible responses to high-frequency environmental variability. Although the timing of the environmental responses among different heterotrophic species seemed synchronous, the specific metabolic genes that were expressed varied from taxon to taxon. In aggregate, these results provide insights into the kinetics, diversity, and functional patterns of microbial community response to environmental change. Our results also suggest a means by which complex multispecies metabolic processes could be coordinated, facilitating the regulation of matter and energy processing in a dynamically

  17. 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...

  18. [Effects of different straw recycling and tillage methods on soil respiration and microbial activity].

    PubMed

    Li, Xiao-sha; Wu, Ning; Liu, Ling; Feng, Yu-peng; Xu, Xu; Han, Hui-fang; Ning, Tang-yuan; Li, Zeng-jia

    2015-06-01

    To explore the effects of different tillage methods and straw recycling on soil respiration and microbial activity in summer maize field during the winter wheat and summer maize double cropping system, substrate induced respiration method and CO2 release method were used to determine soil microbial biomass carbon, microbial activity, soil respiration, and microbial respiratory quotient. The experiment included 3 tillage methods during the winter wheat growing season, i.e., no-tillage, subsoiling and conventional tillage. Each tillage method was companied with 2 straw management patterns, i.e., straw recycling and no straw. The results indicated that the conservation tillage methods and straw recycling mainly affected 0-10 cm soil layer. Straw recycling could significantly improve the microbial biomass carbon and microbial activity, while decrease microbial respiratory quotient. Straw recycling could improve the soil respiration at both seedling stage and anthesis, however, it could reduce the soil respiration at filling stage, wax ripeness, and harvest stage. Under the same straw application, compared with conventional tillage, the soil respiration and microbial respiratory quotient in both subsoiling and no-tillage were reduced, while the microbial biomass carbon and microbial activity were increased. During the summer maize growing season, soil microbial biomass carbon and microbial activity were increased in straw returning with conservation tillage, while the respiratory quotient was reduced. In 0-10 cm soil layer, compared with conventional tillage, straw recycling with subsoiling and no-tillage significantly increased soil microbial biomass carbon by 95.8% and 74.3%, and increased soil microbial activity by 97.1% and 74.2%, respectively.

  19. 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

  20. 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.

  1. Assessment of microbial populations in methyl ethyl ketone degrading biofilters by denaturing gradient gel electrophoresis.

    PubMed

    Li, C; Moe, W M

    2004-05-01

    Denaturing gradient gel electrophoresis (DGGE) analysis of polymerase chain reaction-amplified genes coding for 16S rRNA was used to assess differences in bacterial community structure as a function of spatial location along the height of two biofilters used to treat a model waste gas stream containing methyl ethyl ketone (MEK). One of the laboratory-scale biofilters was operated as a conventional continuous-flow biofilter (CFB) and the other was operated as a sequencing batch biofilter (SBB). Both biofilters, inoculated with an identical starting culture and operated over a period lasting more than 300 days, received the same influent MEK concentration and same mass of MEK on a daily basis. The systems differed, however, in terms of the fraction of time during which contaminated air was supplied and the overall operating strategy employed. DGGE analysis indicated that microbial community structures differed as a function of height in each of the biofilters. The DGGE banding patterns also differed between the two biofilters, suggesting that operating strategies imposed on the biofilters imparted a sufficiently large selective pressure to influence microbial community structures. This may explain, in part, the superior performance of the SBB over the CFB during model transient loading conditions, and it may open new possibilities for purposely manipulating the microbial populations in biofilters treating gas-phase contaminants in a manner that leads to more favorable treatment performance.

  2. Microbial population dynamics in an anaerobic CSTR treating a chemical synthesis-based pharmaceutical wastewater.

    PubMed

    Oz, Nilgun Ayman; Ince, Orhan; Ince, Bahar Kasapgil; Akarsubasi, Alper Tunga; Eyice, Ozge

    2003-01-01

    Effects of a chemical synthesis based pharmaceutical wastewater on performance of an anaerobic completely stirred tank reactor (CSTR), activity of acetoclastic methanogens and microbial composition were evaluated under various influent compositions. Initially, the CSTR was fed with glucose up to an organic loading rate (OLR) of 6 kg COD/m3 x d corresponding to an F/M ratio of 0.43 with a hydraulic retention time (HRT) of 2.5 days. A COD removal efficiency of 92% and a methane yield of 0.32 m3 CH4/kg COD(removed) were achieved whilst specific methanogenic activity (SMA) was found to be 336mL CH4/gTVS x d. After the CSTR was fed with pre-aerated wastewater diluted by glucose in different dilution ratios of 10% (w/v), 30% (w/v), 70% (w/v), and 100% (w/v) pre-aerated wastewater, gradual decreases in COD removal efficiency to 71%, methane yield to 0.28 m3CH4/kg COD(removed) and SMA to 166 mL CH4/gTVS d occurred whilst volatile fatty acid concentration reached to 1474 mg/L. After the raw wastewater diluted with the pre-aerated wastewater was fed into the CSTR in increasing ratios of 10% (w/v), 30% (w/v), and 60% (w/v), there was a proportional deterioration in performance in terms of COD removal efficiency, methane yield and acetoclastic methanogenic activity. Epifluorescence microscopy of the seed sludge revealed that Methanococcus-like species, short, and medium rods were found to be equally dominant. The short and medium rod species remained equally dominant groups in the CSTR throughout the feeding regime whilst Methanococcus-like species and long rods were found to be in insignificant numbers at the end of the study. Changes in archael diversity were determined using molecular analyses such as polymerase chain reaction (PCR), and denaturent gradient gel electrophoresis (DGGE). Results showed that overall archeal diversity did not change much whereas changes in composition of eubacterial population occurred.

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. Geophysical monitoring of microbial activity during stimulated subsurface bioremediation

    NASA Astrophysics Data System (ADS)

    Williams, K. H.; Kemna, A.; Wilkins, M.; Druhan, J.; Arntzen, E.; N'guessan, L.; Long, P.; Hubbard, S.; Banfield, J.

    2007-12-01

    Understanding how microorganisms alter their physical and chemical environment during bioremediation is hindered by our inability to resolve subsurface microbial activity with high spatial resolution. Here we demonstrate the use of a minimally invasive geophysical technique to monitor microbe-mediated iron and sulfate reduction during acetate amendment of a uranium-contaminated aquifer near Rifle, CO. During induced polarization (IP) measurements, spatiotemporal variations in the phase response between applied and measured voltages correlated with changes in groundwater geochemistry indicative of microbial iron and sulfate reduction and sulfide mineral precipitation. The enhanced sensitivity of the high and low frequency phase responses to accumulated aqueous iron and sulfide, respectively, provide the ability to discriminate the dominant subsurface biogeochemical process. The spectral effect was verified and calibrated using a biostimulated column experiment containing Rifle sediments and groundwater. Sediments and fluids recovered from regions of the field site exhibiting an anomalous phase response were enriched in sorbed Fe(II) and cell-associated 2-4 nm diameter FeS nanoparticles. These mineral precipitates and accumulated electroactive ions altered the ability of pore fluids to conduct electrical charge, accounting for the IP response. The results reveal the usefulness of multi-frequency IP measurements for discriminating mineralogical and geochemical changes during stimulated subsurface bioremediation.

  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 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

  16. Population activities of the United States government.

    PubMed

    Miles Re, J

    1971-08-01

    The editor's comment in this issue of the journal cites 5 overlapping phases in the evolution of population and family planning programs in the United States. The phases are 1) collecting census data and vital statistics, 1790-, 2) family planning assistance to developing nations, 1963, 3) family planning assistance to the U.S. "disadvantaged," 1964-, 4) overpopulation as a national concern, 1969-, and 5) the multiple action phase, 197? (phase including diverse steps to limit population growth and occurring after basic attitudes toward human reproduction have changed). The issue of the journal focuses on total population size and rates of population increase rather than on the distribution of population, and on federal action rather than on the activities of state and local governments. The editor's comment is followed by an extensive discussion of population activities of the United States government, especially since 1963. Topics discussed include demographic data, international programs, research, federally subsidized family planning services, medical care programs, educational and international programs, national growth policy, and the roles of the legislative and executive branches of government. A directory listing federal agencies with substantial and identifiable programs concerned with population and family planning is appended.

  17. 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

  18. 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.

  19. 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.

  20. Evolutionary consequences of intra-patient phage predation on microbial populations.

    PubMed

    Seed, Kimberley D; Yen, Minmin; Shapiro, B Jesse; Hilaire, Isabelle J; Charles, Richelle C; Teng, Jessica E; Ivers, Louise C; Boncy, Jacques; Harris, Jason B; Camilli, Andrew

    2014-08-26

    The impact of phage predation on bacterial pathogens in the context of human disease is not currently appreciated. Here, we show that predatory interactions of a phage with an important environmentally transmitted pathogen, Vibrio cholerae, can modulate the evolutionary trajectory of this pathogen during the natural course of infection within individual patients. We analyzed geographically and temporally disparate cholera patient stool samples from Haiti and Bangladesh and found that phage predation can drive the genomic diversity of intra-patient V. cholerae populations. Intra-patient phage-sensitive and phage-resistant isolates were isogenic except for mutations conferring phage resistance, and moreover, phage-resistant V. cholerae populations were composed of a heterogeneous mix of many unique mutants. We also observed that phage predation can significantly alter the virulence potential of V. cholerae shed from cholera patients. We provide the first molecular evidence for predatory phage shaping microbial community structure during the natural course of infection in humans.

  1. Methane production and microbial community structure for alkaline pretreated waste activated sludge.

    PubMed

    Sun, Rui; Xing, Defeng; Jia, Jianna; Zhou, Aijuan; Zhang, Lu; Ren, Nanqi

    2014-10-01

    Alkaline pretreatment was studied to analyze the influence on waste activated sludge (WAS) reduction, methane production and microbial community structure during anaerobic digestion. Methane production from alkaline pretreated sludge (A-WAS) (pH = 12) increased from 251.2 mL/Ld to 362.2 mL/Ld with the methane content of 68.7% compared to raw sludge (R-WAS). Sludge reduction had been improved, and volatile suspended solids (VSS) removal rate and protein reduction had increased by ∼ 10% and ∼ 35%, respectively. The bacterial and methanogenic communities were analyzed using 454 pyrosequencing and clone libraries of 16S rRNA gene. Remarkable shifts were observed in microbial community structures after alkaline pretreatment, especially for Archaea. The dominant methanogenic population changed from Methanosaeta for R-WAS to Methanosarcina for A-WAS. In addition to the enhancement of solubilization and hydrolysis of anaerobic digestion of WAS, alkaline pretreatment showed significant impacts on the enrichment and syntrophic interactions between microbial communities.

  2. 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.

  3. Division synchrony and the dynamics of microbial populations: a size-specific model.

    PubMed

    Gage, T B; Williams, F M; Horton, J B

    1984-12-01

    A discrete, environmentally coupled, size-specific model of microbial population dynamics in continuous culture is presented. It is mathematically simpler than other models based on similar assumptions and lends itself to numerical and analytic solutions. It displays several phenomena which have been reported in the experimental literature but which are not well understood; specifically, a loose relationship between biomass and numbers (i.e., a time lag between mass growth and cell division) and a critical damping of biomass while numbers continue to oscillate. In addition, the model provides several new predictions: The stable biomass distribution is independent of the environmental factors considered in the model and uniformly distributes the biomass among the size classes. The rate of approach to stability and the frequency of waves through the size distributions are a function of the flow rate and the variance in rate of growth and size at division. The model should provide a useful basis for studying the effects of size specificity on the dynamics of microbial populations cultured in chemostats.

