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Sample records for fixing bacterial species

  1. Bacterial adhesion of porphyromonas gingivalis on provisional fixed prosthetic materials

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    Mustafa Zortuk

    2010-01-01

    Conclusion : The quantity of bacterial adhesion and surface roughness differed among the assessed provisional fixed prosthodontic materials. The light-polymerized provisional material Revotek LC had rougher surface and more bacterial adhesion compared with the others.

  2. Nitrogen fixing bacterial diversity in a tropical estuarine sediments.

    Science.gov (United States)

    Thajudeen, Jabir; Yousuf, Jesmi; Veetil, Vipindas Puthiya; Varghese, Sherin; Singh, Arvind; Abdulla, Mohamed Hatha

    2017-02-01

    Microorganisms play a significant role in biogeochemical cycles, especially in the benthic and pelagic ecosystems. Role of environmental parameters in regulating the diversity, distribution and physiology of these microorganisms in tropical marine environment is not well understood. In this study, we have identified dinitrogen (N2) fixing bacterial communities in the sediments by constructing clone libraries of nitrogenase (nifH) gene from four different stations in the Cochin estuary, along the southeastern Arabian Sea. N2 fixing bacterial clones revealed that over 20 putative diazotrophs belong to alpha-, beta-, gamma-, delta- and epsilon- proteobacteria and firmicutes. Predominant genera among these were Bradyrhizobium sp. (α-proteobacteria), Dechloromonas sp. (β-proteobacteria); Azotobactor sp., Teredinibacter sp., Methylobacter sp., Rheinheimera sp. and Marinobacterium sp. (γ-proteobacteria); Desulfobacter sp., Desulfobulbus sp. and Desulfovibrio sp. (δ -proteobacteria); Arcobacter sp. and Sulfurospirillum sp. (ε-proteobacteria). Nostoc sp. was solely identified among the cyanobacterial phylotype. Nitrogen fixing Sulfate reducing bacteria (SRBs) such as Desulfobulbus sp., Desulfovibrio sp., Desulfuromonas sp., Desulfosporosinus sp., Desulfobacter sp., were also observed in the study. Most of the bacterial nifH sequences revealed that the identities of N2 fixing bacteria were less than 95% similar to that available in the GenBank database, which suggested that the sequences were of novel N2 fixing microorganisms. Shannon-Weiner diversity index of nifH gene ranged from 2.95 to 3.61, indicating an inflated diversity of N2 fixing bacteria. Canonical correspondence analysis (CCA) implied positive correlation among nifH diversity, N2 fixation rate and other environmental variables.

  3. Competition and facilitation between the marine nitrogen-fixing cyanobacterium Cyanothece and its associated bacterial community.

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    Brauer, Verena S; Stomp, Maayke; Bouvier, Thierry; Fouilland, Eric; Leboulanger, Christophe; Confurius-Guns, Veronique; Weissing, Franz J; Stal, LucasJ; Huisman, Jef

    2014-01-01

    N2-fixing cyanobacteria represent a major source of new nitrogen and carbon for marine microbial communities, but little is known about their ecological interactions with associated microbiota. In this study we investigated the interactions between the unicellular N2-fixing cyanobacterium Cyanothece sp. Miami BG043511 and its associated free-living chemotrophic bacteria at different concentrations of nitrate and dissolved organic carbon and different temperatures. High temperature strongly stimulated the growth of Cyanothece, but had less effect on the growth and community composition of the chemotrophic bacteria. Conversely, nitrate and carbon addition did not significantly increase the abundance of Cyanothece, but strongly affected the abundance and species composition of the associated chemotrophic bacteria. In nitrate-free medium the associated bacterial community was co-dominated by the putative diazotroph Mesorhizobium and the putative aerobic anoxygenic phototroph Erythrobacter and after addition of organic carbon also by the Flavobacterium Muricauda. Addition of nitrate shifted the composition toward co-dominance by Erythrobacter and the Gammaproteobacterium Marinobacter. Our results indicate that Cyanothece modified the species composition of its associated bacteria through a combination of competition and facilitation. Furthermore, within the bacterial community, niche differentiation appeared to play an important role, contributing to the coexistence of a variety of different functional groups. An important implication of these findings is that changes in nitrogen and carbon availability due to, e.g., eutrophication and climate change are likely to have a major impact on the species composition of the bacterial community associated with N2-fixing cyanobacteria.

  4. Multiple bacterial species reside in chronic wounds

    DEFF Research Database (Denmark)

    Gjødsbøl, Kristine; Christensen, Jens Jørgen; Karlsmark, Tonny;

    2006-01-01

    species present were identified. More than one bacterial species were detected in all the ulcers. The most common bacteria found were Staphylococcus aureus (found in 93.5% of the ulcers), Enterococcus faecalis (71.7%), Pseudomonas aeruginosa (52.2%), coagulase-negative staphylococci (45.7%), Proteus...

  5. Competition and facilitation between the marine nitrogen-fixing cyanobacterium Cyanothece and its associated bacterial community

    Science.gov (United States)

    Brauer, Verena S.; Stomp, Maayke; Bouvier, Thierry; Fouilland, Eric; Leboulanger, Christophe; Confurius-Guns, Veronique; Weissing, Franz J.; Stal, LucasJ.; Huisman, Jef

    2014-01-01

    N2-fixing cyanobacteria represent a major source of new nitrogen and carbon for marine microbial communities, but little is known about their ecological interactions with associated microbiota. In this study we investigated the interactions between the unicellular N2-fixing cyanobacterium Cyanothece sp. Miami BG043511 and its associated free-living chemotrophic bacteria at different concentrations of nitrate and dissolved organic carbon and different temperatures. High temperature strongly stimulated the growth of Cyanothece, but had less effect on the growth and community composition of the chemotrophic bacteria. Conversely, nitrate and carbon addition did not significantly increase the abundance of Cyanothece, but strongly affected the abundance and species composition of the associated chemotrophic bacteria. In nitrate-free medium the associated bacterial community was co-dominated by the putative diazotroph Mesorhizobium and the putative aerobic anoxygenic phototroph Erythrobacter and after addition of organic carbon also by the Flavobacterium Muricauda. Addition of nitrate shifted the composition toward co-dominance by Erythrobacter and the Gammaproteobacterium Marinobacter. Our results indicate that Cyanothece modified the species composition of its associated bacteria through a combination of competition and facilitation. Furthermore, within the bacterial community, niche differentiation appeared to play an important role, contributing to the coexistence of a variety of different functional groups. An important implication of these findings is that changes in nitrogen and carbon availability due to, e.g., eutrophication and climate change are likely to have a major impact on the species composition of the bacterial community associated with N2-fixing cyanobacteria. PMID:25642224

  6. Effect of vegetation types on soil arbuscular mycorrhizal fungi and nitrogen-fixing bacterial communities in a karst region.

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    Liang, Yueming; Pan, Fujing; He, Xunyang; Chen, Xiangbi; Su, Yirong

    2016-09-01

    Arbuscular mycorrhizal (AM) fungi and nitrogen-fixing bacteria play important roles in plant growth and recovery in degraded ecosystems. The desertification in karst regions has become more severe in recent decades. Evaluation of the fungal and bacterial diversity of such regions during vegetation restoration is required for effective protection and restoration in these regions. Therefore, we analyzed relationships among AM fungi and nitrogen-fixing bacteria abundances, plant species diversity, and soil properties in four typical ecosystems of vegetation restoration (tussock (TK), shrub (SB), secondary forest (SF), and primary forest (PF)) in a karst region of southwest China. Abundance of AM fungi and nitrogen-fixing bacteria, plant species diversity, and soil nutrient levels increased from the tussock to the primary forest. The AM fungus, nitrogen-fixing bacterium, and plant community composition differed significantly between vegetation types (p fungi and nitrogen-fixing bacteria, respectively. Available phosphorus, total nitrogen, and soil organic carbon levels and plant richness were positively correlated with the abundance of AM fungi and nitrogen-fixing bacteria (p fungi and nitrogen-fixing bacteria increased from the tussock to the primary forest and highlight the essentiality of these communities for vegetation restoration.

  7. Final Report: The Rhizosphere Association of the Nitrogen Fixing Bacterial Species Azotobacter Paspali with the Tropical Grass Paspalum Notatum: Specificity of Colonization and Contribution to Plant Nutrition, July 1, 1995 - February 14, 1997

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    Kennedy, Christina K.

    1997-02-14

    The nitrogen fixing bacterium azotobacter paspali was first isolated from the roots of the sub-tropical grass, palpium notatum, and added to the clenus in 1996, by Dr. J. Dobereiner (Brazil). It is mentioned that this root association bacteria shows remarkable signs of host-plant specificity to one eco-type of this grass. This specificity is rare in non-symbiotic plant microbe interactions so far identified.

  8. Effects of three different PAHs on nitrogen-fixing bacterial diversity in mangrove sediment.

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    Sun, Fu-Lin; Wang, You-Shao; Sun, Cui-Ci; Peng, Ya-Lan; Deng, Chao

    2012-08-01

    Polycyclic aromatic hydrocarbons (PAHs) are of great environmental and human health concerns due to their widespread occurrence, persistence and carcinogenic properties. There is now compelling evidence that the mangrove sediment microbial structure is susceptible to PAHs contamination. The study aimed to assess the effects of PAHs on the nitrogen-fixing bacterial community of mangrove sediment. Three types of PAHs, naphthalene (NAP), a two-ring PAH; fluorene (FLU), a three-ring PAH; and pyrene (PYR), a four-ring PAH; were applied at three doses. After 7 and 24 days of incubation, the nitrogen-fixing bacterial population and diversity were evidenced in the nifH gene polymerase chain reaction denaturing gradient gel electrophoresis profile. DGGE pattern shows that the nitrogen-fixing bacterial community changed significantly with the types and doses of PAHs, and the incubation time. As far as single PAH is concerned, high concentration of PAH has larger impact on the nitrogen-fixing bacteria than low concentration of PAH. Besides, among the three types of PAHs, NAP has the greatest short term toxicity; PYR has the strongest long-term impact, whereas FLU has relatively higher long-time effect. Multidimensional scaling analysis and correspondence analysis are two reliable multivariate analysis methods for investigating the relationship between the nitrogen-fixing bacterial community and PAHs contamination. Investigating the effect of PAHs on the nitrogen-fixing bacterial diversity could yield useful information for understanding the process of biogeochemical cycling of nitrogen in mangrove sediment. The present study reveals that nitrogen-fixing bacterial community can be used as an important parameter indicating the impact of PAHs on mangrove sediment ecosystem.

  9. Rhizosphere-bacterial community in Eperua falcata (Caesalpiniaceae) a putative nitrogen-fixing tree from French Guiana rainforest.

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    Villadas, P J; Fernández-López, M; Ramírez-Saad, H; Toro, N

    2007-02-01

    The rainforest of French Guiana is still largely unaffected by human activity. Various pristine sites like the Paracou Research Station are devoted to study this tropical ecosystem. We used culture-independent techniques, like polymerase chain reaction-temperature gradient gel electrophoresis, and construction of clone libraries of partial 16S rRNA and nifH genes, to analyze the composition of the bacterial community in the rhizosphere of mature trees of Eperua falcata and Dicorynia guianensis, both species within the Caesalpiniaceae family. E. falcata is one of the more abundant pioneer tree species in this ecosystem and so far, no root nodules have ever been found. However, its nitrogen-fixing status is regarded as "uncertain", whereas D. guianensis is clearly considered a non-nitrogen-fixing plant. The rhizospheres of these mature trees contain specific bacterial communities, including several currently found uncultured microorganisms. In these communities, there are putative nitrogen-fixing bacteria specifically associated to each tree: D. guianensis harbors several Rhizobium spp. and E. falcata members of the genera Burkholderia and Bradyrhizobium. In addition, nifH sequences in the rhizosphere of the latter tree were very diverse. Retrieved sequences were related to bacteria belonging to the alpha-, beta-, and gamma-Proteobacteria in the E. falcata rhizoplane, whereas only two sequences related to gamma-Proteobacteria were found in D. guianensis. Differences in the bacterial communities and the abundance and diversity of nifH sequences in E. falcata rhizosphere suggest that this tree could obtain nitrogen through a nonnodulating bacterial interaction.

  10. Nitrogen fertilization has a stronger effect on soil nitrogen-fixing bacterial communities than elevated atmospheric CO2.

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    Berthrong, Sean T; Yeager, Chris M; Gallegos-Graves, Laverne; Steven, Blaire; Eichorst, Stephanie A; Jackson, Robert B; Kuske, Cheryl R

    2014-05-01

    Biological nitrogen fixation is the primary supply of N to most ecosystems, yet there is considerable uncertainty about how N-fixing bacteria will respond to global change factors such as increasing atmospheric CO2 and N deposition. Using the nifH gene as a molecular marker, we studied how the community structure of N-fixing soil bacteria from temperate pine, aspen, and sweet gum stands and a brackish tidal marsh responded to multiyear elevated CO2 conditions. We also examined how N availability, specifically, N fertilization, interacted with elevated CO2 to affect these communities in the temperate pine forest. Based on data from Sanger sequencing and quantitative PCR, the soil nifH composition in the three forest systems was dominated by species in the Geobacteraceae and, to a lesser extent, Alphaproteobacteria. The N-fixing-bacterial-community structure was subtly altered after 10 or more years of elevated atmospheric CO2, and the observed shifts differed in each biome. In the pine forest, N fertilization had a stronger effect on nifH community structure than elevated CO2 and suppressed the diversity and abundance of N-fixing bacteria under elevated atmospheric CO2 conditions. These results indicate that N-fixing bacteria have complex, interacting responses that will be important for understanding ecosystem productivity in a changing climate.

  11. Multiple bacterial species reside in chronic wounds

    DEFF Research Database (Denmark)

    Gjødsbøl, Kristine; Christensen, Jens Jørgen; Karlsmark, Tonny;

    2006-01-01

    The aim of the study was to investigate the bacterial profile of chronic venous leg ulcers and the importance of the profile to ulcer development. Patients with persisting venous leg ulcers were included and followed for 8 weeks. Every second week, ulcer samples were collected and the bacterial s...

  12. Symbiotic nitrogen-fixing bacterial populations trapped from soils under agroforestry systems in the Western Amazon

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    Paula Marcela Duque Jaramillo

    2013-12-01

    Full Text Available Cowpea (Vigna unguiculata is an important grain-producing legume that can forego nitrogen fertilization by establishing an efficient symbiosis with nitrogen-fixing bacteria. Although inoculating strains have already been selected for this species, little is known about the genotypic and symbiotic diversity of native rhizobia. Recently, Bradyrhizobium has been shown to be the genus most frequently trapped by cowpea in agricultural soils of the Amazon region. We investigated the genetic and symbiotic diversity of 148 bacterial strains with different phenotypic and cultural properties isolated from the nodules of the trap species cowpea, which was inoculated with samples from soils under agroforestry systems from the western Amazon. Sixty non-nodulating strains indicated a high frequency of endophytic strains in the nodules. The 88 authenticated strains had varying symbiotic efficiency. The SPAD (Soil Plant Analysis Development index (indirect measurement of chlorophyll content was more efficient at evaluating the contribution of symbiotic N2-fixation than shoot dry matter under axenic conditions. Cowpea-nodulating bacteria exhibited a high level of genetic diversity, with 68 genotypes identified by BOX-PCR. Sequencing of the 16S rRNA gene showed a predominance of the genus Bradyrhizobium, which accounted for 70 % of all strains sequenced. Other genera identified were Rhizobium, Ochrobactrum, Paenibacillus, Bosea, Bacillus, Enterobacter, and Stenotrophomonas. These results support the promiscuity of cowpea and demonstrate the high genetic and symbiotic diversity of rhizobia in soils under agroforestry systems, with some strains exhibiting potential for use as inoculants. The predominance of Bradyrhizobium in land uses with different plant communities and soil characteristics reflects the adaptation of this genus to the Amazon region.

  13. Temporal variation of the total nitrogen concentration in aereal organs of nitrogen fixing and non fixing riparian species

    OpenAIRE

    Llinares, F.

    1992-01-01

    Changes in nitrogen concentration was determinated in samples of Alnus glutinosa, Elaeagnus angustifolia, Populus x canadiensis and Ailanthus altissima leaves, petioles and branches periodically during a year. Maximum nitrogen percentage was found in diazotrophic species (Alnus and Elaeagnus) and the nitrogen retranslocation form branches was higher (2.5 times) in no fixing species. Se estudian 10s cambios en la concentración de nitrógeno en Alnus glutinosa, Elaeagnus angustifolia, Populus...

  14. Competition and facilitation between unicellular nitrogen-fixing cyanobacteria and non-nitrogen-fixing phytoplankton species

    NARCIS (Netherlands)

    Agawin, N.S.; Rabouille, S.; Veldhuis, M.; Servatius, L.; Hol, S.; van Overzee, H.M.J.; Huisman, J.

    2007-01-01

    Abstract: Recent discoveries show that small unicellular nitrogen-fixing cyanobacteria are more widespread than previously thought and can make major contributions to the nitrogen budget of the oceans. We combined theory and experiments to investigate competition for nitrogen and light between these

  15. Bacterial Diversity and Community Structure in Two Bornean Nepenthes Species with Differences in Nitrogen Acquisition Strategies.

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    Sickel, Wiebke; Grafe, T Ulmar; Meuche, Ivonne; Steffan-Dewenter, Ingolf; Keller, Alexander

    2016-05-01

    Carnivorous plants of the genus Nepenthes have been studied for over a century, but surprisingly little is known about associations with microorganisms. The two species Nepenthes rafflesiana and Nepenthes hemsleyana differ in their pitcher-mediated nutrient sources, sequestering nitrogen from arthropod prey and arthropods as well as bat faeces, respectively. We expected bacterial communities living in the pitchers to resemble this diet difference. Samples were taken from different parts of the pitchers (leaf, peristome, inside, outside, digestive fluid) of both species. Bacterial communities were determined using culture-independent high-throughput amplicon sequencing. Bacterial richness and community structure were similar in leaves, peristomes, inside and outside walls of both plant species. Regarding digestive fluids, bacterial richness was higher in N. hemsleyana than in N. rafflesiana. Additionally, digestive fluid communities were highly variable in structure, with strain-specific differences in community composition between replicates. Acidophilic taxa were mostly of low abundance, except the genus Acidocella, which strikingly reached extremely high levels in two N. rafflesiana fluids. In N. hemsleyana fluid, some taxa classified as vertebrate gut symbionts as well as saprophytes were enriched compared to N. rafflesiana, with saprophytes constituting potential competitors for nutrients. The high variation in community structure might be caused by a number of biotic and abiotic factors. Nitrogen-fixing bacteria were present in both study species, which might provide essential nutrients to the plant at times of low prey capture and/or rare encounters with bats.

  16. Bacterial acquisition in juveniles of several broadcast spawning coral species.

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    Koty H Sharp

    Full Text Available Coral animals harbor diverse microorganisms in their tissues, including archaea, bacteria, viruses, and zooxanthellae. The extent to which coral-bacterial associations are specific and the mechanisms for their maintenance across generations in the environment are unknown. The high diversity of bacteria in adult coral colonies has made it challenging to identify species-specific patterns. Localization of bacteria in gametes and larvae of corals presents an opportunity for determining when bacterial-coral associations are initiated and whether they are dynamic throughout early development. This study focuses on the early onset of bacterial associations in the mass spawning corals Montastraea annularis, M. franksi, M. faveolata, Acropora palmata, A. cervicornis, Diploria strigosa, and A. humilis. The presence of bacteria and timing of bacterial colonization was evaluated in gametes, swimming planulae, and newly settled polyps by fluorescence in situ hybridization (FISH using general eubacterial probes and laser-scanning confocal microscopy. The coral species investigated in this study do not appear to transmit bacteria via their gametes, and bacteria are not detectable in or on the corals until after settlement and metamorphosis. This study suggests that mass-spawning corals do not acquire, or are not colonized by, detectable numbers of bacteria until after larval settlement and development of the juvenile polyp. This timing lays the groundwork for developing and testing new hypotheses regarding general regulatory mechanisms that control bacterial colonization and infection of corals, and how interactions among bacteria and juvenile polyps influence the structure of bacterial assemblages in corals.

  17. Bacterial acquisition in juveniles of several broadcast spawning coral species.

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    Sharp, Koty H; Ritchie, Kim B; Schupp, Peter J; Ritson-Williams, Raphael; Paul, Valerie J

    2010-05-28

    Coral animals harbor diverse microorganisms in their tissues, including archaea, bacteria, viruses, and zooxanthellae. The extent to which coral-bacterial associations are specific and the mechanisms for their maintenance across generations in the environment are unknown. The high diversity of bacteria in adult coral colonies has made it challenging to identify species-specific patterns. Localization of bacteria in gametes and larvae of corals presents an opportunity for determining when bacterial-coral associations are initiated and whether they are dynamic throughout early development. This study focuses on the early onset of bacterial associations in the mass spawning corals Montastraea annularis, M. franksi, M. faveolata, Acropora palmata, A. cervicornis, Diploria strigosa, and A. humilis. The presence of bacteria and timing of bacterial colonization was evaluated in gametes, swimming planulae, and newly settled polyps by fluorescence in situ hybridization (FISH) using general eubacterial probes and laser-scanning confocal microscopy. The coral species investigated in this study do not appear to transmit bacteria via their gametes, and bacteria are not detectable in or on the corals until after settlement and metamorphosis. This study suggests that mass-spawning corals do not acquire, or are not colonized by, detectable numbers of bacteria until after larval settlement and development of the juvenile polyp. This timing lays the groundwork for developing and testing new hypotheses regarding general regulatory mechanisms that control bacterial colonization and infection of corals, and how interactions among bacteria and juvenile polyps influence the structure of bacterial assemblages in corals.

