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Sample records for estimating bacterial abundances

  1. Spectral unmixing: estimating partial abundances

    CSIR Research Space (South Africa)

    Debba, Pravesh

    2009-01-01

    Full Text Available techniques is complicated when considering very similar spectral signatures. Iron-bearing oxide/hydroxide/sulfate minerals have similar spectral signatures. The study focuses on how could estimates of abundances of spectrally similar iron-bearing oxide...

  2. Abundance estimation and conservation biology

    Science.gov (United States)

    Nichols, J.D.; MacKenzie, D.I.

    2004-01-01

    Abundance is the state variable of interest in most population–level ecological research and in most programs involving management and conservation of animal populations. Abundance is the single parameter of interest in capture–recapture models for closed populations (e.g., Darroch, 1958; Otis et al., 1978; Chao, 2001). The initial capture–recapture models developed for partially (Darroch, 1959) and completely (Jolly, 1965; Seber, 1965) open populations represented efforts to relax the restrictive assumption of population closure for the purpose of estimating abundance. Subsequent emphases in capture–recapture work were on survival rate estimation in the 1970’s and 1980’s (e.g., Burnham et al., 1987; Lebreton et al.,1992), and on movement estimation in the 1990’s (Brownie et al., 1993; Schwarz et al., 1993). However, from the mid–1990’s until the present time, capture–recapture investigators have expressed a renewed interest in abundance and related parameters (Pradel, 1996; Schwarz & Arnason, 1996; Schwarz, 2001). The focus of this session was abundance, and presentations covered topics ranging from estimation of abundance and rate of change in abundance, to inferences about the demographic processes underlying changes in abundance, to occupancy as a surrogate of abundance. The plenary paper by Link & Barker (2004) is provocative and very interesting, and it contains a number of important messages and suggestions. Link & Barker (2004) emphasize that the increasing complexity of capture–recapture models has resulted in large numbers of parameters and that a challenge to ecologists is to extract ecological signals from this complexity. They offer hierarchical models as a natural approach to inference in which traditional parameters are viewed as realizations of stochastic processes. These processes are governed by hyperparameters, and the inferential approach focuses on these hyperparameters. Link & Barker (2004) also suggest that our attention

  3. Abundance estimation and Conservation Biology

    Directory of Open Access Journals (Sweden)

    Nichols, J. D.

    2004-06-01

    Full Text Available Abundance is the state variable of interest in most population–level ecological research and in most programs involving management and conservation of animal populations. Abundance is the single parameter of interest in capture–recapture models for closed populations (e.g., Darroch, 1958; Otis et al., 1978; Chao, 2001. The initial capture–recapture models developed for partially (Darroch, 1959 and completely (Jolly, 1965; Seber, 1965 open populations represented efforts to relax the restrictive assumption of population closure for the purpose of estimating abundance. Subsequent emphases in capture–recapture work were on survival rate estimation in the 1970’s and 1980’s (e.g., Burnham et al., 1987; Lebreton et al.,1992, and on movement estimation in the 1990’s (Brownie et al., 1993; Schwarz et al., 1993. However, from the mid–1990’s until the present time, capture–recapture investigators have expressed a renewed interest in abundance and related parameters (Pradel, 1996; Schwarz & Arnason, 1996; Schwarz, 2001. The focus of this session was abundance, and presentations covered topics ranging from estimation of abundance and rate of change in abundance, to inferences about the demographic processes underlying changes in abundance, to occupancy as a surrogate of abundance. The plenary paper by Link & Barker (2004 is provocative and very interesting, and it contains a number of important messages and suggestions. Link & Barker (2004 emphasize that the increasing complexity of capture–recapture models has resulted in large numbers of parameters and that a challenge to ecologists is to extract ecological signals from this complexity. They offer hierarchical models as a natural approach to inference in which traditional parameters are viewed as realizations of stochastic processes. These processes are governed by hyperparameters, and the inferential approach focuses on these hyperparameters. Link & Barker (2004 also suggest that

  4. Bracken: estimating species abundance in metagenomics data

    Directory of Open Access Journals (Sweden)

    Jennifer Lu

    2017-01-01

    Full Text Available Metagenomic experiments attempt to characterize microbial communities using high-throughput DNA sequencing. Identification of the microorganisms in a sample provides information about the genetic profile, population structure, and role of microorganisms within an environment. Until recently, most metagenomics studies focused on high-level characterization at the level of phyla, or alternatively sequenced the 16S ribosomal RNA gene that is present in bacterial species. As the cost of sequencing has fallen, though, metagenomics experiments have increasingly used unbiased shotgun sequencing to capture all the organisms in a sample. This approach requires a method for estimating abundance directly from the raw read data. Here we describe a fast, accurate new method that computes the abundance at the species level using the reads collected in a metagenomics experiment. Bracken (Bayesian Reestimation of Abundance after Classification with KrakEN uses the taxonomic assignments made by Kraken, a very fast read-level classifier, along with information about the genomes themselves to estimate abundance at the species level, the genus level, or above. We demonstrate that Bracken can produce accurate species- and genus-level abundance estimates even when a sample contains multiple near-identical species.

  5. Abundance of bacterial and diatom fouling on various surfaces

    Digital Repository Service at National Institute of Oceanography (India)

    PrabhaDevi

    Abundance of bacterial and diatom fouling on aluminium, fibreglass and stainless steel were studied from Dona Paula waters of the Zuari Estuary. Both these forms were reversibly attached in large numbers to surfaces during the initial 24 hr...

  6. Abundance estimation of spectrally similar minerals

    CSIR Research Space (South Africa)

    Debba, Pravesh

    2009-07-01

    Full Text Available This paper evaluates a spectral unmixing method for estimating the partial abundance of spectrally similar minerals in complex mixtures. The method requires formulation of a linear function of individual spectra of individual minerals. The first...

  7. 2015-2016 Palila abundance estimates

    Science.gov (United States)

    Camp, Richard J.; Brinck, Kevin W.; Banko, Paul C.

    2016-01-01

    The palila (Loxioides bailleui) population was surveyed annually during 1998−2016 on Mauna Kea Volcano to determine abundance, population trend, and spatial distribution. In the latest surveys, the 2015 population was estimated at 852−1,406 birds (point estimate: 1,116) and the 2016 population was estimated at 1,494−2,385 (point estimate: 1,934). Similar numbers of palila were detected during the first and subsequent counts within each year during 2012−2016; the proportion of the total annual detections in each count ranged from 46% to 56%; and there was no difference in the detection probability due to count sequence. Furthermore, conducting repeat counts improved the abundance estimates by reducing the width of the confidence intervals between 9% and 32% annually. This suggests that multiple counts do not affect bird or observer behavior and can be continued in the future to improve the precision of abundance estimates. Five palila were detected on supplemental survey stations in the Ka‘ohe restoration area, outside the core survey area but still within Palila Critical Habitat (one in 2015 and four in 2016), suggesting that palila are present in habitat that is recovering from cattle grazing on the southwest slope. The average rate of decline during 1998−2016 was 150 birds per year. Over the 18-year monitoring period, the estimated rate of change equated to a 58% decline in the population.

  8. Bacterial community profiles in low microbial abundance sponges

    KAUST Repository

    Giles, Emily

    2012-09-04

    It has long been recognized that sponges differ in the abundance of associated microorganisms, and they are therefore termed either \\'low microbial abundance\\' (LMA) or \\'high microbial abundance\\' (HMA) sponges. Many previous studies concentrated on the dense microbial communities in HMA sponges, whereas little is known about microorganisms in LMA sponges. Here, two LMA sponges from the Red Sea, two from the Caribbean and one from the South Pacific were investigated. With up to only five bacterial phyla per sponge, all LMA sponges showed lower phylum-level diversity than typical HMA sponges. Interestingly, each LMA sponge was dominated by a large clade within either Cyanobacteria or different classes of Proteobacteria. The overall similarity of bacterial communities among LMA sponges determined by operational taxonomic unit and UniFrac analysis was low. Also the number of sponge-specific clusters, which indicate bacteria specifically associated with sponges and which are numerous in HMA sponges, was low. A biogeographical or host-dependent distribution pattern was not observed. In conclusion, bacterial community profiles of LMA sponges are clearly different from profiles of HMA sponges and, remarkably, each LMA sponge seems to harbour its own unique bacterial community. © 2012 Federation of European Microbiological Societies.

  9. Bacterial community profiles in low microbial abundance sponges

    KAUST Repository

    Giles, Emily; Kamke, Janine; Moitinho-Silva, Lucas; Taylor, Michael W.; Hentschel, Ute T E; Ravasi, Timothy; Schmitt, Susanne

    2012-01-01

    It has long been recognized that sponges differ in the abundance of associated microorganisms, and they are therefore termed either 'low microbial abundance' (LMA) or 'high microbial abundance' (HMA) sponges. Many previous studies concentrated

  10. Estimating the relationship between abundance and distribution

    DEFF Research Database (Denmark)

    Rindorf, Anna; Lewy, Peter

    2012-01-01

    based on Euclidean distance to the centre of gravity of the spatial distribution. Only the proportion of structurally empty areas, Lloyds index, and indices of the distance to the centre of gravity of the spatial distribution are unbiased at all levels of abundance. The remaining indices generate...

  11. Acidification of calf bedding reduces fly development and bacterial abundance.

    Science.gov (United States)

    Calvo, M S; Gerry, A C; McGarvey, J A; Armitage, T L; Mitloehner, F M

    2010-03-01

    Environmental stressors, such as high fly density, can affect calf well-being. Sodium bisulfate (SBS) is an acidifier that reduces the pH of flooring and bedding, creating a medium that neither bacteria nor immature flies (also known as larvae or maggots) can thrive in. Two experiments were conducted to investigate the application of SBS to a mixture of rice hull calf bedding and calf slurry (BED) to reduce house fly (Musca domestica L.) larval density and the abundance of bacteria. In experiment 1, dish pans containing 1L of BED and 3,000 house fly eggs were treated with SBS at concentrations of 0, 8.9, 17.7, and 26.5g of SBS/0.05m(2) of BED (CON, LOW, MED, and HIGH, respectively), with each SBS concentration applied to 4 individual pans (16 pans total). Reapplication of the same SBS concentrations in each pan occurred 3 times/wk throughout the 23-d trial. Larval house fly survival was significantly reduced in all pans with SBS relative to CON pans, with lowest survival rates in the MED and HIGH pans (99% and 100% reduction, respectively). The mean pH for each treatment was inversely related to the SBS concentration. In experiment 2, pans containing 1L of BED and 3,000 house fly eggs were treated with either 0g of SBS (CON), 8.9g of SBS/0.05m(2) of BED with reapplication of the acidifier 3 times/wk (SB3x), or 8.9g of SBS/0.05m(2) of BED applied only once at 48h before the end of the 8 d-trial (SB48). Larval house fly survival and bacterial concentrations were reduced (90% larval reduction and 68% bacterial reduction) in the SB3x treatment relative to the CON. Mean pH was also reduced in SB3x pans relative to CON or SB48 pans. Overall, acidification of calf BED using the acidifier SBS resulted in a reduction of bacteria and house fly larval survival. This form of fly control might be expected to reduce adult fly production and, therefore, fly-related stress in calves.

  12. Estimating bacterial diversity for ecological studies: methods, metrics, and assumptions.

    Directory of Open Access Journals (Sweden)

    Julia Birtel

    Full Text Available Methods to estimate microbial diversity have developed rapidly in an effort to understand the distribution and diversity of microorganisms in natural environments. For bacterial communities, the 16S rRNA gene is the phylogenetic marker gene of choice, but most studies select only a specific region of the 16S rRNA to estimate bacterial diversity. Whereas biases derived from from DNA extraction, primer choice and PCR amplification are well documented, we here address how the choice of variable region can influence a wide range of standard ecological metrics, such as species richness, phylogenetic diversity, β-diversity and rank-abundance distributions. We have used Illumina paired-end sequencing to estimate the bacterial diversity of 20 natural lakes across Switzerland derived from three trimmed variable 16S rRNA regions (V3, V4, V5. Species richness, phylogenetic diversity, community composition, β-diversity, and rank-abundance distributions differed significantly between 16S rRNA regions. Overall, patterns of diversity quantified by the V3 and V5 regions were more similar to one another than those assessed by the V4 region. Similar results were obtained when analyzing the datasets with different sequence similarity thresholds used during sequences clustering and when the same analysis was used on a reference dataset of sequences from the Greengenes database. In addition we also measured species richness from the same lake samples using ARISA Fingerprinting, but did not find a strong relationship between species richness estimated by Illumina and ARISA. We conclude that the selection of 16S rRNA region significantly influences the estimation of bacterial diversity and species distributions and that caution is warranted when comparing data from different variable regions as well as when using different sequencing techniques.

  13. Seasonal and spatial variation of bacterial production and abundance in the northern Levantine Sea

    Directory of Open Access Journals (Sweden)

    N. YUCEL

    2017-03-01

    Full Text Available Spatial and temporal heterogeneity in bacterial production and abundance in relation to ambient bio-physicochemical parameters has been investigated in the Levantine Sea. Five stations with different trophic states in an area extending from highly eutrophic Mersin bay to the mesotrophic Rhodes gyre area including the oligotrophic offshore waters were sampled four times. Integrated bacterial production varied between 6.1 and 90.3 µg C m-2 d-1 with higher rates occurring during September 2012 in offshore waters. Bacterial abundance ranged between 0.18 and 7.3 x 105 cells ml-1 within the euphotic zone and was generally higher up to 100 meters throughout the study period. In offshore waters, bacterial production (0.401 to 0.050 µg C m-3 d-1, abundance (4.5 to 1.6 x 105 cells ml-1 and depth of the productive layer decreased from 150 to 75 meters westward along the transect. Although the highest abundance was observed in July 2012 in offshore waters, the highest activity was measured in September 2012. These results indicated that the temperature played a key role in regulating bacterial abundance and production in the area. High chlorophyll concentrations in March did not correspond to high bacterial abundance and production at the same time. Increase in dissolved organic carbon content following spring phytoplankton bloom and the increase in temperature in the mean time might have enhanced the bacterial activity towards summer.

  14. Revised estimates of abundance of South African sardine and ...

    African Journals Online (AJOL)

    Hydro-acoustic surveys have been used to provide annual estimates of May recruitment and November spawner biomass of the South African sardine Sardinops sagax and anchovy Engraulis encrasicolus resources since 1984. These time-series of abundance estimates form the backbone of the assessment of these ...

  15. Bacterial Abundance and Activity across Sites within Two Northern Wisconsin Sphagnum Bogs.

    Science.gov (United States)

    Fisher; Graham; Graham

    1998-11-01

    Abstract Bacterial abundance, temperature, pH, and dissolved organic carbon (DOC) concentration were compared across surface sites within and between two northern Wisconsin Sphagnum peatlands over the summer seasons in 1995 and 1996. Sites of interest were the Sphagnum mat surface, the water-filled moat (lagg) at the bog margin, and the bog lake littoral zone. Significant differences in both bacterial populations and water chemistry were observed between sites. pH was highest in the lake and lowest in the mat at both bogs; the opposite was true for DOC. Large populations of bacteria were present in surface interstitial water from the mat; abundance in this site was consistently higher than in the moat or lake. Bacterial abundance also increased across sites of increasing DOC concentration and declining pH. Bacterial activities (rates of [3H]leucine incorporation) and growth in dilution cultures (with grazers removed) were also assessed in lake, moat, and mat sites. Results using these measures generally supported the trends observed in abundance, although high rates of [3H]leucine incorporation were recorded in the moat at one of the bogs. Our results indicate that bacterial populations in Sphagnum peatlands are not adversely affected by acidity, and that DOC may be more important than pH in determining bacterial abundance in these environments.

  16. Asteroseismic estimate of helium abundance of 16 Cyg A, B

    Directory of Open Access Journals (Sweden)

    Verma Kuldeep

    2015-01-01

    Full Text Available The helium ionization zone in a star leaves a characteristic signature on its oscillation frequencies, which can be used to estimate the helium content in the envelope of the star. We use the oscillation frequencies of 16 Cyg A and B, obtained using 2.5 years of Kepler data, to estimate the envelope helium abundance of these stars. We find the envelope helium abundance to lie in the range 0.231–0.251 for 16 Cyg A and 0.218–0.266 for 16 Cyg B.

  17. A collaborative approach for estimating terrestrial wildlife abundance

    Science.gov (United States)

    Ransom, Jason I.; Kaczensky, Petra; Lubow, Bruce C.; Ganbaatar, Oyunsaikhan; Altansukh, Nanjid

    2012-01-01

    Accurately estimating abundance of wildlife is critical for establishing effective conservation and management strategies. Aerial methodologies for estimating abundance are common in developed countries, but they are often impractical for remote areas of developing countries where many of the world's endangered and threatened fauna exist. The alternative terrestrial methodologies can be constrained by limitations on access, technology, and human resources, and have rarely been comprehensively conducted for large terrestrial mammals at landscape scales. We attempted to overcome these problems by incorporating local peoples into a simultaneous point count of Asiatic wild ass (Equus hemionus) and goitered gazelle (Gazella subgutturosa) across the Great Gobi B Strictly Protected Area, Mongolia. Paired observers collected abundance and covariate metrics at 50 observation points and we estimated population sizes using distance sampling theory, but also assessed individual observer error to examine potential bias introduced by the large number of minimally trained observers. We estimated 5671 (95% CI = 3611–8907) wild asses and 5909 (95% CI = 3762–9279) gazelle inhabited the 11,027 km2 study area at the time of our survey and found that the methodology developed was robust at absorbing the logistical challenges and wide range of observer abilities. This initiative serves as a functional model for estimating terrestrial wildlife abundance while integrating local people into scientific and conservation projects. This, in turn, creates vested interest in conservation by the people who are most influential in, and most affected by, the outcomes.

  18. Estimates of cetacean abundance in European Atlantic waters in summer

    OpenAIRE

    Hammond, P.S. (Phil) et al. (incl. Santos, M.B. (Maria Begoña)

    2017-01-01

    This report summarises design-based estimates of abundance for those cetacean species for which sufficient data were obtained during SCANS-III: harbour porpoise, bottlenose dolphin, Risso’s dolphin, white-beaked dolphin, white-sided dolphin, common dolphin, striped dolphin, pilot whale, all beaked whale species combined, sperm whale, minke whale and fin whale.

  19. Fishery characteristics and abundance estimates of the mangrove ...

    African Journals Online (AJOL)

    The mud crab Scylla serrata is lightly exploited along the East African seaboard. This study reports on fishing practices and gives preliminary estimates of abundance and size structures of the mud crab populations in Utende, Chole Island and Juani Island, Tanzania, and west of Quirimba and Ibo Island, Moçambique.

  20. Estimating Cape hare occupancy and abundance in southern ...

    African Journals Online (AJOL)

    This study outlines the importance of integrating spotlighting data and occupancy modelling to estimate the spatial occupancy, abundance and habitat preferences of Cape hares Lepus capensis in southern Tunisia. Exploring the spatial distribution pattern of this species is problematic because of its nocturnal and secretive ...

  1. Heterotrophic activity, bacterial types and abundance in different ecosystems of the Queen Maud Land

    Digital Repository Service at National Institute of Oceanography (India)

    Ramaiah, N.; Kodagali, J.; Nair, S.; Sheelu, G.; Chandramohan, D.

    Microbiological studies from the marine, limnetic, terrestrial and glacial ecosystems were carried out during the Ninth Indian Expedition (1989-90) to estimate the bacterial numbers, to characterise the generic types and also to estimate the uptake...

  2. Continuously Monocropped Jerusalem Artichoke Changed Soil Bacterial Community Composition and Ammonia-Oxidizing and Denitrifying Bacteria Abundances.

    Science.gov (United States)

    Zhou, Xingang; Wang, Zhilin; Jia, Huiting; Li, Li; Wu, Fengzhi

    2018-01-01

    Soil microbial communities have profound effects on the growth, nutrition and health of plants in agroecosystems. Understanding soil microbial dynamics in cropping systems can assist in determining how agricultural practices influence soil processes mediated by microorganisms. In this study, soil bacterial communities were monitored in a continuously monocropped Jerusalem artichoke (JA) system, in which JA was successively monocropped for 3 years in a wheat field. Soil bacterial community compositions were estimated by amplicon sequencing of the 16S rRNA gene. Abundances of ammonia-oxidizing and denitrifying bacteria were estimated by quantitative PCR analysis of the amoA , nirS , and nirK genes. Results showed that 1-2 years of monocropping of JA did not significantly impact the microbial alpha diversity, and the third cropping of JA decreased the microbial alpha diversity ( P < 0.05). Principal coordinates analysis and permutational multivariate analysis of variance analyses revealed that continuous monocropping of JA changed soil bacterial community structure and function profile ( P < 0.001). At the phylum level, the wheat field was characterized with higher relative abundances of Latescibacteria , Planctomycetes , and Cyanobacteria , the first cropping of JA with Actinobacteria , the second cropping of JA with Acidobacteria , Armatimonadetes , Gemmatimonadetes , and Proteobacteria . At the genus level, the first cropping of JA was enriched with bacterial species with pathogen-antagonistic and/or plant growth promoting potentials, while members of genera that included potential denitrifiers increased in the second and third cropping of JA. The first cropping of JA had higher relative abundances of KO terms related to lignocellulose degradation and phosphorus cycling, the second cropping of JA had higher relative abundances of KO terms nitrous-oxide reductase and nitric-oxide reductase, and the third cropping of JA had higher relative abundances of KO terms

  3. Continuously Monocropped Jerusalem Artichoke Changed Soil Bacterial Community Composition and Ammonia-Oxidizing and Denitrifying Bacteria Abundances

    Directory of Open Access Journals (Sweden)

    Xingang Zhou

    2018-04-01

    Full Text Available Soil microbial communities have profound effects on the growth, nutrition and health of plants in agroecosystems. Understanding soil microbial dynamics in cropping systems can assist in determining how agricultural practices influence soil processes mediated by microorganisms. In this study, soil bacterial communities were monitored in a continuously monocropped Jerusalem artichoke (JA system, in which JA was successively monocropped for 3 years in a wheat field. Soil bacterial community compositions were estimated by amplicon sequencing of the 16S rRNA gene. Abundances of ammonia-oxidizing and denitrifying bacteria were estimated by quantitative PCR analysis of the amoA, nirS, and nirK genes. Results showed that 1–2 years of monocropping of JA did not significantly impact the microbial alpha diversity, and the third cropping of JA decreased the microbial alpha diversity (P < 0.05. Principal coordinates analysis and permutational multivariate analysis of variance analyses revealed that continuous monocropping of JA changed soil bacterial community structure and function profile (P < 0.001. At the phylum level, the wheat field was characterized with higher relative abundances of Latescibacteria, Planctomycetes, and Cyanobacteria, the first cropping of JA with Actinobacteria, the second cropping of JA with Acidobacteria, Armatimonadetes, Gemmatimonadetes, and Proteobacteria. At the genus level, the first cropping of JA was enriched with bacterial species with pathogen-antagonistic and/or plant growth promoting potentials, while members of genera that included potential denitrifiers increased in the second and third cropping of JA. The first cropping of JA had higher relative abundances of KO terms related to lignocellulose degradation and phosphorus cycling, the second cropping of JA had higher relative abundances of KO terms nitrous-oxide reductase and nitric-oxide reductase, and the third cropping of JA had higher relative abundances of KO

  4. New aerial survey and hierarchical model to estimate manatee abundance

    Science.gov (United States)

    Langimm, Cahterine A.; Dorazio, Robert M.; Stith, Bradley M.; Doyle, Terry J.

    2011-01-01

    Monitoring the response of endangered and protected species to hydrological restoration is a major component of the adaptive management framework of the Comprehensive Everglades Restoration Plan. The endangered Florida manatee (Trichechus manatus latirostris) lives at the marine-freshwater interface in southwest Florida and is likely to be affected by hydrologic restoration. To provide managers with prerestoration information on distribution and abundance for postrestoration comparison, we developed and implemented a new aerial survey design and hierarchical statistical model to estimate and map abundance of manatees as a function of patch-specific habitat characteristics, indicative of manatee requirements for offshore forage (seagrass), inland fresh drinking water, and warm-water winter refuge. We estimated the number of groups of manatees from dual-observer counts and estimated the number of individuals within groups by removal sampling. Our model is unique in that we jointly analyzed group and individual counts using assumptions that allow probabilities of group detection to depend on group size. Ours is the first analysis of manatee aerial surveys to model spatial and temporal abundance of manatees in association with habitat type while accounting for imperfect detection. We conducted the study in the Ten Thousand Islands area of southwestern Florida, USA, which was expected to be affected by the Picayune Strand Restoration Project to restore hydrology altered for a failed real-estate development. We conducted 11 surveys in 2006, spanning the cold, dry season and warm, wet season. To examine short-term and seasonal changes in distribution we flew paired surveys 1–2 days apart within a given month during the year. Manatees were sparsely distributed across the landscape in small groups. Probability of detection of a group increased with group size; the magnitude of the relationship between group size and detection probability varied among surveys. Probability

  5. Diversity and abundance of the bacterial community of the red Macroalga Porphyra umbilicalis: did bacterial farmers produce macroalgae?

    Directory of Open Access Journals (Sweden)

    Lilibeth N Miranda

    Full Text Available Macroalgae harbor microbial communities whose bacterial biodiversity remains largely uncharacterized. The goals of this study were 1 to examine the composition of the bacterial community associated with Porphyra umbilicalis Kützing from Schoodic Point, ME, 2 determine whether there are seasonal trends in species diversity but a core group of bacteria that are always present, and 3 to determine how the microbial community associated with a laboratory strain (P.um.1 established in the presence of antibiotics has changed. P. umbilicalis blades (n = 5, fall 2010; n = 5, winter 2011; n = 2, clonal P.um.1 were analyzed by pyrosequencing over two variable regions of the 16 S rDNA (V5-V6 and V8; 147,880 total reads. The bacterial taxa present were classified at an 80% confidence threshold into eight phyla (Bacteroidetes, Proteobacteria, Planctomycetes, Chloroflexi, Actinobacteria, Deinococcus-Thermus, Firmicutes, and the candidate division TM7. The Bacteroidetes comprised the majority of bacterial sequences on both field and lab blades, but the Proteobacteria (Alphaproteobacteria, Gammaproteobacteria were also abundant. Sphingobacteria (Bacteroidetes and Flavobacteria (Bacteroidetes had inverse abundances on natural versus P.um.1 blades. Bacterial communities were richer and more diverse on blades sampled in fall compared to winter. Significant differences were observed between microbial communities among all three groups of blades examined. Only two OTUs were found on all 12 blades, and only one of these, belonging to the Saprospiraceae (Bacteroidetes, was abundant. Lewinella (as 66 OTUs was found on all field blades and was the most abundant genus. Bacteria from the Bacteroidetes, Proteobacteria and Planctomycetes that are known to digest the galactan sulfates of red algal cell walls were well-represented. Some of these taxa likely provide essential morphogenetic and beneficial nutritive factors to P. umbilicalis and may have had

  6. Generalized estimators of avian abundance from count survey data

    Directory of Open Access Journals (Sweden)

    Royle, J. A.

    2004-01-01

    Full Text Available I consider modeling avian abundance from spatially referenced bird count data collected according to common protocols such as capture-recapture, multiple observer, removal sampling and simple point counts. Small sample sizes and large numbers of parameters have motivated many analyses that disregard the spatial indexing of the data, and thus do not provide an adequate treatment of spatial structure. I describe a general framework for modeling spatially replicated data that regards local abundance as a random process, motivated by the view that the set of spatially referenced local populations (at the sample locations constitute a metapopulation. Under this view, attention can be focused on developing a model for the variation in local abundance independent of the sampling protocol being considered. The metapopulation model structure, when combined with the data generating model, define a simple hierarchical model that can be analyzed using conventional methods. The proposed modeling framework is completely general in the sense that broad classes of metapopulation models may be considered, site level covariates on detection and abundance may be considered, and estimates of abundance and related quantities may be obtained for sample locations, groups of locations, unsampled locations. Two brief examples are given, the first involving simple point counts, and the second based on temporary removal counts. Extension of these models to open systems is briefly discussed.

  7. Archaeal and bacterial H-GDGTs are abundant in peat and their relative abundance is positively correlated with temperature

    Science.gov (United States)

    Naafs, B. D. A.; McCormick, D.; Inglis, G. N.; Pancost, R. D.; T-GRES Peat Database Collaborators

    2018-04-01

    Glycerol monoalkyl glycerol tetraether lipids (GMGTs; also called 'H-GDGTs') differ from the more commonly studied glycerol dialkyl glycerol tetraether (GDGTs) in that they have an additional covalent bond that links the two alkyl chains. Six different archaeal isoprenoidal H-GDGTs (H-isoGDGTs) and one branched H-GDGT (H-brGDGT), presumably produced by bacteria, have previously been found. However, the function of H-GDGTs in both domains of life is unknown. It is thought that the formation of this additional covalent bond results in enhanced membrane stability, accounting for the high abundance of H-GDGTs in extreme environments such as geothermal settings, but so far there has been little evidence to support this hypothesis. Here we report the distribution of H-GDGTs in a global peat database (n = 471) with a broad range in mean annual air temperature (MAAT) and pH. This is the first finding of H-GDGTs in soils (specifically, peat), highlighting that H-GDGTs are widespread in mesophilic settings. In addition, we report the presence of two new H-brGDGTs with one (H-1034) and two (H-1048) additional methyl groups, respectively. Our results suggest that the relative abundance of both bacterial and archaeal H-GDGTs compared to regular GDGTs is related to temperature with the highest relative abundance of H-GDGTs in tropical peats. Although other factors besides temperature likely also play a role, these results do support the hypothesis that H-GDGTs are an adaptation to temperature to maintain membrane stability. The observation that both bacterial and archaeal membrane lipids respond to temperature indicates the same adaption across the lipid divide between these two domains of life, suggesting parallel or convergent evolution (potentially facilitated by lateral gene transfer).

  8. Estimating abundance of mountain lions from unstructured spatial sampling

    Science.gov (United States)

    Russell, Robin E.; Royle, J. Andrew; Desimone, Richard; Schwartz, Michael K.; Edwards, Victoria L.; Pilgrim, Kristy P.; Mckelvey, Kevin S.

    2012-01-01

    Mountain lions (Puma concolor) are often difficult to monitor because of their low capture probabilities, extensive movements, and large territories. Methods for estimating the abundance of this species are needed to assess population status, determine harvest levels, evaluate the impacts of management actions on populations, and derive conservation and management strategies. Traditional mark–recapture methods do not explicitly account for differences in individual capture probabilities due to the spatial distribution of individuals in relation to survey effort (or trap locations). However, recent advances in the analysis of capture–recapture data have produced methods estimating abundance and density of animals from spatially explicit capture–recapture data that account for heterogeneity in capture probabilities due to the spatial organization of individuals and traps. We adapt recently developed spatial capture–recapture models to estimate density and abundance of mountain lions in western Montana. Volunteers and state agency personnel collected mountain lion DNA samples in portions of the Blackfoot drainage (7,908 km2) in west-central Montana using 2 methods: snow back-tracking mountain lion tracks to collect hair samples and biopsy darting treed mountain lions to obtain tissue samples. Overall, we recorded 72 individual capture events, including captures both with and without tissue sample collection and hair samples resulting in the identification of 50 individual mountain lions (30 females, 19 males, and 1 unknown sex individual). We estimated lion densities from 8 models containing effects of distance, sex, and survey effort on detection probability. Our population density estimates ranged from a minimum of 3.7 mountain lions/100 km2 (95% Cl 2.3–5.7) under the distance only model (including only an effect of distance on detection probability) to 6.7 (95% Cl 3.1–11.0) under the full model (including effects of distance, sex, survey effort, and

  9. Coral Bacterial-Core Abundance and Network Complexity as Proxies for Anthropogenic Pollution

    Directory of Open Access Journals (Sweden)

    Deborah C. A. Leite

    2018-04-01

    Full Text Available Acclimatization via changes in the stable (core or the variable microbial diversity and/or abundance is an important element in the adaptation of coral species to environmental changes. Here, we explored the spatial-temporal dynamics, diversity and interactions of variable and core bacterial populations associated with the coral Mussismilia hispida and the surrounding water. This survey was performed on five reefs along a transect from the coast (Reef 1 to offshore (Reef 5, representing a gradient of influence of the river mouth, for almost 12 months (4 sampling times, in the dry and rainy seasons. A clear increasing gradient of organic-pollution proxies (nitrogen content and fecal coliforms was observed from Reef 1 to Reef 5, during both seasons, and was highest at the Buranhém River mouth (Reef 1. Conversely, a clear inverse gradient of the network analysis of the whole bacterial communities also revealed more-complex network relationships at Reef 5. Our data also indicated a higher relative abundance of members of the bacterial core, dominated by Acinetobacter sp., at Reef 5, and higher diversity of site-stable bacterial populations, likely related to the higher abundance of total coliforms and N content (proxies of sewage or organic pollution at Reef 1, during the rainy season. Thus, the less “polluted” areas may show a more-complex network and a high relative abundance of members of the bacterial core (almost 97% in some cases, resulting in a more-homogeneous and well-established bacteriome among sites/samples, when the influence of the river is stronger (rainy seasons.

  10. Negative binomial models for abundance estimation of multiple closed populations

    Science.gov (United States)

    Boyce, Mark S.; MacKenzie, Darry I.; Manly, Bryan F.J.; Haroldson, Mark A.; Moody, David W.

    2001-01-01

    Counts of uniquely identified individuals in a population offer opportunities to estimate abundance. However, for various reasons such counts may be burdened by heterogeneity in the probability of being detected. Theoretical arguments and empirical evidence demonstrate that the negative binomial distribution (NBD) is a useful characterization for counts from biological populations with heterogeneity. We propose a method that focuses on estimating multiple populations by simultaneously using a suite of models derived from the NBD. We used this approach to estimate the number of female grizzly bears (Ursus arctos) with cubs-of-the-year in the Yellowstone ecosystem, for each year, 1986-1998. Akaike's Information Criteria (AIC) indicated that a negative binomial model with a constant level of heterogeneity across all years was best for characterizing the sighting frequencies of female grizzly bears. A lack-of-fit test indicated the model adequately described the collected data. Bootstrap techniques were used to estimate standard errors and 95% confidence intervals. We provide a Monte Carlo technique, which confirms that the Yellowstone ecosystem grizzly bear population increased during the period 1986-1998.

  11. Are owl pellets good estimators of prey abundance?

    Directory of Open Access Journals (Sweden)

    Analia Andrade

    2016-07-01

    Full Text Available Some ecologists have been skeptics about the use of owl pellets to estimate small mammal’s fauna. This is due to the assumptions required by this method: (a that owls hunt at random, and (b that pellets represent a random sample from the environment. We performed statistical analysis to test these assumptions and to assess the effectiveness of Barn owl pellets as a useful estimator of field abundances of its preys. We used samples collected in the arid Extra-Andean Patagonia along an altitudinal environmental gradient from lower Monte ecoregion to upper Patagonian steppe ecoregion, with a mid-elevation ecotone. To test if owls hunt at random, we estimated expected pellet frequency by creating a distribution of random pellets, which we compared with data using a simulated chi-square. To test if pellets represent a random sample from the environment, differences between ecoregions were evaluated by PERMANOVAs with Bray–Curtis dissimilarities. We did not find evidence that owls foraged non-randomly. Therefore, we can assume that the proportions of the small mammal’s species in the diet are representative of the proportions of the species in their communities. Only Monte is different from other ecoregions. The ecotone samples are grouped with those of Patagonian steppes. There are no real differences between localities in the small mammal’s abundances in each of these ecoregions and/or Barn owl pellets cannot detect patterns at a smaller spatial scale. Therefore, we have no evidence to invalidate the use of owl pellets at an ecoregional scale.

  12. Abundances of Clinically Relevant Antibiotic Resistance Genes and Bacterial Community Diversity in the Weihe River, China

    Directory of Open Access Journals (Sweden)

    Xiaojuan Wang

    2018-04-01

    Full Text Available The spread of antibiotic resistance genes in river systems is an emerging environmental issue due to their potential threat to aquatic ecosystems and public health. In this study, we used droplet digital polymerase chain reaction (ddPCR to evaluate pollution with clinically relevant antibiotic resistance genes (ARGs at 13 monitoring sites along the main stream of the Weihe River in China. Six clinically relevant ARGs and a class I integron-integrase (intI1 gene were analyzed using ddPCR, and the bacterial community was evaluated based on the bacterial 16S rRNA V3–V4 regions using MiSeq sequencing. The results indicated Proteobacteria, Actinobacteria, Cyanobacteria, and Bacteroidetes as the dominant phyla in the water samples from the Weihe River. Higher abundances of blaTEM, strB, aadA, and intI1 genes (103 to 105 copies/mL were detected in the surface water samples compared with the relatively low abundances of strA, mecA, and vanA genes (0–1.94 copies/mL. Eight bacterial genera were identified as possible hosts of the intI1 gene and three ARGs (strA, strB, and aadA based on network analysis. The results suggested that the bacterial community structure and horizontal gene transfer were associated with the variations in ARGs.

  13. Identification of prophages in bacterial genomes by dinucleotide relative abundance difference.

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    K V Srividhya

    Full Text Available BACKGROUND: Prophages are integrated viral forms in bacterial genomes that have been found to contribute to interstrain genetic variability. Many virulence-associated genes are reported to be prophage encoded. Present computational methods to detect prophages are either by identifying possible essential proteins such as integrases or by an extension of this technique, which involves identifying a region containing proteins similar to those occurring in prophages. These methods suffer due to the problem of low sequence similarity at the protein level, which suggests that a nucleotide based approach could be useful. METHODOLOGY: Earlier dinucleotide relative abundance (DRA have been used to identify regions, which deviate from the neighborhood areas, in genomes. We have used the difference in the dinucleotide relative abundance (DRAD between the bacterial and prophage DNA to aid location of DNA stretches that could be of prophage origin in bacterial genomes. Prophage sequences which deviate from bacterial regions in their dinucleotide frequencies are detected by scanning bacterial genome sequences. The method was validated using a subset of genomes with prophage data from literature reports. A web interface for prophage scan based on this method is available at http://bicmku.in:8082/prophagedb/dra.html. Two hundred bacterial genomes which do not have annotated prophages have been scanned for prophage regions using this method. CONCLUSIONS: The relative dinucleotide distribution difference helps detect prophage regions in genome sequences. The usefulness of this method is seen in the identification of 461 highly probable loci pertaining to prophages which have not been annotated so earlier. This work emphasizes the need to extend the efforts to detect and annotate prophage elements in genome sequences.

  14. Are grazer-induced adaptations of bacterial abundance and morphology timedependent?

    Directory of Open Access Journals (Sweden)

    Gianluca CORNO

    2006-02-01

    predators belong to two voracious species: Spumella sp. and Ochromonas sp., strictly heterotrophic and mixotrophic, respectively. For all the treatments, it was impossible to find any clear evidence of a morphological adaptation stimulated by the mere presence of flagellates. On the other hand, for all bacterial strains the enrichment of the media due to the release of exudates, resulted in higher growth rates and higher abundances, confirming that grazers are fundamental actors involved in the inner recycling of the microbial loop.

  15. Bacterial Succession on Rat Carcasses and Applications for PMI Estimation.

    Science.gov (United States)

    Zhang, Lin; Guo, Juan-juan; Telet-Siyit; Peng, Yu-long; Xie, Dan; Guo, Ya-dong; Yan, Jie; Zha, Lagabaiyila; Cai, Ji-feng

    2016-02-01

    Abstract: To investigate the bacterial succession on rat carcasses and to evaluate the use of bacterial succession for postmortem interval (PMI) estimation. Adult female SD rat remains were placed in carton boxes. The bacterial colonization of circumocular skin, mouth and vagina was collected to be identified using culture-dependent biochemical methods. The changes in community composition were regularly documented. The bacterial succession in three habitats showed that Staphylococcus and Neisseria were predominated in early PMI, especially Staphylococcus aureus and Neisseria lactamica in 6 hours after death. Lactobacillus casei developed on the 3-4 days regularly, and kept stable at a certain level in late PMI. The involvement of normal and putrefactive bacteria in three body habitats of rat remains can be used for PMI estimation.

  16. Bacterial abundance and activity in deep-sea sediments from the eastern North Atlantic

    Science.gov (United States)

    Eardly, D. F.; Carton, M. W.; Gallagher, J. M.; Patching, J. W.

    Results are presented from four cruises to the Porcupine Abyssal Plain (PAP site) that took place during the BENGAL project from September 1996 to March 1998, and two cruises to the PAP and an oligotrophic site (EUMELI) that took place during the DEEPSEAS project between September 1993 and March 1994. Bacterial abundances in sediment and sediment contact water were measured by epifluorescence microscopy. Bacterial activity was determined by 3H-thymidine incorporation as a measure of DNA synthesis, and by 3H-leucine incorporation as a measure of protein synthesis. Activities were measured under atmospheric and in situ pressures and temperatures. Bacterial activity was usually higher in samples incubated at in situ pressure than those incubated at atmospheric pressure indicating that a barophilic community was dominant. Inter-cruise comparisons of abundance and activity during the BENGAL project showed no firm evidence of there being a seasonal response in the benthic microbial community to any episodic phytodetritus event. This was probably because of inter-annual variations in the quality and quantity of phytodetritus deposition at the PAP site, the rapid remineralization of fresh organic material by the microbial communities and the timing of cruises to the study area. 3H-thymidine and 3H-leucine incorporation in sediments was higher during the BENGAL period than the DEEPSEAS programme. A methodological change in the 3H-thymidine incorporation technique for sediments may explain the differences in DNA synthesis observed between the two projects, whereas the lower levels of protein synthesis observed during the DEEPSEAS programme probably reflected both inter-annual variations in activity at the PAP site and the lower productivity that prevailed at surface at the EUMELI oligotrophic site. Rates of 3H-thymidine incorporation in sediment contact water were similar during both projects.

  17. Relative Abundance in Bacterial and Fungal Gut Microbes in Obese Children: A Case Control Study.

    Science.gov (United States)

    Borgo, Francesca; Verduci, Elvira; Riva, Alessandra; Lassandro, Carlotta; Riva, Enrica; Morace, Giulia; Borghi, Elisa

    2017-02-01

    Differences in relative proportions of gut microbial communities in adults have been correlated with intestinal diseases and obesity. In this study we evaluated the gut microbiota biodiversity, both bacterial and fungal, in obese and normal-weight school-aged children. We studied 28 obese (mean age 10.03 ± 0.68) and 33 age- and sex-matched normal-weight children. BMI z-scores were calculated, and the obesity condition was defined according to the WHO criteria. Fecal samples were analyzed by 16S rRNA amplification followed by denaturing gradient gel electrophoresis (DGGE) analysis and sequencing. Real-time polymerase chain reaction (PCR) was performed to quantify the most representative microbial species and genera. DGGE profiles showed high bacterial biodiversity without significant correlations with BMI z-score groups. Compared to bacterial profiles, we observed lower richness in yeast species. Sequence of the most representative bands gave back Eubacterium rectale, Saccharomyces cerevisiae, Candida albicans, and C. glabrata as present in all samples. Debaryomyces hansenii was present only in two obese children. Obese children revealed a significantly lower abundance in Akkermansia muciniphyla, Faecalibacterium prausnitzii, Bacteroides/Prevotella group, Candida spp., and Saccharomyces spp. (P = 0.031, P = 0.044, P = 0.003, P = 0.047, and P = 0.034, respectively). Taking into account the complexity of obesity, our data suggest that differences in relative abundance of some core microbial species, preexisting or diet driven, could actively be part of its etiology. This study improved our knowledge about the fungal population in the pediatric school-age population and highlighted the need to consider the influence of cross-kingdom relationships.

  18. A Convenient Method for Estimation of the Isotopic Abundance in Uranium Bearing Samples

    International Nuclear Information System (INIS)

    AI -Saleh, F.S.; AI-Mukren, Alj.H.; Farouk, M.A.

    2008-01-01

    A convenient and simple method for estimation of the isotopic abundance in some uranium bearing samples using gamma-ray spectrometry is developed using a hyper pure germanium spectrometer and a standard uranium sample with known isotopic abundance

  19. Long term repeated fire disturbance alters soil bacterial diversity but not the abundance in an Australian wet sclerophyll forest.

    Science.gov (United States)

    Shen, Ju-pei; Chen, C R; Lewis, Tom

    2016-01-20

    Effects of fire on biogeochemical cycling in terrestrial ecosystem are widely acknowledged, while few studies have focused on the bacterial community under the disturbance of long-term frequent prescribed fire. In this study, three treatments (burning every two years (B2), burning every four years (B4) and no burning (B0)) were applied for 38 years in an Australian wet sclerophyll forest. Results showed that bacterial alpha diversity (i.e. bacterial OTU) in the top soil (0-10 cm) was significantly higher in the B2 treatment compared with the B0 and B4 treatments. Non-metric multidimensional analysis (NMDS) of bacterial community showed clear separation of the soil bacterial community structure among different fire frequency regimes and between the depths. Different frequency fire did not have a substantial effect on bacterial composition at phylum level or bacterial 16S rRNA gene abundance. Soil pH and C:N ratio were the major drivers for bacterial community structure in the most frequent fire treatment (B2), while other factors (EC, DOC, DON, MBC, NH4(+), TC and TN) were significant in the less frequent burning and no burning treatments (B4 and B0). This study suggested that burning had a dramatic impact on bacterial diversity but not abundance with more frequent fire.

  20. "Capture" Me if You Can: Estimating Abundance of Dolphin Populations

    Science.gov (United States)

    Thompson, Jessica; Curran, Mary Carla; Cox, Tara

    2016-01-01

    Animal populations are monitored over time to assess the effects of environmental disaster and disease, as well as the efficacy of laws designed to protect them. Determining the abundance of a species within a defined area is one method of monitoring a population. In "Capture" Me if You Can, middle school students will use data collected…

  1. Bacterial pathogen gene abundance and relation to recreational water quality at seven Great Lakes beaches.

    Science.gov (United States)

    Oster, Ryan J; Wijesinghe, Rasanthi U; Haack, Sheridan K; Fogarty, Lisa R; Tucker, Taaja R; Riley, Stephen C

    2014-12-16

    Quantitative assessment of bacterial pathogens, their geographic variability, and distribution in various matrices at Great Lakes beaches are limited. Quantitative PCR (qPCR) was used to test for genes from E. coli O157:H7 (eaeO157), shiga-toxin producing E. coli (stx2), Campylobacter jejuni (mapA), Shigella spp. (ipaH), and a Salmonella enterica-specific (SE) DNA sequence at seven Great Lakes beaches, in algae, water, and sediment. Overall, detection frequencies were mapA>stx2>ipaH>SE>eaeO157. Results were highly variable among beaches and matrices; some correlations with environmental conditions were observed for mapA, stx2, and ipaH detections. Beach seasonal mean mapA abundance in water was correlated with beach seasonal mean log10 E. coli concentration. At one beach, stx2 gene abundance was positively correlated with concurrent daily E. coli concentrations. Concentration distributions for stx2, ipaH, and mapA within algae, sediment, and water were statistically different (Non-Detect and Data Analysis in R). Assuming 10, 50, or 100% of gene copies represented viable and presumably infective cells, a quantitative microbial risk assessment tool developed by Michigan State University indicated a moderate probability of illness for Campylobacter jejuni at the study beaches, especially where recreational water quality criteria were exceeded. Pathogen gene quantification may be useful for beach water quality management.

  2. Effects of High Hydrostatic Pressure on Coastal Bacterial Community Abundance and Diversity

    Science.gov (United States)

    Marietou, Angeliki

    2014-01-01

    Hydrostatic pressure is an important parameter influencing the distribution of microbial life in the ocean. In this study, the response of marine bacterial populations from surface waters to pressures representative of those under deep-sea conditions was examined. Southern California coastal seawater collected 5 m below the sea surface was incubated in microcosms, using a range of temperatures (16 to 3°C) and hydrostatic pressure conditions (0.1 to 80 MPa). Cell abundance decreased in response to pressure, while diversity increased. The morphology of the community also changed with pressurization to a predominant morphotype of small cocci. The pressure-induced community changes included an increase in the relative abundance of Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, and Flavobacteria largely at the expense of Epsilonproteobacteria. Culturable high-pressure-surviving bacteria were obtained and found to be phylogenetically similar to isolates from cold and/or deep-sea environments. These results provide novel insights into the response of surface water bacteria to changes in hydrostatic pressure. PMID:25063663

  3. Estimation of bacterial hydrogen sulfide production in vitro

    Directory of Open Access Journals (Sweden)

    Amina Basic

    2015-06-01

    Full Text Available Oral bacterial hydrogen sulfide (H2S production was estimated comparing two different colorimetric methods in microtiter plate format. High H2S production was seen for Fusobacterium spp., Treponema denticola, and Prevotella tannerae, associated with periodontal disease. The production differed between the methods indicating that H2S production may follow different pathways.

  4. Combining Inverse and Transport Modeling to Estimate Bacterial Loading and Transport in a Tidal Embayment

    Directory of Open Access Journals (Sweden)

    Mac Sisson

    2016-11-01

    Full Text Available Poquoson River is a tidal coastal embayment located along the Western Shore of the Chesapeake Bay about 4 km south of the York River mouth in the City of Poquoson and in York County, Virginia. Its drainage area has diversified land uses, including high densities of residence, agricultural, salt marsh land uses, as well as a National Wildlife Refuge. This embayment experiences elevated bacterial concentration due to excess bacterial inputs from storm water runoff, nonpoint sources, and wash off from marshes due to tide and wind-induced set-up and set-down. Bacteria can also grow in the marsh and small tributaries. It is difficult to use a traditional watershed model to simulate bacterial loading, especially in this low-lying marsh area with abundant wildlife, while runoff is not solely driven by precipitation. An inverse approach is introduced to estimate loading from unknown sources based on observations in the embayment. The estimated loadings were combined with loadings estimated from different sources (human, wildlife, agriculture, pets, etc. and input to the watershed model. The watershed model simulated long-term flow and bacterial loading and discharged to a three-dimensional transport model driven by tide, wind, and freshwater discharge. The transport model efficiently simulates the transport and fate of the bacterial concentration in the embayment and is capable of determining the loading reduction needed to improve the water quality condition of the embayment. Combining inverse, watershed, and transport models is a sound approach for simulating bacterial transport correctly in the coastal embayment with complex unknown bacterial sources, which are not solely driven by precipitation.

  5. Archaeal abundance across a pH gradient in an arable soil and its relationship to bacterial and fungal growth rates.

    Science.gov (United States)

    Bengtson, Per; Sterngren, Anna E; Rousk, Johannes

    2012-08-01

    Soil pH is one of the most influential factors for the composition of bacterial and fungal communities, but the influence of soil pH on the distribution and composition of soil archaeal communities has yet to be systematically addressed. The primary aim of this study was to determine how total archaeal abundance (quantitative PCR [qPCR]-based estimates of 16S rRNA gene copy numbers) is related to soil pH across a pH gradient (pH 4.0 to 8.3). Secondarily, we wanted to assess how archaeal abundance related to bacterial and fungal growth rates across the same pH gradient. We identified two distinct and opposite effects of pH on the archaeal abundance. In the lowest pH range (pH 4.0 to 4.7), the abundance of archaea did not seem to correspond to pH. Above this pH range, there was a sharp, almost 4-fold decrease in archaeal abundance, reaching a minimum at pH 5.1 to 5.2. The low abundance of archaeal 16S rRNA gene copy numbers at this pH range then sharply increased almost 150-fold with pH, resulting in an increase in the ratio between archaeal and bacterial copy numbers from a minimum of 0.002 to more than 0.07 at pH 8. The nonuniform archaeal response to pH could reflect variation in the archaeal community composition along the gradient, with some archaea adapted to acidic conditions and others to neutral to slightly alkaline conditions. This suggestion is reinforced by observations of contrasting outcomes of the (competitive) interactions between archaea, bacteria, and fungi toward the lower and higher ends of the examined pH gradient.

  6. A method for estimating abundance of mobile populations using telemetry and counts of unmarked animals

    Science.gov (United States)

    Clement, Matthew; O'Keefe, Joy M; Walters, Brianne

    2015-01-01

    While numerous methods exist for estimating abundance when detection is imperfect, these methods may not be appropriate due to logistical difficulties or unrealistic assumptions. In particular, if highly mobile taxa are frequently absent from survey locations, methods that estimate a probability of detection conditional on presence will generate biased abundance estimates. Here, we propose a new estimator for estimating abundance of mobile populations using telemetry and counts of unmarked animals. The estimator assumes that the target population conforms to a fission-fusion grouping pattern, in which the population is divided into groups that frequently change in size and composition. If assumptions are met, it is not necessary to locate all groups in the population to estimate abundance. We derive an estimator, perform a simulation study, conduct a power analysis, and apply the method to field data. The simulation study confirmed that our estimator is asymptotically unbiased with low bias, narrow confidence intervals, and good coverage, given a modest survey effort. The power analysis provided initial guidance on survey effort. When applied to small data sets obtained by radio-tracking Indiana bats, abundance estimates were reasonable, although imprecise. The proposed method has the potential to improve abundance estimates for mobile species that have a fission-fusion social structure, such as Indiana bats, because it does not condition detection on presence at survey locations and because it avoids certain restrictive assumptions.

  7. Estimating Bacterial and Cellular Load in FCFM Imaging

    Directory of Open Access Journals (Sweden)

    Sohan Seth

    2018-01-01

    Full Text Available We address the task of estimating bacterial and cellular load in the human distal lung with fibered confocal fluorescence microscopy (FCFM. In pulmonary FCFM some cells can display autofluorescence, and they appear as disc like objects in the FCFM images, whereas bacteria, although not autofluorescent, appear as bright blinking dots when exposed to a targeted smartprobe. Estimating bacterial and cellular load becomes a challenging task due to the presence of background from autofluorescent human lung tissues, i.e., elastin, and imaging artifacts from motion etc. We create a database of annotated images for both these tasks where bacteria and cells were annotated, and use these databases for supervised learning. We extract image patches around each pixel as features, and train a classifier to predict if a bacterium or cell is present at that pixel. We apply our approach on two datasets for detecting bacteria and cells respectively. For the bacteria dataset, we show that the estimated bacterial load increases after introducing the targeted smartprobe in the presence of bacteria. For the cell dataset, we show that the estimated cellular load agrees with a clinician’s assessment.

  8. Bacterial pathogen gene abundance and relation to recreational water quality at seven Great Lakes beaches

    Science.gov (United States)

    Oster, Ryan J.; Wijesinghe, Rasanthi U.; Fogarty, Lisa Reynolds; Haack, Sheridan K.; Fogarty, Lisa R.; Tucker, Taaja R.; Riley, Stephen

    2014-01-01

    Quantitative assessment of bacterial pathogens, their geographic variability, and distribution in various matrices at Great Lakes beaches are limited. Quantitative PCR (qPCR) was used to test for genes from E. coli O157:H7 (eaeO157), shiga-toxin producing E. coli (stx2), Campylobacter jejuni (mapA), Shigella spp. (ipaH), and a Salmonella enterica-specific (SE) DNA sequence at seven Great Lakes beaches, in algae, water, and sediment. Overall, detection frequencies were mapA>stx2>ipaH>SE>eaeO157. Results were highly variable among beaches and matrices; some correlations with environmental conditions were observed for mapA, stx2, and ipaH detections. Beach seasonal mean mapA abundance in water was correlated with beach seasonal mean log10E. coli concentration. At one beach, stx2 gene abundance was positively correlated with concurrent daily E. coli concentrations. Concentration distributions for stx2, ipaH, and mapA within algae, sediment, and water were statistically different (Non-Detect and Data Analysis in R). Assuming 10, 50, or 100% of gene copies represented viable and presumably infective cells, a quantitative microbial risk assessment tool developed by Michigan State University indicated a moderate probability of illness for Campylobacter jejuni at the study beaches, especially where recreational water quality criteria were exceeded. Pathogen gene quantification may be useful for beach water quality management.

  9. Bacterial and enchytraeid abundance accelerate soil carbon turnover along a lowland vegetation gradient in interior Alaska

    Science.gov (United States)

    Waldrop, M.P.; Harden, Jennifer W.; Turetsky, M.R.; Petersen, D.G.; McGuire, A.D.; Briones, M.J.I.; Churchill, A.C.; Doctor, D.H.; Pruett, L.E.

    2012-01-01

    Boreal wetlands are characterized by a mosaic of plant communities, including forests, shrublands, grasslands, and fens, which are structured largely by changes in topography and water table position. The soil associated with these plant communities contain quantitatively and qualitatively different forms of soil organic matter (SOM) and nutrient availability that drive changes in biogeochemical cycling rates. Therefore different boreal plant communities likely contain different soil biotic communities which in turn affect rates of organic matter decomposition. We examined relationships between plant communities, microbial communities, enchytraeids, and soil C turnover in near-surface soils along a shallow topographic soil moisture and vegetation gradient in interior Alaska. We tested the hypothesis that as soil moisture increases along the gradient, surface soils would become increasingly dominated by bacteria and mesofauna and have more rapid rates of C turnover. We utilized bomb radiocarbon techniques to infer rates of C turnover and the 13C isotopic composition of SOM and respired CO2 to infer the degree of soil humification. Soil phenol oxidase and peroxidase enzyme activities were generally higher in the rich fen compared with the forest and bog birch sites. Results indicated greater C fluxes and more rapid C turnover in the surface soils of the fen sites compared to the wetland forest and shrub sites. Quantitative PCR analyses of soil bacteria and archaea, combined with enchytraeid counts, indicated that surface soils from the lowland fen ecosystems had higher abundances of these microbial and mesofaunal groups. Fungal abundance was highly variable and not significantly different among sites. Microbial data was utilized in a food web model that confirmed that rapidly cycling systems are dominated by bacterial activity and enchytraeid grazing. However, our results also suggest that oxidative enzymes play an important role in the C mineralization process in

  10. Changes in diversity, abundance, and structure of soil bacterial communities in Brazilian Savanna under different land use systems.

    Science.gov (United States)

    Rampelotto, Pabulo Henrique; de Siqueira Ferreira, Adão; Barboza, Anthony Diego Muller; Roesch, Luiz Fernando Wurdig

    2013-10-01

    The Brazilian Savanna, also known as "Cerrado", is the richest and most diverse savanna in the world and has been ranked as one of the main hotspots of biodiversity. The Cerrado is a representative biome in Central Brazil and the second largest biome in species diversity of South America. Nevertheless, large areas of native vegetation have been converted to agricultural land including grain production, livestock, and forestry. In this view, understanding how land use affects microbial communities is fundamental for the sustainable management of agricultural ecosystems. The aim of this work was to analyze and compare the soil bacterial communities from the Brazilian Cerrado associated with different land use systems using high throughput pyrosequencing of 16S rRNA genes. Relevant differences were observed in the abundance and structure of bacterial communities in soils under different land use systems. On the other hand, the diversity of bacterial communities was not relevantly changed among the sites studied. Land use systems had also an important impact on specific bacterial groups in soil, which might change the soil function and the ecological processes. Acidobacteria, Proteobacteria, and Actinobacteria were the most abundant groups in the Brazilian Cerrado. These findings suggest that more important than analyzing the general diversity is to analyze the composition of the communities. Since soil type was the same among the sites, we might assume that land use was the main factor defining the abundance and structure of bacterial communities.

  11. Hankin and Reeves' approach to estimating fish abundance in small streams: limitations and alternatives

    Science.gov (United States)

    William L. Thompson

    2003-01-01

    Hankin and Reeves' (1988) approach to estimating fish abundance in small streams has been applied in stream fish studies across North America. However, their population estimator relies on two key assumptions: (1) removal estimates are equal to the true numbers of fish, and (2) removal estimates are highly correlated with snorkel counts within a subset of sampled...

  12. Estimating Lion Abundance using N-mixture Models for Social Species.

    Science.gov (United States)

    Belant, Jerrold L; Bled, Florent; Wilton, Clay M; Fyumagwa, Robert; Mwampeta, Stanslaus B; Beyer, Dean E

    2016-10-27

    Declining populations of large carnivores worldwide, and the complexities of managing human-carnivore conflicts, require accurate population estimates of large carnivores to promote their long-term persistence through well-informed management We used N-mixture models to estimate lion (Panthera leo) abundance from call-in and track surveys in southeastern Serengeti National Park, Tanzania. Because of potential habituation to broadcasted calls and social behavior, we developed a hierarchical observation process within the N-mixture model conditioning lion detectability on their group response to call-ins and individual detection probabilities. We estimated 270 lions (95% credible interval = 170-551) using call-ins but were unable to estimate lion abundance from track data. We found a weak negative relationship between predicted track density and predicted lion abundance from the call-in surveys. Luminosity was negatively correlated with individual detection probability during call-in surveys. Lion abundance and track density were influenced by landcover, but direction of the corresponding effects were undetermined. N-mixture models allowed us to incorporate multiple parameters (e.g., landcover, luminosity, observer effect) influencing lion abundance and probability of detection directly into abundance estimates. We suggest that N-mixture models employing a hierarchical observation process can be used to estimate abundance of other social, herding, and grouping species.

  13. Bacterial abundance, communities and heterotrophic activities in the coastal waters off Tamil Nadu

    Digital Repository Service at National Institute of Oceanography (India)

    Ramaiah, N.; Raghukumar, C.; Sheelu, G.; Chandramohan, D.

    Culturable aerobic heterotrophic bacterial (CAHB) numbers, total direct counts (TDC), bacterial generic composition and uptake of labelled glucose by natural microbial assemblages were studied from a few selected coastal sites off Tamil Nadu. A high...

  14. Dynamic N -occupancy models: estimating demographic rates and local abundance from detection-nondetection data

    Science.gov (United States)

    Sam Rossman; Charles B. Yackulic; Sarah P. Saunders; Janice Reid; Ray Davis; Elise F. Zipkin

    2016-01-01

    Occupancy modeling is a widely used analytical technique for assessing species distributions and range dynamics. However, occupancy analyses frequently ignore variation in abundance of occupied sites, even though site abundances affect many of the parameters being estimated (e.g., extinction, colonization, detection probability). We introduce a new model (“dynamic

  15. Can we estimate bacterial growth rates from ribosomal RNA content?

    Energy Technology Data Exchange (ETDEWEB)

    Kemp, P.F.

    1995-12-31

    Several studies have demonstrated a strong relationship between the quantity of RNA in bacterial cells and their growth rate under laboratory conditions. It may be possible to use this relationship to provide information on the activity of natural bacterial communities, and in particular on growth rate. However, if this approach is to provide reliably interpretable information, the relationship between RNA content and growth rate must be well-understood. In particular, a requisite of such applications is that the relationship must be universal among bacteria, or alternately that the relationship can be determined and measured for specific bacterial taxa. The RNA-growth rate relationship has not been used to evaluate bacterial growth in field studies, although RNA content has been measured in single cells and in bulk extracts of field samples taken from coastal environments. These measurements have been treated as probable indicators of bacterial activity, but have not yet been interpreted as estimators of growth rate. The primary obstacle to such interpretations is a lack of information on biological and environmental factors that affect the RNA-growth rate relationship. In this paper, the available data on the RNA-growth rate relationship in bacteria will be reviewed, including hypotheses regarding the regulation of RNA synthesis and degradation as a function of growth rate and environmental factors; i.e. the basic mechanisms for maintaining RNA content in proportion to growth rate. An assessment of the published laboratory and field data, the current status of this research area, and some of the remaining questions will be presented.

  16. Variable effects of oxytetracycline on antibiotic resistance gene abundance and the bacterial community during aerobic composting of cow manure.

    Science.gov (United States)

    Qian, Xun; Sun, Wei; Gu, Jie; Wang, Xiao-Juan; Sun, Jia-Jun; Yin, Ya-Nan; Duan, Man-Li

    2016-09-05

    Livestock manure is often subjected to aerobic composting but little is known about the variation in antibiotic resistance genes (ARGs) during the composting process under different concentrations of antibiotics. This study compared the effects of three concentrations of oxytetracycline (OTC; 10, 60, and 200mg/kg) on ARGs and the succession of the bacterial community during composting. Very similar trends were observed in the relative abundances (RAs) of each ARG among the OTC treatments and the control during composting. After composting, the RAs of tetC, tetX, sul1, sul2, and intI1 increased 2-43 times, whereas those of tetQ, tetM, and tetW declined by 44-99%. OTC addition significantly increased the absolute abundances and RAs of tetC and intI1, while 200mg/kg OTC also enhanced those of tetM, tetQ, and drfA7. The bacterial community could be grouped according to the composting time under different treatments. The highest concentration of OTC had a more persistent effect on the bacterial community. In the present study, the succession of the bacterial community appeared to have a greater influence on the variation of ARGs during composting than the presence of antibiotics. Aerobic composting was not effective in reducing most of the ARGs, and thus the compost product should be considered as an important reservoir for ARGs. Copyright © 2016 Elsevier B.V. All rights reserved.

  17. Visual Estimation of Bacterial Growth Level in Microfluidic Culture Systems

    Directory of Open Access Journals (Sweden)

    Kyukwang Kim

    2018-02-01

    Full Text Available Microfluidic devices are an emerging platform for a variety of experiments involving bacterial cell culture, and has advantages including cost and convenience. One inevitable step during bacterial cell culture is the measurement of cell concentration in the channel. The optical density measurement technique is generally used for bacterial growth estimation, but it is not applicable to microfluidic devices due to the small sample volumes in microfluidics. Alternately, cell counting or colony-forming unit methods may be applied, but these do not work in situ; nor do these methods show measurement results immediately. To this end, we present a new vision-based method to estimate the growth level of the bacteria in microfluidic channels. We use Fast Fourier transform (FFT to detect the frequency level change of the microscopic image, focusing on the fact that the microscopic image becomes rough as the number of cells in the field of view increases, adding high frequencies to the spectrum of the image. Two types of microfluidic devices are used to culture bacteria in liquid and agar gel medium, and time-lapsed images are captured. The images obtained are analyzed using FFT, resulting in an increase in high-frequency noise proportional to the time passed. Furthermore, we apply the developed method in the microfluidic antibiotics susceptibility test by recognizing the regional concentration change of the bacteria that are cultured in the antibiotics gradient. Finally, a deep learning-based data regression is performed on the data obtained by the proposed vision-based method for robust reporting of data.

  18. Visual Estimation of Bacterial Growth Level in Microfluidic Culture Systems.

    Science.gov (United States)

    Kim, Kyukwang; Kim, Seunggyu; Jeon, Jessie S

    2018-02-03

    Microfluidic devices are an emerging platform for a variety of experiments involving bacterial cell culture, and has advantages including cost and convenience. One inevitable step during bacterial cell culture is the measurement of cell concentration in the channel. The optical density measurement technique is generally used for bacterial growth estimation, but it is not applicable to microfluidic devices due to the small sample volumes in microfluidics. Alternately, cell counting or colony-forming unit methods may be applied, but these do not work in situ; nor do these methods show measurement results immediately. To this end, we present a new vision-based method to estimate the growth level of the bacteria in microfluidic channels. We use Fast Fourier transform (FFT) to detect the frequency level change of the microscopic image, focusing on the fact that the microscopic image becomes rough as the number of cells in the field of view increases, adding high frequencies to the spectrum of the image. Two types of microfluidic devices are used to culture bacteria in liquid and agar gel medium, and time-lapsed images are captured. The images obtained are analyzed using FFT, resulting in an increase in high-frequency noise proportional to the time passed. Furthermore, we apply the developed method in the microfluidic antibiotics susceptibility test by recognizing the regional concentration change of the bacteria that are cultured in the antibiotics gradient. Finally, a deep learning-based data regression is performed on the data obtained by the proposed vision-based method for robust reporting of data.

  19. When are genetic methods useful for estimating contemporary abundance and detecting population trends?

    Science.gov (United States)

    David A. Tallmon; Dave Gregovich; Robin S. Waples; C. Scott Baker; Jennifer Jackson; Barbara L. Taylor; Eric Archer; Karen K. Martien; Fred W. Allendorf; Michael K. Schwartz

    2010-01-01

    The utility of microsatellite markers for inferring population size and trend has not been rigorously examined, even though these markers are commonly used to monitor the demography of natural populations. We assessed the ability of a linkage disequilibrium estimator of effective population size (Ne) and a simple capture-recapture estimator of abundance (N) to quantify...

  20. An integrated data model to estimate spatiotemporal occupancy, abundance, and colonization dynamics

    Science.gov (United States)

    Williams, Perry J.; Hooten, Mevin B.; Womble, Jamie N.; Esslinger, George G.; Bower, Michael R.; Hefley, Trevor J.

    2017-01-01

    Ecological invasions and colonizations occur dynamically through space and time. Estimating the distribution and abundance of colonizing species is critical for efficient management or conservation. We describe a statistical framework for simultaneously estimating spatiotemporal occupancy and abundance dynamics of a colonizing species. Our method accounts for several issues that are common when modeling spatiotemporal ecological data including multiple levels of detection probability, multiple data sources, and computational limitations that occur when making fine-scale inference over a large spatiotemporal domain. We apply the model to estimate the colonization dynamics of sea otters (Enhydra lutris) in Glacier Bay, in southeastern Alaska.

  1. Estimates of the abundance of minke whales (Balaenoptera acutorostrata from Faroese and Icelandic NASS shipboard surveys

    Directory of Open Access Journals (Sweden)

    Daniel G Pike

    2009-09-01

    Full Text Available North Atlantic Sightings Surveys for cetaceans were carried out Northeast and Central Atlantic in 1987, 1989, 1995 and 2001. Here we provide estimates of density and abundance for minke whales from the Faroese and Icelandic ship surveys. The estimates are not corrected for availability or perception biases. Double platform data collected in 2001 indicates that perception bias is likely considerable for this species. However comparison of corrected estimates of densityfrom aerial surveys with a ship survey estimate from the same area suggests that ship surveys can be nearly unbiased under optimal survey conditions with high searching effort. There were some regional changes in density over the period but no overall changes in density and abundance. Given the recent catch history for minke whales in this area, we would not expect to see changes in abundance due to exploitation that would be detectable with these surveys.

  2. Time-dependent effect of graphene on the structure, abundance, and function of the soil bacterial community.

    Science.gov (United States)

    Ren, Wenjie; Ren, Gaidi; Teng, Ying; Li, Zhengao; Li, Lina

    2015-10-30

    The increased application of graphene raises concerns about its environmental impact, but little information is available on the effect of graphene on the soil microbial community. This study evaluated the impact of graphene on the structure, abundance and function of the soil bacterial community based on quantitative real-time polymerase chain reaction (qPCR), pyrosequencing and soil enzyme activities. The results show that the enzyme activities of dehydrogenase and fluorescein diacetate (FDA) esterase and the biomass of the bacterial populations were transiently promoted by the presence of graphene after 4 days of exposure, but these parameters recovered completely after 21 days. Pyrosequencing analysis suggested a significant shift in some bacterial populations after 4 days, and the shift became weaker or disappeared as the exposure time increased to 60 days. During the entire exposure process, the majority of bacterial phylotypes remained unaffected. Some bacterial populations involved in nitrogen biogeochemical cycles and the degradation of organic compounds can be affected by the presence of graphene. Copyright © 2015 Elsevier B.V. All rights reserved.

  3. Gene and transcript abundances of bacterial type III secretion systems from the rumen microbiome are correlated with methane yield in sheep.

    Science.gov (United States)

    Kamke, Janine; Soni, Priya; Li, Yang; Ganesh, Siva; Kelly, William J; Leahy, Sinead C; Shi, Weibing; Froula, Jeff; Rubin, Edward M; Attwood, Graeme T

    2017-08-08

    Ruminants are important contributors to global methane emissions via microbial fermentation in their reticulo-rumens. This study is part of a larger program, characterising the rumen microbiomes of sheep which vary naturally in methane yield (g CH 4 /kg DM/day) and aims to define differences in microbial communities, and in gene and transcript abundances that can explain the animal methane phenotype. Rumen microbiome metagenomic and metatranscriptomic data were analysed by Gene Set Enrichment, sparse partial least squares regression and the Wilcoxon Rank Sum test to estimate correlations between specific KEGG bacterial pathways/genes and high methane yield in sheep. KEGG genes enriched in high methane yield sheep were reassembled from raw reads and existing contigs and analysed by MEGAN to predict their phylogenetic origin. Protein coding sequences from Succinivibrio dextrinosolvens strains were analysed using Effective DB to predict bacterial type III secreted proteins. The effect of S. dextrinosolvens strain H5 growth on methane formation by rumen methanogens was explored using co-cultures. Detailed analysis of the rumen microbiomes of high methane yield sheep shows that gene and transcript abundances of bacterial type III secretion system genes are positively correlated with methane yield in sheep. Most of the bacterial type III secretion system genes could not be assigned to a particular bacterial group, but several genes were affiliated with the genus Succinivibrio, and searches of bacterial genome sequences found that strains of S. dextrinosolvens were part of a small group of rumen bacteria that encode this type of secretion system. In co-culture experiments, S. dextrinosolvens strain H5 showed a growth-enhancing effect on a methanogen belonging to the order Methanomassiliicoccales, and inhibition of a representative of the Methanobrevibacter gottschalkii clade. This is the first report of bacterial type III secretion system genes being associated with high

  4. Seagrass vegetation and meiofauna enhance the bacterial abundance in the Baltic Sea sediments (Puck Bay)

    OpenAIRE

    Jankowska, Emilia; Jankowska, Katarzyna; Włodarska-Kowalczuk, Maria

    2015-01-01

    This study presents the first report on bacterial communities in the sediments of eelgrass (Zostera marina) meadows in the shallow southern Baltic Sea (Puck Bay). Total bacterial cell numbers (TBNs) and bacteria biomass (BBM) assessed with the use of epifluorescence microscope and Norland’s formula were compared between bare and vegetated sediments at two localities and in two sampling summer months. Significantly higher TBNs and BBM (PERMANOVA tests, P 

  5. ON ESTIMATING INTERSTELLAR POLYCYCLIC AROMATIC HYDROCARBON ABUNDANCES WITH CALCULATED OSCILLATOR STRENGTHS

    International Nuclear Information System (INIS)

    Tan Xiaofeng; Bernstein, Lawrence; Cami, Jan; Salama, Farid

    2011-01-01

    Vibronic bands of polycyclic aromatic hydrocarbons (PAHs) in the UV/visible range are often used to estimate the abundances of PAHs in the interstellar medium by comparing laboratory-measured spectra with astronomical observations. We investigate the errors introduced by associating theoretical electronic oscillator strengths with individual vibronic bands when estimating the abundances of interstellar PAHs. The vibronic oscillator strengths of the 0-0 bands of nine PAHs with two to seven benzene rings, spanning in the 2800-6700 A spectral range, have been calculated using the Franck-Condon approximation and compared to their electronic oscillator strengths. It is found that the use of calculated electronic oscillator strengths rather than the more physically relevant vibronic oscillator strengths underestimates interstellar abundances of the nine PAHs under study, on average by a factor of about 2.4. It is recommended that vibronic oscillator strengths should be systematically used to analyze the vibronic spectra of specific PAHs and to estimate their abundances in the interstellar medium. An empirical correcting factor is suggested for the cases where the vibronic oscillator strengths are unknown for more realistic estimation of interstellar PAH abundances.