  4. 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

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

    PubMed

    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

  6. Population genomics and local adaptation in wild isolates of a model microbial eukaryote.

    PubMed

    Ellison, Christopher E; Hall, Charles; Kowbel, David; Welch, Juliet; Brem, Rachel B; Glass, N L; Taylor, John W

    2011-02-15

    Elucidating the connection between genotype, phenotype, and adaptation in wild populations is fundamental to the study of evolutionary biology, yet it remains an elusive goal, particularly for microscopic taxa, which comprise the majority of life. Even for microbes that can be reliably found in the wild, defining the boundaries of their populations and discovering ecologically relevant phenotypes has proved extremely difficult. Here, we have circumvented these issues in the microbial eukaryote Neurospora crassa by using a "reverse-ecology" population genomic approach that is free of a priori assumptions about candidate adaptive alleles. We performed Illumina whole-transcriptome sequencing of 48 individuals to identify single nucleotide polymorphisms. From these data, we discovered two cryptic and recently diverged populations, one in the tropical Caribbean basin and the other endemic to subtropical Louisiana. We conducted high-resolution scans for chromosomal regions of extreme divergence between these populations and found two such genomic "islands." Through growth-rate assays, we found that the subtropical Louisiana population has a higher fitness at low temperature (10 °C) and that several of the genes within these distinct regions have functions related to the response to cold temperature. These results suggest the divergence islands may be the result of local adaptation to the 9 °C difference in average yearly minimum temperature between these two populations. Remarkably, another of the genes identified using this unbiased, whole-genome approach is the well-known circadian oscillator frequency, suggesting that the 2.4°-10.6° difference in latitude between the populations may be another important environmental parameter. PMID:21282627

  7. ILO and its population information activities.

    PubMed

    1982-04-01

    The International Labor Organisation (ILO) has authorized population activities since 1968. During the 1970s a population "focal point" was set up for promoting, programming, coordinating and monitoring population activities, and a large scale research program on population and employment was initiated as part of the World Employment Program. Both aspects were incorporated in a Population and Labor Policies Branch in 1975. Population documentation in the ILO is the concern of the Documentation Unit in that Branch, and the Central Library and Documentation Branch of the General Analysis of Labor Problems Department. The Documentation Unit collects materials on population in relation to employment, income and mobility; development planning models, role of women; and population and family welfare education, including printed, visual and audiovisual materials. Available reference tools include subject indexes using terms from the ILO Thesaurus. Monthly accessions lists and periodic bibliographies of relevant ILO publications are produced. The Central Library collects materials on a wide range of related subjects and has been automated since 1965. Its machine readable library file, LABORDOC, is available through Systems Development Corporation. It also produces an abstract journal (International Labor Documentation), a bibliographic list of international organization documents of interest to ILO officials (IGODOC), and a machine readable file describing the 9000 periodicals received or published by the ILO. Publications of the ILO's Bureau of Statistics include Bulletin and Year Book of Labor Statistics and regional volumes of Labor Force Estimates and Projections. The ILO recognizes that much relevant material produced by ILO field offices and other external offices may not reach and be collected at headquarters; the Population Information Network might provide a means of filling this gap.

  8. A combination method to study the effects of petroleum on soil microbial activity.

    PubMed

    She, Wen Wen; Yao, Jun; Wang, Fei; Cai, Min Min; Wang, Jing Wei; Song, Chang Shun

    2013-01-01

    TAM III multi-channel calorimetry was applied to study the effect of different concentrations petroleum on soil microbial activity and community. The microbial activities of the soil samples were recorded as power-time curves. The thermokinetic parameters such as microbial growth rate constant k, total heat evolution Q(T), metabolic enthalpy ∆H (met) and mass specific heat rate J(Q/S) were calculated. Results showed that petroleum had a certain extent effects to soil microorganisms. The results indicate that the soil microbial activity was promoted with a petroleum concentration lower than 0.52 % ± 0.24 %, but inhibited with further increase in petroleum.

  9. 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.

  10. Effects of plant species coexistence on soil enzyme activities and soil microbial community structure under Cd and Pb combined pollution.

    PubMed

    Gao, Yang; Zhou, Pei; Mao, Liang; Zhi, Yueer; Zhang, Chunhua; Shi, Wanjun

    2010-01-01

    The relationship between plant species coexistence and soil microbial communities under heavy metal pollution has attracted much attention in ecology. However, whether plant species coexistence could offset the impacts of heavy metal combined pollution on soil microbial community structure and soil enzymes activities is not well studied. The modified ecological dose model and PCR-RAPD method were used to assess the effects of two plant species coexistence on soil microbial community and enzymes activities subjected to Cd and Pb combined stress. The results indicated that monoculture and mixed culture would increased microbe populations under Cd and Pb combined stress, and the order of sensitivity of microbial community responding to heavy metal stress was: actinomycetes > bacteria > fungi. The respirations were significantly higher in planted soil than that in unplanted soil. The plant species coexistence could enhance soil enzyme activities under Cd and Pb combined. Furthermore, planted soil would be helpful to enhance soil genetic polymorphisms, but Cd and Pb pollution would cause a decrease on soil genetic polymorphisms. Mixed culture would increase the ecological dose 50% (EDs50) values, and the ED50 values for soil enzyme activities decreased with increasing culture time. The dehydrogenase was most sensitive to metal addition and easily loses activity under low dose of heavy metal. However, it was difficult to fully inhibit the phoshpatase activity, and urease responded similarly with phosphatase.

  11. 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.

  12. Citrate and malonate increase microbial activity and alter microbial community composition in uncontaminated and diesel-contaminated soil microcosms

    NASA Astrophysics Data System (ADS)

    Martin, Belinda C.; George, Suman J.; Price, Charles A.; Shahsavari, Esmaeil; Ball, Andrew S.; Tibbett, Mark; Ryan, Megan H.

    2016-09-01

    Petroleum hydrocarbons (PHCs) are among the most prevalent sources of environmental contamination. It has been hypothesized that plant root exudation of low molecular weight organic acid anions (carboxylates) may aid degradation of PHCs by stimulating heterotrophic microbial activity. To test their potential implication for bioremediation, we applied two commonly exuded carboxylates (citrate and malonate) to uncontaminated and diesel-contaminated microcosms (10 000 mg kg-1; aged 40 days) and determined their impact on the microbial community and PHC degradation. Every 48 h for 18 days, soil received 5 µmol g-1 of (i) citrate, (ii) malonate, (iii) citrate + malonate or (iv) water. Microbial activity was measured daily as the flux of CO2. After 18 days, changes in the microbial community were assessed by a community-level physiological profile (CLPP) and 16S rRNA bacterial community profiles determined by denaturing gradient gel electrophoresis (DGGE). Saturated PHCs remaining in the soil were assessed by gas chromatography-mass spectrometry (GC-MS). Cumulative soil respiration increased 4- to 6-fold with the addition of carboxylates, while diesel contamination resulted in a small, but similar, increase across all carboxylate treatments. The addition of carboxylates resulted in distinct changes to the microbial community in both contaminated and uncontaminated soils but only a small increase in the biodegradation of saturated PHCs as measured by the n-C17 : pristane biomarker. We conclude that while the addition of citrate and malonate had little direct effect on the biodegradation of saturated hydrocarbons present in diesel, their effect on the microbial community leads us to suggest further studies using a variety of soils and organic acids, and linked to in situ studies of plants, to investigate the role of carboxylates in microbial community dynamics.

  13. Influence of pulsed magnetic field on soybean (Glycine max L.) seed germination, seedling growth and soil microbial population.

    PubMed

    Radhakrishnan, Ramalingam; Kumari, Bollipo Dyana Ranjitha

    2013-08-01

    The effects of pulsed magnetic field (PMF) treatment of soybean (Glycine max L. cv CO3) seeds were investigated on rate of seed germination, seedling growth, physico-chemical properties of seed leachates and soil microbial population under laboratory conditions. Seeds were exposed to PMF of 1500 nT at 0.1, 1.0 10.0 and 100.0 Hz for 5 h per day for 20 days, induced by enclosure coil systems. Non-treated seeds were considered as controls. All PMF treatments significantly increased the rate of seed germination, while 10 and 100 Hz PMFs showed the most effective response. The 1.0 and 10 Hz PMFs remarkably improved the fresh weight of shoots and roots, leaf area and plant height from seedlings from magnetically-exposed seeds compared to the control, while 10 Hz PMF increased the total soluble sugar, total protein and phenol contents. The leaf chlorophyll a, b and total chlorophyll were higher in PMF (10 and 100 Hz) pretreated plants, as compared to other treatments. In addition, activities of alpha-amylase, acid phosphatase, alkaline phosphatase, nitrate reductase, peroxidase and polyphenoloxidase were increased, while beta-amylase and protease activities were declined in PMF (10 Hz)-exposed soybean plants. Similarly, the capacity of absorbance of water by seeds and electrical conductivity of seed leachates were significantly enhanced by 10 Hz PMF exposure, whereas PMF (10 Hz) pretreated plants did not affect the microbial population in rhizosphere soil. The results suggested the potential of 10 Hz PMF treatment to enhance the germination and seedling growth of soybean.

  14. Influence of pulsed magnetic field on soybean (Glycine max L.) seed germination, seedling growth and soil microbial population.

    PubMed

    Radhakrishnan, Ramalingam; Kumari, Bollipo Dyana Ranjitha

    2013-08-01

    The effects of pulsed magnetic field (PMF) treatment of soybean (Glycine max L. cv CO3) seeds were investigated on rate of seed germination, seedling growth, physico-chemical properties of seed leachates and soil microbial population under laboratory conditions. Seeds were exposed to PMF of 1500 nT at 0.1, 1.0 10.0 and 100.0 Hz for 5 h per day for 20 days, induced by enclosure coil systems. Non-treated seeds were considered as controls. All PMF treatments significantly increased the rate of seed germination, while 10 and 100 Hz PMFs showed the most effective response. The 1.0 and 10 Hz PMFs remarkably improved the fresh weight of shoots and roots, leaf area and plant height from seedlings from magnetically-exposed seeds compared to the control, while 10 Hz PMF increased the total soluble sugar, total protein and phenol contents. The leaf chlorophyll a, b and total chlorophyll were higher in PMF (10 and 100 Hz) pretreated plants, as compared to other treatments. In addition, activities of alpha-amylase, acid phosphatase, alkaline phosphatase, nitrate reductase, peroxidase and polyphenoloxidase were increased, while beta-amylase and protease activities were declined in PMF (10 Hz)-exposed soybean plants. Similarly, the capacity of absorbance of water by seeds and electrical conductivity of seed leachates were significantly enhanced by 10 Hz PMF exposure, whereas PMF (10 Hz) pretreated plants did not affect the microbial population in rhizosphere soil. The results suggested the potential of 10 Hz PMF treatment to enhance the germination and seedling growth of soybean. PMID:24772951

  15. Spatial distribution of microbial populations and carbon cycle in the subsurface environment of the Horonobe area, Hokkaido, Japan

    NASA Astrophysics Data System (ADS)

    Amano, Y.; Ise, K.; Terashima, M.; Sasaki, Y.; Amamiya, H.; Yoshikawa, H.