  18. Antibiogram of bacterial species isolated from canine pyometra

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    Madhu Swamy

    2013-06-01

    Full Text Available Aim: The aim of the present work was to ascertain the bacterial flora causing pyometra in female dogs and their antibiotic sensitivity. Materials and Methods: A study was conducted to determine the antibiogram of bacterial species isolated from 20 female dogs diagnosed with pyometra. The vaginal discharge was collected by sterile swab and streaked smoothly over Mueller Hinton medium and sensitivity towards antibiotics was determined by measuring the zone of inhibition using a Hi-media scale. Results: The antobiogram showed that Gentamicin was the most sensitive (85% antibiotic followed by Enrofloxacin, Ciprofloxacin and Amoxicillin (65%, 65% and 55%, respectively. The isolates were most resistant to Oxytetracycline (85% followed by Tetracycline, Ampicillin, Chloramphenicol, Cloxacillin and Erythromycin (80%, 80%, 75%, 70% and 70%, respectively. Conclusion: Gentamicin was found to be most effective antibiotic against the bacterial species isolated from canine pyometra. [Vet World 2013; 6(8.000: 546-549

  19. Prevalent bacterial species and novel phylotypes in advanced noma lesions.

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    Paster, B J; Falkler Jr, W A; Enwonwu, C O; Idigbe, E O; Savage, K O; Levanos, V A; Tamer, M A; Ericson, R L; Lau, C N; Dewhirst, F E

    2002-06-01

    The purpose of this study was to determine the bacterial diversity in advanced noma lesions using culture-independent molecular methods. 16S ribosomal DNA bacterial genes from DNA isolated from advanced noma lesions of four Nigerian children were PCR amplified with universally conserved primers and spirochetal selective primers and cloned into Escherichia coli. Partial 16S rRNA sequences of approximately 500 bases from 212 cloned inserts were used initially to determine species identity or closest relatives by comparison with sequences of known species or phylotypes. Nearly complete sequences of approximately 1,500 bases were obtained for most of the potentially novel species. A total of 67 bacterial species or phylotypes were detected, 25 of which have not yet been grown in vitro. Nineteen of the species or phylotypes, including Propionibacterium acnes, Staphylococcus spp., and the opportunistic pathogens Stenotrophomonas maltophilia and Ochrobactrum anthropi were detected in more than one subject. Other known species that were detected included Achromobacter spp., Afipia spp., Brevundimonas diminuta, Capnocytophaga spp., Cardiobacterium sp., Eikenella corrodens, Fusobacterium spp., Gemella haemoylsans, and Neisseria spp. Phylotypes that were unique to noma infections included those in the genera Eubacterium, Flavobacterium, Kocuria, Microbacterium, and Porphyromonas and the related Streptococcus salivarius and genera Sphingomonas and TREPONEMA: Since advanced noma lesions are infections open to the environment, it was not surprising to detect species not commonly associated with the oral cavity, e.g., from soil. Several species previously implicated as putative pathogens of noma, such as spirochetes and Fusobacterium spp., were detected in at least one subject. However, due to the limited number of available noma subjects, it was not possible at this time to associate specific species with the disease.

  20. Panamanian frog species host unique skin bacterial communities

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    Lisa K. Belden

    2015-10-01

    Full Text Available Vertebrates, including amphibians, host diverse symbiotic microbes that contribute to host disease resistance. Globally, and especially in montane tropical systems, many amphibian species are threatened by a chytrid fungus, Batrachochytrium dendrobatidis (Bd, that causes a lethal skin disease. Bd therefore may be a strong selective agent on the diversity and function of the microbial communities inhabiting amphibian skin. In Panamá, amphibian population declines and the spread of Bd have been tracked. In 2012, we completed a field survey in Panamá to examine frog skin microbiota in the context of Bd infection. We focused on three frog species and collected two skin swabs per frog from a total of 136 frogs across four sites that varied from west to east in the time since Bd arrival. One swab was used to assess bacterial community structure using 16S rRNA amplicon sequencing and to determine Bd infection status, and one was used to assess metabolite diversity, as the bacterial production of anti-fungal metabolites is an important disease resistance function. The skin microbiota of the three Panamanian frog species differed in OTU (operational taxonomic unit, ~bacterial species community composition and metabolite profiles, although the pattern was less strong for the metabolites. Comparisons between frog skin bacterial communities from Panamá and the US suggest broad similarities at the phylum level, but key differences at lower taxonomic levels. In our field survey in Panamá, across all four sites, only 35 individuals (~26% were Bd infected. There was no clustering of OTUs or metabolite profiles based on Bd infection status and no clear pattern of west-east changes in OTUs or metabolite profiles across the four sites. Overall, our field survey data suggest that different bacterial communities might be producing broadly similar sets of metabolites across frog hosts and sites. Community structure and function may not be as tightly coupled in

  1. Patterns of Gut Bacterial Colonization in Three Primate Species

    Science.gov (United States)

    McKenney, Erin A.; Rodrigo, Allen; Yoder, Anne D.

    2015-01-01

    Host fitness is impacted by trillions of bacteria in the gastrointestinal tract that facilitate development and are inextricably tied to life history. During development, microbial colonization primes the gut metabolism and physiology, thereby setting the stage for adult nutrition and health. However, the ecological rules governing microbial succession are poorly understood. In this study, we examined the relationship between host lineage, captive diet, and life stage and gut microbiota characteristics in three primate species (infraorder, Lemuriformes). Fecal samples were collected from captive lemur mothers and their infants, from birth to weaning. Microbial DNA was extracted and the v4 region of 16S rDNA was sequenced on the Illumina platform using protocols from the Earth Microbiome Project. Here, we show that colonization proceeds along different successional trajectories in developing infants from species with differing dietary regimes and ecological profiles: frugivorous (fruit-eating) Varecia variegata, generalist Lemur catta, and folivorous (leaf-eating) Propithecus coquereli. Our analyses reveal community membership and succession patterns consistent with previous studies of human infants, suggesting that lemurs may serve as a useful model of microbial ecology in the primate gut. Each lemur species exhibits distinct species-specific bacterial diversity signatures correlating to life stages and life history traits, implying that gut microbial community assembly primes developing infants at species-specific rates for their respective adult feeding strategies. PMID:25970595

  2. Patterns of gut bacterial colonization in three primate species.

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    Erin A McKenney

    Full Text Available Host fitness is impacted by trillions of bacteria in the gastrointestinal tract that facilitate development and are inextricably tied to life history. During development, microbial colonization primes the gut metabolism and physiology, thereby setting the stage for adult nutrition and health. However, the ecological rules governing microbial succession are poorly understood. In this study, we examined the relationship between host lineage, captive diet, and life stage and gut microbiota characteristics in three primate species (infraorder, Lemuriformes. Fecal samples were collected from captive lemur mothers and their infants, from birth to weaning. Microbial DNA was extracted and the v4 region of 16S rDNA was sequenced on the Illumina platform using protocols from the Earth Microbiome Project. Here, we show that colonization proceeds along different successional trajectories in developing infants from species with differing dietary regimes and ecological profiles: frugivorous (fruit-eating Varecia variegata, generalist Lemur catta, and folivorous (leaf-eating Propithecus coquereli. Our analyses reveal community membership and succession patterns consistent with previous studies of human infants, suggesting that lemurs may serve as a useful model of microbial ecology in the primate gut. Each lemur species exhibits distinct species-specific bacterial diversity signatures correlating to life stages and life history traits, implying that gut microbial community assembly primes developing infants at species-specific rates for their respective adult feeding strategies.

  3. Desulfovibrio bacterial species are increased in ulcerative colitis.

    LENUS (Irish Health Repository)

    Rowan, Fiachra

    2012-02-01

    BACKGROUND: Debate persists regarding the role of Desulfovibrio subspecies in ulcerative colitis. Combined microscopic and molecular techniques enable this issue to be investigated by allowing precise enumeration of specific bacterial species within the colonic mucous gel. The aim of this study was to combine laser capture microdissection and quantitative polymerase chain reaction to determine Desulfovibrio copy number in crypt-associated mucous gel in health and in acute and chronic ulcerative colitis. METHODS: Colonic mucosal biopsies were harvested from healthy controls (n = 19) and patients with acute (n = 10) or chronic (n = 10) ulcerative colitis. Crypt-associated mucous gel was obtained by laser capture microdissection throughout the colon. Pan-bacterial 16S rRNA and Desulfovibrio copy number\\/mm were obtained by polymerase chain reaction at each locus. Bacterial copy numbers were interrogated for correlation with location and disease activity. Data were evaluated using a combination of ordinary linear methods and linear mixed-effects models to cater for multiple interactions. RESULTS: Desulfovibrio positivity was significantly increased in acute and chronic ulcerative colitis at multiple levels within the colon, and after normalization with total bacterial signal, the relative Desulfovibrio load was increased in acute colitis compared with controls. Desulfovibrio counts did not significantly correlate with age, disease duration, or disease activity but interlevel correlations were found in adjacent colonic segments in the healthy control and chronic ulcerative colitis groups. CONCLUSION: The presence of Desulfovibrio subspecies is increased in ulcerative colitis and the data presented suggest that these bacteria represent an increased percentage of the colonic microbiome in acute ulcerative colitis.

  4. Bacterial-induced calcium oscillations are common to nitrogen-fixing associations of nodulating legumes and nonlegumes.

    Science.gov (United States)

    Granqvist, Emma; Sun, Jongho; Op den Camp, Rik; Pujic, Petar; Hill, Lionel; Normand, Philippe; Morris, Richard J; Downie, J Allan; Geurts, Rene; Oldroyd, Giles E D

    2015-08-01

    Plants that form root-nodule symbioses are within a monophyletic 'nitrogen-fixing' clade and associated signalling processes are shared with the arbuscular mycorrhizal symbiosis. Central to symbiotic signalling are nuclear-associated oscillations in calcium ions (Ca(2+) ), occurring in the root hairs of several legume species in response to the rhizobial Nod factor signal. In this study we expanded the species analysed for activation of Ca(2+) oscillations, including nonleguminous species within the nitrogen-fixing clade. We showed that Ca(2+) oscillations are a common feature of legumes in their association with rhizobia, while Cercis, a non-nodulating legume, does not show Ca(2+) oscillations in response to Nod factors from Sinorhizobium fredii NGR234. Parasponia andersonii, a nonlegume that can associate with rhizobia, showed Nod factor-induced calcium oscillations to S. fredii NGR234 Nod factors, but its non-nodulating sister species, Trema tomentosa, did not. Also within the nitrogen-fixing clade are actinorhizal species that associate with Frankia bacteria and we showed that Alnus glutinosa induces Ca(2+) oscillations in root hairs in response to exudates from Frankia alni, but not to S. fredii NGR234 Nod factors. We conclude that the ability to mount Ca(2+) oscillations in response to symbiotic bacteria is a common feature of nodulating species within the nitrogen-fixing clade.

  5. Bacterial communities of two ubiquitous Great Barrier Reef corals reveals both site- and species-specificity of common bacterial associates.

    Directory of Open Access Journals (Sweden)

    E Charlotte E Kvennefors

    Full Text Available BACKGROUND: Coral-associated bacteria are increasingly considered to be important in coral health, and altered bacterial community structures have been linked to both coral disease and bleaching. Despite this, assessments of bacterial communities on corals rarely apply sufficient replication to adequately describe the natural variability. Replicated data such as these are crucial in determining potential roles of bacteria on coral. METHODOLOGY/PRINCIPAL FINDINGS: Denaturing Gradient Gel Electrophoresis (DGGE of the V3 region of the 16S ribosomal DNA was used in a highly replicated approach to analyse bacterial communities on both healthy and diseased corals. Although site-specific variations in the bacterial communities of healthy corals were present, host species-specific bacterial associates within a distinct cluster of gamma-proteobacteria could be identified, which are potentially linked to coral health. Corals affected by "White Syndrome" (WS underwent pronounced changes in their bacterial communities in comparison to healthy colonies. However, the community structure and bacterial ribotypes identified in diseased corals did not support the previously suggested theory of a bacterial pathogen as the causative agent of the syndrome. CONCLUSIONS/SIGNIFICANCE: This is the first study to employ large numbers of replicated samples to assess the bacterial communities of healthy and diseased corals, and the first culture-independent assessment of bacterial communities on WS affected Acroporid corals on the GBR. Results indicate that a minimum of 6 replicate samples are required in order to draw inferences on species, spatial or health-related changes in community composition, as a set of clearly distinct bacterial community profiles exist in healthy corals. Coral bacterial communities may be both site and species specific. Furthermore, a cluster of gamma-proteobacterial ribotypes may represent a group of specific common coral and marine

  6. Extensive Identification of Bacterial Riboflavin Transporters and Their Distribution across Bacterial Species.

    Directory of Open Access Journals (Sweden)

    Ana Gutiérrez-Preciado

    Full Text Available Riboflavin, the precursor for the cofactors flavin mononucleotide (FMN and flavin adenine dinucleotide, is an essential metabolite in all organisms. While the functions for de novo riboflavin biosynthesis and riboflavin import may coexist in bacteria, the extent of this co-occurrence is undetermined. The RibM, RibN, RfuABCD and the energy-coupling factor-RibU bacterial riboflavin transporters have been experimentally characterized. In addition, ImpX, RfnT and RibXY are proposed as riboflavin transporters based on positional clustering with riboflavin biosynthetic pathway (RBP genes or conservation of the FMN riboswitch regulatory element. Here, we searched for the FMN riboswitch in bacterial genomes to identify genes encoding riboflavin transporters and assessed their distribution among bacteria. Two new putative riboflavin transporters were identified: RibZ in Clostridium and RibV in Mesoplasma florum. Trans-complementation of an Escherichia coli riboflavin auxotroph strain confirmed the riboflavin transport activity of RibZ from Clostridium difficile, RibXY from Chloroflexus aurantiacus, ImpX from Fusobacterium nucleatum and RfnT from Ochrobactrum anthropi. The analysis of the genomic distribution of all known bacterial riboflavin transporters revealed that most occur in species possessing the RBP and that some bacteria may even encode functional riboflavin transporters from two different families. Our results indicate that some species possess ancestral riboflavin transporters, while others possess transporters that appear to have evolved recently. Moreover, our data suggest that unidentified riboflavin transporters also exist. The present study doubles the number of experimentally characterized riboflavin transporters and suggests a specific, non-accessory role for these proteins in riboflavin-prototrophic bacteria.

  7. Validation of hierarchical cluster analysis for identification of bacterial species using 42 bacterial isolates

    Science.gov (United States)

    Ghebremedhin, Meron; Yesupriya, Shubha; Luka, Janos; Crane, Nicole J.

    2015-03-01

    Recent studies have demonstrated the potential advantages of the use of Raman spectroscopy in the biomedical field due to its rapidity and noninvasive nature. In this study, Raman spectroscopy is applied as a method for differentiating between bacteria isolates for Gram status and Genus species. We created models for identifying 28 bacterial isolates using spectra collected with a 785 nm laser excitation Raman spectroscopic system. In order to investigate the groupings of these samples, partial least squares discriminant analysis (PLSDA) and hierarchical cluster analysis (HCA) was implemented. In addition, cluster analyses of the isolates were performed using various data types consisting of, biochemical tests, gene sequence alignment, high resolution melt (HRM) analysis and antimicrobial susceptibility tests of minimum inhibitory concentration (MIC) and degree of antimicrobial resistance (SIR). In order to evaluate the ability of these models to correctly classify bacterial isolates using solely Raman spectroscopic data, a set of 14 validation samples were tested using the PLSDA models and consequently the HCA models. External cluster evaluation criteria of purity and Rand index were calculated at different taxonomic levels to compare the performance of clustering using Raman spectra as well as the other datasets. Results showed that Raman spectra performed comparably, and in some cases better than, the other data types with Rand index and purity values up to 0.933 and 0.947, respectively. This study clearly demonstrates that the discrimination of bacterial species using Raman spectroscopic data and hierarchical cluster analysis is possible and has the potential to be a powerful point-of-care tool in clinical settings.

  8. Periodic Colony Formation by Bacterial Species Bacillus subtilis

    Science.gov (United States)

    Wakita, Jun-ichi; Shimada, Hirotoshi; Itoh, Hiroto; Matsuyama, Tohey; Matsushita, Mitsugu

    2001-03-01

    We have investigated the periodic colony growth of bacterial species Bacillus subtilis. A colony grows cyclically with the interface repeating an advance (migration phase) and a rest (consolidation phase) alternately on a surface of semi-solid agar plate under appropriate environmental conditions, resulting in a concentric ring-like colony. It was found from macroscopic observations that the characteristic quantities for the periodic growth such as the migration time, the consolidation time and the terrace spacing do not depend so much on nutrient concentration Cn, but do on agar concentration Ca. The consolidation time was a weakly increasing function of Ca, while the migration time and the terrace spacing were, respectively, weakly and strongly decreasing function of Ca. Overall, the cycle (migration-plus-consolidation) time seems to be constant, and does not depend so much on both Cn and Ca. Microscopically, bacterial cells inside the growing front of a colony keep increasing their population during both migration and consolidation phases. It was also confirmed that their secreting surfactant called surfactin does not affect their periodic growth qualitatively, i.e., mutant cells which cannot secrete surfactin produce a concentric ring-like colony. All these results suggest that the diffusion of the nutrient and the surfactin are irrelevant to their periodic growth.

  9. Competition and facilitation between the marine nitrogen-fixing cyanobacterium Cyanothece and its associated bacterial community

    NARCIS (Netherlands)

    Brauer, Verena S; Stomp, Maayke; Bouvier, Thierry; Fouilland, Eric; Leboulanger, Christophe; Confurius-Guns, Veronique; Weissing, Franz J; Stal, Lucas J; Huisman, Jef

    2015-01-01

    N2-fixing cyanobacteria represent a major source of new nitrogen and carbon for marine microbial communities, but little is known about their ecological interactions with associated microbiota. In this study we investigated the interactions between the unicellular N2-fixing cyanobacterium Cyanothece

  10. Nitrogen-fixing aerobic bacteria have higher genomic GC content than non-fixing species within the same genus

    OpenAIRE

    McEwan, Catriona E.; Gatherer, Derek; McEwan, Neil R.

    1998-01-01

    The genomic GC contents of both nitrogen-fixing and non-fixing members of eight genera of bacteria are investigated. Analysis by t-tests showed that in the two aerobic genera investigated (Aquaspirillum and Vibrio) there is a significantly higher GC content in the nitrogen-fixing members of the genus than in those unable to Fix nitrogen, whilst in anaerobic genera there is either no GC bias, or in the case of two genera (Rhodospirillum and Clostridium) there is a significantly higher GC conte...

  11. 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.

    Accurate measurement of bacterial and viral abundance in coastal marine environments is important to understand the dynamics of microbial communities in these ecosystems. In this study, the effect of formaldehyde preservation on the abundance...

  12. Cupriavidus necator isolates are able to fix nitrogen in symbiosis with different legume species.

    Science.gov (United States)

    da Silva, Krisle; Florentino, Ligiane Aparecida; da Silva, Karina Barroso; de Brandt, Evie; Vandamme, Peter; de Souza Moreira, Fatima Maria

    2012-05-01

    The aim of the present study was to identify a collection of 35 Cupriavidus isolates at the species level and to examine their capacity to nodulate and fix N(2). These isolates were previously obtained from the root nodules of two promiscuous trap species, Phaseolus vulgaris and Leucaena leucocephala, inoculated with soil samples collected near Sesbania virgata plants growing in Minas Gerais (Brazil) pastures. Phenotypic and genotypic methods applied for this study were SDS-PAGE of whole-cell proteins, and 16S rRNA and gyrB gene sequencing. To confirm the ability to nodulate and fix N(2), the presence of the nodC and nifH genes was also determined, and an experiment was carried out with two representative isolates in order to authenticate them as legume nodule symbionts. All 35 isolates belonged to the betaproteobacterium Cupriavidus necator, they possessed the nodC and nifH genes, and two representative isolates were able to nodulate five different promiscuous legume species: Mimosa caesalpiniaefolia, L. leucocephala, Macroptilium atropurpureum, P. vulgaris and Vigna unguiculata. This is the first study to demonstrate that C. necator can nodulate legume species. Copyright © 2012 Elsevier GmbH. All rights reserved.

  13. Predicting genetic and ecological characteristics of bacterial species by comparing the trajectories of dN/dS and dI/dS in bacterial genomes.

    Science.gov (United States)

    Feng, Ye; Chiu, Cheng-Hsun

    2014-02-01

    Indel (insertion/deletion) causes gene disruption and is considered to be deleterious like non-synonymous mutation during the evolution of bacterial genomes. The trajectory of dN/dS (the ratio of non-synonymous to synonymous mutation) has been found to decrease exponentially over time, but the trajectory of dI/dS (the ratio of indel to synonymous mutation) has not been thoroughly explored yet. Here we compared the patterns of dN/dS and dI/dS for several bacterial species. The majority of them showed a much steeper dI/dS trajectory than the dN/dS trajectory, suggesting that indel was more deleterious than non-synonymous mutation and therefore was more difficult to fix in genomes. However, the naturally competent bacteria, or those with a much lower genetic barrier for DNA exchange, presented a reverse relationship between dI/dS and dN/dS, indicative of an exceptional ability to tolerate horizontal genetic transfer. The result suggests that plotting of dN/dS and dI/dS trajectories can help to predict the genetic and ecological characteristics of bacterial species.