  6. Accounting for imperfect detection of groups and individuals when estimating abundance.

    Science.gov (United States)

    Clement, Matthew J; Converse, Sarah J; Royle, J Andrew

    2017-09-01

    If animals are independently detected during surveys, many methods exist for estimating animal abundance despite detection probabilities account for imperfect detection of groups, while assuming that individuals within groups are detected perfectly. However, this assumption is often unsupported. We introduce an abundance estimator for grouped animals when detection of groups is imperfect and group size may be under-counted, but not over-counted. The estimator combines an MRDS model with an N-mixture model to account for imperfect detection of individuals. The new MRDS-Nmix model requires the same data as an MRDS model (independent detection histories, an estimate of distance to transect, and an estimate of group size), plus a second estimate of group size provided by the second observer. We extend the model to situations in which detection of individuals within groups declines with distance. We simulated 12 data sets and used Bayesian methods to compare the performance of the new MRDS-Nmix model to an MRDS model. Abundance estimates generated by the MRDS-Nmix model exhibited minimal bias and nominal coverage levels. In contrast, MRDS abundance estimates were biased low and exhibited poor coverage. Many species of conservation interest reside in groups and could benefit from an estimator that better accounts for imperfect detection. Furthermore, the ability to relax the assumption of perfect detection of individuals within detected groups may allow surveyors to re-allocate resources toward detection of new groups instead of extensive surveys of known groups. We believe the proposed estimator is feasible because the only additional field data required are a second estimate of group size.

  7. Optimum sample size to estimate mean parasite abundance in fish parasite surveys

    Directory of Open Access Journals (Sweden)

    Shvydka S.

    2018-03-01

    Full Text Available To reach ethically and scientifically valid mean abundance values in parasitological and epidemiological studies this paper considers analytic and simulation approaches for sample size determination. The sample size estimation was carried out by applying mathematical formula with predetermined precision level and parameter of the negative binomial distribution estimated from the empirical data. A simulation approach to optimum sample size determination aimed at the estimation of true value of the mean abundance and its confidence interval (CI was based on the Bag of Little Bootstraps (BLB. The abundance of two species of monogenean parasites Ligophorus cephali and L. mediterraneus from Mugil cephalus across the Azov-Black Seas localities were subjected to the analysis. The dispersion pattern of both helminth species could be characterized as a highly aggregated distribution with the variance being substantially larger than the mean abundance. The holistic approach applied here offers a wide range of appropriate methods in searching for the optimum sample size and the understanding about the expected precision level of the mean. Given the superior performance of the BLB relative to formulae with its few assumptions, the bootstrap procedure is the preferred method. Two important assessments were performed in the present study: i based on CIs width a reasonable precision level for the mean abundance in parasitological surveys of Ligophorus spp. could be chosen between 0.8 and 0.5 with 1.6 and 1x mean of the CIs width, and ii the sample size equal 80 or more host individuals allows accurate and precise estimation of mean abundance. Meanwhile for the host sample size in range between 25 and 40 individuals, the median estimates showed minimal bias but the sampling distribution skewed to the low values; a sample size of 10 host individuals yielded to unreliable estimates.

  8. Estimation of lunar FeO abundance based on imaging by LRO Diviner

    International Nuclear Information System (INIS)

    Tang, Xiao; Zhang, Xue-Wei; Chen, Yuan; Zhang, Xiao-Meng; Cai, Wei; Wu, Yun-Zhao; Luo, Xiao-Xing; Jiang, Yun; Xu, Ao-Ao; Wang, Zhen-Chao

    2016-01-01

    Understanding the abundance and distribution characteristics of FeO on the surface of the Moon is important for investigating its evolution. The current high resolution maps of the global FeO abundance are mostly produced with visible and near infrared reflectance spectra. The Christiansen Feature (CF) in mid-infrared has strong sensitivity to lunar minerals and correlates to major elements composing minerals. This paper investigates the possibility of mapping global FeO abundance using the CF values from the Diviner Lunar Radiometer Experiment aboard the Lunar Reconnaissance Orbiter (LRO) mission. A high correlation between the CF values and FeO abundances from the Apollo samples was found. Based on this high correlation, a new global map (±60°) of FeO was produced using the CF map. The results show that the global FeO average is 8.2 wt.%, the highland average is 4.7 wt.%, the global modal abundance is 5.4 wt.% and the lunar mare mode is 15.7 wt.%. These results are close to those derived from data provided by Clementine, the Lunar Prospector Gamma Ray Spectrometer (LP-GRS) and the Chang'e-1 Interference Imaging Spectrometer (IIM), demonstrating the feasibility of estimating FeO abundance based on the Diviner CF data. The near global FeO abundance map shows an enrichment of lunar major elements. (paper)

  9. Estimating species occurrence, abundance, and detection probability using zero-inflated distributions.

    Science.gov (United States)

    Wenger, Seth J; Freeman, Mary C

    2008-10-01

    Researchers have developed methods to account for imperfect detection of species with either occupancy (presence absence) or count data using replicated sampling. We show how these approaches can be combined to simultaneously estimate occurrence, abundance, and detection probability by specifying a zero-inflated distribution for abundance. This approach may be particularly appropriate when patterns of occurrence and abundance arise from distinct processes operating at differing spatial or temporal scales. We apply the model to two data sets: (1) previously published data for a species of duck, Anas platyrhynchos, and (2) data for a stream fish species, Etheostoma scotti. We show that in these cases, an incomplete-detection zero-inflated modeling approach yields a superior fit to the data than other models. We propose that zero-inflated abundance models accounting for incomplete detection be considered when replicate count data are available.

  10. Short-term variability in bacterial abundance, cell properties, and incorporation of leucine and thymidine in subarctic sea ice

    DEFF Research Database (Denmark)

    Kaartokallio, H.; Sogaard, D. H.; Norman, L.

    2013-01-01

    Sea ice is a biome of immense size and provides a range of habitats for diverse microbial communities, many of which are adapted to living at low temperatures and high salinities in brines. We measured simultaneous incorporation of thymidine (TdR) and leucine (Leu), bacterial cell abundance...... and cell population properties (by flow cytometry) in subarctic sea ice in SW Greenland. Short-term temporal variability was moderate, and steep environmental gradients, typical for sea ice, were the main drivers of the variability in bacterial cell properties and activity. Low nucleic acid (LNA) bacteria...... and marine biofilm systems. Leu: TdR ratios were high (up to >300) in lowermost ice layers, and when compared to published respiration measurements, these results suggest non-specific Leu incorporation. There was evidence of polyhydroxyalkanoate (PHA)-containing bacteria in the sea ice, shown by brightly...

  11. Molecular assessment of bacterial vaginosis by Lactobacillus abundance and species diversity

    NARCIS (Netherlands)

    J.A.M. Dols (Joke); D. Molenaar (Douwe); van der Helm, J.J. (Jannie J.); Caspers, M.P.M. (Martien P.M.); Angelino-Bart, A.K. (Alie de Kat); F.H.J. Schuren (Frank); Speksnijder, A.G.C.L. (Adrianus G.C.L.); Westerhoff, H.V. (Hans V.); J.H. Richardus (Jan Hendrik); Boon, M.E. (Mathilde E.); G. Reid (Gregor); de Vries, H.J.C. (Henry J.C.); R. Kort (Remco)

    2016-01-01

    markdownabstract__Background:__ To date, women are most often diagnosed with bacterial vaginosis (BV) using microscopy based Nugent scoring or Amsel criteria. However, the accuracy is less than optimal. The aim of the present study was to confirm the identity of known BV-associated composition

  12. Bacterial abundance and production in the central and eastern Arabian Sea

    Digital Repository Service at National Institute of Oceanography (India)

    Ramaiah, N.; Raghukumar, S.; Gauns, M.

    bacterial densities of about 1 x 10 sup(9) cells L sup(-1) were observed during the intermonsoon periods of September and April/May compared to the southwest monsoon period of July/August and the winter period of February/March. Although primary production...

  13. Bacterial diversity and abundance of a creek valley sites reflected soil pH and season

    Czech Academy of Sciences Publication Activity Database

    Ságová-Marečková, M.; Čermák, L.; Omelka, M.; Kyselková, Martina; Kopecký, J.

    2015-01-01

    Roč. 10, č. 1 (2015), s. 61-70 ISSN 2391-5412 Grant - others:GA AV ČR(CZ) IAA603020901 Program:IA Institutional support: RVO:60077344 Keywords : bacterial communities * actinobacteria * OM quantity and quality * T-RFLP Subject RIV: EE - Microbiology, Virology

  14. Estimating abundance of Sitka black-tailed deer using DNA from fecal pellets

    Science.gov (United States)

    Todd J. Brinkman; David K. Person; F. Stuart Chapin; Winston Smith; Kris J. Hundertmark

    2011-01-01

    Densely vegetated environments have hindered collection of basic population parameters on forest-dwelling ungulates. Our objective was to develop a mark-recapture technique that used DNA from fecal pellets to overcome constraints associated with estimating abundance of ungulates in landscapes where direct observation is difficult. We tested our technique on Sitka black...

  15. Quantification of bacterial and archaeal symbionts in high and low microbial abundance sponges using real-time PCR

    KAUST Repository

    Bayer, Kristina

    2014-07-09

    In spite of considerable insights into the microbial diversity of marine sponges, quantitative information on microbial abundances and community composition remains scarce. Here, we established qPCR assays for the specific quantification of four bacterial phyla of representative sponge symbionts as well as the kingdoms Eubacteria and Archaea. We could show that the 16S rRNA gene numbers of Archaea, Chloroflexi, and the candidate phylum Poribacteria were 4-6 orders of magnitude higher in high microbial abundance (HMA) than in low microbial abundance (LMA) sponges and that actinobacterial 16S rRNA gene numbers were 1-2 orders higher in HMA over LMA sponges, while those for Cyanobacteria were stable between HMA and LMA sponges. Fluorescence in situ hybridization of Aplysina aerophoba tissue sections confirmed the numerical dominance of Chloroflexi, which was followed by Poribacteria. Archaeal and actinobacterial cells were detected in much lower numbers. By use of fluorescence-activated cell sorting as a primer- and probe-independent approach, the dominance of Chloroflexi, Proteobacteria, and Poribacteria in A. aerophoba was confirmed. Our study provides new quantitative insights into the microbiology of sponges and contributes to a better understanding of the HMA/LMA dichotomy. The authors quantified sponge symbionts in eight sponge species from three different locations by real time PCR targetting 16S rRNA genes. Additionally, FISH was performed and diversity and abundance of singularized microbial symbionts from Aplysina aerophoba was determined for a comprehensive quantification work. © 2014 Federation of European Microbiological Societies.

  16. Estimating animal abundance in ground beef batches assayed with molecular markers.

    Directory of Open Access Journals (Sweden)

    Xin-Sheng Hu

    Full Text Available Estimating animal abundance in industrial scale batches of ground meat is important for mapping meat products through the manufacturing process and for effectively tracing the finished product during a food safety recall. The processing of ground beef involves a potentially large number of animals from diverse sources in a single product batch, which produces a high heterogeneity in capture probability. In order to estimate animal abundance through DNA profiling of ground beef constituents, two parameter-based statistical models were developed for incidence data. Simulations were applied to evaluate the maximum likelihood estimate (MLE of a joint likelihood function from multiple surveys, showing superiority in the presence of high capture heterogeneity with small sample sizes, or comparable estimation in the presence of low capture heterogeneity with a large sample size when compared to other existing models. Our model employs the full information on the pattern of the capture-recapture frequencies from multiple samples. We applied the proposed models to estimate animal abundance in six manufacturing beef batches, genotyped using 30 single nucleotide polymorphism (SNP markers, from a large scale beef grinding facility. Results show that between 411∼1367 animals were present in six manufacturing beef batches. These estimates are informative as a reference for improving recall processes and tracing finished meat products back to source.

  17. Estimating breeding season abundance of golden-cheeked warblers in Texas, USA

    KAUST Repository

    Mathewson, Heather A.

    2012-02-15

    Population abundance estimates using predictive models are important for describing habitat use and responses to population-level impacts, evaluating conservation status of a species, and for establishing monitoring programs. The golden-cheeked warbler (Setophaga chrysoparia) is a neotropical migratory bird that was listed as federally endangered in 1990 because of threats related to loss and fragmentation of its woodland habitat. Since listing, abundance estimates for the species have mainly relied on localized population studies on public lands and qualitative-based methods. Our goal was to estimate breeding population size of male warblers using a predictive model based on metrics for patches of woodland habitat throughout the species\\' breeding range. We first conducted occupancy surveys to determine range-wide distribution. We then conducted standard point-count surveys on a subset of the initial sampling locations to estimate density of males. Mean observed patch-specific density was 0.23 males/ha (95% CI = 0.197-0.252, n = 301). We modeled the relationship between patch-specific density of males and woodland patch characteristics (size and landscape composition) and predicted patch occupancy. The probability of patch occupancy, derived from a model that used patch size and landscape composition as predictor variables while addressing effects of spatial relatedness, best predicted patch-specific density. We predicted patch-specific densities as a function of occupancy probability and estimated abundance of male warblers across 63,616 woodland patches accounting for 1.678 million ha of potential warbler habitat. Using a Monte Carlo simulation, our approach yielded a range-wide male warbler population estimate of 263,339 (95% CI: 223,927-302,620). Our results provide the first abundance estimate using habitat and count data from a sampling design focused on range-wide inference. Managers can use the resulting model as a tool to support conservation planning

  18. Diversity and relative abundance of the bacterial pathogen, Flavobacterium spp., infecting reproductive ecotypes of kokanee salmon.

    Science.gov (United States)

    Lemay, Matthew A; Russello, Michael A

    2014-11-04

    Understanding the distribution and abundance of pathogens can provide insight into the evolution and ecology of their host species. Previous research in kokanee, the freshwater form of sockeye salmon (Oncorhynchus nerka), found evidence that populations spawning in streams may experience a greater pathogen load compared with populations that spawn on beaches. In this study we tested for differences in the abundance and diversity of the gram-negative bacteria, Flavobacterium spp., infecting tissues of kokanee in both of these spawning habitats (streams and beaches). Molecular assays were carried out using primers designed to amplify a ~200 nucleotide region of the gene encoding the ATP synthase alpha subunit (AtpA) within the genus Flavobacterium. Using a combination of DNA sequencing and quantitative PCR (qPCR) we compared the diversity and relative abundance of Flavobacterium AtpA amplicons present in DNA extracted from tissue samples of kokanee collected from each spawning habitat. We identified 10 Flavobacterium AtpA haplotypes among the tissues of stream-spawning kokanee and seven haplotypes among the tissues of beach-spawning kokanee, with only two haplotypes shared between spawning habitats. Haplotypes occurring in the same clade as F. psychrophilum were the most prevalent (92% of all reads, 60% of all haplotypes), and occurred in kokanee from both spawning habitats (streams and beaches). Subsequent qPCR assays did not find any significant difference in the relative abundance of Flavobacterium AtpA amplicons between samples from the different spawning habitats. We confirmed the presence of Flavobacterium spp. in both spawning habitats and found weak evidence for increased Flavobacterium diversity in kokanee sampled from stream-spawning sites. However, the quantity of Flavobacterium DNA did not differ between spawning habitats. We recommend further study aimed at quantifying pathogen diversity and abundance in population-level samples of kokanee combined with

  19. Aryl Polyenes, a Highly Abundant Class of Bacterial Natural Products, Are Functionally Related to Antioxidative Carotenoids.

    Science.gov (United States)

    Schöner, Tim A; Gassel, Sören; Osawa, Ayako; Tobias, Nicholas J; Okuno, Yukari; Sakakibara, Yui; Shindo, Kazutoshi; Sandmann, Gerhard; Bode, Helge B

    2016-02-02

    Bacterial pigments of the aryl polyene type are structurally similar to the well-known carotenoids with respect to their polyene systems. Their biosynthetic gene cluster is widespread in taxonomically distant bacteria, and four classes of such pigments have been found. Here we report the structure elucidation of the aryl polyene/dialkylresorcinol hybrid pigments of Variovorax paradoxus B4 by HPLC-UV-MS, MALDI-MS and NMR. Furthermore, we show for the first time that this pigment class protects the bacterium from reactive oxygen species, similarly to what is known for carotenoids. An analysis of the distribution of biosynthetic genes for aryl polyenes and carotenoids in bacterial genomes is presented; it shows a complementary distribution of these protective pigments in bacteria. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Seagrass vegetation and meiofauna enhance the bacterial abundance in the Baltic Sea sediments (Puck Bay).

    Science.gov (United States)

    Jankowska, Emilia; Jankowska, Katarzyna; Włodarska-Kowalczuk, Maria

    2015-09-01

    This study presents the first report on bacterial communities in the sediments of eelgrass (Zostera marina) meadows in the shallow southern Baltic Sea (Puck Bay). Total bacterial cell numbers (TBNs) and bacteria biomass (BBM) assessed with the use of epifluorescence microscope and Norland's formula were compared between bare and vegetated sediments at two localities and in two sampling summer months. Significantly higher TBNs and BBM (PERMANOVA tests, P PERMANOVA distance-based linear model (DISTLM) procedures and showed that the main factors explaining bacteria characteristics are bottom type (vegetated vs. unvegetated) and meiofauna density. These two factors explained together 48.3% of variability in TBN and 40.5% in BBM, and their impacts did not overlap (as indicated by DISTLM sequential tests) demonstrating the different natures of these relationships. The effects of seagrass were most probably related to the increase of organic matter and providing habitat while higher numbers of meiofauna organisms may have stimulated the bacterial growth by increased grazing.

  1. Estimating abundance without recaptures of marked pallid sturgeon in the Mississippi River.

    Science.gov (United States)

    Friedenberg, Nicholas A; Hoover, Jan Jeffrey; Boysen, Krista; Killgore, K Jack

    2018-04-01

    Abundance estimates are essential for assessing the viability of populations and the risks posed by alternative management actions. An effort to estimate abundance via a repeated mark-recapture experiment may fail to recapture marked individuals. We devised a method for obtaining lower bounds on abundance in the absence of recaptures for both panmictic and spatially structured populations. The method assumes few enough recaptures were expected to be missed by random chance. The upper Bayesian credible limit on expected recaptures allows probabilistic statements about the minimum number of individuals present in the population. We applied this method to data from a 12-year survey of pallid sturgeon (Scaphirhynchus albus) in the lower and middle Mississippi River (U.S.A.). None of the 241 individuals marked was recaptured in the survey. After accounting for survival and movement, our model-averaged estimate of the total abundance of pallid sturgeon ≥3 years old in the study area had a 1%, 5%, or 25% chance of being <4,600, 7,000, or 15,000, respectively. When we assumed fish were distributed in proportion to survey catch per unit effort, the farthest downstream reach in the survey hosted at least 4.5-15 fish per river kilometer (rkm), whereas the remainder of the reaches in the lower and middle Mississippi River hosted at least 2.6-8.5 fish/rkm for all model variations examined. The lower Mississippi River had an average density of pallid sturgeon ≥3 years old of at least 3.0-9.8 fish/rkm. The choice of Bayesian prior was the largest source of uncertainty we considered but did not alter the order of magnitude of lower bounds. Nil-recapture estimates of abundance are highly uncertain and require careful communication but can deliver insights from experiments that might otherwise be considered a failure. © 2017 Society for Conservation Biology.

  2. Striped bass ichthyoplankton abundance, mortality, and production estimation for the Potomac River population

    International Nuclear Information System (INIS)

    Polgar, T.T.

    1977-01-01

    Methods are developed for estimating, from field survey data, the mortality rate and production for each successive ichthyoplanktonic stage. The abundance estimators used in the computation of these quantities are also derived. An age-dependent, ichthyoplankton population model is developed assuming either a uniform age distribution or an exponential age distribution within each stage. Striped bass egg and larval data from a 1974 ichthyoplankton survey in the Potomac River are used in model computations. The various model estimates are evaluated qualitatively, and the usefulness and limitations of the models are discussed

  3. Sulfamethoxazole and COD increase abundance of sulfonamide resistance genes and change bacterial community structures within sequencing batch reactors.

    Science.gov (United States)

    Guo, Xueping; Pang, Weihai; Dou, Chunling; Yin, Daqiang

    2017-05-01

    The abundant microbial community in biological treatment processes in wastewater treatment plants (WWTPs) may potentially enhance the horizontal gene transfer of antibiotic resistance genes with the presence of antibiotics. A lab-scale sequencing batch reactor was designed to investigate response of sulfonamide resistance genes (sulI, sulII) and bacterial communities to various concentrations of sulfamethoxazole (SMX) and chemical oxygen demand (COD) of wastewater. The SMX concentrations (0.001 mg/L, 0.1 mg/L and 10 mg/L) decreased with treatment time and higher SMX level was more difficult to remove. The presence of SMX also significantly reduced the removal efficiency of ammonia nitrogen, affecting the normal function of WWTPs. All three concentrations of SMX raised both sulI and sulII genes with higher concentrations exhibiting greater increases. The abundance of sul genes was positive correlated with treatment time and followed the second-order reaction kinetic model. Interestingly, these two genes have rather similar activity. SulI and sulII gene abundance also performed similar response to COD. Simpson index and Shannon-Weiner index did not show changes in the microbial community diversity. However, the 16S rRNA gene cloning and sequencing results showed the bacterial community structures varied during different stages. The results demonstrated that influent antibiotics into WWTPs may facilitate selection of ARGs and affect the wastewater conventional treatment as well as the bacteria community structures. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. Estimate of symbiotically fixed nitrogen in field grown soybeans using variations in 15N natural abundance

    International Nuclear Information System (INIS)

    Amarger, N.; Durr, J.C.; Bourguignon, C.; Lagacherie, B.; Mariotti, A.; Mariotti, F.

    1979-01-01

    The use of variations in natural abundance of 15 N between nitrogen fixing and non nitrogen fixing soybeans was investigated for quantitative estimate of symbiotic nitrogen fixation. Isotopic analysis of 4 varieties of inoculated and non-inoculated soybeans growing under field conditions, with and without N-fertilizer was determined. It was found that inoculated soybeans had a significantly lower 15 N content than non-inoculated ones. Estimates of the participation of fixed N to the total nitrogen content of inoculated soybeans were calculated from these differences. They were compared to estimates calculated from differences in N yield between inoculated and non-inoculated plants and to the nitrogenase activity, measured by the C 2 H 2 reduction assay over the growing season. Estimates given by the 15 N measurements were correlated with the C 2 H 2 reducing activity but not with the differences in the N yield. This shows that the isotopic composition was dependent on the amount of fixed nitrogen and consequently that the estimates of fixed nitrogen based on natural 15 N abundance should be reliable. The absence of correlation between estimates based on 15 N content and estimates based on N yield was explained by differences in the uptake of soil nitrogen between inoculated and non inoculated soybeans. (Auth.)

  5. Preliminary estimates of the abundance and fidelity of dolphins associating with a demersal trawl fishery.

    Science.gov (United States)

    Allen, Simon J; Pollock, Kenneth H; Bouchet, Phil J; Kobryn, Halina T; McElligott, Deirdre B; Nicholson, Krista E; Smith, Joshua N; Loneragan, Neil R

    2017-07-10

    The incidental capture of wildlife in fishing gear presents a global conservation challenge. As a baseline to inform assessments of the impact of bycatch on bottlenose dolphins (Tursiops truncatus) interacting with an Australian trawl fishery, we conducted an aerial survey to estimate dolphin abundance across the fishery. Concurrently, we carried out boat-based dolphin photo-identification to assess short-term fidelity to foraging around trawlers, and used photographic and genetic data to infer longer-term fidelity to the fishery. We estimated abundance at ≈ 2,300 dolphins (95% CI = 1,247-4,214) over the ≈ 25,880-km 2 fishery. Mark-recapture estimates yielded 226 (SE = 38.5) dolphins associating with one trawler and some individuals photographed up to seven times over 12 capture periods. Moreover, photographic and genetic re-sampling over three years confirmed that some individuals show long-term fidelity to trawler-associated foraging. Our study presents the first abundance estimate for any Australian pelagic dolphin community and documents individuals associating with trawlers over days, months and years. Without trend data or correction factors for dolphin availability, the impact of bycatch on this dolphin population's conservation status remains unknown. These results should be taken into account by management agencies assessing the impact of fisheries-related mortality on this protected species.

  6. Estimating the abundance of the Southern Hudson Bay polar bear subpopulation with aerial surveys

    Science.gov (United States)

    Obbard, Martyn E.; Stapleton, Seth P.; Middel, Kevin R.; Thibault, Isabelle; Brodeur, Vincent; Jutras, Charles

    2015-01-01

    The Southern Hudson Bay (SH) polar bear subpopulation occurs at the southern extent of the species’ range. Although capture–recapture studies indicate abundance was likely unchanged between 1986 and 2005, declines in body condition and survival occurred during the period, possibly foreshadowing a future decrease in abundance. To obtain a current estimate of abundance, we conducted a comprehensive line transect aerial survey of SH during 2011–2012. We stratified the study site by anticipated densities and flew coastal contour transects and systematically spaced inland transects in Ontario and on Akimiski Island and large offshore islands in 2011. Data were collected with double-observer and distance sampling protocols. We surveyed small islands in James Bay and eastern Hudson Bay and flew a comprehensive transect along the Québec coastline in 2012. We observed 667 bears in Ontario and on Akimiski Island and nearby islands in 2011, and we sighted 80 bears on offshore islands during 2012. Mark–recapture distance sampling and sight–resight models yielded an estimate of 860 (SE = 174) for the 2011 study area. Our estimate of abundance for the entire SH subpopulation (943; SE = 174) suggests that abundance is unlikely to have changed significantly since 1986. However, this result should be interpreted cautiously because of the methodological differences between historical studies (physical capture–recapture) and this survey. A conservative management approach is warranted given previous increases in duration of the ice-free season, which are predicted to continue in the future, and previously documented declines in body condition and vital rates.

  7. Estimating abundance of the Southern Hudson Bay polar bear subpopulation using aerial surveys, 2011 and 2012

    Science.gov (United States)

    Obbard, Martyn E.; Middel, Kevin R.; Stapleton, Seth P.; Thibault, Isabelle; Brodeur, Vincent; Jutras, Charles

    2013-01-01

    The Southern Hudson Bay (SH) polar bear subpopulation occurs at the southern extent of the species’ range. Although capture-recapture studies indicate that abundance remained stable between 1986 and 2005, declines in body condition and survival were documented during the period, possibly foreshadowing a future decrease in abundance. To obtain a current estimate of abundance, we conducted a comprehensive line transect aerial survey of SH during 2011–2012. We stratified the study site by anticipated densities and flew coastal contour transects and systematically spaced inland transects in Ontario and on Akimiski Island and large offshore islands in 2011. Data were collected with double observer and distance sampling protocols. We also surveyed small islands in Hudson Bay and James Bay and flew a comprehensive transect along the Québec coastline in 2012. We observed 667 bears in Ontario and on Akimiski Island and nearby islands in 2011, and we sighted 80 bears on offshore islands during 2012. Mark-recapture distance sampling and sightresight models yielded a model-averaged estimate of 868 (SE: 177) for the 2011 study area. Our estimate of abundance for the entire SH subpopulation (951; SE: 177) suggests that abundance has remained unchanged. However, this result should be interpreted cautiously because of the methodological differences between historical studies (physical capture) and this survey. A conservative management approach is warranted given the previous increases in the duration of the ice-free season, which are predicted to continue in the future, and previously documented declines in body condition and vital rates.

  8. Estimating abundance and density of Amur tigers along the Sino-Russian border.

    Science.gov (United States)

    Xiao, Wenhong; Feng, Limin; Mou, Pu; Miquelle, Dale G; Hebblewhite, Mark; Goldberg, Joshua F; Robinson, Hugh S; Zhao, Xiaodan; Zhou, Bo; Wang, Tianming; Ge, Jianping

    2016-07-01

    As an apex predator the Amur tiger (Panthera tigris altaica) could play a pivotal role in maintaining the integrity of forest ecosystems in Northeast Asia. Due to habitat loss and harvest over the past century, tigers rapidly declined in China and are now restricted to the Russian Far East and bordering habitat in nearby China. To facilitate restoration of the tiger in its historical range, reliable estimates of population size are essential to assess effectiveness of conservation interventions. Here we used camera trap data collected in Hunchun National Nature Reserve from April to June 2013 and 2014 to estimate tiger density and abundance using both maximum likelihood and Bayesian spatially explicit capture-recapture (SECR) methods. A minimum of 8 individuals were detected in both sample periods and the documentation of marking behavior and reproduction suggests the presence of a resident population. Using Bayesian SECR modeling within the 11 400 km(2) state space, density estimates were 0.33 and 0.40 individuals/100 km(2) in 2013 and 2014, respectively, corresponding to an estimated abundance of 38 and 45 animals for this transboundary Sino-Russian population. In a maximum likelihood framework, we estimated densities of 0.30 and 0.24 individuals/100 km(2) corresponding to abundances of 34 and 27, in 2013 and 2014, respectively. These density estimates are comparable to other published estimates for resident Amur tiger populations in the Russian Far East. This study reveals promising signs of tiger recovery in Northeast China, and demonstrates the importance of connectivity between the Russian and Chinese populations for recovering tigers in Northeast China. © 2016 International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and John Wiley & Sons Australia, Ltd.

  9. Estimating animal abundance with N-mixture models using the R-INLA package for R

    KAUST Repository

    Meehan, Timothy D.

    2017-05-03

    Successful management of wildlife populations requires accurate estimates of abundance. Abundance estimates can be confounded by imperfect detection during wildlife surveys. N-mixture models enable quantification of detection probability and often produce abundance estimates that are less biased. The purpose of this study was to demonstrate the use of the R-INLA package to analyze N-mixture models and to compare performance of R-INLA to two other common approaches -- JAGS (via the runjags package), which uses Markov chain Monte Carlo and allows Bayesian inference, and unmarked, which uses Maximum Likelihood and allows frequentist inference. We show that R-INLA is an attractive option for analyzing N-mixture models when (1) familiar model syntax and data format (relative to other R packages) are desired, (2) survey level covariates of detection are not essential, (3) fast computing times are necessary (R-INLA is 10 times faster than unmarked, 300 times faster than JAGS), and (4) Bayesian inference is preferred.

  10. Abundance, size distribution and bacterial colonization of transparent exopolymeric particles (TEP) during spring in the Kattegat

    DEFF Research Database (Denmark)

    Mari, X.; Kiørboe, Thomas

    1996-01-01

    of beta differed significantly from three, probably because TEP are fractal. All TEP were colonized by bacteria, and bacteria were both attached to the surface of and embedded in TEP. Yet the number of attached bacteria per TEP was related neither to the surface area nor the volume, but rather scaled.......p.m.; they were most abundant in the surface waters subsequent to the spring phytoplankton bloom. The range of TEP (encased) volume concentration was similar to that of the phytoplankton, although at times TEP volume concentration exceeded that of the phytoplankton by two orders of magnitude. The TEP size...... to be formed from colloidal organic material exuded by phytoplankton and bacteria, and may have significant implications for pelagic flux processes. During this study, the number concentration of TEP (>1 mu m) ranged from 3 x 10(3) to 6 x 10(4) ml(-1) and the volume concentration between 0.3 and 9.0 p...

  11. Estimating disperser abundance using open population models that incorporate data from continuous detection PIT arrays

    Science.gov (United States)

    Dzul, Maria C.; Yackulic, Charles B.; Korman, Josh

    2017-01-01

    Autonomous passive integrated transponder (PIT) tag antenna systems continuously detect individually marked organisms at one or more fixed points over long time periods. Estimating abundance using data from autonomous antennae can be challenging, because these systems do not detect unmarked individuals. Here we pair PIT antennae data from a tributary with mark-recapture sampling data in a mainstem river to estimate the number of fish moving from the mainstem to the tributary. We then use our model to estimate abundance of non-native rainbow trout Oncorhynchus mykiss that move from the Colorado River to the Little Colorado River (LCR), the latter of which is important spawning and rearing habitat for federally-endangered humpback chub Gila cypha. We estimate 226 rainbow trout (95% CI: 127-370) entered the LCR from October 2013-April 2014. We discuss the challenges of incorporating detections from autonomous PIT antenna systems into mark-recapture population models, particularly in regards to using information about spatial location to estimate movement and detection probabilities.

  12. Hankin and Reeves' approach to estimating fish abundance in small streams: limitations and potential options; TOPICAL

    International Nuclear Information System (INIS)

    Thompson, William L.

    2000-01-01

    Hankin and Reeves' (1988) approach to estimating fish abundance in small streams has been applied in stream-fish studies across North America. However, as with any method of population estimation, there are important assumptions that must be met for estimates to be minimally biased and reasonably precise. Consequently, I investigated effects of various levels of departure from these assumptions via simulation based on results from an example application in Hankin and Reeves (1988) and a spatially clustered population. Coverage of 95% confidence intervals averaged about 5% less than nominal when removal estimates equaled true numbers within sampling units, but averaged 62% - 86% less than nominal when they did not, with the exception where detection probabilities of individuals were and gt;0.85 and constant across sampling units (95% confidence interval coverage= 90%). True total abundances averaged far (20% - 41%) below the lower confidence limit when not included within intervals, which implies large negative bias. Further, average coefficient of variation was about 1.5 times higher when removal estimates did not equal true numbers within sampling units (C(bar V)0.27[SE= 0.0004]) than when they did (C(bar V)= 0.19[SE= 0.0002]). A potential modification to Hankin and Reeves' approach is to include environmental covariates that affect detection rates of fish into the removal model or other mark-recapture model. A potential alternative is to use snorkeling in combination with line transect sampling to estimate fish densities. Regardless of the method of population estimation, a pilot study should be conducted to validate the enumeration method, which requires a known (or nearly so) population of fish to serve as a benchmark to evaluate bias and precision of population estimates

  13. A framework for establishing predictive relationships between specific bacterial 16S rRNA sequence abundances and biotransformation rates.

    Science.gov (United States)

    Helbling, Damian E; Johnson, David R; Lee, Tae Kwon; Scheidegger, Andreas; Fenner, Kathrin

    2015-03-01

    The rates at which wastewater treatment plant (WWTP) microbial communities biotransform specific substrates can differ by orders of magnitude among WWTP communities. Differences in taxonomic compositions among WWTP communities may predict differences in the rates of some types of biotransformations. In this work, we present a novel framework for establishing predictive relationships between specific bacterial 16S rRNA sequence abundances and biotransformation rates. We selected ten WWTPs with substantial variation in their environmental and operational metrics and measured the in situ ammonia biotransformation rate constants in nine of them. We isolated total RNA from samples from each WWTP and analyzed 16S rRNA sequence reads. We then developed multivariate models between the measured abundances of specific bacterial 16S rRNA sequence reads and the ammonia biotransformation rate constants. We constructed model scenarios that systematically explored the effects of model regularization, model linearity and non-linearity, and aggregation of 16S rRNA sequences into operational taxonomic units (OTUs) as a function of sequence dissimilarity threshold (SDT). A large percentage (greater than 80%) of model scenarios resulted in well-performing and significant models at intermediate SDTs of 0.13-0.14 and 0.26. The 16S rRNA sequences consistently selected into the well-performing and significant models at those SDTs were classified as Nitrosomonas and Nitrospira groups. We then extend the framework by applying it to the biotransformation rate constants of ten micropollutants measured in batch reactors seeded with the ten WWTP communities. We identified phylogenetic groups that were robustly selected into all well-performing and significant models constructed with biotransformation rates of isoproturon, propachlor, ranitidine, and venlafaxine. These phylogenetic groups can be used as predictive biomarkers of WWTP microbial community activity towards these specific

  14. Towards rationally redesigning bacterial signaling systems using information encoded in abundant sequence data

    Science.gov (United States)

    Cheng, Ryan; Morcos, Faruck; Levine, Herbert; Onuchic, Jose

    2014-03-01

    An important challenge in biology is to distinguish the subset of residues that allow bacterial two-component signaling (TCS) proteins to preferentially interact with their correct TCS partner such that they can bind and transfer signal. Detailed knowledge of this information would allow one to search sequence-space for mutations that can systematically tune the signal transmission between TCS partners as well as re-encode a TCS protein to preferentially transfer signals to a non-partner. Motivated by the notion that this detailed information is found in sequence data, we explore the mutual sequence co-evolution between signaling partners to infer how mutations can positively or negatively alter their interaction. Using Direct Coupling Analysis (DCA) for determining evolutionarily conserved interprotein interactions, we apply a DCA-based metric to quantify mutational changes in the interaction between TCS proteins and demonstrate that it accurately correlates with experimental mutagenesis studies probing the mutational change in the in vitro phosphotransfer. Our methodology serves as a potential framework for the rational design of TCS systems as well as a framework for the system-level study of protein-protein interactions in sequence-rich systems. This research has been supported by the NSF INSPIRE award MCB-1241332 and by the CTBP sponsored by the NSF (Grant PHY-1308264).

  15. Relative abundance estimations of Chengal trees in a tropical rainforest by using modified canopy fractional cover (mCFC)

    International Nuclear Information System (INIS)

    Hassan, N

    2014-01-01

    Tree species composition estimations are important to sustain forest management. This study estimates relative abundance of useful timber tree species (chengal) using Hyperion EO-1 satellite data. For the estimation, modified Canopy Fractional Cover (mCFC) was developed using Canopy Fractional Cover (CFC). mCFC was more sensitive to estimate relative abundance of chengal trees rather than Mixture Tuned Matched Filtering (MTMF). Meanwhile, MTMF was more sensitive to estimate the relative abundance of undisturbed forest. Accuracy suggests that the mCFC model is better to explain relative abundance of chengal trees than MTMF. Therefore, it can be concluded that relative abundance of tree species extracted from Hyperion EO-1 satellite data using modified Canopy Fractional Cover is an obtrusive approach used for identifying tree species composition

  16. Relative abundance estimations of chengal tree in a tropical rainforest by using modified Canopy Fractional Cover (mCFC)

    International Nuclear Information System (INIS)

    Hassan, N

    2014-01-01

    Tree species composition estimations are important to sustain forest management. This study challenged estimates of relative abundance of useful timber tree species (chengal) using Hyperion EO-1 satellite data. For the estimation, modified Canopy Fractional Cover (mCFC) was developed using Canopy Fractional Cover (CFC). mCFC was more sensitive to estimate relative abundance of chengal trees rather than Mixture Tuned Matched Filtering (MTMF). Meanwhile, MTMF was more sensitive to estimate the relative abundance of undisturbed forest. Accuracy suggests that the mCFC model is better to explain relative abundance of chengal trees than MTMF. Therefore, it can be concluded that relative abundance of trees species extracted from Hyperion EO-1 satellite data using modified Canopy Fractional Cover is an obtrusive approach used for identifying trees species composition

  17. Lateral-delivered organic matter boosts hadal bacterial abundance in the Mariana Trench: A hypothesis

    Science.gov (United States)

    Zhang, C.; Liu, H.; Lu, F.; Zou, L.; Tian, J.

    2017-12-01

    Hadal trenches are part of the least investigated biosphere on Earth due to the great challenge of sampling. Limited studies on microbiology by far have suggested that the hadalsphere hosts a heterotrophic microbial community that is likely fed by organic matter from surface-sinking biomass or re-suspended and laterally transported sediments. The uniqueness of trench environment and its potential role in global carbon sequestration entitle a detailed study on microbial-driven carbon cycle of the trench system. In this study, we conducted a vertical sampling of the microbial community and measured the environmental factors from the epipelagic zone down to the hadal zone at the Mariana Trench. 16S rRNA gene composition showed high stratification at the first 1000 meters below surface (mbs) but a nearly uniformed microbial community composition was observed at the abyssopelagic and the hadalpelagic water columns. The deep-sea bacteria were generally chemoheterotrophs and the majority of them were similar to those present at the ocean surface, suggesting influence of epipelagic primary production on deep sea bacterial communication at the trench location. Several deep-sea-enriched but surface-depleted bacteria could be characterized by potential degraders of polysaccharides and n-alkanes. Therefore, recalcitrant hydrocarbons or carbohydrates are likely important carbon sources supporting the deep-sea biosphere. In spite of consistent community composition, a remarkable increase in biomass of small-sized microbial aggregates was detected at 8727 mbs. Enhanced CDOM proportions in the trench imply intensified microbial activity in hadal water compared to the above water column, which agree with the notion of possible extra carbon input from lateral transportation of slope material. These observations extend our understanding in carbon cycle driven by metabolically diverse microorganisms at the trench and may shed light on the complexity of hadal biogeochemistry.

  18. Estimating abundance of adult striped bass in reservoirs using mobile hydroacoustics

    Science.gov (United States)

    Hightower, Joseph E.; Taylor, J. Christopher; Degan, Donald J.

    2013-01-01

    Hydroacoustic surveys have proven valuable for estimating reservoir forage fish abundance but are more challenging for adult predators such as striped bass Morone saxatilis. Difficulties in assessing striped bass in reservoirs include their low density and the inability to distinguish species with hydroacoustic data alone. Despite these difficulties, mobile hydroacoustic surveys have potential to provide useful data for management because of the large sample volume compared to traditional methods such as gill netting and the ability to target specific areas where striped bass are aggregated. Hydroacoustic estimates of reservoir striped bass have been made using mobile surveys, with data analysis using a threshold for target strength in order to focus on striped bass-sized targets, and auxiliary sampling with nets to obtain species composition. We provide recommendations regarding survey design, based in part on simulations that provide insight on the level of effort that would be required to achieve reasonable estimates of abundance. Future surveys may be able to incorporate telemetry or other sonar techniques such as side-scan or multibeam in order to focus survey efforts on productive habitats (within lake and vertically). However, species apportionment will likely remain the main source of error, and we see no hydroacoustic system on the horizon that will identify fish by species at the spatial and temporal scale required for most reservoir surveys. In situations where species composition can be reliably assessed using traditional gears, abundance estimates from hydroacoustic methods should be useful to fishery managers interested in developing harvest regulations, assessing survival of stocked juveniles, identifying seasonal aggregations, and examining predator–prey balance.

  19. Estimating time-based instantaneous total mortality rate based on the age-structured abundance index

    Science.gov (United States)

    Wang, Yingbin; Jiao, Yan

    2015-05-01

    The instantaneous total mortality rate ( Z) of a fish population is one of the important parameters in fisheries stock assessment. The estimation of Z is crucial to fish population dynamics analysis, abundance and catch forecast, and fisheries management. A catch curve-based method for estimating time-based Z and its change trend from catch per unit effort (CPUE) data of multiple cohorts is developed. Unlike the traditional catch-curve method, the method developed here does not need the assumption of constant Z throughout the time, but the Z values in n continuous years are assumed constant, and then the Z values in different n continuous years are estimated using the age-based CPUE data within these years. The results of the simulation analyses show that the trends of the estimated time-based Z are consistent with the trends of the true Z, and the estimated rates of change from this approach are close to the true change rates (the relative differences between the change rates of the estimated Z and the true Z are smaller than 10%). Variations of both Z and recruitment can affect the estimates of Z value and the trend of Z. The most appropriate value of n can be different given the effects of different factors. Therefore, the appropriate value of n for different fisheries should be determined through a simulation analysis as we demonstrated in this study. Further analyses suggested that selectivity and age estimation are also two factors that can affect the estimated Z values if there is error in either of them, but the estimated change rates of Z are still close to the true change rates. We also applied this approach to the Atlantic cod ( Gadus morhua) fishery of eastern Newfoundland and Labrador from 1983 to 1997, and obtained reasonable estimates of time-based Z.

  20. Line transect estimates of Irrawaddy dolphin abundance along the eastern Gulf Coast of Thailand.

    Directory of Open Access Journals (Sweden)

    Ellen eHines

    2015-09-01

    Full Text Available Effective conservation of coastal marine mammals is largely dependent on reliable knowledge of their abundance, as well as the ecological and human factors driving their distribution. In developing countries, lack of resources and capacity frequently impedes research needed to estimate abundance and to determine the ecological requirements of coastal marine mammals and the impact of threats related to coastal development and fisheries. Over the course of five years, we developed practical research methods and trained local scientists in Thailand to use accepted line transect distance sampling methods for abundance assessment. The study focused on a little-known coastal and freshwater species found throughout Southeast Asia, namely the Irrawaddy dolphin, which has been sighted regularly along the coast of the eastern Gulf of Thailand. During five years of line transect boat surveys in Trat Province, the eastern-most province in Thailand, we found an average of 423 dolphins distributed within 12km of the coast. Compared to other abundance estimates of coastal Irrawaddy dolphins in Southeast Asia, this is a relatively large number. This population could extend into the northern coast of Cambodia, where surveys are currently being planned. The Thai government has begun talks with Cambodia about a transboundary marine protected area that would include areas in both countries where coastal Irrawaddy dolphins are found. Other analyses include photo-identification, modeling environmental factors that determine presence, determination of fresh vs. salt water foraging using stable isotopes, and an assessment of threats. Collaboration between scientists in Thailand, Cambodia and Vietnam is further needed to determine dolphin movement and habitat use across borders.

  1. A doubling of microphytobenthos biomass coincides with a tenfold increase in denitrifier and total bacterial abundances in intertidal sediments of a temperate estuary.

    Directory of Open Access Journals (Sweden)

    Helen Decleyre

    Full Text Available Surface sediments are important systems for the removal of anthropogenically derived inorganic nitrogen in estuaries. They are often characterized by the presence of a microphytobenthos (MPB biofilm, which can impact bacterial communities in underlying sediments for example by secretion of extracellular polymeric substances (EPS and competition for nutrients (including nitrogen. Pyrosequencing and qPCR was performed on two intertidal surface sediments of the Westerschelde estuary characterized by a two-fold difference in MPB biomass but no difference in MPB composition. Doubling of MPB biomass was accompanied by a disproportionately (ten-fold increase in total bacterial abundances while, unexpectedly, no difference in general community structure was observed, despite significantly lower bacterial richness and distinct community membership, mostly for non-abundant taxa. Denitrifier abundances corresponded likewise while community structure, both for nirS and nirK denitrifiers, remained unchanged, suggesting that competition with diatoms for nitrate is negligible at concentrations in the investigated sediments (appr. 1 mg/l NO3-. This study indicates that MPB biomass increase has a general, significantly positive effect on total bacterial and denitrifier abundances, with stimulation or inhibition of specific bacterial groups that however do not result in a re-structured community.

  2. READSCAN: A fast and scalable pathogen discovery program with accurate genome relative abundance estimation

    KAUST Repository

    Naeem, Raeece

    2012-11-28

    Summary: READSCAN is a highly scalable parallel program to identify non-host sequences (of potential pathogen origin) and estimate their genome relative abundance in high-throughput sequence datasets. READSCAN accurately classified human and viral sequences on a 20.1 million reads simulated dataset in <27 min using a small Beowulf compute cluster with 16 nodes (Supplementary Material). Availability: http://cbrc.kaust.edu.sa/readscan Contact: or raeece.naeem@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online. 2012 The Author(s).

  3. READSCAN: A fast and scalable pathogen discovery program with accurate genome relative abundance estimation

    KAUST Repository

    Naeem, Raeece; Rashid, Mamoon; Pain, Arnab

    2012-01-01

    Summary: READSCAN is a highly scalable parallel program to identify non-host sequences (of potential pathogen origin) and estimate their genome relative abundance in high-throughput sequence datasets. READSCAN accurately classified human and viral sequences on a 20.1 million reads simulated dataset in <27 min using a small Beowulf compute cluster with 16 nodes (Supplementary Material). Availability: http://cbrc.kaust.edu.sa/readscan Contact: or raeece.naeem@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online. 2012 The Author(s).

  4. ELM: an Algorithm to Estimate the Alpha Abundance from Low-resolution Spectra

    Science.gov (United States)

    Bu, Yude; Zhao, Gang; Pan, Jingchang; Bharat Kumar, Yerra

    2016-01-01

    We have investigated a novel methodology using the extreme learning machine (ELM) algorithm to determine the α abundance of stars. Applying two methods based on the ELM algorithm—ELM+spectra and ELM+Lick indices—to the stellar spectra from the ELODIE database, we measured the α abundance with a precision better than 0.065 dex. By applying these two methods to the spectra with different signal-to-noise ratios (S/Ns) and different resolutions, we found that ELM+spectra is more robust against degraded resolution and ELM+Lick indices is more robust against variation in S/N. To further validate the performance of ELM, we applied ELM+spectra and ELM+Lick indices to SDSS spectra and estimated α abundances with a precision around 0.10 dex, which is comparable to the results given by the SEGUE Stellar Parameter Pipeline. We further applied ELM to the spectra of stars in Galactic globular clusters (M15, M13, M71) and open clusters (NGC 2420, M67, NGC 6791), and results show good agreement with previous studies (within 1σ). A comparison of the ELM with other widely used methods including support vector machine, Gaussian process regression, artificial neural networks, and linear least-squares regression shows that ELM is efficient with computational resources and more accurate than other methods.

  5. ELM: AN ALGORITHM TO ESTIMATE THE ALPHA ABUNDANCE FROM LOW-RESOLUTION SPECTRA

    International Nuclear Information System (INIS)

    Bu, Yude; Zhao, Gang; Kumar, Yerra Bharat; Pan, Jingchang

    2016-01-01

    We have investigated a novel methodology using the extreme learning machine (ELM) algorithm to determine the α abundance of stars. Applying two methods based on the ELM algorithm—ELM+spectra and ELM+Lick indices—to the stellar spectra from the ELODIE database, we measured the α abundance with a precision better than 0.065 dex. By applying these two methods to the spectra with different signal-to-noise ratios (S/Ns) and different resolutions, we found that ELM+spectra is more robust against degraded resolution and ELM+Lick indices is more robust against variation in S/N. To further validate the performance of ELM, we applied ELM+spectra and ELM+Lick indices to SDSS spectra and estimated α abundances with a precision around 0.10 dex, which is comparable to the results given by the SEGUE Stellar Parameter Pipeline. We further applied ELM to the spectra of stars in Galactic globular clusters (M15, M13, M71) and open clusters (NGC 2420, M67, NGC 6791), and results show good agreement with previous studies (within 1σ). A comparison of the ELM with other widely used methods including support vector machine, Gaussian process regression, artificial neural networks, and linear least-squares regression shows that ELM is efficient with computational resources and more accurate than other methods

  6. ELM: AN ALGORITHM TO ESTIMATE THE ALPHA ABUNDANCE FROM LOW-RESOLUTION SPECTRA

    Energy Technology Data Exchange (ETDEWEB)

    Bu, Yude [School of Mathematics and Statistics, Shandong University, Weihai, 264209, Shandong (China); Zhao, Gang; Kumar, Yerra Bharat [Key Laboratory for Optical Astronomy, National Astronomical Observatories, Chinese Academy of Sciences, Beijing, 100012 (China); Pan, Jingchang, E-mail: ydbu@bao.ac.cn, E-mail: gzhao@nao.cas.cn [School of Mechanical, Electrical and Information Engineering, Shandong University, Weihai, 264209, Shandong (China)

    2016-01-20

    We have investigated a novel methodology using the extreme learning machine (ELM) algorithm to determine the α abundance of stars. Applying two methods based on the ELM algorithm—ELM+spectra and ELM+Lick indices—to the stellar spectra from the ELODIE database, we measured the α abundance with a precision better than 0.065 dex. By applying these two methods to the spectra with different signal-to-noise ratios (S/Ns) and different resolutions, we found that ELM+spectra is more robust against degraded resolution and ELM+Lick indices is more robust against variation in S/N. To further validate the performance of ELM, we applied ELM+spectra and ELM+Lick indices to SDSS spectra and estimated α abundances with a precision around 0.10 dex, which is comparable to the results given by the SEGUE Stellar Parameter Pipeline. We further applied ELM to the spectra of stars in Galactic globular clusters (M15, M13, M71) and open clusters (NGC 2420, M67, NGC 6791), and results show good agreement with previous studies (within 1σ). A comparison of the ELM with other widely used methods including support vector machine, Gaussian process regression, artificial neural networks, and linear least-squares regression shows that ELM is efficient with computational resources and more accurate than other methods.

  7. Estimating species – area relationships by modeling abundance and frequency subject to incomplete sampling

    Science.gov (United States)

    Yamaura, Yuichi; Connor, Edward F.; Royle, Andy; Itoh, Katsuo; Sato, Kiyoshi; Taki, Hisatomo; Mishima, Yoshio

    2016-01-01

    Models and data used to describe species–area relationships confound sampling with ecological process as they fail to acknowledge that estimates of species richness arise due to sampling. This compromises our ability to make ecological inferences from and about species–area relationships. We develop and illustrate hierarchical community models of abundance and frequency to estimate species richness. The models we propose separate sampling from ecological processes by explicitly accounting for the fact that sampled patches are seldom completely covered by sampling plots and that individuals present in the sampling plots are imperfectly detected. We propose a multispecies abundance model in which community assembly is treated as the summation of an ensemble of species-level Poisson processes and estimate patch-level species richness as a derived parameter. We use sampling process models appropriate for specific survey methods. We propose a multispecies frequency model that treats the number of plots in which a species occurs as a binomial process. We illustrate these models using data collected in surveys of early-successional bird species and plants in young forest plantation patches. Results indicate that only mature forest plant species deviated from the constant density hypothesis, but the null model suggested that the deviations were too small to alter the form of species–area relationships. Nevertheless, results from simulations clearly show that the aggregate pattern of individual species density–area relationships and occurrence probability–area relationships can alter the form of species–area relationships. The plant community model estimated that only half of the species present in the regional species pool were encountered during the survey. The modeling framework we propose explicitly accounts for sampling processes so that ecological processes can be examined free of sampling artefacts. Our modeling approach is extensible and could be applied

  8. Assessment of distribution and abundance estimates for Mariana swiftlets (Aerodramus bartschi) via examination of survey methods

    Science.gov (United States)

    Johnson, Nathan C.; Haig, Susan M.; Mosher, Stephen M.

    2018-01-01

    We described past and present distribution and abundance data to evaluate the status of the endangered Mariana Swiftlet (Aerodramus bartschi), a little-known echolocating cave swiftlet that currently inhabits 3 of 5 formerly occupied islands in the Mariana archipelago. We then evaluated the survey methods used to attain these estimates via fieldwork carried out on an introduced population of Mariana Swiftlets on the island of O'ahu, Hawaiian Islands, to derive better methods for future surveys. We estimate the range-wide population of Mariana Swiftlets to be 5,704 individuals occurring in 15 caves on Saipan, Aguiguan, and Guam in the Marianas; and 142 individuals occupying one tunnel on O'ahu. We further confirm that swiftlets have been extirpated from Rota and Tinian and have declined on Aguiguan. Swiftlets have remained relatively stable on Guam and Saipan in recent years. Our assessment of survey methods used for Mariana Swiftlets suggests overestimates depending on the technique used. We suggest the use of night vision technology and other changes to more accurately reflect their distribution, abundance, and status.

  9. Influence of soil properties on the toxicity of TiO₂ nanoparticles on carbon mineralization and bacterial abundance.

    Science.gov (United States)

    Simonin, Marie; Guyonnet, Julien P; Martins, Jean M F; Ginot, Morgane; Richaume, Agnès

    2015-01-01

    Information regarding the impact of low concentration of engineered nanoparticles on soil microbial communities is currently limited and the importance of soil characteristics is often neglected in ecological risk assessment. To evaluate the impact of TiO2 nanoparticles (NPs) on soil microbial communities (measured on bacterial abundance and carbon mineralization activity), 6 agricultural soils exhibiting contrasted textures and organic matter contents were exposed for 90 days to a low environmentally relevant concentration or to an accidental spiking of TiO2-NPs (1 and 500mgkg(-1) dry soil, respectively) in microcosms. In most soils, TiO2-NPs did not impact the activity and abundance of microbial communities, except in the silty-clay soil (high OM) where C-mineralization was significantly lowered, even with the low NPs concentration. Our results suggest that TiO2-NPs toxicity does not depend on soil texture but likely on pH and OM content. We characterized TiO2-NPs aggregation and zeta potential in soil solutions, in order to explain the difference of TiO2-NPs effects on soil C-mineralization. Zeta potential and aggregation of TiO2-NPs in the silty-clay (high OM) soil solution lead to a lower stability of TiO2-NP-aggregates than in the other soils. Further experiments would be necessary to evaluate the relationship between TiO2-NPs stability and toxicity in the soil. Copyright © 2014 Elsevier B.V. All rights reserved.

  10. Host specificity for bacterial, archaeal and fungal communities determined for high- and low-microbial abundance sponge species in two genera

    NARCIS (Netherlands)

    Mares, De Maryam Chaib; Sipkema, Detmer; Huang, Sixing; Bunk, Boyke; Overmann, Jörg; Elsas, van Jan Dirk

    2017-01-01

    Sponges are engaged in intimate symbioses with a diversity of microorganisms from all three domains of life, namely Bacteria, Archaea and Eukarya. Sponges have been well studied and categorized for their bacterial communities, some displaying a high microbial abundance (HMA), while others show

  11. An abundance estimate of ling ( Molva molva ) and cod ( Gadus morhua ) in the Skagerrak and the northeastern North Sea, 1872

    DEFF Research Database (Denmark)

    Poulsen, R.T.; Cooper, A.B.; Holm, P.

    2007-01-01

    that long-term, historical abundance estimates are relevant to the determination of biomass reference points in fisheries management. Situated within the field of historical ecology, this paper presents findings on the abundance of ling and cod in 1872. Calculations are based on historical CPUE and catch...

  12. Accounting for non-independent detection when estimating abundance of organisms with a Bayesian approach

    Science.gov (United States)

    Martin, Julien; Royle, J. Andrew; MacKenzie, Darryl I.; Edwards, Holly H.; Kery, Marc; Gardner, Beth

    2011-01-01

    Summary 1. Binomial mixture models use repeated count data to estimate abundance. They are becoming increasingly popular because they provide a simple and cost-effective way to account for imperfect detection. However, these models assume that individuals are detected independently of each other. This assumption may often be violated in the field. For instance, manatees (Trichechus manatus latirostris) may surface in turbid water (i.e. become available for detection during aerial surveys) in a correlated manner (i.e. in groups). However, correlated behaviour, affecting the non-independence of individual detections, may also be relevant in other systems (e.g. correlated patterns of singing in birds and amphibians). 2. We extend binomial mixture models to account for correlated behaviour and therefore to account for non-independent detection of individuals. We simulated correlated behaviour using beta-binomial random variables. Our approach can be used to simultaneously estimate abundance, detection probability and a correlation parameter. 3. Fitting binomial mixture models to data that followed a beta-binomial distribution resulted in an overestimation of abundance even for moderate levels of correlation. In contrast, the beta-binomial mixture model performed considerably better in our simulation scenarios. We also present a goodness-of-fit procedure to evaluate the fit of beta-binomial mixture models. 4. We illustrate our approach by fitting both binomial and beta-binomial mixture models to aerial survey data of manatees in Florida. We found that the binomial mixture model did not fit the data, whereas there was no evidence of lack of fit for the beta-binomial mixture model. This example helps illustrate the importance of using simulations and assessing goodness-of-fit when analysing ecological data with N-mixture models. Indeed, both the simulations and the goodness-of-fit procedure highlighted the limitations of the standard binomial mixture model for aerial

  13. Evaluation of natural 15N abundance method in estimating symbiotic dinitrogen fixation by leguminous grasses

    International Nuclear Information System (INIS)

    Yao Yunyin; Cheng Ming; Ma Changlin; Wang Zhidong; Hou Jinqin; Zhang Lihong; Luo Yongyun

    1991-01-01

    Natural 15 N abundance method was used to estimate contribution of symbiotic dinitrogen fixation by leguminous grasses. With the method the expensive 15 N fertilizer did not need to be applied to the soil and the normal ecosystem was not disturbed. Collecting samples of shoots of leguminous grasses and measuring the content of 15 N in them wee all to do for estimating potential of symbiotically fixed N 2 . Isotopic fractionation associated with N 2 fixation by legumes was studied. Values for 7 cultivars of alfalfa were ranged between 1.0000 ∼ 1.0015 (δ 15 N values were -0.05 ∼ 1.47 per mille); and the values for white clover, mung bean and whitepopinac lead tree were 0.0079, 0.9983 and 1.0018 (δ 15 N values: 2.15, 1.74 and -1.81 per mille) respectively. According to the δ 15 N values of grasses tested, the potential of N 2 fixation for 6 cultivars of alfalfa was estimated. Glory and rambler had higher potential of N 2 fixation; Baoding, Aigonquin and Minto had lower potential, and Peru was the lowest.N 2 fixing activity of alfalfa varied with different periods. The peak was found between June and July. Effects of non-N 2 -fixing references and different methods on estimates of %Ndfa of leguminous grasses were also discussed

  14. Differential distribution and abundance of diazotrophic bacterial communities across different soil niches using a gene-targeted clone library approach.

    Science.gov (United States)

    Yousuf, Basit; Kumar, Raghawendra; Mishra, Avinash; Jha, Bhavanath

    2014-11-01

    Diazotrophs are key players of the globally important biogeochemical nitrogen cycle, having a significant role in maintaining ecosystem sustainability. Saline soils are pristine and unexplored habitats representing intriguing ecosystems expected to harbour potential diazotrophs capable of adapting in extreme conditions, and these implicated organisms are largely obscure. Differential occurrence of diazotrophs was studied by the nifH gene-targeted clone library approach. Four nifH gene clone libraries were constructed from different soil niches, that is saline soils (low and high salinity; EC 3.8 and 7.1 ds m(-1) ), and agricultural and rhizosphere soil. Additionally, the abundance of diazotrophic community members was assessed using quantitative PCR. Results showed environment-dependent metabolic versatility and the presence of nitrogen-fixing bacteria affiliated with a range of taxa, encompassing members of the Alphaproteobacteria, Betaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, Cyanobacteria and Firmicutes. The analyses unveiled the dominance of Alphaproteobacteria and Gammaproteobacteria (Pseudomonas, Halorhodospira, Ectothiorhodospira, Bradyrhizobium, Agrobacterium, Amorphomonas) as nitrogen fixers in coastal-saline soil ecosystems, and Alphaproteobacteria and Betaproteobacteria (Bradyrhizobium, Azohydromonas, Azospirillum, Ideonella) in agricultural/rhizosphere ecosystems. The results revealed a repertoire of novel nitrogen-fixing bacterial guilds particularly in saline soil ecosystems. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  15. Intrinsic bacterial biodegradation of petroleum contamination demonstrated in situ using natural abundance, molecular-level 14C analysis

    International Nuclear Information System (INIS)

    Slater, G.F.; Nelson, R.K.; Kile, B.M.; Reddy, C.M.

    2006-01-01

    Natural abundance, molecular-level C 14 analysis was combined with comprehensive gas chromatography (GC x GC) to investigate, in situ, the role of intrinsic biodegradation in the loss of petroleum hydrocarbons from the rocky, inter-tidal zone impacted by the Bouchard 120 oil spill. GC x GC analysis indicated accelerated losses of n-alkane components of the residual petroleum hydrocarbons between day 40 and day 50 after the spill. 14 C analysis of bacterial phospholipid fatty acids (PLFA) from the impacted zone on day 44 showed that the polyunsaturated fatty acids attributed to the photoautotrophic component of the microbial community had the same ( 14 C as the local dissolved inorganic carbon (DIG), indicating that this DIG was their carbon source. In contrast there was significant (C depletion in the saturated and mono-unsaturated PLFA indicating incorporation of petroleum carbon. This correlation between the observed accelerated n-alkane losses and microbial incorporation of (C-depleted carbon directly demonstrated, in situ, that intrinsic biodegradation was affecting the petroleum. Since the majority of organic contaminants originate from petroleum feed-stocks, in situ molecular-level 14 C analysis of microbial PLFA can provide insights into the occurrence and pathways of biodegradation of a wide range of organic contaminants. (Author)

  16. Abundance and composition of indigenous bacterial communities in a multi-step biofiltration-based drinking water treatment plant.

    Science.gov (United States)

    Lautenschlager, Karin; Hwang, Chiachi; Ling, Fangqiong; Liu, Wen-Tso; Boon, Nico; Köster, Oliver; Egli, Thomas; Hammes, Frederik

    2014-10-01

    Indigenous bacterial communities are essential for biofiltration processes in drinking water treatment systems. In this study, we examined the microbial community composition and abundance of three different biofilter types (rapid sand, granular activated carbon, and slow sand filters) and their respective effluents in a full-scale, multi-step treatment plant (Zürich, CH). Detailed analysis of organic carbon degradation underpinned biodegradation as the primary function of the biofilter biomass. The biomass was present in concentrations ranging between 2-5 × 10(15) cells/m(3) in all filters but was phylogenetically, enzymatically and metabolically diverse. Based on 16S rRNA gene-based 454 pyrosequencing analysis for microbial community composition, similar microbial taxa (predominantly Proteobacteria, Planctomycetes, Acidobacteria, Bacteriodetes, Nitrospira and Chloroflexi) were present in all biofilters and in their respective effluents, but the ratio of microbial taxa was different in each filter type. This change was also reflected in the cluster analysis, which revealed a change of 50-60% in microbial community composition between the different filter types. This study documents the direct influence of the filter biomass on the microbial community composition of the final drinking water, particularly when the water is distributed without post-disinfection. The results provide new insights on the complexity of indigenous bacteria colonizing drinking water systems, especially in different biofilters of a multi-step treatment plant. Copyright © 2014 Elsevier Ltd. All rights reserved.

  17. Estimates of Abundance and Trend of Chilean Blue Whales off Isla de Chiloé, Chile.

    Directory of Open Access Journals (Sweden)

    Barbara Galletti Vernazzani

    Full Text Available Since 1970, blue whales (Balaenoptera musculus have been seen feeding in the waters off southern Chile during the summer and autumn (December to May. Investigation of the genetic, acoustic and morphological characteristics of these blue whales shows that they are a distinct but unnamed subspecies, called the Chilean blue whales. Photo-identification surveys have been conducted in the waters off northwestern Isla Grande de Chiloé, southern Chile from 2004-2012 and Isla Chañaral, central Chile in 2012. Over this time, 1,070 blue whales were encountered yielding, after photo-quality control, 318 and 267 unique photographs of the left and right side of the flank respectively. Using mark-recapture analysis of left and right side photographs collected from Isla Grande de Chiloé (2004-2012, open population models estimate that ~570-760 whales are feeding seasonally in this region. POPAN superpopulation abundance estimates for the same feeding ground in 2012 are 762 (95% confidence intervals, CI = 638-933 and 570 (95% CI 475-705 for left and right side datasets respectively, very similar to results from closed population models. Estimates of trend revealed strong variation in abundance, peaking in 2009 and [suggesting] fluctuating use in the survey area over time, likely related to the density of their prey. High inter-annual return rates suggest a degree of site-fidelity of individuals to Isla Grande de Chiloé and that the number of whales using this feeding ground is relatively small.

  18. A spatially explicit estimate of the prewhaling abundance of the endangered North Atlantic right whale.

    Science.gov (United States)

    Monsarrat, Sophie; Pennino, M Grazia; Smith, Tim D; Reeves, Randall R; Meynard, Christine N; Kaplan, David M; Rodrigues, Ana S L

    2016-08-01

    The North Atlantic right whale (NARW) (Eubalaena glacialis) is one of the world's most threatened whales. It came close to extinction after nearly a millennium of exploitation and currently persists as a population of only approximately 500 individuals. Setting appropriate conservation targets for this species requires an understanding of its historical population size, as a baseline for measuring levels of depletion and progress toward recovery. This is made difficult by the scarcity of records over this species' long whaling history. We sought to estimate the preexploitation population size of the North Atlantic right whale and understand how this species was distributed across its range. We used a spatially explicit data set on historical catches of North Pacific right whales (NPRWs) (Eubalaena japonica) to model the relationship between right whale relative density and the environment during the summer feeding season. Assuming the 2 right whale species select similar environments, we projected this model to the North Atlantic to predict how the relative abundance of NARWs varied across their range. We calibrated these relative abundances with estimates of the NPRW total prewhaling population size to obtain high and low estimates for the overall NARW population size prior to exploitation. The model predicted 9,075-21,328 right whales in the North Atlantic. The current NARW population is thus <6% of the historical North Atlantic carrying capacity and has enormous potential for recovery. According to the model, in June-September NARWs concentrated in 2 main feeding areas: east of the Grand Banks of Newfoundland and in the Norwegian Sea. These 2 areas may become important in the future as feeding grounds and may already be used more regularly by this endangered species than is thought. © 2015 Society for Conservation Biology.

  19. Aerial Survey as a Tool to Estimate Abundance and Describe Distribution of a Carcharhinid Species, the Lemon Shark, Negaprion brevirostris

    Directory of Open Access Journals (Sweden)

    S. T. Kessel

    2013-01-01

    Full Text Available Aerial survey provides an important tool to assess the abundance of both terrestrial and marine vertebrates. To date, limited work has tested the effectiveness of this technique to estimate the abundance of smaller shark species. In Bimini, Bahamas, the lemon shark (Negaprion brevirostris shows high site fidelity to a shallow sandy lagoon, providing an ideal test species to determine the effectiveness of localised aerial survey techniques for a Carcharhinid species in shallow subtropical waters. Between September 2007 and September 2008, visual surveys were conducted from light aircraft following defined transects ranging in length between 8.8 and 4.4 km. Count results were corrected for “availability”, “perception”, and “survey intensity” to provide unbiased abundance estimates. The abundance of lemon sharks was greatest in the central area of the lagoon during high tide, with a change in abundance distribution to the east and western regions of the lagoon with low tide. Mean abundance of sharks was estimated at 49 (±8.6 individuals, and monthly abundance was significantly positively correlated with mean water temperature. The successful implementation of the aerial survey technique highlighted the potential of further employment for shark abundance assessments in shallow coastal marine environments.

  20. Estimation and Bias Correction of Aerosol Abundance using Data-driven Machine Learning and Remote Sensing

    Science.gov (United States)

    Malakar, Nabin K.; Lary, D. L.; Moore, A.; Gencaga, D.; Roscoe, B.; Albayrak, Arif; Petrenko, Maksym; Wei, Jennifer

    2012-01-01

    Air quality information is increasingly becoming a public health concern, since some of the aerosol particles pose harmful effects to peoples health. One widely available metric of aerosol abundance is the aerosol optical depth (AOD). The AOD is the integrated light extinction coefficient over a vertical atmospheric column of unit cross section, which represents the extent to which the aerosols in that vertical profile prevent the transmission of light by absorption or scattering. The comparison between the AOD measured from the ground-based Aerosol Robotic Network (AERONET) system and the satellite MODIS instruments at 550 nm shows that there is a bias between the two data products. We performed a comprehensive analysis exploring possible factors which may be contributing to the inter-instrumental bias between MODIS and AERONET. The analysis used several measured variables, including the MODIS AOD, as input in order to train a neural network in regression mode to predict the AERONET AOD values. This not only allowed us to obtain an estimate, but also allowed us to infer the optimal sets of variables that played an important role in the prediction. In addition, we applied machine learning to infer the global abundance of ground level PM2.5 from the AOD data and other ancillary satellite and meteorology products. This research is part of our goal to provide air quality information, which can also be useful for global epidemiology studies.

  1. Re-constructing historical Adélie penguin abundance estimates by retrospectively accounting for detection bias.

    Science.gov (United States)

    Southwell, Colin; Emmerson, Louise; Newbery, Kym; McKinlay, John; Kerry, Knowles; Woehler, Eric; Ensor, Paul

    2015-01-01

    Seabirds and other land-breeding marine predators are considered to be useful and practical indicators of the state of marine ecosystems because of their dependence on marine prey and the accessibility of their populations at breeding colonies. Historical counts of breeding populations of these higher-order marine predators are one of few data sources available for inferring past change in marine ecosystems. However, historical abundance estimates derived from these population counts may be subject to unrecognised bias and uncertainty because of variable attendance of birds at breeding colonies and variable timing of past population surveys. We retrospectively accounted for detection bias in historical abundance estimates of the colonial, land-breeding Adélie penguin through an analysis of 222 historical abundance estimates from 81 breeding sites in east Antarctica. The published abundance estimates were de-constructed to retrieve the raw count data and then re-constructed by applying contemporary adjustment factors obtained from remotely operating time-lapse cameras. The re-construction process incorporated spatial and temporal variation in phenology and attendance by using data from cameras deployed at multiple sites over multiple years and propagating this uncertainty through to the final revised abundance estimates. Our re-constructed abundance estimates were consistently higher and more uncertain than published estimates. The re-constructed estimates alter the conclusions reached for some sites in east Antarctica in recent assessments of long-term Adélie penguin population change. Our approach is applicable to abundance data for a wide range of colonial, land-breeding marine species including other penguin species, flying seabirds and marine mammals.

  2. Re-constructing historical Adélie penguin abundance estimates by retrospectively accounting for detection bias.

    Directory of Open Access Journals (Sweden)

    Colin Southwell

    Full Text Available Seabirds and other land-breeding marine predators are considered to be useful and practical indicators of the state of marine ecosystems because of their dependence on marine prey and the accessibility of their populations at breeding colonies. Historical counts of breeding populations of these higher-order marine predators are one of few data sources available for inferring past change in marine ecosystems. However, historical abundance estimates derived from these population counts may be subject to unrecognised bias and uncertainty because of variable attendance of birds at breeding colonies and variable timing of past population surveys. We retrospectively accounted for detection bias in historical abundance estimates of the colonial, land-breeding Adélie penguin through an analysis of 222 historical abundance estimates from 81 breeding sites in east Antarctica. The published abundance estimates were de-constructed to retrieve the raw count data and then re-constructed by applying contemporary adjustment factors obtained from remotely operating time-lapse cameras. The re-construction process incorporated spatial and temporal variation in phenology and attendance by using data from cameras deployed at multiple sites over multiple years and propagating this uncertainty through to the final revised abundance estimates. Our re-constructed abundance estimates were consistently higher and more uncertain than published estimates. The re-constructed estimates alter the conclusions reached for some sites in east Antarctica in recent assessments of long-term Adélie penguin population change. Our approach is applicable to abundance data for a wide range of colonial, land-breeding marine species including other penguin species, flying seabirds and marine mammals.

  3. Bacterial 16S rRNA gene analysis revealed that bacteria related to Arcobacter spp. constitute an abundant and common component of the oyster microbiota (Tiostrea chilensis).

    Science.gov (United States)

    Romero, J; García-Varela, M; Laclette, J P; Espejo, R T

    2002-11-01

    To explore the bacterial microbiota in Chilean oyster (Tiostrea chilensis), a molecular approach that permits detection of different bacteria, independently of their capacity to grow in culture media, was used. Bacterial diversity was assessed by analysis of both the 16S rDNA and the 16S-23S intergenic region, obtained by PCR amplifications of DNA extracted from depurated oysters. RFLP of the PCR amplified 16S rDNA showed a prevailing pattern in most of the individuals analyzed, indicating that a few bacterial species were relatively abundant and common in oysters. Cloning and sequencing of the 16S rDNA with the prevailing RFLP pattern indicated that this rRNA was most closely related to Arcobacter spp. However, analysis by the size of the amplified 16S-23S rRNA intergenic regions revealed not Arcobacter spp. but Staphylococcus spp. related bacteria as a major and common component in oyster. These different results may be caused by the absence of target for one of the primers employed for amplification of the intergenic region. Neither of the two bacteria species found in large abundance was recovered after culturing under aerobic, anaerobic, or microaerophilic conditions. This result, however, is expected because the number of bacteria recovered after cultivation was less than 0.01% of the total. All together, these observations suggest that Arcobacter-related strains are probably abundant and common in the Chilean oyster bacterial microbiota.