    2014-12-01

    Microorganisms are widely distributed in the subsurface environments. However, the distribution, role and rate of metabolisms, and the source of their activity are not well known. In this study, we investigated deep groundwater samples from sedimentary rocks, containing saturated methane and CO2, using boreholes at the Horonobe Underground Research Laboratory (URL), northern Hokkaido, Japan. The hydrochemical conditions of groundwaters, such as in-situ water pressure, temperature, electric conductivity, pH, redox potential, were monitored without degassing at multiple intervals along the borehole. Groundwater samples were taken periodically and chemical composition was analyzed using ICP-MS, etc. Cell counts were in the range of 103 to 105 cells ml-1. Molecular analyses revealed the spatial distribution and heterogeneity of the microbial population. Abundant methanogens were detected in the groundwater, and 80% of them were related to either Methanoregula boonei or Methanobacterium flexile that can utilize H2/CO2 by methanogenesis. Phylotypes clustered within the phylum Firmicutes, beta-Proteobacteria, delta-Proteobacteria and candidate division TM7 were dominant in the groundwater samples. Laboratory experiments using a culture technique showed that humic substances purified from the groundwater at Horonobe area appear to be degraded by microorganisms. Our results suggest that microbial spatial distributions in the subsurface environment were correlated closely with geochemical conditions, such as redox condition and carbon sources. In addition, it is inferred that humic substances are one of the important carbon sources for the subsurface microbial redox processes in the environment. This study was partly funded by the Ministry of Economy, Trade and Industry of Japan.

  16. Archaeal Populations in Hypersaline Sediments Underlying Orange Microbial Mats in the Napoli Mud Volcano▿†

    PubMed Central

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

    2011-01-01

    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

  17. 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.

  18. Impact of nanoscale zero valent iron on geochemistry and microbial populations in trichloroethylene contaminated aquifer materials.

    PubMed

    Kirschling, Teresa L; Gregory, Kelvin B; Minkley, Edwin G; Lowry, Gregory V; Tilton, Robert D

    2010-05-01

    Nanoscale zerovalent iron (NZVI) particles are a promising technology for reducing trichloroethylene (TCE) contamination in the subsurface. Prior to injecting large quantities of nanoparticles into the groundwater it is important to understand what impact the particles will have on the geochemistry and indigenous microbial communities. Microbial populations are important not only for nutrient cycling, but also for contaminant remediation and heavy metal immobilization. Microcosms were used to determine the effects of NZVI addition on three different aquifer materials from TCE contaminated sites in Alameda Point, CA, Mancelona, MI, and Parris Island, SC. The oxidation and reduction potential of the microcosms consistently decreased by more than 400 mV when NZVI was added at 1.5 g/L concentrations. Sulfate concentrations decreased in the two coastal aquifer materials, and methane was observed in the presence of NZVI in Alameda Point microcosms, but not in the other two materials. Denaturing gradient gel electrophoresis (DGGE) showed significant shifts in Eubacterial diversity just after the Fe(0) was exhausted, and quantitative polymerase chain reaction (qPCR) analyses showed increases of the dissimilatory sulfite reductase gene (dsrA) and Archaeal 16s rRNA genes, indicating that reducing conditions and hydrogen created by NZVI stimulate both sulfate reducer and methanogen populations. Adding NZVI had no deleterious effect on total bacterial abundance in the microcosms. NZVI with a biodegradable polyaspartate coating increased bacterial populations by an order of magnitude relative to controls. The lack of broad bactericidal effect, combined with the stimulatory effect of polyaspartate coatings, has positive implications for NZVI field applications.

  19. Effects of replacing dietary starch with neutral detergent-soluble fibre on ruminal fermentation, microbial synthesis and populations of ruminal cellulolytic bacteria using the rumen simulation technique (RUSITEC).

    PubMed

    Zhao, X H; Liu, C J; Liu, Y; Li, C Y; Yao, J H

    2013-12-01

    A rumen simulation technique (RUSITEC) apparatus with eight 800 ml fermenters was used to investigate the effects of replacing dietary starch with neutral detergent-soluble fibre (NDSF) by inclusion of sugar beet pulp in diets on ruminal fermentation, microbial synthesis and populations of ruminal cellulolytic bacteria. Experimental diets contained 12.7, 16.4, 20.1 or 23.8% NDSF substituted for starch on a dry matter basis. The experiment was conducted over two independent 15-day incubation periods with the last 8 days used for data collection. There was a tendency that 16.4% NDSF in the diet increased the apparent disappearance of organic matter (OM) and neutral detergent fibre (NDF). Increasing dietary NDSF level increased carboxymethylcellulase and xylanase activity in the solid fraction and apparent disappearance of acid detergent fibre (ADF) but reduced the 16S rDNA copy numbers of Ruminococcus albus in both liquid and solid fractions and R. flavefaciens in the solid fraction. The apparent disappearance of dietary nitrogen (N) was reduced by 29.6% with increased dietary NDSF. Substituting NDSF for starch appeared to increase the ratios of acetate/propionate and methane/volatile fatty acids (VFA) (mol/mol). Replacing dietary starch with NDSF reduced the daily production of ammonia-N and increased the growth of the solid-associated microbial pellets (SAM). Total microbial N flow and efficiency of microbial synthesis (EMS), expressed as g microbial N/kg OM fermented, tended to increase with increased dietary NDSF, but the numerical increase did not continue as dietary NDSF exceeded 20.1% of diet DM. Results suggested that substituting NDSF for starch up to 16.4% of diet DM increased digestion of nutrients (except for N) and microbial synthesis, and further increases (from 16.4% to 23.8%) in dietary NDSF did not repress microbial synthesis but did significantly reduce digestion of dietary N.

  20. 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

  1. 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

  2. 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

  3. Perspectives for microbial community composition in anaerobic digestion: from abundance and activity to connectivity.

    PubMed

    De Vrieze, Jo; Verstraete, Willy

    2016-09-01

    Microbial management in anaerobic digestion is mainly focused on physically present and metabolically active species. Because of its complexity and operation near the thermodynamic equilibria, it is equally important to address functional regulation, based on spatial organisation and interspecies communication. Further establishment of the knowledge on microbial communication in anaerobic digestion through quorum sensing and nanowires is needed. Methods to detect centres of concentrated activity, related to the presence of highly active and well-connected species that take a central role in the anaerobic digestion process, have to be optimized. Bioaugmentation could serve as a crucial tool to introduce keystone species that may create or sustain such centres. Functional stability can be maintained by keeping the microbial community active. This results in a clear trade-off between functionally active and redundant microorganisms as primary basis for microbial community organization. Finally, a microbial community based prediction strategy for advanced process control is formulated. PMID:27376701

  4. 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.

  5. 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.

  6. 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

  7. Possible interactions between bacterial diversity, microbial activity and supraglacial hydrology of cryoconite holes in Svalbard

    PubMed Central

    Edwards, Arwyn; Anesio, Alexandre M; Rassner, Sara M; Sattler, Birgit; Hubbard, Bryn; Perkins, William T; Young, Michael; Griffith, Gareth W

    2011-01-01

    The diversity of highly active bacterial communities in cryoconite holes on three Arctic glaciers in Svalbard was investigated using terminal restriction fragment length polymorphism (T-RFLP) of the 16S rRNA locus. Construction and sequencing of clone libraries allowed several members of these communities to be identified, with Proteobacteria being the dominant one, followed by Cyanobacteria and Bacteroidetes. T-RFLP data revealed significantly different communities in holes on the (cold) valley glacier Austre Brøggerbreen relative to two adjacent (polythermal) valley glaciers, Midtre Lovénbreen and Vestre Brøggerbreen. These population compositions correlate with differences in organic matter content, temperature and the metabolic activity of microbial communities concerned. No within-glacier spatial patterns were observed in the communities identified over the 2-year period and with the 1 km-spaced sampling. We infer that surface hydrology is an important factor in the development of cryoconite bacterial communities. PMID:20664552

  8. Possible interactions between bacterial diversity, microbial activity and supraglacial hydrology of cryoconite holes in Svalbard.

    PubMed

    Edwards, Arwyn; Anesio, Alexandre M; Rassner, Sara M; Sattler, Birgit; Hubbard, Bryn; Perkins, William T; Young, Michael; Griffith, Gareth W

    2011-01-01

    The diversity of highly active bacterial communities in cryoconite holes on three Arctic glaciers in Svalbard was investigated using terminal restriction fragment length polymorphism (T-RFLP) of the 16S rRNA locus. Construction and sequencing of clone libraries allowed several members of these communities to be identified, with Proteobacteria being the dominant one, followed by Cyanobacteria and Bacteroidetes. T-RFLP data revealed significantly different communities in holes on the (cold) valley glacier Austre Brøggerbreen relative to two adjacent (polythermal) valley glaciers, Midtre Lovénbreen and Vestre Brøggerbreen. These population compositions correlate with differences in organic matter content, temperature and the metabolic activity of microbial communities concerned. No within-glacier spatial patterns were observed in the communities identified over the 2-year period and with the 1 km-spaced sampling. We infer that surface hydrology is an important factor in the development of cryoconite bacterial communities.

  9. 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/.

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

    PubMed Central

    Malki, Kema; Bruder, Katherine; Putonti, Catherine

    2015-01-01

    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

  11. Effect of moisture, organic matter, microbial population and fortification level on dissipation of pyraclostrobin in soils.

    PubMed

    Reddy, S Navakishore; Gupta, Suman; Gajbhiye, Vijay T

    2013-09-01

    The dissipation of pyraclostrobin, a strobilurin fungicide, in soil was found to be influenced by soil moisture, organic matter content and microbial population. Among the different moisture regimes, dissipation was faster under submerged condition (T1/2 10 days) followed by field capacity (T1/2 28.7 days) and in dry soil (T1/2 41.8 days). Use of sludge at 5 % level to Inceptisol favoured a faster dissipation of pyraclostrobin, whereas a slower rate of dissipation was observed in partial organic matter removed soil as compared to normal soil. Slower rate of dissipation was also observed in sterile soil (T1/2 47 days) compared to normal soil. Pyraclostrobin dissipated faster in Vertisol (T1/2 21.8 days) than in Inceptisol (T1/2 28.7 days). No significant difference in the dissipation rate was observed at 1 and 10 μg g(-1) fortification levels.

  12. 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

  13. 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

  14. Response of microbial community of tundra soil to global warming: Simulation of seasonal and long-term population dynamics

    SciTech Connect

    Panikov, N.S.

    1994-11-01

    A mathematical model has been constructed and verified to simulate dynamics of a microbial community in typical tundra. The model contains the following state variables: the population densities of three competing microbial species (exemplified by Arthrobacter, Pseudomonas, and Bacillus), indexes of their physiological state, concentration of available organic substrate, plant litter reserves, the amount of microbiovorous protozoans, and temperature. The mathematical model simulates adequately the qualitative features of microbial seasonal dynamics observed in tundra. The global warming and associated increase in primary productivity, as predicted by simulation, will relieve the pressure of L-selection and thus result in stabilization of the tundra microbial community. The model also predicts that aerobic decomposition of dead organic matter in solid will be accelerated compared to its formation. 24 refs., 7 figs., 1 tab.

  15. Linking TFT-LCD wastewater treatment performance to microbial population abundance of Hyphomicrobium and Thiobacillus spp.