  14. Bacterial Responses to Glyoxal and Methylglyoxal: Reactive Electrophilic Species

    Science.gov (United States)

    Lee, Changhan; Park, Chankyu

    2017-01-01

    Glyoxal (GO) and methylglyoxal (MG), belonging to α-oxoaldehydes, are produced by organisms from bacteria to humans by glucose oxidation, lipid peroxidation, and DNA oxidation. Since glyoxals contain two adjacent reactive carbonyl groups, they are referred to as reactive electrophilic species (RES), and are damaging to proteins and nucleotides. Therefore, glyoxals cause various diseases in humans, such as diabetes and neurodegenerative diseases, from which all living organisms need to be protected. Although the glyoxalase system has been known for some time, details on how glyoxals are sensed and detoxified in the cell have not been fully elucidated, and are only beginning to be uncovered. In this review, we will summarize the current knowledge on bacterial responses to glyoxal, and specifically focus on the glyoxal-associated regulators YqhC and NemR, as well as their detoxification mediated by glutathione (GSH)-dependent/independent glyoxalases and NAD(P)H-dependent reductases. Furthermore, we will address questions and future directions. PMID:28106725

  15. Broad spectrum microarray for fingerprint-based bacterial species identification

    Directory of Open Access Journals (Sweden)

    Frey Jürg E

    2010-02-01

    Full Text Available Abstract Background Microarrays are powerful tools for DNA-based molecular diagnostics and identification of pathogens. Most target a limited range of organisms and are based on only one or a very few genes for specific identification. Such microarrays are limited to organisms for which specific probes are available, and often have difficulty discriminating closely related taxa. We have developed an alternative broad-spectrum microarray that employs hybridisation fingerprints generated by high-density anonymous markers distributed over the entire genome for identification based on comparison to a reference database. Results A high-density microarray carrying 95,000 unique 13-mer probes was designed. Optimized methods were developed to deliver reproducible hybridisation patterns that enabled confident discrimination of bacteria at the species, subspecies, and strain levels. High correlation coefficients were achieved between replicates. A sub-selection of 12,071 probes, determined by ANOVA and class prediction analysis, enabled the discrimination of all samples in our panel. Mismatch probe hybridisation was observed but was found to have no effect on the discriminatory capacity of our system. Conclusions These results indicate the potential of our genome chip for reliable identification of a wide range of bacterial taxa at the subspecies level without laborious prior sequencing and probe design. With its high resolution capacity, our proof-of-principle chip demonstrates great potential as a tool for molecular diagnostics of broad taxonomic groups.

  16. Non-random species loss in bacterial communities reduces antifungal volatile production.

    Science.gov (United States)

    Hol, W H Gera; Garbeva, Paolina; Hordijk, Cornelis; Hundscheid, P J; Gunnewiek, Paulien J A Klein; Van Agtmaal, Maaike; Kuramae, Eiko E; De Boer, Wietse

    2015-08-01

    The contribution of low-abundance microbial species to soil ecosystems is easily overlooked because there is considerable overlap between metabolic abilities (functional redundancy) of dominant and subordinate microbial species. Here we studied how loss of less abundant soil bacteria affected the production of antifungal volatiles, an important factor in the natural control of soil-borne pathogenic fungi. We provide novel empirical evidence that the loss of soil bacterial species leads to a decline in the production of volatiles that suppress root pathogens. By using dilution-to-extinction for seven different soils we created bacterial communities with a decreasing number of species and grew them under carbon-limited conditions. Communities with high bacterial species richness produced volatiles that strongly reduced the hyphal growth of the pathogen Fusarium oxysporum. For most soil origins loss of bacterial species resulted in loss of antifungal volatile production. Analysis of the volatiles revealed that several known antifungal compounds were only produced in the more diverse bacterial communities. Our results suggest that less abundant bacterial species play an important role in antifungal volatile production by soil bacterial communities and, consequently, in the natural suppression of soil-borne pathogens.

  17. Climate change affects key nitrogen-fixing bacterial populations on coral reefs.

    Science.gov (United States)

    Santos, Henrique F; Carmo, Flávia L; Duarte, Gustavo; Dini-Andreote, Francisco; Castro, Clovis B; Rosado, Alexandre S; van Elsas, Jan Dirk; Peixoto, Raquel S

    2014-11-01

    Coral reefs are at serious risk due to events associated with global climate change. Elevated ocean temperatures have unpredictable consequences for the ocean's biogeochemical cycles. The nitrogen cycle is driven by complex microbial transformations, including nitrogen fixation. This study investigated the effects of increased seawater temperature on bacteria able to fix nitrogen (diazotrophs) that live in association with the mussid coral Mussismilia harttii. Consistent increases in diazotroph abundances and diversities were found at increased temperatures. Moreover, gradual shifts in the dominance of particular diazotroph populations occurred as temperature increased, indicating a potential future scenario of climate change. The temperature-sensitive diazotrophs may provide useful bioindicators of the effects of thermal stress on coral reef health, allowing the impact of thermal anomalies to be monitored. In addition, our findings support the development of research on different strategies to improve the fitness of corals during events of thermal stress, such as augmentation with specific diazotrophs.

  18. Diversity and localization of bacterial endosymbionts from whitefly species collected in Brazil.

    Directory of Open Access Journals (Sweden)

    Julio Massaharu Marubayashi

    Full Text Available Whiteflies (Hemiptera: Aleyrodidae are sap-sucking insect pests, and some cause serious damage in agricultural crops by direct feeding and by transmitting plant viruses. Whiteflies maintain close associations with bacterial endosymbionts that can significantly influence their biology. All whitefly species harbor a primary endosymbiont, and a diverse array of secondary endosymbionts. In this study, we surveyed 34 whitefly populations collected from the states of Sao Paulo, Bahia, Minas Gerais and Parana in Brazil, for species identification and for infection with secondary endosymbionts. Sequencing the mitochondrial Cytochrome Oxidase I gene revealed the existence of five whitefly species: The sweetpotato whitefly Bemisia tabaci B biotype (recently termed Middle East-Asia Minor 1 or MEAM1, the greenhouse whitefly Trialeurodes vaporariorum, B. tabaci A biotype (recently termed New World 2 or NW2 collected only from Euphorbia, the Acacia whitefly Tetraleurodes acaciae and Bemisia tuberculata both were detected only on cassava. Sequencing rRNA genes showed that Hamiltonella and Rickettsia were highly prevalent in all MEAM1 populations, while Cardinium was close to fixation in only three populations. Surprisingly, some MEAM1 individuals and one NW2 population were infected with Fritschea. Arsenopnohus was the only endosymbiont detected in T. vaporariorum. In T. acaciae and B. tuberculata populations collected from cassava, Wolbachia was fixed in B. tuberculata and was highly prevalent in T. acaciae. Interestingly, while B. tuberculata was additionally infected with Arsenophonus, T. acaciae was infected with Cardinium and Fritschea. Fluorescence in situ hybridization analysis on representative individuals showed that Hamiltonella, Arsenopnohus and Fritschea were localized inside the bacteriome, Cardinium and Wolbachia exhibited dual localization patterns inside and outside the bacteriome, and Rickettsia showed strict localization outside the

  19. Diversity and localization of bacterial endosymbionts from whitefly species collected in Brazil.

    Science.gov (United States)

    Marubayashi, Julio Massaharu; Kliot, Adi; Yuki, Valdir Atsushi; Rezende, Jorge Alberto Marques; Krause-Sakate, Renate; Pavan, Marcelo Agenor; Ghanim, Murad

    2014-01-01

    Whiteflies (Hemiptera: Aleyrodidae) are sap-sucking insect pests, and some cause serious damage in agricultural crops by direct feeding and by transmitting plant viruses. Whiteflies maintain close associations with bacterial endosymbionts that can significantly influence their biology. All whitefly species harbor a primary endosymbiont, and a diverse array of secondary endosymbionts. In this study, we surveyed 34 whitefly populations collected from the states of Sao Paulo, Bahia, Minas Gerais and Parana in Brazil, for species identification and for infection with secondary endosymbionts. Sequencing the mitochondrial Cytochrome Oxidase I gene revealed the existence of five whitefly species: The sweetpotato whitefly Bemisia tabaci B biotype (recently termed Middle East-Asia Minor 1 or MEAM1), the greenhouse whitefly Trialeurodes vaporariorum, B. tabaci A biotype (recently termed New World 2 or NW2) collected only from Euphorbia, the Acacia whitefly Tetraleurodes acaciae and Bemisia tuberculata both were detected only on cassava. Sequencing rRNA genes showed that Hamiltonella and Rickettsia were highly prevalent in all MEAM1 populations, while Cardinium was close to fixation in only three populations. Surprisingly, some MEAM1 individuals and one NW2 population were infected with Fritschea. Arsenopnohus was the only endosymbiont detected in T. vaporariorum. In T. acaciae and B. tuberculata populations collected from cassava, Wolbachia was fixed in B. tuberculata and was highly prevalent in T. acaciae. Interestingly, while B. tuberculata was additionally infected with Arsenophonus, T. acaciae was infected with Cardinium and Fritschea. Fluorescence in situ hybridization analysis on representative individuals showed that Hamiltonella, Arsenopnohus and Fritschea were localized inside the bacteriome, Cardinium and Wolbachia exhibited dual localization patterns inside and outside the bacteriome, and Rickettsia showed strict localization outside the bacteriome. This study is

  20. Crustose coralline algal species host distinct bacterial assemblages on their surfaces.

    Science.gov (United States)

    Sneed, Jennifer M; Ritson-Williams, Raphael; Paul, Valerie J

    2015-11-01

    Crustose coralline algae (CCA) are important components of many marine ecosystems. They aid in reef accretion and stabilization, create habitat for other organisms, contribute to carbon sequestration and are important settlement substrata for a number of marine invertebrates. Despite their ecological importance, little is known about the bacterial communities associated with CCA or whether differences in bacterial assemblages may have ecological implications. This study examined the bacterial communities on four different species of CCA collected in Belize using bacterial tag-encoded FLX amplicon pyrosequencing of the V1-V3 region of the 16S rDNA. CCA were dominated by Alphaproteobacteria, Gammaproteobacteria and Actinomycetes. At the operational taxonomic unit (OTU) level, each CCA species had a unique bacterial community that was significantly different from all other CCA species. Hydrolithon boergesenii and Titanoderma prototypum, CCA species that facilitate larval settlement in multiple corals, had higher abundances of OTUs related to bacteria that inhibit the growth and/or biofilm formation of coral pathogens. Fewer coral larvae settle on the surfaces of Paragoniolithon solubile and Porolithon pachydermum. These CCA species had higher abundances of OTUs related to known coral pathogens and cyanobacteria. Coral larvae may be able to use the observed differences in bacterial community composition on CCA species to assess the suitability of these substrata for settlement and selectively settle on CCA species that contain beneficial bacteria.

  1. The bacterial carbon-fixing organelle is formed by shell envelopment of preassembled cargo.

    Directory of Open Access Journals (Sweden)

    Anna H Chen

    Full Text Available BACKGROUND: Cyanobacteria play a significant role in the global carbon cycle. In Synechococcuselongatus, the carbon-fixing enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO is concentrated into polyhedral, proteinaceous compartments called carboxysomes. METHODOLOGY/PRINCIPAL FINDINGS: Using live cell fluorescence microscopy, we show that carboxysomes are first detected as small seeds of RuBisCO that colocalize with existing carboxysomes. These seeds contain little or no shell protein, but increase in RuBisCO content over several hours, during which time they are exposed to the solvent. The maturing seed is then enclosed by shell proteins, a rapid process that seals RuBisCO from the cytosol to establish a distinct, solvent-protected microenvironment that is oxidizing relative to the cytosol. These closure events can be spatially and temporally coincident with the appearance of a nascent daughter RuBisCO seed. CONCLUSIONS/SIGNIFICANCE: Carboxysomes assemble in a stepwise fashion, inside-to-outside, revealing that cargo is the principle organizer of this compartment's biogenesis. Our observations of the spatial relationship of seeds to previously formed carboxysomes lead us to propose a model for carboxysome replication via sequential fission, polymerization, and encapsulation of their internal cargo.

  2. “Lachnoclostridium touaregense,” a new bacterial species isolated from the human gut microbiota

    OpenAIRE

    M. Tidjani Alou; S. Khelaifia; B. La Scola; Cassir, N.

    2016-01-01

    We report the main characteristics of “Lachnoclostridium touaregense” strain Marseille-P2415T (= CSUR P2415 = DSM 102219), a new bacterial species isolated from the gut microbiota of a healthy young girl from Niger.

  3. ‘Lachnoclostridium massiliosenegalense’, a new bacterial species isolated from the human gut microbiota

    OpenAIRE

    M. Tidjani Alou; J.-C. Lagier; B. La Scola; Cassir, N.

    2016-01-01

    We report the main characteristics of ‘Lachnoclostridium massiliosenegalense’ strain mt23T (=CSUR P299 =DSM 102084), a new bacterial species isolated from the gut microbiota of a healthy young girl from Senegal.

  4. Effects of Host Plant Factors on the Bacterial Communities Associated with Two Whitefly Sibling Species.

    Science.gov (United States)

    Su, Ming-Ming; Guo, Lei; Tao, Yun-Li; Zhang, You-Jun; Wan, Fang-Hao; Chu, Dong

    2016-01-01

    Although discrepancy in the specific traits and ecological characteristics of Bemisia tabaci between species are partially attributed to the B. tabaci-associated bacteria, the factors that affect the diversity of B. tabaci-associated bacteria are not well-understood. We used the metagenomic approach to characterize the B. tabaci-associated bacterial community because the approach is an effective tool to identify the bacteria. To investigate the effects of the host plant and a virus, tomato yellow leaf curl virus (TYLCV), on the bacterial communities of B. tabaci sibling species B and Q, we analyzed the bacterial communities associated with whitefly B and Q collected from healthy cotton, healthy tomato, and TYLCV-infected tomato. The analysis used miseq-based sequencing of a variable region of the bacterial 16S rDNA gene. For the bacteria associated with B. tabaci, we found that the influence of the host plant species was greater than that of the whitefly cryptic species. With further analysis of host plants infected with the TYLCV, the virus had no significant effects on the B. tabaci-associated bacterial community. The effects of different plant hosts and TYLCV-infection on the diversity of B. tabaci-associated bacterial communities were successfully analyzed in this study. To explain why B. tabaci sibling species with different host ranges differ in performance, the analysis of the bacterial community may be essential to the explanation.

  5. Confocal Raman microscopy for identification of bacterial species in biofilms

    Science.gov (United States)

    Beier, Brooke D.; Quivey, Robert G.; Berger, Andrew J.

    2011-03-01

    Implemented through a confocal microscope, Raman spectroscopy has been used to distinguish between biofilm samples of two common oral bacteria species, Streptococcus sanguinis and mutans, which are associated with healthy and cariogenic plaque, respectively. Biofilms of these species are studied as a model of dental plaque. A prediction model has been calibrated and validated using pure biofilms. This model has been used to identify the species of transferred and dehydrated samples (much like a plaque scraping) as well as hydrated biofilms in situ. Preliminary results of confocal Raman mapping of species in an intact two-species biofilm will be shown.

  6. Identification of Bacterial Species in Kuwaiti Waters Through DNA Sequencing

    Science.gov (United States)

    Chen, K.

    2017-01-01

    With an objective of identifying the bacterial diversity associated with ecosystem of various Kuwaiti Seas, bacteria were cultured and isolated from 3 water samples. Due to the difficulties for cultured and isolated fecal coliforms on the selective agar plates, bacterial isolates from marine agar plates were selected for molecular identification. 16S rRNA genes were successfully amplified from the genome of the selected isolates using Universal Eubacterial 16S rRNA primers. The resulted amplification products were subjected to automated DNA sequencing. Partial 16S rDNA sequences obtained were compared directly with sequences in the NCBI database using BLAST as well as with the sequences available with Ribosomal Database Project (RDP).

  7. (15)N natural abundance of non-fixing woody species in the Brazilian dry forest (caatinga).

    Science.gov (United States)

    de Freitas, Ana Dolores Santiago; de Sa Barretto Sampaio, Everardo Valadares; Menezes, Romulo Simoes Cezar; Tiessen, Holm

    2010-06-01

    Foliar delta(15)N values are useful to calculate N(2) fixation and N losses from ecosystems. However, a definite pattern among vegetation types is not recognised and few data are available for semi-arid areas. We sampled four sites in the Brazilian caatinga, along a water availability gradient. Sites with lower annual rainfall (700 mm) but more uniform distribution (six months) had delta(15)N values of 9.4 and 10.1 per thousand, among the highest already reported, and significantly greater than those (6.5 and 6.3 per thousand) of sites with higher rainfall (800 mm) but less uniform distribution (three months). There were no significant differences at each site among species or between non-fixing legume and non-legume species, in spite of the higher N content of the first group. Therefore, they constitute ideal reference plants in estimations of legume N(2) fixation. The higher values could result from higher losses of (15)N depleted gases or lower losses of enriched (15)N material.

  8. Bacterial profiling of White Plague Disease in a comparative coral species framework.

    KAUST Repository

    Roder, Cornelia

    2014-01-01

    Coral reefs are threatened throughout the world. A major factor contributing to their decline is outbreaks and propagation of coral diseases. Due to the complexity of coral-associated microbe communities, little is understood in terms of disease agents, hosts and vectors. It is known that compromised health in corals is correlated with shifts in bacterial assemblages colonizing coral mucus and tissue. However, general disease patterns remain, to a large extent, ambiguous as comparative studies over species, regions, or diseases are scarce. Here, we compare bacterial assemblages of samples from healthy (HH) colonies and such displaying signs of White Plague Disease (WPD) of two different coral species (Pavona duerdeni and Porites lutea) from the same reef in Koh Tao, Thailand, using 16S rRNA gene microarrays. In line with other studies, we found an increase of bacterial diversity in diseased (DD) corals, and a higher abundance of taxa from the families that include known coral pathogens (Alteromonadaceae, Rhodobacteraceae, Vibrionaceae). In our comparative framework analysis, we found differences in microbial assemblages between coral species and coral health states. Notably, patterns of bacterial community structures from HH and DD corals were maintained over species boundaries. Moreover, microbes that differentiated the two coral species did not overlap with microbes that were indicative of HH and DD corals. This suggests that while corals harbor distinct species-specific microbial assemblages, disease-specific bacterial abundance patterns exist that are maintained over coral species boundaries.

  9. Interactions between Lactobacillus crispatus and Bacterial Vaginosis (BV)-Associated Bacterial Species in Initial Attachment and Biofilm Formation

    Science.gov (United States)

    Machado, António; Jefferson, Kimberly Kay; Cerca, Nuno

    2013-01-01

    Certain anaerobic bacterial species tend to predominate the vaginal flora during bacterial vaginosis (BV), with Gardnerella vaginalis being the most common. However, the exact role of G. vaginalis in BV has not yet been determined. The main goal of this study was to test the hypothesis that G. vaginalis is an early colonizer, paving the way for intermediate (e.g., Fusobacterium nucleatum) and late colonizers (e.g., Prevotella bivia). Theoretically, in order to function as an early colonizer, species would need to be able to adhere to vaginal epithelium, even in the presence of vaginal lactobacilli. Therefore, we quantified adherence of G. vaginalis and other BV-associated bacteria to an inert surface pre-coated with Lactobacillus crispatus using a new Peptide Nucleic Acid (PNA) Fluorescence In Situ Hybridization (FISH) methodology. We found that G. vaginalis had the greatest capacity to adhere in the presence of L. crispatus. Theoretically, an early colonizer would contribute to the adherence and/or growth of additional species, so we next quantified the effect of G. vaginalis biofilms on the adherence and growth of other BV-associated species by quantitative Polymerase Chain Reaction (qPCR) technique. Interestingly, G. vaginalis derived a growth benefit from the addition of a second species, regardless of the species. Conversely, G. vaginalis biofilms enhanced the growth of P. bivia, and to a minor extent of F. nucleatum. These results contribute to our understanding of BV biofilm formation and the progression of the disorder. PMID:23739678

  10. Antimicrobial effect of probiotics on bacterial species from dental plaque.

    Science.gov (United States)

    Zambori, Csilla; Morvay, Attila Alexandru; Sala, Claudia; Licker, Monica; Gurban, Camelia; Tanasie, Gabriela; Tirziu, Emil

    2016-03-31

    The antimicrobial role of probiotic Lactobacillus casei subspecies casei DG (L. casei DG) and of the mix culture of probiotic Lactobacillus acidophilus LA-5 and Bifidobacterium BB-12 was tested on species of Staphylococcus, Streptococcus, Pasteurella, and Neisseria genera from supragingival sites from dogs with dental disease of different breed, age, sex, weight, and diet. The research was conducted on these four genera because of their importance in zoonotic infections after dog bites. Species from Staphylococcus, Streptococcus, Pasteurella, and Neisseria genera were isolated and identified. To test the antimicrobial efficacy of L. casei DG and the mixed culture of probiotic L. acidophilus LA-5 and Bifidobacterium bifidum BB-12 on the pathogenic species, the agar overlay method was used. L. casei DG had a bactericidal effect on all analyzed species isolated from Staphylococcus, Streptococcus, Pasteurella, and Neisseria genera after 24 hours of incubation. The mixed probiotic culture made up of L. acidophilus LA-5 and Bifidobacterium BB-12 species had no bactericidal effect on the species of Staphylococcus and Streptococcus genera, which were resistant. However, it had a bacteriostatic effect on several species of Pasteurella and Neisseria genera. This work highlights the antimicrobial potential of probiotics in vitro, demonstrating that the probiotic L. casei DG has a bactericidal effect on all analyzed species isolated from dental plaque and that the mix culture of probiotic L. acidophilus LA-5 and Bifidobacterium BB-12 has only a bacteriostatic effect.

  11. Paenibacillus jilunlii sp. nov., a nitrogen-fixing species isolated from the rhizosphere of Begonia semperflorens.

    Science.gov (United States)

    Jin, Hao-Jie; Zhou, Yu-Guang; Liu, Hong-Can; Chen, San-Feng

    2011-06-01

    A nitrogen-fixing bacterium, designated strain Be17(T), was isolated from rhizosphere soil of Begonia semperflorens planted in Beijing Botanical Garden, PR China. Phylogenetic analyses based on a segment of the nifH gene sequence and a full-length 16S rRNA gene sequence revealed that strain Be17(T) was a member of the genus Paenibacillus. High levels of 16S rRNA gene sequence similarity were found between strain Be17(T) and Paenibacillus graminis RSA19(T) (97.9 %), Paenibacillus sonchi LMG 24727(T) (97.8 %), Paenibacillus riograndensis CECT 7330(T) (96.2 %) and Paenibacillus borealis DSM 13188(T) (96.1 %), respectively. Levels of 16S rRNA gene sequence similarity between strain Be17(T) and the type strains of other recognized members of the genus Paenibacillus were below 96.0 %. However, the DNA-DNA hybridization values between strain Be17(T) and P. graminis RSA19(T), P. sonchi LMG 24727(T) and P. riograndensis CECT 7330(T) were 47.9 %, 38.7 % and 37.5 %, respectively. The DNA G+C content of strain Be17(T) was 52.9 mol%. The major fatty acid component of strain Be17(T) was anteiso-branched C(15 : 0) (30.92 %). The major isoprenoid quinone was MK-7. The cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. On the basis of its phenotypic characteristics, 16S rRNA gene sequences, DNA G+C content, DNA-DNA relatedness, chemotaxonomic properties and nifH gene sequence, strain Be17(T) represents a nitrogen-fixing strain of a novel species of the genus Paenibacillus, for which the name Paenibacillus jilunlii sp. nov. is proposed. The type strain is Be17(T) ( = CGMCC 1.10239(T) = DSM 23019(T)).