  4. Validation of abundance estimates from mark–recapture and removal techniques for rainbow trout captured by electrofishing in small streams

    Science.gov (United States)

    Rosenberger, Amanda E.; Dunham, Jason B.

    2005-01-01

    Estimation of fish abundance in streams using the removal model or the Lincoln - Peterson mark - recapture model is a common practice in fisheries. These models produce misleading results if their assumptions are violated. We evaluated the assumptions of these two models via electrofishing of rainbow trout Oncorhynchus mykiss in central Idaho streams. For one-, two-, three-, and four-pass sampling effort in closed sites, we evaluated the influences of fish size and habitat characteristics on sampling efficiency and the accuracy of removal abundance estimates. We also examined the use of models to generate unbiased estimates of fish abundance through adjustment of total catch or biased removal estimates. Our results suggested that the assumptions of the mark - recapture model were satisfied and that abundance estimates based on this approach were unbiased. In contrast, the removal model assumptions were not met. Decreasing sampling efficiencies over removal passes resulted in underestimated population sizes and overestimates of sampling efficiency. This bias decreased, but was not eliminated, with increased sampling effort. Biased removal estimates based on different levels of effort were highly correlated with each other but were less correlated with unbiased mark - recapture estimates. Stream size decreased sampling efficiency, and stream size and instream wood increased the negative bias of removal estimates. We found that reliable estimates of population abundance could be obtained from models of sampling efficiency for different levels of effort. Validation of abundance estimates requires extra attention to routine sampling considerations but can help fisheries biologists avoid pitfalls associated with biased data and facilitate standardized comparisons among studies that employ different sampling methods.

  5. Allometric Equations for Estimating Biomass of Euterpe precatoria, the Most Abundant Palm Species in the Amazon

    Directory of Open Access Journals (Sweden)

    Fernando Da Silva

    2015-02-01

    Full Text Available Allometric models to estimate biomass components such as stem mass Ms, foliage mass Ml, root mass Mr and aboveground mass Ma, were developed for the palm species Euterpe precatoria Mart., which is the most abundant tree species in the Amazon. We harvested twenty palms including above- and below-ground parts in an old growth Amazonian forest in Brazil. The diameter at breast height D ranged from 3.9–12.7 cm, and the stem height H ranged from 2.3–16.4 m. The D, diameter at ground basis D0, crown diameter CD, H, stem specific gravity ρ, and number of fronds Nf were considered as independent variables and incorporated into a power function model. The best predictors were D2Hρ for Ms and Ma, D2HNf for Ml, and D for Mr. Slender index (H/D ranged from 0.56–1.46 m·cm−1, and the D-H relationship suggested that the stem shape becomes more slender with increasing D. On the other hand, ρ increased with D implying a stiffening of stem tissue. The average root/shoot ratio was estimated as 0.29 which was higher than that reported for the non-palm tree species in the Amazon. Comparisons of several models to estimate Ma of different palm species, suggested that the variations of the D-H relationship and ρ should be considered to develop allometric models for estimating biomass in palm species. In particular the ρ largely varied depending on individual size, which should be important to consider, when developing the allometric models for palms.

  6. Trap array configuration influences estimates and precision of black bear density and abundance.

    Directory of Open Access Journals (Sweden)

    Clay M Wilton

    Full Text Available Spatial capture-recapture (SCR models have advanced our ability to estimate population density for wide ranging animals by explicitly incorporating individual movement. Though these models are more robust to various spatial sampling designs, few studies have empirically tested different large-scale trap configurations using SCR models. We investigated how extent of trap coverage and trap spacing affects precision and accuracy of SCR parameters, implementing models using the R package secr. We tested two trapping scenarios, one spatially extensive and one intensive, using black bear (Ursus americanus DNA data from hair snare arrays in south-central Missouri, USA. We also examined the influence that adding a second, lower barbed-wire strand to snares had on quantity and spatial distribution of detections. We simulated trapping data to test bias in density estimates of each configuration under a range of density and detection parameter values. Field data showed that using multiple arrays with intensive snare coverage produced more detections of more individuals than extensive coverage. Consequently, density and detection parameters were more precise for the intensive design. Density was estimated as 1.7 bears per 100 km2 and was 5.5 times greater than that under extensive sampling. Abundance was 279 (95% CI = 193-406 bears in the 16,812 km2 study area. Excluding detections from the lower strand resulted in the loss of 35 detections, 14 unique bears, and the largest recorded movement between snares. All simulations showed low bias for density under both configurations. Results demonstrated that in low density populations with non-uniform distribution of population density, optimizing the tradeoff among snare spacing, coverage, and sample size is of critical importance to estimating parameters with high precision and accuracy. With limited resources, allocating available traps to multiple arrays with intensive trap spacing increased the amount of

  7. Estimating DNA coverage and abundance in metagenomes using a gamma approximation

    Energy Technology Data Exchange (ETDEWEB)

    Hooper, Sean D; Dalevi, Daniel; Pati, Amrita; Mavromatis, Konstantinos; Ivanova, Natalia N; Kyrpides, Nikos C

    2010-01-01

    Shotgun sequencing generates large numbers of short DNA reads from either an isolated organism or, in the case of metagenomics projects, from the aggregate genome of a microbial community. These reads are then assembled based on overlapping sequences into larger, contiguous sequences (contigs). The feasibility of assembly and the coverage achieved (reads per nucleotide or distinct sequence of nucleotides) depend on several factors: the number of reads sequenced, the read length and the relative abundances of their source genomes in the microbial community. A low coverage suggests that most of the genomic DNA in the sample has not been sequenced, but it is often difficult to estimate either the extent of the uncaptured diversity or the amount of additional sequencing that would be most efficacious. In this work, we regard a metagenome as a population of DNA fragments (bins), each of which may be covered by one or more reads. We employ a gamma distribution to model this bin population due to its flexibility and ease of use. When a gamma approximation can be found that adequately fits the data, we may estimate the number of bins that were not sequenced and that could potentially be revealed by additional sequencing. We evaluated the performance of this model using simulated metagenomes and demonstrate its applicability on three recent metagenomic datasets.

  8. Carbon dynamics in corn-soybean sequences as estimated from natural carbon-13 abundance

    International Nuclear Information System (INIS)

    Huggins, D.R.; Clapp, C.E.; Allmaras, R.R.; Lamb, J.A.; Layese, M.F.

    1998-01-01

    Carbon flow in terrestrial ecosystems regulates partitioning between soil organic C (SOC) and atmospheric CO2. Our objectives were to assess SOC dynamics using natural 13C abundance in corn (Zea mays L., a C4 species)-soybean [Glycine max (L.) Merr., a C3 species] sequences. Fifteen treatments of continuous corn, continuous soybean, various sequences of corn and soybean, and fallow were initiated in 1981 at Lamberton, MN, on a Webster clay loam (fine-loamy, mixed, mesic Typic Haplaquoll). In 1991, soil and aboveground shoot samples from all treatments were analyzed for total organic C and delta 13C. Carbon inputs, delta 13C, and SOC were integrated into a two-pool model to evaluate C dynamics of corn and soybean. Total SOC was similar across all treatments after 10 yr; however, differences in soil delta 13C occurred between continuous corn (delta 13C = -17.2 per thous and) and continuous soybean (delta 13C = -18.2 per thousand). Modeled C dynamics showed SOC decay rates of 0.011 yr-1 for C4-derived C and 0.007 yr-1 for C3-derived C, and humification rates of 0.16 yr-1 for corn and 0.11 yr-1 for soybean. Decay and humification rates were slightly lower than those found in other Corn Belt studies. Levels of SOC were predicted to decline an additional 7 to 18% with current C inputs from either corn or soybean, respectively. Annual C additions required for SOC maintenance averaged 5.6 Mg C ha-1, 1.4 to 2.1 times greater than previously reported estimates. Controlled variation in natural 13C abundance in corn-soybean rotations during a 10-yr period adequately traced C dynamics

  9. Effects of sampling conditions on DNA-based estimates of American black bear abundance

    Science.gov (United States)

    Laufenberg, Jared S.; Van Manen, Frank T.; Clark, Joseph D.

    2013-01-01

    DNA-based capture-mark-recapture techniques are commonly used to estimate American black bear (Ursus americanus) population abundance (N). Although the technique is well established, many questions remain regarding study design. In particular, relationships among N, capture probability of heterogeneity mixtures A and B (pA and pB, respectively, or p, collectively), the proportion of each mixture (π), number of capture occasions (k), and probability of obtaining reliable estimates of N are not fully understood. We investigated these relationships using 1) an empirical dataset of DNA samples for which true N was unknown and 2) simulated datasets with known properties that represented a broader array of sampling conditions. For the empirical data analysis, we used the full closed population with heterogeneity data type in Program MARK to estimate N for a black bear population in Great Smoky Mountains National Park, Tennessee. We systematically reduced the number of those samples used in the analysis to evaluate the effect that changes in capture probabilities may have on parameter estimates. Model-averaged N for females and males were 161 (95% CI = 114–272) and 100 (95% CI = 74–167), respectively (pooled N = 261, 95% CI = 192–419), and the average weekly p was 0.09 for females and 0.12 for males. When we reduced the number of samples of the empirical data, support for heterogeneity models decreased. For the simulation analysis, we generated capture data with individual heterogeneity covering a range of sampling conditions commonly encountered in DNA-based capture-mark-recapture studies and examined the relationships between those conditions and accuracy (i.e., probability of obtaining an estimated N that is within 20% of true N), coverage (i.e., probability that 95% confidence interval includes true N), and precision (i.e., probability of obtaining a coefficient of variation ≤20%) of estimates using logistic regression. The capture probability

  10. Distribution, diversity and abundance of bacterial laccase-like genes in different particle size fractions of sediments in a subtropical mangrove ecosystem.

    Science.gov (United States)

    Luo, Ling; Zhou, Zhi-Chao; Gu, Ji-Dong

    2015-10-01

    This study investigated the diversity and abundance of bacterial lacasse-like genes in different particle size fractions, namely sand, silt, and clay of sediments in a subtropical mangrove ecosystem. Moreover, the effects of nutrient conditions on bacterial laccase-like communities as well as the correlation between nutrients and, both the abundance and diversity indices of laccase-like bacteria in particle size fractions were also studied. Compared to bulk sediments, Bacteroidetes, Caldithrix, Cyanobacteria and Chloroflexi were dominated in all 3 particle-size fractions of intertidal sediment (IZ), but Actinobacteria and Firmicutes were lost after the fractionation procedures used. The diversity index of IZ fractions decreased in the order of bulk > clay > silt > sand. In fractions of mangrove forest sediment (MG), Verrucomicrobia was found in silt, and both Actinobacteria and Bacteroidetes appeared in clay, but no new species were found in sand. The declining order of diversity index in MG fractions was clay > silt > sand > bulk. Furthermore, the abundance of lacasse-like bacteria varied with different particle-size fractions significantly (p clay > silt in both IZ and MG fractions. Additionally, nutrient availability was found to significantly affect the diversity and community structure of laccase-like bacteria (p fractions (p < 0.05). Therefore, this study further provides evidence that bacterial laccase plays a vital role in turnover of sediment organic matter and cycling of nutrients.

  11. Variability in abundance of temperate reef fishes estimated by visual census.

    Directory of Open Access Journals (Sweden)

    Alejo J Irigoyen

    Full Text Available Identifying sources of sampling variation and quantifying their magnitude is critical to the interpretation of ecological field data. Yet, most monitoring programs of reef fish populations based on underwater visual censuses (UVC consider only a few of the factors that may influence fish counts, such as the diver or census methodology. Recent studies, however, have drawn attention to a broader range of processes that introduce variability at different temporal scales. This study analyzes the magnitude of different sources of variation in UVCs of temperate reef fishes off Patagonia (Argentina. The variability associated with time-of-day, tidal state, and time elapsed between censuses (minutes, days, weeks and months was quantified for censuses conducted on the five most conspicuous and common species: Pinguipes brasilianus, Pseudopercis semifasciata, Sebastes oculatus, Acanthistius patachonicus and Nemadactylus bergi. Variance components corresponding to spatial heterogeneity and to the different temporal scales were estimated using nested random models. The levels of variability estimated for the different species were related to their life history attributes and behavior. Neither time-of-day nor tidal state had a significant effect on counts, except for the influence of tide on P. brasilianus. Spatial heterogeneity was the dominant source of variance in all but one species. Among the temporal scales, the intra-annual variation was the highest component for most species due to marked seasonal fluctuations in abundance, followed by the weekly and the instantaneous variation; the daily component was not significant. The variability between censuses conducted at different tidal levels and time-of-day was similar in magnitude to the instantaneous variation, reinforcing the conclusion that stochastic variation at very short time scales is non-negligible and should be taken into account in the design of monitoring programs and experiments. The present

  12. Measurement of the incorporation rates of four amino acids into proteins for estimating bacterial production.

    Science.gov (United States)

    Servais, P

    1995-03-01

    In aquatic ecosystems, [(3)H]thymidine incorporation into bacterial DNA and [(3)H]leucine incorporation into proteins are usually used to estimate bacterial production. The incorporation rates of four amino acids (leucine, tyrosine, lysine, alanine) into proteins of bacteria were measured in parallel on natural freshwater samples from the basin of the river Meuse (Belgium). Comparison of the incorporation into proteins and into the total macromolecular fraction showed that these different amino acids were incorporated at more than 90% into proteins. From incorporation measurements at four subsaturated concentrations (range, 2-77 nm), the maximum incorporation rates were determined. Strong correlations (r > 0.91 for all the calculated correlations) were found between the maximum incorporation rates of the different tested amino acids over a range of two orders of magnitude of bacterial activity. Bacterial production estimates were calculated using theoretical and experimental conversion factors. The productions calculated from the incorporation rates of the four amino acids were in good concordance, especially when the experimental conversion factors were used (slope range, 0.91-1.11, and r > 0.91). This study suggests that the incorporation of various amino acids into proteins can be used to estimate bacterial production.

  13. Abundance and activity of 16S rRNA, amoA and nifH bacterial genes during assisted phytostabilization of mine tailings

    Science.gov (United States)

    Nelson, Karis N.; Neilson, Julia W.; Root, Robert A.; Chorover, Jon; Maier, Raina M.

    2014-01-01

    Mine tailings in semiarid regions are highly susceptible to erosion and are sources of dust pollution and potential avenues of human exposure to toxic metals. One constraint to revegetation of tailings by phytostabilization is the absence of microbial communities critical for biogeochemical cycling of plant nutrients. The objective of this study was to evaluate specific genes as in situ indicators of biological soil response during phytoremediation. The abundance and activity of 16S rRNA, nifH, and amoA were monitored during a nine month phytostabilization study using buffalo grass and quailbush grown in compost-amended, metalliferous tailings. The compost amendment provided a greater than 5-log increase in bacterial abundance, and survival of this compost-inoculum was more stable in planted treatments. Despite increased abundance, the activity of the introduced community was low, and significant increases were not detected until six and nine months in quailbush, and unplanted compost and buffalo grass treatments, respectively. In addition, increased abundances of nitrogen-fixation (nifH) and ammonia-oxidizing (amoA) genes were observed in rhizospheres of buffalo grass and quailbush, respectively. Thus, plant establishment facilitated the short term stabilization of introduced bacterial biomass and supported the growth of two key nitrogen-cycling populations in compost-amended tailings. PMID:25495940

  14. Abundance and Activity of 16S rRNA, AmoA and NifH Bacterial Genes During Assisted Phytostabilization of Mine Tailings.

    Science.gov (United States)

    Nelson, Karis N; Neilson, Julia W; Root, Robert A; Chorover, Jon; Maier, Raina M

    2015-01-01

    Mine tailings in semiarid regions are highly susceptible to erosion and are sources of dust pollution and potential avenues of human exposure to toxic metals. One constraint to revegetation of tailings by phytostabilization is the absence of microbial communities critical for biogeochemical cycling of plant nutrients. The objective of this study was to evaluate specific genes as in situ indicators of biological soil response during phytoremediation. The abundance and activity of 16S rRNA, nifH, and amoA were monitored during a nine month phytostabilization study using buffalo grass and quailbush grown in compost-amended, metalliferous tailings. The compost amendment provided a greater than 5-log increase in bacterial abundance, and survival of this compost-inoculum was more stable in planted treatments. Despite increased abundance, the activity of the introduced community was low, and significant increases were not detected until six and nine months in quailbush, and unplanted compost and buffalo grass treatments, respectively. In addition, increased abundances of nitrogen-fixation (nifH) and ammonia-oxidizing (amoA) genes were observed in rhizospheres of buffalo grass and quailbush, respectively. Thus, plant establishment facilitated the short term stabilization of introduced bacterial biomass and supported the growth of two key nitrogen-cycling populations in compost-amended tailings.

  15. Submerged macrophytes shape the abundance and diversity of bacterial denitrifiers in bacterioplankton and epiphyton in the Shallow Fresh Lake Taihu, China.

    Science.gov (United States)

    Fan, Zhou; Han, Rui-Ming; Ma, Jie; Wang, Guo-Xiang

    2016-07-01

    nirK and nirS genes are important functional genes involved in the denitrification pathway. Recent studies about these two denitrifying genes are focusing on sediment and wastewater microbe. In this study, we conducted a comparative analysis of the abundance and diversity of denitrifiers in the epiphyton of submerged macrophytes Potamogeton malaianus and Ceratophyllum demersum as well as in bacterioplankton in the shallow fresh lake Taihu, China. Results showed that nirK and nirS genes had significant different niches in epiphyton and bacterioplankton. Bacterioplankton showed greater abundance of nirK gene in terms of copy numbers and lower abundance of nirS gene. Significant difference in the abundance of nirK and nirS genes also existed between the epiphyton from different submerged macrophytes. Similar community diversity yet different community abundance was observed between epiphytic bacteria and bacterioplankton. No apparent seasonal variation was found either in epiphytic bacteria or bacterioplankton; however, environmental parameters seemed to have direct relevancy with nirK and nirS genes. Our study suggested that submerged macrophytes have greater influence than seasonal parameters in shaping the presence and abundance of bacterial denitrifiers. Further investigation needs to focus on the potential contact and relative contribution between denitrifiers and environmental factors.

  16. Estimating cavity tree and snag abundance using negative binomial regression models and nearest neighbor imputation methods

    Science.gov (United States)

    Bianca N.I. Eskelson; Hailemariam Temesgen; Tara M. Barrett

    2009-01-01

    Cavity tree and snag abundance data are highly variable and contain many zero observations. We predict cavity tree and snag abundance from variables that are readily available from forest cover maps or remotely sensed data using negative binomial (NB), zero-inflated NB, and zero-altered NB (ZANB) regression models as well as nearest neighbor (NN) imputation methods....

  17. Use of Atlantic Forest protected areas by free-ranging dogs: estimating abundance and persistence of use

    Science.gov (United States)

    Paschoal, Ana Maria; Massara, Rodrigo; Bailey, Larissa L.; Kendall, William L.; Doherty, Paul F.; Hirsch, Andre; Chiarello, Adriano; Paglia, Adriano

    2016-01-01

    Worldwide, domestic dogs (Canis familiaris) are one of the most common carnivoran species in natural areas and their populations are still increasing. Dogs have been shown to impact wildlife populations negatively, and their occurrence can alter the abundance, behavior, and activity patterns of native species. However, little is known about abundance and density of the free-ranging dogs that use protected areas. Here, we used camera trap data with an open-robust design mark–recapture model to estimate the number of dogs that used protected areas in Brazilian Atlantic Forest. We estimated the time period these dogs used the protected areas, and explored factors that influenced the probability of continued use (e.g., season, mammal richness, proportion of forest), while accounting for variation in detection probability. Dogs in the studied system were categorized as rural free-ranging, and their abundance varied widely across protected areas (0–73 individuals). Dogs used protected areas near human houses for longer periods (e.g., >50% of sampling occasions) compared to more distant areas. We found no evidence that their probability of continued use varied with season or mammal richness. Dog detection probability decreased linearly among occasions, possibly due to the owners confining their dogs after becoming aware of our presence. Comparing our estimates to those for native carnivoran, we found that dogs were three to 85 times more abundant than ocelots (Leopardus pardalis), two to 25 times more abundant than puma (Puma concolor), and approximately five times more abundant than the crab-eating fox (Cerdocyon thous). Combining camera trapping data with modern mark–recapture methods provides important demographic information on free-ranging dogs that can guide management strategies to directly control dogs' abundance and ranging behavior.

  18. Estimating abundance of an open population with an N-mixture model using auxiliary data on animal movements.

    Science.gov (United States)

    Ketz, Alison C; Johnson, Therese L; Monello, Ryan J; Mack, John A; George, Janet L; Kraft, Benjamin R; Wild, Margaret A; Hooten, Mevin B; Hobbs, N Thompson

    2018-04-01

    Accurate assessment of abundance forms a central challenge in population ecology and wildlife management. Many statistical techniques have been developed to estimate population sizes because populations change over time and space and to correct for the bias resulting from animals that are present in a study area but not observed. The mobility of individuals makes it difficult to design sampling procedures that account for movement into and out of areas with fixed jurisdictional boundaries. Aerial surveys are the gold standard used to obtain data of large mobile species in geographic regions with harsh terrain, but these surveys can be prohibitively expensive and dangerous. Estimating abundance with ground-based census methods have practical advantages, but it can be difficult to simultaneously account for temporary emigration and observer error to avoid biased results. Contemporary research in population ecology increasingly relies on telemetry observations of the states and locations of individuals to gain insight on vital rates, animal movements, and population abundance. Analytical models that use observations of movements to improve estimates of abundance have not been developed. Here we build upon existing multi-state mark-recapture methods using a hierarchical N-mixture model with multiple sources of data, including telemetry data on locations of individuals, to improve estimates of population sizes. We used a state-space approach to model animal movements to approximate the number of marked animals present within the study area at any observation period, thereby accounting for a frequently changing number of marked individuals. We illustrate the approach using data on a population of elk (Cervus elaphus nelsoni) in Northern Colorado, USA. We demonstrate substantial improvement compared to existing abundance estimation methods and corroborate our results from the ground based surveys with estimates from aerial surveys during the same seasons. We develop a

  19. Estimating bacterial production in marine waters from the simultaneous incorporation of thymidine and leucine.

    Science.gov (United States)

    Chin-Leo, G; Kirchman, D L

    1988-08-01

    We examined the simultaneous incorporation of [H]thymidine and [C]leucine to obtain two independent indices of bacterial production (DNA and protein syntheses) in a single incubation. Incorporation rates of leucine estimated by the dual-label method were generally higher than those obtained by the single-label method, but the differences were small (dual/single = 1.1 +/- 0.2 [mean +/- standard deviation]) and were probably due to the presence of labeled leucyl-tRNA in the cold trichloroacetic acid-insoluble fraction. There were no significant differences in thymidine incorporation between dual- and single-label incubations (dual/ single = 1.03 +/- 0.13). Addition of the two substrates in relatively large amounts (25 nM) did not apparently increase bacterial activity during short incubations (leucine incorporation rates covaried over depth profiles of the Chesapeake Bay. Estimates of bacterial production based on thymidine and leucine differed by less than 25%. Although the need for appropriate conversion factors has not been eliminated, the dual-label approach can be used to examine the variation in bacterial production while ensuring that the observed variation in incorporation rates is due to real changes in bacterial production rather than changes in conversion factors or introduction of other artifacts.

  20. A guide to the use of distance sampling to estimate abundance of Karner blue butterflies

    Science.gov (United States)

    Grundel, Ralph

    2015-01-01

    This guide is intended to describe the use of distance sampling as a method for evaluating the abundance of Karner blue butterflies at a location. Other methods for evaluating abundance exist, including mark-release-recapture and index counts derived from Pollard-Yates surveys, for example. Although this guide is not intended to be a detailed comparison of the pros and cons of each type of method, there are important preliminary considerations to think about before selecting any method for evaluating the abundance of Karner blue butterflies.

  1. The improvement of precision for estimating the abundance of standing dead trees using auxiliary information under the FIA pot design

    Science.gov (United States)

    Hong Su An; David W. MacFarlane; Christopher W. Woodall

    2012-01-01

    Standing dead trees are an important component of forest ecosystems. However, reliable estimates of standing dead tree population parameters can be difficult to obtain due to their low abundance and spatial and temporal variation. After 1999, the Forest Inventory and Analysis (FIA) Program began collecting data for standing dead trees at the Phase 2 stage of sampling....

  2. Validation of abundance estimates from mark-recapture and removal techniques for rainbow trout captured by electrofishing in small streams

    Science.gov (United States)

    Amanda E. Rosenberger; Jason B. Dunham

    2005-01-01

    Estimation of fish abundance in streams using the removal model or the Lincoln–Peterson mark–recapture model is a common practice in fisheries. These models produce misleading results if their assumptions are violated. We evaluated the assumptions of these two models via electrofishing of rainbow trout Oncorhynchus mykiss in central Idaho streams....

  3. Estimating bighorn sheep (Ovis Canadensis) abundance using noninvasive sampling at a mineral lick within a national park wilderness area

    Science.gov (United States)

    Kathryn A. Schoenecker; Mary Kay Watry; Laura E. Ellison; Michael K. Schwartz; Gordon L. Luikart

    2015-01-01

    Conservation of species requires accurate population estimates. We used genetic markers from feces to determine bighorn sheep abundance for a herd that was hypothesized to be declining and in need of population status monitoring. We sampled from a small but accessible portion of the population’s range where animals naturally congregate at a natural mineral lick to test...

  4. Estimation of survival rates and abundance of green turtles along the U.S. West Coast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — To determine abundance and survival rates of the east Pacific green turtles in the northern most foraging grounds, the turtle research groups at SWFSC have been...

  5. Asteroseismic estimate of helium abundance of a solar analog binary system

    Energy Technology Data Exchange (ETDEWEB)

    Verma, Kuldeep; Antia, H. M. [Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400005 (India); Faria, João P.; Monteiro, Mário J. P. F. G. [Centro de Astrofísica da Universidade do Porto, Rua das Estrelas, 4150-762 Porto (Portugal); Basu, Sarbani [Astronomy Department, Yale University, P. O. Box 208101, New Haven, CT 065208101 (United States); Mazumdar, Anwesh [Homi Bhabha Centre for Science Education, TIFR, V. N. Purav Marg, Mankhurd, Mumbai 400088 (India); Appourchaux, Thierry [Institut d' Astrophysique Spatiale, Université Paris XI-CNRS (UMR8617), Batiment 121, F-91405 Orsay Cedex (France); Chaplin, William J. [School of Physics and Astronomy, University of Birmingham, B15 2TT (United Kingdom); García, Rafael A. [Laboratoire AIM, CEA/DSM, CNRS, Université Paris Diderot, IRFU/SAp, Centre de Saclay, F-91191 Gif-sur-Yvette Cedex (France); Metcalfe, Travis S. [Stellar Astrophysics Centre, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, DK-8000 Aarhus C (Denmark)

    2014-08-01

    16 Cyg A and B are among the brightest stars observed by Kepler. What makes these stars more interesting is that they are solar analogs. 16 Cyg A and B exhibit solar-like oscillations. In this work we use oscillation frequencies obtained using 2.5 yr of Kepler data to determine the current helium abundance of these stars. For this we use the fact that the helium ionization zone leaves a signature on the oscillation frequencies and that this signature can be calibrated to determine the helium abundance of that layer. By calibrating the signature of the helium ionization zone against models of known helium abundance, the helium abundance in the envelope of 16 Cyg A is found to lie in the range of 0.231 to 0.251 and that of 16 Cyg B lies in the range of 0.218 to 0.266.

  6. Quantification of bacterial and archaeal symbionts in high and low microbial abundance sponges using real-time PCR

    KAUST Repository

    Bayer, Kristina; Kamke, Janine; Hentschel, Ute

    2014-01-01

    In spite of considerable insights into the microbial diversity of marine sponges, quantitative information on microbial abundances and community composition remains scarce. Here, we established qPCR assays for the specific quantification of four

  7. Metabolomics of tomato xylem sap during bacterial wilt reveals Ralstonia solanacearum produces abundant putrescine, a metabolite that accelerates wilt disease

    NARCIS (Netherlands)

    Lowe-Power, Tiffany M.; Hendrich, Connor G.; Roepenack-Lahaye, von Edda; Li, Bin; Wu, Dousheng; Mitra, Raka; Dalsing, Beth L.; Ricca, Patrizia; Naidoo, Jacinth; Cook, David; Jancewicz, Amy; Masson, Patrick; Thomma, Bart; Lahaye, Thomas; Michael, Anthony J.; Allen, Caitilyn

    2018-01-01

    Ralstonia solanacearum thrives in plant xylem vessels and causes bacterial wilt disease despite the low nutrient content of xylem sap. We found that R. solanacearum manipulates its host to increase nutrients in tomato xylem sap, enabling it to grow better in sap from infected plants than in sap from

  8. Spatial patterns of bacterial abundance, activity and community composition in relation to water masses in the eastern Mediterranean Sea

    NARCIS (Netherlands)

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

    2010-01-01

    To determine the variation of bacterial activity and community composition between and within specific water masses, samples were collected throughout the water column at 5 stations in the eastern Mediterranean Sea corresponding to the regions of the northern Aegean, mid-Aegean, western Cretan,

  9. Combining counts and incidence data: an efficient approach for estimating the log-normal species abundance distribution and diversity indices.

    Science.gov (United States)

    Bellier, Edwige; Grøtan, Vidar; Engen, Steinar; Schartau, Ann Kristin; Diserud, Ola H; Finstad, Anders G

    2012-10-01

    Obtaining accurate estimates of diversity indices is difficult because the number of species encountered in a sample increases with sampling intensity. We introduce a novel method that requires that the presence of species in a sample to be assessed while the counts of the number of individuals per species are only required for just a small part of the sample. To account for species included as incidence data in the species abundance distribution, we modify the likelihood function of the classical Poisson log-normal distribution. Using simulated community assemblages, we contrast diversity estimates based on a community sample, a subsample randomly extracted from the community sample, and a mixture sample where incidence data are added to a subsample. We show that the mixture sampling approach provides more accurate estimates than the subsample and at little extra cost. Diversity indices estimated from a freshwater zooplankton community sampled using the mixture approach show the same pattern of results as the simulation study. Our method efficiently increases the accuracy of diversity estimates and comprehension of the left tail of the species abundance distribution. We show how to choose the scale of sample size needed for a compromise between information gained, accuracy of the estimates and cost expended when assessing biological diversity. The sample size estimates are obtained from key community characteristics, such as the expected number of species in the community, the expected number of individuals in a sample and the evenness of the community.

  10. Estimate of symbiotically fixed nitrogen in field grown soybeans using variations in /sup 15/N natural abundance

    Energy Technology Data Exchange (ETDEWEB)

    Amarger, N; Durr, J C; Bourguignon, C; Lagacherie, B [INRA Centre de Recherches de Dijon, 21 (France). Lab. de Microbiologie des Sols; Mariotti, A; Mariotti, F [Paris-6 Univ., 75 (France). Lab. de Geologie Dynamique

    1979-07-01

    The use of variations in natural abundance of /sup 15/N between nitrogen fixing and non nitrogen fixing soybeans was investigated for quantitative estimate of symbiotic nitrogen fixation. Isotopic analysis of 4 varieties of inoculated and non-inoculated soybeans growing under field conditions, with and without N-fertilizer was determined. It was found that inoculated soybeans had a significantly lower /sup 15/N content than non-inoculated ones. Estimates of the participation of fixed N to the total nitrogen content of inoculated soybeans were calculated from these differences. They were compared to estimates calculated from differences in N yield between inoculated and non-inoculated plants and to the nitrogenase activity, measured by the C/sub 2/H/sub 2/ reduction assay over the growing season. Estimates given by the /sup 15/N measurements were correlated with the C/sub 2/H/sub 2/ reducing activity but not with the differences in the N yield. This shows that the isotopic composition was dependent on the amount of fixed nitrogen and consequently that the estimates of fixed nitrogen based on natural /sup 15/N abundance should be reliable. The absence of correlation between estimates based on /sup 15/N content and estimates based on N yield was explained by differences in the uptake of soil nitrogen between inoculated and non inoculated soybeans.

  11. Effects of superabsorbent polymers on the abundances of antibiotic resistance genes, mobile genetic elements, and the bacterial community during swine manure composting.

    Science.gov (United States)

    Guo, Aiyun; Gu, Jie; Wang, Xiaojuan; Zhang, Ranran; Yin, Yanan; Sun, Wei; Tuo, Xiaxia; Zhang, Li

    2017-11-01

    Superabsorbent polymers (SAPs) are considered suitable amendments for reducing the selection pressure due to heavy metals and the abundances of antibiotic resistance genes (ARGs) during composting. In this study, three SAP (sodium polyacrylate) levels (0, 5, and 15mgkg -1 of compost) were applied and their effects on the abundances of ARGs, mobile genetic elements (MGEs), and the bacterial community were investigated. After composting, the abundances of ARGs and MGEs decreased to different extent, where the removal efficiencies for tetW, dfrA7, ermX, aac(6')-ib-cr and MGEs exceeded 90%. The high SAP concentration significantly reduced the abundances of ARGs and MGEs, and changed the microbial community. Redundancy analysis indicated that the moisture content mainly explained the changes in ARGs and MGEs. Network analysis determined the potential hosts of ARGs and MGEs, and their co-occurrence. The results suggested that applying 15mgkg -1 SAP is appropriate for reducing ARGs in compost. Copyright © 2017. Published by Elsevier Ltd.

  12. Estimates of zooplankton abundance and size distribution with the Optical Plankton Counter (OPC)

    DEFF Research Database (Denmark)

    Wieland, Kai; Petersen, D.; Schnack, D.

    1997-01-01

    The capability of the Optical Plankton Count er (OPC) to examine the abundance and size distribution of zooplankton was tested in Storfjorden, Norway, in June 1993. Selected material obtained from net sampling was measured with a laboratory version of the OPC and compared with microscope analysis...

  13. Factors influencing ruminal bacterial community diversity and composition and microbial fibrolytic enzyme abundance in lactating dairy cows with a focus on the role of active dry yeast.

    Science.gov (United States)

    AlZahal, Ousama; Li, Fuyong; Guan, Le Luo; Walker, Nicola D; McBride, Brian W

    2017-06-01

    The objective of the current study was to employ a DNA-based sequencing technology to study the effect of active dry yeast (ADY) supplementation, diet type, and sample location within the rumen on rumen bacterial community diversity and composition, and to use an RNA-based method to study the effect of ADY supplementation on rumen microbial metabolism during high-grain feeding (HG). Our previous report demonstrated that the supplementation of lactating dairy cows with ADY attenuated the effect of subacute ruminal acidosis. Therefore, we used samples from that study, where 16 multiparous, rumen-cannulated lactating Holstein cows were randomly assigned to 1 of 2 dietary treatments: ADY (Saccharomyces cerevisiae strain Y1242, 80 billion cfu/animal per day) or control (carrier only). Cows received a high-forage diet (77:23, forage:concentrate), then were abruptly switched to HG (49:51, forage:concentrate). Rumen bacterial community diversity and structure were highly influenced by diet and sampling location (fluid, solids, epimural). The transition to HG reduced bacterial diversity, but epimural bacteria maintained a greater diversity than fluid and solids. Analysis of molecular variance indicated a significant separation due to diet × sampling location, but not due to treatment. Across all samples, the analysis yielded 6,254 nonsingleton operational taxonomic units (OTU), which were classified into several phyla: mainly Firmicutes, Bacteroidetes, Fibrobacteres, Tenericutes, and Proteobacteria. High forage and solids were dominated by OTU from Fibrobacter, whereas HG and fluid were dominated by OTU from Prevotella. Epimural samples, however, were dominated in part by Campylobacter. Active dry yeast had no effect on bacterial community diversity or structure. The phylum SR1 was more abundant in all ADY samples regardless of diet or sampling location. Furthermore, on HG, OTU2 and OTU3 (both classified into Fibrobacter succinogenes) were more abundant with ADY in fluid

  14. The diversity and abundance of phytase genes (beta-propeller phytases) in bacterial communities of the maize rhizosphere

    NARCIS (Netherlands)

    Cotta, S.R.; Cavalcante Franco Dias, A.; Seldin, L.; Andreote, F. D.; van Elsas, J. D.

    The ecology of microbial communities associated with organic phosphorus (P) mineralization in soils is still understudied. Here, we assessed the abundance and diversity of bacteria harbouring genes encoding beta-propeller phytases (BPP) in the rhizosphere of traditional and transgenic maize

  15. Bacterial traits, organism mass, and numerical abundance in the detrital soil food web of Dutch agricultural grasslands

    NARCIS (Netherlands)

    Mulder, C.; Cohen, J.E.; Setälä, H.; Bloem, J.; Breure, A.M.

    2005-01-01

    This paper compares responses to environmental stress of the ecophysiological traits of organisms in the detrital soil food webs of grasslands in the Netherlands, using the relationship between average body mass M and numerical abundance N. The microbial biomass and biodiversity of belowground fauna

  16. Estimation of occupancy, breeding success, and predicted abundance of golden eagles (Aquila chrysaetos) in the Diablo Range, California, 2014

    Science.gov (United States)

    Wiens, J. David; Kolar, Patrick S.; Fuller, Mark R.; Hunt, W. Grainger; Hunt, Teresa

    2015-01-01

    We used a multistate occupancy sampling design to estimate occupancy, breeding success, and abundance of territorial pairs of golden eagles (Aquila chrysaetos) in the Diablo Range, California, in 2014. This method uses the spatial pattern of detections and non-detections over repeated visits to survey sites to estimate probabilities of occupancy and successful reproduction while accounting for imperfect detection of golden eagles and their young during surveys. The estimated probability of detecting territorial pairs of golden eagles and their young was less than 1 and varied with time of the breeding season, as did the probability of correctly classifying a pair’s breeding status. Imperfect detection and breeding classification led to a sizeable difference between the uncorrected, naïve estimate of the proportion of occupied sites where successful reproduction was observed (0.20) and the model-based estimate (0.30). The analysis further indicated a relatively high overall probability of landscape occupancy by pairs of golden eagles (0.67, standard error = 0.06), but that areas with the greatest occupancy and reproductive potential were patchily distributed. We documented a total of 138 territorial pairs of golden eagles during surveys completed in the 2014 breeding season, which represented about one-half of the 280 pairs we estimated to occur in the broader 5,169-square kilometer region sampled. The study results emphasize the importance of accounting for imperfect detection and spatial heterogeneity in studies of site occupancy, breeding success, and abundance of golden eagles.

  17. Investigation of Endophytic Bacterial Community in Supposedly Axenic Cultures of Pineapple and Orchids with Evidence on Abundant Intracellular Bacteria.

    Science.gov (United States)

    Esposito-Polesi, Natalia Pimentel; de Abreu-Tarazi, Monita Fiori; de Almeida, Cristina Vieira; Tsai, Siu Mui; de Almeida, Marcílio

    2017-01-01

    Asepsis, defined as the absence of microbial contamination, is one of the most important requirements of plant micropropagation. In long-term micropropagated cultures, there may occasionally occur scattered microorganism growth in the culture medium. These microorganisms are common plant components and are known as latent endophytes. Thus, the aim of this research was to investigate the presence of endophytic bacteria in asymptomatic pineapple and orchid microplants, which were cultivated in three laboratories for 1 year. Isolation and characterization of bacterial isolates, PCR-DGGE from total genomic DNA of microplants and ultrastructural analysis of leaves were performed. In the culture-dependent technique, it was only possible to obtain bacterial isolates from pineapple microplants. In this case, the bacteria genera identified in the isolation technique were Bacillus, Acinetobacter, and Methylobacterium. The scanning electron microscopy and transmission electron microscopy (SEM and TEM) analyses revealed the presence of endophytic bacteria in intracellular spaces in the leaves of pineapple and orchid microplants, independent of the laboratory or cultivation protocol. Our results strongly indicate that there are endophytic bacterial communities inhabiting the microplants before initiation of the in vitro culture and that some of these endophytes persist in their latent form and can also grow in the culture medium even after long-term micropropagation, thus discarding the concept of "truly axenic plants."

  18. Abundance and diversity of bacterial nitrifiers and denitrifiers and their functional genes in tannery wastewater treatment plants revealed by high-throughput sequencing.

    Directory of Open Access Journals (Sweden)

    Zhu Wang

    Full Text Available Biological nitrification/denitrification is frequently used to remove nitrogen from tannery wastewater containing high concentrations of ammonia. However, information is limited about the bacterial nitrifiers and denitrifiers and their functional genes in tannery wastewater treatment plants (WWTPs due to the low-throughput of the previously used methods. In this study, 454 pyrosequencing and Illumina high-throughput sequencing, combined with molecular methods, were used to comprehensively characterize structures and functions of nitrification and denitrification bacterial communities in aerobic and anaerobic sludge of two full-scale tannery WWTPs. Pyrosequencing of 16S rRNA genes showed that Proteobacteria and Synergistetes dominated in the aerobic and anaerobic sludge, respectively. Ammonia-oxidizing bacteria (AOB amoA gene cloning revealed that Nitrosomonas europaea dominated the ammonia-oxidizing community in the WWTPs. Metagenomic analysis showed that the denitrifiers mainly included the genera of Thauera, Paracoccus, Hyphomicrobium, Comamonas and Azoarcus, which may greatly contribute to the nitrogen removal in the two WWTPs. It is interesting that AOB and ammonia-oxidizing archaea had low abundance although both WWTPs demonstrated high ammonium removal efficiency. Good correlation between the qPCR and metagenomic analysis is observed for the quantification of functional genes amoA, nirK, nirS and nosZ, indicating that the metagenomic approach may be a promising method used to comprehensively investigate the abundance of functional genes of nitrifiers and denitrifiers in the environment.

  19. Use of the robust design to estimate seasonal abundance and demographic parameters of a coastal bottlenose dolphin (Tursiops aduncus population.

    Directory of Open Access Journals (Sweden)

    Holly C Smith

    Full Text Available As delphinid populations become increasingly exposed to human activities we rely on our capacity to produce accurate abundance estimates upon which to base management decisions. This study applied mark-recapture methods following the Robust Design to estimate abundance, demographic parameters, and temporary emigration rates of an Indo-Pacific bottlenose dolphin (Tursiops aduncus population off Bunbury, Western Australia. Boat-based photo-identification surveys were conducted year-round over three consecutive years along pre-determined transect lines to create a consistent sampling effort throughout the study period and area. The best fitting capture-recapture model showed a population with a seasonal Markovian temporary emigration with time varying survival and capture probabilities. Abundance estimates were seasonally dependent with consistently lower numbers obtained during winter and higher during summer and autumn across the three-year study period. Specifically, abundance estimates for all adults and juveniles (combined varied from a low of 63 (95% CI 59 to 73 in winter of 2007 to a high of 139 (95% CI 134 to148 in autumn of 2009. Temporary emigration rates (γ' for animals absent in the previous period ranged from 0.34 to 0.97 (mean  =  0.54; ±SE 0.11 with a peak during spring. Temporary emigration rates for animals present during the previous period (γ'' were lower, ranging from 0.00 to 0.29, with a mean of 0.16 (± SE 0.04. This model yielded a mean apparent survival estimate for juveniles and adults (combined of 0.95 (± SE 0.02 and a capture probability from 0.07 to 0.51 with a mean of 0.30 (± SE 0.04. This study demonstrates the importance of incorporating temporary emigration to accurately estimate abundance of coastal delphinids. Temporary emigration rates were high in this study, despite the large area surveyed, indicating the challenges of sampling highly mobile animals which range over large spatial areas.

  20. Corn cob biochar increases soil culturable bacterial abundance without enhancing their capacities in utilizing carbon sources in Biolog Eco-plates

    Institute of Scientific and Technical Information of China (English)

    JIANG Lin-lin; HAN Guang-ming; LAN Yu; LIU Sai-nan; GAO Ji-ping; YANG Xu; MENG Jun; CHEN Wen-fu

    2017-01-01

    Biochar has been shown to influence soil microbial communities in terms of their abundance and diversity.However,the relationship among microbial abundance,structure and C metabolic traits is not well studied under biochar application.Here it was hypothesized that the addition of biochar with intrinsic properties (i.e.,porous structure) could affect the proliferation of culturable microbes and the genetic structure of soil bacterial communities.In the meantime,the presence of available organic carbon in biochar may influence the C utilization capacities of microbial community in Biolog Eco-plates.A pot experiment was conducted with differenct biochar application (BC) rates:control (0 t ha-1),BC1 (20 t ha-1) and BC2 (40 t ha-1).Culturable microorganisms were enumerated via the plate counting method.Bacterial diversity was examined using denaturing gradient gel electrophoresis (DGGE).Microbial capacity in using C sources was assessed using Biolog Eco-plates.The addition of biochar stimulated the growth of actinomyces and bacteria,especially the ammonifying bacteria and azotobacteria,but had no significant effect on fungi proliferation.The phylogenetic distribution of the operational taxonomic units could be divided into the following groups with the biochar addition:Firmicutes,Acidobacteria,Gemmatimonadetes,Actinobacteria,Cyanobacteria and α-,β-,γ-and δ-Proteobacteria (average similarity >95%).Biochar application had a higher capacity utilization for L-asparagine,Tween 80,D-mannitol,L-serine,γ-hydroxybutyric acid,N-acetyI-D-glucosamine,glycogen,itaconic acid,glycyl-L-glutamic acid,α-ketobutyricacid and putrescine,whereas it had received decreased capacities in using the other 20 carbon sources in Biolog Eco-plates.Redundancy analysis (RDA) revealed that the physico-chemical properties,indices of bacterial diversity,and C metabolic traits were positively correlated with the appearance of novel sequences under BC2 treatment.Our study indicates that the

  1. Capture-recapture abundance and survival estimates of three cetacean species in Icelandic coastal waters using trained scientist-volunteers

    Science.gov (United States)

    Bertulli, Chiara G.; Guéry, Loreleï; McGinty, Niall; Suzuki, Ailie; Brannan, Naomi; Marques, Tania; Rasmussen, Marianne H.; Gimenez, Olivier

    2018-01-01

    Knowledge of abundance and survival of humpback whales, white-beaked dolphins and minke whales are essential to manage and conserve these species in Icelandic coastal shelf waters. Our main goal was to test the feasibility of employing inexpensive research methods (data collected by trained-scientist volunteers onboard opportunistic vessels) to assess abundance and apparent survival. No previous studies in Iceland have investigated these two demographic parameters in these three cetacean species using open capture-recapture models accounting for imperfect and possibly heterogeneous detection. A transient effect was accounted for whenever required to estimate the population of resident individuals. Identification photographs were collected by scientist-trained volunteers for 7 years (2006-2013) from onboard commercial whale-watching vessels in the coastal waters of Faxaflói (southwest coast, 4400 km2) and Skjálfandi (northeast coast, 1100 km2), Iceland. We estimated an average abundance of 83 humpback whales (Mn; 95% confidence interval: 54-130) in Skjálfandi; 238 white-beaked dolphins (La; [163-321]) in Faxaflói; and 67 minke whales (Ba; [53-82]) in Faxaflói and 24 (14-31) in Skjálfandi. We also found that apparent survival was constant for all three species (Mn: 0.52 [0.41-0.63], La: 0.79 [0.64-0.88], Ba-Faxaflói: 0.80 [0.67-0.88], Ba-Skjálfandi: 0.96 [0.60-0.99]). Our results showed inter-annual variation in abundance estimates which were small for all species, and the presence of transience for minke whales. A significant increase in abundance during the study period was solely found in minke whale data from Skjálfandi. Humpback whales and white-beaked dolphins showed lower apparent survival rates compared to similar baleen whale and dolphin populations. Our results show data collected by trained-scientist volunteers can produce viable estimates of abundance and survival although bias in the methods we employed exist and need to be addressed. With the

  2. A hierarchical model for estimating the spatial distribution and abundance of animals detected by continuous-time recorders.

    Directory of Open Access Journals (Sweden)

    Robert M Dorazio

    Full Text Available Several spatial capture-recapture (SCR models have been developed to estimate animal abundance by analyzing the detections of individuals in a spatial array of traps. Most of these models do not use the actual dates and times of detection, even though this information is readily available when using continuous-time recorders, such as microphones or motion-activated cameras. Instead most SCR models either partition the period of trap operation into a set of subjectively chosen discrete intervals and ignore multiple detections of the same individual within each interval, or they simply use the frequency of detections during the period of trap operation and ignore the observed times of detection. Both practices make inefficient use of potentially important information in the data.We developed a hierarchical SCR model to estimate the spatial distribution and abundance of animals detected with continuous-time recorders. Our model includes two kinds of point processes: a spatial process to specify the distribution of latent activity centers of individuals within the region of sampling and a temporal process to specify temporal patterns in the detections of individuals. We illustrated this SCR model by analyzing spatial and temporal patterns evident in the camera-trap detections of tigers living in and around the Nagarahole Tiger Reserve in India. We also conducted a simulation study to examine the performance of our model when analyzing data sets of greater complexity than the tiger data.Our approach provides three important benefits: First, it exploits all of the information in SCR data obtained using continuous-time recorders. Second, it is sufficiently versatile to allow the effects of both space use and behavior of animals to be specified as functions of covariates that vary over space and time. Third, it allows both the spatial distribution and abundance of individuals to be estimated, effectively providing a species distribution model, even in

  3. Estimating grizzly and black bear population abundance and trend in Banff National Park using noninvasive genetic sampling.

    Directory of Open Access Journals (Sweden)

    Michael A Sawaya

    Full Text Available We evaluated the potential of two noninvasive genetic sampling methods, hair traps and bear rub surveys, to estimate population abundance and trend of grizzly (Ursus arctos and black bear (U. americanus populations in Banff National Park, Alberta, Canada. Using Huggins closed population mark-recapture models, we obtained the first precise abundance estimates for grizzly bears (N= 73.5, 95% CI = 64-94 in 2006; N= 50.4, 95% CI = 49-59 in 2008 and black bears (N= 62.6, 95% CI = 51-89 in 2006; N= 81.8, 95% CI = 72-102 in 2008 in the Bow Valley. Hair traps had high detection rates for female grizzlies, and male and female black bears, but extremely low detection rates for male grizzlies. Conversely, bear rubs had high detection rates for male and female grizzlies, but low rates for black bears. We estimated realized population growth rates, lambda, for grizzly bear males (λ= 0.93, 95% CI = 0.74-1.17 and females (λ= 0.90, 95% CI = 0.67-1.20 using Pradel open population models with three years of bear rub data. Lambda estimates are supported by abundance estimates from combined hair trap/bear rub closed population models and are consistent with a system that is likely driven by high levels of human-caused mortality. Our results suggest that bear rub surveys would provide an efficient and powerful means to inventory and monitor grizzly bear populations in the Central Canadian Rocky Mountains.

  4. Estimating grizzly and black bear population abundance and trend in Banff National Park using noninvasive genetic sampling.

    Science.gov (United States)

    Sawaya, Michael A; Stetz, Jeffrey B; Clevenger, Anthony P; Gibeau, Michael L; Kalinowski, Steven T

    2012-01-01

    We evaluated the potential of two noninvasive genetic sampling methods, hair traps and bear rub surveys, to estimate population abundance and trend of grizzly (Ursus arctos) and black bear (U. americanus) populations in Banff National Park, Alberta, Canada. Using Huggins closed population mark-recapture models, we obtained the first precise abundance estimates for grizzly bears (N= 73.5, 95% CI = 64-94 in 2006; N= 50.4, 95% CI = 49-59 in 2008) and black bears (N= 62.6, 95% CI = 51-89 in 2006; N= 81.8, 95% CI = 72-102 in 2008) in the Bow Valley. Hair traps had high detection rates for female grizzlies, and male and female black bears, but extremely low detection rates for male grizzlies. Conversely, bear rubs had high detection rates for male and female grizzlies, but low rates for black bears. We estimated realized population growth rates, lambda, for grizzly bear males (λ= 0.93, 95% CI = 0.74-1.17) and females (λ= 0.90, 95% CI = 0.67-1.20) using Pradel open population models with three years of bear rub data. Lambda estimates are supported by abundance estimates from combined hair trap/bear rub closed population models and are consistent with a system that is likely driven by high levels of human-caused mortality. Our results suggest that bear rub surveys would provide an efficient and powerful means to inventory and monitor grizzly bear populations in the Central Canadian Rocky Mountains.

  5. Hankin and Reeves' Approach to Estimating Fish Abundance in Small Streams : Limitations and Potential Options.

    Energy Technology Data Exchange (ETDEWEB)

    Thompson, William L. [Bonneville Power Administration, Portland, OR (US). Environment, Fish and Wildlife

    2000-11-01

    Hankin and Reeves' (1988) approach to estimating fish abundance in small streams has been applied in stream-fish studies across North America. However, as with any method of population estimation, there are important assumptions that must be met for estimates to be minimally biased and reasonably precise. Consequently, I investigated effects of various levels of departure from these assumptions via simulation based on results from an example application in Hankin and Reeves (1988) and a spatially clustered population. Coverage of 95% confidence intervals averaged about 5% less than nominal when removal estimates equaled true numbers within sampling units, but averaged 62% - 86% less than nominal when they did not, with the exception where detection probabilities of individuals were >0.85 and constant across sampling units (95% confidence interval coverage = 90%). True total abundances averaged far (20% - 41%) below the lower confidence limit when not included within intervals, which implies large negative bias. Further, average coefficient of variation was about 1.5 times higher when removal estimates did not equal true numbers within sampling units (C{bar V} = 0.27 [SE = 0.0004]) than when they did (C{bar V} = 0.19 [SE = 0.0002]). A potential modification to Hankin and Reeves' approach is to include environmental covariates that affect detection rates of fish into the removal model or other mark-recapture model. A potential alternative is to use snorkeling in combination with line transect sampling to estimate fish densities. Regardless of the method of population estimation, a pilot study should be conducted to validate the enumeration method, which requires a known (or nearly so) population of fish to serve as a benchmark to evaluate bias and precision of population estimates.

  6. Limitations to estimating bacterial cross-speciestransmission using genetic and genomic markers: inferencesfrom simulation modeling

    Science.gov (United States)

    Julio Andre, Benavides; Cross, Paul C.; Luikart, Gordon; Scott, Creel

    2014-01-01

    Cross-species transmission (CST) of bacterial pathogens has major implications for human health, livestock, and wildlife management because it determines whether control actions in one species may have subsequent effects on other potential host species. The study of bacterial transmission has benefitted from methods measuring two types of genetic variation: variable number of tandem repeats (VNTRs) and single nucleotide polymorphisms (SNPs). However, it is unclear whether these data can distinguish between different epidemiological scenarios. We used a simulation model with two host species and known transmission rates (within and between species) to evaluate the utility of these markers for inferring CST. We found that CST estimates are biased for a wide range of parameters when based on VNTRs and a most parsimonious reconstructed phylogeny. However, estimations of CST rates lower than 5% can be achieved with relatively low bias using as low as 250 SNPs. CST estimates are sensitive to several parameters, including the number of mutations accumulated since introduction, stochasticity, the genetic difference of strains introduced, and the sampling effort. Our results suggest that, even with whole-genome sequences, unbiased estimates of CST will be difficult when sampling is limited, mutation rates are low, or for pathogens that were recently introduced.

  7. Fishery-independent surface abundance and density estimates of swordfish (Xiphias gladius) from aerial surveys in the Central Mediterranean Sea

    Science.gov (United States)

    Lauriano, Giancarlo; Pierantonio, Nino; Kell, Laurence; Cañadas, Ana; Donovan, Gregory; Panigada, Simone

    2017-07-01

    Fishery-independent surface density and abundance estimates for the swordfish were obtained through aerial surveys carried out over a large portion of the Central Mediterranean, implementing distance sampling methodologies. Both design- and model-based abundance and density showed an uneven occurrence of the species throughout the study area, with clusters of higher density occurring near converging fronts, strong thermoclines and/or underwater features. The surface abundance was estimated for the Pelagos Sanctuary for Mediterranean Marine Mammals in the summer of 2009 (n=1152; 95%CI=669.0-1981.0; %CV=27.64), the Sea of Sardinia, the Pelagos Sanctuary and the Central Tyrrhenian Sea for the summer of 2010 (n=3401; 95%CI=2067.0-5596.0; %CV=25.51), and for the Southern Tyrrhenian Sea during the winter months of 2010-2011 (n=1228; 95%CI=578-2605; %CV=38.59). The Mediterranean swordfish stock deserves special attention in light of the heavy fishing pressures. Furthermore, the unreliability of fishery-related data has, to date, hampered our ability to effectively inform long-term conservation in the Mediterranean Region. Considering that the European countries have committed to protect the resources and all the marine-related economic and social dynamics upon which they depend, the information presented here constitute useful data towards the international legal requirements under the Marine Strategy Framework Directory, the Common Fisheries Policy, the Habitats and Species Directive and the Directive on Maritime Spatial Planning, among the others.

  8. Relative Abundance and Diversity of Bacterial Methanotrophs at the Oxic?Anoxic Interface of the Congo Deep-Sea Fan

    OpenAIRE

    Bessette, Sandrine; Moalic, Yann; Gautey, S?bastien; Lesongeur, Fran?oise; Godfroy, Anne; Toffin, Laurent

    2017-01-01

    Sitting at ∼5,000 m water depth on the Congo-Angola margin and ∼760 km offshore of the West African coast, the recent lobe complex of the Congo deep-sea fan receives large amounts of fluvial sediments (3–5% organic carbon). This organic-rich sedimentation area harbors habitats with chemosynthetic communities similar to those of cold seeps. In this study, we investigated relative abundance, diversity and distribution of aerobic methane-oxidizing bacteria (MOB) communities at the oxic–anoxic in...

  9. Estimating breeding season abundance of golden-cheeked warblers in Texas, USA

    KAUST Repository

    Mathewson, Heather A.; Groce, Julie E.; Mcfarland, Tiffany M.; Morrison, Michael L.; Newnam, J. Cal; Snelgrove, R. Todd; Collier, Bret A.; Wilkins, R. Neal

    2012-01-01

    relied on localized population studies on public lands and qualitative-based methods. Our goal was to estimate breeding population size of male warblers using a predictive model based on metrics for patches of woodland habitat throughout the species

  10. Estimating Bacterial Production in Marine Waters from the Simultaneous Incorporation of Thymidine and Leucine

    OpenAIRE

    Chin-Leo, Gerardo; Kirchman, David L.

    1988-01-01

    We examined the simultaneous incorporation of [3H]thymidine and [14C]leucine to obtain two independent indices of bacterial production (DNA and protein syntheses) in a single incubation. Incorporation rates of leucine estimated by the dual-label method were generally higher than those obtained by the single-label method, but the differences were small (dual/single = 1.1 ± 0.2 [mean ± standard deviation]) and were probably due to the presence of labeled leucyl-tRNA in the cold trichloroacetic ...

  11. ARK: Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition.

    Science.gov (United States)

    Koslicki, David; Chatterjee, Saikat; Shahrivar, Damon; Walker, Alan W; Francis, Suzanna C; Fraser, Louise J; Vehkaperä, Mikko; Lan, Yueheng; Corander, Jukka

    2015-01-01

    Estimation of bacterial community composition from high-throughput sequenced 16S rRNA gene amplicons is a key task in microbial ecology. Since the sequence data from each sample typically consist of a large number of reads and are adversely impacted by different levels of biological and technical noise, accurate analysis of such large datasets is challenging. There has been a recent surge of interest in using compressed sensing inspired and convex-optimization based methods to solve the estimation problem for bacterial community composition. These methods typically rely on summarizing the sequence data by frequencies of low-order k-mers and matching this information statistically with a taxonomically structured database. Here we show that the accuracy of the resulting community composition estimates can be substantially improved by aggregating the reads from a sample with an unsupervised machine learning approach prior to the estimation phase. The aggregation of reads is a pre-processing approach where we use a standard K-means clustering algorithm that partitions a large set of reads into subsets with reasonable computational cost to provide several vectors of first order statistics instead of only single statistical summarization in terms of k-mer frequencies. The output of the clustering is then processed further to obtain the final estimate for each sample. The resulting method is called Aggregation of Reads by K-means (ARK), and it is based on a statistical argument via mixture density formulation. ARK is found to improve the fidelity and robustness of several recently introduced methods, with only a modest increase in computational complexity. An open source, platform-independent implementation of the method in the Julia programming language is freely available at https://github.com/dkoslicki/ARK. A Matlab implementation is available at http://www.ee.kth.se/ctsoftware.

  12. The abundance of functional genes, cbbL, nifH, amoA and apsA, and bacterial community structure of intertidal soil from Arabian Sea.

    Science.gov (United States)

    Keshri, Jitendra; Yousuf, Basit; Mishra, Avinash; Jha, Bhavanath

    2015-06-01

    The Gulf of Cambay is a trumpet-shaped inlet of the Arabian Sea, located along the west coast of India and confronts a high tidal range with strong water currents. The region belongs to a semi-arid zone and saline alkaline intertidal soils are considered biologically extreme. The selected four soil types (S1-S4) were affected by salinity, alkalinity and sodicity. Soil salinity ranged from 20 to 126 dS/m, soil pH 8.6-10.0 with high sodium adsorption ratio (SAR) and exchangeable sodium percentage (ESP). Abundance of the key functional genes like cbbL, nifH, amoA and apsA involved in biogeochemical cycling were targeted using qPCR, which varied from (2.36 ± 0.03) × 10(4) to (2.87 ± 0.26) × 10(8), (1.18 ± 0.28) × 10(6) to (1.01 ± 0.26) × 10(9), (1.41 ± 0.21) × 10(6) to (1.29 ± 0.05) × 10(8) and (8.47 ± 0.23) × 10(4) to (1.73 ± 0.01) × 10(6) per gram dry weight, respectively. The microbial community structure revealed that soils S1 and S3 were dominated by phylum Firmicutes whereas S4 and S2 showed an abundance of Proteobacterial clones. These soils also represented Bacteroidetes, Chloroflexi, Actinobacteria, Planctomycetes and Acidobacteria clones. Molecular phylogeny showed a significant variation in the bacterial community distribution among the intertidal soil types. A high number of novel taxonomic units were observed which makes the intertidal zone a unique reservoir of unidentified bacterial taxa that may be explored further. Copyright © 2015 Elsevier GmbH. All rights reserved.

  13. In vitro estimation of rumen protein degradability using 35S to label the bacterial mass

    International Nuclear Information System (INIS)

    Khristov, A.; Aleksandrov, S.; Aleksiev, I.

    1994-01-01

    An experiment was carried out in order to simplify a previously developed 15 N-method for in vitro estimation of rumen protein degradability. Casein (Cas), whole soybeans (Sb) heated at 120 o C for 20 min (SbTherm) and sunflower (Sfl) were incubated at 39 o C for 4 hours in a water bathshaker with the following media: McDougall's buffer, strained and enriched with particle associated bacteria rumen fluid (2:1), rapidly (maltose, sucrose, glucose) and more slowly (pectin, soluble starch) degradable carbohydrates with final concentration of 815 mg/100 ml and 21.7 μCi/100 ml of 35 S (from Na 2 35 SO 4 ). After the incubation had been ceased, a bacterial fraction was isolated through differential centrifugation and specific activity of bacterial (Bac) and high speed total solids (TS) nitrogen was measured. The ratio was used to calculate bacterial mass in TS and through the Kjeldahl nitrogen concentration in TS - the net bacterial growth (against control vessels without protein). The level of ammonia-N in the supernate after blank correction was used to find the ammonia-N released from protein degradation. The data showed that the rate (and extend) of degradation for the Cas (as a standard protein) was lower compared to those obtained through the 15 N-method but it was higher than the rate derived through another in vitro method. The Cas equivalent of the Sb was higher than the figure we found in a previous experiment with solvent extracted soybean meal suggesting that the 35 S-method underestimated the degradability of the Cas. After being tested on a wider range of foodstuffs, the proposed 35 S-method might be considered as an alternative procedure which is less laborous than the 15 N-method. (author)

  14. Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes.

    Directory of Open Access Journals (Sweden)

    Stephen Nayfach

    2015-11-01

    Full Text Available Shotgun metagenomic DNA sequencing is a widely applicable tool for characterizing the functions that are encoded by microbial communities. Several bioinformatic tools can be used to functionally annotate metagenomes, allowing researchers to draw inferences about the functional potential of the community and to identify putative functional biomarkers. However, little is known about how decisions made during annotation affect the reliability of the results. Here, we use statistical simulations to rigorously assess how to optimize annotation accuracy and speed, given parameters of the input data like read length and library size. We identify best practices in metagenome annotation and use them to guide the development of the Shotgun Metagenome Annotation Pipeline (ShotMAP. ShotMAP is an analytically flexible, end-to-end annotation pipeline that can be implemented either on a local computer or a cloud compute cluster. We use ShotMAP to assess how different annotation databases impact the interpretation of how marine metagenome and metatranscriptome functional capacity changes across seasons. We also apply ShotMAP to data obtained from a clinical microbiome investigation of inflammatory bowel disease. This analysis finds that gut microbiota collected from Crohn's disease patients are functionally distinct from gut microbiota collected from either ulcerative colitis patients or healthy controls, with differential abundance of metabolic pathways related to host-microbiome interactions that may serve as putative biomarkers of disease.

  15. Metabolomics of tomato xylem sap during bacterial wilt reveals Ralstonia solanacearum produces abundant putrescine, a metabolite that accelerates wilt disease.

    Science.gov (United States)

    Lowe-Power, Tiffany M; Hendrich, Connor G; von Roepenack-Lahaye, Edda; Li, Bin; Wu, Dousheng; Mitra, Raka; Dalsing, Beth L; Ricca, Patrizia; Naidoo, Jacinth; Cook, David; Jancewicz, Amy; Masson, Patrick; Thomma, Bart; Lahaye, Thomas; Michael, Anthony J; Allen, Caitilyn

    2018-04-01

    Ralstonia solanacearum thrives in plant xylem vessels and causes bacterial wilt disease despite the low nutrient content of xylem sap. We found that R. solanacearum manipulates its host to increase nutrients in tomato xylem sap, enabling it to grow better in sap from infected plants than in sap from healthy plants. Untargeted GC/MS metabolomics identified 22 metabolites enriched in R. solanacearum-infected sap. Eight of these could serve as sole carbon or nitrogen sources for R. solanacearum. Putrescine, a polyamine that is not a sole carbon or nitrogen source for R. solanacearum, was enriched 76-fold to 37 µM in R. solanacearum-infected sap. R. solanacearum synthesized putrescine via a SpeC ornithine decarboxylase. A ΔspeC mutant required ≥ 15 µM exogenous putrescine to grow and could not grow alone in xylem even when plants were treated with putrescine. However, co-inoculation with wildtype rescued ΔspeC growth, indicating R. solanacearum produced and exported putrescine to xylem sap. Intriguingly, treating plants with putrescine before inoculation accelerated wilt symptom development and R. solanacearum growth and systemic spread. Xylem putrescine concentration was unchanged in putrescine-treated plants, so the exogenous putrescine likely accelerated disease indirectly by affecting host physiology. These results indicate that putrescine is a pathogen-produced virulence metabolite. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  16. Estimating cetacean density and abundance in the Central and Western Mediterranean Sea through aerial surveys: Implications for management

    Science.gov (United States)

    Panigada, Simone; Lauriano, Giancarlo; Donovan, Greg; Pierantonio, Nino; Cañadas, Ana; Vázquez, José Antonio; Burt, Louise

    2017-07-01

    Systematic, effective monitoring of animal population parameters underpins successful conservation strategy and wildlife management, but it is often neglected in many regions, including much of the Mediterranean Sea. Nonetheless, a series of systematic multispecies aerial surveys was carried out in the seas around Italy to gather important baseline information on cetacean occurrence, distribution and abundance. The monitored areas included the Pelagos Sanctuary, the Tyrrhenian Sea, portions of the Seas of Corsica and Sardinia, the Ionian Seas as well as the Gulf of Taranto. Overall, approximately 48,000 km were flown in either spring, summer and winter between 2009-2014, covering an area of 444,621 km2. The most commonly observed species were the striped dolphin and the fin whale, with 975 and 83 recorded sightings, respectively. Other sighted cetacean species were the common bottlenose dolphin, the Risso's dolphin, the sperm whale, the pilot whale and the Cuvier's beaked whale. Uncorrected model- and design-based estimates of density and abundance for striped dolphins and fin whales were produced, resulting in a best estimate (model-based) of around 95,000 striped dolphins (CV=11.6%; 95% CI=92,900-120,300) occurring in the Pelagos Sanctuary, Central Tyrrhenian and Western Seas of Corsica and Sardinia combined area in summer 2010. Estimates were also obtained for each individual study region and year. An initial attempt to estimate perception bias for striped dolphins is also provided. The preferred summer 2010 uncorrected best estimate (design-based) for the same areas for fin whales was around 665 (CV=33.1%; 95% CI=350-1260). Estimates are also provided for the individual study regions and years. The results represent baseline data to develop efficient, long-term, systematic monitoring programmes, essential to evaluate trends, as required by a number of national and international frameworks, and stress the need to ensure that surveys are undertaken regularly and

  17. Soil water availability and microsite mediate fungal and bacterial phospholipid fatty acid biomarker abundances in Mojave Desert soils exposed to elevated atmospheric CO2

    Science.gov (United States)

    Jin, V. L.; Schaeffer, S. M.; Ziegler, S. E.; Evans, R. D.

    2011-06-01

    Changes in the rates of nitrogen (N) cycling, microbial carbon (C) substrate use, and extracellular enzyme activities in a Mojave Desert ecosystem exposed to elevated atmospheric CO2 suggest shifts in the size and/or functional characteristics of microbial assemblages in two dominant soil microsites: plant interspaces and under the dominant shrub Larrea tridentata. We used ester-linked phospholipid fatty acid (PLFA) biomarkers as a proxy for microbial biomass to quantify spatial and temporal differences in soil microbial communities from February 2003 to May 2005. Further, we used the 13C signature of the fossil CO2 source for elevated CO2 plots to trace recent plant C inputs into soil organic matter (SOM) and broad microbial groups using δ13C (‰). Differences between individual δ13CPLFA and δ13CSOM for fungal biomarkers indicated active metabolism of newer C in elevated CO2 soils. Total PLFA-C was greater in shrub microsites compared to plant interspaces, and CO2 treatment differences within microsites increased under higher soil water availability. Total, fungal, and bacterial PLFA-C increased with decreasing soil volumetric water content (VWC) in both microsites, suggesting general adaptations to xeric desert conditions. Increases in fungal-to-bacterial PLFA-C ratio with decreasing VWC reflected functional group-specific responses to changing soil water availability. While temporal and spatial extremes in resource availability in desert ecosystems contribute to the difficulty in identifying common trends or mechanisms driving microbial responses in less extreme environments, we found that soil water availability and soil microsite interacted with elevated CO2 to shift fungal and bacterial biomarker abundances in Mojave Desert soils.

  18. Relative Abundance and Diversity of Bacterial Methanotrophs at the Oxic–Anoxic Interface of the Congo Deep-Sea Fan

    Directory of Open Access Journals (Sweden)

    Laurent Toffin

    2017-04-01

    Full Text Available Sitting at ∼5,000 m water depth on the Congo-Angola margin and ∼760 km offshore of the West African coast, the recent lobe complex of the Congo deep-sea fan receives large amounts of fluvial sediments (3–5% organic carbon. This organic-rich sedimentation area harbors habitats with chemosynthetic communities similar to those of cold seeps. In this study, we investigated relative abundance, diversity and distribution of aerobic methane-oxidizing bacteria (MOB communities at the oxic–anoxic interface of sedimentary habitats by using fluorescence in situ hybridization and comparative sequence analysis of particulate mono-oxygenase (pmoA genes. Our findings revealed that sedimentary habitats of the recent lobe complex hosted type I and type II MOB cells and comparisons of pmoA community compositions showed variations among the different organic-rich habitats. Furthermore, the pmoA lineages were taxonomically more diverse compared to methane seep environments and were related to those found at cold seeps. Surprisingly, MOB phylogenetic lineages typical of terrestrial environments were observed at such water depth. In contrast, MOB cells or pmoA sequences were not detected at the previous lobe complex that is disconnected from the Congo River inputs.

  19. Lunar mare TiO2 abundances estimated from UV/Vis reflectance

    Science.gov (United States)

    Sato, Hiroyuki; Robinson, Mark S.; Lawrence, Samuel J.; Denevi, Brett W.; Hapke, Bruce; Jolliff, Bradley L.; Hiesinger, Harald

    2017-11-01

    The visible (400-700 nm) and near-infrared (700-2800 nm) reflectance of the lunar regolith is dominantly controlled by variations in the abundance of plagioclase, iron-bearing silicate minerals, opaque minerals (e.g., ilmenite), and maturation products (e.g., agglutinate glass, radiation-produced rims on soil grains, and Fe-metal). The same materials control reflectance into the near-UV (250-400 nm) with varying degrees of importance. A key difference is that while ilmenite is spectrally neutral in the visible to near-infrared, it exhibits a diagnostic upturn in reflectance in the near-UV, at wavelengths shorter than about 450 nm. The Lunar Reconnaissance Orbiter Wide Angle Camera (WAC) filters were specifically designed to take advantage of this spectral feature to enable more accurate mapping of ilmenite within mare soils than previously possible. Using the reflectance measured at 321 and 415 nm during 62 months of repeated near-global WAC observations, first we found a linear correlation between the TiO2 contents of the lunar soil samples and the 321/415 nm ratio of each sample return site. We then used the coefficients from the linear regression and the near-global WAC multispectral mosaic to derive a new TiO2 map. The average TiO2 content is 3.9 wt% for the 17 major maria. The highest TiO2 values were found in Mare Tranquillitatis (∼12.6 wt%) and Oceanus Procellarum (∼11.6 wt%). Regions contaminated by highland ejecta, lunar swirls, and the low-TiO2 maria (e.g., Mare Frigoris, the northeastern units of Mare Imbrium) exhibit very low TiO2 values (2.6 Ga), whereas only medium to high TiO2 values (average = 6.8 wt%, minimum = 4.5 wt%) are found for younger mare units (<2.6 Ga).