    PubMed

    Fukushima, Toshikazu; Whang, Liang-Ming; Chen, Po-Chun; Putri, Dyah Wulandari; Chang, Ming-Yu; Wu, Yi-Ju; Lee, Ya-Ching

    2013-08-01

    This study investigated the linkage between performance of two full-scale membrane bioreactor (MBR) systems treating thin-film transistor liquid crystal display (TFT-LCD) wastewater and the population dynamics of dimethylsulfoxide (DMSO)/dimethylsulfide (DMS) degrading bacteria. High DMSO degradation efficiencies were achieved in both MBRs, while the levels of nitrification inhibition due to DMS production from DMSO degradation were different in the two MBRs. The results of real-time PCR targeting on DMSO/DMS degrading populations, including Hyphomicrobium and Thiobacillus spp., indicated that a higher DMSO oxidation efficiency occurred at a higher Hyphomicrobium spp. abundance in the systems, suggesting that Hyphomicrobium spp. may be more important for complete DMSO oxidation to sulfate compared with Thiobacillus spp. Furthermore, Thiobacillus spp. was more abundant during poor nitrification, while Hyphomicrobium spp. was more abundant during good nitrification. It is suggested that microbial population of DMSO/DMS degrading bacteria is closely linking to both DMSO/DMS degradation efficiency and nitrification performance. PMID:23628318

  16. 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.

  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. 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.

  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. Suppression of Rhizoctonia solani on Impatiens by Enhanced Microbial Activity in Composted Swine Waste-Amended Potting Mixes.

    PubMed

    Diab, H G; Hu, S; Benson, D M

    2003-09-01

    ABSTRACT Peat moss-based potting mix was amended with either of two composted swine wastes, CSW1 and CSW2, at rates from 4 to 20% (vol/vol) to evaluate suppression of pre-emergence damping-off of impatiens (Impatiens balsamina) caused by Rhizoctonia solani (anastomosis group-4). A cucumber bioassay was used prior to each impatiens experiment to monitor maturity of compost as the compost aged in a curing pile by evaluating disease suppression toward both Pythium ultimum and R. solani. At 16, 24, 32, and 37 weeks after composting, plug trays filled with compost-amended potting mix were seeded with impatiens and infested with R. solani to determine suppression of damping-off. Pre-emergence damping-off was lower for impatiens grown in potting mix amended with 20% CSW1 than in CSW2-amended and nonamended mixes. To identify relationships between disease suppression and microbial parameters, samples of mixes were collected to determine microbial activity, biomass carbon and nitrogen, functional diversity, and population density. Higher rates of microbial activity were observed with increasing rates of CSW1 amendment than with CSW2 amendments. Microbial biomass carbon and nitrogen also were higher in CSW1-amended mixes than in CSW2-amended potting mixes 1 day prior to seeding and 5 weeks after seeding. Principal component analysis of Biolog-GN2 profiles showed different functional diversities between CSW1- and CSW2-amended mixes. Furthermore, mixes amended with CSW1 had higher colony forming units of fungi, endospore-forming bacteria, and oligotrophic bacteria. Our results suggest that enhanced microbial activity, functional and population diversity of stable compost-amended mix were associated with suppressiveness to Rhizoctonia damping-off in impatiens. PMID:18944095

  1. Suppression of Rhizoctonia solani on Impatiens by Enhanced Microbial Activity in Composted Swine Waste-Amended Potting Mixes.

    PubMed

    Diab, H G; Hu, S; Benson, D M

    2003-09-01

    ABSTRACT Peat moss-based potting mix was amended with either of two composted swine wastes, CSW1 and CSW2, at rates from 4 to 20% (vol/vol) to evaluate suppression of pre-emergence damping-off of impatiens (Impatiens balsamina) caused by Rhizoctonia solani (anastomosis group-4). A cucumber bioassay was used prior to each impatiens experiment to monitor maturity of compost as the compost aged in a curing pile by evaluating disease suppression toward both Pythium ultimum and R. solani. At 16, 24, 32, and 37 weeks after composting, plug trays filled with compost-amended potting mix were seeded with impatiens and infested with R. solani to determine suppression of damping-off. Pre-emergence damping-off was lower for impatiens grown in potting mix amended with 20% CSW1 than in CSW2-amended and nonamended mixes. To identify relationships between disease suppression and microbial parameters, samples of mixes were collected to determine microbial activity, biomass carbon and nitrogen, functional diversity, and population density. Higher rates of microbial activity were observed with increasing rates of CSW1 amendment than with CSW2 amendments. Microbial biomass carbon and nitrogen also were higher in CSW1-amended mixes than in CSW2-amended potting mixes 1 day prior to seeding and 5 weeks after seeding. Principal component analysis of Biolog-GN2 profiles showed different functional diversities between CSW1- and CSW2-amended mixes. Furthermore, mixes amended with CSW1 had higher colony forming units of fungi, endospore-forming bacteria, and oligotrophic bacteria. Our results suggest that enhanced microbial activity, functional and population diversity of stable compost-amended mix were associated with suppressiveness to Rhizoctonia damping-off in impatiens.

  2. Molecular characterization of microbial populations in full-scale biofilters treating iron, manganese and ammonia containing groundwater in Harbin, China.

    PubMed

    Li, Xiang-kun; Chu, Zhao-rui; Liu, Ya-jun; Zhu, Meng-ting; Yang, Liu; Zhang, Jie

    2013-11-01

    In iron and manganese-containing groundwater treatment for drinking water production, biological filter is an effective process to remove such pollutants. Until now the exact microbial mechanism of iron and manganese removal, especially coupled with other pollutants, such as ammonia, has not been clearly understood. To assess this issue, the performance of a full-scale biofilter located in Harbin, China was monitored over four months. Microbial populations in the biofilter were investigated using T-RFLP and clone library technique. Results suggested that Gallionella, Leptothrix, Nitrospira, Hyphomicrobium and Pseudomonas are dominant in the biofilter and play major roles in the removal of iron, manganese and ammonia. The spatial distribution of microbial populations along the depth of the biofilter demonstrated the stratification of the removal of iron, manganese and ammonia. Additionally, the absence of ammonia-oxidizing bacteria in the biofilter implicated that ammonia-oxidizing archaea might be responsible for the oxidation of ammonia to nitrite. PMID:23994965

  3. Molecular characterization of microbial populations in full-scale biofilters treating iron, manganese and ammonia containing groundwater in Harbin, China.

    PubMed

    Li, Xiang-kun; Chu, Zhao-rui; Liu, Ya-jun; Zhu, Meng-ting; Yang, Liu; Zhang, Jie

    2013-11-01

    In iron and manganese-containing groundwater treatment for drinking water production, biological filter is an effective process to remove such pollutants. Until now the exact microbial mechanism of iron and manganese removal, especially coupled with other pollutants, such as ammonia, has not been clearly understood. To assess this issue, the performance of a full-scale biofilter located in Harbin, China was monitored over four months. Microbial populations in the biofilter were investigated using T-RFLP and clone library technique. Results suggested that Gallionella, Leptothrix, Nitrospira, Hyphomicrobium and Pseudomonas are dominant in the biofilter and play major roles in the removal of iron, manganese and ammonia. The spatial distribution of microbial populations along the depth of the biofilter demonstrated the stratification of the removal of iron, manganese and ammonia. Additionally, the absence of ammonia-oxidizing bacteria in the biofilter implicated that ammonia-oxidizing archaea might be responsible for the oxidation of ammonia to nitrite.

  4. 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

  5. Sediment Microbial Enzyme Activity as an Indicator of Nutrient Limitation in Great Lakes Coastal Wetlands

    EPA Science Inventory

    This study, the first to link microbial enzyme activities to regional-scale anthropogenic stressors, suggests that microbial enzyme regulation of carbon and nutrient dynamics may be sensitive indicators of nutrient dynamics in aquatic ecosystems, but further work is needed to elu...

  6. Microbial Survey of a Full-Scale, Biologically Active Filter for Treatment of Drinking Water

    PubMed Central

    DeBry, Ronald W.; Lytle, Darren A.

    2012-01-01

    The microbial community of a full-scale, biologically active drinking water filter was surveyed using molecular techniques. Nitrosomonas, Nitrospira, Sphingomonadales, and Rhizobiales dominated the clone libraries. The results elucidate the microbial ecology of biological filters and demonstrate that biological treatment of drinking water should be considered a viable alternative to physicochemical methods. PMID:22752177

  7. 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

  8. Detecting rare structural variation in evolving microbial populations from new sequence junctions using breseq

    PubMed Central

    Deatherage, Daniel E.; Traverse, Charles C.; Wolf, Lindsey N.; Barrick, Jeffrey E.

    2014-01-01

    New mutations leading to structural variation (SV) in genomes—in the form of mobile element insertions, large deletions, gene duplications, and other chromosomal rearrangements—can play a key role in microbial evolution. Yet, SV is considerably more difficult to predict from short-read genome resequencing data than single-nucleotide substitutions and indels (SN), so it is not yet routinely identified in studies that profile population-level genetic diversity over time in evolution experiments. We implemented an algorithm for detecting polymorphic SV as part of the breseq computational pipeline. This procedure examines split-read alignments, in which the two ends of a single sequencing read match disjoint locations in the reference genome, in order to detect structural variants and estimate their frequencies within a sample. We tested our algorithm using simulated Escherichia coli data and then applied it to 500- and 1000-generation population samples from the Lenski E. coli long-term evolution experiment (LTEE). Knowledge of genes that are targets of selection in the LTEE and mutations present in previously analyzed clonal isolates allowed us to evaluate the accuracy of our procedure. Overall, SV accounted for ~25% of the genetic diversity found in these samples. By profiling rare SV, we were able to identify many cases where alternative mutations in key genes transiently competed within a single population. We also found, unexpectedly, that mutations in two genes that rose to prominence at these early time points always went extinct in the long term. Because it is not limited by the base-calling error rate of the sequencing technology, our approach for identifying rare SV in whole-population samples may have a lower detection limit than similar predictions of SNs in these data sets. We anticipate that this functionality of breseq will be useful for providing a more complete picture of genome dynamics during evolution experiments with haploid microorganisms

  9. 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...

  10. 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...

  11. Microbial populations of an upflow anaerobic sludge blanket reactor treating wastewater from a gelatin industry.

    PubMed

    Vieira, A M; Bergamasco, R; Gimenes, M L; Nakamura, C V; Dias Filho, B P

    2001-12-01

    The microbial populations of an upflow anaerobic sludge blanket reactor, used for treating wastewater from the gelatin industry, were studied by microbiological methods and phase-contrast and electron microscopy. Microscopy examination of the sludge showed a complex mixture of various rod-shaped and coccoid bacterial pluslong filaments and verymobile curved rods. In addition free-living anaerobic ciliates and flagellates were also observed. The trophic group population observed in decreasing order of dominance were hydrolytic and acetogenic at 10(6) and sulfate reducing and methanogenic at 10(5). The rate of methane production in anaerobic granular sludge cultivated in growth medium supplement with formate pressurized with H2:CO2 showed a significant increase in methane yield compared with theseed culture containingthe same substrate and atmosphere of N2:CO2. Similar rates of methane production were observed when the growth medium was supplemented with acetate pressurized either with H2:CO2 or N2:CO2. The number of total anaerobic bacteria at 10(7), fecal coliforms and total coliforms at 10(6), and fecal streptococci at 10(3) is based on colony counts on solid media. The four prevalent species of facultative anaerobic gram-negative bacteria that belong to the family of Enterobacteriaceae were identified as Escherichia coli, Esherichia fergusonii, Klebsiella oxytoca, and Citrobacter freundii. The species Aeromonas hydrophila, Aeromonas veronii, Acinetobacter iwoffi and Stenotrophomonas maltophila were the most frequently isolated glucose fermenting and nonfermenting gram-negative bacilli.

  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. 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

  16. Dynamic response of microbial activity to irregular disturbance: effects of dormancy in biogeochemical simulations of multispecies systems.