  12. Association between Lactobacillus species and bacterial vaginosis-related bacteria, and bacterial vaginosis scores in pregnant Japanese women

    Directory of Open Access Journals (Sweden)

    Yamada Hideto

    2007-11-01

    Full Text Available Abstract Background Bacterial vaginosis (BV, the etiology of which is still uncertain, increases the risk of preterm birth. Recent PCR-based studies suggested that BV is associated with complex vaginal bacterial communities, including many newly recognized bacterial species in non-pregnant women. Methods To examine whether these bacteria are also involved in BV in pregnant Japanese women, vaginal fluid samples were taken from 132 women, classified as normal (n = 98, intermediate (n = 21, or BV (n = 13 using the Nugent gram stain criteria, and studied. DNA extracted from these samples was analyzed for bacterial sequences of any Lactobacillus, four Lactobacillus species, and four BV-related bacteria by PCR with primers for 16S ribosomal DNA including a universal Lactobacillus primer, Lactobacillus species-specific primers for L. crispatus, L. jensenii, L. gasseri, and L. iners, and BV-related bacterium-specific primers for BVAB2, Megasphaera, Leptotrichia, and Eggerthella-like bacterium. Results The prevalences of L. crispatus, L. jensenii, and L. gasseri were significantly higher, while those of BVAB2, Megasphaera, Leptotrichia, and Eggerthella-like bacterium were significantly lower in the normal group than in the BV group. Unlike other Lactobacillus species, the prevalence of L. iners did not differ between the three groups and women with L. iners were significantly more likely to have BVAB2, Megasphaera, Leptotrichia, and Eggerthella-like bacterium. Linear regression analysis revealed associations of BVAB2 and Megasphaera with Nugent score, and multivariate regression analyses suggested a close relationship between Eggerthella-like bacterium and BV. Conclusion The BV-related bacteria, including BVAB2, Megasphaera, Leptotrichia, and Eggerthella-like bacterium, are common in the vagina of pregnant Japanese women with BV. The presence of L. iners may be correlated with vaginal colonization by these BV-related bacteria.

  13. Seabird nutrient subsidies benefit non-nitrogen fixing trees and alter species composition in South American coastal dry forests.

    Directory of Open Access Journals (Sweden)

    Gilles Havik

    Full Text Available Marine-derived nutrients can increase primary productivity and change species composition of terrestrial plant communities in coastal and riverine ecosystems. We hypothesized that sea nutrient subsidies have a positive effect on nitrogen assimilation and seedling survival of non-nitrogen fixing species, increasing the relative abundance of non-nitrogen fixing species close to seashore. Moreover, we proposed that herbivores can alter the effects of nutrient supplementation by preferentially feeding on high nutrient plants. We studied the effects of nutrient fertilization by seabird guano on tree recruitment and how these effects can be modulated by herbivorous lizards in the coastal dry forests of northwestern Peru. We combined field studies, experiments and stable isotope analysis to study the response of the two most common tree species in these forests, the nitrogen-fixing Prosopis pallida and the non-nitrogen-fixing Capparis scabrida. We did not find differences in herbivore pressure along the sea-inland gradient. We found that the non-nitrogen fixing C. scabrida assimilates marine-derived nitrogen and is more abundant than P. pallida closer to guano-rich soil. We conclude that the input of marine-derived nitrogen through guano deposited by seabirds feeding in the Pacific Ocean affects the two dominant tree species of the coastal dry forests of northern Peru in contrasting ways. The non-nitrogen fixing species, C. scabrida may benefit from sea nutrient subsidies by incorporating guano-derived nitrogen into its foliar tissues, whereas P. pallida, capable of atmospheric fixation, does not.

  14. Bacterial Contaminants of Poultry Meat: Sources, Species, and Dynamics.

    Science.gov (United States)

    Rouger, Amélie; Tresse, Odile; Zagorec, Monique

    2017-08-25

    With the constant increase in poultry meat consumption worldwide and the large variety of poultry meat products and consumer demand, ensuring the microbial safety of poultry carcasses and cuts is essential. In the present review, we address the bacterial contamination of poultry meat from the slaughtering steps to the use-by-date of the products. The different contamination sources are identified. The contaminants occurring in poultry meat cuts and their behavior toward sanitizing treatments or various storage conditions are discussed. A list of the main pathogenic bacteria of concern for the consumer and those responsible for spoilage and waste of poultry meat is established.

  15. Bacterial endophyte communities of three agricultural important grass species differ in their response towards management regimes

    Science.gov (United States)

    Wemheuer, Franziska; Kaiser, Kristin; Karlovsky, Petr; Daniel, Rolf; Vidal, Stefan; Wemheuer, Bernd

    2017-01-01

    Endophytic bacteria are critical for plant growth and health. However, compositional and functional responses of bacterial endophyte communities towards agricultural practices are still poorly understood. Hence, we analyzed the influence of fertilizer application and mowing frequency on bacterial endophytes in three agriculturally important grass species. For this purpose, we examined bacterial endophytic communities in aerial plant parts of Dactylis glomerata L., Festuca rubra L., and Lolium perenne L. by pyrotag sequencing of bacterial 16S rRNA genes over two consecutive years. Although management regimes influenced endophyte communities, observed responses were grass species-specific. This might be attributed to several bacteria specifically associated with a single grass species. We further predicted functional profiles from obtained 16S rRNA data. These profiles revealed that predicted abundances of genes involved in plant growth promotion or nitrogen metabolism differed between grass species and between management regimes. Moreover, structural and functional community patterns showed no correlation to each other indicating that plant species-specific selection of endophytes is driven by functional rather than phylogenetic traits. The unique combination of 16S rRNA data and functional profiles provided a holistic picture of compositional and functional responses of bacterial endophytes in agricultural relevant grass species towards management practices. PMID:28102323

  16. Bacterial endophyte communities of three agricultural important grass species differ in their response towards management regimes

    Science.gov (United States)

    Wemheuer, Franziska; Kaiser, Kristin; Karlovsky, Petr; Daniel, Rolf; Vidal, Stefan; Wemheuer, Bernd

    2017-01-01

    Endophytic bacteria are critical for plant growth and health. However, compositional and functional responses of bacterial endophyte communities towards agricultural practices are still poorly understood. Hence, we analyzed the influence of fertilizer application and mowing frequency on bacterial endophytes in three agriculturally important grass species. For this purpose, we examined bacterial endophytic communities in aerial plant parts of Dactylis glomerata L., Festuca rubra L., and Lolium perenne L. by pyrotag sequencing of bacterial 16S rRNA genes over two consecutive years. Although management regimes influenced endophyte communities, observed responses were grass species-specific. This might be attributed to several bacteria specifically associated with a single grass species. We further predicted functional profiles from obtained 16S rRNA data. These profiles revealed that predicted abundances of genes involved in plant growth promotion or nitrogen metabolism differed between grass species and between management regimes. Moreover, structural and functional community patterns showed no correlation to each other indicating that plant species-specific selection of endophytes is driven by functional rather than phylogenetic traits. The unique combination of 16S rRNA data and functional profiles provided a holistic picture of compositional and functional responses of bacterial endophytes in agricultural relevant grass species towards management practices.

  17. Arthrobacter Species as a Prey Cell Reservoir for Nonobligate Bacterial Predators in Soil

    Science.gov (United States)

    1989-01-01

    species as a prey cell reservoir for nonobligate bacterial predators in soil. Can. J. Microbiol. 35 : 559--564, tine investigation at etc entreprise sur...8217 .Stieprom tice ~s species and Bad//uhs instead of’ A. glohifrbrmis. to provide 1 .0 mng/g soil did not nivoie from the soil did not interfecre because

  18. A new mathematical model of bacterial interactions in two-species oral biofilms.

    Science.gov (United States)

    Martin, Bénédicte; Tamanai-Shacoori, Zohreh; Bronsard, Julie; Ginguené, Franck; Meuric, Vincent; Mahé, Fabrice; Bonnaure-Mallet, Martine

    2017-01-01

    Periodontitis are bacterial inflammatory diseases, where the bacterial biofilms present on the tooth-supporting tissues switch from a healthy state towards a pathogenic state. Among bacterial species involved in the disease, Porphyromonas gingivalis has been shown to induce dysbiosis, and to induce virulence of otherwise healthy bacteria like Streptococcus gordonii. During biofilm development, primary colonizers such as S. gordonii first attach to the surface and allow the subsequent adhesion of periodontal pathogens such as P. gingivalis. Interactions between those two bacteria have been extensively studied during the adhesion step of the biofilm. The aim of the study was to understand interactions of both species during the growing phase of the biofilm, for which little knowledge is available, using a mathematical model. This two-species biofilm model was based on a substrate-dependent growth, implemented with damage parameters, and validated thanks to data obtained on experimental biofilms. Three different hypothesis of interactions were proposed and assayed using this model: independence, competition between both bacteria species, or induction of toxicity by one species for the other species. Adequacy between experimental and simulated biofilms were found with the last hypothetic mathematical model. This new mathematical model of two species bacteria biofilms, dependent on different substrates for growing, can be applied to any bacteria species, environmental conditions, or steps of biofilm development. It will be of great interest for exploring bacterial interactions in biofilm conditions.

  19. A new mathematical model of bacterial interactions in two-species oral biofilms

    Science.gov (United States)

    Martin, Bénédicte; Tamanai-Shacoori, Zohreh; Bronsard, Julie; Ginguené, Franck; Meuric, Vincent

    2017-01-01

    Periodontitis are bacterial inflammatory diseases, where the bacterial biofilms present on the tooth-supporting tissues switch from a healthy state towards a pathogenic state. Among bacterial species involved in the disease, Porphyromonas gingivalis has been shown to induce dysbiosis, and to induce virulence of otherwise healthy bacteria like Streptococcus gordonii. During biofilm development, primary colonizers such as S. gordonii first attach to the surface and allow the subsequent adhesion of periodontal pathogens such as P. gingivalis. Interactions between those two bacteria have been extensively studied during the adhesion step of the biofilm. The aim of the study was to understand interactions of both species during the growing phase of the biofilm, for which little knowledge is available, using a mathematical model. This two-species biofilm model was based on a substrate-dependent growth, implemented with damage parameters, and validated thanks to data obtained on experimental biofilms. Three different hypothesis of interactions were proposed and assayed using this model: independence, competition between both bacteria species, or induction of toxicity by one species for the other species. Adequacy between experimental and simulated biofilms were found with the last hypothetic mathematical model. This new mathematical model of two species bacteria biofilms, dependent on different substrates for growing, can be applied to any bacteria species, environmental conditions, or steps of biofilm development. It will be of great interest for exploring bacterial interactions in biofilm conditions. PMID:28253369

  20. Comparative molecular analysis of bacterial species associated with periodontal disease.

    Science.gov (United States)

    De Iuliis, V; Ursi, S; Di Tommaso, L M; Caruso, M; Marino, A; D Ercole, S; Caputi, S; Sinjari, B; Festa, F; Macri, M; Martinotti, S; Vitullo, G; Toniato, E

    2016-01-01

    Periodontal disease is an inflammatory disorder affecting the supporting teeth structures, including gingiva, periodontal ligament and alveolar bone, causing loss of connective tissue, reabsorption of alveolar bone and formation of periodontal pockets. The aim of this study is to find a correlation between bacterial growth and periodontal disease. Fifty-seven patients aged between 21 and 65 years, median age 46 years, were enrolled. According to gingival pocket depth, ranging from 3 to 7 mm, patients were divided into two groups: the first (30 patients, 53%) with deep pockets ³ 5 mm and the second (27 patients, 47%) less than 5 mm. The samples taken were processed for microbiological analysis by absolute quantitative real-time Taq-Man technique. Patients affected by periodontal disease were 32 (56%) and patients with gingival bleeding were 35 (61%). This data showed that the presence, the type and the bacterial load in gingival pockets were strongly correlated with gingival depth, periodontal disease and gingival bleeding. Quantitative microbiological analysis is a key point to improve patient compliance, allowing to choose the specific antibiotic treatment. avoiding antibiotic resistance and ensuring the successful outcome of therapy for periodontal disease.

  1. Identification of nif genes in N2-fixing bacterial strains isolated from rice fields along the Yangtze River Plain.

    Science.gov (United States)

    Xie, Guang Hui; Cui, Zongjun; Yu, Jun; Yan, Jing; Hai, Weili; Steinberger, Yosef

    2006-01-01

    The aim of this research was to identify nifH and nifHDKYE ' genes in twenty strains of N2-fixing heterotrophic bacteria isolated from rice fields in the Yangtze River Plain. Southern hybridization of the total DNA from each strain was performed with the Klebsiella pneumoniae nifHDKYE ' gene probe (6.2 kb Eco RI fragment from pSA30) and the Azospirillum brasilense nifH gene probe (0.6 kb Eco RI-Hin dIII fragment from pHU8). We found that Eco RI fragments of total DNA from Aeromonas hydrophila HY2, Bacillus azotoformans FD, Bacillus licheniformis NCH1, NCH5, WH4, Bacillus brevis NC2, Bacillus pumilus NC12, Bacillus cereus NCH2, Citrobacter freundii HY5, HY9, Derxia gummosa HZ5, Pseudomonas mendocina HZ1 and Pseudomonas pseudoalcaligenes WH3 were positively hybridized with both of the probes. Agrobacterium radiobacter HY17, Corynebacterium sp. HY12, YZ and Pseudomonas sp. HY11 had Eco RI fragments hybridized with the K. pneumoniae nifHDKYE ' gene probe. An Eco RI fragment of total DNA from Bacillus megaterium YY4 was positively hybridized to the A. brasilense nifH gene probe. No hybridization sign was found in the total DNA fragments from Alcaligenes cupidus YY6 and Corynebacterium sp. NC11 hybridized with either of the gene probes. The data provide the number and size of EcoRI fragments of the total DNA hybridized with the nif gene probes for these strains of rarely studied species, suggesting additional evidence for N2 fixing and nif gene diversity of N2-fixing bacteria in rice fields along the Yangtze River Plain.

  2. Antibacterial effects of some commmercial fixed and essential oils on causal agent of tomato bacterial cancer and wilt disease

    Directory of Open Access Journals (Sweden)

    Meral YILMAZ

    2014-06-01

    Full Text Available Tomato (S. Lycopersicum L. is the most widely cultivated vegetable grown in the World and is economically important in Turkey. Within seed-borne pathogens, bacteria are the most important ones and threating seed industry and its control is difficult.. One of these pathogens Clavibacter michiganensis subsp. michiganensis (Cmm causing tomato bacterial cancer and wilt causes yield loss upto 100 percent. Particularly it affects the plant in whole growing season from seedling stage to harvest. In this study, inhibitory activity of some commercial essential oils on Cmm has been investigated. Antibacterial effect of essential oils has been determineted using agar well diffusion method considering the inhibition zone as diameter (mm. 18 out of 34 essential oils showed 67 % and higher inhibitory effect on Cmm. None of commercial fixed oils and all of essential oils were showed antibacterial effect. Essential oils (S. officinalis L. and R. officinalis L., which is provided at different times from the same company were observed different antibacterial effects.Thyme oils of Origanum spp. are the most effective oils within all tested esential oils. Therefore they can be suggested as biopesticides and control of Cmm on seeds.

  3. Transcriptional responses of Treponema denticola to other oral bacterial species.

    Science.gov (United States)

    Sarkar, Juni; McHardy, Ian H; Simanian, Emil J; Shi, Wenyuan; Lux, Renate

    2014-01-01

    The classic organization by Socransky and coworkers categorized the oral bacteria of the subgingival plaque into different complexes. Treponema denticola, Porphyromonas gingivalis and Tannerella forsythia are grouped into the red complex that is highly correlated with periodontal disease. Socransky's work closely associates red with orange complex species such as Fusobacterium nucleatum and Prevotella intermedia but not with members of the other complexes. While the relationship between species contained by these complexes is in part supported by their ability to physically attach to each other, the physiological consequences of these interactions and associations are less clear. In this study, we employed T. denticola as a model organism to analyze contact-dependent responses to interactions with species belonging to the same complex (P. gingivalis and T. forsythia), the closely associated orange complex (using F. nucleatum and P. intermedia as representatives) and the unconnected yellow complex (using Streptococcus sanguinis and S. gordonii as representatives). RNA was extracted from T. denticola alone as well as after pairwise co-incubation for 5 hrs with representatives of the different complexes, and the respective gene expression profiles were determined using microarrays. Numerous genes related to motility, metabolism, transport, outer membrane and hypothetical proteins were differentially regulated in T. denticola in the presence of the tested partner species. Further analysis revealed a significant overlap in the affected genes and we identified a general response to the presence of other species, those specific to two of the three complexes as well as individual complexes. Most interestingly, many predicted major antigens (e.g. flagella, Msp, CTLP) were suppressed in responses that included red complex species indicating that the presence of the most closely associated species induces immune-evasive strategies. In summary, the data presented here provide

  4. Transcriptional responses of Treponema denticola to other oral bacterial species.

    Directory of Open Access Journals (Sweden)

    Juni Sarkar

    Full Text Available The classic organization by Socransky and coworkers categorized the oral bacteria of the subgingival plaque into different complexes. Treponema denticola, Porphyromonas gingivalis and Tannerella forsythia are grouped into the red complex that is highly correlated with periodontal disease. Socransky's work closely associates red with orange complex species such as Fusobacterium nucleatum and Prevotella intermedia but not with members of the other complexes. While the relationship between species contained by these complexes is in part supported by their ability to physically attach to each other, the physiological consequences of these interactions and associations are less clear. In this study, we employed T. denticola as a model organism to analyze contact-dependent responses to interactions with species belonging to the same complex (P. gingivalis and T. forsythia, the closely associated orange complex (using F. nucleatum and P. intermedia as representatives and the unconnected yellow complex (using Streptococcus sanguinis and S. gordonii as representatives. RNA was extracted from T. denticola alone as well as after pairwise co-incubation for 5 hrs with representatives of the different complexes, and the respective gene expression profiles were determined using microarrays. Numerous genes related to motility, metabolism, transport, outer membrane and hypothetical proteins were differentially regulated in T. denticola in the presence of the tested partner species. Further analysis revealed a significant overlap in the affected genes and we identified a general response to the presence of other species, those specific to two of the three complexes as well as individual complexes. Most interestingly, many predicted major antigens (e.g. flagella, Msp, CTLP were suppressed in responses that included red complex species indicating that the presence of the most closely associated species induces immune-evasive strategies. In summary, the data

  5. Genetic Diversity of Nitrogen-Fixing and Plant Growth Promoting Pseudomonas Species Isolated from Sugarcane Rhizosphere

    Directory of Open Access Journals (Sweden)

    Hai-Bi Li

    2017-07-01

    Full Text Available The study was designed to isolate and characterize Pseudomonas spp. from sugarcane rhizosphere, and to evaluate their plant- growth- promoting (PGP traits and nitrogenase activity. A biological nitrogen-fixing microbe has great potential to replace chemical fertilizers and be used as a targeted biofertilizer in a plant. A total of 100 isolates from sugarcane rhizosphere, belonging to different species, were isolated; from these, 30 isolates were selected on the basis of preliminary screening, for in vitro antagonistic activities against sugarcane pathogens and for various PGP traits, as well as nitrogenase activity. The production of IAA varied from 312.07 to 13.12 μg mL−1 in tryptophan supplemented medium, with higher production in AN15 and lower in CN20 strain. The estimation of ACC deaminase activity, strains CY4 and BA2 produced maximum and minimum activity of 77.0 and 15.13 μmoL mg−1 h−1. For nitrogenase activity among the studied strains, CoA6 fixed higher and AY1 fixed lower in amounts (108.30 and 6.16 μmoL C2H2 h−1 mL−1. All the strains were identified on the basis of 16S rRNA gene sequencing, and the phylogenetic diversity of the strains was analyzed. The results identified all strains as being similar to Pseudomonas spp. Polymerase chain reaction (PCR amplification of nifH and antibiotic genes was suggestive that the amplified strains had the capability to fix nitrogen and possessed biocontrol activities. Genotypic comparisons of the strains were determined by BOX, ERIC, and REP PCR profile analysis. Out of all the screened isolates, CY4 (Pseudomonas koreensis and CN11 (Pseudomonas entomophila showed the most prominent PGP traits, as well as nitrogenase activity. Therefore, only these two strains were selected for further studies; Biolog profiling; colonization through green fluorescent protein (GFP-tagged bacteria; and nifH gene expression using quantitative real-time polymerase chain reaction (qRT-PCR analysis. The

  6. Genetic Diversity of Nitrogen-Fixing and Plant Growth Promoting Pseudomonas Species Isolated from Sugarcane Rhizosphere.