  20. Seasonal changes in the abundance of bacterial genes related to dimethylsulfoniopropionate catabolism in seawater from Ofunato Bay revealed by metagenomic analysis

    KAUST Repository

    Kudo, Toshiaki

    2018-04-26

    Ofunato Bay is located in the northeastern Pacific Ocean area of Japan, and it has the highest biodiversity of marine organisms in the world, primarily due to tidal influences from the cold Oyashio and warm Kuroshio currents. Our previous results from performing shotgun metagenomics indicated that Candidatus Pelagibacter ubique and Planktomarina temperata were the dominant bacteria (Reza et al., 2018a, 2018b). These bacteria are reportedly able to catabolize dimethylsulfoniopropionate (DMSP) produced from phytoplankton into dimethyl sulfide (DMS) or methanethiol (MeSH). This study was focused on seasonal changes in the abundances of bacterial genes (dddP, dmdA) related to DMSP catabolism in the seawater of Ofunato Bay by BLAST+ analysis using shotgun metagenomic datasets. We found seasonal changes among the Candidatus Pelagibacter ubique strains, including those of the HTCC1062 type and the Red Sea type. A good correlation was observed between the chlorophyll a concentrations and the abundances of the catabolic genes, suggesting that the bacteria directly interact with phytoplankton in the marine material cycle system and play important roles in producing DMS and MeSH from DMSP as signaling molecules for the possible formation of the scent of the tidewater or as fish attractants.

  1. Seasonal changes in the abundance of bacterial genes related to dimethylsulfoniopropionate catabolism in seawater from Ofunato Bay revealed by metagenomic analysis

    KAUST Repository

    Kudo, Toshiaki; Kobiyama, Atsushi; Rashid, Jonaira; Reza, Shaheed; Yamada, Yuichiro; Ikeda, Yuri; Ikeda, Daisuke; Mizusawa, Nanami; Ikeo, Kazuho; Sato, Shigeru; Ogata, Takehiko; Jimbo, Mitsuru; Kaga, Shinnosuke; Watanabe, Shiho; Naiki, Kimiaki; Kaga, Yoshimasa; Segawa, Satoshi; Mineta, Katsuhiko; Bajic, Vladimir B.; Gojobori, Takashi; Watabe, Shugo

    2018-01-01

    Ofunato Bay is located in the northeastern Pacific Ocean area of Japan, and it has the highest biodiversity of marine organisms in the world, primarily due to tidal influences from the cold Oyashio and warm Kuroshio currents. Our previous results from performing shotgun metagenomics indicated that Candidatus Pelagibacter ubique and Planktomarina temperata were the dominant bacteria (Reza et al., 2018a, 2018b). These bacteria are reportedly able to catabolize dimethylsulfoniopropionate (DMSP) produced from phytoplankton into dimethyl sulfide (DMS) or methanethiol (MeSH). This study was focused on seasonal changes in the abundances of bacterial genes (dddP, dmdA) related to DMSP catabolism in the seawater of Ofunato Bay by BLAST+ analysis using shotgun metagenomic datasets. We found seasonal changes among the Candidatus Pelagibacter ubique strains, including those of the HTCC1062 type and the Red Sea type. A good correlation was observed between the chlorophyll a concentrations and the abundances of the catabolic genes, suggesting that the bacteria directly interact with phytoplankton in the marine material cycle system and play important roles in producing DMS and MeSH from DMSP as signaling molecules for the possible formation of the scent of the tidewater or as fish attractants.

  2. Accounting for subgroup structure in line-transect abundance estimates of false killer whales (Pseudorca crassidens in Hawaiian waters.

    Directory of Open Access Journals (Sweden)

    Amanda L Bradford

    Full Text Available For biological populations that form aggregations (or clusters of individuals, cluster size is an important parameter in line-transect abundance estimation and should be accurately measured. Cluster size in cetaceans has traditionally been represented as the total number of individuals in a group, but group size may be underestimated if group members are spatially diffuse. Groups of false killer whales (Pseudorca crassidens can comprise numerous subgroups that are dispersed over tens of kilometers, leading to a spatial mismatch between a detected group and the theoretical framework of line-transect analysis. Three stocks of false killer whales are found within the U.S. Exclusive Economic Zone of the Hawaiian Islands (Hawaiian EEZ: an insular main Hawaiian Islands stock, a pelagic stock, and a Northwestern Hawaiian Islands (NWHI stock. A ship-based line-transect survey of the Hawaiian EEZ was conducted in the summer and fall of 2010, resulting in six systematic-effort visual sightings of pelagic (n = 5 and NWHI (n = 1 false killer whale groups. The maximum number and spatial extent of subgroups per sighting was 18 subgroups and 35 km, respectively. These sightings were combined with data from similar previous surveys and analyzed within the conventional line-transect estimation framework. The detection function, mean cluster size, and encounter rate were estimated separately to appropriately incorporate data collected using different methods. Unlike previous line-transect analyses of cetaceans, subgroups were treated as the analytical cluster instead of groups because subgroups better conform to the specifications of line-transect theory. Bootstrap values (n = 5,000 of the line-transect parameters were randomly combined to estimate the variance of stock-specific abundance estimates. Hawai'i pelagic and NWHI false killer whales were estimated to number 1,552 (CV = 0.66; 95% CI = 479-5,030 and 552 (CV = 1.09; 95% CI = 97

  3. Gear and seasonal bias associated with abundance and size structure estimates for lentic freshwater fishes

    Science.gov (United States)

    Fischer, Jesse R.; Quist, Michael C.

    2014-01-01

    All freshwater fish sampling methods are biased toward particular species, sizes, and sexes and are further influenced by season, habitat, and fish behavior changes over time. However, little is known about gear-specific biases for many common fish species because few multiple-gear comparison studies exist that have incorporated seasonal dynamics. We sampled six lakes and impoundments representing a diversity of trophic and physical conditions in Iowa, USA, using multiple gear types (i.e., standard modified fyke net, mini-modified fyke net, sinking experimental gill net, bag seine, benthic trawl, boat-mounted electrofisher used diurnally and nocturnally) to determine the influence of sampling methodology and season on fisheries assessments. Specifically, we describe the influence of season on catch per unit effort, proportional size distribution, and the number of samples required to obtain 125 stock-length individuals for 12 species of recreational and ecological importance. Mean catch per unit effort generally peaked in the spring and fall as a result of increased sampling effectiveness in shallow areas and seasonal changes in habitat use (e.g., movement offshore during summer). Mean proportional size distribution decreased from spring to fall for white bass Morone chrysops, largemouth bass Micropterus salmoides, bluegill Lepomis macrochirus, and black crappie Pomoxis nigromaculatus, suggesting selectivity for large and presumably sexually mature individuals in the spring and summer. Overall, the mean number of samples required to sample 125 stock-length individuals was minimized in the fall with sinking experimental gill nets, a boat-mounted electrofisher used at night, and standard modified nets for 11 of the 12 species evaluated. Our results provide fisheries scientists with relative comparisons between several recommended standard sampling methods and illustrate the effects of seasonal variation on estimates of population indices that will be critical to

  4. Examination of an indicative tool for rapidly estimating viable organism abundance in ballast water

    Science.gov (United States)

    Vanden Byllaardt, Julie; Adams, Jennifer K.; Casas-Monroy, Oscar; Bailey, Sarah A.

    2018-03-01

    Regulatory discharge standards stipulating a maximum allowable number of viable organisms in ballast water have led to a need for rapid, easy and accurate compliance assessment tools and protocols. Some potential tools presume that organisms present in ballast water samples display the same characteristics of life as the native community (e.g. rates of fluorescence). This presumption may not prove true, particularly when ships' ballast tanks present a harsh environment and long transit times, negatively impacting organism health. Here, we test the accuracy of a handheld pulse amplitude modulated (PAM) fluorometer, the Hach BW680, for detecting photosynthetic protists at concentrations above or below the discharge standard (< 10 cells·ml- 1) in comparison to microscopic counts using fluorescein diacetate as a viability probe. Testing was conducted on serial dilutions of freshwater harbour samples in the lab and in situ untreated ballast water samples originating from marine, freshwater and brackish sources utilizing three preprocessing techniques to target organisms in the size range of ≥ 10 and < 50 μm. The BW680 numeric estimates were in agreement with microscopic counts when analyzing freshly collected harbour water at all but the lowest concentrations (< 38 cells·ml- 1). Chi-square tests determined that error is not independent of preprocessing methods: using the filtrate method or unfiltered water, in addition to refining the conversion factor of raw fluorescence to cell size, can decrease the grey area where exceedance of the discharge standard cannot be measured with certainty (at least for the studied populations). When examining in situ ballast water, the BW680 detected significantly fewer viable organisms than microscopy, possibly due to factors such as organism size or ballast water age. Assuming both the BW680 and microscopy with FDA stain were measuring fluorescence and enzymatic activity/membrane integrity correctly, the observed discrepancy

  5. EMSAR: estimation of transcript abundance from RNA-seq data by mappability-based segmentation and reclustering.

    Science.gov (United States)

    Lee, Soohyun; Seo, Chae Hwa; Alver, Burak Han; Lee, Sanghyuk; Park, Peter J

    2015-09-03

    RNA-seq has been widely used for genome-wide expression profiling. RNA-seq data typically consists of tens of millions of short sequenced reads from different transcripts. However, due to sequence similarity among genes and among isoforms, the source of a given read is often ambiguous. Existing approaches for estimating expression levels from RNA-seq reads tend to compromise between accuracy and computational cost. We introduce a new approach for quantifying transcript abundance from RNA-seq data. EMSAR (Estimation by Mappability-based Segmentation And Reclustering) groups reads according to the set of transcripts to which they are mapped and finds maximum likelihood estimates using a joint Poisson model for each optimal set of segments of transcripts. The method uses nearly all mapped reads, including those mapped to multiple genes. With an efficient transcriptome indexing based on modified suffix arrays, EMSAR minimizes the use of CPU time and memory while achieving accuracy comparable to the best existing methods. EMSAR is a method for quantifying transcripts from RNA-seq data with high accuracy and low computational cost. EMSAR is available at https://github.com/parklab/emsar.

  6. Associations of hypoosmotic swelling test, relative sperm volume shift, aquaporin7 mRNA abundance and bull fertility estimates.

    Science.gov (United States)

    Kasimanickam, R K; Kasimanickam, V R; Arangasamy, A; Kastelic, J P

    2017-02-01

    Mammalian sperm are exposed to a natural hypoosmotic environment during male-to-female reproductive tract transition; although this activates sperm motility in vivo, excessive swelling can harm sperm structure and function. Aquaporins (AQPs) is a family of membrane-channel proteins implicated in sperm osmoregulation. The objective was to determine associations among relative sperm volume shift, hypoosmotic swelling test (HOST), sperm aquaporin (AQP) 7 mRNA abundances, and sire conception rate (SCR; fertility estimate) in Holstein bulls at a commercial artificial insemination center. Three or four sires for each full point SCR score from -4 to +4 were included. Each SCR estimate for study bulls (N = 30) was based on > 500 services (mean ± SEM) of 725 ± 13 services/sire). Sperm from a single collection day (two ejaculates) from these commercial Holstein bulls were used. Relative mRNA expression of AQP7 in sperm was determined by polymerase chain reaction. Mean relative sperm volume shift and percentage of sperm reacted in a HOST (% HOST) were determined (400 sperm per bull) after incubating in isoosmotic (300 mOsm/kg) and hypoosmotic (100 mOsm/kg) solutions for 30 min. There was no correlation between %HOST and SCR (r = 0.28 P > 0.1). However, there was a positive correlation between relative sperm volume shift and SCR (r = 0.65, P 2) fertility sire groups. In conclusion, bulls with higher SCR had significantly greater AQP7 mRNA abundance in frozen-thawed sperm. This plausibly contributed to greater regulation of sperm volume shift, which apparently conferred protection from detrimental swelling and impaired functions. Copyright © 2016 Elsevier Inc. All rights reserved.

  7. Use of metabolic inhibitors to estimate protozooplankton grazing and bacterial production in a monomictic eutrophic lake with an anaerobic hypolimnion

    International Nuclear Information System (INIS)

    Sanders, R.W.; Porter, K.G.

    1986-01-01

    Inhibitors of eucaryotes (cycloheximide and amphotericin B) and procaryotes (penicillin and chloramphenical) were used to estimate bacterivory and bacterial production in a eutrophic lake. Bacterial production appeared to be slightly greater than protozoan grazing in the aerobic waters of Lake Oglethorpe. Use of penicillin and cycloheximide yielded inconsistent results in anaerobic water and in aerobic water when bacterial production was low. Production measured by inhibiting eucaryotes with cycloheximide did not always agree with [ 3 H]thymidine estimates or differential filtration methods. Laboratory experiments showed that several common freshwater protozoans continued to swim and ingest bacterium-size latex beads in the presence of the eucaryote inhibitor. Penicillin also affected grazing rates of some ciliates. The authors recommended that caution and a corroborating method be used when estimating ecologically important parameters with specific inhibitors

  8. Compensating for geographic variation in detection probability with water depth improves abundance estimates of coastal marine megafauna.

    Science.gov (United States)

    Hagihara, Rie; Jones, Rhondda E; Sobtzick, Susan; Cleguer, Christophe; Garrigue, Claire; Marsh, Helene

    2018-01-01

    The probability of an aquatic animal being available for detection is typically probability of detection is important for obtaining robust estimates of the population abundance and determining its status and trends. The dugong (Dugong dugon) is a bottom-feeding marine mammal and a seagrass community specialist. We hypothesized that the probability of a dugong being available for detection is dependent on water depth and that dugongs spend more time underwater in deep-water seagrass habitats than in shallow-water seagrass habitats. We tested this hypothesis by quantifying the depth use of 28 wild dugongs fitted with GPS satellite transmitters and time-depth recorders (TDRs) at three sites with distinct seagrass depth distributions: 1) open waters supporting extensive seagrass meadows to 40 m deep (Torres Strait, 6 dugongs, 2015); 2) a protected bay (average water depth 6.8 m) with extensive shallow seagrass beds (Moreton Bay, 13 dugongs, 2011 and 2012); and 3) a mixture of lagoon, coral and seagrass habitats to 60 m deep (New Caledonia, 9 dugongs, 2013). The fitted instruments were used to measure the times the dugongs spent in the experimentally determined detection zones under various environmental conditions. The estimated probability of detection was applied to aerial survey data previously collected at each location. In general, dugongs were least available for detection in Torres Strait, and the population estimates increased 6-7 fold using depth-specific availability correction factors compared with earlier estimates that assumed homogeneous detection probability across water depth and location. Detection probabilities were higher in Moreton Bay and New Caledonia than Torres Strait because the water transparency in these two locations was much greater than in Torres Strait and the effect of correcting for depth-specific detection probability much less. The methodology has application to visual survey of coastal megafauna including surveys using Unmanned

  9. Short-range spatial variability of soil δ15N natural abundance – effects on symbiotic N2-fixation estimates in pea

    DEFF Research Database (Denmark)

    Holdensen, Lars; Hauggaard-Nielsen, Henrik; Jensen, Erik Steen

    2007-01-01

    abundance in spring barley and N2-fixing pea was measured within the 0.15-4 m scale at flowering and at maturity. The short-range spatial variability of soil δ15N natural abundance and symbiotic nitrogen fixation were high at both growth stages. Along a 4-m row, the δ15N natural abundance in barley......-abundance are that estimates of symbiotic N2-fixation can be obtained from the natural abundance method if at least half a square meter of crop and reference plants is sampled for the isotopic analysis. In fields with small amounts of representative reference crops (weeds) it might be necessary to sow in reference crop...

  10. Fate and effect of imidacloprid on vermicompost-amended soils under dissimilar conditions: Risk for soil functions, structure, and bacterial abundance.

    Science.gov (United States)

    Castillo Diaz, Jean Manuel; Martin-Laurent, Fabrice; Beguet, Jérèmie; Nogales, Rogelio; Romero, Esperanza

    2017-02-01

    The fate and impact of pesticide on soil depend partly on the agricultural practices, such as prior treatment with pesticide and/or organic amendments. As a means of determining how the previous soil conditions can affect the fate of imidacloprid (IMI) and its effect on soil functions, experiments were made with soil samples, double-amended or not with either vine-shoot (W) or olive cake (O) vermicompost or contaminated or not with IMI. These soil samples, incubated for 3months, were placed in two microcosms (M1 with the pre-amended soils and M2 with the pre-exposed soils), treated with IMI and amended with vermicomposts and then incubated for 3months. The IMI distribution on soil fractions, sorption processes, dissipation kinetics, and biochemical as well as genetic structure and bacterial abundance were determined to assess the fate and impact of IMI on the soil. The addition of W vermicompost to the soil reduced the IMI availability. The dissipation kinetic in soils from M1 and M2 followed, respectively, a single first-order and a double first-order in parallel models. The lowest IMI persistence corresponded to the soil from M2 amended with O-vermicompost with DT50 and DT90 values of 67d and 265d, while in the other soils 90% dissipation required >512d. The vermicomposts-amended contaminated soils increased the dehydrogenase activity by 2- and 4-fold respect the control soils. However, the urease activity decreased due to the IMI influence. The changes in the bacterial community in the contaminated soil amended with O-vermicompost during incubation were correlated with the dissipation rate constant of IMI, suggesting a better tolerance of microorganisms to IMI. Thus, in the soil contaminated with IMI, the amendment with the vermicompost from olive cake can mitigate the impact of this insecticide on soil functions and promote its depuration capability while minimizing environmental risks. Copyright © 2016 Elsevier B.V. All rights reserved.

  11. Data reconstruction can improve abundance index estimation: An example using Taiwanese longline data for Pacific bluefin tuna.

    Directory of Open Access Journals (Sweden)

    Shui-Kai Chang

    Full Text Available Catch-per-unit-effort (CPUE is often the main piece of information used in fisheries stock assessment; however, the catch and effort data that are traditionally compiled from commercial logbooks can be incomplete or unreliable due to many reasons. Pacific bluefin tuna (PBF is a seasonal target species in the Taiwanese longline fishery. Since 2010, detailed catch information for each PBF has been made available through a catch documentation scheme. However, previously, only market landing data with a low coverage of logbooks were available. Therefore, several nontraditional procedures were performed to reconstruct catch and effort data from many alternative data sources not directly obtained from fishers for 2001-2015: (1 Estimating the catch number from the landing weight for 2001-2003, for which the catch number information was incomplete, based on Monte Carlo simulation; (2 deriving fishing days for 2007-2009 from voyage data recorder data, based on a newly developed algorithm; and (3 deriving fishing days for 2001-2006 from vessel trip information, based on linear relationships between fishing and at-sea days. Subsequently, generalized linear mixed models were developed with the delta-lognormal assumption for standardizing the CPUE calculated from the reconstructed data, and three-stage model evaluation was performed using (1 Akaike and Bayesian information criteria to determine the most favorable variable composition of standardization models, (2 overall R2 via cross-validation to compare fitting performance between area-separated and area-combined standardizations, and (3 system-based testing to explore the consistency of the standardized CPUEs with auxiliary data in the PBF stock assessment model. The last stage of evaluation revealed high consistency among the data, thus demonstrating improvements in data reconstruction for estimating the abundance index, and consequently the stock assessment.

  12. Carbon-enhanced Metal-poor Stars in SDSS/SEGUE. I. Carbon Abundance Estimation and Frequency of CEMP Stars

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Young Sun [NMSU, Las Cruces; Beers, Timothy C. [Michigan State U., JINA; Masseron, Thomas [Brussels U.; Plez, Bertrand [U. Montpellier 2, LUPM; Rockosi, Constance M. [Lick Observ.; Sobeck, Jennifer [Chicago U.; Yanny, Brian [Fermilab; Lucatello, Sara [Padua Observ.; Sivarani, Thirupathi [Bangalore, Indian Inst. Astrophys.; Placco, Vinicius M. [Sao Paulo U., IAG; Carollo, Daniela [Macquarie U.

    2013-10-17

    We describe a method for the determination of stellar [C/Fe] abundance ratios using low-resolution (R = 2000) stellar spectra from the SDSS and SEGUE. By means of a star-by-star comparison with a set of SDSS/SEGUE spectra with available estimates of [C/Fe] based on published high-resolution analyses, we demonstrate that we can measure [C/Fe] from SDSS/SEGUE spectra with S/N > 15 to a precision better than 0.35 dex. Using the measured carbon-to-iron abundance ratios obtained by this technique, we derive the frequency of carbon-enhanced stars ([C/Fe] > +0.7) as a function of [Fe/H], for both the SDSS/SEGUE stars and other samples from the literature. We find that the differential frequency slowly rises from almost zero to about 14% at [Fe/H] ~ -2.4, followed by a sudden increase, by about a factor of three, to 39% from [Fe/H] ~ -2.4 to [Fe/H] ~ -3.7. We also examine how the cumulative frequency of CEMP stars varies across different luminosity classes. The giant sample exhibits a cumulative CEMP frequency of 32% for [Fe/H] < -2.5, 31% for [Fe/H] < -3.0, and 33% for [Fe/H] < -3.5. For the main-sequence turnoff stars, we obtain a lower cumulative CEMP frequency, around 10% for [Fe/H] < -2.5. The dwarf population displays a large change in the cumulative frequency for CEMP stars below [Fe/H] = -2.5, jumping from 15% for [Fe/H] < -2.5 to about 75% for [Fe/H] < -3.0. When we impose a restriction with respect to distance from the Galactic mid-plane (|Z| < 5 kpc), the frequency of the CEMP giants does not increase at low metallicity ([Fe/H] < -2.5), but rather, decreases, due to the dilution of C-rich material in stars that have undergone mixing with CNO-processed material from their interiors. The frequency of CEMP stars near the main-sequence turnoff, which are not expected to have experienced mixing, increases for [Fe/H] < -3.0. [abridged

  13. Multiple marker abundance profiling

    DEFF Research Database (Denmark)

    Hooper, Cornelia M.; Stevens, Tim J.; Saukkonen, Anna

    2017-01-01

    proteins and the scoring accuracy of lower-abundance proteins in Arabidopsis. NPAS was combined with subcellular protein localization data, facilitating quantitative estimations of organelle abundance during routine experimental procedures. A suite of targeted proteomics markers for subcellular compartment...

  14. A Novel Statistical Approach for Ocean Colour Estimation of Inherent Optical Properties and Cyanobacteria Abundance in Optically Complex Waters

    Directory of Open Access Journals (Sweden)

    Monika Soja-Woźniak

    2017-04-01

    Full Text Available Eutrophication is an increasing problem in coastal waters of the Baltic Sea. Moreover, algal blooms, which occur every summer in the Gulf of Gdansk can deleteriously impact human health, the aquatic environment, and economically important fisheries, tourism, and recreation industries. Traditional laboratory-based techniques for water monitoring are expensive and time consuming, which usually results in limited numbers of observations and discontinuity in space and time. The use of hyperspectral radiometers for coastal water observation provides the potential for more detailed remote optical monitoring. A statistical approach to develop local models for the estimation of optically significant components from in situ measured hyperspectral remote sensing reflectance in case 2 waters is presented in this study. The models, which are based on empirical orthogonal function (EOF analysis and stepwise multilinear regression, allow for the estimation of parameters strongly correlated with phytoplankton (pigment concentration, absorption coefficient and coloured detrital matter abundance (absorption coefficient directly from reflectance spectra measured in situ. Chlorophyll a concentration, which is commonly used as a proxy for phytoplankton biomass, was retrieved with low error (median percent difference, MPD = 17%, root mean square error RMSE = 0.14 in log10 space and showed a high correlation with chlorophyll a measured in situ (R = 0.84. Furthermore, phycocyanin and phycoerythrin, both characteristic pigments for cyanobacteria species, were also retrieved reliably from reflectance with MPD = 23%, RMSE = 0.23, R2 = 0.77 and MPD = 24%, RMSE = 0.15, R2 = 0.74, respectively. The EOF technique proved to be accurate in the derivation of the absorption spectra of phytoplankton and coloured detrital matter (CDM, with R2 (λ above 0.83 and RMSE around 0.10. The approach was also applied to satellite multispectral remote sensing reflectance data, thus allowing

  15. Estimating juvenile Chinook salmon (Oncorhynchus tshawytscha) abundance from beach seine data collected in the Sacramento–San Joaquin Delta and San Francisco Bay, California

    Science.gov (United States)

    Perry, Russell W.; Kirsch, Joseph E.; Hendrix, A. Noble

    2016-06-17

    Resource managers rely on abundance or density metrics derived from beach seine surveys to make vital decisions that affect fish population dynamics and assemblage structure. However, abundance and density metrics may be biased by imperfect capture and lack of geographic closure during sampling. Currently, there is considerable uncertainty about the capture efficiency of juvenile Chinook salmon (Oncorhynchus tshawytscha) by beach seines. Heterogeneity in capture can occur through unrealistic assumptions of closure and from variation in the probability of capture caused by environmental conditions. We evaluated the assumptions of closure and the influence of environmental conditions on capture efficiency and abundance estimates of Chinook salmon from beach seining within the Sacramento–San Joaquin Delta and the San Francisco Bay. Beach seine capture efficiency was measured using a stratified random sampling design combined with open and closed replicate depletion sampling. A total of 56 samples were collected during the spring of 2014. To assess variability in capture probability and the absolute abundance of juvenile Chinook salmon, beach seine capture efficiency data were fitted to the paired depletion design using modified N-mixture models. These models allowed us to explicitly test the closure assumption and estimate environmental effects on the probability of capture. We determined that our updated method allowing for lack of closure between depletion samples drastically outperformed traditional data analysis that assumes closure among replicate samples. The best-fit model (lowest-valued Akaike Information Criterion model) included the probability of fish being available for capture (relaxed closure assumption), capture probability modeled as a function of water velocity and percent coverage of fine sediment, and abundance modeled as a function of sample area, temperature, and water velocity. Given that beach seining is a ubiquitous sampling technique for

  16. Variation in pre-treatment count lead time and its effect on baseline estimates of cage-level sea lice abundance.

    Science.gov (United States)

    Gautam, R; Boerlage, A S; Vanderstichel, R; Revie, C W; Hammell, K L

    2016-11-01

    Treatment efficacy studies typically use pre-treatment sea lice abundance as the baseline. However, the pre-treatment counting window often varies from the day of treatment to several days before treatment. We assessed the effect of lead time on baseline estimates, using historical data (2010-14) from a sea lice data management programme (Fish-iTrends). Data were aggregated at the cage level for three life stages: (i) chalimus, (ii) pre-adult and adult male and (iii) adult female. Sea lice counts were log-transformed, and mean counts by lead time relative to treatment day were computed and compared separately for each life stage, using linear mixed models. There were 1,658 observations (treatment events) from 56 sites in 5 Bay Management Areas. Our study showed that lead time had a significant effect on the estimated sea lice abundance, which was moderated by season. During the late summer and autumn periods, counting on the day of treatment gave significantly higher values than other days and would be a more appropriate baseline estimate, while during spring and early summer abundance estimates were comparable among counts within 5 days of treatment. A season-based lead time window may be most appropriate when estimating baseline sea lice levels. © 2016 John Wiley & Sons Ltd.

  17. The diagnostic value of c-reactive protein estimation in differentiating bacterial from viral meningitis

    International Nuclear Information System (INIS)

    Sheikh, A.

    2001-01-01

    Objective: To evaluate the efficacy of serum and CSF C-reactive protein (C-rp) in differentiating bacterial from viral meningitis. Design: An observational, respective hospital-based study. Place and duration of study: It was conducted at the Department of Medicine and Department of Pediatrics, Shaikh Zayed Postgraduate Medical Institute Lahore, Over a Period of one year between march, 1999 and March, 2000. Subject and Methods: A randomized group of thirty patients, who presented with clinical features, suggestive of meningitis, were included in the study. C-reactive protein determinations were performed by latex agglutination method on the serum and cerebrospinal fluid (CSF) of these patients. Results: In the present study, c-reactive protein was found to be a more sensitive test for differentiating bacterial from non-bacterial meningitis on initial examination than the usual conventional methods used to diagnose bacterial meningitis. CSF C-reactive protein had a greater sensitivity (92% as compared to serum C-reactive protein (71%). Conclusion: C-reactive protein determination in CSF was found to be a useful indicator of bacterial meningitis that can be used to distinguish it from viral meningitis. (author)

  18. Estimating the abundance of airborne pollen and fungal spores at variable elevations using an aircraft: how high can they fly?

    Science.gov (United States)

    Damialis, Athanasios; Kaimakamis, Evangelos; Konoglou, Maria; Akritidis, Ioannis; Traidl-Hoffmann, Claudia; Gioulekas, Dimitrios

    2017-03-16

    Airborne pollen and fungal spores are monitored mainly in highly populated, urban environments, for allergy prevention purposes. However, their sources can frequently be located outside cities' fringes with more vegetation. So as to shed light to this paradox, we investigated the diversity and abundance of airborne pollen and fungal spores at various environmental regimes. We monitored pollen and spores using an aircraft and a car, at elevations from sea level to 2,000 m above ground, in the region of Thesssaloniki, Greece. We found a total of 24 pollen types and more than 15 spore types. Pollen and spores were detected throughout the elevational transect. Lower elevations exhibited higher pollen concentrations in only half of plant taxa and higher fungal spore concentrations in only Ustilago. Pinaceae and Quercus pollen were the most abundant recorded by airplane (>54% of the total). Poaceae pollen were the most abundant via car measurements (>77% of the total). Cladosporium and Alternaria spores were the most abundant in all cases (aircraft: >69% and >17%, car: >45% and >27%, respectively). We conclude that pollen and fungal spores can be diverse and abundant even outside the main source area, evidently because of long-distance transport incidents.

  19. Pan-Antarctic analysis aggregating spatial estimates of Adélie penguin abundance reveals robust dynamics despite stochastic noise.

    Science.gov (United States)

    Che-Castaldo, Christian; Jenouvrier, Stephanie; Youngflesh, Casey; Shoemaker, Kevin T; Humphries, Grant; McDowall, Philip; Landrum, Laura; Holland, Marika M; Li, Yun; Ji, Rubao; Lynch, Heather J

    2017-10-10

    Colonially-breeding seabirds have long served as indicator species for the health of the oceans on which they depend. Abundance and breeding data are repeatedly collected at fixed study sites in the hopes that changes in abundance and productivity may be useful for adaptive management of marine resources, but their suitability for this purpose is often unknown. To address this, we fit a Bayesian population dynamics model that includes process and observation error to all known Adélie penguin abundance data (1982-2015) in the Antarctic, covering >95% of their population globally. We find that process error exceeds observation error in this system, and that continent-wide "year effects" strongly influence population growth rates. Our findings have important implications for the use of Adélie penguins in Southern Ocean feedback management, and suggest that aggregating abundance across space provides the fastest reliable signal of true population change for species whose dynamics are driven by stochastic processes.Adélie penguins are a key Antarctic indicator species, but data patchiness has challenged efforts to link population dynamics to key drivers. Che-Castaldo et al. resolve this issue using a pan-Antarctic Bayesian model to infer missing data, and show that spatial aggregation leads to more robust inference regarding dynamics.

  20. A predictive model to estimate the risk of serious bacterial infections in febrile infants

    NARCIS (Netherlands)

    Berger, RMF; Berger, MY; vanSteenselMoll, HA; DzoljicDanilovic, G; DerksenLubsen, G

    Low risk criteria have been defined to identify febrile infants unlikely to have serious bacterial infection (SBI). Using these criteria approximately 40% of all febrile infants can be defined as being at low risk. Of the remaining infants (60%) only 10%-20% have an SBI. No adequate criteria exists

  1. Estimation of Throughfall and Stemflow Bacterial Flux in a Subtropical Oak-Cedar Forest

    Science.gov (United States)

    Bittar, Thais B.; Pound, Preston; Whitetree, Ansley; Moore, L. Dean; Van Stan, John T.

    2018-02-01

    Transport pathways of microbes between ecosystem spheres (atmosphere, phyllosphere, and pedosphere) represent major fluxes in nutrient cycles and have the potential to affect microbially mediated biogeochemical processes. Novel data on bacterial fluxes from the phyllosphere to the pedosphere during rainfall via throughfall (rain dripping from/through the canopy) and stemflow (rain funneled down tree stems) are reported. Bacterial concentrations were quantified using flow cytometry and validated with quantitative polymerase chain reaction assays in rainfall samples from an oak-cedar forest in coastal Georgia (southeastern U.S.). Bacteria concentrations (cells mL-1) and storm-normalized fluxes (cells m-2 h-1, cells m-2 mm-1) were greater for cedar versus oak. Total bacterial flux was 1.5 × 1016 cells ha-1 yr-1. These previously unexamined bacterial fluxes are interpreted in the context of major elemental pools and fluxes in forests and could represent inoculum-level sources of bacteria (if alive), and organic matter and inorganic solute inputs (if lysed) to soils.

  2. [3H] Thymidine incorporation to estimate growth rates of anaerobic bacterial strains

    International Nuclear Information System (INIS)

    Winding, A.

    1992-01-01

    The incorporation of [ 3 H] thymidine by axenic cultures of anaerobic bacteria was investigated as a means to measure growth. The three fermentative strains and one of the methanogenic strains tested incorporated [ 3 H] thymidine during growth. It is concluded that the [ 3 H] thymidine incorporation method underestimates bacterial growth in anaerobic environments

  3. Can Airborne Laser Scanning (ALS and Forest Estimates Derived from Satellite Images Be Used to Predict Abundance and Species Richness of Birds and Beetles in Boreal Forest?

    Directory of Open Access Journals (Sweden)

    Eva Lindberg

    2015-04-01

    Full Text Available In managed landscapes, conservation planning requires effective methods to identify high-biodiversity areas. The objective of this study was to evaluate the potential of airborne laser scanning (ALS and forest estimates derived from satellite images extracted at two spatial scales for predicting the stand-scale abundance and species richness of birds and beetles in a managed boreal forest landscape. Multiple regression models based on forest data from a 50-m radius (i.e., corresponding to a homogenous forest stand had better explanatory power than those based on a 200-m radius (i.e., including also parts of adjacent stands. Bird abundance and species richness were best explained by the ALS variables “maximum vegetation height” and “vegetation cover between 0.5 and 3 m” (both positive. Flying beetle abundance and species richness, as well as epigaeic (i.e., ground-living beetle richness were best explained by a model including the ALS variable “maximum vegetation height” (positive and the satellite-derived variable “proportion of pine” (negative. Epigaeic beetle abundance was best explained by “maximum vegetation height” at 50 m (positive and “stem volume” at 200 m (positive. Our results show that forest estimates derived from satellite images and ALS data provide complementary information for explaining forest biodiversity patterns. We conclude that these types of remote sensing data may provide an efficient tool for conservation planning in managed boreal landscapes.

  4. Harmonizing methods for wildlife abundance estimation and pathogen detection in Europe-a questionnaire survey on three selected host-pathogen combinations

    DEFF Research Database (Denmark)

    Schulz, Jana; Ryser-Degiorgis, Marie-Pierre; Kuiken, Thijs

    2017-01-01

    Background: The need for wildlife health surveillance as part of disease control in wildlife, domestic animals and humans on the global level is widely recognized. However, the objectives, methods and intensity of existing wildlife health surveillance programs vary greatly among European countries......, resulting in a patchwork of data that are difficult to merge and compare. This survey aimed at evaluating the need and potential for data harmonization in wildlife health in Europe. The specific objective was to collect information on methods currently used to estimate host abundance and pathogen prevalence...... estimation, there is an urgent need to develop tools for the routine collection of host abundance data in a harmonized way. Wildlife health experts are encouraged to apply the harmonized APHAEA protocols in epidemiological studies in wildlife and to increase cooperation....

  5. Evaluation of alternative age-based methods for estimating relative abundance from survey data in relation to assessment models

    DEFF Research Database (Denmark)

    Berg, Casper Willestofte; Nielsen, Anders; Kristensen, Kasper

    2014-01-01

    Indices of abundance from fishery-independent trawl surveys constitute an important source of information for many fish stock assessments. Indices are often calculated using area stratified sample means on age-disaggregated data, and finally treated in stock assessment models as independent...... observations. We evaluate a series of alternative methods for calculating indices of abundance from trawl survey data (delta-lognormal, delta-gamma, and Tweedie using Generalized Additive Models) as well as different error structures for these indices when used as input in an age-based stock assessment model...... the different indices produced. The stratified mean method is found much more imprecise than the alternatives based on GAMs, which are found to be similar. Having time-varying index variances is found to be of minor importance, whereas the independence assumption is not only violated but has significant impact...

  6. Density surface fitting to estimate the abundance of humpback whales based on the NASS-95 and NASS- 2001 aerial and shipboard surveys

    Directory of Open Access Journals (Sweden)

    Charles GM Paxton

    2009-09-01

    The estimated humpback whale abundance for the region covered by the aerial and shipboard surveys in 1995 was 10,521 (95% CI: 3,716–24,636 using all available data and 7,625 (3,641–22,424 if survey blocks with 0 sightings around the Faroes and south of 60˚ N where no humpback whales were detected were excluded from the analysis. The estimate for the total survey region in 2001 was 14,662 (9,441–29,879. The high upper bounds of the confidence intervals were thought to be caused by a paucity of effort over wide areas of the survey leading to interpolation. Overall, the uncertainty associated with these abundance estimates was approximately equal to, or greater than, that associated with a stratified distance analysis. Given these wide CIs the evidence for a substantial difference in abundance between years was equivocal. However there was evidence to suggest that humpback whales congregated in shallower waters between 6–8˚C.

  7. Estimates of abundance and diversity of Shewanella genus in natural and engineered aqueous environments with newly designed primers.

    Science.gov (United States)

    Li, Bing-Bing; Cheng, Yuan-Yuan; Fan, Yang-Yang; Liu, Dong-Feng; Fang, Cai-Yun; Wu, Chao; Li, Wen-Wei; Yang, Zong-Chuang; Yu, Han-Qing

    2018-05-12

    Shewanella species have a diverse respiratory ability and wide distribution in environments and play an important role in bioremediation and the biogeochemical cycles of elements. Primers with more accuracy and broader coverage are required with consideration of the increasing number of Shewanella species and evaluation of their roles in various environments. In this work, a new primer set of 640F/815R was developed to quantify the abundance of Shewanella species in natural and engineered environments. In silico tools for primer evaluation, quantitative polymerase chain reaction (qPCR) and clone library results showed that 640F/815R had a higher specificity and coverage than the previous primers in quantitative analysis of Shewanella. Another newly developed primer pair of 211F/815cR was also adopted to analyze the Shewanella diversity and demonstrated to be the best candidate in terms of specificity and coverage. We detected more Shewanella-related species in freshwater environments and found them to be substantially different from those in marine environments. Abundance and diversity of Shewanella species in wastewater treatment plants were largely affected by the process and operating conditions. Overall, this study suggests that investigations of abundance and diversity of Shewanella in various environments are of great importance to evaluate their ecophysiology and potential ecological roles. Copyright © 2018 Elsevier B.V. All rights reserved.

  8. [Estimation of small intestinal bacterial overgrowth in patients with constipation and diarrhea irritable bowel syndrome].

    Science.gov (United States)

    Łokieć, Katarzyna; Klupińska, Grazyna; Walecka-Kapica, Ewa; Błońska, Aleksandra

    2014-05-01

    Irritable bowel syndrome (IBS) is one of the most common reason for gastroenterology consultations. The diverse in symptomatology of the disease comes from its rich etiopathogenesis. Recently studies talk about infectious etiology of IBS and because of that it is necessary to expand its diagnostics by small intestinal bacterial overgrowth (SIBO) test. The aim of this study was to evaluate the prevalence of small intestinal bacterial overgrowth in patients with constipation (IBS-C) and diarrhea (IBS-D) irritable bowel syndrome with regard to nutrition. The study involved 46 subjects (33 women and 13 men) in average age of 44 years, which were divided into two groups: diarrhea and constipation IBS. All patients underwent hydrogen breath test studying bacterial overgrowth in the small intestine. In addition, each person had fulfilled a feeding questionnaire. Student's t-test, Pearson test. It has been shown that there is no statistical significances between the prevalence of SIBO in form of diarrheal IBS and constipation IBS and gender. Average value of increments of hydrogen in breath during the test was higher in IBS-C in comparison with IBS-D, which was the highest in the intestine bacterial overgrowth in patients with IBS-C. STATISTICAL ANALYSIS showed that there is no relationship between the type and frequency of consumption of milk, meat, fruit and vegetables, sweets and coffee and the prevalence of SIBO in form of diarrhea and constipation IBS. The occurrence of constipation or diarrhea irritable bowel syndrome is not related to gender. SIBO is more common in patients with IBS-C than in IBS-D group. There is no relationship between the type of food consumed and the amount of SIBO in people with IBS. Type of food intake do not affect the status of the intestinal flora of people with IBS.

  9. More than 9,000,000 unique genes in human gut bacterial community: estimating gene numbers inside a human body.

    Science.gov (United States)

    Yang, Xing; Xie, Lu; Li, Yixue; Wei, Chaochun

    2009-06-29

    Estimating the number of genes in human genome has been long an important problem in computational biology. With the new conception of considering human as a super-organism, it is also interesting to estimate the number of genes in this human super-organism. We presented our estimation of gene numbers in the human gut bacterial community, the largest microbial community inside the human super-organism. We got 552,700 unique genes from 202 complete human gut bacteria genomes. Then, a novel gene counting model was built to check the total number of genes by combining culture-independent sequence data and those complete genomes. 16S rRNAs were used to construct a three-level tree and different counting methods were introduced for the three levels: strain-to-species, species-to-genus, and genus-and-up. The model estimates that the total number of genes is about 9,000,000 after those with identity percentage of 97% or up were merged. By combining completed genomes currently available and culture-independent sequencing data, we built a model to estimate the number of genes in human gut bacterial community. The total number of genes is estimated to be about 9 million. Although this number is huge, we believe it is underestimated. This is an initial step to tackle this gene counting problem for the human super-organism. It will still be an open problem in the near future. The list of genomes used in this paper can be found in the supplementary table.

  10. Changes in bacterial diversity and community structure following pesticides addition to soil estimated by cultivation technique.

    Science.gov (United States)

    Cycoń, Mariusz; Piotrowska-Seget, Zofia

    2009-07-01

    An experiment was conducted under laboratory conditions to investigate the effect of increasing concentrations of fenitrothion (2, 10 and 200 mg a.i./kg soil), diuron (1.5, 7.5 and 150 mg a.i./kg soil) and thiram (3.5, 17.5 and 350 mg a.i./kg soil) on soil respiration, bacterial counts and changes in culturable fraction of soil bacteria. To ascertain these changes, the community structure, bacterial biodiversity and process of colony formation, based on the r/K strategy concept, EP- and CD-indices and the FOR model, respectively, were determined. The results showed that the measured parameters were generally unaffected by the lowest dosages of pesticides, corresponding to the recommended field rates. The highest dosages of fenitrothion and thiram suppressed the peak SIR by 15-70% and 20-80%, respectively, while diuron increased respiration rate by 17-25% during the 28-day experiment. Also, the total numbers of bacteria increased in pesticide-treated soils. However, the reverse effect on day 1 and, in addition, in case of the highest dosages of insecticide on days 14 and 28, was observed. Analysis of the community structure revealed that in all soil treatments bacterial communities were generally dominated by K-strategists. Moreover, differences in the distribution of individual bacteria classes and the gradual domination of bacteria populations belonging to r-strategists during the experiment, as compared to control, was observed. However, on day 1, at the highest pesticide dosages, fast growing bacteria constituted only 1-10% of the total colonies number during 48 h of plate incubation, whereas in remaining samples they reached from 20 to 40% of total cfu. This effect, in case of fenitrothion, lasted till the end of the experiment. At the highest dosages of fenitrothion, diuron and at all dosages of thiram the decrease of biodiversity, as indicated by EP- and CD-indices on day 1, was found. At the next sampling time, no significant retarding or stimulating effect

  11. Comparison of the effects of two bongo net mesh sizes on the estimation of abundance and size of Engraulidae eggs

    Directory of Open Access Journals (Sweden)

    Jana Menegassi del Favero

    2015-06-01

    Full Text Available Abstract Studies of ichthyoplankton retention by nets of different mesh sizes are important because they help in choosing a sampler when planning collection and the establishment of correction factors. These factors make it possible to compare studies performed with nets of different mesh sizes. In most studies of mesh retention of fish eggs, the taxonomic identification is done at the family level, resulting in the loss of detailed information. We separated Engraulidae eggs, obtained with 0.333 mm and 0.505 mm mesh bongo nets at 172 oceanographic stations in the southeastern Brazilian Bight, into four groups based on their morphometric characteristics. The difference in the abundance of eggs caught by the two nets was not significant for those groups with highest volume, types A and B, but in type C (Engraulis anchoita, the most eccentric, and in type D, of the smallest volume, the difference was significant. However, no significant difference was observed in the egg size sampled with each net for E. anchoita and type D, which exhibited higher abundance in the 0.333 mm mesh net and minor axis varying from 0.45-0.71 mm, smaller than the 0.505 mm mesh aperture and the mesh diagonal.

  12. Constrained Maximum Likelihood Estimation of Relative Abundances of Protein Conformation in a Heterogeneous Mixture from Small Angle X-Ray Scattering Intensity Measurements

    Science.gov (United States)

    Onuk, A. Emre; Akcakaya, Murat; Bardhan, Jaydeep P.; Erdogmus, Deniz; Brooks, Dana H.; Makowski, Lee

    2015-01-01

    In this paper, we describe a model for maximum likelihood estimation (MLE) of the relative abundances of different conformations of a protein in a heterogeneous mixture from small angle X-ray scattering (SAXS) intensities. To consider cases where the solution includes intermediate or unknown conformations, we develop a subset selection method based on k-means clustering and the Cramér-Rao bound on the mixture coefficient estimation error to find a sparse basis set that represents the space spanned by the measured SAXS intensities of the known conformations of a protein. Then, using the selected basis set and the assumptions on the model for the intensity measurements, we show that the MLE model can be expressed as a constrained convex optimization problem. Employing the adenylate kinase (ADK) protein and its known conformations as an example, and using Monte Carlo simulations, we demonstrate the performance of the proposed estimation scheme. Here, although we use 45 crystallographically determined experimental structures and we could generate many more using, for instance, molecular dynamics calculations, the clustering technique indicates that the data cannot support the determination of relative abundances for more than 5 conformations. The estimation of this maximum number of conformations is intrinsic to the methodology we have used here. PMID:26924916

  13. Effects of a .i.Microcystis aeruginosa./i. bloom and bacterivory on bacterial abundance and activity in a eutrophic reservoir

    Czech Academy of Sciences Publication Activity Database

    Horňák, Karel; Jezbera, Jan; Šimek, Karel

    2008-01-01

    Roč. 52, č. 2 (2008), s. 107-117 ISSN 0948-3055 R&D Projects: GA ČR(CZ) GA206/08/0015; GA ČR(CZ) GA206/05/0007; GA AV ČR(CZ) 1QS600170504 Institutional research plan: CEZ:AV0Z60170517 Keywords : reservoir * Microcystis aeruginosa * bacterial activity * leucine incorporation Subject RIV: DA - Hydrology ; Limnology Impact factor: 2.190, year: 2008

  14. Abundance and activity of 16S rRNA, amoA and nifH bacterial genes during assisted phytostabilization of mine tailings

    OpenAIRE

    Nelson, Karis N.; Neilson, Julia W.; Root, Robert A.; Chorover, Jon; Maier, Raina M.

    2015-01-01

    Mine tailings in semiarid regions are highly susceptible to erosion and are sources of dust pollution and potential avenues of human exposure to toxic metals. One constraint to revegetation of tailings by phytostabilization is the absence of microbial communities critical for biogeochemical cycling of plant nutrients. The objective of this study was to evaluate specific genes as in situ indicators of biological soil response during phytoremediation. The abundance and activity of 16S rRNA, nif...

  15. Using bacterial and necrophagous insect dynamics for post-mortem interval estimation during cold season: Novel case study in Romania.

    Science.gov (United States)

    Iancu, Lavinia; Carter, David O; Junkins, Emily N; Purcarea, Cristina

    2015-09-01

    Considering the biogeographical characteristics of forensic entomology, and the recent development of forensic microbiology as a complementary approach for post-mortem interval estimation, the current study focused on characterizing the succession of necrophagous insect species and bacterial communities inhabiting the rectum and mouth cavities of swine (Sus scrofa domesticus) carcasses during a cold season outdoor experiment in an urban natural environment of Bucharest, Romania. We monitored the decomposition process of three swine carcasses during a 7 month period (November 2012-May 2013) corresponding to winter and spring periods of a temperate climate region. The carcasses, protected by wire cages, were placed on the ground in a park type environment, while the meteorological parameters were constantly recorded. The succession of necrophagous Diptera and Coleoptera taxa was monitored weekly, both the adult and larval stages, and the species were identified both by morphological and genetic characterization. The structure of bacterial communities from swine rectum and mouth tissues was characterized during the same time intervals by denaturing gradient gel electrophoresis (DGGE) and sequencing of 16S rRNA gene fragments. We observed a shift in the structure of both insect and bacterial communities, primarily due to seasonal effects and the depletion of the carcass. A total of 14 Diptera and 6 Coleoptera species were recorded on the swine carcasses, from which Calliphora vomitoria and C. vicina (Diptera: Calliphoridae), Necrobia violacea (Coleoptera: Cleridae) and Thanatophilus rugosus (Coleoptera: Silphidae) were observed as predominant species. The first colonizing wave, primarily Calliphoridae, was observed after 15 weeks when the temperature increased to 13°C. This was followed by Muscidae, Fanniidae, Anthomyiidae, Sepsidae and Piophilidae. Families belonging to Coleoptera Order were observed at week 18 when temperatures raised above 18°C, starting with

  16. Seagrass (Zostera marina) Colonization Promotes the Accumulation of Diazotrophic Bacteria and Alters the Relative Abundances of Specific Bacterial Lineages Involved in Benthic Carbon and Sulfur Cycling.

    Science.gov (United States)

    Sun, Feifei; Zhang, Xiaoli; Zhang, Qianqian; Liu, Fanghua; Zhang, Jianping; Gong, Jun

    2015-10-01

    Seagrass colonization changes the chemistry and biogeochemical cycles mediated by microbes in coastal sediments. In this study, we molecularly characterized the diazotrophic assemblages and entire bacterial community in surface sediments of a Zostera marina-colonized coastal lagoon in northern China. Higher nitrogenase gene (nifH) copy numbers were detected in the sediments from the vegetated region than in the sediments from the unvegetated region nearby. The nifH phylotypes detected were mostly affiliated with the Geobacteraceae, Desulfobulbus, Desulfocapsa, and Pseudomonas. Redundancy analysis based on terminal restriction fragment length polymorphism analysis showed that the distribution of nifH genotypes was mostly shaped by the ratio of total organic carbon to total organic nitrogen, the concentration of cadmium in the sediments, and the pH of the overlying water. High-throughput sequencing and phylogenetic analyses of bacterial 16S rRNA genes also indicated the presence of Geobacteraceae and Desulfobulbaceae phylotypes in these samples. A comparison of these results with those of previous studies suggests the prevalence and predominance of iron(III)-reducing Geobacteraceae and sulfate-reducing Desulfobulbaceae diazotrophs in coastal sedimentary environments. Although the entire bacterial community structure was not significantly different between these two niches, Desulfococcus (Deltaproteobacteria) and Anaerolineae (Chloroflexi) presented with much higher proportions in the vegetated sediments, and Flavobacteriaceae (Bacteroidetes) occurred more frequently in the bare sediments. These data suggest that the high bioavailability of organic matter (indicated by relatively lower carbon-to-nitrogen ratios) and the less-reducing anaerobic condition in vegetated sediments may favor Desulfococcus and Anaerolineae lineages, which are potentially important populations in benthic carbon and sulfur cycling in the highly productive seagrass ecosystem. Copyright © 2015

  17. Towards abundance estimates for jack mackerel in the South Pacific based on acoustic data collected by the commercial vessels

    NARCIS (Netherlands)

    Brunel, T.P.A.; Faessler, S.M.M.; Haan, de D.; Hintzen, N.T.; Kamp, van der P.H.J.; Ybema, M.S.

    2010-01-01

    Pelagic trawlers make intensive use of echosounders and therefore could potentially be used as acoustic data collection platforms. This project investigated the possibility of collecting acoustic data and its potential utility to estimate fish stock biomass. The scope of the project was to develop

  18. Comparison of two methods for estimating the abundance, diversity and habitat preference of fluvial macroinvertebrates in contrasting habitats

    NARCIS (Netherlands)

    Alonso, A.; Camargo, J.A.

    2010-01-01

    In this research we evaluate the effects of the method used for estimating the potential surface available for benthic macroinvertebrates in macrophyte and unvegetated habitats on several metrics and habitat preference of aquatic macroinvertebrates in the upper catchment of the Henares River

  19. MetaGaAP: A Novel Pipeline to Estimate Community Composition and Abundance from Non-Model Sequence Data

    Directory of Open Access Journals (Sweden)

    Christopher Noune

    2017-02-01

    Full Text Available Next generation sequencing and bioinformatic approaches are increasingly used to quantify microorganisms within populations by analysis of ‘meta-barcode’ data. This approach relies on comparison of amplicon sequences of ‘barcode’ regions from a population with public-domain databases of reference sequences. However, for many organisms relevant ‘barcode’ regions may not have been identified and large databases of reference sequences may not be available. A workflow and software pipeline, ‘MetaGaAP,’ was developed to identify and quantify genotypes through four steps: shotgun sequencing and identification of polymorphisms in a metapopulation to identify custom ‘barcode’ regions of less than 30 polymorphisms within the span of a single ‘read’, amplification and sequencing of the ‘barcode’, generation of a custom database of polymorphisms, and quantitation of the relative abundance of genotypes. The pipeline and workflow were validated in a ‘wild type’ Alphabaculovirus isolate, Helicoverpa armigera single nucleopolyhedrovirus (HaSNPV-AC53 and a tissue-culture derived strain (HaSNPV-AC53-T2. The approach was validated by comparison of polymorphisms in amplicons and shotgun data, and by comparison of predicted dominant and co-dominant genotypes with Sanger sequences. The computational power required to generate and search the database effectively limits the number of polymorphisms that can be included in a barcode to 30 or less. The approach can be used in quantitative analysis of the ecology and pathology of non-model organisms.

  20. Using SPIRAL (Single Pollen Isotope Ratio AnaLysis) to estimate C 3- and C 4-grass abundance in the paleorecord

    Science.gov (United States)

    Nelson, David M.; Hu, Feng Sheng; Scholes, Daniel R.; Joshi, Neeraj; Pearson, Ann

    2008-05-01

    C 3 and C 4 grasses differ greatly in their responses to environmental controls and influences on biogeochemical processes (e.g. water, carbon, and nutrient cycling). Difficulties in distinguishing between these two functional groups of grasses have hindered paleoecological studies of grass-dominated ecosystems. Stable carbon isotopic analysis of individual grains of grass pollen using a spooling-wire microcombustion device interfaced with an isotope-ratio mass spectrometer holds promise for improving C 3 and C 4 grass reconstructions. This technique, SPIRAL (Single Pollen Isotope Ratio AnaLysis), has only been evaluated using pollen of known C 3 and C 4 grasses. To test the ability of SPIRAL to reproduce the abundance of C 3 and C 4 grasses on the landscape, we measured δ13C values of > 1500 individual grains of grass pollen isolated from the surface sediments of ten lakes in areas that span a large gradient of C 3- and C 4-grass abundance, as determined from vegetation surveys. Results indicate a strong positive correlation between the δ13C-based estimates of % C 4-grass pollen and the abundance of C 4 grasses on the landscape. The % C 4-grass pollen slightly underestimates the actual abundance of C 4 grasses at sites with high proportions of C 4 grasses, which can be corrected using regression analysis. Comparison of the % C 4-grass pollen with C/N and δ13C measurements of bulk organic matter illustrates the distinct advantages of grass-pollen δ13C as a proxy for distinguishing C 3 and C 4 shifts within the grass family. Thus SPIRAL promises to advance our understanding of grassland ecology and evolution.

  1. Distribution and abundance of archaeal and bacterial ammonia oxidizers in the sediments of the Dongjiang River, a drinking water supply for Hong Kong.

    Science.gov (United States)

    Sun, Wei; Xia, Chunyu; Xu, Meiying; Guo, Jun; Wang, Aijie; Sun, Guoping

    2013-01-01

    Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play important roles in nitrification. However, limited information about the characteristics of AOA and AOB in the river ecosystem is available. The distribution and abundance of AOA and AOB in the sediments of the Dongjiang River, a drinking water source for Hong Kong, were investigated by clone library analysis and quantitative real-time PCR. Phylogenetic analysis showed that Group 1.1b- and Group 1.1b-associated sequences of AOA predominated in sediments with comparatively high carbon and nitrogen contents (e.g. total carbon (TC) >13 g kg(-1) sediment, NH4(+)-N >144 mg kg(-1) sediment), while Group 1.1a- and Group 1.1a-associated sequences were dominant in sediments with opposite conditions (e.g. TC <4 g kg(-1) sediment, NH4(+)-N <93 mg kg(-1) sediment). Although Nitrosomonas- and Nitrosospira-related sequences of AOB were detected in the sediments, nearly 70% of the sequences fell into the Nitrosomonas-like B cluster, suggesting similar sediment AOB communities along the river. Higher abundance of AOB than AOA was observed in almost all of the sediments in the Dongjiang River, while significant correlations were only detected between the distribution of AOA and the sediment pH and TC, which suggested that AOA responded more sensitively than AOB to variations of environmental factors. These results extend our knowledge about the environmental responses of ammonia oxidizers in the river ecosystem.

  2. Acoustic surveys for juvenile anchovy in the Bay of Biscay: Abundance estimate as an indicator of the next year's recruitment and spatial distribution patterns

    KAUST Repository

    Boyra, Guillermo; Martí nez, U.; Cotano, Unai; Begoñ a Santos, Maria; Irigoien, Xabier; Uriarte, André s

    2013-01-01

    A series of acoustic surveys (JUVENA) began in 2003 targeting juvenile anchovy (Engraulis encrasicolus) in the Bay of Biscay. A specific methodology was designed for mapping and estimating juvenile abundance annually, four months after the spawning season. After eight years of the survey, a consistent picture of the spatial pattern of the juvenile anchovy has emerged. Juveniles show a vertical and horizontal distribution pattern that depends on size. The younger individuals are found isolated from other species in waters closer to the surface, mainly off the shelf within the mid-southern region of the bay. The largest juveniles are usually found deeper and closer to the shore in the company of adult anchovy and other pelagic species. In these eight years, the survey has covered a wide range of juvenile abundances, and the estimates show a significant positive relationship between the juvenile biomasses and the one-year-old recruits of the following year. This demonstrates that the JUVENA index provides an early indication of the strength of next year's recruitment to the fishery and can therefore be used to improve the management advice for the fishery of this short-lived species. © 2013 International Council for the Exploration of the Sea.

  3. Acoustic surveys for juvenile anchovy in the Bay of Biscay: Abundance estimate as an indicator of the next year's recruitment and spatial distribution patterns

    KAUST Repository

    Boyra, Guillermo

    2013-08-16

    A series of acoustic surveys (JUVENA) began in 2003 targeting juvenile anchovy (Engraulis encrasicolus) in the Bay of Biscay. A specific methodology was designed for mapping and estimating juvenile abundance annually, four months after the spawning season. After eight years of the survey, a consistent picture of the spatial pattern of the juvenile anchovy has emerged. Juveniles show a vertical and horizontal distribution pattern that depends on size. The younger individuals are found isolated from other species in waters closer to the surface, mainly off the shelf within the mid-southern region of the bay. The largest juveniles are usually found deeper and closer to the shore in the company of adult anchovy and other pelagic species. In these eight years, the survey has covered a wide range of juvenile abundances, and the estimates show a significant positive relationship between the juvenile biomasses and the one-year-old recruits of the following year. This demonstrates that the JUVENA index provides an early indication of the strength of next year\\'s recruitment to the fishery and can therefore be used to improve the management advice for the fishery of this short-lived species. © 2013 International Council for the Exploration of the Sea.

  4. Abundance, Distribution and Estimated Consumption (kg fish) of Piscivorous Birds Along the Yakima River, Washington State; Implications for Fisheries Management, 2002 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Major, III, Walter; Grassley, James M.; Ryding, Kristen E. (University of Washington, Quantitive Ecology Program, Seattle, WA)

    2003-05-01

    This report is divided into two chapters. The abstract for chapter one is--Understanding of the abundance and spatial and temporal distributions of piscivorous birds and their potential consumption of fish is an increasingly important aspect of fisheries management. During 1999-2002, we determined the abundance and distribution and estimated the maximum consumption (kg biomass) of fish-eating birds along the length of the Yakima River in Washington State. Sixteen different species were observed during the 4-yr study, but only half of those were observed during all years. Abundance and estimated consumption of fish within the upper and middle sections of the river were dominated by common mergansers (Mergus merganser) which are known to breed in those reaches. Common mergansers accounted for 78 to 94% of the estimated total fish take for the upper river or approximately 28,383 {+-} 1,041 kg over the 4 yrs. A greater diversity of avian piscivores occurred in the lower river and potential impacts to fish populations was more evenly distributed among the species. In 1999-2000, great blue herons potentially accounted for 29 and 36% of the fish consumed, whereas in 2001-2002 American white pelicans accounted for 53 and 55%. We estimated that approximately 75,878 {+-} 6,616 kg of fish were consumed by piscivorous birds in the lower sections of the river during the study. Bird assemblages differed spatially along the river with a greater abundance of colonial nesting species within the lower sections of the river, especially during spring and the nesting season. The abundance of avian piscivores and consumption estimates are discussed within the context of salmonid supplementation efforts on the river and juvenile out-migration. The abstract for chapter two is--Consumption of fish by piscivorous birds may be a significant constraint on efforts to enhance salmonid populations within tributaries to the Columbia River in Washington State. During 1999-2002, we determined the

  5. Estimates of Free-tropospheric NO2 Abundance from the Aura Ozone Monitoring Instrument (OMI) Using Cloud Slicing Technique

    Science.gov (United States)

    Choi, S.; Joiner, J.; Krotkov, N. A.; Choi, Y.; Duncan, B. N.; Celarier, E. A.; Bucsela, E. J.; Vasilkov, A. P.; Strahan, S. E.; Veefkind, J. P.; Cohen, R. C.; Weinheimer, A. J.; Pickering, K. E.

    2013-12-01

    Total column measurements of NO2 from space-based sensors are of interest to the atmospheric chemistry and air quality communities; the relatively short lifetime of near-surface NO2 produces satellite-observed hot-spots near pollution sources including power plants and urban areas. However, estimates of NO2 concentrations in the free-troposphere, where lifetimes are longer and the radiative impact through ozone formation is larger, are severely lacking. Such information is critical to evaluate chemistry-climate and air quality models that are used for prediction of the evolution of tropospheric ozone and its impact of climate and air quality. Here, we retrieve free-tropospheric NO2 volume mixing ratio (VMR) using the cloud slicing technique. We use cloud optical centroid pressures (OCPs) as well as collocated above-cloud vertical NO2 columns (defined as the NO2 column from top of the atmosphere to the cloud OCP) from the Ozone Monitoring Instrument (OMI). The above-cloud NO2 vertical columns used in our study are retrieved independent of a priori NO2 profile information. In the cloud-slicing approach, the slope of the above-cloud NO2 column versus the cloud optical centroid pressure is proportional to the NO2 volume mixing ratio (VMR) for a given pressure (altitude) range. We retrieve NO2 volume mixing ratios and compare the obtained NO2 VMRs with in-situ aircraft profiles measured during the NASA Intercontinental Chemical Transport Experiment Phase B (INTEX-B) campaign in 2006. The agreement is good when proper data screening is applied. In addition, the OMI cloud slicing reports a high NO2 VMR where the aircraft reported lightning NOx during the Deep Convection Clouds and Chemistry (DC3) campaign in 2012. We also provide a global seasonal climatology of free-tropospheric NO2 VMR in cloudy conditions. Enhanced NO2 in free troposphere commonly appears near polluted urban locations where NO2 produced in the boundary layer may be transported vertically out of the

  6. Proposed Method for Estimating Health-Promoting Glucosinolates and Hydrolysis Products in Broccoli (Brassica oleracea var. italica) Using Relative Transcript Abundance.

    Science.gov (United States)

    Becker, Talon M; Jeffery, Elizabeth H; Juvik, John A

    2017-01-18

    Due to the importance of glucosinolates and their hydrolysis products in human nutrition and plant defense, optimizing the content of these compounds is a frequent breeding objective for Brassica crops. Toward this goal, we investigated the feasibility of using models built from relative transcript abundance data for the prediction of glucosinolate and hydrolysis product concentrations in broccoli. We report that predictive models explaining at least 50% of the variation for a number of glucosinolates and their hydrolysis products can be built for prediction within the same season, but prediction accuracy decreased when using models built from one season's data for prediction of an opposing season. This method of phytochemical profile prediction could potentially allow for lower phytochemical phenotyping costs and larger breeding populations. This, in turn, could improve selection efficiency for phase II induction potential, a type of chemopreventive bioactivity, by allowing for the quick and relatively cheap content estimation of phytochemicals known to influence the trait.

  7. Raft and floating radio frequency identification (RFID) antenna systems for detecting and estimating abundance of PIT-tagged fish in rivers

    Science.gov (United States)

    Fetherman, Eric R.; Avila, Brian W.; Winkelman, Dana L.

    2016-01-01

    Portable radio frequency identification (RFID) PIT tag antenna systems are increasingly being used in studies examining aquatic animal movement, survival, and habitat use, and their design flexibility permits application in a wide variety of settings. We describe the construction, use, and performance of two portable floating RFID PIT tag antenna systems designed to detect fish that were unavailable for recapture using stationary antennas or electrofishing. A raft antenna system was designed to detect and locate PIT-tagged fish in relatively long (i.e., ≥10 km) river reaches, and consisted of two antennas: (1) a horizontal antenna (4 × 1.2 m) installed on the bottom of the raft and used to detect fish in shallower river reaches (raft antenna system, which covered 21% of the wetted area, was 0.14 ± 0.14. A shore-deployed floating antenna (14.6 × 0.6 m), which covered 100% of the wetted area, was designed for use by two operators for detecting and locating PIT-tagged fish in shorter (i.e., <2 km) river reaches. Detection distances of the shore-deployed floating antenna were between 0.7 and 0.8 m, and detection probabilities during field deployment in the St. Vrain River exceeded 0.52. The shore-deployed floating antenna was also used to estimate abundance of PIT-tagged fish. Results suggest that the shore-deployed floating antenna could be used as an alternative to estimating abundance using traditional sampling methods such as electrofishing.

  8. World Health Organization Estimates of the Global and Regional Disease Burden of 22 Foodborne Bacterial, Protozoal, and Viral Diseases, 2010 : A Data Synthesis

    NARCIS (Netherlands)

    Kirk, Martyn D; Pires, Sara M; Black, Robert E; Caipo, Marisa; Crump, John A; Devleesschauwer, Brecht; Döpfer, Dörte; Fazil, Aamir; Fischer-Walker, Christa L; Hald, Tine; Hall, Aron J; Keddy, Karen H; Lake, Robin J; Lanata, Claudio F; Torgerson, Paul R; Havelaar, Arie H|info:eu-repo/dai/nl/072306122; Angulo, Frederick J

    2015-01-01

    BACKGROUND: Foodborne diseases are important worldwide, resulting in considerable morbidity and mortality. To our knowledge, we present the first global and regional estimates of the disease burden of the most important foodborne bacterial, protozoal, and viral diseases. METHODS AND FINDINGS: We

  9. World Health Organization Estimates of the Global and Regional Disease Burden of 22 Foodborne Bacterial, Protozoal, and Viral Diseases, 2010: A Data Synthesis

    DEFF Research Database (Denmark)

    Kirk, Martyn D.; Pires, Sara Monteiro; Black, Robert E.

    2015-01-01

    Foodborne diseases are important worldwide, resulting in considerable morbidity and mortality. To our knowledge, we present the first global and regional estimates of the disease burden of the most important foodborne bacterial, protozoal, and viral diseases. We synthesized data on the number of ...

  10. Validity of the tritiated thymidine method for estimating bacterial growth rates: measurement of isotope dilution during DNA synthesis

    International Nuclear Information System (INIS)

    Pollard, P.C.; Moriarty, D.J.W.

    1984-01-01

    The rate of tritiated thymidine incorporation into DNA was used to estimate bacterial growth rates in aquatic environments. To be accurate, the calculation of growth rates has to include a factor for the dilution of isotope before incorporation. The validity of an isotope dilution analysis to determine this factor was verified in experiments reported here with cultures of a marine bacterium growing in a chemostat. Growth rates calculated from data on chemostat dilution rates and cell density agreed well with rates calculated by tritiated thymidine incorporation into DNA and isotope dilution analysis. With sufficiently high concentrations of exogenous thymidine, de novo synthesis of deoxythymidine monophosphate was inhibited, thereby preventing the endogenous dilution of isoope. The thymidine technique was also shown to be useful for measuring growth rates of mixed suspensions of bacteria growing anaerobically. Thymidine was incorporated into the DNA of a range of marine pseudomonads that were investigated. Three species did not take up thymidine. The common marine cyanobacterium Synechococcus species did not incorporate thymidine into DNA

  11. Combining split-beam and dual-frequency identification sonars to estimate abundance of anadromous fishes in the Roanoke River, North Carolina

    Science.gov (United States)

    Hughes, Jacob B.; Hightower, Joseph E.

    2015-01-01

    Riverine hydroacoustic techniques are an effective method for evaluating abundance of upstream migrating anadromous fishes. To use these methods in the Roanoke River, North Carolina, at a wide site with uneven bottom topography, we used a combination of split-beam sonar and dual-frequency identification sonar (DIDSON) deployments. We aimed a split-beam sonar horizontally to monitor midchannel and near-bottom zones continuously over the 3-month spring monitoring periods in 2010 and 2011. The DIDSON was rotated between seven cross-channel locations (using a vertical aim) and nearshore regions (using horizontal aims). Vertical deployment addressed blind spots in split-beam coverage along the bottom and provided reliable information about the cross-channel and vertical distributions of upstream migrants. Using a Bayesian framework, we modeled sonar counts within four cross-channel strata and apportioned counts by species using species proportions from boat electrofishing and gill netting. Modeled estimates (95% credible intervals [CIs]) of total upstream migrants in 2010 and 2011 were 2.5 million (95% CI, 2.4–2.6 million) and 3.6 million (95% CI, 3.4–3.9 million), respectively. Results indicated that upstream migrants are extremely shore- and bottom-oriented, suggesting nearshore DIDSON monitoring improved the accuracy and precision of our estimates. This monitoring protocol and model may be widely applicable to river systems regardless of their cross-sectional width or profile.

  12. Urine Proteomics Revealed a Significant Correlation Between Urine-Fibronectin Abundance and Estimated-GFR Decline in Patients with Bardet-Biedl Syndrome

    Directory of Open Access Journals (Sweden)

    Marianna Caterino

    2018-03-01

    Full Text Available Background:/Aims: Renal disease is a common cause of morbidity in patients with Bardet-Biedl syndrome (BBS, however the severity of kidney dysfunction is highly variable. To date, there is little information on the pathogenesis, the risk and predictor factors for poor renal outcome in this setting. The present study aims to analyze the spectrum of urinary proteins in BBS patients, in order to potentially identify 1 disease-specific proteomic profiles that may differentiate the patients from normal subjects; 2 urinary markers of renal dysfunction. Methods: Fourteen individuals (7 males and 7 females with a clinical diagnosis of BBS have been selected in this study. A pool of 10 aged-matched males and 10 aged-matched females have been used as controls for proteomic analysis. The glomerular filtration rate (eGFR has been estimated using the CKD-EPI formula. Variability of eGFR has been retrospectively assessed calculating average annual eGFR decline (ΔeGFR in a mean follow-up period of 4 years (3-7. Results: 42 proteins were significantly over- or under-represented in BBS patients compared with controls; the majority of these proteins are involved in fibrosis, cell adhesion and extracellular matrix organization. Statistic studies revealed a significant correlation between urine fibronectin (u-FN (r2=0.28; p<0.05, CD44 antigen (r2 =0.35; p<0.03 and lysosomal alfa glucosidase ( r20.27; p<0.05 abundance with the eGFR. In addition, u-FN (r2 =0.2389; p<0.05 was significantly correlated with ΔeGFR. Conclusion: The present study demonstrates that urine proteome of BBS patients differs from that of normal subjects; in addition, kidney dysfunction correlated with urine abundance of known markers of renal fibrosis.

  13. Understanding Aggregation and Estimating Seasonal Abundance of Chrysaora quinquecirrha Medusae from a Fixed-station Time Series in the Choptank River, Chesapeake Bay

    Science.gov (United States)

    Tay, J.; Hood, R. R.

    2016-02-01

    Although jellyfish exert strong control over marine plankton dynamics (Richardson et al. 2009, Robison et al. 2014) and negatively impact human commercial and recreational activities (Purcell et al. 2007, Purcell 2012), jellyfish biomass is not well quantified due primarily to sampling difficulties with plankton nets or fisheries trawls (Haddock 2004). As a result, some of the longest records of jellyfish are visual shore-based surveys, such as the fixed-station time series of Chrysaora quinquecirrha that began in 1960 in the Patuxent River in Chesapeake Bay, USA (Cargo and King 1990). Time series counts from fixed-station surveys capture two signals: 1) demographic change at timescales on the order of reproductive processes and 2) spatial patchiness at shorter timescales as different parcels of water move in and out of the survey area by tidal and estuarine advection and turbulent mixing (Lee and McAlice 1979). In this study, our goal was to separate these two signals using a 4-year time series of C. quinquecirrha medusa counts from a fixed-station in the Choptank River, Chesapeake Bay. Idealized modeling of tidal and estuarine advection was used to conceptualize the sampling scheme. Change point and time series analysis was used to detect demographic changes. Indices of aggregation (Negative Binomial coefficient, Taylor's Power Law coefficient, and Morisita's Index) were calculated to describe the spatial patchiness of the medusae. Abundance estimates revealed a bloom cycle that differed in duration and magnitude for each of the study years. Indices of aggregation indicated that medusae were aggregated and that patches grew in the number of individuals, and likely in size, as abundance increased. Further inference from the conceptual modeling suggested that medusae patch structure was generally homogenous over the tidal extent. This study highlights the benefits of using fixed-station shore-based surveys for understanding the biology and ecology of jellyfish.

  14. Partial least squares methods for spectrally estimating lunar soil FeO abundance: A stratified approach to revealing nonlinear effect and qualitative interpretation

    Science.gov (United States)

    Li, Lin

    2008-12-01

    Partial least squares (PLS) regressions were applied to lunar highland and mare soil data characterized by the Lunar Soil Characterization Consortium (LSCC) for spectral estimation of the abundance of lunar soil chemical constituents FeO and Al2O3. The LSCC data set was split into a number of subsets including the total highland, Apollo 16, Apollo 14, and total mare soils, and then PLS was applied to each to investigate the effect of nonlinearity on the performance of the PLS method. The weight-loading vectors resulting from PLS were analyzed to identify mineral species responsible for spectral estimation of the soil chemicals. The results from PLS modeling indicate that the PLS performance depends on the correlation of constituents of interest to their major mineral carriers, and the Apollo 16 soils are responsible for the large errors of FeO and Al2O3 estimates when the soils were modeled along with other types of soils. These large errors are primarily attributed to the degraded correlation FeO to pyroxene for the relatively mature Apollo 16 soils as a result of space weathering and secondary to the interference of olivine. PLS consistently yields very accurate fits to the two soil chemicals when applied to mare soils. Although Al2O3 has no spectrally diagnostic characteristics, this chemical can be predicted for all subset data by PLS modeling at high accuracies because of its correlation to FeO. This correlation is reflected in the symmetry of the PLS weight-loading vectors for FeO and Al2O3, which prove to be very useful for qualitative interpretation of the PLS results. However, this qualitative interpretation of PLS modeling cannot be achieved using principal component regression loading vectors.