    NASA Astrophysics Data System (ADS)

    Stolpovsky, Konstantin; Fetzer, Ingo; van Cappellen, Philippe; Thullner, Martin

    2010-05-01

    Motivation Soil habitats as many other environmental systems are characterized by frequent changes of living conditions of the microbial community. Microorganisms are known to respond to such changes by switching their physiological state between activity and dormancy. This allows them to endure periods of unfavorable environmental conditions. As a consequence, the competitiveness of microbial species is not only controlled by their growth performance under plentiful conditions but also by their ability and readiness to respond to periods of unfavorable environmental conditions. To our knowledge, the effects of dormancy and reactivation of individual microbial species on the composition of microbial communities and their biodegradation activity have hardly been addressed conceptually, especially not in the context of biogeochemical simulations of environmental systems. The aim of this study is to simulate the response of microbial model systems - containing two competing species with different growth and de-/reactivation efficiencies - on intermittent changes of environmental conditions. Approach Microbial respiration and population dynamics are modeled using the numerical simulation software BRNS (Biogeochemical Reaction Network Simulator). Active and dormant biomasses are included as state variables, growth of microorganisms is described by established approached and is combined with kinetic expressions derived to account for the deactivation and reactivation of the microorganisms. The kinetic expressions are functionally linked to the energy yields of the corresponding respiration pathways, as well as to the maintenance requirements of the organisms. We also take into consideration variation in the yield factor, depending on the energy budget and consider loss of biomass during reactivation. The model was used to simulate the dynamics of the microbial models systems for different/irregular frequencies of feeding events. Results Model simulation show that - as

  17. 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

  18. Soybean oligosaccharides alter colon short-chain fatty acid production and microbial population in vitro.

    PubMed

    Zhou, X L; Kong, X F; Yang, X J; Yin, Y L

    2012-12-01

    This study was conducted to the determine fermentation characteristics of soybean oligosaccharides (SBOS) in an in vitro system. Digesta collected from the colon of Huanjiang mini-pigs was used as inoculums, and SBOS (0.2 g per 10 mL fermentation broth) was used as substrate during the in vitro fermentation. The inoculum or inoculum + glucose (0.2 g) was used as negative or positive control, respectively. The slurry was fermented in an anaerobic chamber and gas production (GP) recording was taken after 48 h of incubation by referring to the moving scale on the plunger of the glass syringes, and then GP parameters, pH value, NH(3)-N content, short chain fatty acid (SCFA) levels, and microbial community in the fermentation broth were determined. For gas production parameters, pH, and fermentation product determination after 1, 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 28, 32, 36, 42, and 48 h of incubation, SBOS and glucose demonstrated similar responses compared to control including increase maximal gas production, decreased lag time, decreased pH, and accumulation of NH(3) and increased SCFA. The exception was rate of GP, which was higher (P < 0.05) for SBOS compared with glucose. Incubation with SBOS increased (P < 0.05) the microbial diversity and population of Bifidobacterium and Lactobacillus but decreased (P < 0.05) Escherichia and Streptococcus when compared with incubation with glucose. These findings suggested that the SBOS can improve the gut microbiota balance in colon and modulate its metabolism. PMID:23365277

  19. 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.

  20. 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.

  1. Metatranscriptome analysis of active microbial communities in produced water samples from the Marcellus Shale.

    PubMed

    Vikram, Amit; Lipus, Daniel; Bibby, Kyle

    2016-10-01

    Controlling microbial activity is a primary concern during the management of the large volumes of wastewater (produced water) generated during high-volume hydraulic fracturing. In this study we analyzed the transcriptional activity (metatranscriptomes) of three produced water samples from the Marcellus Shale. The goal of this study was to describe active metabolic pathways of industrial concern for produced water management and reuse, and to improve understanding of produced water microbial activity. Metatranscriptome analysis revealed active biofilm formation, sulfide production, and stress management mechanisms of the produced water microbial communities. Biofilm-formation and sulfate-reduction pathways were identified in all samples. Genes related to a diverse array of stress response mechanisms were also identified with implications for biocide efficacy. Additionally, active expression of a methanogenesis pathway was identified in a sample of produced water collected prior to holding pond storage. The active microbial community identified by metatranscriptome analysis was markedly different than the community composition as identified by 16S rRNA sequencing, highlighting the value of evaluating the active microbial fraction during assessments of produced water biofouling potential and evaluation of biocide application strategies. These results indicate biofouling and corrosive microbial processes are active in produced water and should be taken into consideration while designing produced water reuse strategies. PMID:27457653

  2. 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.

  3. 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

  4. 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

  5. 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

  6. 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.

  7. 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

  8. 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.

  9. Microbial extracellular enzyme activities in HUMEX Lake Skjervatjern

    SciTech Connect

    Muenster, U. )

    1992-01-01

    Two microbial extracellular enzyme activities (MEEA) were studied in HUMEX Lake Skjervatjern: acid phosphatase (APHA) and leucine aminopeptidase (LeuAMPA). Both enzyme activities varied in the vertical and horizontal scale in both lake sites. APHA varied in the acidfied Basin A between 945-1706 nmol L[sup [minus]1] h[sup [minus]1] and LeuAMPA between 3.7-25 nmol L[sup [minus]1] h[sup [minus]1]. Both MEEA reached maxima in 0.5 m depth. In the control site (Basin B), APHA was lower by a factor of two, and varied between 156-669 nmol L[sup [minus]1] h[sup [minus]1]. LeuAMPA reached similar values as in Basin A and varied between 7.8-34.8 nmol L[sup [minus]1] h[sup [minus]1]. Maxima of APHA were found in the upper layer (0-2 m), while LeuAMPA had only one distinct maxima at 2-2.5 m depth. The number of bacteria (AFDC) varied between 4.4-8.8 10[sup 6] cells mL[sup [minus]1] and was not significantly different in either side, but both had maxima in the thermocline. Highest specific LeuAMPA activities were found in the thermocline (3.2-4.5 fmol L[sup [minus]1] h[sup [minus]1] cell[sup [minus]1]) in both sides and varied between 0.4-4.5 fmol L[sup [minus]1] h[sup [minus]1] cell[sup [minus]1] in both water columns. The main contributor (60-70%) to LeuAMPA was found in the microplankton fraction, retained on Nuclepore filters with pore sizes between 2.0-0.2 [mu]m. APHA was retained less even on a filter with pore size smaller than 0.2 [mu]m. About 50-70% of APHA passed through 0.2 [mu]m-0.1 [mu]m Nuclepore filters and could be found in the dissolved organic matter (DOM) fraction. APHA and bacteria counts (AFDC) showed a distinct gradient from the littoral zone to the pelagial in the surface water samples (0.2 m depth). APHA and LeuAMPA are regarded as important regulators for nutrient availabilty to microplankton. 40 refs., 6 figs.

  10. 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

  11. 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.

  12. 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...

  13. 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...

  14. Impacts of Human Activity on the Microbial Communities of Devon Island, Canadian High Arctic

    NASA Astrophysics Data System (ADS)

    Bywaters, K. B.; Burton, A. S.; Wallace, S. L.; Glass, B. J.

    2016-09-01

    The impacts of human activities on microbial communities in arctic environments are poorly understood. This project compares the distribution of microbes at the HMP Mars analog site prior to and after human settlement.

  15. Functional Diversity and Electron Donor Dependence of Microbial Populations Capable of U(VI) Reduction in Radionuclide-Contaminated Subsurface Sediments▿

    PubMed Central

    Akob, Denise M.; Mills, Heath J.; Gihring, Thomas M.; Kerkhof, Lee; Stucki, Joseph W.; Anastácio, Alexandre S.; Chin, Kuk-Jeong; Küsel, Kirsten; Palumbo, Anthony V.; Watson, David B.; Kostka, Joel E.

    2008-01-01

    In order to elucidate the potential mechanisms of U(VI) reduction for the optimization of bioremediation strategies, the structure-function relationships of microbial communities were investigated in microcosms of subsurface materials cocontaminated with radionuclides and nitrate. A polyphasic approach was used to assess the functional diversity of microbial populations likely to catalyze electron flow under conditions proposed for in situ uranium bioremediation. The addition of ethanol and glucose as supplemental electron donors stimulated microbial nitrate and Fe(III) reduction as the predominant terminal electron-accepting processes (TEAPs). U(VI), Fe(III), and sulfate reduction overlapped in the glucose treatment, whereas U(VI) reduction was concurrent with sulfate reduction but preceded Fe(III) reduction in the ethanol treatments. Phyllosilicate clays were shown to be the major source of Fe(III) for microbial respiration by using variable-temperature Mössbauer spectroscopy. Nitrate- and Fe(III)-reducing bacteria (FeRB) were abundant throughout the shifts in TEAPs observed in biostimulated microcosms and were affiliated with the genera Geobacter, Tolumonas, Clostridium, Arthrobacter, Dechloromonas, and Pseudomonas. Up to two orders of magnitude higher counts of FeRB and enhanced U(VI) removal were observed in ethanol-amended treatments compared to the results in glucose-amended treatments. Quantification of citrate synthase (gltA) levels demonstrated a stimulation of Geobacteraceae activity during metal reduction in carbon-amended microcosms, with the highest expression observed in the glucose treatment. Phylogenetic analysis indicated that the active FeRB share high sequence identity with Geobacteraceae members cultivated from contaminated subsurface environments. Our results show that the functional diversity of populations capable of U(VI) reduction is dependent upon the choice of electron donor. PMID:18378664

  16. 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

  17. 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

  18. 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

  19. 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.

  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. 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

  2. Mild salinization stimulated glyphosate degradation and microbial activities in a riparian soil from Chongming Island, China.

    PubMed

    Yang, Changming; Shen, Shuo; Wang, Mengmeng; Li, Jianhua

    2013-04-01

    An incubation experiment was conducted to investigate the effects of simulated saltwater treatment with different percentages of artificial seawater on degradation dynamics of herbicide glyphosate and microbial activities in a riparian soil in Chongming Island, China. The results showed that 10% seawater treatment showed significantly enhancing effects on degradation efficiency of glyphosate with the lowest residual concentration among all the treatments. However, glyphosate degradation was markedly decreased in the riparian soil with 20% and 50% seawater treatments. The half-lives for 20% and 50% seawater treatments were prolonged by 12.1 and 39.0%, respectively, as compared to control. Microbial investigation indicated that 10% seawater treatment significantly stimulated microbial activities in the glyphosate-spiked riparian soil throughout the incubation period. At 42 day of incubation experiment, flourescein diacetate (FDA) hydrolysis rate, microbial adenosine triphosphate (ATP), and basal soil respiration (BSR) in the glyphosate-spiked riparian soil with 10% seawater were 59.2, 42.5 and 31.8% higher than those with no saltwater treatment, respectively. In contrast, saltwater treatment with 50% seawater significantly inhibited microbial activities. Especially, FDA hydrolysis rate, microbial ATP and BSR were decreased by 66.4, 58.6 and 66.8%, respectively, as compared to control. The results indicate that levels of simulated saltwater can exert variable effects on herbicide degradation dynamics and microbial parameters in the riparian soil.

  3. [Effect of straw pretreatment on soil microbial biomass and respiration activity].