    Science.gov (United States)

    Li, Hai-Bi; Singh, Rajesh K; Singh, Pratiksha; Song, Qi-Qi; Xing, Yong-Xiu; Yang, Li-Tao; Li, Yang-Rui

    2017-01-01

    The study was designed to isolate and characterize Pseudomonas spp. from sugarcane rhizosphere, and to evaluate their plant- growth- promoting (PGP) traits and nitrogenase activity. A biological nitrogen-fixing microbe has great potential to replace chemical fertilizers and be used as a targeted biofertilizer in a plant. A total of 100 isolates from sugarcane rhizosphere, belonging to different species, were isolated; from these, 30 isolates were selected on the basis of preliminary screening, for in vitro antagonistic activities against sugarcane pathogens and for various PGP traits, as well as nitrogenase activity. The production of IAA varied from 312.07 to 13.12 μg mL(-1) in tryptophan supplemented medium, with higher production in AN15 and lower in CN20 strain. The estimation of ACC deaminase activity, strains CY4 and BA2 produced maximum and minimum activity of 77.0 and 15.13 μmoL mg(-1) h(-1). For nitrogenase activity among the studied strains, CoA6 fixed higher and AY1 fixed lower in amounts (108.30 and 6.16 μmoL C2H2 h(-1) mL(-1)). All the strains were identified on the basis of 16S rRNA gene sequencing, and the phylogenetic diversity of the strains was analyzed. The results identified all strains as being similar to Pseudomonas spp. Polymerase chain reaction (PCR) amplification of nifH and antibiotic genes was suggestive that the amplified strains had the capability to fix nitrogen and possessed biocontrol activities. Genotypic comparisons of the strains were determined by BOX, ERIC, and REP PCR profile analysis. Out of all the screened isolates, CY4 (Pseudomonas koreensis) and CN11 (Pseudomonas entomophila) showed the most prominent PGP traits, as well as nitrogenase activity. Therefore, only these two strains were selected for further studies; Biolog profiling; colonization through green fluorescent protein (GFP)-tagged bacteria; and nifH gene expression using quantitative real-time polymerase chain reaction (qRT-PCR) analysis. The Biolog phenotypic

  7. Paenibacillus sonchi sp. nov., a nitrogen-fixing species isolated from the rhizosphere of Sonchus oleraceus.

    Science.gov (United States)

    Hong, Yuan-Yuan; Ma, Yu-Chao; Zhou, Yu-Guang; Gao, Fei; Liu, Hong-Can; Chen, San-Feng

    2009-11-01

    A nitrogen-fixing bacterium, designated strain X19-5(T), was isolated from rhizosphere soil of Sonchus oleraceus. Phylogenetic analysis based on a fragment of the nifH gene and the full-length 16S rRNA gene sequence revealed that strain X19-5(T) was a member of the genus Paenibacillus. Strain X19-5(T) showed the highest 16S rRNA gene sequence similarity (98.8 %) with Paenibacillus graminis RSA19(T) and below 97 % similarity with other recognized members of the genus. The level of DNA-DNA relatedness between strain X19-5(T) and P. graminis RSA19(T) was 45.7 %. The DNA G+C content of strain X19-5(T) was 46.8 mol%. The major fatty acids were anteiso-C(15 : 0), C(16 : 0) and iso-C(16 : 0). On the basis of its phenotypic characteristics and the level of DNA-DNA hybridization, strain X19-5(T) is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus sonchi sp. nov. is proposed. The type strain is X19-5(T) (=CCBAU 83901(T)=LMG 24727(T)).

  8. Fumaric acid: an overlooked form of fixed carbon in Arabidopsis and other plant species

    Energy Technology Data Exchange (ETDEWEB)

    Chia, D.W.; Yoder, T.J.; Reiter, W.D.; Gibson, S.I.

    2000-10-01

    Photoassimilates are used by plants for production of energy, as carbon skeletons and in transport of fixed carbon between different plant organs. Many studies have been devoted to characterizing the factors that. regulate photoassimilate concentrations in different plant species. Most studies examining photoassimilate concentrations in C{sub 3} plants have focused on analyzing starch and soluble sugars. However, work presented here demonstrates that a number of C{sub 3} plants, including the popular model organism Arabidopsis thaliana (L.) Heynh., and agriculturally important plants, such as soybean [Glycine ma (L.) Merr.], contain significant quantities of furnaric acid. In fact, furnaric acid can accumulate to levels of several mg per g fresh weight in A-abidopsis leaves, often exceeding starch and soluble sugar levels. Furnaric acid is a component of the tricarboxylic acid cycle and, like starch and soluble sugars, can be metabolized to yield energy and carbon skeletons for production of other compounds. Fumaric acid concentrations increase with plant age and light intensity in Arabidopsis leaves. Arabidopsis phloem exudates contain significant quantities of fumaric acid, raising the possibility that fumaric acid may function in carbon transport.

  9. Oral toxicity of bacterial toxins against thrips species

    NARCIS (Netherlands)

    Gerritsen, L.J.M.; Visser, J.H.; Jongsma, M.A.

    2004-01-01

    The oral toxicity of excretion products of several Photorhabdus and Xenorhabdus strains was tested on two thrips species: Frankliniella occidentalis and Thrips tabaci. Out of 46 Photorhabdus isolates and 6 Xenorhabdus isolates only 6 North American P. temperata isolates were toxic to the thrips spec

  10. Oral toxicity of bacterial toxins against thrips species

    NARCIS (Netherlands)

    Gerritsen, L.J.M.; Visser, J.H.; Jongsma, M.A.

    2004-01-01

    The oral toxicity of excretion products of several Photorhabdus and Xenorhabdus strains was tested on two thrips species: Frankliniella occidentalis and Thrips tabaci. Out of 46 Photorhabdus isolates and 6 Xenorhabdus isolates only 6 North American P. temperata isolates were toxic to the thrips

  11. Systematic determination of the mosaic structure of bacterial genomes: species backbone versus strain-specific loops

    Directory of Open Access Journals (Sweden)

    Gendrault-Jacquemard A

    2005-07-01

    Full Text Available Abstract Background Public databases now contain multitude of complete bacterial genomes, including several genomes of the same species. The available data offers new opportunities to address questions about bacterial genome evolution, a task that requires reliable fine comparison data of closely related genomes. Recent analyses have shown, using pairwise whole genome alignments, that it is possible to segment bacterial genomes into a common conserved backbone and strain-specific sequences called loops. Results Here, we generalize this approach and propose a strategy that allows systematic and non-biased genome segmentation based on multiple genome alignments. Segmentation analyses, as applied to 13 different bacterial species, confirmed the feasibility of our approach to discern the 'mosaic' organization of bacterial genomes. Segmentation results are available through a Web interface permitting functional analysis, extraction and visualization of the backbone/loops structure of documented genomes. To illustrate the potential of this approach, we performed a precise analysis of the mosaic organization of three E. coli strains and functional characterization of the loops. Conclusion The segmentation results including the backbone/loops structure of 13 bacterial species genomes are new and available for use by the scientific community at the URL: http://genome.jouy.inra.fr/mosaic.

  12. Seabird nutrient subsidies benefit non-nitrogen fixing trees and alter species composition in South American coastal dry forests

    NARCIS (Netherlands)

    Havik, G.; Catenazzi, A.; Holmgren, M.

    2014-01-01

    Marine-derived nutrients can increase primary productivity and change species composition of terrestrial plant communities in coastal and riverine ecosystems. We hypothesized that sea nutrient subsidies have a positive effect on nitrogen assimilation and seedling survival of non-nitrogen fixing spec

  13. Application of methods for identifying broiler chicken gut bacterial species linked with increased energy metabolism.

    Science.gov (United States)

    Torok, Valeria A; Ophel-Keller, Kathy; Loo, Maylene; Hughes, Robert J

    2008-02-01

    A high-throughput microbial profiling tool based on terminal restriction fragment length polymorphism was developed to monitor the poultry gut microbiota in response to dietary manipulations. Gut microbial communities from the duodena, jejuna, ilea, and ceca of 48 birds fed either a barley control diet or barley diet supplemented with exogenous enzymes for degrading nonstarch polysaccharide were characterized by using multivariate statistical methods. Analysis of samples showed that gut microbial communities varied significantly among gut sections, except between the duodenum and jejunum. Significant diet-associated differences in gut microbial communities were detected within the ileum and cecum only. The dissimilarity in bacterial community composition between diets was 73 and 66% within the ileum and cecum, respectively. Operational taxonomic units, representing bacterial species or taxonomically related groups, contributing to diet-associated differences were identified. Several bacterial species contributed to differences between diet-related gut microbial community composition, with no individual bacterial species contributing more than 1 to 5% of the total. Using canonical analysis of principal coordinates biplots, we correlated differences in gut microbial community composition within the ileum and cecum to improved performance, as measured by apparent metabolizable energy. This is the first report that directly links differences in the composition of the gut microbial community with improved performance, which implies that the presence of specific beneficial and/or absence of specific detrimental bacterial species may contribute to the improved performance in these birds.

  14. A highly precise and portable genome engineering method allows comparison of mutational effects across bacterial species.

    Science.gov (United States)

    Nyerges, Ákos; Csörgő, Bálint; Nagy, István; Bálint, Balázs; Bihari, Péter; Lázár, Viktória; Apjok, Gábor; Umenhoffer, Kinga; Bogos, Balázs; Pósfai, György; Pál, Csaba

    2016-03-01

    Currently available tools for multiplex bacterial genome engineering are optimized for a few laboratory model strains, demand extensive prior modification of the host strain, and lead to the accumulation of numerous off-target modifications. Building on prior development of multiplex automated genome engineering (MAGE), our work addresses these problems in a single framework. Using a dominant-negative mutant protein of the methyl-directed mismatch repair (MMR) system, we achieved a transient suppression of DNA repair in Escherichia coli, which is necessary for efficient oligonucleotide integration. By integrating all necessary components into a broad-host vector, we developed a new workflow we term pORTMAGE. It allows efficient modification of multiple loci, without any observable off-target mutagenesis and prior modification of the host genome. Because of the conserved nature of the bacterial MMR system, pORTMAGE simultaneously allows genome editing and mutant library generation in other biotechnologically and clinically relevant bacterial species. Finally, we applied pORTMAGE to study a set of antibiotic resistance-conferring mutations in Salmonella enterica and E. coli. Despite over 100 million y of divergence between the two species, mutational effects remained generally conserved. In sum, a single transformation of a pORTMAGE plasmid allows bacterial species of interest to become an efficient host for genome engineering. These advances pave the way toward biotechnological and therapeutic applications. Finally, pORTMAGE allows systematic comparison of mutational effects and epistasis across a wide range of bacterial species.

  15. Effect of species, breed, and age on bacterial load in bovine and bubaline semen

    Directory of Open Access Journals (Sweden)

    Chandrahas Sannat

    2015-04-01

    Full Text Available Aim: The present study was conducted to investigate the effect of species, breed and age on bacterial load in fresh and frozen semen of Cattle and Buffalo bull. Materials and Methods: Present study covered 56 cow and 10 buffalo bulls stationed at Central Semen Station Anjora, Durg (Chhattisgarh. Impact of breeds on bacterial load in semen was assessed using six breeds of cattle viz. Sahiwal, Gir, Red Sindhi, Tharparkar, Jersey and Holstein Friesian (HF cross. Cow bulls were categorized into four different groups based on their age ( 6 years to study variation among age groups. Bacterial load was measured in fresh and frozen semen samples from these bulls using the standard plate count (SPC method and count was expressed as colony forming unit (CFU per ml of semen. Results: Higher bacterial load was reported in fresh (2.36 × 104 ± 1943 CFU/ml and frozen (1.00 × 10 ± 90 CFU/ml semen of cow bulls as compared to buffalo bulls (1.95 × 104 ± 2882 and 7.75 × 102 ± 160 CFU/ml in fresh and frozen semen, respectively. Jersey bull showed significantly higher bacterial count (p < 0.05 both in fresh (4.07 × 104 ± 13927 CFU/ ml and frozen (1.92 × 103 ± 178 CFU/ml semen followed by HF cross, Sahiwal, Gir, Red Sindhi and Tharparkar bull. Bulls aged < 4 years and more than 6 years yielded increased bacterial load in their semen. Although a minor variation was reported between species and among age groups, no significant differences were measured. Conclusion: Bacterial load in semen did not differ significantly between species and age groups; however significant variation was reported among different breeds. Bulls of Jersey breed showed significantly higher bacterial load in semen as compared to the crossbred and indigenous bull.

  16. Protist predation can favour cooperation within bacterial species

    Science.gov (United States)

    Friman, Ville-Petri; Diggle, Stephen P.; Buckling, Angus

    2013-01-01

    Here, we studied how protist predation affects cooperation in the opportunistic pathogen bacterium Pseudomonas aeruginosa, which uses quorum sensing (QS) cell-to-cell signalling to regulate the production of public goods. By competing wild-type bacteria with QS mutants (cheats), we show that a functioning QS system confers an elevated resistance to predation. Surprisingly, cheats were unable to exploit this resistance in the presence of cooperators, which suggests that resistance does not appear to result from activation of QS-regulated public goods. Instead, elevated resistance of wild-type bacteria was related to the ability to form more predation-resistant biofilms. This could be explained by the expression of QS-regulated resistance traits in densely populated biofilms and floating cell aggregations, or alternatively, by a pleiotropic cost of cheating where less resistant cheats are selectively removed from biofilms. These results show that trophic interactions among species can maintain cooperation within species, and have further implications for P. aeruginosa virulence in environmental reservoirs by potentially enriching the cooperative and highly infective strains with functional QS system. PMID:23945212

  17. Gut bacterial community structure of two Australian tropical fruit fly species (Diptera: Tephritidae

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    Narit Thaochan

    2015-12-01

    Full Text Available The community structure of the alimentary tract bacteria of two Australian fruit fly species, Bactrocera cacuminata (Hering and Bactrocera tryoni (Froggatt, was studied using a molecular cloning method based on the 16S rRNA gene. Differences in the bacterial community structure were shown between the crops and midguts of the two species and sexes of each species. Proteobacteria was the dominant bacterial phylum in the flies, especially bacteria in the order Gammaproteobacteria which was prominent in all clones. The total bacterial community consisted of Proteobacteria (more than 75% of clones, except in the crop of B. cacuminata where more than 50% of clones belonged to Firmicutes. Firmicutes gave the number of the secondary community structure in the fly’s gut. Four orders, Alpha-, Beta-, Delta- and Gammaproteobacteria and the phyla Firmicutes and Actinobacteria were found in both fruit fly species, while the order Epsilonproteobacteria and the phylum Bacteroidetes were found only in B. tryoni. Two phyla, Actinobacteria and Bacteroidetes, were rare and less frequent in the flies. There was a greater diversity of bacteria in the crop of the two fruit fly species than in the midgut. The midgut of B. tryoni females and the midgut of B. cacuminata males had the lowest bacterial diversity.

  18. Identification of different bacterial species in biofilms using confocal Raman microscopy

    Science.gov (United States)

    Beier, Brooke D.; Quivey, Robert G.; Berger, Andrew J.

    2010-11-01

    Confocal Raman microspectroscopy is used to discriminate between different species of bacteria grown in biofilms. Tests are performed using two bacterial species, Streptococcus sanguinis and Streptococcus mutans, which are major components of oral plaque and of particular interest due to their association with healthy and cariogenic plaque, respectively. Dehydrated biofilms of these species are studied as a simplified model of dental plaque. A prediction model based on principal component analysis and logistic regression is calibrated using pure biofilms of each species and validated on pure biofilms grown months later, achieving 96% accuracy in prospective classification. When biofilms of the two species are partially mixed together, Raman-based identifications are achieved within ~2 μm of the boundaries between species with 97% accuracy. This combination of spatial resolution and predication accuracy should be suitable for forming images of species distributions within intact two-species biofilms.

  19. Bacterial persistence induced by salicylate via reactive oxygen species

    Science.gov (United States)

    Wang, Tiebin; El Meouche, Imane; Dunlop, Mary J.

    2017-01-01

    Persisters are phenotypic variants of regular cells that exist in a dormant state with low metabolic activity, allowing them to exhibit high tolerance to antibiotics. Despite increasing recognition of their role in chronic and recalcitrant infections, the mechanisms that induce persister formation are not fully understood. In this study, we find that salicylate can induce persister formation in Escherichia coli via generation of reactive oxygen species (ROS). Salicylate-induced ROS cause a decrease in the membrane potential, reduce metabolism and lead to an increase in persistence. These effects can be recovered by culturing cells in the presence of a ROS quencher or in an anaerobic environment. Our findings reveal that salicylate-induced oxidative stress can lead to persistence, suggesting that ROS, and their subsequent impact on membrane potential and metabolism, may play a broad role in persister formation. PMID:28281556

  20. Anti-bacterial effect of Mentha spicata L. essential oil on eight standard species of gastrointestinal pathogens

    National Research Council Canada - National Science Library

    Majid Zare Bidaki; Mina Arab; Mohtarame Khazaei; Ehsan Afkar

    2014-01-01

    .... We aimed to study antibacterial effects of Mentha spicata L essential oil on 8 standard bacterial species including Escherichia coli, Bacillus cereus, Klebsiella pneumoniae, Pseudomonas aeruginosa...

  1. Bacterial community in sclerotia of Cenococcum species and soil in sub-alpine forest, central Japan

    Science.gov (United States)

    Nonoyama, Y.; Narisawa, K.; Ohta, H.; Watanabe, M.

    2009-04-01

    Species of Cenococcum, ectomycorrhizal fungi, may be particularly abundant in cold- or nutrient-stressed habitats. The fungus is easily recognized by its jet-black hyphae, and distinct compact masses of fungal mycelium called sclerotia. They are hard, black, comparatively smooth and mostly spherical. Sclerotia are formed in rhizosphere and can provide sufficient inoculums for several years. The purpose of this study is to investigate bacterial community inside sclerotia, with an interest on contribution of sclerotia to microbial diversity in rhizosphere. To investigate bacterial community inside of the fungal sclerotia by 16S rDNA gene clone library, several hundred of sclerotia (ca. 1g) were collected from sub-alpine forest soil in central Japan. Furthermore, three sclerotium grains were applied to investigate internal bacteria community by culture method. The isolated bacterial strains were then proceeded to determine their 16S rDNA partial sequences. The predominant group determined by clone library analysis of 16S ribosomal RNA genes with DNA from the sclerotia was Acidobacteria in both sclerotia and soil. Bacterial community of sclerotia showed higher diversity compared to soil. On the contrary, bacterial flora isolated from single sclerotium differed each other. Additionally, the bacterial community was composed by limited species of related genus.

  2. Differing prevalence and diversity of bacterial species in fetal membranes from very preterm and term labor.

    Directory of Open Access Journals (Sweden)

    Hannah E Jones

    Full Text Available BACKGROUND: Intrauterine infection may play a role in preterm delivery due to spontaneous preterm labor (PTL and preterm prolonged rupture of membranes (PPROM. Because bacteria previously associated with preterm delivery are often difficult to culture, a molecular biology approach was used to identify bacterial DNA in placenta and fetal membranes. METHODOLOGY/PRINCIPAL FINDINGS: We used broad-range 16S rDNA PCR and species-specific, real-time assays to amplify bacterial DNA from fetal membranes and placenta. 74 women were recruited to the following groups: PPROM <32 weeks (n = 26; 11 caesarean; PTL with intact membranes <32 weeks (n = 19; all vaginal birth; indicated preterm delivery <32 weeks (n = 8; all caesarean; term (n = 21; 11 caesarean. 50% (5/10 of term vaginal deliveries were positive for bacterial DNA. However, little spread was observed through tissues and species diversity was restricted. Minimal bacteria were detected in term elective section or indicated preterm deliveries. Bacterial prevalence was significantly increased in samples from PTL with intact membranes [89% (17/19 versus 50% (5/10 in term vaginal delivery p = 0.03] and PPROM (CS [55% (6/11 versus 0% (0/11 in term elective CS, p = 0.01]. In addition, bacterial spread and diversity was greater in the preterm groups with 68% (13/19 PTL group having 3 or more positive samples and over 60% (12/19 showing two or more bacterial species (versus 20% (2/10 in term vaginal deliveries. Blood monocytes from women with PTL with intact membranes and PPROM who were 16S bacterial positive showed greater level of immune paresis (p = 0.03. A positive PCR result was associated with histological chorioamnionitis in preterm deliveries. CONCLUSION/SIGNIFICANCE: Bacteria are found in both preterm and term fetal membranes. A greater spread and diversity of bacterial species were found in tissues of women who had very preterm births. It is unclear to what extent the greater bacterial prevalence

  3. Assessing variation in bacterial composition between the rhizospheres of two mangrove tree species

    Science.gov (United States)

    Gomes, Newton C. M.; Cleary, Daniel F. R.; Pires, Ana C. C.; Almeida, Adelaide; Cunha, Angela; Mendonça-Hagler, Leda C. S.; Smalla, Kornelia

    2014-02-01

    This study aimed to determine to what extent roots from the common mangrove tree species Avicennia schaueriana and Laguncularia racemosa are able to impose a selective force on the composition of sediment bacterial communities in mangrove intertidal sediments using barcoded pyrosequencing analysis of 16S rRNA gene fragments (V4 hyper-variable region). The novel results showed that root systems of A. schaueriana and L. racemosa are associated with increased bacterial dominance, lower richness and compositional shifts of sediment bacterial communities. The proportion of OTUs (operational taxonomc units) belonging to the orders Rhizobiales and Vibrionales were enriched in rhizosphere samples from both plant species and sulphur-reducing bacteria (SRB) belonging to the order Desulfobacterales and Desulfuromonadales were enriched in the rhizosphere of A. schaueriana. In addition, Clostridium and Vibrio populations were more abundant in different mangrove rhizospheres. A. schaueriana and L. racemosa roots appear to be able to impose a selective force on the composition of mangrove sediment bacterial communities and this phenomenon appears to be plant species specific. Our findings provide new insights into the potential ecological roles of bacterial guilds in plant-microbe interactions and may aid rhizoengineering approaches for replanting impacted mangrove areas.

  4. An X-ray Absorption Fine Structure study of Au adsorbed onto the non-metabolizing cells of two soil bacterial species

    Energy Technology Data Exchange (ETDEWEB)

    Song, Zhen; Kenney, Janice P.L.; Fein, Jeremy B.; Bunker, Bruce A. (Notre)

    2015-02-09

    Gram-positive and Gram-negative bacterial cells can remove Au from Au(III)-chloride solutions, and the extent of removal is strongly pH dependent. In order to determine the removal mechanisms, X-ray Absorption Fine Structure (XAFS) spectroscopy experiments were conducted on non-metabolizing biomass of Bacillus subtilis and Pseudomonas putida with fixed Au(III) concentrations over a range of bacterial concentrations and pH values. X-ray Absorption Near Edge Structure (XANES) and Extended X-ray Absorption Fine Structure (EXAFS) data on both bacterial species indicate that more than 90% of the Au atoms on the bacterial cell walls were reduced to Au(I). In contrast to what has been observed for Au(III) interaction with metabolizing bacterial cells, no Au(0) or Au-Au nearest neighbors were observed in our experimental systems. All of the removed Au was present as adsorbed bacterial surface complexes. For both species, the XAFS data suggest that although Au-chloride-hydroxide aqueous complexes dominate the speciation of Au in solution, Au on the bacterial cell wall is characterized predominantly by binding of Au atoms to sulfhydryl functional groups and amine and/or carboxyl functional groups, and the relative importance of the sulfhydryl groups increases with increasing pH and with decreasing Au loading. The XAFS data for both microorganism species suggest that adsorption is the first step in the formation of Au nanoparticles by bacteria, and the results enhance our ability to account for the behavior of Au in bacteria-bearing geologic systems.