  15. Raft and floating radio frequency identification (RFID) antenna systems for detecting and estimating abundance of PIT-tagged fish in rivers

    Science.gov (United States)

    Fetherman, Eric R.; Avila, Brian W.; Winkelman, Dana L.

    2016-01-01

    Portable radio frequency identification (RFID) PIT tag antenna systems are increasingly being used in studies examining aquatic animal movement, survival, and habitat use, and their design flexibility permits application in a wide variety of settings. We describe the construction, use, and performance of two portable floating RFID PIT tag antenna systems designed to detect fish that were unavailable for recapture using stationary antennas or electrofishing. A raft antenna system was designed to detect and locate PIT-tagged fish in relatively long (i.e., ≥10 km) river reaches, and consisted of two antennas: (1) a horizontal antenna (4 × 1.2 m) installed on the bottom of the raft and used to detect fish in shallower river reaches (<1 m), and (2) a vertical antenna (2.7 × 1.2 m) for detecting fish in deeper pools (≥1 m). Detection distances of the horizontal antenna were between 0.7 and 1.0 m, and detection probability was 0.32 ± 0.02 (mean ± SE) in a field test using rocks marked with 32-mm PIT tags. Detection probability of PIT-tagged fish in the Cache la Poudre River, Colorado, using the raft antenna system, which covered 21% of the wetted area, was 0.14 ± 0.14. A shore-deployed floating antenna (14.6 × 0.6 m), which covered 100% of the wetted area, was designed for use by two operators for detecting and locating PIT-tagged fish in shorter (i.e., <2 km) river reaches. Detection distances of the shore-deployed floating antenna were between 0.7 and 0.8 m, and detection probabilities during field deployment in the St. Vrain River exceeded 0.52. The shore-deployed floating antenna was also used to estimate abundance of PIT-tagged fish. Results suggest that the shore-deployed floating antenna could be used as an alternative to estimating abundance using traditional sampling methods such as electrofishing.

  16. Bacterial Community Structure in a Mollisol Under Long-Term Natural Restoration, Cropping, and Bare Fallow History Estimated by PCR-DGGE

    Institute of Scientific and Technical Information of China (English)

    WANG Guang-Hua; JIN Jian; LIU Jun-Jie; CHEN Xue-Li; LIU Ju-Dong; LIU Xiao-Bing

    2009-01-01

    Soil microbial biomass and community structures are commonly used as indicators for soil quality and fertility.A investigation was performed to study the effects of long-term natural restoration,cropping,and bare fallow managements on the soil microbial biomass and bacterial community structures in depths of 0-10,20-30,and 40-50 cm in a black soil (Mollisol).Microbial biomass was estimated from chloroform fumigation-extraction,and bacterial community structures were determined by analysis of 16S rDNA using polymerase chain reaction-denaturing gradient gel electrophoresis (PCRDGGE).Experimental results showed that microbial biomass significantly declined with soil depth in the managements of restoration and cropping,but not in the bare fallow.DGGE profiles indicated that the band number in top 0-10 cm soils was less than that in depth of 20-30 or 40-50 cm.These suggested that the microbial population was high but the bacterial community structure was simple in the topsoil.Cluster and principle component analysis based on DGGE banding patterns showed that the bacterial community structure was affected by soil depth more primarily than by managements,and the succession of bacterial community as increase of soil depth has a similar tendency in the three managements.Fourteen predominating DGGE bands were excised and sequenced,in which 6 bands were identified as the taxa of Verrucomicrobia,2 bands as Actinobacteria,2 bands as α-Proteobacteria,and the other 4 bands as δ-Proteobacteria,Acidobacteria,Nitrospira,and unclassified bacteria.In addition,the sequences of 11 DGGE bands were closely related to uncultured bacteria.Thus,the bacterial community structure in black soil was stable,and the predominating bacterial groups were uncultured.

  17. Modeling number of bacteria per food unit in comparison to bacterial concentration in quantitative risk assessment: impact on risk estimates.

    Science.gov (United States)

    Pouillot, Régis; Chen, Yuhuan; Hoelzer, Karin

    2015-02-01

    When developing quantitative risk assessment models, a fundamental consideration for risk assessors is to decide whether to evaluate changes in bacterial levels in terms of concentrations or in terms of bacterial numbers. Although modeling bacteria in terms of integer numbers may be regarded as a more intuitive and rigorous choice, modeling bacterial concentrations is more popular as it is generally less mathematically complex. We tested three different modeling approaches in a simulation study. The first approach considered bacterial concentrations; the second considered the number of bacteria in contaminated units, and the third considered the expected number of bacteria in contaminated units. Simulation results indicate that modeling concentrations tends to overestimate risk compared to modeling the number of bacteria. A sensitivity analysis using a regression tree suggests that processes which include drastic scenarios consisting of combinations of large bacterial inactivation followed by large bacterial growth frequently lead to a >10-fold overestimation of the average risk when modeling concentrations as opposed to bacterial numbers. Alternatively, the approach of modeling the expected number of bacteria in positive units generates results similar to the second method and is easier to use, thus potentially representing a promising compromise. Published by Elsevier Ltd.

  18. Using GIS mapping of the extent of nearshore rocky reefs to estimate the abundance and reproductive output of important fishery species.

    Directory of Open Access Journals (Sweden)

    Jeremy T Claisse

    Full Text Available Kelp Bass (Paralabrax clathratus and California Sheephead (Semicossyphus pulcher are economically and ecologically valuable rocky reef fishes in southern California, making them likely indicator species for evaluating resource management actions. Multiple spatial datasets, aerial and satellite photography, underwater observations and expert judgment were used to produce a comprehensive map of nearshore natural rocky reef habitat for the Santa Monica Bay region (California, USA. It was then used to examine the relative contribution of individual reefs to a regional estimate of abundance and reproductive potential of the focal species. For the reefs surveyed for fishes (i.e. 18 out of the 22 in the region, comprising 82% the natural rocky reef habitat 30% was produced from a relatively small proportion of the regional reef area (c. 10%. Natural nearshore rocky reefs make up only 11% of the area in the newly designated MPAs in this region, but results provide some optimism that regional fisheries could benefit through an increase in overall reproductive output, if adequate increases in size structure of targeted species are realized.

  19. Evaluation of single and two-stage adaptive sampling designs for estimation of density and abundance of freshwater mussels in a large river

    Science.gov (United States)

    Smith, D.R.; Rogala, J.T.; Gray, B.R.; Zigler, S.J.; Newton, T.J.

    2011-01-01

    Reliable estimates of abundance are needed to assess consequences of proposed habitat restoration and enhancement projects on freshwater mussels in the Upper Mississippi River (UMR). Although there is general guidance on sampling techniques for population assessment of freshwater mussels, the actual performance of sampling designs can depend critically on the population density and spatial distribution at the project site. To evaluate various sampling designs, we simulated sampling of populations, which varied in density and degree of spatial clustering. Because of logistics and costs of large river sampling and spatial clustering of freshwater mussels, we focused on adaptive and non-adaptive versions of single and two-stage sampling. The candidate designs performed similarly in terms of precision (CV) and probability of species detection for fixed sample size. Both CV and species detection were determined largely by density, spatial distribution and sample size. However, designs did differ in the rate that occupied quadrats were encountered. Occupied units had a higher probability of selection using adaptive designs than conventional designs. We used two measures of cost: sample size (i.e. number of quadrats) and distance travelled between the quadrats. Adaptive and two-stage designs tended to reduce distance between sampling units, and thus performed better when distance travelled was considered. Based on the comparisons, we provide general recommendations on the sampling designs for the freshwater mussels in the UMR, and presumably other large rivers.

  20. Estimation of decay rates for fecal indicator bacteria and bacterial pathogens in agricultural field-applied manure

    Science.gov (United States)

    Field-applied manure is an important source of pathogenic exposure in surface water bodies for humans and ecological receptors. We analyzed the persistence and decay of fecal indicator bacteria and bacterial pathogens from three sources (cattle, poultry, swine) for agricultural f...

  1. Quantitative estimation of net rates of production of bacterial and protozoal nitrogen and their interconversion in the rumen

    International Nuclear Information System (INIS)

    El-Fouly, H.A.

    1983-01-01

    A technique is described using 35 S-labelled bacteria or protozoa by which the rates of production of microbial and protozoal protein N may be calculated. The results indicate an average microbial protein yield of about 13.7gN.d -1 in sheep maintained on a diet consisting largely of cottonseed cake and wheat and rice bran. Evidence is presented that protozoa made little contribution to the microbial protein-N leaving the rumen. Also, the average rate of N flow from the protozoal to the bacterial pool was about 3.5g.d -1 , whereas about 1.4g.d -1 of bacterial N was consumed by protozoa. (author)

  2. Classic, fuzzy and predictive dtc strategies for the PMSM using the bacterial foraging algorithmas an online parameter estimator

    Directory of Open Access Journals (Sweden)

    Gabriel Noriega

    2012-01-01

    Full Text Available Este trabajo presenta una comparación entre cuatro técnicas de control directo de par (DTC aplicadas al accionamiento de la máquina sincrónica deimán permanente: Clásico, Modificado con un sistema de inferencia difusa, Predictivo y Predictivo con inferencia difusa. La estimación de parámetros para las estrategias predictivas es realizado utilizando un algoritmo de búsqueda poblacional basado en Forraje Bacterial, el cuál es capaz de calcular en línea los parámetros de la máquina sincrónica de imán permanente. Los resultados experimentales del par eléctrico y de los enlaces de flujo del estator muestran mejoras significativas para las estrategias predictivas que utilizan algoritmos de estimación paramétrica mediante Forraje Bacterial cuando se comparan con técnicas no predictivas.

  3. A short review of the distribution of short-beaked common dolphins (Delphinus delphis in the central and eastern North Atlantic with an abundance estimate for part of this area

    Directory of Open Access Journals (Sweden)

    Ana Cañadas

    2009-09-01

    Full Text Available This paper uses data from 3 programmes: (1 the North Atlantic Sightings Surveys (NASS surveys undertaken throughout much of the central and eastern North Atlantic north of about 40° N in 1987, 1989, 1995 and 2001; (2 the MICA-93 programme; and (3 the north eastern Atlantic segment of the Small Cetacean Abundance in the North Sea (SCANS survey in 1994. The data from all surveys were used to examine the distribution of common dolphins in the NE Atlantic. No sightings were made north of 57° N. An initial attempt to examine distribution against 4 potential non biological explanatory variables was made. A simple interpretation of the preliminary analyses presented here is that the primary areas for groups of common dolphins were in waters over 15° C and depths of 400-1,000 m (there does appear a link with shelf features, between around 49°-55° N especially between 20°-30°W. An illustrative example of spatial modelling is presented. Only for 1 year (and part of the total survey area were there sufficient data to attempt to estimate abundance: 1995. The estimated abundance in the W Block of the NASS-95 Faroese survey was 273,159 (cv=0.26; 95% CI=153,392-435,104 short-beaked common dolphins. This estimate is corrected for animals missed on the trackline (g(0 and for responsive movement.

  4. Bacterial diversity in a soil sample from Uranium mining waste pile as estimated via a culture-independent 16S rDNA approach

    International Nuclear Information System (INIS)

    Satchanska, G.; Golovinsky, E.; Selenska-Pobell, S.

    2004-01-01

    Bacterial diversity was studied in a soil sample collected from a uranium mining waste pile situated near the town of Johanngeorgenstadt, Germany. As estimated by ICP-MS analysis the studied sample was highly contaminated with Fe, Al, Mn, Zn, As, Pb and U. The 16S rDNA retrieval, applied in this study, demonstrated that more than the half of the clones of the constructed 16S rDNA library were represented by individual RFLP profiles. This indicates that the composition of the bacterial community in the sample was very complex. However, several 16S rDNA RFLP groups were found to be predominant and they were subjected to a sequence analysis. The most predominant group, which represented about 13% of the clones of the 16S rDNA library, was affiliated with the Holophaga/Acidobacterium phylum. Significant was also the number of the proteobacterial sequences which were distributed in one predominant α-proteobacterial cluster representing 11% of the total number of clones and in two equal-sized β- and γ-proteobacterial clusters representing each 6% of the clones. Two smaller groups representing both 2% of the clones were affiliated with Nitrospira and with the novel division WS3. Three of the analysed sequences were evaluated as a novel, not yet described lineage and one as a putative chimera. (authors)

  5. Synthesis of multiple data structures for improved accuracy of abundance and demographic estimates form white-tailed at Savannah River Site.

    Energy Technology Data Exchange (ETDEWEB)

    Conroy, Michael J. [USDA Forest Service, New Ellenton, SC (United States)

    2014-12-08

    The goal of this study was to provide a framework for combining existing data (from camera trapping, harvest surveys, and spotlight counts) into an integrated system that produces the most accurate estimates possible for use in setting harvest goals. A summary of the key data components that were available is included.

  6. The regional abundance and size distribution of lakes and reservoirs in the United States and implication for estimates of global lake extent

    Science.gov (United States)

    McDonald, Cory P.; Rover, Jennifer; Stets, Edward G.; Striegl, Robert G.

    2012-01-01

    We analyzed complete geospatial data for the 3.5 million lakes and reservoirs larger than 0.001 km2, with a combined surface area of 131,000 km2, in the contiguous United States (excluding the Laurentian Great Lakes) and identified their regional distribution characteristics. For Alaska, we also analyzed (1) incomplete data that suggest that the state contains 1–2.5 million lakes larger than 0.001 km2 covering over 50,000 km2 and (2) localized high-resolution (5 m) data that suggest that the number of very small water bodies ( 0.001 km2 in some areas. The Pareto distribution cannot accurately describe the lake abundance-size relationship across the entire size spectrum, and extrapolation of this density function to small size classes has likely resulted in the overestimation of the number of small lakes in the world. While small water bodies dominate in terms of numbers, they are not numerous enough to dominate in terms of surface area, as has been previously suggested. Extending our results to the global scale suggests that there are on the order of 64 million water bodies larger than 0.001 km2 in the world, with a total surface area of approximately 3.8 million km2.

  7. World Health Organization Estimates of the Global and Regional Disease Burden of 22 Foodborne Bacterial, Protozoal, and Viral Diseases, 2010: A Data Synthesis.

    Science.gov (United States)

    Kirk, Martyn D; Pires, Sara M; Black, Robert E; Caipo, Marisa; Crump, John A; Devleesschauwer, Brecht; Döpfer, Dörte; Fazil, Aamir; Fischer-Walker, Christa L; Hald, Tine; Hall, Aron J; Keddy, Karen H; Lake, Robin J; Lanata, Claudio F; Torgerson, Paul R; Havelaar, Arie H; Angulo, Frederick J

    2015-12-01

    Foodborne diseases are important worldwide, resulting in considerable morbidity and mortality. To our knowledge, we present the first global and regional estimates of the disease burden of the most important foodborne bacterial, protozoal, and viral diseases. We synthesized data on the number of foodborne illnesses, sequelae, deaths, and Disability Adjusted Life Years (DALYs), for all diseases with sufficient data to support global and regional estimates, by age and region. The data sources included varied by pathogen and included systematic reviews, cohort studies, surveillance studies and other burden of disease assessments. We sought relevant data circa 2010, and included sources from 1990-2012. The number of studies per pathogen ranged from as few as 5 studies for bacterial intoxications through to 494 studies for diarrheal pathogens. To estimate mortality for Mycobacterium bovis infections and morbidity and mortality for invasive non-typhoidal Salmonella enterica infections, we excluded cases attributed to HIV infection. We excluded stillbirths in our estimates. We estimate that the 22 diseases included in our study resulted in two billion (95% uncertainty interval [UI] 1.5-2.9 billion) cases, over one million (95% UI 0.89-1.4 million) deaths, and 78.7 million (95% UI 65.0-97.7 million) DALYs in 2010. To estimate the burden due to contaminated food, we then applied proportions of infections that were estimated to be foodborne from a global expert elicitation. Waterborne transmission of disease was not included. We estimate that 29% (95% UI 23-36%) of cases caused by diseases in our study, or 582 million (95% UI 401-922 million), were transmitted by contaminated food, resulting in 25.2 million (95% UI 17.5-37.0 million) DALYs. Norovirus was the leading cause of foodborne illness causing 125 million (95% UI 70-251 million) cases, while Campylobacter spp. caused 96 million (95% UI 52-177 million) foodborne illnesses. Of all foodborne diseases, diarrheal and

  8. World Health Organization Estimates of the Global and Regional Disease Burden of 22 Foodborne Bacterial, Protozoal, and Viral Diseases, 2010: A Data Synthesis.

    Directory of Open Access Journals (Sweden)

    Martyn D Kirk

    2015-12-01

    Full Text Available Foodborne diseases are important worldwide, resulting in considerable morbidity and mortality. To our knowledge, we present the first global and regional estimates of the disease burden of the most important foodborne bacterial, protozoal, and viral diseases.We synthesized data on the number of foodborne illnesses, sequelae, deaths, and Disability Adjusted Life Years (DALYs, for all diseases with sufficient data to support global and regional estimates, by age and region. The data sources included varied by pathogen and included systematic reviews, cohort studies, surveillance studies and other burden of disease assessments. We sought relevant data circa 2010, and included sources from 1990-2012. The number of studies per pathogen ranged from as few as 5 studies for bacterial intoxications through to 494 studies for diarrheal pathogens. To estimate mortality for Mycobacterium bovis infections and morbidity and mortality for invasive non-typhoidal Salmonella enterica infections, we excluded cases attributed to HIV infection. We excluded stillbirths in our estimates. We estimate that the 22 diseases included in our study resulted in two billion (95% uncertainty interval [UI] 1.5-2.9 billion cases, over one million (95% UI 0.89-1.4 million deaths, and 78.7 million (95% UI 65.0-97.7 million DALYs in 2010. To estimate the burden due to contaminated food, we then applied proportions of infections that were estimated to be foodborne from a global expert elicitation. Waterborne transmission of disease was not included. We estimate that 29% (95% UI 23-36% of cases caused by diseases in our study, or 582 million (95% UI 401-922 million, were transmitted by contaminated food, resulting in 25.2 million (95% UI 17.5-37.0 million DALYs. Norovirus was the leading cause of foodborne illness causing 125 million (95% UI 70-251 million cases, while Campylobacter spp. caused 96 million (95% UI 52-177 million foodborne illnesses. Of all foodborne diseases, diarrheal

  9. Molecular bacterial diversity and bioburden of commercial airliner cabin air

    Energy Technology Data Exchange (ETDEWEB)

    La Duc, M.T.; Stuecker, T.; Venkateswaran, K. [California Inst. of Technology, Pasadena, CA (United States). Jet Propulsion Laboratory, Biotechnology and Planetary Protection Group

    2007-11-15

    Microorganisms that exist in aircraft air systems are considered to be the primary source of microbial contamination that can lead to illness shortly after flying. More than 600 million passengers board commercial airline flights annually in the United States alone. In this study, culture-independent, biomarker-targeted bacterial enumeration and identification strategies were used to estimate total bacterial burden and diversity within the cabin air of commercial airliners. Air-impingement was used to collect samples of microorganisms from 4 flights on 2 commercial carriers. The total viable microbial population ranged from below detection limits to 4.1 x 10{sup 6} cells/m{sup 3} of air. Microbes were found to gradually accumulate from the time of passenger boarding through mid-flight. A sharp decline in bacterial abundance was then observed. Representatives of the {alpha}, {beta} and {gamma} Proteobacteria, as well as Gram-positive bacteria, were isolated in varying abundance. Airline A had large abundances of Neisseria meningitidis rRNA gene sequences and Streptococcus oralis/mitis sequences. Airline B was dominated by pseudomonas synxantha sequences as well as N. meningitidis and S. oralis/mitis. The cabin air samples housed low bacterial diversity and were typically dominated by a particular subset of bacteria, notably opportunistic pathogenic inhabitants of the human respiratory tract and oral cavity. The microbes were found largely around the ventilation ducts and gasper conduits that supply cabin air. 45 refs., 4 tabs., 3 figs.

  10. Copper effects on bacterial activity of estuarine silty sediments

    Science.gov (United States)

    Almeida, Adelaide; Cunha, Ângela; Fernandes, Sandra; Sobral, Paula; Alcântara, Fernanda

    2007-07-01

    Bacteria of silty estuarine sediments were spiked with copper to 200 μg Cu g -1 dry weight sediment in order to assess the impact of copper on bacterial degradation of organic matter and on bacterial biomass production. Bacterial density was determined by direct counting under epifluorescence microscopy and bacterial production by the incorporation of 3H-Leucine. Leucine turnover rate was evaluated by 14C-leucine incorporation and ectoenzymatic activities were estimated as the hydrolysis rate of model substrates for β-glucosidase and leucine-aminopeptidase. The presence of added copper in the microcosms elicited, after 21 days of incubation, generalised anoxia and a decrease in organic matter content. The non-eroded surface of the copper-spiked sediment showed, when compared to the control, a decrease in bacterial abundance and significant lower levels of bacterial production and of leucine turnover rate. Bacterial production and leucine turnover rate decreased to 1.4% and 13% of the control values, respectively. Ectoenzymatic activities were also negatively affected but by smaller factors. After erosion by the water current in laboratory flume conditions, the eroded surface of the control sediment showed a generalised decline in all bacterial activities. The erosion of the copper-spiked sediment showed, however, two types of responses with respect to bacterial activities at the exposed surface: positive responses of bacterial production and leucine turnover rate contrasting with slight negative responses of ectoenzymatic activities. The effects of experimental erosion in the suspended cells were also different in the control and in the copper-spiked sediment. Bacterial cells in the control microcosm exhibited, when compared to the non-eroded sediment cells, decreases in all activities after the 6-h suspension. The response of the average suspended copper-spiked sediment cell differed from the control by a less sharp decrease in ectoenzymatic activities and

  11. Bacterial production and growth rate estimation from [3H]thymidine incorporation for attached and free-living bacteria in aquatic systems

    International Nuclear Information System (INIS)

    Iriberri, J.; Unanue, M.; Ayo, B.; Barcina, I.; Egea, L.

    1990-01-01

    Production and specific growth rates of attached and free-living bacteria were estimated in an oligotrophic marine system, La Salvaje Beach, Vizcaya, Spain, and in a freshwater system having a higher nutrient concentration, Butron River, Vizcaya, Spain. Production was calculated from [methyl- 3 H]thymidine incorporation by estimating specific conversion factors (cells or micrograms of C produced per mole of thymidine incorporated) for attached and free-living bacteria, respectively, in each system. Conversion factors were not statistically different between attached and free-living bacteria: 6.812 x 10 11 and 8.678 x 10 11 μg of C mol -1 for free-living and attached bacteria in the freshwater system, and 1.276 x 10 11 and 1.354 x 10 11 μg of C mol -1 for free-living and attached bacteria in the marine system. Therefore, use of a unique conversion factor for the mixed bacterial population is well founded. However, conversion factors were higher in the freshwater system than in the marine system. This could be due to the different tropic conditions of the two systems. Free-living bacteria contributed the most to production in the two systems (85% in the marine system and 67% in the freshwater system) because of their greater contribution to total biomass. Specific growth rates calculated from production data and biomass data were similar for attached and free-living bacteria

  12. Measurements of Neuronal Soma Size and Estimated Peptide Concentrations in Addition to Cell Abundance Offer a Higher Resolution of Seasonal and Reproductive Influences of GnRH-I and GnIH in European Starlings.

    Science.gov (United States)

    Amorin, Nelson; Calisi, Rebecca M

    2015-08-01

    Hypothalamic neuropeptides involved in vertebrate reproduction, gonadotropin releasing hormone (GnRH-I) and gonadotropin-inhibitory hormone (GnIH), can vary in the abundance of immunoreactive cells as a function of the reproductive status and nest box occupation of European starlings (Sturnus vulgaris). While using the abundance of cells as an indicator of the activity of neurohormones is informative, incorporating information on cell size (readily observed using immunohistochemistry) can offer a more detailed understanding of environmentally-mediated changes in hormonal dynamics. In this study, we tested the hypothesis that the size of cells' somas and the estimated concentration of peptides in cells immunoreactive (ir) for GnRH-I and GnIH would vary throughout the breeding season and as a function of nest-box status (resident or not). In the absence of a direct assay of protein, we estimated an index of the concentration of hypothalamic peptides via the relative optical density (i.e., the difference between the mean optical density and the optical density of background staining). In support of our hypothesis, we found that GnRH-I- and GnIH-ir soma size and peptide concentration changed both in males and females throughout the breeding season. Somas were largest and estimated peptide concentration was highest mid-season when compared with earlier in the season or to the non-breeding period. For nest-box residents, GnIH-ir soma size and peptide concentration were higher during the middle of the breeding season than earlier in the breeding season, although residence in the nest box was not related to GnRH-I-ir variables. Our results confirm that previously reported changes in cell abundance mimic changes we see in GnRH-I and GnIH-ir soma size and our proxy for peptide concentration. However, investigating changes in the soma of GnRH-I-ir cells revealed a peak in size during the middle of the breeding season, a change not evident when solely examining data on the

  13. Infrared spectroscopy, vibrational predissociation dynamics and stability of the hydrogen trioxy (HOOO) radical and estimation of its abundance in the atmosphere

    Science.gov (United States)

    Derro, Erika L.

    .31 kcal/mol. The atmospheric abundance of HOOO is assessed using a statistical mechanical approach employing the experimentally determined binding energy and spectroscopic properties, which suggests that HOOO may be a significant sink for atmospheric OH radicals, specifically under the low temperature and moderate pressure conditions of the tropopause.

  14. Estimating the contribution of surfactant replacement therapy to the alveolar pool: an in vivo study based on 13 C natural abundance in rabbits.

    Science.gov (United States)

    Giambelluca, Sonia; Ricci, Francesca; Simonato, Manuela; Correani, Alessio; Casiraghi, Costanza; Storti, Matteo; Cogo, Paola; Salomone, Fabrizio; Carnielli, Virgilio Paolo

    2018-04-06

    Variation of the isotopic abundance of selected nutrients and molecules have been used for pharmacological and kinetics studies under the premise that the administered molecule has a different isotopic enrichment from the isotopic background of the recipient subject. The aim of this study is to test the feasibility of assessing the contribution of exogenous surfactant phospholipids to the endogenous alveolar pool in vivo after exogenous surfactant replacement therapy in rabbits. The study consisted in measuring the consistency of 13 C/ 12 C ratio of disaturated-phosphatidylcholine palmitate (DSPC-PA) in 7 lots of poractant alfa, produced over a year, and among bronchoalveolar lavages of 20 rabbits fed with a standard chow. A pilot study was performed in a rabbit model of lavage-induced surfactant deficiency: 7 control rabbits and 4 treated with exogenous surfactant. The contribution of exogenous surfactant to the alveolar pool was assessed after intra-tracheal administration of 200 mg/kg of poractant alfa. The 13 C content of DSPC-PA was measured by Isotope Ratio Mass Spectrometry. The mean DSPC-PA 13 C/ 12 C ratio of the 7 lots of poractant alfa was -18.8 ‰ with a SD of 0.1 ‰ [Range: -18.9 ‰; -18.6 ‰]. The mean 13 C/ 12 C ratio of surfactant DSPC recovered from the lung lavage of 20 rabbits was -28.8±1.2 ‰ [Range: -31.7 ‰; -25.7 ‰]. The contribution of exogenous surfactant to the total alveolar surfactant could be calculated in the treated rabbits and it ranged from 83.9 to 89.6 %. This pilot study describes a novel method to measure the contribution of the exogenous surfactant to the alveolar pool. This method is based on the natural variation of 13 C and therefore it does not require the use of chemically synthetized tracers. This method could be useful in human research and especially in surfactant replacement studies in preterm infants. This article is protected by copyright. All rights reserved.

  15. THE SEGUE STELLAR PARAMETER PIPELINE. V. ESTIMATION OF ALPHA-ELEMENT ABUNDANCE RATIOS FROM LOW-RESOLUTION SDSS/SEGUE STELLAR SPECTRA

    International Nuclear Information System (INIS)

    Lee, Young Sun; Beers, Timothy C.; Prieto, Carlos Allende; Lai, David K.; Rockosi, Constance M.; Morrison, Heather L.; Johnson, Jennifer A.; An, Deokkeun; Sivarani, Thirupathi; Yanny, Brian

    2011-01-01

    We present a method for the determination of [α/Fe] ratios from low-resolution (R = 2000) SDSS/SEGUE stellar spectra. By means of a star-by-star comparison with degraded spectra from the ELODIE spectral library and with a set of moderately high-resolution (R = 15, 000) and medium-resolution (R = 6000) spectra of SDSS/SEGUE stars, we demonstrate that we are able to measure [α/Fe] from SDSS/SEGUE spectra (with S/N>20/1) to a precision of better than 0.1 dex, for stars with atmospheric parameters in the range T eff = [4500, 7000] K, log g = [1.5, 5.0], and [Fe/H] = [-1.4, +0.3], over the range [α/Fe] = [-0.1, +0.6]. For stars with [Fe/H] 25/1). Over the full temperature range considered, the lowest metallicity star for which a confident estimate of [α/Fe] can be obtained from our approach is [Fe/H] ∼-2.5; preliminary tests indicate that a metallicity limit as low as [Fe/H] ∼-3.0 may apply to cooler stars. As a further validation of this approach, weighted averages of [α/Fe] obtained for SEGUE spectra of likely member stars of Galactic globular clusters (M15, M13, and M71) and open clusters (NGC 2420, M67, and NGC 6791) exhibit good agreement with the values of [α/Fe] from previous studies. The results of the comparison with NGC 6791 imply that the metallicity range for the method may extend to ∼+0.5.

  16. Bacterial meningitis

    NARCIS (Netherlands)

    Roos, Karen L.; van de Beek, Diederik

    2010-01-01

    Bacterial meningitis is a neurological emergency. Empiric antimicrobial and adjunctive therapy should be initiated as soon as a single set of blood cultures has been obtained. Clinical signs suggestive of bacterial meningitis include fever, headache, meningismus, vomiting, photophobia, and an

  17. Estimation of the incidence of bacterial vaginosis and other vaginal infections and its consequences on maternal/fetal outcome in pregnant women attending an antenatal clinic in a tertiary care hospital in North India

    Directory of Open Access Journals (Sweden)

    Lata Indu

    2010-01-01

    Full Text Available Aims: This study was undertaken to estimate the incidence of bacterial vaginosis (BV and other vaginal infections during pregnancy and its association with urinary tract infections (UTI and its consequences on pregnancy outcome, maternal and fetal morbidity and mortality. Settings and Design: Prospective cohort study. Materials and Methods: The present prospective cohort study was conducted on 200 women attending the antenatal clinic (ANC of a tertiary hospital. All pertinent obstetric and neonatal data covering antenatal events during the course of pregnancy, delivery, puerperium and condition of each newborn at the time of birth were collected. BV was detected by both Gram stain and gold standard clinical criteria (Amsel′s composite criteria. Statistical analysis used: Data were analyzed using SPSS version 9. Fischer′s exact test, chi square tests and Student′s′ test has been used for analysis. The probability of 5% was considered as significant for continuous variables such as age, period of gestation and birth weight. Odds ratio (OR and confidence interval (CI with 95% probability were determined. Results: The incidence of bacterial vaginosis was 41 in 200 patients. Adverse outcomes such as preterm labor, PROM and fetal complications were found more in pregnant women who had bacterial vaginosis (N=41, bacterial vaginosis with UTI (N=14 as compared to those without bacterial vaginosis (N=118. Conclusions: The incidence of poor pregnancy outcome was higher in bacterial vaginosis with UTI. Prevention of BV and UTI is cost effective to minimize the pregnancy-related complications and preterm labor to decrease in perinatal and maternal mortality and morbidity. We recommend all antenatal patients should be screened for the presence of bacterial vaginosis, other infections and UTI.

  18. Responsiveness of soil nitrogen fractions and bacterial communities to afforestation in the Loess Hilly Region (LHR) of China

    Science.gov (United States)

    Ren, Chengjie; Sun, Pingsheng; Kang, Di; Zhao, Fazhu; Feng, Yongzhong; Ren, Guangxin; Han, Xinhui; Yang, Gaihe

    2016-06-01

    In the present paper, we investigated the effects of afforestation on nitrogen fractions and microbial communities. A total of 24 soil samples were collected from farmland (FL) and three afforested lands, namely Robinia pseudoacacia L (RP), Caragana korshinskii Kom (CK), and abandoned land (AL), which have been arable for the past 40 years. Quantitative PCR and Illumina sequencing of 16S rRNA genes were used to analyze soil bacterial abundance, diversity, and composition. Additionally, soil nitrogen (N) stocks and fractions were estimated. The results showed that soil N stock, N fractions, and bacterial abundance and diversity increased following afforestation. Proteobacteria, Acidobacteria, and Actinobacteria were the dominant phyla of soil bacterial compositions. Overall, soil bacterial compositions generally changed from Actinobacteria (Acidobacteria)-dominant to Proteobacteria-dominant following afforestation. Soil N fractions, especially for dissolved organic nitrogen (DON), were significantly correlated with most bacterial groups and bacterial diversity, while potential competitive interactions between Proteobacteria (order Rhizobiales) and Cyanobacteria were suggested. In contrast, nitrate nitrogen (NO3--N) influenced soil bacterial compositions less than other N fractions. Therefore, the present study demonstrated that bacterial diversity and specific species respond to farmland-to-forest conversion and hence have the potential to affect N dynamic processes in the Loess Plateau.

  19. Differential growth responses of soil bacterial taxa to carbon substrates of varying chemical recalcitrance

    Energy Technology Data Exchange (ETDEWEB)

    Goldfarb, K.C.; Karaoz, U.; Hanson, C.A.; Santee, C.A.; Bradford, M.A.; Treseder, K.K.; Wallenstein, M.D.; Brodie, E.L.

    2011-04-18

    Soils are immensely diverse microbial habitats with thousands of co-existing bacterial, archaeal, and fungal species. Across broad spatial scales, factors such as pH and soil moisture appear to determine the diversity and structure of soil bacterial communities. Within any one site however, bacterial taxon diversity is high and factors maintaining this diversity are poorly resolved. Candidate factors include organic substrate availability and chemical recalcitrance, and given that they appear to structure bacterial communities at the phylum level, we examine whether these factors might structure bacterial communities at finer levels of taxonomic resolution. Analyzing 16S rRNA gene composition of nucleotide analog-labeled DNA by PhyloChip microarrays, we compare relative growth rates on organic substrates of increasing chemical recalcitrance of >2,200 bacterial taxa across 43 divisions/phyla. Taxa that increase in relative abundance with labile organic substrates (i.e., glycine, sucrose) are numerous (>500), phylogenetically clustered, and occur predominantly in two phyla (Proteobacteria and Actinobacteria) including orders Actinomycetales, Enterobacteriales, Burkholderiales, Rhodocyclales, Alteromonadales, and Pseudomonadales. Taxa increasing in relative abundance with more chemically recalcitrant substrates (i.e., cellulose, lignin, or tannin-protein) are fewer (168) but more phylogenetically dispersed, occurring across eight phyla and including Clostridiales, Sphingomonadalaes, Desulfovibrionales. Just over 6% of detected taxa, including many Burkholderiales increase in relative abundance with both labile and chemically recalcitrant substrates. Estimates of median rRNA copy number per genome of responding taxa demonstrate that these patterns are broadly consistent with bacterial growth strategies. Taken together, these data suggest that changes in availability of intrinsically labile substrates may result in predictable shifts in soil bacterial composition.

  20. SWFSC/MMTD: Vaquita Abundance Survey 1997

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — In 1997, the Southwest Fisheries Science Center (SWFSC) conducted a survey designed to estimate the abundance of vaquita, the Gulf of California harbor porpoise...

  1. Abundances in field dwarf stars. II. Carbon and nitrogen abundances

    Energy Technology Data Exchange (ETDEWEB)

    Laird, J.B.

    1985-02-15

    Intermediate-dispersion spectra of 116 field dwarf stars, plus 10 faint field giants and 3 Hyades dwarfs, have been used to derive carbon and nitrogen abundances relative to iron. The program sample includes both disk and halo stars, spanning a range in (Fe/H) of +0.50 to -2.45. Synthetic spectra of CH and NH bands have been used to determine carbon and nitrogen abundances. The C/Fe ratio is solar over the range of metallicity studied, with an estimated intrinsic scatter of 0.10 dex. Down to (Fe/H)roughly-equal-1.8, below which the nitrogen abundance could not be measured, the N/Fe ratio is also constant for the majority of stars, indicating that nitrogen production is largely primary. Four halo stars are found to be enhanced in nitrogen relative to iron, by factors between 5 and 50, although their carbon abundances appear to be normal. These results are discussed in connection with the chemical evolution of the Galaxy and the sites of C, N, and Fe nucleosynthesis. The results require that C, N, and Fe be produced in stars of similar mass. Our current understanding of N production, then, implies that most Type I supernovae have intermediate-mass progenitors. The nitrogen in the N-enhanced halo stars is very probably primordial, indicating that the interstellar medium at early epochs contained substantial inhomogeneities.

  2. Abundances in field dwarf stars. II. Carbon and nitrogen abundances

    International Nuclear Information System (INIS)

    Laird, J.B.

    1985-01-01

    Intermediate-dispersion spectra of 116 field dwarf stars, plus 10 faint field giants and 3 Hyades dwarfs, have been used to derive carbon and nitrogen abundances relative to iron. The program sample includes both disk and halo stars, spanning a range in [Fe/H] of +0.50 to -2.45. Synthetic spectra of CH and NH bands have been used to determine carbon and nitrogen abundances. The C/Fe ratio is solar over the range of metallicity studied, with an estimated intrinsic scatter of 0.10 dex. Down to [Fe/H]roughly-equal-1.8, below which the nitrogen abundance could not be measured, the N/Fe ratio is also constant for the majority of stars, indicating that nitrogen production is largely primary. Four halo stars are found to be enhanced in nitrogen relative to iron, by factors between 5 and 50, although their carbon abundances appear to be normal. These results are discussed in connection with the chemical evolution of the Galaxy and the sites of C, N, and Fe nucleosynthesis. The results require that C, N, and Fe be produced in stars of similar mass. Our current understanding of N production, then, implies that most Type I supernovae have intermediate-mass progenitors. The nitrogen in the N-enhanced halo stars is very probably primordial, indicating that the interstellar medium at early epochs contained substantial inhomogeneities

  3. Methow River Studies, Washington: abundance estimates from Beaver Creek and the Chewuch River screw trap, methodology testing in the Whitefish Island side channel, and survival and detection estimates from hatchery fish releases, 2013

    Science.gov (United States)

    Martens, Kyle D.; Fish, Teresa M.; Watson, Grace A.; Connolly, Patrick J.

    2014-01-01

    , leaving one large pool near the bottom of the side channel and several shallow isolated pools that may or may not go dry. In seasonally connected side channels, juvenile salmonid survival in pools less than 100 cm average depth was lower than in pools greater than 100 cm average depth (Martens and Connolly, 2014). In this report, we document our field work and analysis completed in 2013. During 2013, USGS sampling efforts were focused on resampling of three reaches in Beaver Creek, testing methodology in the Whitefish Island side channel, conducting hatchery survival estimates, and operating a screw trap on the Chewuch River (funded by Yakama Nation; fig. 1). The Beaver Creek sampling effort was a revisit of three index sites sampled continuously from 2004 to 2007 to look at the fish response to barrier removal. Methodology testing in Whitefish Island side channel was done to determine the best method for evaluating fish populations after restoration efforts in side channels (previous sampling methods were determined to be ineffective after pools were deepened). Hatchery survival estimates were completed to monitor fish survival in the Methow and Columbia Rivers, while the screw trap was operated to estimate migrating fish populations in the Chewuch River and track passive integrated transponder (PIT)-tagged fish. In addition, we maintained a network of PIT-tag interrogation systems (PTIS), assisted Reclamation with fish removal events associated with stream restoration (two people for 9 days; 14 percent of summer field season), and conducted a stream metabolism study designed to help parameterize and calibrate the stream productivity model (Bellmore and others, 2014) with model validation.

  4. Bacterial communities in the fruit bodies of ground basidiomycetes

    Science.gov (United States)

    Zagryadskaya, Yu. A.; Lysak, L. V.; Chernov, I. Yu.

    2015-06-01

    Fruit bodies of basidiomycetes at different stages of decomposition serve as specific habitats in forest biocenoses for bacteria and differ significantly with respect to the total bacterial population and abundance of particular bacterial genera. A significant increase in the total bacterial population estimated by the direct microscopic method with acridine orange staining and in the population of saprotrophic bacteria (inoculation of glucose peptone yeast agar) in fruit bodies of basidiomycetes Armillaria mellea and Coprinus comatus was recorded at the final stage of their decomposition in comparison with the initial stage. Gramnegative bacteria predominated in the tissues of fruit bodies at all the stages of decomposition and were represented at the final stage by the Aeromonas, Vibrio, and Pseudomonas genera (for fruit bodies of A. mellea) the Pseudomonas genus (for fruit bodies of C. comatus). The potential influence of bacterial communities in the fruit bodies of soil basidiomycetes on the formation of bacterial communities in the upper soil horizons in forest biocenoses is discussed. The loci connected with the development and decomposition of fruit bodies of basidiomycetes on the soil surface are promising for targeted search of Gram-negative bacteria, the important objects of biotechnology.

  5. Bacterial prostatitis.

    Science.gov (United States)

    Gill, Bradley C; Shoskes, Daniel A

    2016-02-01

    The review provides the infectious disease community with a urologic perspective on bacterial prostatitis. Specifically, the article briefly reviews the categorization of prostatitis by type and provides a distillation of new findings published on bacterial prostatitis over the past year. It also highlights key points from the established literature. Cross-sectional prostate imaging is becoming more common and may lead to more incidental diagnoses of acute bacterial prostatitis. As drug resistance remains problematic in this condition, the reemergence of older antibiotics such as fosfomycin, has proven beneficial. With regard to chronic bacterial prostatitis, no clear clinical risk factors emerged in a large epidemiological study. However, bacterial biofilm formation has been associated with more severe cases. Surgery has a limited role in bacterial prostatitis and should be reserved for draining of a prostatic abscess or the removal of infected prostatic stones. Prostatitis remains a common and bothersome clinical condition. Antibiotic therapy remains the basis of treatment for both acute and chronic bacterial prostatitis. Further research into improving prostatitis treatment is indicated.

  6. Benthic bacterial biomass and production in the Hudson River estuary

    International Nuclear Information System (INIS)

    Austin, H.K.; Findlay, S.E.G.

    1989-01-01

    Bacterial biomass, production, and turnover were determined for two freshwater march sites and a site in the main river channel along the tidally influenced Hudson River. The incorporation of [methyl- 3 H]thymidine into DNA was used to estimate the growth rate of surface and anaerobic bacteria. Bacterial production at marsh sites was similar to, and in some cases considerably higher than, production estimates reported for other aquatic wetland and marine sediment habitats. Production averaged 1.8-2.8 mg C·m -2 · hour -1 in marsh sediments. Anaerobic bacteria in marsh sediment incorporated significant amounts of [methyl- 3 H]thymidine into DNA. Despite differences in dominant vegatation and tidal regime, bacterial biomass was similar (1 x 10 3 ± 0.08 mg C·m -2 ) in Trapa, Typha, and Nuphar aquatic macrophyte communities. Bacterial abundance and productivity were lower in sandy sediments associated with Scirpus communities along the Hudson River (0.2 x 10 3 ± 0.05 mg C·m -2 and 0.3 ± 0.23 mg C · m -2 · hour -1 , respectively)

  7. Bacterial membrane proteomics.

    Science.gov (United States)

    Poetsch, Ansgar; Wolters, Dirk

    2008-10-01

    About one quarter to one third of all bacterial genes encode proteins of the inner or outer bacterial membrane. These proteins perform essential physiological functions, such as the import or export of metabolites, the homeostasis of metal ions, the extrusion of toxic substances or antibiotics, and the generation or conversion of energy. The last years have witnessed completion of a plethora of whole-genome sequences of bacteria important for biotechnology or medicine, which is the foundation for proteome and other functional genome analyses. In this review, we discuss the challenges in membrane proteome analysis, starting from sample preparation and leading to MS-data analysis and quantification. The current state of available proteomics technologies as well as their advantages and disadvantages will be described with a focus on shotgun proteomics. Then, we will briefly introduce the most abundant proteins and protein families present in bacterial membranes before bacterial membrane proteomics studies of the last years will be presented. It will be shown how these works enlarged our knowledge about the physiological adaptations that take place in bacteria during fine chemical production, bioremediation, protein overexpression, and during infections. Furthermore, several examples from literature demonstrate the suitability of membrane proteomics for the identification of antigens and different pathogenic strains, as well as the elucidation of membrane protein structure and function.

  8. Distribution, abundance and density estimates of franciscanas, Pontoporia blainvillei (Cetacea: Pontoporiidae, in Babitonga bay, southern Brazil Distribuição e estimativas de abundância e densidade de franciscanas, Pontoporia blainvillei (Cetacea: Pontoporiidae, na baía da Babitonga, sul do Brasil

    Directory of Open Access Journals (Sweden)

    Marta J. Cremer

    2008-09-01

    Full Text Available Pontoporia blainvillei (Gervais & d'Orbigny, 1844 is threatened throughout its distribution. The species can be found year-round in the Babitonga bay estuary (26º 02'-26º 28'S and 48º28'-48º50'W, in the north coast of the state of Santa Catarina, Brazil. Boat surveys were conducted in order to evaluate its abundance and density between 2000 and 2003. Sampling was random and stratified, with 46 transects in five sub-areas, comprising a total area of 160 km². Data collection was conducted following the linear transect method with distance sampling. A total of 1174.7 km was scanned and 38 groups were observed. Franciscanas were not uniformly distributed in Babitonga bay. Group size ranged from one to 13 animals (mean ± SD = 5.02 ± 3.62. Model 1 (Half-Normal showed the best fit to the data. The estimated population size was 50 animals and the density was 0.32 individuals km-2. Density estimates evaluated in the sub-areas where franciscanas occurred resulted in a density of 0.46 individuals km-2. Monitoring this population is of considerable importance due to the constant threats that this species faces in this bay.Pontoporia blainvillei (Gervais & d'Orbigny, 1844 ocorre ao longo de todo o ano no estuário da baía da Babitonga, no litoral norte de Santa Catarina, sul do Brasil. Foram realizadas amostragens com o objetivo de obter informações sobre sua abundância e densidade populacional nesta área entre os anos de 2000 e 2003. A amostragem foi aleatória e estratificada, com 46 transecções estabelecidas em cinco grandes sub-áreas, compreendendo 160 km². A coleta de dados foi conduzida utilizando o método de transecções lineares com amostragem de distância. Foram percorridos 1174,7 km e 38 grupos foram registrados. As franciscanas não apresentaram uma distribuição uniforme na baía da Babitonga. O tamanho de grupo variou de um a 13 animais (5,02 ± 3,62. O Modelo 1 (Meio-Normal promoveu o melhor ajustamento dos parâmetros. A

  9. Bacterial Vaginosis

    Science.gov (United States)

    ... Archive STDs Home Page Bacterial Vaginosis (BV) Chlamydia Gonorrhea Genital Herpes Hepatitis HIV/AIDS & STDs Human Papillomavirus ( ... of getting other STDs, such as chlamydia and gonorrhea . These bacteria can sometimes cause pelvic inflammatory disease ( ...

  10. Mechanical Homogenization Increases Bacterial Homogeneity in Sputum

    Science.gov (United States)

    Stokell, Joshua R.; Khan, Ammad

    2014-01-01

    Sputum obtained from patients with cystic fibrosis (CF) is highly viscous and often heterogeneous in bacterial distribution. Adding dithiothreitol (DTT) is the standard method for liquefaction prior to processing sputum for molecular detection assays. To determine if DTT treatment homogenizes the bacterial distribution within sputum, we measured the difference in mean total bacterial abundance and abundance of Burkholderia multivorans between aliquots of DTT-treated sputum samples with and without a mechanical homogenization (MH) step using a high-speed dispersing element. Additionally, we measured the effect of MH on bacterial abundance. We found a significant difference between the mean bacterial abundances in aliquots that were subjected to only DTT treatment and those of the aliquots which included an MH step (all bacteria, P = 0.04; B. multivorans, P = 0.05). There was no significant effect of MH on bacterial abundance in sputum. Although our results are from a single CF patient, they indicate that mechanical homogenization increases the homogeneity of bacteria in sputum. PMID:24759710

  11. OXYGEN ABUNDANCES IN CEPHEIDS

    International Nuclear Information System (INIS)

    Luck, R. E.; Andrievsky, S. M.; Korotin, S. N.; Kovtyukh, V. V.

    2013-01-01

    Oxygen abundances in later-type stars, and intermediate-mass stars in particular, are usually determined from the [O I] line at 630.0 nm, and to a lesser extent, from the O I triplet at 615.7 nm. The near-IR triplets at 777.4 nm and 844.6 nm are strong in these stars and generally do not suffer from severe blending with other species. However, these latter two triplets suffer from strong non-local thermodynamic equilibrium (NLTE) effects and thus see limited use in abundance analyses. In this paper, we derive oxygen abundances in a large sample of Cepheids using the near-IR triplets from an NLTE analysis, and compare those abundances to values derived from a local thermodynamic equilibrium (LTE) analysis of the [O I] 630.0 nm line and the O I 615.7 nm triplet as well as LTE abundances for the 777.4 nm triplet. All of these lines suffer from line strength problems making them sensitive to either measurement complications (weak lines) or to line saturation difficulties (strong lines). Upon this realization, the LTE results for the [O I] lines and the O I 615.7 nm triplet are in adequate agreement with the abundance from the NLTE analysis of the near-IR triplets.

  12. BACTERIAL CONSORTIUM

    Directory of Open Access Journals (Sweden)

    Payel Sarkar

    2013-01-01

    Full Text Available Petroleum aromatic hydrocarbons like benzen e, toluene, ethyl benzene and xylene, together known as BTEX, has almost the same chemical structure. These aromatic hydrocarbons are released as pollutants in th e environment. This work was taken up to develop a solvent tolerant bacterial cons ortium that could degrade BTEX compounds as they all share a common chemical structure. We have isolated almost 60 different types of bacterial strains from different petroleum contaminated sites. Of these 60 bacterial strains almost 20 microorganisms were screene d on the basis of capability to tolerate high concentration of BTEX. Ten differe nt consortia were prepared and the compatibility of the bacterial strains within the consortia was checked by gram staining and BTEX tolerance level. Four successful mi crobial consortia were selected in which all the bacterial strains concomitantly grew in presence of high concentration of BTEX (10% of toluene, 10% of benzene 5% ethyl benzene and 1% xylene. Consortium #2 showed the highest growth rate in pr esence of BTEX. Degradation of BTEX by consortium #2 was monitored for 5 days by gradual decrease in the volume of the solvents. The maximum reduction observed wa s 85% in 5 days. Gas chromatography results also reveal that could completely degrade benzene and ethyl benzene within 48 hours. Almost 90% degradation of toluene and xylene in 48 hours was exhibited by consortium #2. It could also tolerate and degrade many industrial solvents such as chloroform, DMSO, acetonitrile having a wide range of log P values (0.03–3.1. Degradation of aromatic hydrocarbon like BTEX by a solvent tolerant bacterial consortium is greatly significant as it could degrade high concentration of pollutants compared to a bacterium and also reduces the time span of degradation.

  13. Orion A helium abundance

    International Nuclear Information System (INIS)

    Tsivilev, A.P.; Ershov, A.A.; Smirnov, G.T.; Sorochenko, R.L.

    1986-01-01

    The 22.4-GHz (H,He)66-alpha and 36.5-GHz (H,He)56-alpha radio recombination lines have been observed at several Jaffe-Pankonin positions in the central part of the Orion A source. The measured relative abundance of ionized helium increases with distance, averaging 11.6 percent at peripheral points. The observed behavior is interpreted by a blister-type model nebula, which implies that Orion A has a true He abundance of 12 percent, is moving with a radial velocity of 5 km/sec, and is expanding. 18 references

  14. Bio-precipitation of uranium by two bacterial isolates recovered from extreme environments as estimated by potentiometric titration, TEM and X-ray absorption spectroscopic analyses

    Energy Technology Data Exchange (ETDEWEB)

    Merroun, Mohamed L., E-mail: merroun@ugr.es [Institute of Radiochemistry, Helmholtz Centre Dresden-Rossendorf, Dresden (Germany); Departamento de Microbiologia, Universidad de Granada, Campus Fuentenueva s/n 18071, Granada (Spain); Nedelkova, Marta [Institute of Radiochemistry, Helmholtz Centre Dresden-Rossendorf, Dresden (Germany); Ojeda, Jesus J. [Cell-Mineral Interface Research Programme, Kroto Research Institute, University of Sheffield, Broad Lane, Sheffield S3 7HQ (United Kingdom); Experimental Techniques Centre, Brunel University, Uxbridge, Middlesex UB8 3PH (United Kingdom); Reitz, Thomas [Institute of Radiochemistry, Helmholtz Centre Dresden-Rossendorf, Dresden (Germany); Fernandez, Margarita Lopez; Arias, Jose M. [Departamento de Microbiologia, Universidad de Granada, Campus Fuentenueva s/n 18071, Granada (Spain); Romero-Gonzalez, Maria [Cell-Mineral Interface Research Programme, Kroto Research Institute, University of Sheffield, Broad Lane, Sheffield S3 7HQ (United Kingdom); Selenska-Pobell, Sonja [Institute of Radiochemistry, Helmholtz Centre Dresden-Rossendorf, Dresden (Germany)

    2011-12-15

    Highlights: Black-Right-Pointing-Pointer Precipitation of uranium as U phosphates by natural bacterial isolates. Black-Right-Pointing-Pointer The uranium biomineralization involves the activity of acidic phosphatase. Black-Right-Pointing-Pointer Uranium bioremediation could be achieved via the biomineralization of U(VI) in phosphate minerals. - Abstract: This work describes the mechanisms of uranium biomineralization at acidic conditions by Bacillus sphaericus JG-7B and Sphingomonas sp. S15-S1 both recovered from extreme environments. The U-bacterial interaction experiments were performed at low pH values (2.0-4.5) where the uranium aqueous speciation is dominated by highly mobile uranyl ions. X-ray absorption spectroscopy (XAS) showed that the cells of the studied strains precipitated uranium at pH 3.0 and 4.5 as a uranium phosphate mineral phase belonging to the meta-autunite group. Transmission electron microscopic (TEM) analyses showed strain-specific localization of the uranium precipitates. In the case of B. sphaericus JG-7B, the U(VI) precipitate was bound to the cell wall. Whereas for Sphingomonas sp. S15-S1, the U(VI) precipitates were observed both on the cell surface and intracellularly. The observed U(VI) biomineralization was associated with the activity of indigenous acid phosphatase detected at these pH values in the absence of an organic phosphate substrate. The biomineralization of uranium was not observed at pH 2.0, and U(VI) formed complexes with organophosphate ligands from the cells. This study increases the number of bacterial strains that have been demonstrated to precipitate uranium phosphates at acidic conditions via the activity of acid phosphatase.

  15. Bacterial Adhesion & Blocking Bacterial Adhesion

    DEFF Research Database (Denmark)

    Vejborg, Rebecca Munk

    2008-01-01

    , which influence the transition from a planktonic lifestyle to a sessile lifestyle, have been studied. Protein conditioning film formation was found to influence bacterial adhesion and subsequent biofilm formation considerable, and an aqueous extract of fish muscle tissue was shown to significantly...... tract to the microbial flocs in waste water treatment facilities. Microbial biofilms may however also cause a wide range of industrial and medical problems, and have been implicated in a wide range of persistent infectious diseases, including implantassociated microbial infections. Bacterial adhesion...... is the first committing step in biofilm formation, and has therefore been intensely scrutinized. Much however, still remains elusive. Bacterial adhesion is a highly complex process, which is influenced by a variety of factors. In this thesis, a range of physico-chemical, molecular and environmental parameters...

  16. Bacterial meningitis

    NARCIS (Netherlands)

    Heckenberg, Sebastiaan G. B.; Brouwer, Matthijs C.; van de Beek, Diederik

    2014-01-01

    Bacterial meningitis is a neurologic emergency. Vaccination against common pathogens has decreased the burden of disease. Early diagnosis and rapid initiation of empiric antimicrobial and adjunctive therapy are vital. Therapy should be initiated as soon as blood cultures have been obtained,

  17. Bacterial lipases

    NARCIS (Netherlands)

    Jaeger, Karl-Erich; Ransac, Stéphane; Dijkstra, Bauke W.; Colson, Charles; Heuvel, Margreet van; Misset, Onno

    Many different bacterial species produce lipases which hydrolyze esters of glycerol with preferably long-chain fatty acids. They act at the interface generated by a hydrophobic lipid substrate in a hydrophilic aqueous medium. A characteristic property of lipases is called interfacial activation,

  18. Bacterial stress

    Indian Academy of Sciences (India)

    First page Back Continue Last page Graphics. Bacterial stress. Physicochemical and chemical parameters: temperature, pressure, pH, salt concentration, oxygen, irradiation. Nutritional depravation: nutrient starvation, water shortage. Toxic compounds: Antibiotics, heavy metals, toxins, mutagens. Interactions with other cells: ...

  19. Bio-precipitation of uranium by two bacterial isolates recovered from extreme environments as estimated by potentiometric titration, TEM and X-ray absorption spectroscopic analyses.

    Science.gov (United States)

    Merroun, Mohamed L; Nedelkova, Marta; Ojeda, Jesus J; Reitz, Thomas; Fernández, Margarita López; Arias, José M; Romero-González, María; Selenska-Pobell, Sonja

    2011-12-15

    This work describes the mechanisms of uranium biomineralization at acidic conditions by Bacillus sphaericus JG-7B and Sphingomonas sp. S15-S1 both recovered from extreme environments. The U-bacterial interaction experiments were performed at low pH values (2.0-4.5) where the uranium aqueous speciation is dominated by highly mobile uranyl ions. X-ray absorption spectroscopy (XAS) showed that the cells of the studied strains precipitated uranium at pH 3.0 and 4.5 as a uranium phosphate mineral phase belonging to the meta-autunite group. Transmission electron microscopic (TEM) analyses showed strain-specific localization of the uranium precipitates. In the case of B. sphaericus JG-7B, the U(VI) precipitate was bound to the cell wall. Whereas for Sphingomonas sp. S15-S1, the U(VI) precipitates were observed both on the cell surface and intracellularly. The observed U(VI) biomineralization was associated with the activity of indigenous acid phosphatase detected at these pH values in the absence of an organic phosphate substrate. The biomineralization of uranium was not observed at pH 2.0, and U(VI) formed complexes with organophosphate ligands from the cells. This study increases the number of bacterial strains that have been demonstrated to precipitate uranium phosphates at acidic conditions via the activity of acid phosphatase. Copyright © 2011 Elsevier B.V. All rights reserved.

  20. Stellar Oxygen Abundances

    Science.gov (United States)

    King, Jeremy

    1994-04-01

    This dissertation addresses several issues concerning stellar oxygen abundances. The 7774 {\\AA} O I triplet equivalent widths of Abia & Rebolo [1989, AJ, 347, 186] for metal-poor dwarfs are found to be systematically too high. I also argue that current effective temperatures used in halo star abundance studies may be ~150 K too low. New color-Teff relations are derived for metal-poor stars. Using the revised Teff values and improved equivalent widths for the 7774A O I triplet, the mean [O/Fe] ratio for a handful of halo stars is found to be +0.52 with no dependence on Teff or [Fe/H]. Possible cosmological implications of the hotter Teff scale are discussed along with additional evidence supporting the need for a higher temperature scale for metal-poor stars. Our Teff scale leads to a Spite Li plateau value of N(Li)=2.28 +/- 0.09. A conservative minimal primordial value of N(Li)=2.35 is inferred. If errors in the observations and models are considered, consistency with standard models of Big Bang nucleosynthesis is still achieved with this larger Li abundance. The revised Teff scale raises the observed B/Be ratio of HD 140283 from 10 to 12, making its value more comfortably consistent with the production of the observed B and Be by ordinary spallation. Our Teff values are found to be in good agreement with values predicted from both the Victoria and Yale isochrone color-Teff relations. Thus, it appears likely that no changes in globular cluster ages would result. Next, we examine the location of the break in the [O/Fe] versus [Fe/H] plane in a quantitative fashion. Analysis of a relatively homogeneous data set does not favor any unique break point in the range -1.7 /= -3), in agreement with the new results for halo dwarfs. We find that the gap in the observed [O/H] distribution, noted by Wheeler et al. [1989, ARAA, 27, 279], persists despite the addition of more O data and may betray the occurrence of a hiatus in star formation between the end of halo formation and

  1. Bacterial growth on macrophyte leachate and fate of bacterial production

    International Nuclear Information System (INIS)

    Findlay, S.; Carlough, L.; Crocker, M.T.; Gill, H.K.; Meyer, J.L.; Smith, P.J.

    1986-01-01

    The role bacteria play in transferring organic carbon to other trophic levels in aquatic ecosystems depends on the efficiency with which they convert dissolved organic [ 14 C]-labelled carbon into bacterial biomass and on the ability of consumers to graze bacteria. The authors have measured the conversion efficiency for bacteria growing on macrophyte-derived dissolved organic carbon and estimated the amount of bacterial production removed by grazing. Bacteria converted this DOC into new tissue with an efficiency of 53%, substantially higher than the apparent conversion efficiency of macrophyte-derived particulate organic carbon or other types of DOC. Two estimates of grazing indicate that the decline in bacterial numbers after the bloom was probably due to grazing by flagellates. These results show the significance of the bacterial link between DOC and other trophic levels

  2. Bacterial contribution to iodine volatilization in the environment

    Energy Technology Data Exchange (ETDEWEB)

    Amachi, S; Kasahara, M; Fujii, T [Chiba Univ., Dept. of Bioresources Chemistry, Matsudo, Chiba (Japan); Muramatsu, Y [National Inst. of Radiological Sciences, Chiba (Japan)

    2003-09-01

    The roles of microorganisms in iodine volatilization from the environment were studied. More than 100 bacterial strains were isolated from various environments such as soils, seawater and marine sediments, and were examined their capacities for volatilizing iodine. Approximately 40% of these bacteria showed significant capacities for volatilizing iodine. Gas chromatographic determinations revealed that the chemical species of gaseous iodine is methyl iodide (CH{sub 3}I). Phylogenetic analysis based on 16S ribosomal DNA showed that these 'iodine-volatilizing bacteria' are widely distributed through the bacterial domain. The iodide-methylating reaction was mediated by an enzyme protein with S-adenosyl-L-methionine (SAM) as the methyl donor. We then estimated bacterial contribution to iodine volatilization from soils. Iodine in soils was volatilized mainly as CH{sub 3}I. CH{sub 3}I emission was enhanced in the presence of glucose or yeast extract, but was inhibited by autoclaving of soils. Little CH{sub 3}I was produced under anaerobic conditions. Furthermore, the addition of streptomycin and tetracycline, antibiotics which inhibit bacterial growth, strongly inhibited CH{sub 3}I emission, while a fungal inhibitor cycloheximide caused little effect. These results suggest that iodine in soils is volatilized as CH{sub 3}I mainly by the action of aerobic soil bacteria. Similar experiment was carried out by using sea water samples. The emission of iodine from sea waters occurred biologically, and bacterial (and also other microbial) contribution was confirmed. Our results suggest that iodine is methylated and volatilized into the atmosphere as a result of bacterial activities. Since bacteria are so abundant and widespread in the environments, they may significantly contribute to global iodine volatilization. This indicates that if {sup 129}I would be released from nuclear facilities, weapons testing or ground storage of nuclear wastes, the pathway of volatilization by

  3. Bacterial anoxygenic photosynthesis on plant leaf surfaces.

    Science.gov (United States)

    Atamna-Ismaeel, Nof; Finkel, Omri; Glaser, Fabian; von Mering, Christian; Vorholt, Julia A; Koblížek, Michal; Belkin, Shimshon; Béjà, Oded

    2012-04-01

    The aerial surface of plants, the phyllosphere, is colonized by numerous bacteria displaying diverse metabolic properties that enable their survival in this specific habitat. Recently, we reported on the presence of microbial rhodopsin harbouring bacteria on the top of leaf surfaces. Here, we report on the presence of additional bacterial populations capable of harvesting light as a means of supplementing their metabolic requirements. An analysis of six phyllosphere metagenomes revealed the presence of a diverse community of anoxygenic phototrophic bacteria, including the previously reported methylobacteria, as well as other known and unknown phototrophs. The presence of anoxygenic phototrophic bacteria was also confirmed in situ by infrared epifluorescence microscopy. The microscopic enumeration correlated with estimates based on metagenomic analyses, confirming both the presence and high abundance of these microorganisms in the phyllosphere. Our data suggest that the phyllosphere contains a phylogenetically diverse assemblage of phototrophic species, including some yet undescribed bacterial clades that appear to be phyllosphere-unique. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

  4. Fluorine Abundances in AGB Carbon Stars: New Results?

    Science.gov (United States)

    Abia, C.; de Laverny, P.; Recio-Blanco, A.; Domínguez, I.; Cristallo, S.; Straniero, O.

    2009-09-01

    A recent reanalysis of the fluorine abundance in three Galactic Asymptotic Giant Branch (AGB) carbon stars (TX Psc, AQ Sgr and R Scl) by Abia et al. (2009) results in estimates of fluorine abundances systematically lower by ~0.8 dex on average, with respect to the sole previous estimates by Jorissen, Smith & Lambert (1992). The new F abundances are in better agreement with the predictions of full-network stellar models of low-mass (<3 Msolar) AGB stars.

  5. Ammonia abundances in comets

    Science.gov (United States)

    Wyckoff, S.; Tegler, S.; Engel, L.

    The emission band strengths of the NH2 bands of Comets Halley, Hartley-Good, Thiele, and Borrelly were measured to determine the NH2 column densities for the comets. Production rates obtained using the Haser and vectorial models are in agreement within the observational errors, suggesting that a simple two-step decay model may be used to approximate the NH2 distribution in a comet's coma. Ammonia-to-water abundance ratios from 0.01 to 0.4 percent were found for the four comets. The ratio in Comet Halley is found to be Q(NH3)/Q(H2O) = 0.002 + or - 0.001. No significant difference in the ammonia abundance was found before or after perihelion in Comet Halley.

  6. Compilation of solar abundance data

    International Nuclear Information System (INIS)

    Hauge, Oe.; Engvold, O.

    1977-01-01

    Interest in the previous compilations of solar abundance data by the same authors (ITA--31 and ITA--39) has led to this third, revised edition. Solar abundance data of 67 elements are tabulated and in addition upper limits for the abundances of 5 elements are listed. References are made to 167 papers. A recommended abundance value is given for each element. (JIW)

  7. Abundances in galaxies

    International Nuclear Information System (INIS)

    Pagel, B.E.J.

    1991-01-01

    Standard (or mildly inhomogeneous) Big Bang nucleosynthesis theory is well confirmed by abundance measurements of light elements up to 7 Li and the resulting upper limit to the number of neutrino families confirmed in accelerator experiments. Extreme inhomogeneous models with a closure density in form of baryons seem to be ruled out and there is no evidence for a cosmic 'floor' to 9 Be or heavier elements predicted in some versions of those models. Galaxies show a correlation between luminous mass and abundance of carbon and heavier elements, usually attributed to escape of hot gas from shallow potential wells. Uncertainties include the role of dark matter and biparametric behaviour of ellipticals. Spirals have radial gradients which may arise from a variety of causes. In our own Galaxy one can distinguish three stellar populations - disk, halo and bulge - characterised by differing metallicity distribution functions. Differential abundance effects are found among different elements in stars as a function of metallicity and presumably age, notably in the ratio of oxygen and α-particle elements to iron. These may eventually be exploitable to set a time scale for the formation of the halo, bulge and disk. (orig.)

  8. [Bacterial vaginosis].

    Science.gov (United States)

    Romero Herrero, Daniel; Andreu Domingo, Antonia

    2016-07-01

    Bacterial vaginosis (BV) is the main cause of vaginal dysbacteriosis in the women during the reproductive age. It is an entity in which many studies have focused for years and which is still open for discussion topics. This is due to the diversity of microorganisms that cause it and therefore, its difficult treatment. Bacterial vaginosis is probably the result of vaginal colonization by complex bacterial communities, many of them non-cultivable and with interdependent metabolism where anaerobic populations most likely play an important role in its pathogenesis. The main symptoms are an increase of vaginal discharge and the unpleasant smell of it. It can lead to serious consequences for women, such as an increased risk of contracting sexually transmitted infections including human immunodeficiency virus and upper genital tract and pregnancy complications. Gram stain is the gold standard for microbiological diagnosis of BV, but can also be diagnosed using the Amsel clinical criteria. It should not be considered a sexually transmitted disease but it is highly related to sex. Recurrence is the main problem of medical treatment. Apart from BV, there are other dysbacteriosis less characterized like aerobic vaginitis of which further studies are coming slowly but are achieving more attention and consensus among specialists. Copyright © 2016 Elsevier España, S.L.U. All rights reserved.

  9. Functional Potential of Bacterial Communities using Gene Context Information

    Directory of Open Access Journals (Sweden)

    Anwesha Mohapatra

    2017-12-01

    Full Text Available Estimation of the functional potential of a bacterial genome can be determined by accurate annotation of its metabolic pathways. Existing homology based methods for pathway annotation fail to account for homologous genes that participate in multiple pathways, causing overestimation of gene copy number. Mere presence of constituent genes of a candidate pathway which are dispersed on a genome often results in incorrect annotation, thereby leading to erroneous gene abundance and pathway estimation. Clusters of evolutionarily conserved coregulated genes are characteristic features in bacterial genomes and their spatial arrangement in the genome is constrained by the pathway encoded by them. Thus, in order to improve the accuracy of pathway prediction, it is important to augment homology based annotation with gene organization information. In this communication, we present a methodology considering prioritization of gene context for improved pathway annotation. Extensive literature mining was performed to confirm conserved juxtaposed arrangement of gene components of various pathways. Our method was utilized to identify and analyse the functional potential of all available completely sequenced bacterial genomes. The accuracy of the predicted gene clusters and their importance in metabolic pathways will be demonstrated using a few case studies. One of such case study corresponds to butyrate production pathways in gut bacteria where it was observed that gut pathogens and commensals possess a distinct set of pathway components. In another example, we will demonstrate how our methodology improves the prediction accuracy of carbohydrate metabolic potential in human microbial communities. Applicability of our method for estimation of functional potential in bacterial communities present in diverse environments will also be illustrated.

  10. Volume changes and electrostriction in the primary photoreactions of various photosynthetic systems: estimation of dielectric coefficient in bacterial reaction centers and of the observed volume changes with the Drude-Nernst equation.

    Science.gov (United States)

    Mauzerall, David; Hou, Jian-Min; Boichenko, Vladimir A

    2002-01-01

    Photoacoustics (PA) allows the determination of enthalpy and volume changes of photoreactions in photosynthetic reaction centers on the 0.1-10 mus time scale. These include the bacterial centers from Rb. sphaeroides, PS I and PS II centers from Synechocystis and in whole cells. In vitro and in vivo PA data on PS I and PS II revealed that both the volume change (-26 A(3)) and reaction enthalpy (-0.4 eV) in PS I are the same as those in the bacterial centers. However the volume change in PS II is small and the enthalpy far larger, -1 eV. Assigning the volume changes to electrostriction allows a coherent explanation of these observations. One can explain the large volume decrease in the bacterial centers with an effective dielectric coefficient of approximately 4. This is a unique approach to this parameter so important in estimation of protein energetics. The value of the volume contraction for PS I can only be explained if the acceptor is the super- cluster (Fe(4)S(4))(Cys(4)) with charge change from -1 to -2. The small volume change in PS II is explained by sub-mus electron transfer from Y(Z) anion to P(680) cation, in which charge is only moved from the Y(Z) anion to the Q(A) with no charge separation or with rapid proton transfer from oxidized Y(Z) to a polar region and thus very little change in electrostriction. At more acid pH equally rapid proton transfer from a neighboring histidine to a polar region may be caused by the electric field of the P(680) cation.

  11. Quasar Elemental Abundances at High Redshifts

    DEFF Research Database (Denmark)

    Dietrich, M.; Hamann, F.; Shields, J. C.

    2003-01-01

    the framework of the most recent photoionization models to estimate the metallicity of the gas associated with the high-z quasars. Standard photoionization parameters and the assumption of secondary nitrogen enrichment indicate an average abundance of Z/Z_sol = 4 to 5 in the line emitting gas. Assuming a time...

  12. Molecular characterization of soil bacterial community in a perhumid, low mountain forest.

    Science.gov (United States)

    Lin, Yu-Te; Whitman, William B; Coleman, David C; Chih-Yu, Chiu

    2011-01-01

    Forest disturbance often results in changes in soil properties and microbial communities. In the present study, we characterized a soil bacterial community subjected to disturbance using 16S rRNA gene clone libraries. The community was from a disturbed broad-leaved, low mountain forest ecosystem at Huoshaoliao (HSL) located in northern Taiwan. This locality receives more than 4,000 mm annual precipitation, one of the highest precipitations in Taiwan. Based on the Shannon diversity index, Chao1 estimator, richness and rarefaction curve analysis, the bacterial community in HSL forest soils was more diverse than those previously investigated in natural and disturbed forest soils with colder or less humid weather conditions. Analysis of molecular variance also revealed that the bacterial community in disturbed soils significantly differed from natural forest soils. Most of the abundant operational taxonomic units (OTUs) in the disturbed soil community at HSL were less abundant or absent in other soils. The disturbances influenced the composition of bacterial communities in natural and disturbed forests and increased the diversity of the disturbed forest soil community. Furthermore, the warmer and humid weather conditions could also increase community diversity in HSL soils.

  13. Bacterial mitosis

    DEFF Research Database (Denmark)

    Møller-Jensen, Jakob; Borch, Jonas; Dam, Mette

    2003-01-01

    Bacterial DNA segregation takes place in an active and ordered fashion. In the case of Escherichia coli plasmid R1, the partitioning system (par) separates paired plasmid copies and moves them to opposite cell poles. Here we address the mechanism by which the three components of the R1 par system...... act together to generate the force required for plasmid movement during segregation. ParR protein binds cooperatively to the centromeric parC DNA region, thereby forming a complex that interacts with the filament-forming actin-like ParM protein in an ATP-dependent manner, suggesting that plasmid...