    PubMed

    Li, Guitong; Zhang, Baogui; Li, Baoguo

    2003-12-01

    Winter wheat straw particles (0.5 ~ 2.0mm) were soaked with 8.0 g.L-1 H202(pH11.0), 12.5 g.L-1 Na0H or H2S04 solution for 8 h and dried at 80 degreeC. Soils amended with the pretreated straw and inorganic N were incubated aerobically at 25 degreeC for 60 days. The C02 emission rate and soil microbial biomass C and N were measured at different time. The results showed that during the earlier stage of incubation, the pretreatments of straw increased soil microbial biomass C by 1.0 ~ 1.4 folds, but decreased soil microbial respiration activity. During the later stage of incubation, the Na0H and H2S04 pretreated straw decreased soil microbial biomass carbon by 28% and 42%, respectively, while increased the soil microbial respiration activity. The straw pretreated by H202 increased soil microbial biomass nitrogen by 90% after the 15th day of incubation. The pretreatments of straw increased the fungi/bacteria ratio at different special time. It could be concluded that soil microbial biomass and respiration activity could be changed after the pretreated straw was added into the soil.

  4. Response of enzyme activities and microbial communities to soil amendment with sugar alcohols.

    PubMed

    Yu, Huili; Si, Peng; Shao, Wei; Qiao, Xiansheng; Yang, Xiaojing; Gao, Dengtao; Wang, Zhiqiang

    2016-08-01

    Changes in microbial community structure are widely known to occur after soil amendment with low-molecular-weight organic compounds; however, there is little information on concurrent changes in soil microbial functional diversity and enzyme activities, especially following sorbitol and mannitol amendment. Soil microbial functional diversity and enzyme activities can be impacted by sorbitol and mannitol, which in turn can alter soil fertility and quality. The objective of this study was to investigate the effects of sorbitol and mannitol addition on microbial functional diversity and enzyme activities. The results demonstrated that sorbitol and mannitol addition altered the soil microbial community structure and improved enzyme activities. Specifically, the addition of sorbitol enhanced the community-level physiological profile (CLPP) compared with the control, whereas the CLPP was significantly inhibited by the addition of mannitol. The results of a varimax rotated component matrix demonstrated that carbohydrates, polymers, and carboxylic acids affected the soil microbial functional structure. Additionally, we found that enzyme activities were affected by both the concentration and type of inputs. In the presence of high concentrations of sorbitol, the urease, catalase, alkaline phosphatase, β-glucosidase, and N-acetyl-β-d-glucosaminidase activities were significantly increased, while invertase activity was decreased. Similarly, this increase in invertase, catalase, and alkaline phosphatase and N-acetyl-β-d-glucosaminidase activities was especially evident after mannitol addition, and urease activity was only slightly affected. In contrast, β-glucosidase activity was suppressed at the highest concentration. These results indicate that microbial community diversity and enzyme activities are significantly affected by soil amendment with sorbitol and mannitol. PMID:27005019

  5. 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

  6. 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...

  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. 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.

  9. 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

  10. 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.

  11. 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

  12. 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.

  13. 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

  14. Information in Support of Population Activities.

    ERIC Educational Resources Information Center

    United Nations Educational, Scientific, and Cultural Organization, Paris (France).

    As part of UNESCO's World Population Year, information services in support of population programs are explained and listed. The information system of the International Planned Parenthood Federation is described and the management of population literature discussed. Information needs of population workers and special aspects of the training and…

  15. 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

  16. Chromospheric Activity in Population II Giants

    NASA Technical Reports Server (NTRS)

    Harper, Graham M.

    2004-01-01

    One of the mysteries of Population II giants is that they still show chromospheric emission despite their great age. The global dynamo which was active during their main-sequence lifetimes is expected to become extremely weak through magnetic rotational braking. The nature of the observed emission is not understood; although acoustic shock waves might provide the heating, acoustic waves are not predicted to drive the observed mass loss - which in turn requires the dissipation of magneto-hydrodynamic waves. This program was designed to search for the faint stellar H Ly beta emission wings and the fluorescent Fe II and H2 emission from one of the brightest, metal poor, Population II stars. These FUSE diagnostics, when combined with existing UV and optical spectra, help determine the major radiative cooling channels for the chromosphere. This observation was to complement that previously planned for the mildly metal deficient giant alpha Boo (K2 III). However, alpha Boo has yet to be observed with FUSE.

  17. 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

  18. Direct profiling of environmental microbial populations by thermal dissociation analysis of native rRNAs hybridized to oligonucleotide microarrays

    NASA Technical Reports Server (NTRS)

    El Fantroussi, Said; Urakawa, Hidetoshi; Bernhard, Anne E.; Kelly, John J.; Noble, Peter A.; Smidt, H.; Yershov, G. M.; Stahl, David A.

    2003-01-01

    Oligonucleotide microarrays were used to profile directly extracted rRNA from environmental microbial populations without PCR amplification. In our initial inspection of two distinct estuarine study sites, the hybridization patterns were reproducible and varied between estuarine sediments of differing salinities. The determination of a thermal dissociation curve (i.e., melting profile) for each probe-target duplex provided information on hybridization specificity, which is essential for confirming adequate discrimination between target and nontarget sequences.

  19. 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.

  20. 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.

  1. 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

  2. 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.

  3. Activated sludge microbial community responses to single-walled carbon nanotubes: community structure does matter.

    PubMed

    Ma, Qiao; Qu, Yuanyuan; Shen, Wenli; Wang, Jingwei; Zhang, Zhaojing; Zhang, Xuwang; Zhou, Hao; Zhou, Jiti

    2015-01-01

    The ecological effects of carbon nanotubes (CNTs) have been a worldwide research focus due to their extensive release and accumulation in environment. Activated sludge acting as an important gathering place will inevitably encounter and interact with CNTs, while the microbial responses have been rarely investigated. Herein, the activated sludges from six wastewater treatment plants were acclimated and treated with single-walled carbon nanotubes (SWCNTs) under identical conditions. Illumina high-throughput sequencing was applied to in-depth analyze microbial changes and results showed SWCNTs differently perturbed the alpha diversity of the six groups (one increase, two decrease, three no change). Furthermore, the microbial community structures were shifted, and specific bacterial performance in each group was different. Since the environmental and operational factors were identical in each group, it could be concluded that microbial responses to SWCNTs were highly depended on the original community structures. PMID:25909735

  4. 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

  5. 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.

  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. 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

  8. 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.

  9. Spatial Heterogeneity of Gut Microbial Composition along the Gastrointestinal Tract in Natural Populations of House Mice

    PubMed Central

    Nachman, Michael W.

    2016-01-01

    There is a growing appreciation of the role of gut microbial communities in host biology. However, the nature of variation in microbial communities among different segments of the gastrointestinal (GI) tract is not well understood. Here, we describe microbial communities from ten different segments of the GI tract (mouth, esophagus, stomach, duodenum, ileum, proximal cecum, distal cecum, colon, rectum, and feces) in wild house mice using 16S rRNA gene amplicon sequencing. We also measured carbon and nitrogen stable isotopic ratios from hair samples of individual mice as a proxy for diet. We identified factors that may explain differences in microbial composition among gut segments, and we tested for differences among individual mice in the composition of the microbiota. Consistent with previous studies, the lower GI tract was characterized by a greater relative abundance of anaerobic bacteria and greater microbial diversity relative to the upper GI tract. The upper and lower GI tracts also differed in the relative abundances of predicted microbial gene functions, including those involved in metabolic pathways. However, when the upper and lower GI tracts were considered separately, gut microbial composition was associated with individual mice. Finally, microbial communities derived from fecal samples were similar to those derived from the lower GI tract of their respective hosts, supporting the utility of fecal sampling for studying the gut microbiota of mice. These results show that while there is substantial heterogeneity among segments of the GI tract, individual hosts play a significant role in structuring microbial communities within particular segments of the GI tract. PMID:27669007

  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. Biodegradation of trichloroethylene and toluene by indigenous microbial populations in soil.

    PubMed

    Fan, S; Scow, K M

    1993-06-01

    The biodegradation of trichloroethylene (TCE) and toluene, incubated separately and in combination, by indigenous microbial populations was measured in three unsaturated soils incubated under aerobic conditions. Sorption and desorption of TCE (0.1 to 10 micrograms ml-1) and toluene (1.0 to 20 micrograms ml-1) were measured in two soils and followed a reversible linear isotherm. At a concentration of 1 micrograms ml-1, TCE was not degraded in the absence of toluene in any of the soils. In combination, both 1 microgram of TCE ml-1 and 20 micrograms of toluene ml-1 were degraded simultaneously after a lag period of approximately 60 to 80 h, and the period of degradation lasted from 70 to 90 h. Usually 60 to 75% of the initial 1 microgram of TCE ml-1 was degraded, whereas 100% of the toluene disappeared. A second addition of 20 micrograms of toluene ml-1 to a flask with residual TCE resulted in another 10 to 20% removal of the chemical. Initial rates of degradation of toluene and TCE were similar at 32, 25, and 18 degrees C; however, the lag period increased with decreasing temperature. There was little difference in degradation of toluene and TCE at soil moisture contents of 16, 25, and 30%, whereas there was no detectable degradation at 5 and 2.5% moisture. The addition of phenol, but not benzoate, stimulated the degradation of TCE in Rindge and Yolo silt loam soils, methanol and ethylene slightly stimulated TCE degradation in Rindge soil, glucose had no effect in either soil, and dissolved organic carbon extracted from soil strongly sorbed TCE but did not affect its rate of biodegradation. PMID:8328806

  13. 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...

  14. Analysis of rumen microbial populations in lactating dairy cattle fed diets varying in carbohydrate profiles and Saccharomyces cerevisiae fermentation product.

    PubMed

    Mullins, C R; Mamedova, L K; Carpenter, A J; Ying, Y; Allen, M S; Yoon, I; Bradford, B J

    2013-09-01

    The rumen microbial ecosystem is a critical factor that links diets to bovine physiology and productivity; however, information about dietary effects on microbial populations has generally been limited to small numbers of samples and qualitative assessment. To assess whether consistent shifts in microbial populations occur in response to common dietary manipulations in dairy cattle, samples of rumen contents were collected from 2 studies for analysis by quantitative real-time PCR (qPCR). In one study, lactating Holstein cows (n=8) were fed diets in which a nonforage fiber source replaced an increasing proportion of forages and concentrates in a 4×4 Latin square design, and samples of ruminal digesta were collected at 9-h intervals over 3 d at the end of each period. In the second study, lactating Holstein cows (n=15) were fed diets with or without the inclusion of a Saccharomyces cerevisiae fermentation product (SCFP) in a crossover design. In this study, rumen liquid and solid samples were collected during total rumen evacuations before and after feeding in a 42-h period. In total, 146 samples of ruminal digesta were used for microbial DNA isolation and analysis by qPCR. Validated primer sets were used to quantify total bacterial and anaerobic fungal populations as well as 12 well-studied bacterial taxa. The relative abundance of the target populations was similar to those previously reported. No significant treatment effects were observed for any target population. A significant interaction of treatment and dry matter intake was observed, however, for the abundance of Eubacterium ruminantium. Increasing dry matter intake was associated with a quadratic decrease in E. ruminantium populations in control animals but with a quadratic increase in E.ruminantium populations in cows fed SCFP. Analysis of sample time effects revealed that Fibrobacter succinogenes and fungal populations were more abundant postfeeding, whereas Ruminococcus albus tended to be more abundant

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. Anomalous electrical signals associated with microbial activity: Results from Iron and Nitrate-Reducing Columns

    NASA Astrophysics Data System (ADS)

    Aaron, R. B.; Zheng, Q.; Flynn, P.; Singha, K.; Brantley, S.