  5. A framework for identifying plant species to be used as 'ecological engineers' for fixing soil on unstable slopes.

    Science.gov (United States)

    Ghestem, Murielle; Cao, Kunfang; Ma, Wenzhang; Rowe, Nick; Leclerc, Raphaëlle; Gadenne, Clément; Stokes, Alexia

    2014-01-01

    Major reforestation programs have been initiated on hillsides prone to erosion and landslides in China, but no framework exists to guide managers in the choice of plant species. We developed such a framework based on the suitability of given plant traits for fixing soil on steep slopes in western Yunnan, China. We examined the utility of 55 native and exotic species with regard to the services they provided. We then chose nine species differing in life form. Plant root system architecture, root mechanical and physiological traits were then measured at two adjacent field sites. One site was highly unstable, with severe soil slippage and erosion. The second site had been replanted 8 years previously and appeared to be physically stable. How root traits differed between sites, season, depth in soil and distance from the plant stem were determined. Root system morphology was analysed by considering architectural traits (root angle, depth, diameter and volume) both up- and downslope. Significant differences between all factors were found, depending on species. We estimated the most useful architectural and mechanical traits for physically fixing soil in place. We then combined these results with those concerning root physiological traits, which were used as a proxy for root metabolic activity. Scores were assigned to each species based on traits. No one species possessed a suite of highly desirable traits, therefore mixtures of species should be used on vulnerable slopes. We also propose a conceptual model describing how to position plants on an unstable site, based on root system traits.

  6. A framework for identifying plant species to be used as 'ecological engineers' for fixing soil on unstable slopes.

    Directory of Open Access Journals (Sweden)

    Murielle Ghestem

    Full Text Available Major reforestation programs have been initiated on hillsides prone to erosion and landslides in China, but no framework exists to guide managers in the choice of plant species. We developed such a framework based on the suitability of given plant traits for fixing soil on steep slopes in western Yunnan, China. We examined the utility of 55 native and exotic species with regard to the services they provided. We then chose nine species differing in life form. Plant root system architecture, root mechanical and physiological traits were then measured at two adjacent field sites. One site was highly unstable, with severe soil slippage and erosion. The second site had been replanted 8 years previously and appeared to be physically stable. How root traits differed between sites, season, depth in soil and distance from the plant stem were determined. Root system morphology was analysed by considering architectural traits (root angle, depth, diameter and volume both up- and downslope. Significant differences between all factors were found, depending on species. We estimated the most useful architectural and mechanical traits for physically fixing soil in place. We then combined these results with those concerning root physiological traits, which were used as a proxy for root metabolic activity. Scores were assigned to each species based on traits. No one species possessed a suite of highly desirable traits, therefore mixtures of species should be used on vulnerable slopes. We also propose a conceptual model describing how to position plants on an unstable site, based on root system traits.

  7. ‘Tidjanibacter massiliensis’ gen. nov., sp. nov., a new bacterial species isolated from human colon

    Directory of Open Access Journals (Sweden)

    M. Mailhe

    2017-05-01

    Full Text Available We report the summary of main characteristics of Tidjanibacter massiliensis strain Marseille-P3084T, a new bacterial species isolated from the liquid sample of the colon of a patient with a history of irritable bowel syndrome.

  8. Detection of bacterial species involved in perimplantitis concerned with cultural and RT-PCR

    Directory of Open Access Journals (Sweden)

    Marcello Gatti

    2010-06-01

    Full Text Available Dental implants offer new treatment options for edentulous either partially or completely, now represent a viable alternative to conventional fixed protheses. Dental implants are colonized by a flora dominated by Gram-positive facultative aerobic, while in patients with bone loss and formation of pockets peri-implant diseases was found a significant difference in the composition of microflora, bacteria, Gram-negative anaerobes in particular Fusobacterium spp., Treponema denticola (Spirochetes, Tannerella forsythensis, Aggregatibacter actinomycetemcomitans, Prevotella intermedia as interim black-pigmented bacteria, Porphyromonas gingivalis, often in high concentrations. Aims. The purpose of this study was to identify those at risk of perimplantitis using 2 techniques: RT-PCR examination of trade and culture. The results were compared taking into consideration the advantages and disadvantages of both methods. Materials and methods.We studied 24 patients (14 women and 10 men, aged, women between 43 and 76 years, with an average of 63.8 + / - 10.9 years, men between 45 and 88 years with a average of 64.3 years + / - 12.5 years. Was performed a double levy of sub-gingival plaque at multiple sites that had an implant CAL (clinical attachment level> 4mm in order to assess the microbiological identification with the two techniques: Examining culture and Real-Time PCR of Commerce ( Gum-Sunstar that identifies 4 bacterial species: A. actinomycetemcomitans (A.a., P.gingivalis (P.g., T.forsythensis (T.f., and T.denticola (T.d.. Results. All patients studied were positive to both tests with charger high: the consideration of tenure, with CFU / ml > 105, was positive in 66.6% of samples by:T.f., and P.g., in 12.5% for A.a., while T.d. not been sought by examining culture, the RT-PCR was positive, with high loads, in 95.8% of samples for T.f., in 79.1% for P.g., in 12.5% for A.a. and 20.8% for T.d.The test crop showed the presence of even P.intermedia in 91

  9. A robust universal method for extraction of genomic DNA from bacterial species.

    Science.gov (United States)

    Atashpaz, Sina; Khani, Sajjad; Barzegari, Abolfazl; Barar, Jaleh; Vahed, Sepideh Zununi; Azarbaijani, Reza; Omidi, Yadollah

    2010-01-01

    The intactness of DNA is the keystone of genome-based clinical investigations, where rapid molecular detection of life-threatening bacteria is largely dependent on the isolation of high-quality DNA. Various protocols have been so far developed for genomic DNA isolation from bacteria, most of which have been claimed to be reproducible with relatively good yields of high-quality DNA. Nonetheless, they are not fully applicable to various types of bacteria, their processing cost is relatively high, and some toxic reagents are used. The routine protocols for DNA extraction appear to be sensitive to species diversity, and may fail to produce high-quality DNA from different species. Such protocols remain time-consuming and tedious, thus to resolve some of these impediments, we report development of a very simple, rapid, and high-throughput protocol for extracting of high-quality DNA from different bacterial species. Based upon our protocol, interfering phenolic compounds were removed from extraction using polyvinylpyrrolidone (PVP) and RNA contamination was precipitated using LiCI. The UV spectrophotometric and gel electrophoresis analysis resulted in high A260/A280 ratio (>1.8) with high intactness of DNA. Subsequent evaluations were performed using some quality-dependent techniques (e.g., RAPD marker and restriction digestions). The isolated DNA from 9 different bacterial species confirmed the accuracy of this protocol which requires no enzymatic processing and accordingly its low-cost making it an appropriate method f r large-scale DNA isolation fromvarious bacterial species.

  10. Bacterial species associated with sound and Botrytis-infected grapes from a Greek vineyard.

    Science.gov (United States)

    Nisiotou, Aspasia A; Rantsiou, Kalliopi; Iliopoulos, Vassilios; Cocolin, Luca; Nychas, George-John E

    2011-02-28

    Grape bacterial microbiota plays central roles in the quality of grapes and wine, yet its diversity remains poorly described. In the present study, bacterial species associated with sound and Botrytis-infected grapes of two cultivars originating from the same vineyard were assessed. Isolates were identified by PCR-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) and sequence analysis of partial 16S rRNA gene. Comparable counts were recorded between Botrytis-infected and sound grape samples. In all cases, the majority of isolates belonged to different species of Enterobacteriaceae. The dominant species in the vineyard was Klebsiella oxytoca that was found in different combinations with Citrobacter freundii, Enterobacter spp., Erwinia sp., Pantoea dispersa, Tatumella ptyseos or other species. In fermenting musts, those populations declined while other species evolved, like Lactobacillus plantarum and Enterobacter ludwigii. Populations in botrytised samples persisted longer during spontaneous fermentations. Present study suggests that bacterial diversity on grapes may be wider than previously described. Copyright © 2011 Elsevier B.V. All rights reserved.

  11. Surface-motility induction, attraction and hitchhiking between bacterial species promote dispersal on solid surfaces.

    Science.gov (United States)

    Hagai, Efrat; Dvora, Reut; Havkin-Blank, Tal; Zelinger, Einat; Porat, Ziv; Schulz, Stefan; Helman, Yael

    2014-05-01

    The ability to move on solid surfaces provides ecological advantages for bacteria, yet many bacterial species lack this trait. We found that Xanthomonas spp. overcome this limitation by making use of proficient motile bacteria in their vicinity. Using X. perforans and Paenibacillus vortex as models, we show that X. perforans induces surface motility, attracts proficient motile bacteria and 'rides' them for dispersal. In addition, X. perforans was able to restore surface motility of strains that lost this mode of motility under multiple growth cycles in the lab. The described interaction occurred both on agar plates and tomato leaves and was observed between several xanthomonads and motile bacterial species. Thus, suggesting that this motility induction and hitchhiking strategy might be widespread and ecologically important. This study provides an example as to how bacteria can rely on the abilities of their neighboring species for their own benefit, signifying the importance of a communal organization for fitness.

  12. Biodegradation of malathion and evaluation of kinetic parameters using three bacterial species

    Directory of Open Access Journals (Sweden)

    S.R. Geed

    2016-12-01

    Full Text Available Efficacy of three different bacterial species for biodegradation of malathion and its secondary products have been investigated. The concentration range of malathion under investigation was 25–200 mg⋅L−1. It has been observed that Pseudomonas putida was found to be most efficient for degradation of malathion. The removal of malathion was 72% at its concentration of 125 mg⋅L−1. The optimum parameters were studied for all three bacterial species in batch mode. The average values of Ks and μmax were obtained for all these species for degradation of malathion. Results indicate that P. putida has high degradation potential than Rhodoccocus rhodochrous and Sphingomonas sp. The degradation of P. putida was maximum at concentration of 125 mg⋅L−1, pH and temperature at 7 ± 0.2, 80 °C respectively. Metabolites were obtained using GCMS analysis.

  13. The bacterial species challenge: making sense of genetic and ecological diversity.

    Science.gov (United States)

    Fraser, Christophe; Alm, Eric J; Polz, Martin F; Spratt, Brian G; Hanage, William P

    2009-02-06

    The Bacteria and Archaea are the most genetically diverse superkingdoms of life, and techniques for exploring that diversity are only just becoming widespread. Taxonomists classify these organisms into species in much the same way as they classify eukaryotes, but differences in their biology-including horizontal gene transfer between distantly related taxa and variable rates of homologous recombination-mean that we still do not understand what a bacterial species is. This is not merely a semantic question; evolutionary theory should be able to explain why species exist at all levels of the tree of life, and we need to be able to define species for practical applications in industry, agriculture, and medicine. Recent studies have emphasized the need to combine genetic diversity and distinct ecology in an attempt to define species in a coherent and convincing fashion. The resulting data may help to discriminate among the many theories of prokaryotic species that have been produced to date.

  14. Studies on interaction of colloidal silver nanoparticles (SNPs) with five different bacterial species.

    Science.gov (United States)

    Khan, S Sudheer; Mukherjee, Amitava; Chandrasekaran, N

    2011-10-01

    Silver nanoparticles (SNPs) are being increasingly used in many consumer products like textile fabrics, cosmetics, washing machines, food and drug products owing to its excellent antimicrobial properties. Here we have studied the adsorption and toxicity of SNPs on bacterial species such as Pseudomonas aeruginosa, Micrococcus luteus, Bacillus subtilis, Bacillus barbaricus and Klebsiella pneumoniae. The influence of zeta potential on the adsorption of SNPs on bacterial cell surface was investigated at acidic, neutral and alkaline pH and with varying salt (NaCl) concentrations (0.05, 0.1, 0.5, 1 and 1.5 M). The survival rate of bacterial species decreased with increase in adsorption of SNPs. Maximum adsorption and toxicity was observed at pH 5, and NaCl concentration of 0.5 M, there by resulting in less toxicity. The zeta potential study suggests that, the adsorption of SNPs on the cell surface was related to electrostatic force of attraction. The equilibrium and kinetics of the adsorption process were also studied. The adsorption equilibrium isotherms fitted well to the Langmuir model. The kinetics of adsorption fitted best to pseudo-first-order. These findings form a basis for interpreting the interaction of nanoparticles with environmental bacterial species.

  15. Impact of lime, nitrogen and plant species on bacterial community structure in grassland microcosms.

    Science.gov (United States)

    Kennedy, Nabla; Brodie, Eoin; Connolly, John; Clipson, Nicholas

    2004-10-01

    A microcosm-based approach was used to study impacts of plant and chemical factors on the bacterial community structure of an upland acidic grassland soil. Seven perennial plant species typical of both natural, unimproved (Nardus stricta, Agrostis capillaris, Festuca ovina and F. rubra) and fertilized, improved (Holcus lanatus, Lolium perenne and Trifolium repens) grasslands were either left unamended or treated with lime, nitrogen, or lime plus nitrogen in a 75-day glasshouse experiment. Lime and nitrogen amendment were shown to have a greater effect on microbial activity, biomass and bacterial ribotype number than plant species. Liming increased soil pH, microbial activity and biomass, while decreasing ribotype number. Nitrogen addition decreased soil pH, microbial activity and ribotype number. Addition of lime plus nitrogen had intermediate effects, which appeared to be driven more by lime than nitrogen. Terminal restriction fragment length polymorphism (TRFLP) analysis revealed that lime and nitrogen addition altered soil bacterial community structure, while plant species had little effect. These results were further confirmed by multivariate redundancy analysis, and suggest that soil lime and nitrogen status are more important controllers of bacterial community structure than plant rhizosphere effects.

  16. Diazotrophic potential among bacterial communities associated with wild and cultivated Agave species.

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    Desgarennes, Damaris; Garrido, Etzel; Torres-Gomez, Miryam J; Peña-Cabriales, Juan J; Partida-Martinez, Laila P

    2014-12-01

    Agaves are major biotic resources in arid and semi-arid ecosystems. Despite their ecological, economical and cultural relevance, many aspects of the microbial communities associated with agaves are still unknown. Here, we investigated the bacterial communities associated with two Agave species by 16S rRNA- Denaturing gradient gel electrophoresis fingerprinting and sequencing. We also evaluated the effects of biotic and abiotic factors in the structure of the bacterial communities. In parallel, we isolated and characterized diazotrophic bacteria associated with agaves, as Agave soils are characterized by their low nitrogen content. Our results demonstrate that in Agave, the structure of prokaryotic assemblages was mostly influenced by the community group, where the soil, episphere, and endosphere were clearly distinct. Proteobacteria (γ and α), Actinobacteria, and Acidobacteria were the dominant phyla. Bacterial communities in the episphere of agaves were mainly influenced by the host species, whereas in the endosphere were affected by the season. Fifteen bacterial taxa were common and abundant in the endosphere of both Agave species during the dry season. Notably, some of the confirmed diazotrophic strains belonged to this group, suggesting a possible beneficial role in planta.

  17. Heavy metals species affect fungal-bacterial synergism during the bioremediation of fluoranthene.

    Science.gov (United States)

    Ma, Xiao-Kui; Ding, Ning; Peterson, Eric Charles; Daugulis, Andrew J

    2016-09-01

    The co-occurrence of polycyclic aromatic hydrocarbons (PAHs) with heavy metals (HMs) is very common in contaminated soils, but the influence of HMs on fungal-bacterial synergism during PAH bioremediation has not been investigated. The bioremediation of fluoranthene-contaminated sand using co-cultures of Acremonium sp. P0997 and Bacillus subtilis showed increases of 109.4 and 9.8 % in degradation compared to pure bacterial and fungal cultures, respectively, removing 64.1 ± 1.4 % fluoanthene in total. The presence of Cu(2+) reduced fluoranthene removal to 53.7 ± 1.7 %, while inhibiting bacterial growth, and reducing translocation of bacteria on fungal hyphae by 49.5 %, in terms of the bacterial translocation ratio. Cu(2+) reduced bacterial diffusion by 46.8 and 31.9 %, as reflected by D (a bulk random motility diffusional coefficient) and D eff (the effective one-dimensional diffusion coefficient) compared to the control without HM supplementation, respectively. However, Mn(2+) resulted in a 78.2 ± 1.9 % fluoranthene degradation, representing an increase of 21.9 %, while enhancing bacterial growth and bacterial translocation on fungal hyphae, showing a 12.0 % increase in translocation ratio, with no observable impact on D and D eff. Hence, the presence of HMs has been shown to affect fungal-bacterial synergism in PAH degradation, and this effect differs with HM species.

  18. Distribution of periodontopathic bacterial species in Japanese children with developmental disabilities

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    Nemoto Hirotoshi

    2009-09-01

    Full Text Available Abstract Background Recent developments in molecular biological techniques have enabled rapid detection of periodontopathic bacterial species in clinical specimens. Accumulated evidence suggests that detection of specific bacterial species enables identification of subjects at high risk for the onset of periodontitis. We investigated the distribution of 10 selected periodontopathic bacterial species in dental plaque specimens obtained from children with disabilities who were attending daycare centers. Methods A total of 187 children (136 boys, 51 girls aged 1-6 years old and diagnosed with such disabilities as mental retardation, cerebral palsy, and autism, participated in the study. Subgingival dental plaque specimens were collected from the buccal side of the maxillary left second primary molar after a clinical examination. Bacterial DNA was extracted from the specimens and PCR analyses were carried out to detect 10 selected periodontopathic species using specific primers for each. In addition, statistical analyses were performed to analyze the correlations among clinical parameters and the detected species. Results The most frequently detected species was Capnocytophaga sputigena (28.3%, followed by Aggregatibacter actinomycetemcomitans (20.9% and Campylobacter rectus (18.2%. Eikenella corrodens, Capnocytophaga ochracea, and Prevotella nigrescence were detected in approximately 10% of the specimens, whereas Treponema denticola, Tannerella forsythia, and Prevotella intermedia were rarely found, and Porphyromonas gingivalis was not detected in any of the subjects. The total numbers of detected species were positively correlated with the age of the subjects. There were 10 subjects with positive reactions for T. denticola and/or T. forsythia, in whom the total number of bacterial species was significantly higher as compared to the other subjects. Furthermore, subjects possessing C. rectus showed significantly greater values for periodontal pocket

  19. Intestinal microbiota in metabolic diseases: from bacterial community structure and functions to species of pathophysiological relevance.

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    Clavel, Thomas; Desmarchelier, Charles; Haller, Dirk; Gérard, Philippe; Rohn, Sascha; Lepage, Patricia; Daniel, Hannelore

    2014-07-01

    The trillions of bacterial cells that colonize the mammalian digestive tract influence both host physiology and the fate of dietary compounds. Gnotobionts and fecal transplantation have been instrumental in revealing the causal role of intestinal bacteria in energy homeostasis and metabolic dysfunctions such as type-2 diabetes. However, the exact contribution of gut bacterial metabolism to host energy balance is still unclear and knowledge about underlying molecular mechanisms is scant. We have previously characterized cecal bacterial community functions and host responses in diet-induced obese mice using omics approaches. Based on these studies, we here discuss issues on the relevance of mouse models, give evidence that the metabolism of cholesterol-derived compounds by gut bacteria is of particular importance in the context of metabolic disorders and that dominant species of the family Coriobacteriaceae are good models to study these functions.

  20. Isolation, cultivation, purification and identification of bacterial species from microfauna of soil

    Directory of Open Access Journals (Sweden)

    Amna Ali

    2011-03-01

    Full Text Available

     

    Abstract:
    Soil is an excellent source of unknown microorganisms since bacteria, algae, protozoans, yeasts, moulds, and microscopic worms are routinely found in this environment. Therefore, soil is a medium in which life is sustained in a fragile biological balance. Bacteria play an important role in nutritional chains that are an important part of biological balance. In the present study, four different soil samples were collected from the rhizosphere of i Sapota zapotilla, ii Eucalyptus species, iii Ficus religiosa from Lahore and iv soil from Changa manga, Pakistan. A Total of 28 bacterial species were isolated and classified in the period between November 2008 and December 2009. All species were cultured on recommended media for verification of biochemical characteristics. The results showed that at least fifteen Gram-positive bacterial species were present in samples and these were considered as the major group constituting the bacterial population strains

  1. Coral-associated bacterial diversity is conserved across two deep-sea Anthothela species

    Science.gov (United States)

    Lawler, Stephanie N.; Kellogg, Christina A.; France, Scott C; Clostio, Rachel W; Brooke, Sandra D.; Ross, Steve W.

    2016-01-01

    Cold-water corals, similar to tropical corals, contain diverse and complex microbial assemblages. These bacteria provide essential biological functions within coral holobionts, facilitating increased nutrient utilization and production of antimicrobial compounds. To date, few cold-water octocoral species have been analyzed to explore the diversity and abundance of their microbial associates. For this study, 23 samples of the family Anthothelidae were collected from Norfolk (n = 12) and Baltimore Canyons (n = 11) from the western Atlantic in August 2012 and May 2013. Genetic testing found that these samples comprised two Anthothela species (Anthothela grandiflora and Anthothela sp.) and Alcyonium grandiflorum. DNA was extracted and sequenced with primers targeting the V4-V5 variable region of the 16S rRNA gene using 454 pyrosequencing with GS FLX Titanium chemistry. Results demonstrated that the coral host was the primary driver of bacterial community composition. Al. grandiflorum, dominated by Alteromonadales and Pirellulales had much higher species richness, and a distinct bacterial community compared to Anthothela samples. Anthothela species (A. grandiflora and Anthothela sp.) had very similar bacterial communities, dominated by Oceanospirillales and Spirochaetes. Additional analysis of core-conserved bacteria at 90% sample coverage revealed genus level conservation across Anthothela samples. This core included unclassified Oceanospirillales, Kiloniellales, Campylobacterales, and genus Spirochaeta. Members of this core were previously recognized for their functional capabilities in nitrogen cycling and suggest the possibility of a nearly complete nitrogen cycle within Anthothela species. Overall, many of the bacterial associates identified in this study have the potential to contribute to the acquisition and cycling of nutrients within the coral holobiont.