  14. Anomalous behavior of tellurium abundances

    Energy Technology Data Exchange (ETDEWEB)

    Cohen, B L

    1984-01-01

    The cosmic abundance of Te is larger than for any element with atomic number greater than 40, but it is one of the least abundant elements in the earth's lithosphere and it is one of the five elements never reported in sea water. On the other hand, it is the fourth most abundant element in the human body (after Fe, Zn and Rb), and is unusually abundant in human food. It is shown that the high abundance in human food combined with the low abundance in soil requires that it be picked up by plant roots very much more efficiently than any other trace element.

  15. Frequency of Pathogenic Paediatric Bacterial Meningitis in Mozambique: The Critical Role of Multiplex Real-Time Polymerase Chain Reaction to Estimate the Burden of Disease.

    Science.gov (United States)

    Nhantumbo, Aquino Albino; Cantarelli, Vlademir Vicente; Caireão, Juliana; Munguambe, Alcides Moniz; Comé, Charlotte Elizabeth; Pinto, Gabriela do Carmo; Zimba, Tomás Francisco; Mandomando, Inácio; Semá, Cynthia Baltazar; Dias, Cícero; Moraes, Milton Ozório; Gudo, Eduardo Samo

    2015-01-01

    In Sub-Saharan Africa, including Mozambique, acute bacterial meningitis (ABM) represents a main cause of childhood mortality. The burden of ABM is seriously underestimated because of the poor performance of culture sampling, the primary method of ABM surveillance in the region. Low quality cerebrospinal fluid (CSF) samples and frequent consumption of antibiotics prior to sample collection lead to a high rate of false-negative results. To our knowledge, this study is the first to determine the frequency of ABM in Mozambique using real-time polymerase chain reaction (qPCR) and to compare results to those of culture sampling. Between March 2013 and March 2014, CSF samples were collected at 3 regional hospitals from patients under 5 years of age, who met World Health Organization case definition criteria for ABM. Macroscopic examination, cytochemical study, culture, and qPCR were performed on all samples. A total of 369 CSF samples were collected from children clinically suspected of ABM. qPCR showed a significantly higher detection rate of ABM-causing pathogens when compared to culture (52.3% [193/369] versus 7.3% [27/369], p = 0.000). The frequency of Streptococcus pneumoniae, Haemophilus influenzae, group B Streptococci, and Neisseria meningitidis were 32.8% (121⁄369), 12.2%, (45⁄369), 3.0% (16⁄369) and 4.3% (11⁄369), respectively, significantly higher compared to that obtained on culture (p < 0.001 for each). Our findings demonstrate that culture is less effective for the diagnosis of ABM than qPCR. The common use of culture rather than qPCR to identify ABM results in serious underestimation of the burden of the disease, and our findings strongly suggest that qPCR should be incorporated into surveillance activities for ABM. In addition, our data showed that S. pneumoniae represents the most common cause of ABM in children under 5 years of age.

  16. Changes in soil physicochemical properties and soil bacterial community in mulberry (Morus alba L.)/alfalfa (Medicago sativa L.) intercropping system.

    Science.gov (United States)

    Zhang, Meng-Meng; Wang, Ning; Hu, Yan-Bo; Sun, Guang-Yu

    2018-04-01

    A better understanding of tree-based intercropping effects on soil physicochemical properties and bacterial community has a potential contribution to improvement of agroforestry productivity and sustainability. In this study, we investigated the effects of mulberry/alfalfa intercropping on soil physicochemical properties and soil bacterial community by MiSeq sequencing of bacterial 16S rRNA gene. The results showed a significant increase in the contents of available nitrogen, available phosphate, available potassium, and total carbon in the rhizosphere soil of the intercropped alfalfa. Sequencing results showed that intercropping improved bacterial richness and diversity of mulberry and alfalfa based on richness estimates and diversity indices. The relative abundances of Proteobacteria, Actinobacteria, and Firmicutes were significantly higher in intercropping mulberry than in monoculture mulberry; and the abundances of Proteobacteria, Bacteroidetes, and Gemmatimonadetes in the intercropping alfalfa were markedly higher than that in monoculture alfalfa. Bacterial taxa with soil nutrients cycling were enriched in the intercropping system. There were higher relative abundances of Bacillus (0.32%), Pseudomonas (0.14%), and Microbacterium (0.07%) in intercropping mulberry soil, and Bradyrhizobium (1.0%), Sphingomonas (0.56%), Pseudomonas (0.18%), Microbacterium (0.15%), Rhizobium (0.09%), Neorhizobium (0.08%), Rhodococcus (0.06%), and Burkholderia (0.04%) in intercropping alfalfa soil. Variance partition analysis showed that planting pattern contributed 26.7% of the total variation of bacterial community, and soil environmental factors explained approximately 56.5% of the total variation. This result indicated that the soil environmental factors were more important than the planting pattern in shaping the bacterial community in the field soil. Overall, mulberry/alfalfa intercropping changed soil bacterial community, which was related to changes in soil total carbon

  17. Good abundances from bad spectra - I. Techniques

    Science.gov (United States)

    Jones, J. Bryn; Gilmore, Gerard; Wyse, Rosemary F. G.

    1996-01-01

    Stellar spectra derived from multiple-object fibre-fed spectroscopic radial-velocity surveys, of the type feasible with, among other examples, AUTOFIB, 2dF, HYDRA, NESSIE, and the Sloan survey, differ significantly from those traditionally used for determination of stellar abundances. The spectra tend to be of moderate resolution (around 1A) and signal-to-noise ratio (around 10-20 per resolution element), and cannot usually have reliable continuum shapes determined over wavelength ranges in excess of a few tens of Angstroms. None the less, with care and a calibration of stellar effective temperature from photometry, independent of the spectroscopy, reliable iron abundances can be derived. We have developed techniques to extract true iron abundances and surface gravities from low-signal-to-noise ratio, intermediate-resolution spectra of G-type stars in the 4000-5000A wavelength region. Spectroscopic indices sensitive to iron abundance and gravity are defined from a set of narrow (few-several A wide) wavelength intervals. The indices are calibrated theoretically using synthetic spectra. Given adequate data and a photometrically determined effective temperature, one can derive estimates of the stellar iron abundance and surface gravity. We have also defined a single abundance indicator for the analysis of very low-signal-to-noise ratio spectra; with the further assumption of a value for the stellar surface gravity, this is able to provide useful iron abundance information from spectra having signal-to-noise ratios as low as 10 (1-A elements). The theoretical basis and calibration using synthetic spectra are described in this paper. The empirical calibration of these techniques by application to observational data is described in a separate paper (Jones, Wyse & Gilmore). The technique provides precise iron abundances, with zero-point correct to ~0.1 dex, and is reliable, with typical uncertainties being <~0.2 dex. A derivation of the in situ thick disc metallicity

  18. Challenges of transferring models of fish abundance between coral reefs.

    Science.gov (United States)

    Sequeira, Ana M M; Mellin, Camille; Lozano-Montes, Hector M; Meeuwig, Jessica J; Vanderklift, Mathew A; Haywood, Michael D E; Babcock, Russell C; Caley, M Julian

    2018-01-01

    Reliable abundance estimates for species are fundamental in ecology, fisheries, and conservation. Consequently, predictive models able to provide reliable estimates for un- or poorly-surveyed locations would prove a valuable tool for management. Based on commonly used environmental and physical predictors, we developed predictive models of total fish abundance and of abundance by fish family for ten representative taxonomic families for the Great Barrier Reef (GBR) using multiple temporal scenarios. We then tested if models developed for the GBR (reference system) could predict fish abundances at Ningaloo Reef (NR; target system), i.e., if these GBR models could be successfully transferred to NR. Models of abundance by fish family resulted in improved performance (e.g., 44.1% fish abundance (9% fish species richness from the GBR to NR, transferability for these fish abundance models was poor. When compared with observations of fish abundance collected in NR, our transferability results had low validation scores ( R 2   0.05). High spatio-temporal variability of patterns in fish abundance at the family and population levels in both reef systems likely affected the transferability of these models. Inclusion of additional predictors with potential direct effects on abundance, such as local fishing effort or topographic complexity, may improve transferability of fish abundance models. However, observations of these local-scale predictors are often not available, and might thereby hinder studies on model transferability and its usefulness for conservation planning and management.

  19. Distribution and life strategies of two bacterial populations in a eutrophic lake

    Science.gov (United States)

    Weinbauer; Hofle

    1998-10-01

    Monoclonal antibodies and epifluorescence microscopy were used to determine the depth distribution of two indigenous bacterial populations in the stratified Lake Plusssee and characterize their life strategies. Populations of Comamonas acidovorans PX54 showed a depth distribution with maximum abundances in the oxic epilimnion, whereas Aeromonas hydrophila PU7718 showed a depth distribution with maximum abundances in the anoxic thermocline layer (metalimnion), i. e., in the water layer with the highest microbial activity. Resistance of PX54 to protist grazing and high metabolic versatility and growth rate of PU7718 were the most important life strategy traits for explaining the depth distribution of the two bacterial populations. Maximum abundance of PX54 was 16,000 cells per ml, and maximum abundance of PU7718 was 20,000 cells per ml. Determination of bacterial productivity in dilution cultures with different-size fractions of dissolved organic matter (DOM) from lake water indicates that low-molecular-weight (LMW) DOM is less bioreactive than total DOM (TDOM). The abundance and growth rate of PU7718 were highest in the TDOM fractions, whereas those of PX54 were highest in the LMW DOM fraction, demonstrating that PX54 can grow well on the less bioreactive DOM fraction. We estimated that 13 to 24% of the entire bacterial community and 14% of PU7718 were removed by viral lysis, whereas no significant effect of viral lysis on PX54 could be detected. Growth rates of PX54 (0.11 to 0.13 h-1) were higher than those of the entire bacterial community (0.04 to 0.08 h-1) but lower than those of PU7718 (0.26 to 0.31 h-1). In undiluted cultures, the growth rates were significantly lower, pointing to density effects such as resource limitation or antibiosis, and the effects were stronger for PU7718 and the entire bacterial community than for PX54. Life strategy characterizations based on data from literature and this study revealed that the fast-growing and metabolically

  20. Soil bacterial community shifts associated with sugarcane straw removal

    Science.gov (United States)

    Pimentel, Laisa; Gumiere, Thiago; Andreote, Fernando; Cerri, Carlos

    2017-04-01

    In Brazil, the adoption of the mechanical unburned sugarcane harvest potentially increase the quantity of residue left in the field after harvesting. Economically, this material has a high potential for second generation ethanol (2G) production. However, crop residues have an essential role in diverse properties and processes in the soil. The greater part of the uncertainties about straw removal for 2G ethanol production is based on its effects in soil microbial community. In this sense, it is important to identify the main impacts of sugarcane straw removal on soil microbial community. Therefore, we conducted a field study, during one year, in Valparaíso (São Paulo state - Brazil) to evaluate the effects of straw decomposition on soil bacterial community. Specifically, we wanted: i) to compare the rates of straw removal and ii) to evaluate the effects of straw decomposition on soil bacterial groups over one year. The experiment was in a randomized block design with treatments arranged in strip plot. The treatments are different rates of sugarcane straw removal, namely: no removal, 50, 75 and 100% of straw removal. Soil sampling was carried out at 0, 4, 8 and 12 months after the sugarcane harvest (August 2015). Total DNA was extracted from soil using the PowersoilTM DNA Isolation kit. And the abundance of bacterial in each soil sample was estimated via quantification of 16S rRNA gene. The composition of the bacterial communities was estimated via terminal restriction fragment length polymorphism (T-RFLP) analysis, and the T-RF sizes were performed on a 3500 Genetic Analyzer. Finally, the results were examined with GeneMapper 4.1 software. There was bacterial community shifts through the time and among the rates of sugarcane straw removal. Bacterial community was firstly determined by the time scale, which explained 29.16% of total variation. Rates of straw removal explained 11.55% of shifts on bacterial community. Distribution through the time is an important

  1. Spatio-temporal variability of airborne bacterial communities and their correlation with particulate matter chemical composition across two urban areas.

    Science.gov (United States)

    Gandolfi, I; Bertolini, V; Bestetti, G; Ambrosini, R; Innocente, E; Rampazzo, G; Papacchini, M; Franzetti, A

    2015-06-01

    The study of spatio-temporal variability of airborne bacterial communities has recently gained importance due to the evidence that airborne bacteria are involved in atmospheric processes and can affect human health. In this work, we described the structure of airborne microbial communities in two urban areas (Milan and Venice, Northern Italy) through the sequencing, by the Illumina platform, of libraries containing the V5-V6 hypervariable regions of the 16S rRNA gene and estimated the abundance of airborne bacteria with quantitative PCR (qPCR). Airborne microbial communities were dominated by few taxa, particularly Burkholderiales and Actinomycetales, more abundant in colder seasons, and Chloroplasts, more abundant in warmer seasons. By partitioning the variation in bacterial community structure, we could assess that environmental and meteorological conditions, including variability between cities and seasons, were the major determinants of the observed variation in bacterial community structure, while chemical composition of atmospheric particulate matter (PM) had a minor contribution. Particularly, Ba, SO4 (2-) and Mg(2+) concentrations were significantly correlated with microbial community structure, but it was not possible to assess whether they simply co-varied with seasonal shifts of bacterial inputs to the atmosphere, or their variation favoured specific taxa. Both local sources of bacteria and atmospheric dispersal were involved in the assembling of airborne microbial communities, as suggested, to the one side by the large abundance of bacteria typical of lagoon environments (Rhodobacterales) observed in spring air samples from Venice and to the other by the significant effect of wind speed in shaping airborne bacterial communities at all sites.

  2. Abundance, Excess, Waste

    Directory of Open Access Journals (Sweden)

    Rox De Luca

    2016-02-01

    Her recent work focuses on the concepts of abundance, excess and waste. These concerns translate directly into vibrant and colourful garlands that she constructs from discarded plastics collected on Bondi Beach where she lives. The process of collecting is fastidious, as is the process of sorting and grading the plastics by colour and size. This initial gathering and sorting process is followed by threading the components onto strings of wire. When completed, these assemblages stand in stark contrast to the ease of disposability associated with the materials that arrive on the shoreline as evidence of our collective human neglect and destruction of the environment around us. The contrast is heightened by the fact that the constructed garlands embody the paradoxical beauty of our plastic waste byproducts, while also evoking the ways by which those byproducts similarly accumulate in randomly assorted patterns across the oceans and beaches of the planet.

  3. pcaH, a molecular marker for estimating the diversity of the protocatechuate-degrading bacterial community in the soil environment

    DEFF Research Database (Denmark)

    El Azhari, Najoi

    2007-01-01

    Microorganisms degrading phenolic compounds play an important role in soil carbon cycling as well as in pesticide degradation. The pcaH gene encoding a key ring-cleaving enzyme of the β-ketoadipate pathway was selected as a functional marker. Using a degenerate primer pair, pcaH fragments were cl......H sequences from Actinobacteria and Proteobacteria phyla. This confirms that the developed primer pair targets a wide diversity of pcaH sequences, thereby constituting a suitable molecular marker to estimate the response of the pca community to agricultural practices....

  4. Bacterial Ecology

    DEFF Research Database (Denmark)

    Fenchel, Tom

    2011-01-01

    compounds these must first be undergo extracellular hydrolysis. Bacteria have a great diversity with respect to types of metabolism that far exceeds the metabolic repertoire of eukaryotic organisms. Bacteria play a fundamental role in the biosphere and certain key processes such as, for example......, the production and oxidation of methane, nitrate reduction and fixation of atmospheric nitrogen are exclusively carried out by different groups of bacteria. Some bacterial species – ‘extremophiles’ – thrive in extreme environments in which no eukaryotic organisms can survive with respect to temperature, salinity...... biogeochemical processes are carried exclusively by bacteria. * Bacteria play an important role in all types of habitats including some that cannot support eukaryotic life....

  5. Bacterial Actins.

    Science.gov (United States)

    Izoré, Thierry; van den Ent, Fusinita

    2017-01-01

    A diverse set of protein polymers, structurally related to actin filaments contributes to the organization of bacterial cells as cytomotive or cytoskeletal filaments. This chapter describes actin homologs encoded by bacterial chromosomes. MamK filaments, unique to magnetotactic bacteria, help establishing magnetic biological compasses by interacting with magnetosomes. Magnetosomes are intracellular membrane invaginations containing biomineralized crystals of iron oxide that are positioned by MamK along the long-axis of the cell. FtsA is widespread across bacteria and it is one of the earliest components of the divisome to arrive at midcell, where it anchors the cell division machinery to the membrane. FtsA binds directly to FtsZ filaments and to the membrane through its C-terminus. FtsA shows altered domain architecture when compared to the canonical actin fold. FtsA's subdomain 1C replaces subdomain 1B of other members of the actin family and is located on the opposite side of the molecule. Nevertheless, when FtsA assembles into protofilaments, the protofilament structure is preserved, as subdomain 1C replaces subdomain IB of the following subunit in a canonical actin filament. MreB has an essential role in shape-maintenance of most rod-shaped bacteria. Unusually, MreB filaments assemble from two protofilaments in a flat and antiparallel arrangement. This non-polar architecture implies that both MreB filament ends are structurally identical. MreB filaments bind directly to membranes where they interact with both cytosolic and membrane proteins, thereby forming a key component of the elongasome. MreB filaments in cells are short and dynamic, moving around the long axis of rod-shaped cells, sensing curvature of the membrane and being implicated in peptidoglycan synthesis.

  6. Diversity and abundance of the arsenite oxidase gene aioA in geothermal areas of Tengchong, Yunnan, China.

    Science.gov (United States)

    Jiang, Zhou; Li, Ping; Jiang, Dawei; Wu, Geng; Dong, Hailiang; Wang, Yanhong; Li, Bing; Wang, Yanxin; Guo, Qinghai

    2014-01-01

    A total of 12 samples were collected from the Tengchong geothermal areas of Yunnan, China, with the goal to assess the arsenite (AsIII) oxidation potential of the extant microbial communities as inferred by the abundance and diversity of the AsIII oxidase large subunit gene aioA relative to geochemical context. Arsenic concentrations were higher (on average 251.68 μg/L) in neutral or alkaline springs than in acidic springs (on average 30.88 μg/L). aioA abundance ranged from 1.63 × 10(1) to 7.08 × 10(3) per ng of DNA and positively correlated with sulfide and the ratios of arsenate (AsV):total dissolved arsenic (AsTot). Based on qPCR estimates of bacterial and archaeal 16S rRNA gene abundance, aioA-harboring organisms comprised as much as ~15% of the total community. Phylogenetically, the major aioA sequences (270 total) in the acidic hot springs (pH 3.3-4.4) were affiliated with Aquificales and Rhizobiales, while those in neutral or alkaline springs (pH 6.6-9.1) were inferred to be primarily bacteria related to Thermales and Burkholderiales. Interestingly, aioA abundance at one site greatly exceeded bacterial 16S rRNA gene abundance, suggesting these aioA genes were archaeal even though phylogenetically these aioA sequences were most similar to the Aquificales. In summary, this study described novel aioA sequences in geothermal features geographically far removed from those in the heavily studied Yellowstone geothermal complex.

  7. Subdwarf ultraviolet excesses and metal abundances

    International Nuclear Information System (INIS)

    Carney, B.W.

    1979-01-01

    The relation between stellar ultraviolet excesses and abundances is reexamined with the aid of new data, and an investigation is made of the accuracy of previous abundance analyses. A high-resolution echellogram of the subdwarf HD 201891 is analyzed to illustrate some of the problems. Generally, the earliest and latest analytical techniques yield consistent results for dwarfs. New UBV data yield normalized ultraviolet excesses, delta (U-B)/sub 0.6/, which are compared to abundances to produce a graphical relation that may be used to estimate [Fe/H] to +- 0.2 dex, given UBV colors accurate to +- 0.01 mag. The relation suggests a possible discontinuity between the halo and old-disk stars

  8. Bacterial growth kinetics

    International Nuclear Information System (INIS)

    Boonkitticharoen, V.; Ehrhardt, J.C.; Kirchner, P.T.

    1989-01-01

    Quantitative measurement of bacterial growth may be made using a radioassay technique. This method measures, by scintillation counting, the 14 CO 2 derived from the bacterial metabolism of a 14 C-labeled substrate. Mathematical growth models may serve as reliable tools for estimation of the generation rate constant (or slope of the growth curve) and provide a basis for evaluating assay performance. Two models, i.e., exponential and logistic, are proposed. Both models yielded an accurate fit to the data from radioactive measurement of bacterial growth. The exponential model yielded high precision values of the generation rate constant, with an average relative standard deviation of 1.2%. Under most conditions the assay demonstrated no changes in the slopes of growth curves when the number of bacteria per inoculation was changed. However, the radiometric assay by scintillation method had a growth-inhibiting effect on a few strains of bacteria. The source of this problem was thought to be hypersensitivity to trace amounts of toluene remaining on the detector

  9. Dynamics of Vaginal Bacterial Communities in Women Developing Bacterial Vaginosis, Candidiasis, or No Infection, Analyzed by PCR-Denaturing Gradient Gel Electrophoresis and Real-Time PCR▿

    Science.gov (United States)

    Vitali, Beatrice; Pugliese, Ciro; Biagi, Elena; Candela, Marco; Turroni, Silvia; Bellen, Gert; Donders, Gilbert G. G.; Brigidi, Patrizia

    2007-01-01

    The microbial flora of the vagina plays a major role in preventing genital infections, including bacterial vaginosis (BV) and candidiasis (CA). An integrated approach based on PCR-denaturing gradient gel electrophoresis (PCR-DGGE) and real-time PCR was used to study the structure and dynamics of bacterial communities in vaginal fluids of healthy women and patients developing BV and CA. Universal eubacterial primers and Lactobacillus genus-specific primers, both targeted at 16S rRNA genes, were used in DGGE and real-time PCR analysis, respectively. The DGGE profiles revealed that the vaginal flora was dominated by Lactobacillus species under healthy conditions, whereas several potentially pathogenic bacteria were present in the flora of women with BV. Lactobacilli were the predominant bacterial population in the vagina for patients affected by CA, but changes in the composition of Lactobacillus species were observed. Real-time PCR analysis allowed the quantitative estimation of variations in lactobacilli associated with BV and CA diseases. A statistically significant decrease in the relative abundance of lactobacilli was found in vaginal fluids of patients with BV compared to the relative abundance of lactobacilli in the vaginal fluids of healthy women and patients with CA. PMID:17644631

  10. Dynamics of vaginal bacterial communities in women developing bacterial vaginosis, candidiasis, or no infection, analyzed by PCR-denaturing gradient gel electrophoresis and real-time PCR.

    Science.gov (United States)

    Vitali, Beatrice; Pugliese, Ciro; Biagi, Elena; Candela, Marco; Turroni, Silvia; Bellen, Gert; Donders, Gilbert G G; Brigidi, Patrizia

    2007-09-01

    The microbial flora of the vagina plays a major role in preventing genital infections, including bacterial vaginosis (BV) and candidiasis (CA). An integrated approach based on PCR-denaturing gradient gel electrophoresis (PCR-DGGE) and real-time PCR was used to study the structure and dynamics of bacterial communities in vaginal fluids of healthy women and patients developing BV and CA. Universal eubacterial primers and Lactobacillus genus-specific primers, both targeted at 16S rRNA genes, were used in DGGE and real-time PCR analysis, respectively. The DGGE profiles revealed that the vaginal flora was dominated by Lactobacillus species under healthy conditions, whereas several potentially pathogenic bacteria were present in the flora of women with BV. Lactobacilli were the predominant bacterial population in the vagina for patients affected by CA, but changes in the composition of Lactobacillus species were observed. Real-time PCR analysis allowed the quantitative estimation of variations in lactobacilli associated with BV and CA diseases. A statistically significant decrease in the relative abundance of lactobacilli was found in vaginal fluids of patients with BV compared to the relative abundance of lactobacilli in the vaginal fluids of healthy women and patients with CA.

  11. Seismological measurement of solar helium abundance

    International Nuclear Information System (INIS)

    Vorontsov, S.V.; Pamyatnykh, A.A.

    1991-01-01

    The internal structure and evolution of the Sun depends on its chemical composition, particularly the helium abundance. In addition, the helium abundance in the solar envelope is thought to represent the protosolar value, making it a datum of cosmological significance. Spectroscopic measurements of the helium abundance are uncertain, and the most reliable estimates until now have come from the calibration of solar evolutionary models. The frequencies of solar acoustic oscillations are sensitive, however, to the behaviour of the speed of sound in the Sun's helium ionization zone, which allows a helioseismological determination of the helium abundance. Sound-speed inversion of helioseismological data can be used for this purpose, but precise frequency measurements of high-degree oscillation modes are needed. Here we describe a new approach based on an analysis of the phase shift of acoustic waves of intermediate-degree modes. From the accurate intermediate-mode data now available, we obtain a helium mass fraction Y=0.25±0.01 in the solar convection zone, significantly smaller than the value Y=0.27-0.29 predicted by recent solar evolutionary models. The discrepancy indicates either that initial helium abundance was reduced in the envelope by downward diffusion or that the protosolar value was lower than currently accepted. (author)

  12. Twilight of Abundance

    Science.gov (United States)

    Archibald, David

    2014-03-01

    Baby boomers enjoyed the most benign period in human history: fifty years of relative peace, cheap energy, plentiful grain supply, and a warming climate due to the highest solar activity for 8,000 years. The party is over - prepare for the twilight of abundance. David Archibald reveals the grim future the world faces on its current trajectory: massive fuel shortages, the bloodiest warfare in human history, a global starvation crisis, and a rapidly cooling planet. Archibald combines pioneering science with keen economic knowledge to predict the global disasters that could destroy civilization as we know it - disasters that are waiting just around the corner. But there's good news, too: We can have a good future if we prepare for it. Advanced, civilized countries can have a permanently high standard of living if they choose to invest in the technologies that will get them there. Archibald, a climate scientist as well as an inventor and a financial specialist, explains which scientific breakthroughs can save civilization in the coming crisis - if we can cut through the special interest opposition to these innovations and allow free markets to flourish.

  13. Inferring recent historic abundance from current genetic diversity

    NARCIS (Netherlands)

    Palsboll, Per J.; Peery, M. Zachariah; Olsen, Morten T.; Beissinger, Steven R.; Berube, Martine

    Recent historic abundance is an elusive parameter of great importance for conserving endangered species and understanding the pre-anthropogenic state of the biosphere. The number of studies that have used population genetic theory to estimate recent historic abundance from contemporary levels of

  14. Can occupancy-abundance models be used to monitor wolf abundance?

    Directory of Open Access Journals (Sweden)

    M Cecilia Latham

    Full Text Available Estimating the abundance of wild carnivores is of foremost importance for conservation and management. However, given their elusive habits, direct observations of these animals are difficult to obtain, so abundance is more commonly estimated from sign surveys or radio-marked individuals. These methods can be costly and difficult, particularly in large areas with heavy forest cover. As an alternative, recent research has suggested that wolf abundance can be estimated from occupancy-abundance curves derived from "virtual" surveys of simulated wolf track networks. Although potentially more cost-effective, the utility of this approach hinges on its robustness to violations of its assumptions. We assessed the sensitivity of the occupancy-abundance approach to four assumptions: variation in wolf movement rates, changes in pack cohesion, presence of lone wolves, and size of survey units. Our simulations showed that occupancy rates and wolf pack abundances were biased high if track surveys were conducted when wolves made long compared to short movements, wolf packs were moving as multiple hunting units as opposed to a cohesive pack, and lone wolves were moving throughout the surveyed landscape. We also found that larger survey units (400 and 576 km2 were more robust to changes in these factors than smaller survey units (36 and 144 km2. However, occupancy rates derived from large survey units rapidly reached an asymptote at 100% occupancy, suggesting that these large units are inappropriate for areas with moderate to high wolf densities (>15 wolves/1,000 km2. Virtually-derived occupancy-abundance relationships can be a useful method for monitoring wolves and other elusive wildlife if applied within certain constraints, in particular biological knowledge of the surveyed species needs to be incorporated into the design of the occupancy surveys. Further, we suggest that the applicability of this method could be extended by directly incorporating some of its

  15. The bias associated with amplicon sequencing does not affect the quantitative assessment of bacterial community dynamics.

    Directory of Open Access Journals (Sweden)

    Federico M Ibarbalz

    Full Text Available The performance of two sets of primers targeting variable regions of the 16S rRNA gene V1-V3 and V4 was compared in their ability to describe changes of bacterial diversity and temporal turnover in full-scale activated sludge. Duplicate sets of high-throughput amplicon sequencing data of the two 16S rRNA regions shared a collection of core taxa that were observed across a series of twelve monthly samples, although the relative abundance of each taxon was substantially different between regions. A case in point was the changes in the relative abundance of filamentous bacteria Thiothrix, which caused a large effect on diversity indices, but only in the V1-V3 data set. Yet the relative abundance of Thiothrix in the amplicon sequencing data from both regions correlated with the estimation of its abundance determined using fluorescence in situ hybridization. In nonmetric multidimensional analysis samples were distributed along the first ordination axis according to the sequenced region rather than according to sample identities. The dynamics of microbial communities indicated that V1-V3 and the V4 regions of the 16S rRNA gene yielded comparable patterns of: 1 the changes occurring within the communities along fixed time intervals, 2 the slow turnover of activated sludge communities and 3 the rate of species replacement calculated from the taxa-time relationships. The temperature was the only operational variable that showed significant correlation with the composition of bacterial communities over time for the sets of data obtained with both pairs of primers. In conclusion, we show that despite the bias introduced by amplicon sequencing, the variable regions V1-V3 and V4 can be confidently used for the quantitative assessment of bacterial community dynamics, and provide a proper qualitative account of general taxa in the community, especially when the data are obtained over a convenient time window rather than at a single time point.

  16. Estimativa da incerteza em ensaio de detecção de endotoxina bacteriana pelo método de gelificação Estimation of uncertainty in the detection of bacterial endotoxin by gel-clot method

    Directory of Open Access Journals (Sweden)

    Felipe Rebello Lourenço

    2005-12-01

    Full Text Available Desde a publicação da ISO 17025:1999, o interesse em métodos para estimativa da incerteza em ensaios qualitativos, do tipo "passa/não passa", têm ganho grande importância. Uma forma de estimar e informar a incerteza deste tipo de ensaio é o uso das probabilidades de respostas-falsas, particularmente falsos-positivos e falsos-negativos, determinados a partir do teorema de Bayes. O objetivo deste artigo é estabelecer um método para a estimativa de incerteza em ensaios de detecção de endotoxina bacteriana pelo método in vitro Limulus Amebocyte Lysate (LAL. Considerando a confirmação da sensibilidade do LAL e a validação do teste, a probabilidade de uma resposta falsa corresponde à soma da probabilidade dos resultados falso-negativos e falso-positivos. A partir dos resultados obtidos foi verificado que a etapa da confirmação da sensibilidade do LAL contribui para a incerteza de forma mais significativa (67,6% que a etapa de validação do teste (32,4%. Através de um procedimento simples, descrito neste artigo, e de dados obtidos a partir da confirmação da sensibilidade do LAL e validação do teste para um produto em questão é possível obter uma estimativa de incerteza razoável para o ensaio de detecção de endotoxinas bacterianas pelo método de gelificação.Since the publication of ISO 17025:1999, the interest in methods for estimation of the uncertainty in qualitative analysis, such as 'pass/fail', have became more important. The usual form of estimating and informing the uncertainty in this kind of analysis is the use of false-response rates, particularly false-positive and false-negative, determinated from Bayes theorem. The aim of this paper is establish a method for estimation of the uncertainty in the detection of bacterial endotoxins by in vitro Limulus Amebocyte Lysate (LAL test. Considering the confirmation of LAL sensitivity and the validation of the test, the probability of a false-response corresponds to the

  17. Estimation of test characteristics of real-time PCR and bacterial culture for diagnosis of subclinical intramammary infections with Streptococcus agalactiae in Danish dairy cattle in 2012 using latent class analysis

    DEFF Research Database (Denmark)

    Mahmmod, Yasser; Toft, Nils; Katholm, Jørgen

    2013-01-01

    threshold (Ct) values against bacterial culture (BC) for diagnosis of S. agalactiae IMI using latent class analysis to avoid the assumption of a perfect reference test. A total of 614 dairy cows were randomly selected from 6 herds with bulk tank PCR Ct value ≤ 39 for S. agalactiae and S. aureus. At milk...... cut-offs, indicating under estimation of S. agalactiae IMI in the examined dairy cows. In conclusion, Se of PCR is always higher than Se of BC at all tested cut-offs. The lower cut-off, the more comparable becomes Se of PCR and Se of BC. The changes in Se in both PCR and BC at different Ct-value cut...... definition of infection may reflect a more general condition of cows being positive for S. agalactiae. Our findings indicate that PCR Ct-value cut-offs should be chosen according to the underlying latent infection definition of interest. Latent class analysis proposes a useful alternative to classic test...

  18. Bacterial diversity of Taxus rhizosphere: culture-independent and culture-dependent approaches.

    Science.gov (United States)

    Hao, Da Cheng; Ge, Guang Bo; Yang, Ling

    2008-07-01

    The regional variability of Taxus rhizosphere bacterial community composition and diversity was studied by comparative analysis of three large 16S rRNA gene clone libraries from the Taxus rhizosphere in different regions of China (subtropical and temperate regions). One hundred and forty-six clones were screened for three libraries. Phylogenetic analysis of 16S rRNA gene sequences demonstrated that the abundance of sequences affiliated with Gammaproteobacteria, Betaproteobacteria, and Actinobacteria was higher in the library from the T. xmedia rhizosphere of the temperate region compared with the subtropical Taxus mairei rhizosphere. On the other hand, Acidobacteria was more abundant in libraries from the subtropical Taxus mairei rhizosphere. Richness estimates and diversity indices of three libraries revealed major differences, indicating a higher richness in the Taxus rhizosphere bacterial communities of the subtropical region and considerable variability in the bacterial community composition within this region. By enrichment culture, a novel Actinobacteria strain DICP16 was isolated from the T. xmedia rhizosphere of the temperate region and was identified as Leifsonia shinshuensis sp. via 16S rRNA gene and gyrase B sequence analyses. DICP16 was able to remove the xylosyl group from 7-xylosyl-10-deacetylbaccatin III and 7-xylosyl-10-deacetylpaclitaxel, thereby making the xylosyltaxanes available as sources of 10-deacetylbaccatin III and the anticancer drug paclitaxel. Taken together, the present studies provide, for the first time, the knowledge of the biodiversity of microorganisms populating Taxus rhizospheres.

  19. Inferring invasive species abundance using removal data from management actions

    Science.gov (United States)

    Davis, Amy J.; Hooten, Mevin B.; Miller, Ryan S.; Farnsworth, Matthew L.; Lewis, Jesse S.; Moxcey, Michael; Pepin, Kim M.

    2016-01-01

    Evaluation of the progress of management programs for invasive species is crucial for demonstrating impacts to stakeholders and strategic planning of resource allocation. Estimates of abundance before and after management activities can serve as a useful metric of population management programs. However, many methods of estimating population size are too labor intensive and costly to implement, posing restrictive levels of burden on operational programs. Removal models are a reliable method for estimating abundance before and after management using data from the removal activities exclusively, thus requiring no work in addition to management. We developed a Bayesian hierarchical model to estimate abundance from removal data accounting for varying levels of effort, and used simulations to assess the conditions under which reliable population estimates are obtained. We applied this model to estimate site-specific abundance of an invasive species, feral swine (Sus scrofa), using removal data from aerial gunning in 59 site/time-frame combinations (480–19,600 acres) throughout Oklahoma and Texas, USA. Simulations showed that abundance estimates were generally accurate when effective removal rates (removal rate accounting for total effort) were above 0.40. However, when abundances were small (<50) the effective removal rate needed to accurately estimates abundances was considerably higher (0.70). Based on our post-validation method, 78% of our site/time frame estimates were accurate. To use this modeling framework it is important to have multiple removals (more than three) within a time frame during which demographic changes are minimized (i.e., a closed population; ≤3 months for feral swine). Our results show that the probability of accurately estimating abundance from this model improves with increased sampling effort (8+ flight hours across the 3-month window is best) and increased removal rate. Based on the inverse relationship between inaccurate abundances and

  20. Inferring invasive species abundance using removal data from management actions.

    Science.gov (United States)

    Davis, Amy J; Hooten, Mevin B; Miller, Ryan S; Farnsworth, Matthew L; Lewis, Jesse; Moxcey, Michael; Pepin, Kim M

    2016-10-01

    Evaluation of the progress of management programs for invasive species is crucial for demonstrating impacts to stakeholders and strategic planning of resource allocation. Estimates of abundance before and after management activities can serve as a useful metric of population management programs. However, many methods of estimating population size are too labor intensive and costly to implement, posing restrictive levels of burden on operational programs. Removal models are a reliable method for estimating abundance before and after management using data from the removal activities exclusively, thus requiring no work in addition to management. We developed a Bayesian hierarchical model to estimate abundance from removal data accounting for varying levels of effort, and used simulations to assess the conditions under which reliable population estimates are obtained. We applied this model to estimate site-specific abundance of an invasive species, feral swine (Sus scrofa), using removal data from aerial gunning in 59 site/time-frame combinations (480-19,600 acres) throughout Oklahoma and Texas, USA. Simulations showed that abundance estimates were generally accurate when effective removal rates (removal rate accounting for total effort) were above 0.40. However, when abundances were small (removal rate needed to accurately estimates abundances was considerably higher (0.70). Based on our post-validation method, 78% of our site/time frame estimates were accurate. To use this modeling framework it is important to have multiple removals (more than three) within a time frame during which demographic changes are minimized (i.e., a closed population; ≤3 months for feral swine). Our results show that the probability of accurately estimating abundance from this model improves with increased sampling effort (8+ flight hours across the 3-month window is best) and increased removal rate. Based on the inverse relationship between inaccurate abundances and inaccurate removal

  1. Bacterial contaminations of informally marketed raw milk in Ghana ...

    African Journals Online (AJOL)

    Background: Milk has an outstanding nutritional quality but is also an excellent medium for bacterial growth and an important source of bacterial infection when consumed without pasteurization. Objective: To estimate the bacterial health risk of milk consumption in Accra and Kumasi, the twomajor cities in Ghana. Method: A ...

  2. Energy abundance and economic progress

    International Nuclear Information System (INIS)

    Schurr, S.H.

    1983-01-01

    A discussion is presented on the benefits of energy abundance and on the links between energy supply, economic growth and human welfare in the United States. It is argued that the restoration of energy abundance with dependable sources of supply should be a major national objective. (U.K.)

  3. Abundances in the Galactic bulge

    Energy Technology Data Exchange (ETDEWEB)

    Barbuy, B; Alves-Brito, A [Universidade de Sao Paulo, IAG, Rua do Matao 1226, Sao Paulo 05508-900 (Brazil); Ortolani, S; Zoccali, M [Dipartimento di Astronomia, Universita di Padova, Vicolo dell' Osservatorio 2, I-35122 Padova (Italy); Hill, V; Gomez, A [Observatoire de Paris-Meudon, 92195 Meudon Cedex (France); Melendez, J [Centro de AstrofIsica da Universidade de Porto, Rua das Estrelas, 4150-762 Porto (Portugal); Asplund, M [Max Planck Institute for Astrophysics, Postfach 1317, 85741 Garching (Germany); Bica, E [Departamento de Astronomia, Universidade Federal do Rio Grande do Sul, CP 15051, Porto Alegre 91501-970 (Brazil); Renzini, A [Osservatorio Astronomico di Padova, Vicolo dell' Osservatorio 5, I-35122 Padova (Italy); Minniti, D [Department of Astronomy and Astrophysics, Universidad Catolica de Chile, Casilla 306, Santiago 22 (Chile)], E-mail: barbuy@astro.iag.usp.br

    2008-12-15

    The metallicity distribution and abundance ratios of the Galactic bulge are reviewed. Issues raised by recent work of different groups, in particular the high metallicity end, the overabundance of {alpha}-elements in the bulge relative to the thick disc and the measurement of giants versus dwarfs, are discussed. Abundances in the old moderately metal-poor bulge globular clusters are described.

  4. Gram stains: a resource for retrospective analysis of bacterial pathogens in clinical studies.

    Science.gov (United States)

    Srinivasan, Usha; Ponnaluri, Sreelatha; Villareal, Lisa; Gillespie, Brenda; Wen, Ai; Miles, Arianna; Bucholz, Brigette; Marrs, Carl F; Iyer, Ram K; Misra, Dawn; Foxman, Betsy

    2012-01-01

    We demonstrate the feasibility of using qPCR on DNA extracted from vaginal Gram stain slides to estimate the presence and relative abundance of specific bacterial pathogens. We first tested Gram stained slides spiked with a mix of 10(8) cfu/ml of Escherichia coli and 10(5) cfu/ml of Lactobacillus acidophilus. Primers were designed for amplification of total and species-specific bacterial DNA based on 16S ribosomal gene regions. Sample DNA was pre-amplified with nearly full length 16S rDNA ribosomal gene fragment, followed by quantitative PCR with genera and species-specific 16S rDNA primers. Pre-amplification PCR increased the bacterial amounts; relative proportions of Escherichia coli and Lactobacillus recovered from spiked slides remained unchanged. We applied this method to forty two archived Gram stained slides available from a clinical trial of cerclage in pregnant women at high risk of preterm birth. We found a high correlation between Nugent scores based on bacterial morphology of Lactobacillus, Gardenerella and Mobiluncus and amounts of quantitative PCR estimated genus specific DNA (rrn copies) from Gram stained slides. Testing of a convenience sample of eight paired vaginal swabs and Gram stains freshly collected from healthy women found similar qPCR generated estimates of Lactobacillus proportions from Gram stained slides and vaginal swabs. Archived Gram stained slides collected from large scale epidemiologic and clinical studies represent a valuable, untapped resource for research on the composition of bacterial communities that colonize human mucosal surfaces.

  5. Evidence of Ash Tree (Fraxinus spp. Specific Associations with Soil Bacterial Community Structure and Functional Capacity

    Directory of Open Access Journals (Sweden)

    Michael P. Ricketts

    2018-04-01

    Full Text Available The spread of the invasive emerald ash borer (EAB across North America has had enormous impacts on temperate forest ecosystems. The selective removal of ash trees (Fraxinus spp. has resulted in abnormally large inputs of coarse woody debris and altered forest tree community composition, ultimately affecting a variety of ecosystem processes. The goal of this study was to determine if the presence of ash trees influences soil bacterial communities and/or functions to better understand the impacts of EAB on forest successional dynamics and biogeochemical cycling. Using 16S rRNA amplicon sequencing of soil DNA collected from ash and non-ash plots in central Ohio during the early stages of EAB infestation, we found that bacterial communities in plots with ash differed from those without ash. These differences were largely driven by Acidobacteria, which had a greater relative abundance in non-ash plots. Functional genes required for sulfur cycling, phosphorus cycling, and carbohydrate metabolism (specifically those which breakdown complex sugars to glucose were estimated to be more abundant in non-ash plots, while nitrogen cycling gene abundance did not differ. This ash-soil microbiome association implies that EAB-induced ash decline may promote belowground successional shifts, altering carbon and nutrient cycling and changing soil properties beyond the effects of litter additions caused by ash mortality.

  6. The bacterial community structure of hydrocarbon-polluted marine environments as the basis for the definition of an ecological index of hydrocarbon exposure.

    Science.gov (United States)

    Lozada, Mariana; Marcos, Magalí S; Commendatore, Marta G; Gil, Mónica N; Dionisi, Hebe M

    2014-09-17

    The aim of this study was to design a molecular biological tool, using information provided by amplicon pyrosequencing of 16S rRNA genes, that could be suitable for environmental assessment and bioremediation in marine ecosystems. We selected 63 bacterial genera that were previously linked to hydrocarbon biodegradation, representing a minimum sample of the bacterial guild associated with this process. We defined an ecological indicator (ecological index of hydrocarbon exposure, EIHE) using the relative abundance values of these genera obtained by pyrotag analysis. This index reflects the proportion of the bacterial community that is potentially capable of biodegrading hydrocarbons. When the bacterial community structures of intertidal sediments from two sites with different pollution histories were analyzed, 16 of the selected genera (25%) were significantly overrepresented with respect to the pristine site, in at least one of the samples from the polluted site. Although the relative abundances of individual genera associated with hydrocarbon biodegradation were generally low in samples from the polluted site, EIHE values were 4 times higher than those in the pristine sample, with at least 5% of the bacterial community in the sediments being represented by the selected genera. EIHE values were also calculated in other oil-exposed marine sediments as well as in seawater using public datasets from experimental systems and field studies. In all cases, the EIHE was significantly higher in oiled than in unpolluted samples, suggesting that this tool could be used as an estimator of the hydrocarbon-degrading potential of microbial communities.

  7. Patterns in Abundance, Cell Size and Pigment Content of Aerobic Anoxygenic Phototrophic Bacteria along Environmental Gradients in Northern Lakes.

    Directory of Open Access Journals (Sweden)

    Lisa Fauteux

    Full Text Available There is now evidence that aerobic anoxygenic phototrophic (AAP bacteria are widespread across aquatic systems, yet the factors that determine their abundance and activity are still not well understood, particularly in freshwaters. Here we describe the patterns in AAP abundance, cell size and pigment content across wide environmental gradients in 43 temperate and boreal lakes of Québec. AAP bacterial abundance varied from 1.51 to 5.49 x 105 cells mL-1, representing <1 to 37% of total bacterial abundance. AAP bacteria were present year-round, including the ice-cover period, but their abundance relative to total bacterial abundance was significantly lower in winter than in summer (2.6% and 7.7%, respectively. AAP bacterial cells were on average two-fold larger than the average bacterial cell size, thus AAP cells made a greater relative contribution to biomass than to abundance. Bacteriochlorophyll a (BChla concentration varied widely across lakes, and was not related to AAP bacterial abundance, suggesting a large intrinsic variability in the cellular pigment content. Absolute and relative AAP bacterial abundance increased with dissolved organic carbon (DOC, whereas cell-specific BChla content was negatively related to chlorophyll a (Chla. As a result, both the contribution of AAP bacteria to total prokaryotic abundance, and the cell-specific BChla pigment content were positively correlated with the DOC:Chla ratio, both peaking in highly colored, low-chlorophyll lakes. Our results suggest that photoheterotrophy might represent a significant ecological advantage in highly colored, low-chlorophyll lakes, where DOC pool is chemically and structurally more complex.

  8. Long-term field application of sewage sludge increases the abundance of antibiotic resistance genes in soil.

    Science.gov (United States)

    Chen, Qinglin; An, Xinli; Li, Hu; Su, Jianqiang; Ma, Yibing; Zhu, Yong-Guan

    2016-01-01

    Sewage sludge and manure are common soil amendments in crop production; however, their impact on the abundance and diversity of the antibiotic resistome in soil remains elusive. In this study, by using high-throughput sequencing and high-throughput quantitative PCR, the patterns of bacterial community and antibiotic resistance genes (ARGs) in a long-term field experiment were investigated to gain insights into these impacts. A total of 130 unique ARGs and 5 mobile genetic elements (MGEs) were detected and the long-term application of sewage sludge and chicken manure significantly increased the abundance and diversity of ARGs in the soil. Genes conferring resistance to beta-lactams, tetracyclines, and multiple drugs were dominant in the samples. Sewage sludge or chicken manure applications caused significant enrichment of 108 unique ARGs and MGEs with a maximum enrichment of up to 3845 folds for mexF. The enrichment of MGEs suggested that the application of sewage sludge or manure may accelerate the dissemination of ARGs in soil through horizontal gene transfer (HGT). Based on the co-occurrence pattern of ARGs subtypes revealed by network analysis, aacC, oprD and mphA-02, were proposed to be potential indicators for quantitative estimation of the co-occurring ARGs subtypes abundance by power functions. The application of sewage sludge and manure resulted in significant increase of bacterial diversity in soil, Proteobacteria, Acidobacteria, Actinobacteria and Chloroflexi were the dominant phyla (>10% in each sample). Five bacterial phyla (Chloroflexi, Planctomycetes, Firmicutes, Gemmatimonadetes and Bacteroidetes) were found to be significantly correlated with the ARGs in soil. Mantel test and variation partitioning analysis (VPA) suggested that bacterial community shifts, rather than MGEs, is the major driver shaping the antibiotic resistome. Additionally, the co-occurrence pattern between ARGs and microbial taxa revealed by network analysis indicated that four

  9. Oxygen abundances in halo stars

    Science.gov (United States)

    Bessell, Michael S.; Sutherland, Ralph S.; Ruan, Kui

    1991-12-01

    The present study determines the oxygen abundance for a sample of metal-poor G dwarfs by analysis of OH lines between 3080 and 3200 A and the permitted high-excitation far-red O I triple. The oxygen abundances determined from the low-excitation OH lines are up to 0.55 dex lower than those measured from the high-excitation O I lines. The abundances for the far-red O I triplet lines agree with those rederived from Abia and Rebolo (1989), and the abundances from the OH lines in dwarfs and giants are in agreement with the rederived O abundances of Barbuy (1988) and others from the forbidden resonance O I line. Because the chi = 0.1.7 eV OH lines are formed in the same layers as the majority of Fe, Ti, and other neutral metal lines used for abundance analyses, it is argued that the OH lines and the forbidden O I line yield the true oxygen abundances relative to the metals.

  10. Estimation of test characteristics of real-time PCR and bacterial culture for diagnosis of subclinical intramammary infections with Streptococcus agalactiae in Danish dairy cattle in 2012 using latent class analysis.

    Science.gov (United States)

    Mahmmod, Yasser S; Toft, Nils; Katholm, Jørgen; Grønbæk, Carsten; Klaas, Ilka C

    2013-05-01

    The misdiagnosis of intramammary infections (IMI) with Streptococcus agalactiae (S. agalactiae) could lead farmers to treat or cull animals unnecessarily. The objective of this field study was to estimate the sensitivity (Se) and specificity (Sp) of real-time PCR at different cut-offs for cycle threshold (Ct) values against bacterial culture (BC) for diagnosis of S. agalactiae IMI using latent class analysis to avoid the assumption of a perfect reference test. A total of 614 dairy cows were randomly selected from 6 herds with bulk tank PCR Ct value ≤ 39 for S. agalactiae and S. aureus. At milk recording, 2456 quarter milk samples were taken aseptically for BC and the routinely taken cow level milk samples were analyzed by PCR. Results showed that 53 cows (8.6%) were positive for S. agalactiae IMI by BC. Sensitivity of PCR at cut-offs; ≤ 39, ≤ 37, ≤ 34, and ≤ 32, was 96.2%, 91.9%, 87.2% and 73.9%, while Se of BC was 25.7%, 29.9%, 59.9% and 72.1%. Specificity of PCR at cut-offs; ≤ 39, ≤ 37, ≤ 34, and ≤ 32, was 96.8%, 96.9%, 96.7%, and 97.22%, while Sp of BC was 99.7%, 99.5%, 99.2%, and 98.9%. The estimated prevalence of S. agalactiae IMI by PCR was higher than the apparent prevalence at the tested cut-offs, indicating under estimation of S. agalactiae IMI in the examined dairy cows. In conclusion, Se of PCR is always higher than Se of BC at all tested cut-offs. The lower cut-off, the more comparable becomes Se of PCR and Se of BC. The changes in Se in both PCR and BC at different Ct-value cut-offs may indicate a change in the definition of the latent infection. The similar Se of both tests at cut-off ≤ 32 may indicate high concentrations of S. agalactiae viable cells, representing a cow truly/heavily infected with S. agalactiae and thus easier to detect with BC. At cut-off ≤ 39 the latent definition of infection may reflect a more general condition of cows being positive for S. agalactiae. Our findings indicate that PCR Ct-value cut-offs should

  11. Attenuation of species abundance distributions by sampling

    Science.gov (United States)

    Shimadzu, Hideyasu; Darnell, Ross

    2015-01-01

    Quantifying biodiversity aspects such as species presence/ absence, richness and abundance is an important challenge to answer scientific and resource management questions. In practice, biodiversity can only be assessed from biological material taken by surveys, a difficult task given limited time and resources. A type of random sampling, or often called sub-sampling, is a commonly used technique to reduce the amount of time and effort for investigating large quantities of biological samples. However, it is not immediately clear how (sub-)sampling affects the estimate of biodiversity aspects from a quantitative perspective. This paper specifies the effect of (sub-)sampling as attenuation of the species abundance distribution (SAD), and articulates how the sampling bias is induced to the SAD by random sampling. The framework presented also reveals some confusion in previous theoretical studies. PMID:26064626

  12. Big-Bang nucleosynthesis and lithium abundance

    International Nuclear Information System (INIS)

    Singh, Vinay; Lahiri, Joydev; Bhowmick, Debasis; Basu, D.N.

    2017-01-01

    The predictions of the standard big-bang nucleosynthesis (BBN) theory depend on the astrophysical nuclear reaction rates and on additional three parameters, the number of flavours of light neutrinos, the neutron lifetime and the baryon-to-photon ratio in the uni- verse. The effect of the modification of thirty-five reaction rates on light element abundance yields in BBN was investigated earlier by us. In the present work we have replaced the neutron lifetime, baryon-to-photon ratio by the most recent values and further modified 3 He( 4 He,γ) 7 Be reaction rate which is used directly for estimating the formation of 7 Li as a result of β + decay by the most recent equation. We find that these modifications reduce the calculated abundance of 7 Li by ∼ 12%

  13. Understanding and reducing statistical uncertainties in nebular abundance determinations

    Science.gov (United States)

    Wesson, R.; Stock, D. J.; Scicluna, P.

    2012-06-01

    Whenever observations are compared to theories, an estimate of the uncertainties associated with the observations is vital if the comparison is to be meaningful. However, many or even most determinations of temperatures, densities and abundances in photoionized nebulae do not quote the associated uncertainty. Those that do typically propagate the uncertainties using analytical techniques which rely on assumptions that generally do not hold. Motivated by this issue, we have developed Nebular Empirical Analysis Tool (NEAT), a new code for calculating chemical abundances in photoionized nebulae. The code carries out a standard analysis of lists of emission lines using long-established techniques to estimate the amount of interstellar extinction, calculate representative temperatures and densities, compute ionic abundances from both collisionally excited lines and recombination lines, and finally to estimate total elemental abundances using an ionization correction scheme. NEATuses a Monte Carlo technique to robustly propagate uncertainties from line flux measurements through to the derived abundances. We show that, for typical observational data, this approach is superior to analytic estimates of uncertainties. NEAT also accounts for the effect of upward biasing on measurements of lines with low signal-to-noise ratio, allowing us to accurately quantify the effect of this bias on abundance determinations. We find not only that the effect can result in significant overestimates of heavy element abundances derived from weak lines, but also that taking it into account reduces the uncertainty of these abundance determinations. Finally, we investigate the effect of possible uncertainties in R, the ratio of selective-to-total extinction, on abundance determinations. We find that the uncertainty due to this parameter is negligible compared to the statistical uncertainties due to typical line flux measurement uncertainties.

  14. Bacterial Rhizosphere Biodiversity from Several Pioneer Desert Sand Plants Near Jizan, Saudi Arabia

    KAUST Repository

    Osman, Jorge R.; Zelicourt, Axel de; Bisseling, Ton; Geurts, Rene; Hirt, Heribert; DuBow, Michael S.

    2016-01-01

    Life in arid regions and, in particular, hot deserts is often limited due to their harsh environmental conditions, such as large temperature fluctuations and low amounts of water. These extreme environments can influence the microbial community present on the surface sands and any rhizosphere members surrounding desert plant roots. The Jizan desert area, located in Saudi Arabia, supports particular vegetation that grows in the large sandy flat terrain. We examined five different samples, four from the rhizosphere of pioneer plants plus a surface sand sample, and used pyrosequencing of PCR-amplified V1-V3 regions of 16S rDNA genes from total extracted DNA to reveal and compare the bacterial population diversity of the samples. The results showed a total of 3,530 OTUs in the five samples, calculated using ≥ 97% sequence similarity levels. The Chao1 estimation of the bacterial diversity fluctuated from 637 to 2,026 OTUs for a given sample. The most abundant members found in the samples belong to the Bacteroidetes, Firmicutes and Proteobacteria phyla. This work shows that the Jizan desert area of Saudi Arabia can contain a diverse bacterial community on the sand and surrounding the roots of pioneer desert plants. It also shows that desert sand microbiomes can vary depending on conditions, with broad implications for sandstone monument bacterial communities

  15. Bacterial diversity of surface sand samples from the Gobi and Taklamaken deserts.

    Science.gov (United States)

    An, Shu; Couteau, Cécile; Luo, Fan; Neveu, Julie; DuBow, Michael S

    2013-11-01

    Arid regions represent nearly 30 % of the Earth's terrestrial surface, but their microbial biodiversity is not yet well characterized. The surface sands of deserts, a subset of arid regions, are generally subjected to large temperature fluctuations plus high UV light exposure and are low in organic matter. We examined surface sand samples from the Taklamaken (China, three samples) and Gobi (Mongolia, two samples) deserts, using pyrosequencing of PCR-amplified 16S V1/V2 rDNA sequences from total extracted DNA in order to gain an assessment of the bacterial population diversity. In total, 4,088 OTUs (using ≥97 % sequence similarity levels), with Chao1 estimates varying from 1,172 to 2,425 OTUs per sample, were discernable. These could be grouped into 102 families belonging to 15 phyla, with OTUs belonging to the Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria phyla being the most abundant. The bacterial population composition was statistically different among the samples, though members from 30 genera were found to be common among the five samples. An increase in phylotype numbers with increasing C/N ratio was noted, suggesting a possible role in the bacterial richness of these desert sand environments. Our results imply an unexpectedly large bacterial diversity residing in the harsh environment of these two Asian deserts, worthy of further investigation.

  16. Bacterial Rhizosphere Biodiversity from Several Pioneer Desert Sand Plants Near Jizan, Saudi Arabia

    KAUST Repository

    Osman, Jorge R.

    2016-04-08

    Life in arid regions and, in particular, hot deserts is often limited due to their harsh environmental conditions, such as large temperature fluctuations and low amounts of water. These extreme environments can influence the microbial community present on the surface sands and any rhizosphere members surrounding desert plant roots. The Jizan desert area, located in Saudi Arabia, supports particular vegetation that grows in the large sandy flat terrain. We examined five different samples, four from the rhizosphere of pioneer plants plus a surface sand sample, and used pyrosequencing of PCR-amplified V1-V3 regions of 16S rDNA genes from total extracted DNA to reveal and compare the bacterial population diversity of the samples. The results showed a total of 3,530 OTUs in the five samples, calculated using ≥ 97% sequence similarity levels. The Chao1 estimation of the bacterial diversity fluctuated from 637 to 2,026 OTUs for a given sample. The most abundant members found in the samples belong to the Bacteroidetes, Firmicutes and Proteobacteria phyla. This work shows that the Jizan desert area of Saudi Arabia can contain a diverse bacterial community on the sand and surrounding the roots of pioneer desert plants. It also shows that desert sand microbiomes can vary depending on conditions, with broad implications for sandstone monument bacterial communities

  17. Ammonia abundances in four comets

    International Nuclear Information System (INIS)

    Wickoff, S.; Tegler, S.C.; Engel, L.

    1991-01-01

    NH2 emission band strengths were measured in four comets and the NH2 column densities were determined in order to measure the ammonia content of the comets. The mean ammonia/water abundance ratio derived for the four comets is found to be 0.13 + or - 0.06 percent, with no significant variation among the comets. The uniformity of this abundance attests to a remarkable degree of chemical homogeneity over large scales in the comet-forming region of the primordial solar nebula, and contrasts with the CO abundance variations found previously in comets. The N2 and NH3 abundances indicate a condensation temperature in the range 20-160 K, consistent with virtually all comet formation hypotheses. 64 refs

  18. Magellanic Clouds Cepheids: Thorium Abundances

    Directory of Open Access Journals (Sweden)

    Yeuncheol Jeong

    2018-03-01

    Full Text Available The analysis of the high-resolution spectra of 31 Magellanic Clouds Cepheid variables enabled the identification of thorium lines. The abundances of thorium were found with spectrum synthesis method. The calculated thorium abundances exhibit correlations with the abundances of other chemical elements and atmospheric parameters of the program stars. These correlations are similar for both Clouds. The correlations of iron abundances of thorium, europium, neodymium, and yttrium relative to the pulsational periods are different in the Large Magellanic Cloud (LMC and the Small Magellanic Cloud (SMC, namely the correlations are negative for LMC and positive or close to zero for SMC. One of the possible explanations can be the higher activity of nucleosynthesis in SMC with respect to LMC in the recent several hundred million years.

  19. NEFSC Survey Indices of Abundance

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Northeast Fisheries Survey Bottom trawl survey indices of abundance such as stratified mean number per tow or mean weight per tow by species stock. Includes indices...

  20. Relative Abundance of Carsonella ruddii (Gamma Proteobacterium) in Females and Males of Cacopsylla pyricola (Hemiptera: Psyllidae) and Bactericera cockerelli (Hemiptera: Triozidae)

    Science.gov (United States)

    Cooper, W. Rodney; Garczynski, Stephen F.; Horton, David R.

    2015-01-01

    Carsonella ruddii (Gamma Proteobacterium) is an obligate bacterial endosymbiont of psyllids that produces essential amino acids that are lacking in the insect’s diet. Accurate estimations of Carsonella populations are important to studies of Carsonella-psyllid interactions and to developing ways to target Carsonella for control of psyllid pests including pear psylla, Cacopsylla pyricola (Förster) (Hemiptera: Psyllidae) and potato psyllid, Bactericera cockerelli (Šulc) (Hemiptera: Triozidae). We used two methods, namely fluorescence in situ hybridization and quantitative polymerase chain reaction (qPCR), to estimate relative abundance of Carsonella in bacteriocytes and whole bodies of psyllids, respectively. Using these two methods, we compared Carsonella populations between female and male insects. Estimations using fluorescence in situ hybridization indicated that Carsonella was more abundant in bacteriocytes of female C. pyricola than in those of males, but Carsonella abundance in bacteriocytes did not differ between sexes of B. cockerelli. Analyses by qPCR using whole-body specimens indicated Carsonella was more abundant in females than in males of both psyllids. Neither fluorescence in situ hybridization nor qPCR indicated that Carsonella populations differed in abundance among adults of different ages (0–3 wk after adult eclosion). Using fluorescence in situ hybridization, Carsonella was observed in ovarioles of newly emerged females and formed an aggregation in the posterior end of mature oocytes. Results of our study indicate that female psyllids harbor greater populations of Carsonella than do males and that sex should be controlled for in studies which require estimations of Carsonella populations. PMID:26056318

  1. Antibiotics promote aggregation within aquatic bacterial communities

    Directory of Open Access Journals (Sweden)

    Gianluca eCorno

    2014-07-01

    Full Text Available The release of antibiotics (AB into the environment poses several threats for human health due to potential development of ABresistant natural bacteria. Even though the use of low-dose antibiotics has been promoted in health care and farming, significant amounts of AB are observed in aquatic environments. Knowledge on the impact of AB on natural bacterial communities is missing both in terms of spread and evolution of resistance mechanisms, and of modifications of community composition and productivity. New approaches are required to study the response of microbial communities rather than individual resistance genes. In this study a chemostat-based experiment with 4 coexisting bacterial strains has been performed to mimicking the response of a freshwater bacterial community to the presence of antibiotics in low and high doses. Bacterial abundance rapidly decreased by 75% in the presence of AB, independently of their concentration, and remained constant until the end of the experiment. The bacterial community was mainly dominated by Aeromonas hydrophila and Brevundimonas intermedia while the other two strains, Micrococcus luteus and Rhodococcus sp. never exceed 10%. Interestingly, the bacterial strains, which were isolated at the end of the experiment, were not AB-resistant, while reassembled communities composed of the 4 strains, isolated from treatments under AB stress, significantly raised their performance (growth rate, abundance in the presence of AB compared to the communities reassembled with strains isolated from the treatment without AB. By investigating the phenotypic adaptations of the communities subjected to the different treatments, we found that the presence of AB significantly increased co-aggregation by 5-6 fold.These results represent the first observation of co-aggregation as a successful strategy of AB resistance based on phenotype in aquatic bacterial communities, and can represent a fundamental step in the understanding of

  2. Characterisation of the gill mucosal bacterial communities of four butterflyfish species: a reservoir of bacterial diversity in coral reef ecosystems.

    Science.gov (United States)

    Reverter, Miriam; Sasal, Pierre; Tapissier-Bontemps, N; Lecchini, D; Suzuki, M

    2017-06-01

    While recent studies have suggested that fish mucus microbiota play an important role in homeostasis and prevention of infections, very few studies have investigated the bacterial communities of gill mucus. We characterised the gill mucus bacterial communities of four butterflyfish species and although the bacterial diversity of gill mucus varied significantly between species, Shannon diversities were high (H = 3.7-5.7) in all species. Microbiota composition differed between butterflyfishes, with Chaetodon lunulatus and C. ornatissimus having the most similar bacterial communities, which differed significantly from C. vagabundus and C. reticulatus. The core bacterial community of all species consisted of mainly Proteobacteria followed by Actinobacteria and Firmicutes. Chaetodonlunulatus and C. ornatissimus bacterial communities were mostly dominated by Gammaproteobacteria with Vibrio as the most abundant genus. Chaetodonvagabundus and C. reticulatus presented similar abundances of Gammaproteobacteria and Alphaproteobacteria, which were well represented by Acinetobacter and Paracoccus, respectively. In conclusion, our results indicate that different fish species present specific bacterial assemblages. Finally, as mucus layers are nutrient hotspots for heterotrophic bacteria living in oligotrophic environments, such as coral reef waters, the high bacterial diversity found in butterflyfish gill mucus might indicate external fish mucus surfaces act as a reservoir of coral reef bacterial diversity. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  3. Hydrocarbon Reserves: Abundance or Scarcity

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2005-07-01

    of reserves and resources (H. Le Leuch); Additional reserves: the role of new technologies - A global perspective on EORIOR (G. Fries); - Updating reservoir models with dynamic data and uncertainty quantification: an integrated approach (F. Roggero); Seismic technology for the OAPEC countries (P. Canal); Exploration knowledge and technologies: impact of progress - Statistical results (N. Alazard); Stratigraphic modelling as a key to find new potentialities in exploration (D. Granjeon); Modelling hydrocarbon migration as a tool for reserve estimation (J-L. Rudkiewicz); The contribution of surface and near surface geology to hydrocarbon discoveries (S.M. Kumati); Contribution of the exploration activity in renewing reserves - The case of Algeria (R. Lounissi); Egypt's petroleum hydrocarbon potential (H. Hataba); Future of hydrocarbon reserves in Syria (T. Hemsh); Natural gas, the fuel of choice for decades to com (M.F. Chabrelie); The role and importance of Arab natural gas in world market (M. Al-Lababidi); LNG and GTL: two pathways for natural gas utilization (C. Cameron); Yet to find hydrocarbon potential (S. Al Menhali); Libyan context of hydrocarbon reserves: abundance or scarcity? (M. Elazi)

  4. Hydrocarbon Reserves: Abundance or Scarcity

    International Nuclear Information System (INIS)

    2005-01-01

    of reserves and resources (H. Le Leuch); Additional reserves: the role of new technologies - A global perspective on EORIOR (G. Fries); - Updating reservoir models with dynamic data and uncertainty quantification: an integrated approach (F. Roggero); Seismic technology for the OAPEC countries (P. Canal); Exploration knowledge and technologies: impact of progress - Statistical results (N. Alazard); Stratigraphic modelling as a key to find new potentialities in exploration (D. Granjeon); Modelling hydrocarbon migration as a tool for reserve estimation (J-L. Rudkiewicz); The contribution of surface and near surface geology to hydrocarbon discoveries (S.M. Kumati); Contribution of the exploration activity in renewing reserves - The case of Algeria (R. Lounissi); Egypt's petroleum hydrocarbon potential (H. Hataba); Future of hydrocarbon reserves in Syria (T. Hemsh); Natural gas, the fuel of choice for decades to com (M.F. Chabrelie); The role and importance of Arab natural gas in world market (M. Al-Lababidi); LNG and GTL: two pathways for natural gas utilization (C. Cameron); Yet to find hydrocarbon potential (S. Al Menhali); Libyan context of hydrocarbon reserves: abundance or scarcity? (M. Elazi)

  5. Hydrocarbon Reserves: Abundance or Scarcity

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2005-07-01

    impact on the growth of reserves and resources (H. Le Leuch); Additional reserves: the role of new technologies - A global perspective on EORIOR (G. Fries); - Updating reservoir models with dynamic data and uncertainty quantification: an integrated approach (F. Roggero); Seismic technology for the OAPEC countries (P. Canal); Exploration knowledge and technologies: impact of progress - Statistical results (N. Alazard); Stratigraphic modelling as a key to find new potentialities in exploration (D. Granjeon); Modelling hydrocarbon migration as a tool for reserve estimation (J-L. Rudkiewicz); The contribution of surface and near surface geology to hydrocarbon discoveries (S.M. Kumati); Contribution of the exploration activity in renewing reserves - The case of Algeria (R. Lounissi); Egypt's petroleum hydrocarbon potential (H. Hataba); Future of hydrocarbon reserves in Syria (T. Hemsh); Natural gas, the fuel of choice for decades to com (M.F. Chabrelie); The role and importance of Arab natural gas in world market (M. Al-Lababidi); LNG and GTL: two pathways for natural gas utilization (C. Cameron); Yet to find hydrocarbon potential (S. Al Menhali); Libyan context of hydrocarbon reserves: abundance or scarcity? (M. Elazi)

  6. Abundance Survey of M and K Dwarf Stars

    Energy Technology Data Exchange (ETDEWEB)

    Woolf, Vincent M. [Astronomy Department, University of Washington, Seattle, WA 98133 (United States); Wallerstein, George [Astronomy Department, University of Washington, Seattle, WA 98133 (United States)

    2005-07-25

    We report the measurement of chemical abundances in 35 low-mass main sequence (M and K dwarf) stars. We have measured the abundance of 12 elements in Kapteyn's Star, a nearby halo M subdwarf. The abundances indicate an iron abundance of [Fe/H] = -0.98, which is about 0.5 dex smaller than that measured in the only previous published measurement using atomic absorption lines. We have measured Fe and Ti abundances in 35 M and K dwarfs with -2.39 [Fe/H] +0.21 using atomic absorption lines, mostly in the 8000A <{lambda} < 8850A range. These will be used to calibrate photometric and low-resolution spectrum metallicity indices for low mass dwarfs, which will make metallicity estimates for these stars more certain. We also describe some difficulties encountered which are not normally necessary to consider when studying warmer stars.

  7. Chemical mediation of bacterial surface colonisation by secondary metabolites from the red alga Delisea pulchra

    DEFF Research Database (Denmark)

    Maximilien, Ria; de Nys, Rocky; Holmström, Carola

    1998-01-01

    -occurring algal species, all of which lack furanones. There was also a strong inverse correlation between bacterial abundance and furanone content (previously determined) for different sections of the thallus of D. pulchra, consistent with inhibition of bacteria by furanones. Based on these observations we....... pulchra the most. As inhibition of growth did not provide an adequate explanation for the inverse relationship between levels of furanones and bacteria abundance on D. pulchra, we proceeded to investigate the effects of these metabolites on other bacterial characteristics relevant to colonisation...... of different bacterial isolates or phenotypes by furanones, as well as affecting overall bacterial abundance on the alga, should have strong effects on the species composition of the bacterial community on the alga's surface. The effects of furanones on specific bacterial colonisation traits are discussed...

  8. C-reactive protein and bacterial meningitis

    DEFF Research Database (Denmark)

    Gerdes, Lars Ulrik; Jørgensen, P E; Nexø, E

    1998-01-01

    The aim of the study was to review published articles on the diagnostic accuracy of C-reactive protein (CRP) tests with cerebrospinal fluid and serum in diagnosing bacterial meningitis. The literature from 1980 and onwards was searched using the electronic databases of MEDLINE, and we used summary...... measured in serum, and 4 in which it had been measured in both cerebrospinal fluid and serum. The odds ratio for bacterial meningitis versus aseptic meningitis for a positive CRP test with cerebrospinal fluid was estimated at 241 (95% confidence interval [CI]: 59-980), and the central tendencies.......06-0.08, respectively, the post-test probability of not having bacterial meningitis given a negative test is very high (> or = 97%), in the range of a pre-test probability (prevalence of bacterial meningitis) from 10 to 30%, whereas the post-test probability of bacterial meningitis given a positive test is considerably...

  9. Detecting significant changes in protein abundance

    Directory of Open Access Journals (Sweden)

    Kai Kammers

    2015-06-01

    Full Text Available We review and demonstrate how an empirical Bayes method, shrinking a protein's sample variance towards a pooled estimate, leads to far more powerful and stable inference to detect significant changes in protein abundance compared to ordinary t-tests. Using examples from isobaric mass labelled proteomic experiments we show how to analyze data from multiple experiments simultaneously, and discuss the effects of missing data on the inference. We also present easy to use open source software for normalization of mass spectrometry data and inference based on moderated test statistics.

  10. Geographical range and local abundance of tree species in China.

    Directory of Open Access Journals (Sweden)

    Haibao Ren

    Full Text Available Most studies on the geographical distribution of species have utilized a few well-known taxa in Europe and North America, with little research in China and its wide range of climate and forest types. We assembled large datasets to quantify the geographic ranges of tree species in China and to test several biogeographic hypotheses: 1 whether locally abundant species tend to be geographically widespread; 2 whether species are more abundant towards their range-centers; and 3 how abundances are correlated between sites. Local abundances of 651 species were derived from four tree plots of 20-25 ha where all individuals ≥1 cm in stem diameter were mapped and identified taxonomically. Range sizes of these species across China were then estimated from over 460,000 geo-referenced records; a Bayesian approach was used, allowing careful measures of error of each range estimate. The log-transformed range sizes had a bell-shaped distribution with a median of 703,000 km(2, and >90% of 651 species had ranges >10(5 km(2. There was no relationship between local abundance and range size, and no evidence for species being more abundant towards their range-centers. Finally, species' abundances were positively correlated between sites. The widespread nature of most tree species in China suggests few are vulnerable to global extinction, and there is no indication of the double-peril that would result if rare species also had narrow ranges.

  11. Analysis of bacterial communities and bacterial pathogens in a biogas plant by the combination of ethidium monoazide, PCR and Ion Torrent sequencing.