    2008-12-01

    Three flow-through columns outfitted with Ag/AgCl electrodes were constructed to test the effects of different microbial processes on the geophysical measurements of self potential (SP), bulk electrical conductivity (σ b), and induced polarization (IP). The columns were filled with sieved, Fe-bearing subsurface sediment from the Delmarva Peninsula near Oyster, VA, inoculated (9:1 ratio) with a freshly-collected, shallow subsurface sediment from a wetland floodplain (Dorn Creek) near Madison, WI. Each of the columns was fed anoxic and sterile PIPES buffered artificial groundwater (PBAGW) containing different concentrations of acetate and nitrate. The medium fed to Column 1 (nitrate-reducing) was amended with 100 μM acetate and 2 mM nitrate. Column 2 (iron-reducing) was run with PBAGW containing 1.0 mM acetate and 0 mM nitrate. Column 3 (alternating redox state) was operated under conditions designed to alternately stimulate nitrate-reducing and iron-reducing populations to provide conditions, i.e., the presence of both nitrate and microbially-produced Fe(II), that would allow growth of nitrate-dependent Fe(II)-oxidizing populations. We operated Column 3 with a cycling strategy of 14-18 days of high C medium (1 mM acetate and 100 μ M nitrate) followed by 14-18 days of low C medium (100 μ M acetate and 2 mM nitrate). Effluent chemistry (NO3-, NO2-, NH4+, acetate, and Fe2+) was sampled daily for four months so as to be concurrent with the electrical measurements. We observed chemical evidence of iron reduction (dissolved [Fe(II)] = 0.2mM) in the effluent from the iron reduction and alternating redox columns. Chemical depletion of NO3- ([NO3-] ranged from 1 to 0.02mM), the production of NO2-, and possible production of NH4+ (0.2 mM) was observed in the nitrate reducing column as well as the alternating redox column. All three columns displayed loss of acetate as microbial activity progressed. σ b remained constant in the alternating redox column (~0.15 S

  1. 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

  2. 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

  3. 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

  4. 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.

  5. 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

  6. 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.

  7. 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

  8. Effect of microbial activity on trace element release from sewage sludge.

    PubMed

    Qureshi, Shabnam; Richards, Brian K; Hay, Anthony G; Tsai, Christine C; McBride, Murray B; Baveye, Philippe; Steenhuis, Tammo S

    2003-08-01

    The microbial role in mobilization of trace elements from land-applied wastewater sludge is not well-defined. Our study examined the leachability of trace elements (Cd, Cr, Cu, Mo, Ni, P, Pb, S, and Zn) from dewatered sludge as affected by treatments designed to alter microbial activity. Different levels of microbial activity were achieved by incubating sludge columns at 4, 16, 28, and 37 degrees C and by the addition of AgNO3 biocide at each temperature. Columns (with inert glass bead support beds) were subjected to six consecutive incubation-leaching cycles, each consisting of 7.3-d incubation followed by 16-h leaching with synthetic acid rain. Glucose mineralization tests were used to assess overall microbial activity. Significant acidification and trace element leaching occurred when conditions favored microbial activity (16 and 28 degrees C). Extent of mobilization was element-specific with Zn, Ni, and Cu showing the greatest mobilization (99, 67, and 57%, respectively). Mobilization was reduced but still substantial at 4 degrees C. Conditions that best inhibited microbial activity (37 degrees C or biocide at any temperature) resulted in the least mobilization. Characterization of enrichments performed using thiosulfate as the sole energy source revealed the presence of both known and putative S-oxidizing bacteria in the sludge. The results suggest that microbial acidification via S oxidation can mobilize trace elements from sludge. Elemental mobility in field situations would also be governed by other factors, including the capacity of soil to buffer acidification and to adsorb mobilized elements.

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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.

  14. Microbial diversity, dynamics and activity throughout manufacturing and ripening of Castelmagno PDO cheese.

    PubMed

    Dolci, P; Alessandria, V; Rantsiou, K; Bertolino, M; Cocolin, L

    2010-09-30

    The diversity, dynamics and activity of Castelmagno PDO cheese microbiota were studied in three batches produced in a floor valley farm, in the Grana Valley (northwest Italy), during the wintertime. Samples of milk, curd and cheese (core and subsurface) at different ripening time were submitted to both culture-dependent and -independent analysis. In particular, DNA and RNA directly extracted from the matrices were studied by PCR-Denaturing gradient gel electrophoresis (DGGE) and reverse transcription (RT)-PCR-DGGE. Culture-dependent methods highlighted the initial dominance of a thermophilic streptococcal population with the species Streptococcus thermophilus and S. agalactiae. Then, mesophilic lactococci occurred among isolates during manufacturing, with Lactococcus lactis which was also well represented in the first month of Castelmagno PDO ripening. At this point and throughout the ripening, lactobacilli prevailed in cheese samples, represented from Lactobacillus plantarum and Lb. casei. Culture-independent analysis underlined the undoubted role of L. lactis, actively involved in both Castelmagno PDO manufacturing and ripening. Despite Lb. helveticus was never isolated on selective media, a DGGE band referred to this microorganism was detected, at RNA level, in samples from ripened cheeses. On the other hand, Lb. plantarum was widely isolated from the plates, among lactobacilli, but never detected by direct analysis. Due to the importance of microbiota in the sensory richness and properties of traditional cheeses, new information have been added, in this work, on microbial diversity of Castelmagno PDO cheese.

  15. Microbial metagenomes from three aquifers in the Fennoscandian shield terrestrial deep biosphere reveal metabolic partitioning among populations

    PubMed Central

    Wu, Xiaofen; Holmfeldt, Karin; Hubalek, Valerie; Lundin, Daniel; Åström, Mats; Bertilsson, Stefan; Dopson, Mark

    2016-01-01

    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

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. Dominant Microbial Populations in Limestone-Corroding Stream Biofilms, Frasassi Cave System, Italy

    PubMed Central

    Macalady, Jennifer L.; Lyon, Ezra H.; Koffman, Bess; Albertson, Lindsey K.; Meyer, Katja; Galdenzi, Sandro; Mariani, Sandro

    2006-01-01

    Waters from an extensive sulfide-rich aquifer emerge in the Frasassi cave system, where they mix with oxygen-rich percolating water and cave air over a large surface area. The actively forming cave complex hosts a microbial community, including conspicuous white biofilms coating surfaces in cave streams, that is isolated from surface sources of C and N. Two distinct biofilm morphologies were observed in the streams over a 4-year period. Bacterial 16S rDNA libraries were constructed from samples of each biofilm type collected from Grotta Sulfurea in 2002. β-, γ-, δ-, and ɛ-proteobacteria in sulfur-cycling clades accounted for ≥75% of clones in both biofilms. Sulfate-reducing and sulfur-disproportionating δ-proteobacterial sequences in the clone libraries were abundant and diverse (34% of phylotypes). Biofilm samples of both types were later collected at the same location and at an additional sample site in Ramo Sulfureo and examined, using fluorescence in situ hybridization (FISH). The biomass of all six stream biofilms was dominated by filamentous γ-proteobacteria with Beggiatoa-like and/or Thiothrix-like cells containing abundant sulfur inclusions. The biomass of ɛ-proteobacteria detected using FISH was consistently small, ranging from 0 to less than 15% of the total biomass. Our results suggest that S cycling within the stream biofilms is an important feature of the cave biogeochemistry. Such cycling represents positive biological feedback to sulfuric acid speleogenesis and related processes that create subsurface porosity in carbonate rocks. PMID:16885314

  1. 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

  2. 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.

  3. 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

  4. 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.

  5. [Population].

    PubMed

    1979-01-01

    Data on the population of Venezuela between 1975 and 1977 are presented in descriptive tables and graphs. Information is included on the employed population according to category, sex, and type of economic activity, and by sex, age, and area on the employment rate and the total, the economically active, and the unemployed population.

  6. Methods for determining the abundance, diversity and activity of soil microbial communities

    NASA Astrophysics Data System (ADS)

    Pereg, Lily

    2014-05-01

    The diversity and abundance of soil microbial communities play important roles in determining soil structure, quality and productivity. The past decade has seen an increase in the number and efficiency of methods for determining microbial diversity, abundance and function. Recognising that only a very small proportion of the soil microbial community can be cultured, most current studies use molecular techniques based on the 16S and 18S rRNA encoding sequences (DGGE, TRFLP, OFRG, ARISA, SSCP) as well as techniques based on the cellular composition of the microbes (PLFA composition). Recent developments include high-throughput sequencing and microarrays, representing major advances in microbial community analysis. While the diversity of microbes can be determined using DNA-based techniques, microbial activity changes under various conditions. Therefore, the analysis of soil function at any given time requires the analysis of gene expression using RNA-based techniques. Molecular techniques have tremendously advanced our knowledge in the field of soil microbiology, however, the limitations should not be underestimated. This presentation will critically review both the advantages and the limitations of techniques used in soil microbial analysis.

  7. 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.

  8. Nematicidal activity of microbial pigment from Serratia marcescens.

    PubMed

    Rahul, Suryawanshi; Chandrashekhar, Patil; Hemant, Borase; Chandrakant, Narkhede; Laxmikant, Shinde; Satish, Patil

    2014-01-01

    Ineffectiveness of available nematicides and the high damage caused by plant-parasitic nematodes result in the urgent need to find some natural remedy for their control. Bioactivity of the pigment extracted from Serratia marcescens was screened for controlling nematodes at their juvenile stage. Test pigment was found effective against juvenile stages of Radopholus similis and Meloidogyne javanica at low concentrations (LC50 values, 83 and 79 μg/mL, respectively) as compared with positive control of copper sulphate (LC50 values, 380 and 280 μg/mL, respectively). The pigment also exhibited inhibition on nematode egg-hatching ability. Characterisation of extracted pigment with TLC, FTIR, HPLC, HPTLC and spectroscopic analysis confirmed the presence of prodigiosin as a bioactive metabolite. Considering the sensory mechanism of pathogen recognition by nematodes, the use of microbial secondary metabolites can be effective for nematode control rather than using whole organism.

  9. 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.

  10. 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

  11. Hydrogeology, chemical and microbial activity measurement through deep permafrost.

    PubMed

    Stotler, Randy L; Frape, Shaun K; Freifeld, Barry M; Holden, Brian; Onstott, Tullis C; Ruskeeniemi, Timo; Chan, Eric

    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 δ(18) O values ∼5‰ lower than the local surface water. The fluid isotopic composition was affected by the permafrost-formation process. Nonbacteriogenic CH(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(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.

  12. 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.

  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. 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

  15. 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

  16. 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

  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.

    2013-02-01

    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.

  18. 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.

  19. 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

  20. [Microbial activity and functional diversity in rhizosphere of cucumber under different subsurface drip irrigation scheduling].

    PubMed

    Li, Hua; He, Hong-Jun; Li, Teng-Fei; Zhang, Zi-Kun

    2014-08-01

    The effects of subsurface drip irrigation scheduling on microbial activity and functional diversity in rhizosphere of cucumber in solar greenhouse were studied in this paper. The results showed that the soil microbial biomass C and N, basal respiration, metabolic quotient and values of AWCD, Shannon and McIntosh indexes were increased at first and then decreased with the increase of irrigation water amount. The values of microbial C and N, basal respiration and metabolic quotient in I2 treatments were significantly higher than those in I1 treatments at the 0.8E(p) irrigation level. The numbers of bacteria, actinomyces and nitrogen-fixing bacteria, and the activities of urease, phosphatase, sucrase, catalase and polyhenoloxidase were significantly higher in the 0.8E(p) treatment than in the other treatments. The numbers of bacteria and nitrogen-fixing bacteria, the activities of urease, phosphatase and sucrase in I2 treatments were significantly higher than in I1 treatment, the actinomyces number and activities of catalase and polyhenoloxidase had no significant difference between I1 and I2 treatments, however, the fungi number in I2 treatments were significantly lower than in I2 treaments at the 0.8E(p) irrigation level. The microbial activity and functional diversity in rhizosphere of cucumber were strengthened in the I20.8E(p) treatment, meanwhile, the soil microflora was improved and the soil enzymes activities were enhanced, therefore, the cucumber growth was promoted as well.