  2. Plant-associated bacterial populations on native and invasive plant species: comparisons between 2 freshwater environments.

    Science.gov (United States)

    Olapade, Ola A; Pung, Kayleigh

    2012-06-01

    Plant-microbial interactions have been well studied because of the ecological importance of such relationships in aquatic systems. However, general knowledge regarding the composition of these biofilm communities is still evolving, partly as a result of several confounding factors that are attributable to plant host properties and to hydrodynamic conditions in aquatic environments. In this study, the occurrences of various bacterial phylogenetic taxa on 2 native plants, i.e., mayapple (Podophyllum peltatum L.) and cow parsnip (Heracleum maximum Bartram), and on an invasive species, i.e., garlic mustard (Alliaria petiolata (M. Bieb.) Cavara & Grande), were quantitatively examined using nucleic acid staining and fluorescence in situ hybridization. The plants were incubated in triplicates for about a week within the Kalamazoo River and Pierce Cedar Creek as well as in microcosms. The bacterial groups targeted for enumeration are known to globally occur in relatively high abundance and are also ubiquitously distributed in freshwater environments. Fluorescence in situ hybridization analyses of the bacterioplankton assemblages revealed that the majority of bacterial cells that hybridized with the different probes were similar between the 2 sites. In contrast, the plant-associated populations while similar on the 3 plants incubated in Kalamazoo River, their representations were highest on the 2 native plants relative to the invasive species in Pierce Cedar Creek. Overall, our results further suggested that epiphytic bacterial assemblages are probably under the influences of and probably subsequently respond to multiple variables and conditions in aquatic milieus.

  3. Bacterial and fungal endophthalmitis in Upper Egypt: related species and risk factors

    OpenAIRE

    2012-01-01

    Objective: To study risk factors, contributing factors of bacterial and fungal endophthalmitis in Upper Egypt, test the isolated species sensitive to some therapeutic agents, and to investigate the air-borne bacteria and fungi in opthalmology operating rooms. Methods: Thirty one cases of endophthalmitis were clinically diagnosed and microbiologically studied. Indoor air-borne bacteria and fungi inside four air-conditioned operating rooms in the Ophthalmology Department at Assiut University...

  4. Biliary fluorescent aromatic compounds (FACs) measured by fixed wavelength fluorescence (FF) in several marine fish species from the NW Mediterranean.

    Science.gov (United States)

    Insausti, David; Carrasson, Maite; Maynou, Francesc; Cartes, Joan E; Solé, Montserrat

    2009-11-01

    The fixed wavelength fluoresce (FF) method was used to estimate the levels of fluorescent aromatic compounds (FACs) in the bile of fourteen fish species of commercial and/or ecological interest. Sampling was carried out in the NW Mediterranean at depths ranging from 50 to 1000 m during four seasonal cruises. During the summer sampling period, some species were also collected from another site (Vilanova fishing grounds) for comparison. Baseline levels of the polycyclic aromatic hydrocarbons (PAHs) naphthalene, phenanthrene, pyrene and benzo[a]pyrene were measured. Some seasonality was observed, with reduced FF levels in summer and no differences among sites, consistent with sediment PAH levels. We discuss our results in relation to fish phylogeny, season, depth, diet, trophic level and swimming capacity. Overall FF levels indicated differences among species; the suprabenthic feeders from shallow and deep communities, and Mullus barbatus in particular, displayed elevated FF values and are potential candidates for additional monitoring studies.

  5. [Finding of the bacterial species Edwardsiella tarda in the aquarium fish Betta splendens].

    Science.gov (United States)

    Vladík, P; Prouza, A; Vítovec, J

    1983-01-01

    A case of the mass occurrence of a disease in the aquarium fish species Betta splendens is described; morphologically the disease was characterized by the finding of large dermal changes located mainly in the dorsal part and by miliary granulomata in liver, spleen and kidneys. The granulomata consisted of epitheloid light cells with centrally located necrosis. Gram-negative bacteria with morphological and biochemical characteristics corresponding to the bacterial species Edwardsiella tarda were isolated from the kidneys, liver and from the dermal lesion. The characteristics of the strains isolated by us were compared with the reference Edwardsiella strain (Bth 1/64) obtained from the Czechoslovak collection of type cultures, Prague.

  6. Effects of viruses on bacterial functions under contrasting nutritional conditions for four species of bacteria isolated from Hong Kong waters

    Science.gov (United States)

    Liu, Hao; Yuan, Xiangcheng; Xu, Jie; Harrison, Paul J.; He, Lei; Yin, Kedong

    2015-09-01

    Free living viruses are ubiquitous in marine waters and concentrations are usually several times higher than the bacterial abundance. These viruses are capable of lysing host bacteria and therefore, play an important role in the microbial loop in oligotrophic waters. However, few studies have been conducted to compare the role of viruses in regulating bacterial abundance and heterotrophic activities between natural oligotrophic waters and anthropogenic influenced eutrophic waters. In this study, we examined viral effects on bacterial functions of four single bacterial species incubated with natural viral assemblages in seawater samples from eutrophic and oligotrophic waters. The viral-lysis of bacteria was significantly higher in eutrophic than oligotrophic waters. This suggests that viruses were capable of controlling bacterial abundance, respiration and production in the eutrophic waters. Cellular bacterial respiration and production was higher with viruses than without viruses, which was more evident in the oligotrophic waters. These results indicate that viruses can slow down bacterial consumption of oxygen and reduce bacteria-induced eutrophication effects in anthropogenic eutrophic waters, but switch to the role of sustaining the bacterial population when nutrients are limiting. There were bacterial species differences in resisting viral attack, which can influence the dominance and biodiversity of bacterial species in coastal waters.

  7. Effects of viruses on bacterial functions under contrasting nutritional conditions for four species of bacteria isolated from Hong Kong waters.

    Science.gov (United States)

    Liu, Hao; Yuan, Xiangcheng; Xu, Jie; Harrison, Paul J; He, Lei; Yin, Kedong

    2015-09-25

    Free living viruses are ubiquitous in marine waters and concentrations are usually several times higher than the bacterial abundance. These viruses are capable of lysing host bacteria and therefore, play an important role in the microbial loop in oligotrophic waters. However, few studies have been conducted to compare the role of viruses in regulating bacterial abundance and heterotrophic activities between natural oligotrophic waters and anthropogenic influenced eutrophic waters. In this study, we examined viral effects on bacterial functions of four single bacterial species incubated with natural viral assemblages in seawater samples from eutrophic and oligotrophic waters. The viral-lysis of bacteria was significantly higher in eutrophic than oligotrophic waters. This suggests that viruses were capable of controlling bacterial abundance, respiration and production in the eutrophic waters. Cellular bacterial respiration and production was higher with viruses than without viruses, which was more evident in the oligotrophic waters. These results indicate that viruses can slow down bacterial consumption of oxygen and reduce bacteria-induced eutrophication effects in anthropogenic eutrophic waters, but switch to the role of sustaining the bacterial population when nutrients are limiting. There were bacterial species differences in resisting viral attack, which can influence the dominance and biodiversity of bacterial species in coastal waters.

  8. BOX-PCR-based identification of bacterial species belonging to Pseudomonas syringae: P. viridiflava group

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    Abi S.A. Marques

    2008-01-01

    Full Text Available The phenotypic characteristics and genetic fingerprints of a collection of 120 bacterial strains, belonging to Pseudomonas syringae sensu lato group, P. viridiflava and reference bacteria were evaluated, with the aim of species identification. The numerical analysis of 119 nutritional characteristics did not show patterns that would help with identification. Regarding the genetic fingerprinting, the results of the present study supported the observation that BOX-PCR seems to be able to identify bacterial strains at species level. After numerical analyses of the bar-codes, all pathovars belonging to each one of the nine described genomospecies were clustered together at a distance of 0.72, and could be separated at genomic species level. Two P. syringae strains of unknown pathovars (CFBP 3650 and CFBP 3662 and the three P. syringae pv. actinidiae strains were grouped in two extra clusters and might eventually constitute two new species. This genomic species clustering was particularly evident for genomospecies 4, which gathered P. syringae pvs. atropurpurea, coronafaciens, garçae, oryzae, porri, striafaciens, and zizaniae at a noticeably low distance.

  9. Investigation of the bacterial communities associated with females of Lutzomyia sand fly species from South America.

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    Mauricio R V Sant'Anna

    Full Text Available Phlebotomine sand flies are vectors of Leishmania that are acquired by the female sand fly during blood feeding on an infected mammal. Leishmania parasites develop exclusively in the gut lumen during their residence in the insect before transmission to a suitable host during the next blood feed. Female phlebotomine sand flies are blood feeding insects but their life style of visiting plants as well as animals, and the propensity for larvae to feed on detritus including animal faeces means that the insect host and parasite are exposed to a range of microorganisms. Thus, the sand fly microbiota may interact with the developing Leishmania population in the gut. The aim of the study was to investigate and identify the bacterial diversity associated with wild adult female Lutzomyia sand flies from different geographical locations in the New World. The bacterial phylotypes recovered from 16S rRNA gene clone libraries obtained from wild caught adult female Lutzomyia sand flies were estimated from direct band sequencing after denaturing gradient gel electrophoresis of bacterial 16 rRNA gene fragments. These results confirm that the Lutzomyia sand flies contain a limited array of bacterial phylotypes across several divisions. Several potential plant-related bacterial sequences were detected including Erwinia sp. and putative Ralstonia sp. from two sand fly species sampled from 3 geographically separated regions in Brazil. Identification of putative human pathogens also demonstrated the potential for sand flies to act as vectors of bacterial pathogens of medical importance in addition to their role in Leishmania transmission.

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

    Science.gov (United States)

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

    2016-04-23

    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 profiles and evaluate indicators for BV using three molecular methods. Evaluation of indicators for BV was carried out by 16S rRNA amplicon sequencing of the V5-V7 region, a tailor-made 16S rRNA oligonucleotide-based microarray, and a PCR-based profiling technique termed IS-profiling, which is based on fragment variability of the 16S-23S rRNA intergenic spacer region. An inventory of vaginal bacterial species was obtained from 40 females attending a Dutch sexually transmitted infection outpatient clinic, of which 20 diagnosed with BV (Nugent score 7-10), and 20 BV negative (Nugent score 0-3). Analysis of the bacterial communities by 16S rRNA amplicon sequencing revealed two clusters in the BV negative women, dominated by either Lactobacillus iners or Lactobacillus crispatus and three distinct clusters in the BV positive women. In the former, there was a virtually complete, negative correlation between L. crispatus and L. iners. BV positive subjects showed cluster profiles that were relatively high in bacterial species diversity and dominated by anaerobic species, including Gardnerella vaginalis, and those belonging to the Families of Lachnospiraceae and Leptotrichiaceae. Accordingly, the Gini-Simpson index of species diversity, and the relative abundance Lactobacillus species appeared consistent indicators for BV. Under the conditions used, only the 16S rRNA amplicon sequencing method was suitable to assess species diversity, while all three molecular composition profiling methods were able to indicate Lactobacillus abundance in the vaginal microbiota. An affordable and simple molecular test showing a depletion of the genus Lactobacillus in combination with an increased species diversity of vaginal

  11. Microbial activity of soil with sulfentrazone associated with phytoremediator species and inoculation with a bacterial consortium

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    Christiane Augusta Diniz Melo

    Full Text Available ABSTRACT Phytostimulation plays a key role in the process of rhizodegradation of herbicides in soil. Additionally, bio-enhancement associated with phytoremediation may increase the efficiency of the decontamination process of soils with herbicides. Therefore, the objective of this study was to evaluate the biomass and microbial activity of soil contaminated with sulfentrazone and cultivated with phytoremediator species plus a bacterial consortium. The experiment was conducted in a greenhouse, carried out with a 2 × 4 × 4 completely randomized factorial design with 4 replications. The first factor consisted of the presence or absence of bio-enhancement with a bacterial consortium composed of Pseudomonas bacteria; the second factor consisted of a monoculture or mixed cultivation of 2 phytoremediator species Canavalia ensiformis and Helianthus annuus, besides the absence of cultivation; the third factor was made up by the bio-remediation time (25, 45, 65, and 85 days after thinning. Uncultivated soils displayed low values of microbial biomass carbon and microbial quotient as well as high values of metabolic quotient throughout the bio-remediation time, indicating the importance of cultivating phytoremediator species for the stimulation of soil microbiota. Bio-enhancement with the bacterial consortium, in general, promoted an increase in the microbial biomass and activity of soil contaminated with sulfentrazone. In the presence of the bacterial consortium, Canavalia ensiformis stimulated a greater activity of associated microbiota and supported a higher microbial biomass. Phytoremediation associated with microbial bio-enhancement are thus promising techniques for the bio-remediation for soils contaminated with sulfentrazone. This technique enhances the biomass and activity of soil microorganisms.

  12. An investigation of the effect of scaling-induced surface roughness on bacterial adhesion in common fixed dental restorative materials.

    Science.gov (United States)

    Checketts, Matthew R; Turkyilmaz, Ilser; Asar, Neset Volkan

    2014-11-01

    Bacterial plaque must be routinely removed from teeth, adjacent structures, and prostheses. However, the removal of this plaque can inadvertently increase the risk of future bacterial adhesion. The purpose of this investigation was to assess the change in the surface roughness of 3 different surfaces after dental prophylactic instrumentation and how this influenced bacterial adhesion. Forty specimens each of Type III gold alloy, lithium disilicate, and zirconia were fabricated in the same dimensions. The specimens were divided into 4 groups: ultrasonic scaler, stainless steel curette, prophylaxis cup, and control. Pretreatment surface roughness measurements were made with a profilometer. Surface treatments in each group were performed with a custom mechanical scaler. Posttreatment surface roughness values were measured. In turn, the specimens were inoculated with Streptococcus mutans, Lactobacillus acidophilus, and Actinomyces viscosus. Bacterial adhesion was assessed by rinsing the specimens with sterile saline to remove unattached cells. The specimens were then placed in sterile tubes with 1 mL of sterile saline. The solution was plated and quantified. Scanning electron microscopy was performed. The statistical analysis of surface roughness was completed by using repeated-measures single-factor ANOVA with a Bonferroni correction. The surface roughness values for gold alloy specimens increased as a result of prophylaxis cup treatment (0.221 to 0.346 Ra) (Padhesion to gold alloy proved inconclusive. A quantitative comparison indicated no statistically significant differences in pretreatment and posttreatment surface roughness values for lithium disilicate and zirconia specimens. In spite of these similarities, the overall bacterial adherence values for lithium disilicate were significantly greater than those recorded for gold alloy or zirconia (Padhesion compared with the control (Padhesion than lithium disilicate, and greater bacterial adhesion was found for the

  13. Biodegradation of BOD and ammonia-free using bacterial consortium in aerated fixed film bioreactor (AF2B)

    Science.gov (United States)

    Prayitno, Rulianah, Sri; Saroso, Hadi; Meilany, Diah

    2017-06-01

    BOD and Ammonia-free (NH3-N) are pollutants of hospital wastewater which often exceed the quality standards. It is because biological processes in wastewater treatment plant (WWTP) have not been effective in degrading BOD and NH3-N. Therefore, a study on factors that influence the biodegradation of BOD and NH3-N by choosing the type of bacteria to improve the mechanisms of biodegradation processes is required. Bacterial consortium is a collection of several types of bacteria obtained from isolation process, which is known to be more effective than a single bacterial in degrading pollutants. On the other hand, AF2B is a type of reactor in wastewater treatment system. The AF2B contains a filter media that has a large surface area so that the biodegradation process of pollutants by microorganism can be improved. The objective of this research is to determine the effect of volume of starter and air supplies on decreasing BOD and NH3-N in hospital wastewater using bacterial consortium in the AF2B on batch process. The research was conducted in three stages: the making of the growth curve of the bacterial consortium, bacterial consortium acclimatization, and hospital wastewater treatment in the AF2B with batch process. The variables used are the volume of starter (65%, 75%, and 85% in volume) and air supplies (2.5, 5, and 7.5 L/min). Meanwhile, the materials used are hospital wastewater, bacterial consortium (Pseudomonas diminuta, Pseudomonas capica, Bacillius sp, and Nitrobacter sp), blower, and AF2B. AF2B is a plastic basin containing a filter media with a wasp-nest shape used as a medium for growing the bacterial consortium. In the process of making the growth curve, a solid form of bacterial consortium was dissolved in sterilized water, then grown in a nutrient broth (NB). Then, shaking and sampling were done at any time to determine the path growth of bacterial consortium. In the acclimatization process, bacterial isolates were grown using hospital wastewater as a

  14. Korean indigenous bacterial species with valid names belonging to the phylum Actinobacteria.

    Science.gov (United States)

    Bae, Kyung Sook; Kim, Mi Sun; Lee, Ji Hee; Kang, Joo Won; Kim, Dae In; Lee, Ji Hee; Seong, Chi Nam

    2016-12-01

    , Gyeonggi, Jeonnam, Daejeon, and Chungnam. A large number of novel actinobacterial species continue to be discovered since the Korean government is encouraging the search for new bacterial species and researchers are endeavoring to find out novel strains from extreme or untapped environments.

  15. What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira.

    Directory of Open Access Journals (Sweden)

    Derrick E Fouts

    2016-02-01

    Full Text Available Leptospirosis, caused by spirochetes of the genus Leptospira, is a globally widespread, neglected and emerging zoonotic disease. While whole genome analysis of individual pathogenic, intermediately pathogenic and saprophytic Leptospira species has been reported, comprehensive cross-species genomic comparison of all known species of infectious and non-infectious Leptospira, with the goal of identifying genes related to pathogenesis and mammalian host adaptation, remains a key gap in the field. Infectious Leptospira, comprised of pathogenic and intermediately pathogenic Leptospira, evolutionarily diverged from non-infectious, saprophytic Leptospira, as demonstrated by the following computational biology analyses: 1 the definitive taxonomy and evolutionary relatedness among all known Leptospira species; 2 genomically-predicted metabolic reconstructions that indicate novel adaptation of infectious Leptospira to mammals, including sialic acid biosynthesis, pathogen-specific porphyrin metabolism and the first-time demonstration of cobalamin (B12 autotrophy as a bacterial virulence factor; 3 CRISPR/Cas systems demonstrated only to be present in pathogenic Leptospira, suggesting a potential mechanism for this clade's refractoriness to gene targeting; 4 finding Leptospira pathogen-specific specialized protein secretion systems; 5 novel virulence-related genes/gene families such as the Virulence Modifying (VM (PF07598 paralogs proteins and pathogen-specific adhesins; 6 discovery of novel, pathogen-specific protein modification and secretion mechanisms including unique lipoprotein signal peptide motifs, Sec-independent twin arginine protein secretion motifs, and the absence of certain canonical signal recognition particle proteins from all Leptospira; and 7 and demonstration of infectious Leptospira-specific signal-responsive gene expression, motility and chemotaxis systems. By identifying large scale changes in infectious (pathogenic and intermediately

  16. Paraburkholderia nodosa is the main N2-fixing species trapped by promiscuous common bean (Phaseolus vulgaris L.) in the Brazilian 'Cerradão'.

    Science.gov (United States)

    Dall'Agnol, Rebeca F; Plotegher, Fábio; Souza, Renata C; Mendes, Iêda C; Dos Reis Junior, Fábio B; Béna, Gilles; Moulin, Lionel; Hungria, Mariangela

    2016-08-01

    The bacterial genus Burkholderia comprises species occupying several habitats, including a group of symbionts of leguminous plants-also called beta-rhizobia-that has been recently ascribed to the new genus Paraburkholderia We used common bean (Phaseolus vulgaris L.) plants to trap rhizobia from an undisturbed soil of the Brazilian Cerrado under the vegetation type 'Cerradão'. Genetic characterization started with the analyses of 181 isolates by BOX-PCR, where the majority revealed unique profiles, indicating high inter- and intra-species diversity. Restriction fragment length polymorphism-PCR of the 16S rRNA of representative strains of the BOX-PCR groups indicated two main clusters, and gene-sequencing analysis identified the minority (27%) as Rhizobium and the majority (73%) as Paraburkholderia Phylogenetic analyses of the 16S rRNA and housekeeping (recA and gyrB) genes positioned all strains of the second cluster in the species P. nodosa, and the phylogeny of a symbiotic gene-nodC-was in agreement with the conserved genes. All isolates were stable vis-à-vis nodulating common bean, but, in general, with a low capacity for fixing N2, although some effective strains were identified. The predominance of P. nodosa might be associated with the edaphic properties of the Cerrado biome, and might represent an important role in terms of maintenance of the ecosystem, which is characterized by acid soils with high saturation of aluminum and low N2 content. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  17. Life history correlates of fecal bacterial species richness in a wild population of the blue tit Cyanistes caeruleus.

    Science.gov (United States)

    Benskin, Clare McW H; Rhodes, Glenn; Pickup, Roger W; Mainwaring, Mark C; Wilson, Kenneth; Hartley, Ian R

    2015-02-01

    Very little is known about the normal gastrointestinal flora of wild birds, or how it might affect or reflect the host's life-history traits. The aim of this study was to survey the species richness of bacteria in the feces of a wild population of blue tits Cyanistes caeruleus and to explore the relationships between bacterial species richness and various life-history traits, such as age, sex, and reproductive success. Using PCR-TGGE, 55 operational taxonomic units (OTUs) were identified in blue tit feces. DNA sequencing revealed that the 16S rRNA gene was amplified from a diverse range of bacteria, including those that shared closest homology with Bacillus licheniformis, Campylobacter lari, Pseudomonas spp., and Salmonella spp. For adults, there was a significant negative relationship between bacterial species richness and the likelihood of being detected alive the following breeding season; bacterial richness was consistent across years but declined through the breeding season; and breeding pairs had significantly more similar bacterial richness than expected by chance alone. Reduced adult survival was correlated with the presence of an OTU most closely resembling C. lari; enhanced adult survival was associated with an OTU most similar to Arthrobacter spp. For nestlings, there was no significant change in bacterial species richness between the first and second week after hatching, and nestlings sharing the same nest had significantly more similar bacterial richness. Collectively, these results provide compelling evidence that bacterial species richness was associated with several aspects of the life history of their hosts.