    Science.gov (United States)

    Luo, Gang; Angelidaki, Irini

    2014-09-01

    The present study investigated the changes of bacterial community composition including bacterial pathogens along a biogas plant, i.e. from the influent, to the biogas reactor and to the post-digester. The effects of post-digestion temperature and time on the changes of bacterial community composition and bacterial pathogens were also studied. Microbial analysis was made by Ion Torrent sequencing of the PCR amplicons from ethidium monoazide treated samples, and ethidium monoazide was used to cleave DNA from dead cells and exclude it from PCR amplification. Both similarity and taxonomic analysis showed that the bacterial community composition in the influent was changed after anaerobic digestion. Firmicutes were dominant in all the samples, while Proteobacteria decreased in the biogas reactor compared with the influent. Variations of bacterial community composition in the biogas reactor with time were also observed. This could be attributed to varying composition of the influent. Batch experiments showed that the methane recovery from the digested residues (obtained from biogas reactor) was mainly related with post-digestion temperature. However, post-digestion time rather than temperature had a significant effect on the changes of bacterial community composition. The changes of bacterial community composition were also reflected in the changes of relative abundance of bacterial pathogens. The richness and relative abundance of bacterial pathogens were reduced after anaerobic digestion in the biogas reactor. It was found in batch experiments that bacterial pathogens showed the highest relative abundance and richness after 30 days' post-digestion. Streptococcus bovis was found in all the samples. Our results showed that special attention should be paid to the post-digestion since the increase in relative abundance of bacterial pathogens after post-digestion might reflect regrowth of bacterial pathogens and limit biosolids disposal vectors. Copyright © 2014 Elsevier

  12. Uranium abundance in some sudanese phosphate ores

    International Nuclear Information System (INIS)

    Adam, A.A.; Eltayeb, M.A.H.

    2009-01-01

    This work was carried out mainly to analysis of some Sudanese phosphate ores, for their uranium abundance and total phosphorus content measured as P 2 O 5 %. For this purpose, 30 samples of two types of phosphate ore from Eastern Nuba Mountains, in Sudan namely, Kurun and Uro areas were examined. In addition, the relationship between uranium and major, and trace elements were obtained, also, the natural radioactivity of the phosphate samples was measured, in order to characterize and differentiate between the two types of phosphate ores. The uranium abundance in Uro phosphate with 20.3% P 2 O 5 is five time higher than in Kurun phosphate with 26.7% P 2 O 5 . The average of uranium content was found to be 56.6 and 310 mg/kg for Kurun and Uro phosphate ore, respectively. The main elements in Kurun and Uro phosphate ore are silicon, aluminum, and phosphorus, while the most abundant trace elements in these two ores are titanium, strontium and barium. Pearson correlation coefficient revealed that uranium in Kurun phosphate shows strong positive correlation with P 2 O 5 , and its distribution is essentially controlled by the variations of P2O5 concentration, whereas uranium in Uro phosphate shows strong positive correlation with strontium, and its distribution is controlled by the variations of Sr concentration. Uranium behaves in different ways in Kurun phosphate and in Uro phosphate. Uro phosphate shows higher concentrations of all the estimated radionuclides than Kurun phosphate. According to the obtained results, it can be concluded that Uro phosphate is consider as secondary uranium source, and is more suitable for uranium recovery, because it has high uranium abundance and low P 2 O 5 %, than Kurun phosphate. (authors) [es

  13. Nitrogen abundance in Comet Halley

    International Nuclear Information System (INIS)

    Wyckoff, S.; Tegler, S.C.; Engel, L.

    1991-01-01

    Data on the nitrogen-containing compounds that observed spectroscopically in the coma of Comet Halley are summarized, and the elemental abundance of nitrogen in the Comet Halley nucleus is derived. It is found that 90 percent of elemental nitrogen is in the dust fraction of the coma, while in the gas fraction, most of the nitrogen is contained in NH3 and CN. The elemental nitrogen abundance in the ice component of the nucleus was found to be deficient by a factor of about 75, relative to the solar photosphere, indicating that the chemical partitioning of N2 into NH3 and other nitrogen compounds during the evolution of the solar nebula cannot account completely for the low abundance ratio N2/NH3 = 0.1, observed in the comet. It is suggested that the low N2/NH3 ratio in Comet Halley may be explained simply by physical fractionation and/or thermal diffusion. 88 refs

  14. CHLORINE ABUNDANCES IN COOL STARS

    Energy Technology Data Exchange (ETDEWEB)

    Maas, Z. G.; Pilachowski, C. A. [Indiana University Bloomington, Astronomy Department, Swain West 319, 727 East Third Street, Bloomington, IN 47405-7105 (United States); Hinkle, K., E-mail: zmaas@indiana.edu, E-mail: cpilacho@indiana.edu, E-mail: hinkle@noao.edu [National Optical Astronomy Observatory, P.O. Box 26732, Tucson, AZ 85726 (United States)

    2016-12-01

    Chlorine abundances are reported in 15 evolved giants and 1 M dwarf in the solar neighborhood. The Cl abundance was measured using the vibration-rotation 1-0 P8 line of H{sup 35}Cl at 3.69851 μ m. The high-resolution L -band spectra were observed using the Phoenix infrared spectrometer on the Kitt Peak Mayall 4 m telescope. The average [{sup 35}Cl/Fe] abundance in stars with −0.72 < [Fe/H] < 0.20 is [{sup 35}Cl/Fe] = (−0.10 ± 0.15) dex. The mean difference between the [{sup 35}Cl/Fe] ratios measured in our stars and chemical evolution model values is (0.16 ± 0.15) dex. The [{sup 35}Cl/Ca] ratio has an offset of ∼0.35 dex above model predictions, suggesting that chemical evolution models are underproducing Cl at the high metallicity range. Abundances of C, N, O, Si, and Ca were also measured in our spectral region and are consistent with F and G dwarfs. The Cl versus O abundances from our sample match Cl abundances measured in planetary nebula and H ii regions. In one star where both H{sup 35}Cl and H{sup 37}Cl could be measured, a {sup 35}Cl/{sup 37}Cl isotope ratio of 2.2 ± 0.4 was found, consistent with values found in the Galactic ISM and predicted chemical evolution models.

  15. Spatial and Species Variations in Bacterial Communities Associated with Corals from the Red Sea as Revealed by Pyrosequencing

    KAUST Repository

    Lee, O. O.

    2012-08-03

    Microbial associations with corals are common and are most likely symbiotic, although their diversity and relationships with environmental factors and host species remain unclear. In this study, we adopted a 16S rRNA gene tag-pyrosequencing technique to investigate the bacterial communities associated with three stony Scleractinea and two soft Octocorallia corals from three locations in the Red Sea. Our results revealed highly diverse bacterial communities in the Red Sea corals, with more than 600 ribotypes detected and up to 1,000 species estimated from a single coral species. Altogether, 21 bacterial phyla were recovered from the corals, of which Gammaproteobacteria was the most dominant group, and Chloroflexi, Chlamydiae, and the candidate phylum WS3 were reported in corals for the first time. The associated bacterial communities varied greatly with location, where environmental conditions differed significantly. Corals from disturbed areas appeared to share more similar bacterial communities, but larger variations in community structures were observed between different coral species from pristine waters. Ordination methods identified salinity and depth as the most influential parameters affecting the abundance of Vibrio, Pseudoalteromonas, Serratia, Stenotrophomonas, Pseudomonas, and Achromobacter in the corals. On the other hand, bacteria such as Chloracidobacterium and Endozoicomonas were more sensitive to the coral species, suggesting that the host species type may be influential in the associated bacterial community, as well. The combined influences of the coral host and environmental factors on the associated microbial communities are discussed. This study represents the first comparative study using tag-pyrosequencing technology to investigate the bacterial communities in Red Sea corals.

  16. [Bacterial diversity within different sections of summer sea-ice samples from the Prydz Bay, Antarctica].

    Science.gov (United States)

    Ma, Jifei; Du, Zongjun; Luo, Wei; Yu, Yong; Zeng, Yixin; Chen, Bo; Li, Huirong

    2013-02-04

    In order to assess bacterial abundance and diversity within three different sections of summer sea-ice samples collected from the Prydz Bay, Antarctica. Fluorescence in situ hybridization was applied to determine the proportions of Bacteria in sea-ice. Bacterial community composition within sea ice was analyzed by 16S rRNA gene clone library construction. Correlation analysis was performed between the physicochemical parameters and the bacterial diversity and abundance within sea ice. The result of fluorescence in situ hybridization shows that bacteria were abundant in the bottom section, and the concentration of total organic carbon, total organic nitrogen and phosphate may be the main factors for bacterial abundance. In bacterial 16S rRNA gene libraries of sea-ice, nearly complete 16S rRNA gene sequences were grouped into three distinct lineages of Bacteria (gamma-Proteobacteria, alpha-Proteobacteria and Bacteroidetes). Most clone sequences were related to cultured bacterial isolates from the marine environment, arctic and Antarctic sea-ice with high similarity. The member of Bacteroidetes was not detected in the bottom section of sea-ice. The bacterial communities within sea-ice were little heterogeneous at the genus-level between different sections, and the concentration of NH4+ may cause this distribution. The number of bacteria was abundant in the bottom section of sea-ice. Gamma-proteobacteria was the dominant bacterial lineage in sea-ice.

  17. Chinook Abundance - Point Features [ds180

    Data.gov (United States)

    California Natural Resource Agency — The CalFish Abundance Database contains a comprehensive collection of anadromous fisheries abundance information. Beginning in 1998, the Pacific States Marine...

  18. Steelhead Abundance - Linear Features [ds185

    Data.gov (United States)

    California Natural Resource Agency — The CalFish Abundance Database contains a comprehensive collection of anadromous fisheries abundance information. Beginning in 1998, the Pacific States Marine...

  19. Steelhead Abundance - Point Features [ds184

    Data.gov (United States)

    California Natural Resource Agency — The CalFish Abundance Database contains a comprehensive collection of anadromous fisheries abundance information. Beginning in 1998, the Pacific States Marine...

  20. Coho Abundance - Linear Features [ds183

    Data.gov (United States)

    California Natural Resource Agency — The CalFish Abundance Database contains a comprehensive collection of anadromous fisheries abundance information. Beginning in 1998, the Pacific States Marine...

  1. Coho Abundance - Point Features [ds182

    Data.gov (United States)

    California Natural Resource Agency — The CalFish Abundance Database contains a comprehensive collection of anadromous fisheries abundance information. Beginning in 1998, the Pacific States Marine...

  2. Distribution and abundance of West Greenland humpback whales ( Megaptera novaeangliae )

    DEFF Research Database (Denmark)

    Larsen, Finn; Hammond, P.S.

    2004-01-01

    Photo-identification surveys of humpback whales Megaptera novaeangliae were conducted at West Greenland during 1988-93, the last 2 years of which were part of the internationally coordinated humpback whale research programme YoNAH, with the primary aim of estimating abundance for the West Greenland...... effort. A total of 670 groups of humpback whales was encountered leading to the identification of 348 individual animals. Three areas of concentration were identified: an area off Nuuk; an area at c. 63degrees30'N; and an area off Frederikshab. Sequential Petersen capture-recapture estimates of abundance...

  3. Autoproteolytic Activation of Bacterial Toxins

    Directory of Open Access Journals (Sweden)

    Aimee Shen

    2010-05-01

    Full Text Available Protease domains within toxins typically act as the primary effector domain within target cells. By contrast, the primary function of the cysteine protease domain (CPD in Multifunctional Autoprocessing RTX-like (MARTX and Clostridium sp. glucosylating toxin families is to proteolytically cleave the toxin and release its cognate effector domains. The CPD becomes activated upon binding to the eukaryotic-specific small molecule, inositol hexakisphosphate (InsP6, which is found abundantly in the eukaryotic cytosol. This property allows the CPD to spatially and temporally regulate toxin activation, making it a prime candidate for developing anti-toxin therapeutics. In this review, we summarize recent findings related to defining the regulation of toxin function by the CPD and the development of inhibitors to prevent CPD-mediated activation of bacterial toxins.

  4. Ecotype diversification of an abundant Roseobacter lineage.

    Science.gov (United States)

    Sun, Ying; Zhang, Yao; Hollibaugh, James T; Luo, Haiwei

    2017-04-01

    The Roseobacter DC5-80-3 cluster (also known as the RCA clade) is among the most abundant bacterial lineages in temperate and polar oceans. Previous studies revealed two phylotypes within this cluster that are distinctly distributed in the Antarctic and other ocean provinces. Here, we report a nearly complete genome co-assembly of three closely related single cells co-occurring in the Antarctic, and compare it to the available genomes of the other phylotype from ocean regions where iron is more accessible but phosphorus and nitrogen are less. The Antarctic phylotype exclusively contains an operon structure consisting of a dicitrate transporter fecBCDE and an upstream regulator likely for iron uptake, whereas the other phylotype consistently carry a high-affinity phosphate pst transporter and the phoB-phoR regulatory system, a high-affinity ammonium amtB transporter, urea and taurine utilization systems. Moreover, the Antarctic phylotype uses proteorhodopsin to acquire light, whereas the other uses bacteriochlorophyll-a and the sulfur-oxidizing sox cluster for energy acquisition. This is potentially an iron-saving strategy for the Antarctic phylotype because only the latter two pathways have iron-requiring cytochromes. Therefore, the two DC5-80-3 phylotypes, while diverging by only 1.1% in their 16S rRNA genes, have evolved systematic differences in metabolism to support their distinct ecologies. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  5. Significant relationship between soil bacterial community structure and incidence of bacterial wilt disease under continuous cropping system.

    Science.gov (United States)

    She, Siyuan; Niu, Jiaojiao; Zhang, Chao; Xiao, Yunhua; Chen, Wu; Dai, Linjian; Liu, Xueduan; Yin, Huaqun

    2017-03-01

    Soil bacteria are very important in biogeochemical cycles and play significant role in soil-borne disease suppression. Although continuous cropping is responsible for soil-borne disease enrichment, its effect on tobacco plant health and how soil bacterial communities change are yet to be elucidated. In this study, soil bacterial communities across tobacco continuous cropping time-series fields were investigated through high-throughput sequencing of 16S ribosomal RNA genes. The results showed that long-term continuous cropping could significantly alter soil microbial communities. Bacterial diversity indices and evenness indices decreased over the monoculture span and obvious variations for community structures across the three time-scale tobacco fields were detected. Compared with the first year, the abundances of Arthrobacter and Lysobacter showed a significant decrease. Besides, the abundance of the pathogen Ralstonia spp. accumulated over the monoculture span and was significantly correlated with tobacco bacterial wilt disease rate. Moreover, Pearson's correlation demonstrated that the abundance of Arthrobacter and Lysobacter, which are considered to be beneficial bacteria had significant negative correlation with tobacco bacterial wilt disease. Therefore, after long-term continuous cropping, tobacco bacterial wilt disease could be ascribed to the alteration of the composition as well as the structure of the soil microbial community.

  6. Bacterial lung abscess

    International Nuclear Information System (INIS)

    Groskin, S.A.; Panicek, D.M.; Ewing, D.K.; Rivera, F.; Math, K.; Teixeira, J.; Heitzman, E.R.

    1987-01-01

    A retrospective review of patients with bacterial lung abscess was carried out. Demographic, clinical, and radiographical features of this patient group are compared with similar data from patients with empyema and/or cavitated lung carcinoma; differential diagnostic points are stressed. The entity of radiographically occult lung abscess is discussed. Complications associated with bacterial lung abscess are discussed. Current therapeutic options and treatment philosophy for patients with bacterial lung abscess are noted

  7. Heterotrophic free-living and particle-bound bacterial cell size in the ...

    Indian Academy of Sciences (India)

    PRAKASH

    the heterotrophic bacterial cell size in the various water bodies studied in this investigation. The possible ... seasonal changes in abundance and cell size of heterotrophic ... data, 1995) physiological stress indicated by the presence of small ...

  8. Microbiological studies in schirmacher oasis, Antarctica: Effect of temperature on bacterial populations

    Digital Repository Service at National Institute of Oceanography (India)

    Matondkar, S.G.P.

    Seasonal and site wise variation in size and diversity of bacterial population was observed in Schirmacher Oasis, Antarctica. Prevailing soil temperature limited the distribution and abundance of groups of bacteria like psychrophiles, psychrotrophs...

  9. Characterization of the bacterial community in shower water before and after chlorination

    KAUST Repository

    Peters, Marjolein C. F. M.; Keuten, Maarten G. A.; Knezev, Aleksandra; van Loosdrecht, Mark C. M.; Vrouwenvelder, Johannes S.; Rietveld, Luuk C.; de Kreuk, Merle K.

    2017-01-01

    Gram-negative. The dominant bacterial families with a relative abundance of ≥10% of the total (non-chlorinated and chlorinated) communities were Flavobacteriaceae (24–21%), Xanthomonadaceae (23–24%), Moraxellaceae (12–11%) and Pseudomonadaceae (10

  10. Contribution of bacterial respiration to plankton respiration from 50°N to 44°S in the Atlantic Ocean

    Science.gov (United States)

    García-Martín, E. E.; Aranguren-Gassis, M.; Hartmann, M.; Zubkov, M. V.; Serret, P.

    2017-11-01

    Marine bacteria play an important role in the global cycling of carbon and therefore in climate regulation. However, the paucity of direct measurements means that our understanding of the magnitude and variability of bacterial respiration in the ocean is poor. Estimations of respiration in the 0.2-0.8 μm size-fraction (considered as bacterial respiration), total plankton community respiration, and the contribution of bacterial respiration to total plankton community respiration were made along two latitudinal transects in the Atlantic Ocean (ca. 50°N-44°S) during 2010 and 2011. Two different methodologies were used: determination of changes in dissolved O2 concentration after standard 24 h dark bottle incubations, and measurements of in vivo reduction of 2-(ρ-iodophenyl)-3-(ρ-nitrophenyl)-5phenyl tetrazolium salt (INT). There was an overall significant correlation (r = 0.44, p community respiration estimated by both methods. Depth-integrated community respiration varied as much as threefold between regions. Maximum rates occurred in waters of the western European shelf and Patagonian shelf, and minimum rates in the North and South oligotrophic gyres. Depth-integrated bacterial respiration followed the same pattern as community respiration. There was a significantly higher cell-specific bacterial respiration in the northern subtropical gyre than in the southern subtropical gyre which suggests that bacterial carbon turnover is faster in the northern gyre. The relationships between plankton respiration and physicochemical and biological variables were different in different years. In general, INTT was correlated to both chlorophyll-a and bacterial abundance, while INT0.2-0.8 was only correlated with bacterial abundance. However, in 2010 INTT and INT0.2-0.8 were also correlated with temperature and primary production while in 2011 they were correlated with nitrate + nitrite concentration. The bacterial contribution to depth integrated community respiration was

  11. Detecting novel low-abundant transcripts in Drosophila

    DEFF Research Database (Denmark)

    Lee, Sanggyu; Bao, Jingyue; Zhou, Guolin

    2005-01-01

    Increasing evidence suggests that low-abundant transcripts may play fundamental roles in biological processes. In an attempt to estimate the prevalence of low-abundant transcripts in eukaryotic genomes, we performed a transcriptome analysis in Drosophila using the SAGE technique. We collected 244......,313 SAGE tags from transcripts expressed in Drosophila embryonic, larval, pupae, adult, and testicular tissue. From these SAGE tags, we identified 40,823 unique SAGE tags. Our analysis showed that 55% of the 40,823 unique SAGE tags are novel without matches in currently known Drosophila transcripts...... in the Drosophila genome. Our study reveals the presence of a significant number of novel low-abundant transcripts in Drosophila, and highlights the need to isolate these novel low-abundant transcripts for further biological studies. Udgivelsesdato: 2005-Jun...

  12. Peritonitis - spontaneous bacterial

    Science.gov (United States)

    Spontaneous bacterial peritonitis (SBP); Ascites - peritonitis; Cirrhosis - peritonitis ... who are on peritoneal dialysis for kidney failure. Peritonitis may have other causes . These include infection from ...

  13. Molecular Analysis of Bacterial Microbiota on Brazilian Currency Note Surfaces

    Directory of Open Access Journals (Sweden)

    Tairacan Augusto Pereira da Fonseca

    2015-10-01

    Full Text Available Currency notes have been implicated as a vehicle for transmitting community-acquired bacterial infections. However, the overall diversity of the bacterial population residing on banknotes is still unknown in Brazil. In this study, we aimed to investigate the overall bacterial population from 150 different Brazilian Rial (R$ notes in circulation using a culture-independent Illumina massively parallel sequencing approach of the 16S rRNA genes. Samples were randomly collected from three different street markets or “feiras” in the metropolitan region of São Paulo. Taxonomical composition revealed the abundance of Proteobacteria phyla, followed by Firmicutes and Streptophyta, with a total of 1193 bacterial families and 3310 bacterial genera. Most of these bacterial genera are of human, animal, and environmental origins. Also, our analysis revealed the presence of some potential pathogenic bacterial genera including Salmonella, Staphylococcus, and Klebsiella. The results demonstrate that there is a tremendous diversity of bacterial contamination on currency notes, including organisms known to be opportunistic pathogens. One of the factors that may contribute to the richness of bacterial diversity in currency notes is personal hygiene. Thus, our results underscore the need to increase public awareness of the importance of personal hygiene of money handlers who also handle food.

  14. Molecular Analysis of Bacterial Microbiota on Brazilian Currency Note Surfaces.

    Science.gov (United States)

    Pereira da Fonseca, Tairacan Augusto; Pessôa, Rodrigo; Sanabani, Sabri Saeed

    2015-10-22

    Currency notes have been implicated as a vehicle for transmitting community-acquired bacterial infections. However, the overall diversity of the bacterial population residing on banknotes is still unknown in Brazil. In this study, we aimed to investigate the overall bacterial population from 150 different Brazilian Rial (R$) notes in circulation using a culture-independent Illumina massively parallel sequencing approach of the 16S rRNA genes. Samples were randomly collected from three different street markets or "feiras" in the metropolitan region of São Paulo. Taxonomical composition revealed the abundance of Proteobacteria phyla, followed by Firmicutes and Streptophyta, with a total of 1193 bacterial families and 3310 bacterial genera. Most of these bacterial genera are of human, animal, and environmental origins. Also, our analysis revealed the presence of some potential pathogenic bacterial genera including Salmonella, Staphylococcus, and Klebsiella. The results demonstrate that there is a tremendous diversity of bacterial contamination on currency notes, including organisms known to be opportunistic pathogens. One of the factors that may contribute to the richness of bacterial diversity in currency notes is personal hygiene. Thus, our results underscore the need to increase public awareness of the importance of personal hygiene of money handlers who also handle food.

  15. Prevention of bacterial adhesion

    DEFF Research Database (Denmark)

    Klemm, Per; Vejborg, Rebecca Munk; Hancock, Viktoria

    2010-01-01

    . As such, adhesion represents the Achilles heel of crucial pathogenic functions. It follows that interference with adhesion can reduce bacterial virulence. Here, we illustrate this important topic with examples of techniques being developed that can inhibit bacterial adhesion. Some of these will become...

  16. Unprecedented evidence for high viral abundance and lytic activity in coral reef waters of the South Pacific Ocean

    Directory of Open Access Journals (Sweden)

    Jérôme P. Payet

    2014-09-01

    Full Text Available Despite nutrient-depleted conditions, coral reef waters harbor abundant and diverse microbes; as major agents of microbial mortality, viruses are likely to influence microbial processes in these ecosystems. However, little is known about marine viruses in these rapidly changing ecosystems. Here we examined spatial and short-term temporal variability in marine viral abundance and viral lytic activity across various reef habitats surrounding Moorea Island (French Polynesia in the South Pacific. Water samples were collected along 4 regional cross-reef transects and during a time-series in Opunohu Bay. Results revealed high viral abundance (range: 5.6 x 106 – 3.6 x 107 viruses ml-1 and lytic viral production (range: 1.5 x 109 – 9.2 x 1010 viruses l-1 d-1. Flow cytometry revealed that viral assemblages were composed of three subsets that each displayed distinct spatiotemporal relationships with nutrient concentrations and autotrophic and heterotrophic microbial abundances. The results highlight dynamic shifts in viral community structure and imply that each of these three subsets is ecologically important and likely to infect distinct microbial hosts in reef waters. Based on viral-reduction approach, we estimate that lytic viruses were responsible for the removal of ca. 24% to 367% of bacterial standing stock d-1 and the release of ca. 1.1 to 62 µg of organic carbon l-1 d-1 in reef waters. Overall, this work demonstrates the highly dynamic distribution of viruses and their critical roles in controlling microbial mortality and nutrient cycling in coral reef water ecosystems.

  17. THE RAVE CATALOG OF STELLAR ELEMENTAL ABUNDANCES: FIRST DATA RELEASE

    International Nuclear Information System (INIS)

    Boeche, C.; Williams, M.; De Jong, R. S.; Steinmetz, M.; Siebert, A.; Bienaymé, O.; Fulbright, J. P.; Ruchti, G. R.; Bland-Hawthorn, J.; Campbell, R.; Freeman, K. C.; Gibson, B. K.; Gilmore, G.; Grebel, E. K.; Helmi, A.; Munari, U.; Navarro, J. F.; Parker, Q. A.; Reid, W.; Seabroke, G. M.

    2011-01-01

    We present chemical elemental abundances for 36,561 stars observed by the RAdial Velocity Experiment (RAVE), an ambitious spectroscopic survey of our Galaxy at Galactic latitudes |b| > 25° and with magnitudes in the range 9 DENIS 2 minimization technique. We plan to extend this pipeline to include estimates for other elements, such as oxygen and sulfur, in future data releases.

  18. Understanding Survival And Abundance Of Overwintering Warblers: Does Rainfall Matter?

    Science.gov (United States)

    Katie M. Dugger; John G Faaborg; Wayne J. Arendt; Keith A. Hobson

    2004-01-01

    We investigated relationships between warbler abundance and survival rates measured on a Puerto Rican wintering site and rainfall patterns measured on the wintering site and in regions where these warblers breed, as estimated using stable-isotope analysis (δD) of feathers collected from wintering birds. We banded birds using constant-effort mist netting...

  19. Bacterial sex in dental plaque.

    Science.gov (United States)

    Olsen, Ingar; Tribble, Gena D; Fiehn, Nils-Erik; Wang, Bing-Yan

    2013-01-01

    Genes are transferred between bacteria in dental plaque by transduction, conjugation, and transformation. Membrane vesicles can also provide a mechanism for horizontal gene transfer. DNA transfer is considered bacterial sex, but the transfer is not parallel to processes that we associate with sex in higher organisms. Several examples of bacterial gene transfer in the oral cavity are given in this review. How frequently this occurs in dental plaque is not clear, but evidence suggests that it affects a number of the major genera present. It has been estimated that new sequences in genomes established through horizontal gene transfer can constitute up to 30% of bacterial genomes. Gene transfer can be both inter- and intrageneric, and it can also affect transient organisms. The transferred DNA can be integrated or recombined in the recipient's chromosome or remain as an extrachromosomal inheritable element. This can make dental plaque a reservoir for antimicrobial resistance genes. The ability to transfer DNA is important for bacteria, making them better adapted to the harsh environment of the human mouth, and promoting their survival, virulence, and pathogenicity.

  20. Bacterial sex in dental plaque

    Directory of Open Access Journals (Sweden)

    Ingar Olsen

    2013-06-01

    Full Text Available Genes are transferred between bacteria in dental plaque by transduction, conjugation, and transformation. Membrane vesicles can also provide a mechanism for horizontal gene transfer. DNA transfer is considered bacterial sex, but the transfer is not parallel to processes that we associate with sex in higher organisms. Several examples of bacterial gene transfer in the oral cavity are given in this review. How frequently this occurs in dental plaque is not clear, but evidence suggests that it affects a number of the major genera present. It has been estimated that new sequences in genomes established through horizontal gene transfer can constitute up to 30% of bacterial genomes. Gene transfer can be both inter- and intrageneric, and it can also affect transient organisms. The transferred DNA can be integrated or recombined in the recipient's chromosome or remain as an extrachromosomal inheritable element. This can make dental plaque a reservoir for antimicrobial resistance genes. The ability to transfer DNA is important for bacteria, making them better adapted to the harsh environment of the human mouth, and promoting their survival, virulence, and pathogenicity.

  1. Influence of Coronal Abundance Variations

    Science.gov (United States)

    Scargle, Jeffrey D. (Technical Monitor); Kashyap, Vinay

    2005-01-01

    The PI of this project was Jeff Scargle of NASA/Ames. Co-I's were Alma Connors of Eureka Scientific/Wellesley, and myself. Part of the work was subcontracted to Eureka Scientific via SAO, with Vinay Kashyap as PI. This project was originally assigned grant number NCC2-1206, and was later changed to NCC2-1350 for administrative reasons. The goal of the project was to obtain, derive, and develop statistical and data analysis tools that would be of use in the analyses of high-resolution, high-sensitivity data that are becoming available with new instruments. This is envisioned as a cross-disciplinary effort with a number of "collaborators" including some at SA0 (Aneta Siemiginowska, Peter Freeman) and at the Harvard Statistics department (David van Dyk, Rostislav Protassov, Xiao-li Meng, Epaminondas Sourlas, et al). We have developed a new tool to reliably measure the metallicities of thermal plasma. It is unfeasible to obtain high-resolution grating spectra for most stars, and one must make the best possible determination based on lower-resolution, CCD-type spectra. It has been noticed that most analyses of such spectra have resulted in measured metallicities that were significantly lower than when compared with analyses of high- resolution grating data where available (see, e.g., Brickhouse et al., 2000, ApJ 530,387). Such results have led to the proposal of the existence of so-called Metal Abundance Deficient, or "MAD" stars (e.g., Drake, J.J., 1996, Cool Stars 9, ASP Conf.Ser. 109, 203). We however find that much of these analyses may be systematically underestimating the metallicities, and using a newly developed method to correctly treat the low-counts regime at the high-energy tail of the stellar spectra (van Dyk et al. 2001, ApJ 548,224), have found that the metallicities of these stars are generally comparable to their photospheric values. The results were reported at the AAS (Sourlas, Yu, van Dyk, Kashyap, and Drake, 2000, BAAS 196, v32, #54.02), and at the

  2. Microdiversity of an Abundant Terrestrial Bacterium Encompasses Extensive Variation in Ecologically Relevant Traits

    Directory of Open Access Journals (Sweden)

    Alexander B. Chase

    2017-11-01

    Full Text Available Much genetic diversity within a bacterial community is likely obscured by microdiversity within operational taxonomic units (OTUs defined by 16S rRNA gene sequences. However, it is unclear how variation within this microdiversity influences ecologically relevant traits. Here, we employ a multifaceted approach to investigate microdiversity within the dominant leaf litter bacterium, Curtobacterium, which comprises 7.8% of the bacterial community at a grassland site undergoing global change manipulations. We use cultured bacterial isolates to interpret metagenomic data, collected in situ over 2 years, together with lab-based physiological assays to determine the extent of trait variation within this abundant OTU. The response of Curtobacterium to seasonal variability and the global change manipulations, specifically an increase in relative abundance under decreased water availability, appeared to be conserved across six Curtobacterium lineages identified at this site. Genomic and physiological analyses in the lab revealed that degradation of abundant polymeric carbohydrates within leaf litter, cellulose and xylan, is nearly universal across the genus, which may contribute to its high abundance in grassland leaf litter. However, the degree of carbohydrate utilization and temperature preference for this degradation varied greatly among clades. Overall, we find that traits within Curtobacterium are conserved at different phylogenetic depths. We speculate that similar to bacteria in marine systems, diverse microbes within this taxon may be structured in distinct ecotypes that are key to understanding Curtobacterium abundance and distribution in the environment.

  3. High fat diet induced atherosclerosis is accompanied with low colonic bacterial diversity and altered abundances that correlates with plaque size, plasma A-FABP and cholesterol: a pilot study of high fat diet and its intervention with Lactobacillus rhamnosus GG (LGG) or telmisartan in ApoE-/- mice.

    Science.gov (United States)

    Chan, Yee Kwan; Brar, Manreetpal Singh; Kirjavainen, Pirkka V; Chen, Yan; Peng, Jiao; Li, Daxu; Leung, Frederick Chi-Ching; El-Nezami, Hani

    2016-11-08

    Atherosclerosis appears to have multifactorial causes - microbial component like lipopolysaccharides (LPS) and other pathogen associated molecular patterns may be plausible factors. The gut microbiota is an ample source of such stimulants, and its dependent metabolites and altered gut metagenome has been an established link to atherosclerosis. In this exploratory pilot study, we aimed to elucidate whether microbial intervention with probiotics L. rhamnosus GG (LGG) or pharmaceuticals telmisartan (TLM) could improve atherosclerosis in a gut microbiota associated manner. Atherosclerotic phenotype was established by 12 weeks feeding of high fat (HF) diet as opposed to normal chow diet (ND) in apolipoprotein E knockout (ApoE -/- ) mice. LGG or TLM supplementation to HF diet was studied. Both LGG and TLM significantly reduced atherosclerotic plaque size and improved various biomarkers including endotoxin to different extents. Colonial microbiota analysis revealed that TLM restored HF diet induced increase in Firmicutes/Bacteroidetes ratio and decrease in alpha diversity; and led to a more distinct microbial clustering closer to ND in PCoA plot. Eubacteria, Anaeroplasma, Roseburia, Oscillospira and Dehalobacteria appeared to be protective against atherosclerosis and showed significant negative correlation with atherosclerotic plaque size and plasma adipocyte - fatty acid binding protein (A-FABP) and cholesterol. LGG and TLM improved atherosclerosis with TLM having a more distinct alteration in the colonic gut microbiota. Altered bacteria genera and reduced alpha diversity had significant correlations to atherosclerotic plaque size, plasma A-FABP and cholesterol. Future studies on such bacterial functional influence in lipid metabolism will be warranted.

  4. A distinct bacterial dysbiosis associated skin inflammation in ovine footrot

    Science.gov (United States)

    Maboni, Grazieli; Blanchard, Adam; Frosth, Sara; Stewart, Ceri; Emes, Richard; Tötemeyer, Sabine

    2017-03-01

    Ovine footrot is a highly prevalent bacterial disease caused by Dichelobacter nodosus and characterised by the separation of the hoof horn from the underlying skin. The role of innate immune molecules and other bacterial communities in the development of footrot lesions remains unclear. This study shows a significant association between the high expression of IL1β and high D. nodosus load in footrot samples. Investigation of the microbial population identified distinct bacterial populations in the different disease stages and also depending on the level of inflammation. Treponema (34%), Mycoplasma (29%) and Porphyromonas (15%) were the most abundant genera associated with high levels of inflammation in footrot. In contrast, Acinetobacter (25%), Corynebacteria (17%) and Flavobacterium (17%) were the most abundant genera associated with high levels of inflammation in healthy feet. This demonstrates for the first time there is a distinct microbial community associated with footrot and high cytokine expression.

  5. Deepwater Horizon MC252 oyster data from the Environmental Response Management Application (ERMA) containing oyster recruitment sampling results, estimates of subtidal habitat, percent cover, nearshore and subtidal abundance data, and other related datasets collected from 2009-01-01 to 2015-01-01 in the Northern Gulf of Mexico (NCEI Accession 0163812)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This Archival Information Package (AIP) contains Environmental Resource Management Application (ERMA) GIS layers that represent oyster recruitment and abundance...

  6. Postviral Complications: Bacterial Pneumonia.

    Science.gov (United States)

    Prasso, Jason E; Deng, Jane C

    2017-03-01

    Secondary bacterial pneumonia after viral respiratory infection remains a significant source of morbidity and mortality. Susceptibility is mediated by a variety of viral and bacterial factors, and complex interactions with the host immune system. Prevention and treatment strategies are limited to influenza vaccination and antibiotics/antivirals respectively. Novel approaches to identifying the individuals with influenza who are at increased risk for secondary bacterial pneumonias are urgently needed. Given the threat of further pandemics and the heightened prevalence of these viruses, more research into the immunologic mechanisms of this disease is warranted with the hope of discovering new potential therapies. Published by Elsevier Inc.

  7. Monitoring waterbird abundance in wetlands: The importance of controlling results for variation in water depth

    Science.gov (United States)

    Bolduc, F.; Afton, A.D.

    2008-01-01

    Wetland use by waterbirds is highly dependent on water depth, and depth requirements generally vary among species. Furthermore, water depth within wetlands often varies greatly over time due to unpredictable hydrological events, making comparisons of waterbird abundance among wetlands difficult as effects of habitat variables and water depth are confounded. Species-specific relationships between bird abundance and water depth necessarily are non-linear; thus, we developed a methodology to correct waterbird abundance for variation in water depth, based on the non-parametric regression of these two variables. Accordingly, we used the difference between observed and predicted abundances from non-parametric regression (analogous to parametric residuals) as an estimate of bird abundance at equivalent water depths. We scaled this difference to levels of observed and predicted abundances using the formula: ((observed - predicted abundance)/(observed + predicted abundance)) ?? 100. This estimate also corresponds to the observed:predicted abundance ratio, which allows easy interpretation of results. We illustrated this methodology using two hypothetical species that differed in water depth and wetland preferences. Comparisons of wetlands, using both observed and relative corrected abundances, indicated that relative corrected abundance adequately separates the effect of water depth from the effect of wetlands. ?? 2008 Elsevier B.V.

  8. Characterization of bacterial functional groups and microbial activity in microcosms with glyphosate application

    Science.gov (United States)

    Moyano, Sofia; Bonetto, Mariana; Baigorria, Tomas; Pegoraro, Vanesa; Ortiz, Jimena; Faggioli, Valeria; Conde, Belen; Cazorla, Cristian; Boccolini, Monica

    2017-04-01

    Glyphosate is a worldwide used herbicide as c. 90% of transgenic crops are tolerant to it. Microbial degradation of glyphosate molecule in soil is considered the most important process that determines its persistence in the environment. However, the impact of this herbicide on target groups of soil biota remains poorly understood. Our objective was to characterize the abundance of bacterial groups and global microbial activity, under controlled conditions with application of increasing doses of glyphosate. A bioassay was carried out in microcosms using an agricultural soil (Typic Argiudoll) with registered history of glyphosate application from National Institute of Agricultural Technology (INTA, EEA Marcos Juarez, Argentina). Glyphosate of commercial formulation (74.7%) was used and the following treatments were evaluated: Soil without glyphosate (control), and Soil with doses equivalent to 1.12 and 11.2 kg ai ha-1. Microbiological parameters were estimated at 3, 7, 14 and 21 days after herbicide application by counting heterotrophic, cellulolytic, nitrogen fixing (N), and nitrifying bacteria; and fluorescein diacetate hydrolysis (FDA), microbial respiration (MR) and microbial biomass (C-BM). The N cycle related bacteria showed greater sensitivity to glyphosate with significant increases in abundance. On the other hand the C cycle parameters were strongly conditioned by the time elapsed since the application of the herbicide, as did the MR. The FDA declined with the highest dose, while the C-BM was not affected. Therefore, we conclude that in the studied experimental conditions glyphosate stimulated bacterial growth (i.e. target abundances) representing a source of N, C and nutrients. On the other hand, enzymatic activity (FDA) decreased when glyphosate was applied in the highest dose, whereas, it had no effect on the MR nor C-BM, which could be attributable to the organic matter content of the soil. However, future research in field conditions is necessary, for

  9. Rare earth element abundances and distribution patterns in plant materials

    International Nuclear Information System (INIS)

    Aidid, S.B.

    1994-01-01

    Eight out of the fourteen rare earth elements were estimated from the leaves of Pelthophorum pterocarpum, the leaves and roots of Impatiens balsamina, and the soils from four sampling sites by instrumental neutron activation analysis. The chondrite normalized rare earth element abundances and distribution patterns in the plant materials were found to be significantly correlated to the abundances of the rare earth elements occurring in the soils. The extent of accumulation of the rare earth elements in some plant materials was also governed by the age of the plants and the plant organs. (author) 16 refs.; 4 figs.; 3 tabs

  10. Bacterial vaginosis - aftercare

    Science.gov (United States)

    Bacterial vaginosis (BV) is a type of vaginal infection. The vagina normally contains both healthy bacteria and unhealthy bacteria. BV occurs when more unhealthy bacteria grow than healthy bacteria. No one knows ...

  11. Bacterial surface adaptation

    Science.gov (United States)

    Utada, Andrew

    2014-03-01

    Biofilms are structured multi-cellular communities that are fundamental to the biology and ecology of bacteria. Parasitic bacterial biofilms can cause lethal infections and biofouling, but commensal bacterial biofilms, such as those found in the gut, can break down otherwise indigestible plant polysaccharides and allow us to enjoy vegetables. The first step in biofilm formation, adaptation to life on a surface, requires a working knowledge of low Reynolds number fluid physics, and the coordination of biochemical signaling, polysaccharide production, and molecular motility motors. These crucial early stages of biofilm formation are at present poorly understood. By adapting methods from soft matter physics, we dissect bacterial social behavior at the single cell level for several prototypical bacterial species, including Pseudomonas aeruginosa and Vibrio cholerae.

  12. Bacterial intermediate filaments

    DEFF Research Database (Denmark)

    Charbon, Godefroid; Cabeen, M.; Jacobs-Wagner, C.

    2009-01-01

    Crescentin, which is the founding member of a rapidly growing family of bacterial cytoskeletal proteins, was previously proposed to resemble eukaryotic intermediate filament (IF) proteins based on structural prediction and in vitro polymerization properties. Here, we demonstrate that crescentin...

  13. Diagnosis of bacterial infection

    African Journals Online (AJOL)

    direct or indirect evidence of a compatible bacterial pathogen. Inflammation may be .... cardinal features (fever, confusion, headache and neck stiffness). .... specificity, inappropriate indications or poor sampling technique may diminish this ...

  14. Effect of diet and absence of protozoa on the rumen microbial community and on the representativeness of bacterial fractions used in the determination of microbial protein synthesis.

    Science.gov (United States)

    Belanche, A; de la Fuente, G; Pinloche, E; Newbold, C J; Balcells, J

    2012-11-01

    Accurate estimates of microbial synthesis in the rumen are vital to optimize ruminant nutrition. Liquid- (LAB) and solid-associated bacterial fractions (SAB) harvested from the rumen are generally considered as microbial references when microbial yield is calculated; however, factors that determine their composition are not completely understood. The aim of this study was to evaluate the effect of diet and absence or presence of rumen protozoa on the rumen microbial community. It was hypothesized that these treatments could modify the composition and representativeness of LAB and SAB. Twenty twin lambs (Ovis aries) were used; one-half of the twins were kept protozoa-free, and each respective twin sibling was faunated. At 6 mo of age, 5 animals from each group were randomly allocated to the experimental diets consisting of either alfalfa hay as the sole diet, or 50:50 mixed with ground barley grain. After 15 d of adaptation to the diet, animals were euthanized, rumen and abomasum contents were sampled, and LAB and SAB isolated. The presence of protozoa buffered the effect of diet on the rumen bacterial population. Faunated animals fed alfalfa hay had a greater abundance of F. succinogenes, anaerobic fungi and methanogens, as well as an enhanced rumen bacterial diversity. Cellulolytic bacteria were more abundant in SAB, whereas the abomasal abundance of most of the microorganisms studied was closer to those values observed in LAB. Rumen and abomasal samples showed similar bacterial DNA concentrations, but the fungal and protozoal DNA concentration in the abomasum was only 69% and 13% of that observed in the rumen, respectively, suggesting fungal and protozoal sequestration in the rumen or possible preferential degradation of fungal and protozoal DNA in the abomasum, or both. In conclusion, absence of protozoa and type of diet extensively modified the chemical composition of LAB and SAB as a consequence of changes in the microbial composition of these fractions.

  15. A search for stars of very low metal abundance. VI. Detailed abundances of 313 metal-poor stars

    International Nuclear Information System (INIS)

    Roederer, Ian U.; Preston, George W.; Thompson, Ian B.; Shectman, Stephen A.; Burley, Gregory S.; Kelson, Daniel D.; Sneden, Christopher

    2014-01-01

    We present radial velocities, equivalent widths, model atmosphere parameters, and abundances or upper limits for 53 species of 48 elements derived from high resolution optical spectroscopy of 313 metal-poor stars. A majority of these stars were selected from the metal-poor candidates of the HK Survey of Beers, Preston, and Shectman. We derive detailed abundances for 61% of these stars for the first time. Spectra were obtained during a 10 yr observing campaign using the Magellan Inamori Kyocera Echelle spectrograph on the Magellan Telescopes at Las Campanas Observatory, the Robert G. Tull Coudé Spectrograph on the Harlan J. Smith Telescope at McDonald Observatory, and the High Resolution Spectrograph on the Hobby-Eberly Telescope at McDonald Observatory. We perform a standard LTE abundance analysis using MARCS model atmospheres, and we apply line-by-line statistical corrections to minimize systematic abundance differences arising when different sets of lines are available for analysis. We identify several abundance correlations with effective temperature. A comparison with previous abundance analyses reveals significant differences in stellar parameters, which we investigate in detail. Our metallicities are, on average, lower by ≈0.25 dex for red giants and ≈0.04 dex for subgiants. Our sample contains 19 stars with [Fe/H] ≤–3.5, 84 stars with [Fe/H] ≤–3.0, and 210 stars with [Fe/H] ≤–2.5. Detailed abundances are presented here or elsewhere for 91% of the 209 stars with [Fe/H] ≤–2.5 as estimated from medium resolution spectroscopy by Beers, Preston, and Shectman. We will discuss the interpretation of these abundances in subsequent papers.

  16. Seasonal dynamics of bacterial biomass and production in a coastal arctic ecosystem: Franklin Bay, western Canadian Arctic

    Science.gov (United States)

    Garneau, Marie-Ã. Ve; Roy, SéBastien; Lovejoy, Connie; Gratton, Yves; Vincent, Warwick F.

    2008-07-01

    The Canadian Arctic Shelf Exchange Study (CASES) included the overwintering deployment of a research platform in Franklin Bay (70°N, 126°W) and provided a unique seasonal record of bacterial dynamics in a coastal region of the Arctic Ocean. Our objectives were (1) to relate seasonal bacterial abundance (BA) and production (BP) to physico-chemical characteristics and (2) to quantify the annual bacterial carbon flux. BA was estimated by epifluorescence microscopy and BP was estimated from 3H-leucine and 3H-thymidine assays. Mean BA values for the water column ranged from 1.0 (December) to 6.8 × 105 cells mL-1 (July). Integral BP varied from 1 (February) to 80 mg C m-2 d-1 (July). During winter-spring, BP was uncorrelated with chlorophyll a (Chl a), but these variables were significantly correlated during summer-autumn (rs = 0.68, p winter, late winter-late spring, and summer. A baseline level of BB and BP was maintained throughout late winter-late spring despite the persistent cold and darkness, with irregular fluctuations that may be related to hydrodynamic events. During this period, BP rates were correlated with colored dissolved organic matter (CDOM) but not Chl a (rs BP.CDOM∣Chl a = 0.20, p < 0.05, N = 176). Annual BP was estimated as 6 g C m-2 a-1, implying a total BP of 4.8 × 1010 g C a-1 for the Franklin Bay region. These results show that bacterial processes continue throughout all seasons and make a large contribution to the total biological carbon flux in this coastal arctic ecosystem.

  17. Bacterial flavin-containing monooxygenase is trimethylamine monooxygenase.

    Science.gov (United States)

    Chen, Yin; Patel, Nisha A; Crombie, Andrew; Scrivens, James H; Murrell, J Colin

    2011-10-25

    Flavin-containing monooxygenases (FMOs) are one of the most important monooxygenase systems in Eukaryotes and have many important physiological functions. FMOs have also been found in bacteria; however, their physiological function is not known. Here, we report the identification and characterization of trimethylamine (TMA) monooxygenase, termed Tmm, from Methylocella silvestris, using a combination of proteomic, biochemical, and genetic approaches. This bacterial FMO contains the FMO sequence motif (FXGXXXHXXXF/Y) and typical flavin adenine dinucleotide and nicotinamide adenine dinucleotide phosphate-binding domains. The enzyme was highly expressed in TMA-grown M. silvestris and absent during growth on methanol. The gene, tmm, was expressed in Escherichia coli, and the purified recombinant protein had high Tmm activity. Mutagenesis of this gene abolished the ability of M. silvestris to grow on TMA as a sole carbon and energy source. Close homologs of tmm occur in many Alphaproteobacteria, in particular Rhodobacteraceae (marine Roseobacter clade, MRC) and the marine SAR11 clade (Pelagibacter ubique). We show that the ability of MRC to use TMA as a sole carbon and/or nitrogen source is directly linked to the presence of tmm in the genomes, and purified Tmm of MRC and SAR11 from recombinant E. coli showed Tmm activities. The tmm gene is highly abundant in the metagenomes of the Global Ocean Sampling expedition, and we estimate that 20% of the bacteria in the surface ocean contain tmm. Taken together, our results suggest that Tmm, a bacterial FMO, plays an important yet overlooked role in the global carbon and nitrogen cycles.

  18. Identification of Differentially Abundant Proteins of Edwardsiella ictaluri during Iron Restriction.

    Directory of Open Access Journals (Sweden)

    Pradeep R Dumpala

    Full Text Available Edwardsiella ictaluri is a Gram-negative facultative anaerobe intracellular bacterium that causes enteric septicemia in channel catfish. Iron is an essential inorganic nutrient of bacteria and is crucial for bacterial invasion. Reduced availability of iron by the host may cause significant stress for bacterial pathogens and is considered a signal that leads to significant alteration in virulence gene expression. However, the precise effect of iron-restriction on E. ictaluri protein abundance is unknown. The purpose of this study was to identify differentially abundant proteins of E. ictaluri during in vitro iron-restricted conditions. We applied two-dimensional difference in gel electrophoresis (2D-DIGE for determining differentially abundant proteins and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF/TOF MS for protein identification. Gene ontology and pathway-based functional modeling of differentially abundant proteins was also conducted. A total of 50 unique differentially abundant proteins at a minimum of 2-fold (p ≤ 0.05 difference in abundance due to iron-restriction were detected. The numbers of up- and down-regulated proteins were 37 and 13, respectively. We noted several proteins, including EsrB, LamB, MalM, MalE, FdaA, and TonB-dependent heme/hemoglobin receptor family proteins responded to iron restriction in E. ictaluri.

  19. Bacterial formation of phosphatic laminites off Peru.

    Science.gov (United States)

    Arning, E T; Birgel, D; Brunner, B; Peckmann, J

    2009-06-01

    Authigenic phosphatic laminites enclosed in phosphorite crusts from the shelf off Peru (10 degrees 01' S and 10 degrees 24' S) consist of carbonate fluorapatite layers, which contain abundant sulfide minerals including pyrite (FeS(2)) and sphalerite (ZnS). Low delta(34)S(pyrite) values (average -28.8 per thousand) agree with bacterial sulfate reduction and subsequent pyrite formation. Stable sulfur isotopic compositions of sulfate bound in carbonate fluorapatite are lower than that of sulfate from ambient sea water, suggesting bacterial reoxidation of sulfide by sulfide-oxidizing bacteria. The release of phosphorus and subsequent formation of the autochthonous phosphatic laminites are apparently caused by the activity of sulfate-reducing bacteria and associated sulfide-oxidizing bacteria. Following an extraction-phosphorite dissolution-extraction procedure, molecular fossils of sulfate-reducing bacteria (mono-O-alkyl glycerol ethers, di-O-alkyl glycerol ethers, as well as the short-chain branched fatty acids i/ai-C(15:0), i/ai-C(17:0) and 10MeC(16:0)) are found to be among the most abundant compounds. The fact that these molecular fossils of sulfate-reducing bacteria are distinctly more abundant after dissolution of the phosphatic laminite reveals that the lipids are tightly bound to the mineral lattice of carbonate fluorapatite. Moreover, compared with the autochthonous laminite, molecular fossils of sulfate-reducing bacteria are: (1) significantly less abundant and (2) not as tightly bound to the mineral lattice in the other, allochthonous facies of the Peruvian crusts consisting of phosphatic coated grains. These observations confirm the importance of sulfate-reducing bacteria in the formation of the phosphatic laminite. Model calculations highlight that organic matter degradation by sulfate-reducing bacteria has the potential to liberate sufficient phosphorus for phosphogenesis.

  20. [The composition of the gastrointestinal bacterial flora of mouse embryos and the placenta tissue bacterial flora].

    Science.gov (United States)

    Lei, D; Lin, Y; Jiang, X; Lan, L; Zhang, W; Wang, B X

    2017-03-02

    Objective: To explore the composition of the gastrointestinal bacterial flora of mouse embryos and the placenta tissue bacterial flora. Method: Twenty-four specimens were collected from pregnant Kunming mouse including 8 mice of early embryonic (12-13 days) gastrointestinal tissues, 8 cases of late embryonic (19-20 days)gastrointestinal tissues, 8 of late pregnancy placental tissues.The 24 samples were extracted by DNeasy Blood & Tissue kit for high-throughput DNA sequencing. Result: The level of Proteobacteria, Bacteroidetes, Actino-bacteria and Firmicutes were predominantin all specimens.The relative content of predominant bacterial phyla in each group: Proteobacteria (95.00%, 88.14%, 87.26%), Bacteroidetes(1.71%, 2.15%, 2.63%), Actino-Bacteria(1.16%, 4.10%, 3.38%), Firmicutes(0.75%, 2.62%, 2.01%). At the level of family, there were nine predominant bacterial families in which Enterobacteriaeae , Shewanel laceae and Moraxellaceae were dominant.The relative content of dominant bacterial family in eachgroup: Enterobacteriaeae (46.99%, 44.34%, 41.08%), Shewanellaceae (21.99%, 21.10%, 19.05%), Moraxellaceae (9.18%, 7.09%, 5.64%). From the species of flora, the flora from fetal gastrointestinal in early pregnancy and late pregnancy (65.44% and 62.73%) were the same as that from placenta tissue in the late pregnancy.From the abundance of bacteria, at the level of family, the same content of bacteria in three groups accounted for 78.16%, 72.53% and 65.78% respectively. Conclusion: It was proved that the gastrointestinal bacterial flora of mouse embryos and the placenta tissue bacterial flora were colonized. At the same time the bacteria are classified.

  1. Nitrogen Abundances and the Distance Moduli of the Pleiades and Hyades

    OpenAIRE

    Miller, Blake; King, Jeremy R.; Chen, Yu; Boesgaard, Ann M.

    2013-01-01

    Recent reanalyses of HIPPARCOS parallax data confirm a previously noted discrepancy with the Pleiades distance modulus estimated from main-sequence fitting in the color-magnitude diagram. One proposed explanation of this distance modulus discrepancy is a Pleiades He abundance that is significantly larger than the Hyades value. We suggest that, based on our theoretical and observational understanding of Galactic chemical evolution, nitrogen abundances may serve as a proxy for helium abundances...

  2. Primordial helium abundance determination using sulphur as metallicity tracer

    Science.gov (United States)

    Fernández, Vital; Terlevich, Elena; Díaz, Angeles I.; Terlevich, Roberto; Rosales-Ortega, F. F.

    2018-05-01

    The primordial helium abundance YP is calculated using sulphur as metallicity tracer in the classical methodology (with YP as an extrapolation of Y to zero metals). The calculated value, YP, S = 0.244 ± 0.006, is in good agreement with the estimate from the Planck experiment, as well as, determinations in the literature using oxygen as the metallicity tracer. The chemical analysis includes the sustraction of the nebular continuum and of the stellar continuum computed from simple stellar population synthesis grids. The S+2 content is measured from the near infrared [SIII]λλ9069Å, 9532Å lines, while an ICF(S3 +) is proposed based on the Ar3 +/Ar2 + fraction. Finally, we apply a multivariable linear regression using simultaneously oxygen, nitrogen and sulphur abundances for the same sample to determine the primordial helium abundance resulting in YP - O, N, S = 0.245 ± 0.007.

  3. A New Sensitive GC-MS-based Method for Analysis of Dipicolinic Acid and Quantifying Bacterial Endospores in Deep Marine Subsurface Sediment

    Science.gov (United States)

    Fang, J.

    2015-12-01

    Marine sediments cover more than two-thirds of the Earth's surface and represent a major part of the deep biosphere. Microbial cells and microbial activity appear to be widespread in these sediments. Recently, we reported the isolation of gram-positive anaerobic spore-forming piezophilic bacteria and detection of bacterial endospores in marine subsurface sediment from the Shimokita coalbed, Japan. However, the modern molecular microbiological methods (e.g., DNA-based microbial detection techniques) cannot detect bacterial endospore, because endospores are impermeable and are not stained by fluorescence DNA dyes or by ribosomal RNA staining techniques such as catalysed reporter deposition fluorescence in situ hybridization. Thus, the total microbial cell abundance in the deep biosphere may has been globally underestimated. This emphasizes the need for a new cultivation independent approach for the quantification of bacterial endospores in the deep subsurface. Dipicolinic acid (DPA, pyridine-2,6-dicarboxylic acid) is a universal and specific component of bacterial endospores, representing 5-15wt% of the dry spore, and therefore is a useful indicator and quantifier of bacterial endospores and permits to estimate total spore numbers in the subsurface biosphere. We developed a sensitive analytical method to quantify DPA content in environmental samples using gas chromatography-mass spectrometry. The method is sensitive and more convenient in use than other traditional methods. We applied this method to analyzing sediment samples from the South China Sea (obtained from IODP Exp. 349) to determine the abundance of spore-forming bacteria in the deep marine subsurface sediment. Our results suggest that gram-positive, endospore-forming bacteria may be the "unseen majority" in the deep biosphere.

  4. Bacterial community composition and predicted functional ecology of sponges, sediment and seawater from the thousand islands reef complex, West Java, Indonesia.

    Science.gov (United States)

    de Voogd, Nicole J; Cleary, Daniel F R; Polónia, Ana R M; Gomes, Newton C M

    2015-04-01

    In the present study, we assessed the composition of Bacteria in four biotopes namely sediment, seawater and two sponge species (Stylissa massa and Xestospongia testudinaria) at four different reef sites in a coral reef ecosystem in West Java, Indonesia. In addition to this, we used a predictive metagenomic approach to estimate to what extent nitrogen metabolic pathways differed among bacterial communities from different biotopes. We observed marked differences in bacterial composition of the most abundant bacterial phyla, classes and orders among sponge species, water and sediment. Proteobacteria were by far the most abundant phylum in terms of both sequences and Operational Taxonomic Units (OTUs). Predicted counts for genes associated with the nitrogen metabolism suggested that several genes involved in the nitrogen cycle were enriched in sponge samples, including nosZ, nifD, nirK, norB and nrfA genes. Our data show that a combined barcoded pyrosequencing and predictive metagenomic approach can provide novel insights into the potential ecological functions of the microbial communities. Not only is this approach useful for our understanding of the vast microbial diversity found in sponges but also to understand the potential response of microbial communities to environmental change. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  5. Bumble bee nest abundance, foraging distance, and host-plant reproduction: implications for management and conservation.

    Science.gov (United States)

    Geib, Jennifer C; Strange, James P; Galenj, Candace

    2015-04-01

    Recent reports of global declines in pollinator species imply an urgent need to assess the abundance of native pollinators and density-dependent benefits for linked plants. In this study, we investigated (1) pollinator nest distributions and estimated colony abundances, (2) the relationship between abundances of foraging workers and the number of nests they represent, (3) pollinator foraging ranges, and (4) the relationship between pollinator abundance and plant reproduction. We examined these questions in an alpine ecosystem in the Colorado Rocky Mountains, focusing on four alpine bumble bee species (Bombus balteatus, B. flavifrons, B. bifarius, and B. sylvicola), and two host plants that differ in their degrees of pollinator specialization (Trifolium dasyphyllum and T. parryi). Using microsatellites, we found that estimated colony abundances among Bombus species ranged from ~18 to 78 colonies/0.01 km2. The long-tongued species B. balteatus was most common, especially high above treeline, but the subalpine species B. bifarius was unexpectedly abundant for this elevation range. Nests detected among sampled foragers of each species were correlated with the number of foragers caught. Foraging ranges were smaller than expected for all Bombus species, ranging from 25 to 110 m. Fruit set for the specialized plant, Trifolium parryi, was positively related to the abundance of its Bombus pollinator. In contrast, fruit set for the generalized plant, T. dasyphyllum, was related to abundance of all Bombus species. Because forager abundance was related to nest abundance of each Bombus species and was an equally effective predictor of plant fecundity, forager inventories are probably suitable for assessing the health of outcrossing plant populations. However, nest abundance, rather than forager abundance, better reflects demographic and genetic health in populations of eusocial pollinators such as bumble bees. Development of models incorporating the parameters we have measured

  6. Diversity, abundance, and possible sources of fecal bacteria in the Yangtze River.

    Science.gov (United States)

    Sun, Haohao; He, Xiwei; Ye, Lin; Zhang, Xu-Xiang; Wu, Bing; Ren, Hongqiang

    2017-03-01

    The fecal bacteria in natural waters may pose serious risks on human health. Although many source tracking methods have been developed and used to determine the possible sources of the fecal pollution, little is known about the overall diversity and abundance of fecal bacterial community in natural waters. In this study, a method based on fecal bacterial sequence library was introduced to evaluate the fecal bacterial profile in the Yangtze River (Nanjing section). Our results suggested that the Yangtze River water harbors diverse fecal bacteria. Fifty-eight fecal operational taxonomic units (97% identity level) were detected in the Yangtze River water samples and the relative abundance of fecal bacteria in these samples ranged from 0.1 to 8%. It was also found that the relative abundances of the fecal bacteria in locations near to the downstream of wastewater treatment plants were obviously higher than those in other locations. However, the high abundance of fecal bacteria could decrease to the normal level in 2~4 km in the river due to degradation or dilution, and the overall fecal bacteria level changed little when the Yangtze River flew through the Nanjing City. Moreover, the fecal bacteria in the Yangtze River water were found to be highly associated (Spearman rho = 0.804, P Yangtze River and advance our understandings of the fecal bacteria community in the natural waters.

  7. Significant biases affecting abundance determinations

    Science.gov (United States)

    Wesson, Roger

    2015-08-01

    I have developed two highly efficient codes to automate analyses of emission line nebulae. The tools place particular emphasis on the propagation of uncertainties. The first tool, ALFA, uses a genetic algorithm to rapidly optimise the parameters of gaussian fits to line profiles. It can fit emission line spectra of arbitrary resolution, wavelength range and depth, with no user input at all. It is well suited to highly multiplexed spectroscopy such as that now being carried out with instruments such as MUSE at the VLT. The second tool, NEAT, carries out a full analysis of emission line fluxes, robustly propagating uncertainties using a Monte Carlo technique.Using these tools, I have found that considerable biases can be introduced into abundance determinations if the uncertainty distribution of emission lines is not well characterised. For weak lines, normally distributed uncertainties are generally assumed, though it is incorrect to do so, and significant biases can result. I discuss observational evidence of these biases. The two new codes contain routines to correctly characterise the probability distributions, giving more reliable results in analyses of emission line nebulae.

  8. Integrating population and genetic monitoring to understand changes in the abundance of a threatened seabird

    Science.gov (United States)

    Catalina Vásquez-Carrillo; R. William Henry; Laird Henkel; M. Zachariah. Peery

    2013-01-01

    Population monitoring programs for threatened species are rarely designed to disentangle the effects of movements from changes in birth and death rates on estimated trends in abundance. Here, we illustrate how population and genetic monitoring can be integrated to understand the cause of large changes in the abundance of a threatened species of seabird, the Marbled...

  9. The abundance of health-associated bacteria is altered in PAH polluted soils-Implications for health in urban areas?

    Directory of Open Access Journals (Sweden)

    Anirudra Parajuli

    Full Text Available Long-term exposure to polyaromatic hydrocarbons (PAHs has been connected to chronic human health disorders. It is also well-known that i PAH contamination alters soil bacterial communities, ii human microbiome is associated with environmental microbiome, and iii alteration in the abundance of members in several bacterial phyla is associated with adverse or beneficial human health effects. We hypothesized that soil pollution by PAHs altered soil bacterial communities that had known associations with human health. The rationale behind our study was to increase understanding and potentially facilitate reconsidering factors that lead to health disorders in areas characterized by PAH contamination. Large containers filled with either spruce forest soil, pine forest soil, peat, or glacial sand were left to incubate or contaminated with creosote. Biological degradation of PAHs was monitored using GC-MS, and the bacterial community composition was analyzed using 454 pyrosequencing. Proteobacteria had higher and Actinobacteria and Bacteroidetes had lower relative abundance in creosote contaminated soils than in non-contaminated soils. Earlier studies have demonstrated that an increase in the abundance of Proteobacteria and decreased abundance of the phyla Actinobacteria and Bacteroidetes are particularly associated with adverse health outcomes and immunological disorders. Therefore, we propose that pollution-induced shifts in natural soil bacterial community, like in PAH-polluted areas, can contribute to the prevalence of chronic diseases. We encourage studies that simultaneously address the classic "adverse toxin effect" paradigm and our novel "altered environmental microbiome" hypothesis.

  10. Bacterial Cell Mechanics.

    Science.gov (United States)

    Auer, George K; Weibel, Douglas B

    2017-07-25

    Cellular mechanical properties play an integral role in bacterial survival and adaptation. Historically, the bacterial cell wall and, in particular, the layer of polymeric material called the peptidoglycan were the elements to which cell mechanics could be primarily attributed. Disrupting the biochemical machinery that assembles the peptidoglycan (e.g., using the β-lactam family of antibiotics) alters the structure of this material, leads to mechanical defects, and results in cell lysis. Decades after the discovery of peptidoglycan-synthesizing enzymes, the mechanisms that underlie their positioning and regulation are still not entirely understood. In addition, recent evidence suggests a diverse group of other biochemical elements influence bacterial cell mechanics, may be regulated by new cellular mechanisms, and may be triggered in different environmental contexts to enable cell adaptation and survival. This review summarizes the contributions that different biomolecular components of the cell wall (e.g., lipopolysaccharides, wall and lipoteichoic acids, lipid bilayers, peptidoglycan, and proteins) make to Gram-negative and Gram-positive bacterial cell mechanics. We discuss the contribution of individual proteins and macromolecular complexes in cell mechanics and the tools that make it possible to quantitatively decipher the biochemical machinery that contributes to bacterial cell mechanics. Advances in this area may provide insight into new biology and influence the development of antibacterial chemotherapies.

  11. Biodegradability of bacterial surfactants.

    Science.gov (United States)

    Lima, Tânia M S; Procópio, Lorena C; Brandão, Felipe D; Carvalho, André M X; Tótola, Marcos R; Borges, Arnaldo C

    2011-06-01

    This work aimed at evaluating the biodegradability of different bacterial surfactants in liquid medium and in soil microcosms. The biodegradability of biosurfactants by pure and mixed bacterial cultures was evaluated through CO(2) evolution. Three bacterial strains, Acinetobacter baumanni LBBMA ES11, Acinetobacter haemolyticus LBBMA 53 and Pseudomonas sp. LBBMA 101B, used the biosurfactants produced by Bacillus sp. LBBMA 111A (mixed lipopeptide), Bacillus subtilis LBBMA 155 (lipopeptide), Flavobacterium sp. LBBMA 168 (mixture of flavolipids), Dietzia Maris LBBMA 191(glycolipid) and Arthrobacter oxydans LBBMA 201(lipopeptide) as carbon sources in minimal medium. The synthetic surfactant sodium dodecyl sulfate (SDS) was also mineralized by these microorganisms, but at a lower rate. CO(2) emitted by a mixed bacterial culture in soil microcosms with biosurfactants was higher than in the microcosm containing SDS. Biosurfactant mineralization in soil was confirmed by the increase in surface tension of the soil aqueous extracts after incubation with the mixed bacterial culture. It can be concluded that, in terms of biodegradability and environmental security, these compounds are more suitable for applications in remediation technologies in comparison to synthetic surfactants. However, more information is needed on structure of biosurfactants, their interaction with soil and contaminants and scale up and cost for biosurfactant production.

  12. Investigations on abundance and activity of microbial sponge symbionts using quantitative real - time PCR

    DEFF Research Database (Denmark)

    Kumala, Lars; Hentschel, Ute; Bayer, Kristina

    Marine sponges are hosts to dense and diverse microbial consortia that are likely to play a key role in the metabolic processes of the host sponge due to their enormous abundance. Common symbioses between nitrogen transforming microorganisms and sponges indicate complex nitrogen cycling within...... the host. Of particular interest is determining the community structure and function of microbial symbionts in order to gain deeper insight into host-symbiont interactions. We investigated the abundance and activity of microbial symbionts in two Mediterranean sponge species using quantitative real-time PCR....... An absolute quantification of functional genes and transcripts in archaeal and bacterial symbionts was conducted to determine their involvement in nitrification and denitrification, comparing the low microbial abundance (LMA) sponge Dysidea avara with the high microbial abundance (HMA) representative Aplysina...

  13. Ice formation and growth shape bacterial community structure in Baltic Sea drift ice.

    Science.gov (United States)

    Eronen-Rasimus, Eeva; Lyra, Christina; Rintala, Janne-Markus; Jürgens, Klaus; Ikonen, Vilma; Kaartokallio, Hermanni

    2015-02-01

    Drift ice, open water and under-ice water bacterial communities covering several developmental stages from open water to thick ice were studied in the northern Baltic Sea. The bacterial communities were assessed with 16S rRNA gene terminal-restriction fragment length polymorphism and cloning, together with bacterial abundance and production measurements. In the early stages, open water and pancake ice were dominated by Alphaproteobacteria and Actinobacteria, which are common bacterial groups in Baltic Sea wintertime surface waters. The pancake ice bacterial communities were similar to the open-water communities, suggesting that the parent water determines the sea-ice bacterial community in the early stages of sea-ice formation. In consolidated young and thick ice, the bacterial communities were significantly different from water bacterial communities as well as from each other, indicating community development in Baltic Sea drift ice along with ice-type changes. The thick ice was dominated by typical sea-ice genera from classes Flavobacteria and Gammaproteobacteria, similar to those in polar sea-ice bacterial communities. Since the thick ice bacterial community was remarkably different from that of the parent seawater, results indicate that thick ice bacterial communities were recruited from the rarer members of the seawater bacterial community. © FEMS 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  14. High level bacterial contamination of secondary school students' mobile phones.

    Science.gov (United States)

    Kõljalg, Siiri; Mändar, Rando; Sõber, Tiina; Rööp, Tiiu; Mändar, Reet

    2017-06-01

    While contamination of mobile phones in the hospital has been found to be common in several studies, little information about bacterial abundance on phones used in the community is available. Our aim was to quantitatively determine the bacterial contamination of secondary school students' mobile phones. Altogether 27 mobile phones were studied. The contact plate method and microbial identification using MALDI-TOF mass spectrometer were used for culture studies. Quantitative PCR reaction for detection of universal 16S rRNA, Enterococcus faecalis 16S rRNA and Escherichia coli allantoin permease were performed, and the presence of tetracycline ( tet A, tet B, tet M), erythromycin ( erm B) and sulphonamide ( sul 1) resistance genes was assessed. We found a high median bacterial count on secondary school students' mobile phones (10.5 CFU/cm 2 ) and a median of 17,032 bacterial 16S rRNA gene copies per phone. Potentially pathogenic microbes ( Staphylococcus aureus , Acinetobacter spp. , Pseudomonas spp., Bacillus cereus and Neisseria flavescens ) were found among dominant microbes more often on phones with higher percentage of E. faecalis in total bacterial 16S rRNA. No differences in contamination level or dominating bacterial species between phone owner's gender and between phone types (touch screen/keypad) were found. No antibiotic resistance genes were detected on mobile phone surfaces. Quantitative study methods revealed high level bacterial contamination of secondary school students' mobile phones.

  15. Maize Endophytic Bacterial Diversity as Affected by Soil Cultivation History.

    Science.gov (United States)

    Correa-Galeote, David; Bedmar, Eulogio J; Arone, Gregorio J

    2018-01-01

    The bacterial endophytic communities residing within roots of maize ( Zea mays L.) plants cultivated by a sustainable management in soils from the Quechua maize belt (Peruvian Andes) were examined using tags pyrosequencing spanning the V4 and V5 hypervariable regions of the 16S rRNA. Across four replicate libraries, two corresponding to sequences of endophytic bacteria from long time maize-cultivated soils and the other two obtained from fallow soils, 793 bacterial sequences were found that grouped into 188 bacterial operational taxonomic units (OTUs, 97% genetic similarity). The numbers of OTUs in the libraries from the maize-cultivated soils were significantly higher than those found in the libraries from fallow soils. A mean of 30 genera were found in the fallow soil libraries and 47 were in those from the maize-cultivated soils. Both alpha and beta diversity indexes showed clear differences between bacterial endophytic populations from plants with different soil cultivation history and that the soils cultivated for long time requires a higher diversity of endophytes. The number of sequences corresponding to main genera Sphingomonas, Herbaspirillum, Bradyrhizobium and Methylophilus in the maize-cultivated libraries were statistically more abundant than those from the fallow soils. Sequences of genera Dyella and Sreptococcus were significantly more abundant in the libraries from the fallow soils. Relative abundance of genera Burkholderia, candidatus Glomeribacter, Staphylococcus, Variovorax, Bacillus and Chitinophaga were similar among libraries. A canonical correspondence analysis of the relative abundance of the main genera showed that the four libraries distributed in two clearly separated groups. Our results suggest that cultivation history is an important driver of endophytic colonization of maize and that after a long time of cultivation of the soil the maize plants need to increase the richness of the bacterial endophytes communities.

  16. Acute Bacterial Prostatitis: Diagnosis and Management.

    Science.gov (United States)

    Coker, Timothy J; Dierfeldt, Daniel M

    2016-01-15

    Acute bacterial prostatitis is an acute infection of the prostate gland that causes pelvic pain and urinary tract symptoms, such as dysuria, urinary frequency, and urinary retention, and may lead to systemic symptoms, such as fevers, chills, nausea, emesis, and malaise. Although the true incidence is unknown, acute bacterial prostatitis is estimated to comprise approximately 10% of all cases of prostatitis. Most acute bacterial prostatitis infections are community acquired, but some occur after transurethral manipulation procedures, such as urethral catheterization and cystoscopy, or after transrectal prostate biopsy. The physical examination should include abdominal, genital, and digital rectal examination to assess for a tender, enlarged, or boggy prostate. Diagnosis is predominantly made based on history and physical examination, but may be aided by urinalysis. Urine cultures should be obtained in all patients who are suspected of having acute bacterial prostatitis to determine the responsible bacteria and its antibiotic sensitivity pattern. Additional laboratory studies can be obtained based on risk factors and severity of illness. Radiography is typically unnecessary. Most patients can be treated as outpatients with oral antibiotics and supportive measures. Hospitalization and broad-spectrum intravenous antibiotics should be considered in patients who are systemically ill, unable to voluntarily urinate, unable to tolerate oral intake, or have risk factors for antibiotic resistance. Typical antibiotic regimens include ceftriaxone and doxycycline, ciprofloxacin, and piperacillin/tazobactam. The risk of nosocomial bacterial prostatitis can be reduced by using antibiotics, such as ciprofloxacin, before transrectal prostate biopsy.

  17. Bacterial meningitis in children

    International Nuclear Information System (INIS)

    Marji, S.

    2007-01-01

    To demonstrate the epidemiology, clinical manifestations and bacteriological profile of bacterial meningitis in children beyond the neonatal period in our hospital. This was a retrospective descriptive study conducted at Prince Rashid Hospital in Irbid, Jordan. The medical records of 50 children with the diagnosis of bacterial meningitis during 4 years period, were reviewed. The main cause of infection was streptococcus pneumoniae, followed by Haemophilus influenza and Niesseria meningitides. Mortality was higher in infants and meningococcal infection, while complications were more encountered in cases of streptococcus pneumoniae. Cerebrospinal fluid culture was positive in 11 cases and Latex agglutination test in 39. There is a significant reduction of the numbers of bacterial meningitis caused by Haemophilus influenza type B species. (author)

  18. SWFSC/MMTD/AK: Structure of Populations, Level of Abundance, and Status of Humpbacks (SPLASH) 2004

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This project was part of a larger international project (SPLASH) designed to estimate the abundance and determine the population structure for humpback whales...