  1. Phenol- and toluene-degrading microbial populations from an aquifer in which successful trichloroethene cometabolism occurred.

    PubMed

    Fries, M R; Forney, L J; Tiedje, J M

    1997-04-01

    - 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.

  2. The effect of malathion on the activity, performance, and microbial ecology of activated sludge.

    PubMed

    Rauglas, Erik; Martin, Seth; Bailey, Kandace; Magnuson, Matthew; Phillips, Rebecca; Harper, Willie F

    2016-12-01

    This study evaluated the effect of a VX (O-ethyl S-[2-(diisopropylamino)ethyl] methylphosphonothioate) surrogate (malathion) on the activity, performance, and ecology of activated sludge bioreactors. In the presence of malathion, the maximum observed respiration rates varied between 43 and 53 μg/O2 min, generally similar to the 49 μg O2/min rates observed in controls. Malathion did not alter the respiration ratio of O2 consumed-to-CO2 produced nor did it impact the shape of the oxygen consumption curves during respirometry. Shorter term (12 h) batch tests showed that both chemical oxygen demand (COD) and ammonia removal were not negatively impacted by the presence of 0.1-3 mg/L malathion. Longer term continuous addition (i.e. 40 days) of 0.1 mg/L of malathion also had no effect on COD and ammonia removal. In contrast to shorter term exposures, longer term continuous addition of 3 mg/L of malathion negatively impacted both COD and nitrogen removal and was associated with shifts in the abundance of species that are common to activated sludge. These results illustrate the impact that chemicals like malathion may have on COD removal, and nitrification, as well as the robustness of activated sludge microbial communities.

  3. The effect of malathion on the activity, performance, and microbial ecology of activated sludge.

    PubMed

    Rauglas, Erik; Martin, Seth; Bailey, Kandace; Magnuson, Matthew; Phillips, Rebecca; Harper, Willie F

    2016-12-01

    This study evaluated the effect of a VX (O-ethyl S-[2-(diisopropylamino)ethyl] methylphosphonothioate) surrogate (malathion) on the activity, performance, and ecology of activated sludge bioreactors. In the presence of malathion, the maximum observed respiration rates varied between 43 and 53 μg/O2 min, generally similar to the 49 μg O2/min rates observed in controls. Malathion did not alter the respiration ratio of O2 consumed-to-CO2 produced nor did it impact the shape of the oxygen consumption curves during respirometry. Shorter term (12 h) batch tests showed that both chemical oxygen demand (COD) and ammonia removal were not negatively impacted by the presence of 0.1-3 mg/L malathion. Longer term continuous addition (i.e. 40 days) of 0.1 mg/L of malathion also had no effect on COD and ammonia removal. In contrast to shorter term exposures, longer term continuous addition of 3 mg/L of malathion negatively impacted both COD and nitrogen removal and was associated with shifts in the abundance of species that are common to activated sludge. These results illustrate the impact that chemicals like malathion may have on COD removal, and nitrification, as well as the robustness of activated sludge microbial communities. PMID:27594690

  4. 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.

  5. 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.

  6. Cow teat skin, a potential source of diverse microbial populations for cheese production.

    PubMed

    Verdier-Metz, Isabelle; 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.

  7. 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

  8. [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.

  9. [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

  10. Recovery of microbial diversity and activity during bioremediation following chemical oxidation of diesel contaminated soils.

    PubMed

    Sutton, Nora B; Langenhoff, Alette A M; Lasso, Daniel Hidalgo; van der Zaan, Bas; van Gaans, Pauline; Maphosa, Farai; Smidt, Hauke; Grotenhuis, Tim; Rijnaarts, Huub H M

    2014-03-01

    To improve the coupling of in situ chemical oxidation and in situ bioremediation, a systematic analysis was performed of the effect of chemical oxidation with Fenton's reagent, modified Fenton's reagent, permanganate, or persulfate, on microbial diversity and activity during 8 weeks of incubation in two diesel-contaminated soils (peat and fill). Chemical oxidant and soil type affected the microbial community diversity and biodegradation activity; however, this was only observed following treatment with Fenton's reagent and modified Fenton's reagent, and in the biotic control without oxidation. Differences in the highest overall removal efficiencies of 69 % for peat (biotic control) and 59 % for fill (Fenton's reagent) were partially explained by changes in contaminant soil properties upon oxidation. Molecular analysis of 16S rRNA and alkane monooxygenase (alkB) gene abundances indicated that oxidation with Fenton's reagent and modified Fenton's reagent negatively affected microbial abundance. However, regeneration occurred, and final relative alkB abundances were 1-2 orders of magnitude higher in chemically treated microcosms than in the biotic control. 16S rRNA gene fragment fingerprinting with DGGE and prominent band sequencing illuminated microbial community composition and diversity differences between treatments and identified a variety of phylotypes within Alpha-, Beta-, and Gammaproteobacteria. Understanding microbial community dynamics during coupled chemical oxidation and bioremediation is integral to improved biphasic field application.

  11. 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

  12. Differential Incorporation of Carbon Substrates among Microbial Populations Identified by Field-Based, DNA Stable-Isotope Probing in South China Sea.

    PubMed

    Zhang, Yao; Deng, Wenchao; 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

  13. Differential Incorporation of Carbon Substrates among Microbial Populations Identified by Field-Based, DNA Stable-Isotope Probing in South China Sea.

    PubMed

    Zhang, Yao; Deng, Wenchao; 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

  14. 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.

  15. Effects of graphene oxides on soil enzyme activity and microbial biomass.

    PubMed

    Chung, Haegeun; Kim, Min Ji; Ko, Kwanyoung; Kim, Jae Hyeuk; Kwon, Hyun-Ah; Hong, Inpyo; Park, Nari; Lee, Seung-Wook; Kim, Woong

    2015-05-01

    Due to recent developments in nanotechnology, nanomaterials (NMs) such as graphene oxide (GO) may enter the soil environment with mostly unknown consequences. We investigated the effects of GO on soil microbial activity in a 59-day soil incubation study. For this, high-purity GO was prepared and characterized. Soils were treated with up to 1 mg GO g(-1) soil, and the changes in the activities of 1,4-β-glucosidase, cellobiohydrolase, xylosidase, 1,4-β-N-acetyl glucosaminidase, and phosphatase and microbial biomass were determined. 0.5-1 mg GO g(-1) soil lowered the activity of xylosidase, 1,4-β-N-acetyl glucosaminidase, and phosphatase by up to 50% when compared to that in the control soils up to 21 days of incubation. Microbial biomass in soils treated with GO was not significantly different from that in control soils throughout the incubation period, and the soil enzyme activity and microbial biomass were not significantly correlated in this study. Our results indicate that soil enzyme activity can be lowered by the entry of GO into soils in short term but it can be recovered afterwards. PMID:25668283

  16. 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.

  17. 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

  18. Microbial ecology of Bacillus thuringiensis: fecal populations recovered from wildlife in Korea.

    PubMed

    Lee, Dong-Hyun; Cha, In Hwan; Woo, Doo Sung; Ohba, Michio

    2003-07-01

    A total of 34 fecal samples, collected from 14 species of wild mammals in Korea, were examined for the occurrence of Bacillus thuringiensis. The organism was detected in 18 (53%) samples. Among the three food-habit groups, herbivorous animals yielded the highest frequency (69%) of samples positive for B. thuringiensis, followed by omnivorous animals (50%). Of the six fecal samples from carnivorous animals, only one sample contained B. thurin giensis. Among 527 isolates belonging to the Bacillus cereus - B. thuringiensis group, 43 (8%) were assigned to B. thurin giensis on the basis of the formation of parasporal inclusions. Of the 43 isolates, 13 were serologically allocated to the nine H-antigenic serotypes: H3ad (serovar sumiyoshiensis), H15 (dakota), H17/27 (tohokuensis/ mexicanensis), H19 (tochigiensis), H21 (colmeri), H29 (amagiensis), H31/49 (toguchini/muju), H42 (jinghongiensis), and H44 (higo). Other isolates were untestable or untypable by the 55 reference H antisera available. Insecticidal activity was associated with 23% of the fecal populations: three isolates killed larvae of the silkworm, Bombyx mori (Lepidoptera), and seven exhibited larvicidal activity against the mosquito, Aedes aegypti (Diptera). There was no larvicidal activity against the three lepidopterous insects: Plutella xylostella, Spodoptera exigua, and Spodoptera litura. The overall results suggest that wild animals in Korea are in contact with naturally occurring B. thuringiensis at high frequencies through the daily food intake of plants.

  19. 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.

  20. 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

  1. 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.

  2. 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

  3. Changes of soil organic matter and microbial activity in irrigated and non irrigated olive groves

    NASA Astrophysics Data System (ADS)

    Kavvadias, Victor; Papadopoulou, Maria; Theocharopoulos, Sideris; Vavoulidou, Evagelia; Doula, Maria; Reppas, Spiros

    2014-05-01

    The implementation of olive cultivation techniques in Greece has not been systematically tested under the prevailing Mediterranean conditions. A LIFE+ project was initiated (oLIVE-CLIMA; LIFE 11/ENV/000942) aiming to introduce new management practices in olive tree crops that lead to increased carbon dioxide uptake by plants as well as carbon sequestration from the atmosphere and reverse the trend of soil organic matter decline, erosion and desertification. This paper presents data on soil organic matter and microbial activity from a soil campaign in a pilot region in Greece, and particularly in the area of Chora, prefecture of Messinia, South west Peloponnese. The soil campaign took place during the period December 2012-February 2013. Twelve soil parcels of olive groves were selected (6 irrigated and 6 rainfed) and in each soil parcel six composite soil samples were taken from 0-10 cm depth at equal intervals along a straight line of the trunk of the tree to the middle of the distance from the nearest tree of the next tree series. The first three samples were under olive tree canopy. An additional composite sample was taken at depth of 10-40 cm. Soil samples were analyzed for soil physicochemical and biological properties. In this study results for total organic carbon (TOC), soil basal microbial respiration (BR), microbial biomass C (MB-C) from the region of Messinia, are presented. Organic matter was determined by dichromate oxidation. The microbial activity was measured by the amount of CO2 evolution, while microbial biomass C was determined by substrate-induced respiration, after the addition of glucose. The results showed considerable differences in TOC, BR and MB-C associated with the sampling position and soil depth. The higher TOC, BR and MB-C values, in most cases, were determined in samples taken from points under the canopy, but not close to the tree trunk compared to the sampling points outside the canopy. This indicates the positive effect of

  4. 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

  5. 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.

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  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. 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...

  13. 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

  14. 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.

  15. 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 ...

  16. 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

  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. 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.

  19. Microbial Content of Nonsterile Therapeutic Agents Containing Natural or Seminatural Active Ingredients

    PubMed Central

    Schiller, I.; Kuntscher, H.; Wolff, A.; Nekola, M.

    1968-01-01

    The relationship was investigated between various chemical or pharmaceutical production processes and the extent of microbial contamination, of natural origin, of the resulting products. The products contained active ingredients of vegetable, enzymatic, or animal origin. It was concluded that (i) vegetable prod