  19. Distributions of Bacterial Generalists among the Guts of Birds ...

    Science.gov (United States)

    Complex distributions of bacterial taxa within diverse animal microbiomes have inspired ecological and biogeographical approaches to revealing the functions of taxa that may be most important for host health. Of particular interest are bacteria that find many diverse habitats suitable for growth and remain competitive amongst finely-tuned host specialists. While previous work has focused on identifying these specialists, here our aims were to 1) identify generalist taxa, 2) identify taxonomic clades with enriched generalist diversity, and 3) describe the distribution of the largest generalist groups among hosts. We analyzed existing bacterial rRNA tag-sequencing data (v6) available on VAMPs (vamps.mbl.edu) from the microbiomes of 12 host species (106 samples total) spanning birds, mammals, and fish for generalist taxa using the CLAM test. OTUs with approximately equal abundance and a minimum of 10 reads in two hosts were classified as generalists. Generalist OTUs (n=2,982) were found in all hosts tested. Bacterial families Alcaligenaceae and Burkholderiaceae were significantly enriched with generalists OTUs compared to other families. Bacterial families such as Bacteroidaceae and Lachnospiraceae significantly lacked generalists OTUs compared to other families. Enterobacteriaceae, Peptostreptococcaceae, and Erysipelotrichaceae more so than other bacterial families were widely distributed and abundant in birds, mammals, and fish suggesting that these taxa mainta

  20. Stellar oxygen abundances. I - A resolution to the 7774 A O I abundance discrepancy

    Science.gov (United States)

    King, Jeremy R.

    1993-09-01

    We investigate the discrepancy between O/Fe abundance ratios of metal-poor stars derived from the 7774 A O I triplet and O/Fe ratios determined from other oxygen lines. We propose a possible resolution to this discrepancy which also eliminates the correlation of O/Fe and T(eff) found in a recent 7774 A O I analysis. The equivalent widths of Abia & Rebolo (1989) are found to be systematically too high by 25 percent. Arguments are presented that current temperature estimates for halo stars are 150-200 K too low. Using the guidance of both model atmospheres and other empirical color-T(eff) relations, we construct new color temperature relations for metal-poor stars. These relations are tied to the temperature scale of Saxner & Hammarback (1985) for metal-rich stars. We use (b-y) and (V-K) indices to redetermine values of T(eff) for a handful of halo stars. (B-V)-T(eff) relations which do not take into account the effects of metallicity are found to be inadequate. Revised O/Fe ratios are determined using the new temperature scale. The mean abundance ratio of the reanalyzed halo dwarfs is about +0.52. There is no trend of O/Fe with Fe/H or T(eff).

  1. Adult bacterial meningitis

    DEFF Research Database (Denmark)

    Meyer, C N; Samuelsson, I S; Galle, M

    2004-01-01

    Episodes of adult bacterial meningitis (ABM) at a Danish hospital in 1991-2000 were identified from the databases of the Department of Clinical Microbiology, and compared with data from the Danish National Patient Register and the Danish National Notification System. Reduced penicillin susceptibi......Episodes of adult bacterial meningitis (ABM) at a Danish hospital in 1991-2000 were identified from the databases of the Department of Clinical Microbiology, and compared with data from the Danish National Patient Register and the Danish National Notification System. Reduced penicillin...

  2. Daily thanatomicrobiome changes in soil as an approach of postmortem interval estimation: An ecological perspective.

    Science.gov (United States)

    Adserias-Garriga, Joe; Hernández, Marta; Quijada, Narciso M; Rodríguez Lázaro, David; Steadman, Dawnie; Garcia-Gil, Jesús

    2017-09-01

    Understanding human decomposition is critical for its use in postmortem interval (PMI) estimation, having a significant impact on forensic investigations. In recognition of the need to establish the scientific basis for PMI estimation, several studies on decomposition have been carried out in the last years. The aims of the present study were: (i) to identify soil microbiota communities involved in human decomposition through high-throughput sequencing (HTS) of DNA sequences from the different bacteria, (ii) to monitor quantitatively and qualitatively the decay of such signature species, and (iii) to describe succesional changes in bacterial populations from the early putrefaction state until skeletonization. Three donated individuals to the University of Tennessee FAC were studied. Soil samples around the body were taken from the placement of the donor until advanced decay/dry remains stage. Bacterial DNA extracts were obtained from the samples, HTS techniques were applied and bioinformatic data analysis was performed. The three cadavers showed similar overall successional changes. At the beginning of the decomposition process the soil microbiome consisted of diverse indigenous soil bacterial communities. As decomposition advanced, Firmicutes community abundance increased in the soil during the bloat stage. The growth curve of Firmicutes from human remains can be used to estimate time since death during Tennessee summer conditions. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. Anaerobic bacterial quantitation of Yucca Mountain, Nevada DOE site samples

    International Nuclear Information System (INIS)

    Clarkson, W.W.; Krumholz, L.R.; Suflita, J.M.

    1996-01-01

    Anaerobic bacteria were studied from samples of excavated rock material as one phase of the overall Yucca Mountain site characterization effort. An indication of the abundance of important groups of anaerobic bacteria would enable inferences to be made regarding the natural history of the site and allow for more complete risk evaluation of the site as a nuclear repository. Six bacterial groups were investigated including anaerobic heterotrophs, acetogens, methanogens, sulfate-, nitrate-, and iron-reducing bacteria. The purpose of this portion of the study was to detect and quantify the aforementioned bacterial groups

  4. High bacterial biodiversity increases degradation performance of hydrocarbons during bioremediation of contaminated harbor marine sediments

    International Nuclear Information System (INIS)

    Dell'Anno, Antonio; Beolchini, Francesca; Rocchetti, Laura; Luna, Gian Marco; Danovaro, Roberto

    2012-01-01

    We investigated changes of bacterial abundance and biodiversity during bioremediation experiments carried out on oxic and anoxic marine harbor sediments contaminated with hydrocarbons. Oxic sediments, supplied with inorganic nutrients, were incubated in aerobic conditions at 20 °C and 35 °C for 30 days, whereas anoxic sediments, amended with organic substrates, were incubated in anaerobic conditions at the same temperatures for 60 days. Results reported here indicate that temperature exerted the main effect on bacterial abundance, diversity and assemblage composition. At higher temperature bacterial diversity and evenness increased significantly in aerobic conditions, whilst decreased in anaerobic conditions. In both aerobic and anaerobic conditions, biodegradation efficiencies of hydrocarbons were significantly and positively related with bacterial richness and evenness. Overall results presented here suggest that bioremediation strategies, which can sustain high levels of bacterial diversity rather than the selection of specific taxa, may significantly increase the efficiency of hydrocarbon degradation in contaminated marine sediments. - Highlights: ► Bioremediation performance was investigated on hydrocarbon contaminated sediments. ► Major changes in bacterial diversity and assemblage composition were observed. ► Temperature exerted the major effect on bacterial assemblages. ► High bacterial diversity increased significantly biodegradation performance. ► This should be considered for sediment remediation by bio-treatments. - Bioremediation strategies which can sustain high levels of bacterial diversity may significantly increase the biodegradation of hydrocarbons in contaminated marine sediments.

  5. Bacterial communities in batch and continuous-flow wetlands treating the herbicide S-metolachlor

    International Nuclear Information System (INIS)

    Elsayed, O.F.; Maillard, E.; Vuilleumier, S.; Imfeld, G.

    2014-01-01

    Knowledge of wetland bacterial communities in the context of pesticide contamination and hydrological regime is scarce. We investigated the bacterial composition in constructed wetlands receiving Mercantor Gold ® contaminated water (960 g L −1 of the herbicide S-metolachlor, > 80% of the S-enantiomer) operated under continuous-flow or batch modes to evaluate the impact of the hydraulic regime. In the continuous-flow wetland, S-metolachlor mass removal was > 40%, whereas in the batch wetland, almost complete removal of S-metolachlor (93–97%) was observed. Detection of ethanesulfonic and oxanilic acid degradation products further indicated S-metolachlor biodegradation in the two wetlands. The dominant bacterial populations were characterised by terminal restriction fragment length polymorphism (T-RFLP) and 454 pyrosequencing. The bacterial profiles evolved during the first 35 days of the experiment, starting from a composition similar to that of inlet water, with the use of nitrate and to a lesser extent sulphate and manganese as terminal electron acceptors for microbial metabolism. Proteobacteria were the most abundant phylum, with Beta-, Alpha- and Gammaproteobacteria representing 26%, 19% and 17% respectively of total bacterial abundance. Bacterial composition in wetland water changed gradually over time in continuous-flow wetland and more abruptly in the batch wetland. Differences in overall bacterial water structure in the two systems were modest but significant (p = 0.008), and S-metolachlor, nitrate, and total inorganic carbon concentrations correlated with changes in the bacterial profiles. Together, the results highlight that bacterial composition profiles and their dynamics may be used as bioindicators of herbicide exposure and hydraulic disturbances in wetland systems. - Highlights: • We evaluated the bacterial composition in wetlands treating S-metolachlor • Hydraulic regime impacted biogeochemical processes and S-metolachlor removal

  6. Abundance of introduced species at home predicts abundance away in herbaceous communities

    Science.gov (United States)

    Firn, Jennifer; Moore, Joslin L.; MacDougall, Andrew S.; Borer, Elizabeth T.; Seabloom, Eric W.; HilleRisLambers, Janneke; Harpole, W. Stanley; Cleland, Elsa E.; Brown, Cynthia S.; Knops, Johannes M.H.; Prober, Suzanne M.; Pyke, David A.; Farrell, Kelly A.; Bakker, John D.; O'Halloran, Lydia R.; Adler, Peter B.; Collins, Scott L.; D'Antonio, Carla M.; Crawley, Michael J.; Wolkovich, Elizabeth M.; La Pierre, Kimberly J.; Melbourne, Brett A.; Hautier, Yann; Morgan, John W.; Leakey, Andrew D.B.; Kay, Adam; McCulley, Rebecca; Davies, Kendi F.; Stevens, Carly J.; Chu, Cheng-Jin; Holl, Karen D.; Klein, Julia A.; Fay, Phillip A.; Hagenah, Nicole; Kirkman, Kevin P.; Buckley, Yvonne M.

    2011-01-01

    Many ecosystems worldwide are dominated by introduced plant species, leading to loss of biodiversity and ecosystem function. A common but rarely tested assumption is that these plants are more abundant in introduced vs. native communities, because ecological or evolutionary-based shifts in populations underlie invasion success. Here, data for 26 herbaceous species at 39 sites, within eight countries, revealed that species abundances were similar at native (home) and introduced (away) sites - grass species were generally abundant home and away, while forbs were low in abundance, but more abundant at home. Sites with six or more of these species had similar community abundance hierarchies, suggesting that suites of introduced species are assembling similarly on different continents. Overall, we found that substantial changes to populations are not necessarily a pre-condition for invasion success and that increases in species abundance are unusual. Instead, abundance at home predicts abundance away, a potentially useful additional criterion for biosecurity programmes.

  7. Comparative analyses of the bacterial community of hydrothermal deposits and seafloor sediments across Okinawa Trough

    Science.gov (United States)

    Wang, Long; Yu, Min; Liu, Yan; Liu, Jiwen; Wu, Yonghua; Li, Li; Liu, Jihua; Wang, Min; Zhang, Xiao-Hua

    2018-04-01

    As an ideal place to study back-arc basins and hydrothermal eco-system, Okinawa Trough has attracted the interests of scientists for decades. However, there are still no in-depth studies targeting the bacterial community of the seafloor sediments and hydrothermal deposits in Okinawa Trough. In the present study, we reported the bacterial community of the surface deposits of a newly found hydrothermal field in the southern Okinawa Trough, and the horizontal and vertical variation of bacterial communities in the sediments of the northern Okinawa Trough. The hydrothermal deposits had a relatively high 16S rRNA gene abundance but low bacterial richness and diversity. Epsilonproteobacteria and Bacteroidetes were predominant in hydrothermal deposits whereas Deltaproteobacteria, Gammaproteobacteria and Chloroflexi were abundant across all samples. The bacterial distribution in the seafloor of Okinawa Trough was significantly correlated to the content of total nitrogen, and had consistent relationship with total carbon. Gradual changes of sulfur-oxidizing bacteria were found with the distance away from hydrothermal fields, while the hydrothermal activity did not influence the distribution of the major clades of sulfate-reducing bacteria. Higher abundance of the sulfur cycle related genes (aprA and dsrB), and lower abundance of the bacterial ammonia-oxidizing related gene (amoA) were quantified in hydrothermal deposits. In addition, the present study also compared the inter-field variation of Epsilonproteobacteria among multi-types of hydrothermal vents, revealing that the proportion and diversity of this clade were quite various.

  8. [Bacterial biofilms and infection].

    Science.gov (United States)

    Lasa, I; Del Pozo, J L; Penadés, J R; Leiva, J

    2005-01-01

    In developed countries we tend to think of heart disease and the numerous forms of cancer as the main causes of mortality, but on a global scale infectious diseases come close, or may even be ahead: 14.9 million deaths in 2002 compared to cardiovascular diseases (16.9 million deaths) and cancer (7.1 million deaths) (WHO report 2004). The infectious agents responsible for human mortality have evolved as medical techniques and hygienic measures have changed. Modern-day acute infectious diseases caused by specialized bacterial pathogens such as diphtheria, tetanus, cholera, plague, which represented the main causes of death at the beginning of XX century, have been effectively controlled with antibiotics and vaccines. In their place, more than half of the infectious diseases that affect mildly immunocompromised patients involve bacterial species that are commensal with the human body; these can produce chronic infections, are resistant to antimicrobial agents and there is no effective vaccine against them. Examples of these infections are the otitis media, native valve endocarditis, chronic urinary infections, bacterial prostatitis, osteomyelitis and all the infections related to medical devices. Direct analysis of the surface of medical devices or of tissues that have been foci of chronic infections shows the presence of large numbers of bacteria surrounded by an exopolysaccharide matrix, which has been named the "biofilm". Inside the biofilm, bacteria grow protected from the action of the antibodies, phagocytic cells and antimicrobial treatments. In this article, we describe the role of bacterial biofilms in human persistent infections.

  9. Interfering with bacterial gossip

    DEFF Research Database (Denmark)

    Bjarnsholt, Thomas; Tolker-Nielsen, Tim; Givskov, Michael

    2011-01-01

    that appropriately target bacteria in their relevant habitat with the aim of mitigating their destructive impact on patients. In this review we describe molecular mechanisms involved in “bacterial gossip” (more scientifically referred to as quorum sensing (QS) and c-di-GMP signaling), virulence, biofilm formation...

  10. Bacterial fingerprints across Europe

    NARCIS (Netherlands)

    Glasner, Corinna

    2014-01-01

    Bacterial pathogens, such as Staphylococcus aureus and carbapenemase-producing Enterobacteriaceae (CPE), impose major threats to human health worldwide. Both have a ‘Jekyll & Hyde’ character, since they can be present as human commensals, but can also become harmful invasive pathogens especially

  11. [Spontaneous bacterial peritonitis].

    Science.gov (United States)

    Velkey, Bálint; Vitális, Eszter; Vitális, Zsuzsanna

    2017-01-01

    Spontaneous bacterial peritonitis occurs most commonly in cirrhotic patients with ascites. Pathogens get into the circulation by intestinal translocation and colonize in peritoneal fluid. Diagnosis of spontaneous bacterial peritonitis is based on elevated polymorphonuclear leukocyte count in the ascites (>0,25 G/L). Ascites culture is often negative but aids to get information about antibiotic sensitivity in positive cases. Treatment in stable patient can be intravenous then orally administrated ciprofloxacin or amoxicillin/clavulanic acid, while in severe cases intravenous III. generation cephalosporin. Nosocomial spontaneous bacterial peritonitis often caused by Gram-positive bacteria and multi-resistant pathogens can also be expected thus carbapenem should be the choice of the empiric treatment. Antibiotic prophylaxis should be considered. Norfloxacin is used most commonly, but changes are expected due to increase in quinolone resistance. As a primary prophylaxis, a short-term antibiotic treatment is recommended after gastrointestinal bleeding for 5 days, while long-term prophylaxis is for patients with low ascites protein, and advanced disease (400 mg/day). Secondary prophylaxis is recommended for all patients recovered from spontaneous bacterial peritonitis. Due to increasing antibiotic use of antibiotics prophylaxis is debated to some degree. Orv. Hetil., 2017, 158(2), 50-57.

  12. Stimulation of bacterial DNA synthesis by algal exudates in attached algal-bacterial consortia

    International Nuclear Information System (INIS)

    Murray, R.E.; Cooksey, K.E.; Priscu, J.C.

    1986-01-01

    Algal-bacterial consortia attached to polystyrene surfaces were prepared in the laboratory by using the marine diatom Amphora coffeaeformis and the marine bacterium Vibrio proteolytica (the approved name of this bacterium is Vibrio proteolyticus. The organisms were attached to the surfaces at cell densities of approximately 5 x 10 4 cells cm -2 (diatoms) and 5 x 10 6 cells cm -2 (bacteria). The algal-bacterial consortia consistently exhibited higher rates of [ 3 H]thymidine incorporation than did biofilms composed solely of bacteria. The rates of [ 3 H]thymidine incorporation by the algal-bacterial consortia were fourfold greater than the rates of incorporation by monobacterial biofilms 16 h after biofilm formation and were 16-fold greater 70 h after biofilm formation. Extracellular material released from the attached Amphora cells supported rates of bacterial activity (0.8 x 10 -21 mol to 17.9 x 10 -21 mol of [ 3 H]thymidine incorporated cell -1 h -1 ) and growth (doubling time, 29.5 to 1.4 days) comparable to values reported for a wide variety of marine and freshwater ecosystems. In the presence of sessile diatom populations, DNA synthesis by attached V. proteolytica cells was light dependent and increased with increasing algal abundance. The metabolic activity of diatoms thus appears to be the rate-limiting process in biofilm development on illuminated surfaces under conditions of low bulk-water dissolved organic carbon

  13. One Percent Determination of the Primordial Deuterium Abundance

    Science.gov (United States)

    Cooke, Ryan J.; Pettini, Max; Steidel, Charles C.

    2018-03-01

    We report a reanalysis of a near-pristine absorption system, located at a redshift {z}abs}=2.52564 toward the quasar Q1243+307, based on the combination of archival and new data obtained with the HIRES echelle spectrograph on the Keck telescope. This absorption system, which has an oxygen abundance [O/H] = ‑2.769 ± 0.028 (≃1/600 of the solar abundance), is among the lowest metallicity systems currently known where a precise measurement of the deuterium abundance is afforded. Our detailed analysis of this system concludes, on the basis of eight D I absorption lines, that the deuterium abundance of this gas cloud is {log}}10({{D}}/{{H}})=-4.622+/- 0.015, which is in very good agreement with the results previously reported by Kirkman et al., but with an improvement on the precision of this single measurement by a factor of ∼3.5. Combining this new estimate with our previous sample of six high precision and homogeneously analyzed D/H measurements, we deduce that the primordial deuterium abundance is {log}}10{({{D}}/{{H}})}{{P}}=-4.5974+/- 0.0052 or, expressed as a linear quantity, {10}5{({{D}}/{{H}})}{{P}}=2.527+/- 0.030; this value corresponds to a one percent determination of the primordial deuterium abundance. Combining our result with a big bang nucleosynthesis (BBN) calculation that uses the latest nuclear physics input, we find that the baryon density derived from BBN agrees to within 2σ of the latest results from the Planck cosmic microwave background data. Based on observations collected at the W.M. Keck Observatory which is operated as a scientific partnership among the California Institute of Technology, the University of California, and the National Aeronautics and Space Administration. The Observatory was made possible by the generous financial support of the W.M. Keck Foundation.

  14. Corticosteroids for Bacterial Keratitis

    Science.gov (United States)

    Srinivasan, Muthiah; Mascarenhas, Jeena; Rajaraman, Revathi; Ravindran, Meenakshi; Lalitha, Prajna; Glidden, David V.; Ray, Kathryn J.; Hong, Kevin C.; Oldenburg, Catherine E.; Lee, Salena M.; Zegans, Michael E.; McLeod, Stephen D.; Lietman, Thomas M.; Acharya, Nisha R.

    2013-01-01

    Objective To determine whether there is a benefit in clinical outcomes with the use of topical corticosteroids as adjunctive therapy in the treatment of bacterial corneal ulcers. Methods Randomized, placebo-controlled, double-masked, multicenter clinical trial comparing prednisolone sodium phosphate, 1.0%, to placebo as adjunctive therapy for the treatment of bacterial corneal ulcers. Eligible patients had a culture-positive bacterial corneal ulcer and received topical moxifloxacin for at least 48 hours before randomization. Main Outcome Measures The primary outcome was best spectacle-corrected visual acuity (BSCVA) at 3 months from enrollment. Secondary outcomes included infiltrate/scar size, reepithelialization, and corneal perforation. Results Between September 1, 2006, and February 22, 2010, 1769 patients were screened for the trial and 500 patients were enrolled. No significant difference was observed in the 3-month BSCVA (−0.009 logarithm of the minimum angle of resolution [logMAR]; 95% CI, −0.085 to 0.068; P = .82), infiltrate/scar size (P = .40), time to reepithelialization (P = .44), or corneal perforation (P > .99). A significant effect of corticosteroids was observed in subgroups of baseline BSCVA (P = .03) and ulcer location (P = .04). At 3 months, patients with vision of counting fingers or worse at baseline had 0.17 logMAR better visual acuity with corticosteroids (95% CI, −0.31 to −0.02; P = .03) compared with placebo, and patients with ulcers that were completely central at baseline had 0.20 logMAR better visual acuity with corticosteroids (−0.37 to −0.04; P = .02). Conclusions We found no overall difference in 3-month BSCVA and no safety concerns with adjunctive corticosteroid therapy for bacterial corneal ulcers. Application to Clinical Practice Adjunctive topical corticosteroid use does not improve 3-month vision in patients with bacterial corneal ulcers. PMID:21987582

  15. Changes in bacterial gut community of Reticulitermes flavipes (Kollar) and Reticulitermes tibialis Banks after feeding on termiticidal bait material

    Science.gov (United States)

    Rachel A. Arango; Frederick Green III; Kenneth F. Raffa

    2014-01-01

    In this study, 454-pyrosequencing was used to evaluate the effect of two termiticidal baits, hexaflumuron and diflubenzuron, on the bacterial gut community in two Reticulitermes flavipes colonies and one Reticulitermes tibialis colony. Results showed two bacterial groups to be most abundant in the gut, the Bacteroidetes and...

  16. Bacterial infec tions in travellers

    African Journals Online (AJOL)

    namely bacterial causes of travellers' diarrhoea and skin infections, as well as .... Vaccination: protective efficacy against typhoid may be overcome by ingesting a high bacterial load. Vaccine ..... preparation such as cream sauce. Only after ...

  17. Inhibition of Pseudogymnoascus destructans growth from conidia and mycelial extension by bacterially produced volatile organic compounds.

    Science.gov (United States)

    Cornelison, Christopher T; Gabriel, Kyle T; Barlament, Courtney; Crow, Sidney A

    2014-02-01

    The recently identified causative agent of white-nose syndrome (WNS), Pseudogymnoascus destructans, has been implicated in the mortality of an estimated 5.5 million North American bats since its initial documentation in 2006 (Frick et al. in Science 329:679-682, 2010). In an effort to identify potential biological and chemical control options for WNS, 6 previously described bacterially produced volatile organic compounds (VOCs) were screened for anti-P. destructans activity. The compounds include decanal; 2-ethyl-1-hexanol; nonanal; benzothiazole; benzaldehyde; andN,N-dimethyloctylamine. P. destructans conidia and mycelial plugs were exposed to the VOCs in a closed air space at 15 and 4 °C and then evaluated for growth inhibition. All VOCs inhibited growth from conidia as well as inhibiting radial mycelial extension, with the greatest effect at 4 °C. Studies of the ecology of fungistatic soils and the natural abundance of the fungistatic VOCs present in these environments suggest a synergistic activity of select VOCs may occur. The evaluation of formulations of two or three VOCs at equivalent concentrations was supportive of synergistic activity in several cases. The identification of bacterially produced VOCs with anti-P. destructans activity indicates disease-suppressive and fungistatic soils as a potentially significant reservoir of biological and chemical control options for WNS and provides wildlife management personnel with tools to combat this devastating disease.

  18. Diversity rankings among bacterial lineages in soil.

    Science.gov (United States)

    Youssef, Noha H; Elshahed, Mostafa S

    2009-03-01

    We used rarefaction curve analysis and diversity ordering-based approaches to rank the 11 most frequently encountered bacterial lineages in soil according to diversity in 5 previously reported 16S rRNA gene clone libraries derived from agricultural, undisturbed tall grass prairie and forest soils (n=26,140, 28 328, 31 818, 13 001 and 53 533). The Planctomycetes, Firmicutes and the delta-Proteobacteria were consistently ranked among the most diverse lineages in all data sets, whereas the Verrucomicrobia, Gemmatimonadetes and beta-Proteobacteria were consistently ranked among the least diverse. On the other hand, the rankings of alpha-Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes and Chloroflexi varied widely in different soil clone libraries. In general, lineages exhibiting largest differences in diversity rankings also exhibited the largest difference in relative abundance in the data sets examined. Within these lineages, a positive correlation between relative abundance and diversity was observed within the Acidobacteria, Actinobacteria and Chloroflexi, and a negative diversity-abundance correlation was observed within the Bacteroidetes. The ecological and evolutionary implications of these results are discussed.

  19. Abundance Tomography of Type Ia Supernovae

    International Nuclear Information System (INIS)

    Stehle, M.; Mazzali, P.A.; Hillebrandt, W.

    2005-01-01

    An analysis of early time spectra of Type Ia Supernovae is presented. A new method to derive a detailed abundance distribution of the SN ejecta through comparison with synthetic spectra, called 'Abundance Tomography' is introduced and applied to the normal SN Ia 2002bo. Conclusions regarding the explosion mechanism are drawn

  20. Diversity, composition and abundance of macroinvertebrates ...

    African Journals Online (AJOL)

    user

    these genera were found at all sampling stations as shown in Table 2. Out of the orders sampled, Hemiptera, Pulmonata and. Coleoptera had the highest number of genera with 5, 4 and 4, respectively. In terms of relative abundance, dipterans and Pulmonata were the most abundant while. Hydracarina (water mites) were ...

  1. Resource Abundance and Resource Dependence in China

    NARCIS (Netherlands)

    Ji, K.; Magnus, J.R.; Wang, W.

    2010-01-01

    This paper reconsiders the ‘curse of resources’ hypothesis for the case of China, and distinguishes between resource abundance, resource rents, and resource dependence. Resource abundance and resource rents are shown to be approximately equivalent, and their association with resource dependence

  2. Determinants of distribution, abundance and reproductive success ...

    African Journals Online (AJOL)

    ... while local vegetation structure determines the abundance of locally established populations. The abundance of trees affects nest site availability and breeding success, based on observations at two oases. Blackbird nests were usually situated on pomegranate trees and olive trees. The Common Blackbird is a successful ...

  3. Diversity and abundance of ammonia-oxidizing

    NARCIS (Netherlands)

    Cardoso, J.F.M.F.; van Bleijswijk, J.D.L.; Witte, H.; van Duyl, F.C.

    2013-01-01

    We analysed the diversity and abundance of ammonia-oxidizing Archaea (AOA) and Bacteria (AOB) in the shallow warm-water sponge Halisarca caerulea and the deep cold-water sponges Higginsia thielei and Nodastrella nodastrella. The abundance of AOA and AOB was analysed using catalyzed reporter

  4. Stellar pulsation and the abundance of helium

    International Nuclear Information System (INIS)

    Schmidt, E.G.

    1978-01-01

    It has been suggested that the appearance of nonvariable stars within the Cepheid strip could be explained by a range in the helium abundance of Population I stars. In order to study this possibility, spectra were obtained of the main-sequence B stars in the galactic cluster NGC 129, which contains a nonvariable Cepheid-strip star, and M25, which contains a relatively hot Cepheid. Unfortunately, several of the stars in these clusters turn out to be helium-weak stars. In NGC 129 two stars which appear normal give a normal abundance, while in M25 all of the observed stars have abnormally low abundances. The significance of the low abundance in M25 is not clear. The abundance in NGC 129 is not low enough to support the above suggestion. 4 figures, 2 tables

  5. Comparing the bacterial diversity of acute and chronic dental root canal infections.

    Directory of Open Access Journals (Sweden)

    Adriana L Santos

    Full Text Available This study performed barcoded multiplex pyrosequencing with a 454 FLX instrument to compare the microbiota of dental root canal infections associated with acute (symptomatic or chronic (asymptomatic apical periodontitis. Analysis of samples from 9 acute abscesses and 8 chronic infections yielded partial 16S rRNA gene sequences that were taxonomically classified into 916 bacterial species-level operational taxonomic units (OTUs (at 3% divergence belonging to 67 genera and 13 phyla. The most abundant phyla in acute infections were Firmicutes (52%, Fusobacteria (17% and Bacteroidetes (13%, while in chronic infections the dominant were Firmicutes (59%, Bacteroidetes (14% and Actinobacteria (10%. Members of Fusobacteria were much more prevalent in acute (89% than in chronic cases (50%. The most abundant/prevalent genera in acute infections were Fusobacterium and Parvimonas. Twenty genera were exclusively detected in acute infections and 18 in chronic infections. Only 18% (n = 165 of the OTUs at 3% divergence were shared by acute and chronic infections. Diversity and richness estimators revealed that acute infections were significantly more diverse than chronic infections. Although a high interindividual variation in bacterial communities was observed, many samples tended to group together according to the type of infection (acute or chronic. This study is one of the most comprehensive in-deep comparisons of the microbiota associated with acute and chronic dental root canal infections and highlights the role of diverse polymicrobial communities as the unit of pathogenicity in acute infections. The overall diversity of endodontic infections as revealed by the pyrosequencing technique was much higher than previously reported for endodontic infections.

  6. Determinants of bacterial communities in Canadian agroforestry systems.

    Science.gov (United States)

    Banerjee, Samiran; Baah-Acheamfour, Mark; Carlyle, Cameron N; Bissett, Andrew; Richardson, Alan E; Siddique, Tariq; Bork, Edward W; Chang, Scott X

    2016-06-01

    Land-use change is one of the most important factors influencing soil microbial communities, which play a pivotal role in most biogeochemical and ecological processes. Using agroforestry systems as a model, this study examined the effects of land uses and edaphic properties on bacterial communities in three agroforestry types covering a 270 km soil-climate gradient in Alberta, Canada. Our results demonstrate that land-use patterns exert stronger effects on soil bacterial communities than soil zones in these agroforestry systems. Plots with trees in agroforestry systems promoted greater bacterial abundance and to some extent species richness, which was associated with more nutrient-rich soil resources. While Acidobacteria, Actinobacteria and Alphaproteobacteria were the dominant bacterial phyla and subphyla across land uses, Arthrobacter, Acidobacteria_Gp16, Burkholderia, Rhodanobacter and Rhizobium were the keystone taxa in these agroforestry systems. Soil pH and carbon contents emerged as the major determinants of bacterial community characteristics. We found non-random co-occurrence and modular patterns of soil bacterial communities, and these patterns were controlled by edaphic factors and not their taxonomy. Overall, this study highlights the drivers and co-occurrence patterns of soil microbial communities in agroforestry systems. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

  7. Bacterial Community Succession in Pine-Wood Decomposition.

    Science.gov (United States)

    Kielak, Anna M; Scheublin, Tanja R; Mendes, Lucas W; van Veen, Johannes A; Kuramae, Eiko E

    2016-01-01

    Though bacteria and fungi are common inhabitants of decaying wood, little is known about the relationship between bacterial and fungal community dynamics during natural wood decay. Based on previous studies involving inoculated wood blocks, strong fungal selection on bacteria abundance and community composition was expected to occur during natural wood decay. Here, we focused on bacterial and fungal community compositions in pine wood samples collected from dead trees in different stages of decomposition. We showed that bacterial communities undergo less drastic changes than fungal communities during wood decay. Furthermore, we found that bacterial community assembly was a stochastic process at initial stage of wood decay and became more deterministic in later stages, likely due to environmental factors. Moreover, composition of bacterial communities did not respond to the changes in the major fungal species present in the wood but rather to the stage of decay reflected by the wood density. We concluded that the shifts in the bacterial communities were a result of the changes in wood properties during decomposition and largely independent of the composition of the wood-decaying fungal communities.

  8. Bacterial community succession in pine-wood decomposition

    Directory of Open Access Journals (Sweden)

    Anna eKielak

    2016-03-01

    Full Text Available Though bacteria and fungi are common inhabitants of decaying wood, little is known about the relationship between bacterial and fungal community dynamics during natural wood decay. Based on previous studies involving inoculated wood blocks, strong fungal selection on bacteria abundance and community composition was expected to occur during natural wood decay. Here we focused on bacterial and fungal community compositions in pine wood samples collected from dead trees in different stages of decomposition. We showed that bacterial communities undergo less drastic changes than fungal communities during wood decay. Furthermore, we found that bacterial community assembly was a stochastic process at initial stage of wood decay and became more deterministic in later stages, likely due to environmental factors. Moreover, composition of bacterial communities did not respond to the changes in the major fungal species present in the wood but rather to the stage of decay reflected by the wood density. We concluded that the shifts in the bacterial communities were a result of the changes in wood properties during decomposition and largely independent of the composition of the wood-decaying fungal communities.

  9. Evaluating abundance and trends in a Hawaiian avian community using state-space analysis

    Science.gov (United States)

    Camp, Richard J.; Brinck, Kevin W.; Gorresen, P.M.; Paxton, Eben H.

    2016-01-01

    Estimating population abundances and patterns of change over time are important in both ecology and conservation. Trend assessment typically entails fitting a regression to a time series of abundances to estimate population trajectory. However, changes in abundance estimates from year-to-year across time are due to both true variation in population size (process variation) and variation due to imperfect sampling and model fit. State-space models are a relatively new method that can be used to partition the error components and quantify trends based only on process variation. We compare a state-space modelling approach with a more traditional linear regression approach to assess trends in uncorrected raw counts and detection-corrected abundance estimates of forest birds at Hakalau Forest National Wildlife Refuge, Hawai‘i. Most species demonstrated similar trends using either method. In general, evidence for trends using state-space models was less strong than for linear regression, as measured by estimates of precision. However, while the state-space models may sacrifice precision, the expectation is that these estimates provide a better representation of the real world biological processes of interest because they are partitioning process variation (environmental and demographic variation) and observation variation (sampling and model variation). The state-space approach also provides annual estimates of abundance which can be used by managers to set conservation strategies, and can be linked to factors that vary by year, such as climate, to better understand processes that drive population trends.

  10. Abundance, viability and culturability of Antarctic bacteria

    Digital Repository Service at National Institute of Oceanography (India)

    LokaBharathi, P.A.; DeSouza, M.J.B.D.; Nair, S.; Chandramohan, D.

    The viability of total number of bacteria decide the mineralisation rate in any ecosystem and ultimately the fertility of the region. This study aims at establishing the extent of viability in the standing stock of the Antarctic bacterial population...

  11. Chlamydia caviae infection alters abundance but not composition of the guinea pig vaginal microbiota.

    Science.gov (United States)

    Neuendorf, Elizabeth; Gajer, Pawel; Bowlin, Anne K; Marques, Patricia X; Ma, Bing; Yang, Hongqiu; Fu, Li; Humphrys, Michael S; Forney, Larry J; Myers, Garry S A; Bavoil, Patrik M; Rank, Roger G; Ravel, Jacques

    2015-06-01

    In humans, the vaginal microbiota is thought to be the first line of defense again pathogens including Chlamydia trachomatis. The guinea pig has been extensively used as a model to study chlamydial infection because it shares anatomical and physiological similarities with humans, such as a squamous vaginal epithelium as well as some of the long-term outcomes caused by chlamydial infection. In this study, we aimed to evaluate the guinea pig-C. caviae model of genital infection as a surrogate for studying the role of the vaginal microbiota in the early steps of C. trachomatis infection in humans. We used culture-independent molecular methods to characterize the relative and absolute abundance of bacterial phylotypes in the guinea pig vaginal microbiota in animals non-infected, mock-infected or infected by C. caviae. We showed that the guinea pig and human vaginal microbiotas are of different bacterial composition and abundance. Chlamydia caviae infection had a profound effect on the absolute abundance of bacterial phylotypes but not on the composition of the guinea pig vaginal microbiota. Our findings compromise the validity of the guinea pig-C. caviae model to study the role of the vaginal microbiota during the early steps of sexually transmitted infection. © FEMS 2015.

  12. Seasonal and spatial variations in heterotrophic nanoflagellate and bacteria abundances in sediments of a freshwater littoral zone

    NARCIS (Netherlands)

    Starink, Mathieu; Bär-Gilissen, M.J.; Cappenberg, T.E.

    1996-01-01

    We studied seasonal variation in heterotrophic nanoflagellates (HNAN) and bacterial, densities at different depths in the sediment of two freshwater littoral stations. Station 1 was in a reed bed of Phragmites australis; station 2 was outside the reed zone in open water. Benthic HNAN abundances

  13. Occurrence, metabolism, metabolic role, and industrial uses of bacterial polyhydroxyalkanoates.

    OpenAIRE

    Anderson, A J; Dawes, E A

    1990-01-01

    Polyhydroxyalkanoates (PHAs), of which polyhydroxybutyrate (PHB) is the most abundant, are bacterial carbon and energy reserve materials of widespread occurrence. They are composed of 3-hydroxyacid monomer units and exist as a small number of cytoplasmic granules per cell. The properties of the C4 homopolymer PHB as a biodegradable thermoplastic first attracted industrial attention more than 20 years ago. Copolymers of C4 (3-hydroxybutyrate [3HB]) and C5 (3-hydroxyvalerate [3HV]) monomer unit...

  14. Structure of bacterial lipopolysaccharides.

    Science.gov (United States)

    Caroff, Martine; Karibian, Doris

    2003-11-14

    Bacterial lipopolysaccharides are the major components of the outer surface of Gram-negative bacteria They are often of interest in medicine for their immunomodulatory properties. In small amounts they can be beneficial, but in larger amounts they may cause endotoxic shock. Although they share a common architecture, their structural details exert a strong influence on their activity. These molecules comprise: a lipid moiety, called lipid A, which is considered to be the endotoxic component, a glycosidic part consisting of a core of approximately 10 monosaccharides and, in "smooth-type" lipopolysaccharides, a third region, named O-chain, consisting of repetitive subunits of one to eight monosaccharides responsible for much of the immunospecificity of the bacterial cell.

  15. Cooperative Bacterial Foraging Optimization

    Directory of Open Access Journals (Sweden)

    Hanning Chen

    2009-01-01

    Full Text Available Bacterial Foraging Optimization (BFO is a novel optimization algorithm based on the social foraging behavior of E. coli bacteria. This paper presents a variation on the original BFO algorithm, namely, the Cooperative Bacterial Foraging Optimization (CBFO, which significantly improve the original BFO in solving complex optimization problems. This significant improvement is achieved by applying two cooperative approaches to the original BFO, namely, the serial heterogeneous cooperation on the implicit space decomposition level and the serial heterogeneous cooperation on the hybrid space decomposition level. The experiments compare the performance of two CBFO variants with the original BFO, the standard PSO and a real-coded GA on four widely used benchmark functions. The new method shows a marked improvement in performance over the original BFO and appears to be comparable with the PSO and GA.

  16. THE RAVE CATALOG OF STELLAR ELEMENTAL ABUNDANCES: FIRST DATA RELEASE

    Energy Technology Data Exchange (ETDEWEB)

    Boeche, C.; Williams, M.; De Jong, R. S.; Steinmetz, M. [Leibniz-Institut fuer Astrophysik Potsdam (AIP), D-14482 Potsdam (Germany); Siebert, A.; Bienayme, O. [Observatoire Astronomique de Strasbourg, Universite de Strasbourg, CNRS, UMR 7550, F-67000 Strasbourg (France); Fulbright, J. P.; Ruchti, G. R. [Department of Physics and Astronomy, Johns Hopkins University, Baltimore, MD 21218 (United States); Bland-Hawthorn, J. [Sydney Institute for Astronomy, School of Physics A28, University of Sydney, NSW 2006 (Australia); Campbell, R. [Department of Physics and Astronomy, Western Kentucky University, Bowling Green, KY (United States); Freeman, K. C. [Research School of Astronomy and Astrophysics, Australia National University, Weston Creek, Canberra ACT 2611 (Australia); Gibson, B. K. [Jeremiah Horrocks Institute, University of Central Lancashire, Preston PR1 2HE (United Kingdom); Gilmore, G. [Institute of Astronomy, University of Cambridge, Madingley Road, Cambridge CB3 0HA (United Kingdom); Grebel, E. K. [Astronomisches Rechen-Institut, Zentrum fuer Astronomie der Universitaet Heidelberg, D-69120 Heidelberg (Germany); Helmi, A. [Kapteyn Astronomical Institute, University of Groningen, 9700 AV Groningen (Netherlands); Munari, U. [INAF Osservatorio Astronomico di Padova, Asiago I-36012 (Italy); Navarro, J. F. [Department of Physics and Astronomy, University of Victoria, Victoria BC V8W 3P6 (Canada); Parker, Q. A.; Reid, W. [Department of Physics and Astronomy, Faculty of Sciences, Macquarie University, Sydney, NSW 2109 (Australia); Seabroke, G. M. [Mullard Space Science Laboratory, University College London, Holmbury, St. Mary RH5 6NT (United Kingdom); and others

    2011-12-15

    We present chemical elemental abundances for 36,561 stars observed by the RAdial Velocity Experiment (RAVE), an ambitious spectroscopic survey of our Galaxy at Galactic latitudes |b| > 25 Degree-Sign and with magnitudes in the range 9 abundances for the elements Mg, Al, Si, Ca, Ti, Fe, and Ni, with a mean error of {approx}0.2 dex, as judged from accuracy tests performed on synthetic and real spectra. Abundances are estimated through a dedicated processing pipeline in which the curve of growth of individual lines is obtained from a library of absorption line equivalent widths to construct a model spectrum that is then matched to the observed spectrum via a {chi}{sup 2} minimization technique. We plan to extend this pipeline to include estimates for other elements, such as oxygen and sulfur, in future data releases.

  17. Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

    KAUST Repository

    Roux, Simon

    2016-05-12

    Ocean microbes drive biogeochemical cycling on a global scale. However, this cycling is constrained by viruses that affect community composition, metabolic activity, and evolutionary trajectories. Owing to challenges with the sampling and cultivation of viruses, genome-level viral diversity remains poorly described and grossly understudied, with less than 1% of observed surface-ocean viruses known. Here we assemble complete genomes and large genomic fragments from both surface-and deep-ocean viruses sampled during the Tara Oceans and Malaspina research expeditions, and analyse the resulting â global ocean virome\\' dataset to present a global map of abundant, double-stranded DNA viruses complete with genomic and ecological contexts. A total of 15,222 epipelagic and mesopelagic viral populations were identified, comprising 867 viral clusters (defined as approximately genus-level groups). This roughly triples the number of known ocean viral populations and doubles the number of candidate bacterial and archaeal virus genera, providing a near-complete sampling of epipelagic communities at both the population and viral-cluster level. We found that 38 of the 867 viral clusters were locally or globally abundant, together accounting for nearly half of the viral populations in any global ocean virome sample. While two-thirds of these clusters represent newly described viruses lacking any cultivated representative, most could be computationally linked to dominant, ecologically relevant microbial hosts. Moreover, we identified 243 viral-encoded auxiliary metabolic genes, of which only 95 were previously known. Deeper analyses of four of these auxiliary metabolic genes (dsrC, soxYZ, P-II (also known as glnB) and amoC) revealed that abundant viruses may directly manipulate sulfur and nitrogen cycling throughout the epipelagic ocean. This viral catalog and functional analyses provide a necessary foundation for the meaningful integration of viruses into ecosystem models where

  18. Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses.

    Science.gov (United States)

    Roux, Simon; Brum, Jennifer R; Dutilh, Bas E; Sunagawa, Shinichi; Duhaime, Melissa B; Loy, Alexander; Poulos, Bonnie T; Solonenko, Natalie; Lara, Elena; Poulain, Julie; Pesant, Stéphane; Kandels-Lewis, Stefanie; Dimier, Céline; Picheral, Marc; Searson, Sarah; Cruaud, Corinne; Alberti, Adriana; Duarte, Carlos M; Gasol, Josep M; Vaqué, Dolors; Bork, Peer; Acinas, Silvia G; Wincker, Patrick; Sullivan, Matthew B

    2016-09-29

    Ocean microbes drive biogeochemical cycling on a global scale. However, this cycling is constrained by viruses that affect community composition, metabolic activity, and evolutionary trajectories. Owing to challenges with the sampling and cultivation of viruses, genome-level viral diversity remains poorly described and grossly understudied, with less than 1% of observed surface-ocean viruses known. Here we assemble complete genomes and large genomic fragments from both surface- and deep-ocean viruses sampled during the Tara Oceans and Malaspina research expeditions, and analyse the resulting 'global ocean virome' dataset to present a global map of abundant, double-stranded DNA viruses complete with genomic and ecological contexts. A total of 15,222 epipelagic and mesopelagic viral populations were identified, comprising 867 viral clusters (defined as approximately genus-level groups). This roughly triples the number of known ocean viral populations and doubles the number of candidate bacterial and archaeal virus genera, providing a near-complete sampling of epipelagic communities at both the population and viral-cluster level. We found that 38 of the 867 viral clusters were locally or globally abundant, together accounting for nearly half of the viral populations in any global ocean virome sample. While two-thirds of these clusters represent newly described viruses lacking any cultivated representative, most could be computationally linked to dominant, ecologically relevant microbial hosts. Moreover, we identified 243 viral-encoded auxiliary metabolic genes, of which only 95 were previously known. Deeper analyses of four of these auxiliary metabolic genes (dsrC, soxYZ, P-II (also known as glnB) and amoC) revealed that abundant viruses may directly manipulate sulfur and nitrogen cycling throughout the epipelagic ocean. This viral catalog and functional analyses provide a necessary foundation for the meaningful integration of viruses into ecosystem models where they

  19. Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

    KAUST Repository

    Roux, Simon; Brum, Jennifer R; Dutilh, Bas E.; Sunagawa, Shinichi; Duhaime, Melissa B; Loy, Alexander; Poulos, Bonnie T; Solonenko, Natalie; Lara, Elena; Poulain, Julie; Pesant, Stephane; Kandels-Lewis, Stefanie; Dimier, Celine; Picheral, Marc; Searson, Sarah; Cruaud, Corinne; Alberti, Adriana; Duarte, Carlos M.; Gasol, Josep M M; Vaque, Dolors; Bork, Peer; Acinas, Silvia G; Wincker, Patrick; Sullivan, Matthew B

    2016-01-01

    Ocean microbes drive biogeochemical cycling on a global scale. However, this cycling is constrained by viruses that affect community composition, metabolic activity, and evolutionary trajectories. Owing to challenges with the sampling and cultivation of viruses, genome-level viral diversity remains poorly described and grossly understudied, with less than 1% of observed surface-ocean viruses known. Here we assemble complete genomes and large genomic fragments from both surface-and deep-ocean viruses sampled during the Tara Oceans and Malaspina research expeditions, and analyse the resulting â global ocean virome' dataset to present a global map of abundant, double-stranded DNA viruses complete with genomic and ecological contexts. A total of 15,222 epipelagic and mesopelagic viral populations were identified, comprising 867 viral clusters (defined as approximately genus-level groups). This roughly triples the number of known ocean viral populations and doubles the number of candidate bacterial and archaeal virus genera, providing a near-complete sampling of epipelagic communities at both the population and viral-cluster level. We found that 38 of the 867 viral clusters were locally or globally abundant, together accounting for nearly half of the viral populations in any global ocean virome sample. While two-thirds of these clusters represent newly described viruses lacking any cultivated representative, most could be computationally linked to dominant, ecologically relevant microbial hosts. Moreover, we identified 243 viral-encoded auxiliary metabolic genes, of which only 95 were previously known. Deeper analyses of four of these auxiliary metabolic genes (dsrC, soxYZ, P-II (also known as glnB) and amoC) revealed that abundant viruses may directly manipulate sulfur and nitrogen cycling throughout the epipelagic ocean. This viral catalog and functional analyses provide a necessary foundation for the meaningful integration of viruses into ecosystem models where they

  20. Bacterial control of cyanobacteria

    CSIR Research Space (South Africa)

    Ndlela, Luyanda L

    2017-08-01

    Full Text Available of biological control appears to be direct contact. • Ndlela, L. L. et al. (2016) ‘An overview of cyanobacterial bloom occurrences and research in Africa over the last decade’, Harmful Algae, 60 • Gumbo, J.R. et al. (2010) The Isolation and identification... of Predatory Bacteria from a Microcystis algal Bloom.. African Journal of Biotechnology, 9. *Special acknowledgement goes to the National Research foundation for funding this presentation Bacterial control of cyanobacteria Luyanda...

  1. Seasonal Variation in Soil Microbial Biomass, Bacterial Community Composition and Extracellular Enzyme Activity in Relation to Soil Respiration in a Northern Great Plains Grassland

    Science.gov (United States)

    Wilton, E.; Flanagan, L. B.

    2014-12-01

    Soil respiration rate is affected by seasonal changes in temperature and moisture, but is this a direct effect on soil metabolism or an indirect effect caused by changes in microbial biomass, bacterial community composition and substrate availability? In order to address this question, we compared continuous measurements of soil and plant CO2 exchange made with an automatic chamber system to analyses conducted on replicate soil samples collected on four dates during June-August. Microbial biomass was estimated from substrate-induced respiration rate, bacterial community composition was determined by 16S rRNA amplicon pyrosequencing, and β-1,4-N-acetylglucosaminidase (NAGase) and phenol oxidase enzyme activities were assayed fluorometrically or by absorbance measurements, respectively. Soil microbial biomass declined from June to August in strong correlation with a progressive decline in soil moisture during this time period. Soil bacterial species richness and alpha diversity showed no significant seasonal change. However, bacterial community composition showed a progressive shift over time as measured by Bray-Curtis dissimilarity. In particular, the change in community composition was associated with increasing relative abundance in the alpha and delta classes, and declining abundance of the beta and gamma classes of the Proteobacteria phylum during June-August. NAGase showed a progressive seasonal decline in potential activity that was correlated with microbial biomass and seasonal changes in soil moisture. In contrast, phenol oxidase showed highest potential activity in mid-July near the time of peak soil respiration and ecosystem photosynthesis, which may represent a time of high input of carbon exudates into the soil from plant roots. This input of exudates may stimulate the activity of phenol oxidase, a lignolytic enzyme involved in the breakdown of soil organic matter. These analyses indicated that seasonal change in soil respiration is a complex

  2. Adaptive Bacterial Foraging Optimization

    Directory of Open Access Journals (Sweden)

    Hanning Chen

    2011-01-01

    Full Text Available Bacterial Foraging Optimization (BFO is a recently developed nature-inspired optimization algorithm, which is based on the foraging behavior of E. coli bacteria. Up to now, BFO has been applied successfully to some engineering problems due to its simplicity and ease of implementation. However, BFO possesses a poor convergence behavior over complex optimization problems as compared to other nature-inspired optimization techniques. This paper first analyzes how the run-length unit parameter of BFO controls the exploration of the whole search space and the exploitation of the promising areas. Then it presents a variation on the original BFO, called the adaptive bacterial foraging optimization (ABFO, employing the adaptive foraging strategies to improve the performance of the original BFO. This improvement is achieved by enabling the bacterial foraging algorithm to adjust the run-length unit parameter dynamically during algorithm execution in order to balance the exploration/exploitation tradeoff. The experiments compare the performance of two versions of ABFO with the original BFO, the standard particle swarm optimization (PSO and a real-coded genetic algorithm (GA on four widely-used benchmark functions. The proposed ABFO shows a marked improvement in performance over the original BFO and appears to be comparable with the PSO and GA.

  3. Disturbance opens recruitment sites for bacterial colonization in activated sludge.

    Science.gov (United States)

    Vuono, David C; Munakata-Marr, Junko; Spear, John R; Drewes, Jörg E

    2016-01-01

    Little is known about the role of immigration in shaping bacterial communities or the factors that may dictate success or failure of colonization by bacteria from regional species pools. To address these knowledge gaps, the influence of bacterial colonization into an ecosystem (activated sludge bioreactor) was measured through a disturbance gradient (successive decreases in the parameter solids retention time) relative to stable operational conditions. Through a DNA sequencing approach, we show that the most abundant bacteria within the immigrant community have a greater probability of colonizing the receiving ecosystem, but mostly as low abundance community members. Only during the disturbance do some of these bacterial populations significantly increase in abundance beyond background levels and in few cases become dominant community members post-disturbance. Two mechanisms facilitate the enhanced enrichment of immigrant populations during disturbance: (i) the availability of resources left unconsumed by established species and (ii) the increased availability of niche space for colonizers to establish and displace resident populations. Thus, as a disturbance decreases local diversity, recruitment sites become available to promote colonization. This work advances our understanding of microbial resource management and diversity maintenance in complex ecosystems. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

  4. Study of changes in bacterial and viral abundance in formaldehyde - Fixed water samples by epifluorescence microscopy

    Digital Repository Service at National Institute of Oceanography (India)

    Parvathi, A.; Radhakrishnan, S.; Sajila, M.P.; Jacob, B.

    of bacteria and viruses in water samples from Cochin Backwater was determined by SYBR Green I staining and epifluorescence microscopy. The counts were determined for 45 days in samples fixed with 1–6% formaldehyde. The results suggest rapid decline in counts...

  5. Widespread abundance of functional bacterial amyloid in Mycolata and other Gram-positive bacteria

    DEFF Research Database (Denmark)

    Jordal, Peter Bruun; Dueholm, Morten Simonsen; Larsen, Poul

    2009-01-01

    extracellular fibrils were also produced. In three cases, FuBA was only revealed after extensive removal of extracellular material by saponification, indicating an integrated attachment within the cellular envelope. Spores from species within the genera Streptomyces, Bacillus and Nocardia were all coated...... analysis. We conclude that amyloid is widespread among Gram-positive bacteria and may in many species constitute a hitherto overlooked integral part of the spores and the cellular envelope....

  6. Molecular hydrogen: An abundant energy source for bacterial activity in nuclear waste repositories

    Science.gov (United States)

    Libert, M.; Bildstein, O.; Esnault, L.; Jullien, M.; Sellier, R.

    A thorough understanding of the energy sources used by microbial systems in the deep terrestrial subsurface is essential since the extreme conditions for life in deep biospheres may serve as a model for possible life in a nuclear waste repository. In this respect, H 2 is known as one of the most energetic substrates for deep terrestrial subsurface environments. This hydrogen is produced from abiotic and biotic processes but its concentration in natural systems is usually maintained at very low levels due to hydrogen-consuming bacteria. A significant amount of H 2 gas will be produced within deep nuclear waste repositories, essentially from the corrosion of metallic components. This will consequently improve the conditions for microbial activity in this specific environment. This paper discusses different study cases with experimental results to illustrate the fact that microorganisms are able to use hydrogen for redox processes (reduction of O 2, NO3-, Fe III) in several waste disposal conditions. Consequences of microbial activity include: alteration of groundwater chemistry and shift in geochemical equilibria, gas production or consumption, biocorrosion, and potential modifications of confinement properties. In order to quantify the impact of hydrogen bacteria, the next step will be to determine the kinetic rate of the reactions in realistic conditions.

  7. Molecular hydrogen: An abundant energy source for bacterial activity in nuclear waste repositories

    International Nuclear Information System (INIS)

    Libert, M.; Bildstein, O.; Esnault, L.; Jullien, M.; Sellier, R.

    2011-01-01

    A thorough understanding of the energy sources used by microbial systems in the deep terrestrial subsurface is essential since the extreme conditions for life in deep biospheres may serve as a model for possible life in a nuclear waste repository. In this respect, H 2 is known as one of the most energetic substrates for deep terrestrial subsurface environments. This hydrogen is produced from abiotic and biotic processes but its concentration in natural systems is usually maintained at very low levels due to hydrogen-consuming bacteria. A significant amount of H 2 gas will be produced within deep nuclear waste repositories, essentially from the corrosion of metallic components. This will consequently improve the conditions for microbial activity in this specific environment. This paper discusses different study cases with experimental results to illustrate the fact that microorganisms are able to use hydrogen for redox processes (reduction of O 2 , NO 3- , Fe III) in several waste disposal conditions. Consequences of microbial activity include: alteration of groundwater chemistry and shift in geochemical equilibria, gas production or consumption, bio-corrosion, and potential modifications of confinement properties. In order to quantify the impact of hydrogen bacteria, the next step will be to determine the kinetic rate of the reactions in realistic conditions. (authors)

  8. A Straightforward Approach for 3D Bacterial Printing.

    Science.gov (United States)

    Lehner, Benjamin A E; Schmieden, Dominik T; Meyer, Anne S

    2017-07-21

    Sustainable and personally tailored materials production is an emerging challenge to society. Living organisms can produce and pattern an extraordinarily wide range of different molecules in a sustainable way. These natural systems offer an abundant source of inspiration for the development of new environmentally friendly materials production techniques. In this paper, we describe the first steps toward the 3-dimensional printing of bacterial cultures for materials production and patterning. This methodology combines the capability of bacteria to form new materials with the reproducibility and tailored approach of 3D printing systems. For this purpose, a commercial 3D printer was modified for bacterial systems, and new alginate-based bioink chemistry was developed. Printing temperature, printhead speed, and bioink extrusion rate were all adapted and customized to maximize bacterial health and spatial resolution of printed structures. Our combination of 3D printing technology with biological systems enables a sustainable approach for the production of numerous new materials.

  9. In Situ Hydrocarbon Degradation by Indigenous Nearshore Bacterial Populations

    International Nuclear Information System (INIS)

    Cherrier, J.

    2005-01-01

    Potential episodic hydrocarbon inputs associated with oil mining and transportation together with chronic introduction of hydrocarbons via urban runoff into the relatively pristine coastal Florida waters poses a significant threat to Florida's fragile marine environment. It is therefore important to understand the extent to which indigenous bacterial populations are able to degrade hydrocarbon compounds and also determine factors that could potentially control and promote the rate at which these compounds are broken down in situ. Previous controlled laboratory experiments carried out by our research group demonstrated that separately both photo-oxidation and cometabolism stimulate bacterial hydrocarbon degradation by natural bacterial assemblages collected from a chronically petroleum contaminated site in Bayboro Bay, Florida. Additionally, we also demonstrated that stable carbon and radiocarbon abundances of respired CO 2 could be used to trace in situ hydrocarbon degradation by indigenous bacterial populations at this same site. This current proposal had two main objectives: (a) to evaluate the cumulative impact of cometabolism and photo-oxidation on hydrocarbon degradation by natural bacterial assemblages collected the same site in Bayboro Bay, Florida and (b) to determine if in situ hydrocarbon degradation by indigenous bacterial populations this site could be traced using natural radiocarbon and stable carbon abundances of assimilated bacterial carbon. Funds were used for 2 years of full support for one ESI Ph.D. student, April Croxton. To address our first objective a series of closed system bacterial incubations were carried out using photo-oxidized petroleum and pinfish (i.e. cometabolite). Bacterial production of CO 2 was used as the indicator of hydrocarbon degradation and (delta) 13 C analysis of the resultant CO 2 was used to evaluate the source of the respired CO 2 (i.e. petroleum hydrocarbons or the pinfish cometabolite). Results from these time

  10. Bacterial diversity is strongly associated with historical penguin activity in an Antarctic lake sediment profile.

    Science.gov (United States)

    Zhu, Renbin; Shi, Yu; Ma, Dawei; Wang, Can; Xu, Hua; Chu, Haiyan

    2015-11-25

    Current penguin activity in Antarctica affects the geochemistry of sediments and their microbial communities; the effects of historical penguin activity are less well understood. Here, bacterial diversity in ornithogenic sediment was investigated using high-throughput pyrosequencing. The relative abundances of dominant phyla were controlled by the amount of historical penguin guano deposition. Significant positive correlations were found between both the bacterial richness and diversity, and the relative penguin number (p penguin activity drove the vertical distribution of the bacterial communities. The lowest relative abundances of individual phyla corresponded to lowest number of penguin population at 1,800-2,300 yr BP during a drier and colder period; the opposite was observed during a moister and warmer climate (1,400-1,800 yr BP). This study shows that changes in the climate over millennia affected penguin populations and the outcomes of these changes affect the sediment bacterial community today.

  11. Risk Assessment and effect of Penicillin-G on bacterial diversity in drinking water

    Science.gov (United States)

    Wu, Qing; Zhao, Xiaofei; Peng, Sen; Wang, Lei; Zhao, Xinhua

    2018-02-01

    Penicillin-G was detected in drinking water by LC-MS/MS and the bacterial diversity was investigated by PCR and high-throughput sequencing. The results showed that bacteria community structure in drinking water has undergone major changes when added different concentrations of penicillin-G. The diversity index of each sample was calculated. The results showed that the total number and abundance of bacterial community species in drinking water samples decreased significantly after the addition of penicillin-G. However, the number and abundance of community structure did not change with the concentration. Penicillin-G inhibits the activity of bacterial community in drinking water and can reduce the bacterial diversity in drinking water.

  12. Bacterial and fungal communities and contribution of physicochemical factors during cattle farm waste composting.

    Science.gov (United States)

    Huhe; Jiang, Chao; Wu, Yanpei; Cheng, Yunxiang

    2017-12-01

    During composting, the composition of microbial communities is subject to constant change owing to interactions with fluctuating physicochemical parameters. This study explored the changes in bacterial and fungal communities during cattle farm waste composting and aimed to identify and prioritize the contributing physicochemical factors. Microbial community compositions were determined by high-throughput sequencing. While the predominant phyla in the bacterial and fungal communities were largely consistent during the composting, differences in relative abundances were observed. Bacterial and fungal community diversity and relative abundance varied significantly, and inversely, over time. Relationships between physicochemical factors and microbial community compositions were evaluated by redundancy analysis. The variation in bacterial community composition was significantly related to water-soluble organic carbon (WSOC), and pile temperature and moisture (p composts. © 2017 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

  13. Defence strategies and antibiotic resistance gene abundance in enterococci under stress by exposure to low doses of peracetic acid.

    Science.gov (United States)

    Turolla, Andrea; Sabatino, Raffaella; Fontaneto, Diego; Eckert, Ester M; Colinas, Noemi; Corno, Gianluca; Citterio, Barbara; Biavasco, Francesca; Antonelli, Manuela; Mauro, Alessandro; Mangiaterra, Gianmarco; Di Cesare, Andrea

    2017-10-01

    Peracetic acid (PAA) is an organic compound used efficiently as disinfectant in wastewater treatments. Yet, at low doses it may cause selection; thus, the effect of low doses of PAA on Enterococcus faecium as a proxy of human-related microbial waste was evaluated. Bacteria were treated with increasing doses of PAA (from 0 to 25 mg L -1 min) and incubated in regrowth experiments under non-growing, limiting conditions and under growing, favorable conditions. The changes in bacterial abundance, in bacterial phenotype (number and composition of small cell clusters), and in the abundance of an antibiotic resistance gene (ARG) was evaluated. The experiment demonstrated that the selected doses of PAA efficiently removed enterococci, and induced a long-lasting effect after PAA inactivation. The relative abundance of small clusters increased during the experiment when compared with that of the inoculum. Moreover, under growing favorable conditions the relative abundance of small clusters decreased and the number of cells per cluster increased with increasing PAA doses. A strong stability of the measured ARG was found, not showing any effect during the whole experiment. The results demonstrated the feasibility of low doses of PAA to inactivate bacteria. However, the stress induced by PAA disinfection promoted a bacterial adaptation, even if potentially without affecting the abundance of the ARG. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. Interstellar Abundances Toward X Per, Revisited

    Science.gov (United States)

    Valencic, Lynne A.; Smith, Randall K.

    2014-01-01

    The nearby X-ray binary X Per (HD 24534) provides a useful beacon with which to measure elemental abundances in the local ISM. We examine absorption features of 0, Mg, and Si along this line of sight using spectra from the Chandra Observatory's LETG/ ACIS-S and XMM-Newton's RGS instruments. In general, we find that the abundances and their ratios are similar to those of young F and G stars and the most recent solar values. We compare our results with abundances required by dust grain models.

  15. Abundance variations in solar active regions

    Science.gov (United States)

    Strong, K. T.; Lemen, J. R.; Linford, G. A.

    1991-01-01

    The diversity in the published values of coronal abundances is unsettling, especially as the range of results seems to be beyond the quoted uncertainties. Measurements of the relative abundance of iron and neon derived from soft X-ray spectra of active regions are presented. From a data base of over 200 spectra taken by the Solar Maximum Mission Flat Crystal Spectrometer, it is found that the relative abundance can vary by as much as a factor of about 7 and can change on timescales of less than 1 h.

  16. NEUTRON-CAPTURE ELEMENT ABUNDANCES IN MAGELLANIC CLOUD PLANETARY NEBULAE

    Energy Technology Data Exchange (ETDEWEB)

    Mashburn, A. L.; Sterling, N. C. [Department of Physics, University of West Georgia, 1601 Maple Street, Carrollton, GA 30118 (United States); Madonna, S. [Instituto de Astrofísica de Canarias, Departamento Astrofísica, Universidad de La Laguna, E-38206 La Laguna, Tenerife (Spain); Dinerstein, Harriet L. [Department of Astronomy, University of Texas, 2515 Speedway, C1400, Austin, TX 78712-1205 (United States); Roederer, I. U. [Department of Astronomy, University of Michigan, 1085 South University Avenue, Ann Arbor, MI 48109 (United States); Geballe, T. R., E-mail: awhite15@my.westga.edu, E-mail: nsterlin@westga.edu, E-mail: smadonna@iac.es, E-mail: harriet@astro.as.utexas.edu, E-mail: iur@umich.edu, E-mail: tgeballe@gemini.edu [Gemini Observatory, 670 N. A’ohoku Place, Hilo, HI 96720 (United States)

    2016-11-01

    We present near-infrared spectra of 10 planetary nebulae (PNe) in the Large and Small Magellanic Clouds (LMC and SMC), acquired with the FIRE and GNIRS spectrometers on the 6.5 m Baade and 8.1 m Gemini South Telescopes, respectively. We detect Se and/or Kr emission lines in eight of these objects, the first detections of n -capture elements in Magellanic Cloud PNe. Our abundance analysis shows large s -process enrichments of Kr (0.6–1.3 dex) in the six PNe in which it was detected, and Se is enriched by 0.5–0.9 dex in five objects. We also estimate upper limits to Rb and Cd abundances in these objects. Our abundance results for the LMC are consistent with the hypothesis that PNe with 2–3 M {sub ⊙} progenitors dominate the bright end of the PN luminosity function in young gas-rich galaxies. We find no significant correlations between s -process enrichments and other elemental abundances, central star temperature, or progenitor mass, though this is likely due to our small sample size. We determine S abundances from our spectra and find that [S/H] agrees with [Ar/H] to within 0.2 dex for most objects, but is lower than [O/H] by 0.2–0.4 dex in some PNe, possibly due to O enrichment via third dredge-up. Our results demonstrate that n -capture elements can be detected in PNe belonging to nearby galaxies with ground-based telescopes, allowing s -process enrichments to be studied in PN populations with well-determined distances.

  17. Biogeography and ecology of the rare and abundant microbial lineages in deep-sea hydrothermal vents.

    Science.gov (United States)

    Anderson, Rika E; Sogin, Mitchell L; Baross, John A

    2015-01-01

    Environmental gradients generate countless ecological niches in deep-sea hydrothermal vent systems, which foster diverse microbial communities. The majority of distinct microbial lineages in these communities occur in very low abundance. However, the ecological role and distribution of rare and abundant lineages, particularly in deep, hot subsurface environments, remain unclear. Here, we use 16S rRNA tag sequencing to describe biogeographic patterning and microbial community structure of both rare and abundant archaea and bacteria in hydrothermal vent systems. We show that while rare archaeal lineages and almost all bacterial lineages displayed geographically restricted community structuring patterns, the abundant lineages of archaeal communities displayed a much more cosmopolitan distribution. Finally, analysis of one high-volume, high-temperature fluid sample representative of the deep hot biosphere described a unique microbial community that differed from microbial populations in diffuse flow fluid or sulfide samples, yet the rare thermophilic archaeal groups showed similarities to those that occur in sulfides. These results suggest that while most archaeal and bacterial lineages in vents are rare and display a highly regional distribution, a small percentage of lineages, particularly within the archaeal domain, are successful at widespread dispersal and colonization. © FEMS 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  18. Emergent macrophytes modify the abundance and community composition of ammonia oxidizers in their rhizosphere sediments.

    Science.gov (United States)

    Zhao, Dayong; He, Xiaowei; Huang, Rui; Yan, Wenming; Yu, Zhongbo

    2017-07-01

    Ammonia oxidation is a crucial process in global nitrogen cycling, which is catalyzed by the ammonia oxidizers. Emergent plants play important roles in the freshwater ecosystem. Therefore, it is meaningful to investigate the effects of emergent macrophytes on the abundance and community composition of ammonia oxidizers. In the present study, two commonly found emergent macrophytes (Zizania caduciflora and Phragmitas communis) were obtained from freshwater lakes and the abundance and community composition of the ammonia-oxidizing prokaryotes in the rhizosphere sediments of these emergent macrophytes were investigated. The abundance of the bacterial amoA gene was higher in the rhizosphere sediments of the emergent macrophytes than those of bulk sediments. Significant positive correlation was found between the potential nitrification rates (PNRs) and the abundance of bacterial amoA gene, suggesting that ammonia-oxidizing bacteria (AOB) might play an important role in the nitrification process of the rhizosphere sediments of emergent macrophytes. The Nitrosotalea cluster is the dominant ammonia-oxidizing archaea (AOA) group in all the sediment samples. Analysis of AOB group showed that the N. europaeal cluster dominated the rhizosphere sediments of Z. caduciflora and the bulk sediments, whereas the Nitrosospira cluster was the dominant AOB group in the rhizosphere sediments of P. communis. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Evaluation of double formalin--Lugol's fixation in assessing number and biomass of ciliates: an example of estimations at mesoscale in NE Atlantic.

    Science.gov (United States)

    Karayanni, Hera; Christaki, Urania; Van Wambeke, France; Dalby, Andrew P

    2004-03-01

    Ciliated protozoa are potential grazers of primary and bacterial production and act as intermediaries between picoplankton and copepods and other large suspension feeders. Accurate determination of ciliate abundance and feeding mode is crucial in oceanic carbon budget estimations. However, the impact of different fixatives on the abundance and cell volume of ciliates has been investigated in only a few studies using either laboratory cultures or natural populations. Lugol's solution and formalin are the most commonly used fixatives for the preservation of ciliates samples. In the present study, the aim was to compare 0.4% Lugol's solution and 2% borated-formalin fixation and evaluate the need of counting duplicate samples each using a different fixative. For this, a large number of samples (n = 110) from the NE Atlantic was analyzed in the frame of POMME program (Multidisciplinary Mesoscale Ocean Program). We established a statistically significant relationship (p Tintinnus spp. did not show any difference between the two treatments. Abundance and biomass of mixotrophic ciliates (chloroplast-bearing cells) were for various reasons underestimated in both treatments. Our results show that unique fixation by formalin may severely underestimate ciliates abundance and biomass although their population may not alter. For this reason, Lugol's solution is best for the estimation of their abundance and biomass. However, for counts of mixotrophs and the evaluation of the ecological role of ciliates in carbon flux, double fixation is essential. Compromises regarding the fixatives have lead to severe underestimations of mixotrophs in studies conducted by now.

  20. The Effect of Long-Term Continuous Cropping of Black Pepper on Soil Bacterial Communities as Determined by 454 Pyrosequencing

    Science.gov (United States)

    Xiong, Wu; Li, Zhigang; Liu, Hongjun; Xue, Chao; Zhang, Ruifu; Wu, Huasong; Li, Rong; Shen, Qirong

    2015-01-01

    In the present study, 3 replanted black pepper orchards with continuously cropping histories for 10, 21, and 55 years in tropical China, were selected for investigating the effect of monoculture on soil physiochemical properties, enzyme activities, bacterial abundance, and bacterial community structures. Results showed long-term continuous cropping led to a significant decline in soil pH, organic matter contents, enzymatic activities, and resulted in a decrease in soil bacterial abundance. 454 pyrosequencing analysis of 16S rRNA genes revealed that the Acidobacteria and Proteobacteria were the main phyla in the replanted black pepper orchard soils, comprising up to 73.82% of the total sequences; the relative abundances of Bacteroidetes and Firmicutes phyla decreased with long-term continuous cropping; and at genus level, the Pseudomonas abundance significantly depleted after 21 years continuous cropping. In addition, bacterial diversity significantly decreased after 55 years black pepper continuous cropping; obvious variations for community structures across the 3 time-scale replanted black pepper orchards were observed, suggesting monoculture duration was the major determinant for bacterial community structure. Overall, continuous cropping during black pepper cultivation led to a significant decline in soil pH, organic matter contents, enzymatic activities, resulted a decrease in soil bacterial abundance, and altered soil microbial community membership and structure, which in turn resulted in black pepper poor growth in the continuous cropping system. PMID:26317364

  1. Shifts in microbial populations in Rusitec fermenters as affected by the type of diet and impact of the method for estimating microbial growth (15N v. microbial DNA).

    Science.gov (United States)

    Mateos, I; Ranilla, M J; Saro, C; Carro, M D

    2017-11-01

    Rusitec fermenters are in vitro systems widely used to study ruminal fermentation, but little is known about the microbial populations establishing in them. This study was designed to assess the time evolution of microbial populations in fermenters fed medium- (MC; 50% alfalfa hay : concentrate) and high-concentrate diets (HC; 15 : 85 barley straw : concentrate). Samples from solid (SOL) and liquid (LIQ) content of fermenters were taken immediately before feeding on days 3, 8 and 14 of incubation for quantitative polymerase chain reaction and automated ribosomal intergenic spacer analysis analyses. In SOL, total bacterial DNA concentration and relative abundance of Ruminococcus flavefaciens remained unchanged over the incubation period, but protozoal DNA concentration and abundance of Fibrobacter succinogenes, Ruminococcus albus and fungi decreased and abundance of methanogenic archaea increased. In LIQ, total bacterial DNA concentration increased with time, whereas concentration of protozoal DNA and abundance of methanogens and fungi decreased. Diet×time interactions were observed for bacterial and protozoal DNA and relative abundance of F. succinogenes and R. albus in SOL, as well as for protozoal DNA in LIQ. Bacterial diversity in SOL increased with time, but no changes were observed in LIQ.