  18. Bacterial and fungal endophthalmitis in Upper Egypt:related species and risk factors

    Institute of Scientific and Technical Information of China (English)

    AA Gharamah; AM Moharram; MA Ismail; AK AL-Hussaini

    2012-01-01

    Objective: To study risk factors, contributing factors of bacterial and fungal endophthalmitis in Upper Egypt, test the isolated species sensitive to some therapeutic agents, and to investigate the air-borne bacteria and fungi in opthalmology operating rooms. Methods: Thirty one cases of endophthalmitis were clinically diagnosed and microbiologically studied. Indoor air-borne bacteria and fungi inside four air-conditioned operating rooms in the Ophthalmology Department at Assiut University Hospitals were also investigated. The isolated microbes from endophthalmitis cases were tested for their ability to produce some extracellular enzymes including protease, lipase, urease, phosphatase and catalase. Also the ability of 5 fungal isolates from endophthalmitis origin to produce mycotoxins and their sensitivity to some therapeutic agents were studied. Results: Results showed that bacteria and fungi were responsihle for infection in 10 and 6 cases of endophthalmitis, respectively and only 2 cases produced a mixture of bacteria and fungi. Trauma was the most prevalent risk factor of endophthalmitis where 58.1% of the 31 cases were due to trauma. In ophthalmology operating rooms, different bacterial and fungal species were isolated. 8 bacterial and 5 fungal isolates showed their ability to produce enzymes while only 3 fungal isolates were able to produce mycotoxins. Terbinafine showed the highest effect against most isolates in vitro. Conclusions: The ability of bacterial and fungal isolates to produce extracellular enzymes and mycotoxins may be aid in the invasion and destruction of eye tissues. Microbial contamination of operating rooms with air-borne bacteria and fungi in the present work may be a source of postoperative endophthalmitis.

  19. Isolation of a lead tolerant novel bacterial species, Achromobacter sp. TL-3: assessment of bioflocculant activity.

    Science.gov (United States)

    Batta, Neha; Subudhi, Sanjukta; Lal, Banwari; Devi, Arundhuti

    2013-11-01

    Lead is one of the four heavy metals that has a profound damaging effects on human health. In the recent past there has been an increasing global concern for development of sustainable bioremediation technologies for detoxification of lead contaminant. Present investigation highlights for lead biosorption by a newly isolated novel bacterial species; Achromobacter sp. TL-3 strain, isolated from activated sludge samples contaminated with heavy metals (collected from oil refinery, Assam, North-East India). For isolation of lead tolerant bacteria, sludge samples were enriched into Luria Broth medium supplemented separately with a range of lead nitrate; 250, 500, 750, 1000, 1250 and 1500 ppm respectively. The bacterial consortium that could tolerate 1500 ppm of lead nitrate was selected further for purification of lead tolerant bacterial isolates. Purified lead tolerant bacterial isolates were then eventually inoculated into production medium supplemented with ethanol and glycerol as carbon and energy source to investigate for bioflocculant production. Bioflocculant production was estimated by monitoring the potential of lead tolerant bacterial isolate to flocculate Kaolin clay in presence of 1% CaCl2. Compared to other isolates, TL-3 isolate demonstrated for maximum bioflocculant activity of 95% and thus was identified based on 16S rRNA gene sequence analysis. TL3 isolate revealed maximum homology (98%) with Achromobacter sp. and thus designated as Achromobacter sp. TL-3. Bioflocculant activity of TL-3 isolate was correlated with the change in pH and growth. Achromobacter sp. TL-3 has significant potential for lead biosorption and can be effectively employed for detoxification of lead contaminated waste effluents/waste waters.

  20. Mineral Types and Tree Species Determine the Functional and Taxonomic Structures of Forest Soil Bacterial Communities.

    Science.gov (United States)

    Colin, Y; Nicolitch, O; Turpault, M-P; Uroz, S

    2017-03-01

    mineralogy influences the diversity, structure, and function of soil bacterial communities in relation to the soil conditions is crucial to better understanding the relative role of the soil bacterial communities in nutrient cycling and plant nutrition in nutrient-poor environments. The present study determined in detail the diversity and structure of bacterial communities associated with different mineral types incubated for 2.5 years in the soil under different tree species using cultivation-dependent and -independent analyses. Our data showed an enrichment of specific bacterial taxa on the minerals, specifically on the most weathered minerals, suggesting that they play key roles in mineral weathering and nutrient cycling in nutrient-poor forest ecosystems. Copyright © 2017 American Society for Microbiology.

  1. Bacterial growth rates are influenced by cellular characteristics of individual species when immersed in electromagnetic fields.

    Science.gov (United States)

    Tessaro, Lucas W E; Murugan, Nirosha J; Persinger, Michael A

    2015-03-01

    Previous studies have shown that exposure to extremely low-frequency electromagnetic fields (ELF-EMFs) have negative effects on the rate of growth of bacteria. In the present study, two Gram-positive and two Gram-negative species were exposed to six magnetic field conditions in broth cultures. Three variations of the 'Thomas' pulsed frequency-modulated pattern; a strong-static "puck" magnet upwards of 5000G in intensity; a pair of these magnets rotating opposite one another at ∼30rpm; and finally a strong dynamic magnetic field generator termed the 'Resonator' with an average intensity of 250μT were used. Growth rate was discerned by optical density (OD) measurements every hour at 600nm. ELF-EMF conditions significantly affected the rates of growth of the bacterial cultures, while the two static magnetic field conditions were not statistically significant. Most interestingly, the 'Resonator' dynamic magnetic field increased the rates of growth of three species (Staphylococcus epidermidis, Staphylococcus aureus, and Escherichia coli), while slowing the growth of one (Serratia marcescens). We suggest that these effects are due to individual biophysical characteristics of the bacterial species.

  2. Development of species-specific primers for detection of Streptococcus mutans in mixed bacterial samples

    OpenAIRE

    Chen, Zhou; Saxena, Deepak; Caufield, Page W.; Ge, Yao; Wang, Minqi; Li, Yihong

    2007-01-01

    Streptococcus mutans is the major microbial pathogen associated with dental caries in children. The objectives of this study were to design and evaluate species-specific primers for the identification of S. mutans. Validation of the best primer set, Sm479F/R, was performed using 7 S. mutans reference strains, 48 ATCC non-S. mutans strains, 92 S. mutans clinical isolates, DNA samples of S. mutans-S. sobrinus or S. mutans-S. sanguinis, and mixed bacterial DNA of saliva samples from 33 18-month-...

  3. Themes and Variations: Regulation of RpoN-Dependent Flagellar Genes across Diverse Bacterial Species

    Directory of Open Access Journals (Sweden)

    Jennifer Tsang

    2014-01-01

    Full Text Available Flagellar biogenesis in bacteria is a complex process in which the transcription of dozens of structural and regulatory genes is coordinated with the assembly of the flagellum. Although the overall process of flagellar biogenesis is conserved among bacteria, the mechanisms used to regulate flagellar gene expression vary greatly among different bacterial species. Many bacteria use the alternative sigma factor σ54 (also known as RpoN to transcribe specific sets of flagellar genes. These bacteria include members of the Epsilonproteobacteria (e.g., Helicobacter pylori and Campylobacter jejuni, Gammaproteobacteria (e.g., Vibrio and Pseudomonas species, and Alphaproteobacteria (e.g., Caulobacter crescentus. This review characterizes the flagellar transcriptional hierarchies in these bacteria and examines what is known about how flagellar gene regulation is linked with other processes including growth phase, quorum sensing, and host colonization.

  4. Individual growth detection of bacterial species in an in vitro oral polymicrobial biofilm model.

    Science.gov (United States)

    Tabenski, L; Maisch, T; Santarelli, F; Hiller, K-A; Schmalz, G

    2014-11-01

    Most in vitro studies on the antibacterial effects of antiseptics have used planktonic bacteria in monocultures. However, this study design does not reflect the in vivo situation in oral cavities harboring different bacterial species that live in symbiotic relationships in biofilms. The aim of this study was to establish a simple in vitro polymicrobial model consisting of only three bacterial strains of different phases of oral biofilm formation to simulate in vivo oral conditions. Therefore, we studied the biofilm formation of Actinomyces naeslundii (An), Fusobacterium nucleatum (Fn), and Enterococcus faecalis (Ef) on 96-well tissue culture plates under static anaerobic conditions using artificial saliva according to the method established by Pratten et al. that was supplemented with 1 g l(-1) sucrose. Growth was separately determined for each bacterial strain after incubation periods of up to 72 h by means of quantitative real-time polymerase chain reaction and live/dead staining. Presence of an extracellular polymeric substance (EPS) was visualized by Concanavalin A staining. Increasing incubation times of up to 72 h showed adhesion and propagation of the bacterial strains with artificial saliva formulation. An and Ef had significantly higher growth rates than Fn. Live/dead staining showed a median of 49.9 % (range 46.0-53.0 %) of living bacteria after 72 h of incubation, and 3D fluorescence microscopy showed a three-dimensional structure containing EPS. An in vitro oral polymicrobial biofilm model was established to better simulate oral conditions and had the advantage of providing the well-controlled experimental conditions of in vitro testing.

  5. The bacterial adhesion on and the cytotoxicity of various dental cements used for implant-supported fixed restorations.

    Science.gov (United States)

    Winkler, Cornelia; Schäfer, Lina; Felthaus, Oliver; Allerdings, Juri; Hahnel, Sebastian; Behr, Michael; Bürgers, Ralf

    2014-05-01

    Bacterial adhesion on and cytotoxicity of eight luting agents used for implant-supported restorations were investigated. Surface roughness (Ra), surface free energy (SFE) values and three-dimensional images by atomic-force microscopy of circular specimens were determined. Bacterial suspensions of Streptococcus sanguinis and Streptococcus epidermidis were incubated at 37°C for 2 h. Adhering bacteria were examined with fluorescence dye CytoX-Violet, stained with 4',6-diamidino-2-phenylindole (DAPI) and visualized by fluorescence-microscopy. Cytotoxicity-testing was done with WST-1-tests (water soluble tetrazolium). No significant differences, neither with regard to Ra nor regarding SFE were determined. Adherence of S. sanguinis was less on titanium, TempBondNE and TempBond. TempBond, TempBondNE, RelyX Unicem and Implantlink Semi Classic presented low amounts of S. epidermidis. WST-testing showed high cytotoxic potential of Harvard, Aqualox, TempBondNE and TempBond. No combination of low adherent bacteria with low cytotoxicity was found. From a biological in-vitro perspective, none of the cements may be recommended for implant-supported restorations.

  6. Responses of soil N-fixing bacteria communities to invasive plant species under different types of simulated acid deposition

    Science.gov (United States)

    Wang, Congyan; Zhou, Jiawei; Jiang, Kun; Liu, Jun; Du, Daolin

    2017-06-01

    Biological invasions have incurred serious threats to native ecosystems in China, and soil N-fixing bacteria communities (SNB) may play a vital role in the successful plant invasion. Meanwhile, anthropogenic acid deposition is increasing in China, which may modify or upgrade the effects that invasive plant species can cause on SNB. We analyzed the structure and diversity of SNB by means of new generation sequencing technology in soils with different simulated acid deposition (SAD), i.e., different SO4 2- to NO3 - ratios, and where the invasive ( Amaranthus retroflexus L.) and the native species ( Amaranthus tricolor L.) grew mixed or isolated for 3 months. A. retroflexus itself did not exert significant effects on the diversity and richness of SNB but did it under certain SO4 2- to NO3 - ratios. Compared to soils where the native species grew isolated, the soils where the invasive A. retroflexus grew isolated showed lower relative abundance of some SNB classes under certain SAD treatments. Some types of SAD can alter soil nutrient content which in turn could affect SNB diversity and abundance. Specifically, greater SO4 2- to NO3 - ratios tended to have more toxic effects on SNB likely due to the higher exchange capacity of hydroxyl groups (OH-) between SO4 2- and NO3 -. As a conclusion, it can be expected a change in the structure of SNB after A. retroflexus invasion under acid deposition rich in sulfuric acid. This change may create a plant soil feedback favoring future A. retroflexus invasions.

  7. Bacterial Species and Biochemical Characteristic Investigations of Nostoc flagelliforme Concentrates during its Storage.

    Science.gov (United States)

    Yue, Lifang; Lv, Hexin; Zhen, Jing; Jiang, Shengping; Jia, Shiru; Shen, Shigang; Gao, Lu; Dai, Yujie

    2016-04-28

    Preservation of fresh algae plays an important role in algae seed subculture and aquaculture. The determination and examination of the changes of cell viability, composition, and bacterial species during storage would help to take suitable preservation methods to prolong the preservation time of fresh algae. Nostoc flagelliforme is a kind of edible cyanobacterium with important herbal and dietary values. This article investigated the changes of bacterial species and biochemical characteristics of fresh N. flagelliforme concentrate during natural storage. It was found that the viability of cells decreased along with the storage time. Fourteen bacteria strains in the algae concentrate were identified by PCR-DGGE and were grouped into four phyla, including Cyanobacteria, Firmicutes, Proteobacteria, and Bacteroidetes. Among them, Enterococcus viikkiensis may be a concern in the preservation. Eleven volatile organic compounds were identified from N. flagelliforme cells, in which geosmin could be treated as an indicator of the freshness of N. flagelliforme. The occurrence of indole compound may be an indicator of the degradation of cells.

  8. Azospirillum fermentarium sp. nov., a nitrogen-fixing species isolated from a fermenter.

    Science.gov (United States)

    Lin, Shih-Yao; Liu, You-Cheng; Hameed, Asif; Hsu, Yi-Han; Lai, Wei-An; Shen, Fo-Ting; Young, Chiu-Chung

    2013-10-01

    An aerobic, Gram-stain-negative, spiral or rod-shaped, non-spore-forming, diazotrophic bacterium (strain CC-LY743(T)) was isolated from a fermentative tank in Taiwan. Strain CC-LY743(T) was able to grow at 20-37 °C and pH 6.0-8.0 and tolerated up to 3.0 % (w/v) NaCl. It was positive for nitrogen fixation, with activity of 10.6 nmol ethylene h(-1). 16S rRNA gene sequence analysis of strain CC-LY743(T) showed highest similarity to Azospirillum picis DSM 19922(T) (96.1 %), Azospirillum oryzae JCM 21588(T) (96.0 %) and Azospirillum rugosum DSM 19657(T) (96.0 %) and lower similarity (Azospirillum species. Highest nifH gene sequence similarities were obtained with Azospirillum brasilense BCRC 12270(T) (92.0 %), Azospirillum formosense BCRC 80273(T) (92.3 %) and A. rugosum DSM 19657(T) (91.8 %). It was positive in the rapid identification by a genus-specific primer set. The predominant quinone system was ubiquinone 10 (Q-10) and the DNA G+C content was 69.6±0.1 mol%. The major fatty acids found in strain CC-LY743(T) were n-C16 : 0, C19 : 0 cyclo ω8c, C14 : 0 3-OH/C16 : 1 iso I, C16 : 1ω7c/C16 : 1ω6c and C18 : 1ω7c/C18 : 1ω6c. Based on its phylogenetic, phenotypic and chemotaxonomic features, strain CC-LY743(T) is considered to represent a novel species within the genus Azospirillum for which the name Azospirillum fermentarium sp. nov. is proposed. The type strain is CC-LY743(T) ( = BCRC 80505(T) = JCM 18688(T) = LMG 27264(T)).

  9. Comparative genomics of non-pseudomonal bacterial species colonising paediatric cystic fibrosis patients

    Directory of Open Access Journals (Sweden)

    Kate L. Ormerod

    2015-09-01

    Full Text Available The genetic disorder cystic fibrosis is a life-limiting condition affecting ∼70,000 people worldwide. Targeted, early, treatment of the dominant infecting species, Pseudomonas aeruginosa, has improved patient outcomes; however, there is concern that other species are now stepping in to take its place. In addition, the necessarily long-term antibiotic therapy received by these patients may be providing a suitable environment for the emergence of antibiotic resistance. To investigate these issues, we employed whole-genome sequencing of 28 non-Pseudomonas bacterial strains isolated from three paediatric patients. We did not find any trend of increasing antibiotic resistance (either by mutation or lateral gene transfer in these isolates in comparison with other examples of the same species. In addition, each isolate contained a virulence gene repertoire that was similar to other examples of the relevant species. These results support the impaired clearance of the CF lung not demanding extensive virulence for survival in this habitat. By analysing serial isolates of the same species we uncovered several examples of strain persistence. The same strain of Staphylococcus aureus persisted for nearly a year, despite administration of antibiotics to which it was shown to be sensitive. This is consistent with previous studies showing antibiotic therapy to be inadequate in cystic fibrosis patients, which may also explain the lack of increasing antibiotic resistance over time. Serial isolates of two naturally multi-drug resistant organisms, Achromobacter xylosoxidans and Stenotrophomonas maltophilia, revealed that while all S. maltophilia strains were unique, A. xylosoxidans persisted for nearly five years, making this a species of particular concern. The data generated by this study will assist in developing an understanding of the non-Pseudomonas species associated with cystic fibrosis.

  10. Novel Perspectives on the Characterization of Species-Dependent Optical Signatures of Bacterial Colonies by Digital Holography.

    Science.gov (United States)

    Buzalewicz, Igor; Kujawińska, Małgorzata; Krauze, Wojciech; Podbielska, Halina

    2016-01-01

    The use of light diffraction for the microbiological diagnosis of bacterial colonies was a significant breakthrough with widespread implications for the food industry and clinical practice. We previously confirmed that optical sensors for bacterial colony light diffraction can be used for bacterial identification. This paper is focused on the novel perspectives of this method based on digital in-line holography (DIH), which is able to reconstruct the amplitude and phase properties of examined objects, as well as the amplitude and phase patterns of the optical field scattered/diffracted by the bacterial colony in any chosen observation plane behind the object from single digital hologram. Analysis of the amplitude and phase patterns inside a colony revealed its unique optical properties, which are associated with the internal structure and geometry of the bacterial colony. Moreover, on a computational level, it is possible to select the desired scattered/diffracted pattern within the entire observation volume that exhibits the largest amount of unique, differentiating bacterial features. These properties distinguish this method from the already proposed sensing techniques based on light diffraction/scattering of bacterial colonies. The reconstructed diffraction patterns have a similar spatial distribution as the recorded Fresnel patterns, previously applied for bacterial identification with over 98% accuracy, but they are characterized by both intensity and phase distributions. Our results using digital holography provide new optical discriminators of bacterial species revealed in one single step in form of new optical signatures of bacterial colonies: digital holograms, reconstructed amplitude and phase patterns, as well as diffraction patterns from all observation space, which exhibit species-dependent features. To the best of our knowledge, this is the first report on bacterial colony analysis via digital holography and our study represents an innovative approach

  11. Novel Perspectives on the Characterization of Species-Dependent Optical Signatures of Bacterial Colonies by Digital Holography.

    Directory of Open Access Journals (Sweden)

    Igor Buzalewicz

    Full Text Available The use of light diffraction for the microbiological diagnosis of bacterial colonies was a significant breakthrough with widespread implications for the food industry and clinical practice. We previously confirmed that optical sensors for bacterial colony light diffraction can be used for bacterial identification. This paper is focused on the novel perspectives of this method based on digital in-line holography (DIH, which is able to reconstruct the amplitude and phase properties of examined objects, as well as the amplitude and phase patterns of the optical field scattered/diffracted by the bacterial colony in any chosen observation plane behind the object from single digital hologram. Analysis of the amplitude and phase patterns inside a colony revealed its unique optical properties, which are associated with the internal structure and geometry of the bacterial colony. Moreover, on a computational level, it is possible to select the desired scattered/diffracted pattern within the entire observation volume that exhibits the largest amount of unique, differentiating bacterial features. These properties distinguish this method from the already proposed sensing techniques based on light diffraction/scattering of bacterial colonies. The reconstructed diffraction patterns have a similar spatial distribution as the recorded Fresnel patterns, previously applied for bacterial identification with over 98% accuracy, but they are characterized by both intensity and phase distributions. Our results using digital holography provide new optical discriminators of bacterial species revealed in one single step in form of new optical signatures of bacterial colonies: digital holograms, reconstructed amplitude and phase patterns, as well as diffraction patterns from all observation space, which exhibit species-dependent features. To the best of our knowledge, this is the first report on bacterial colony analysis via digital holography and our study represents an

  12. Both plant and bacterial nitrate reductases contribute to nitric oxide production in Medicago truncatula nitrogen-fixing nodules.

    Science.gov (United States)

    Horchani, Faouzi; Prévot, Marianne; Boscari, Alexandre; Evangelisti, Edouard; Meilhoc, Eliane; Bruand, Claude; Raymond, Philippe; Boncompagni, Eric; Aschi-Smiti, Samira; Puppo, Alain; Brouquisse, Renaud

    2011-02-01

    Nitric oxide (NO) is a signaling and defense molecule of major importance in living organisms. In the model legume Medicago truncatula, NO production has been detected in the nitrogen fixation zone of the nodule, but the systems responsible for its synthesis are yet unknown and its role in symbiosis is far from being elucidated. In this work, using pharmacological and genetic approaches, we explored the enzymatic source of NO production in M. truncatula-Sinorhizobium meliloti nodules under normoxic and hypoxic conditions. When transferred from normoxia to hypoxia, nodule NO production was rapidly increased, indicating that NO production capacity is present in functioning nodules and may be promptly up-regulated in response to decreased oxygen availability. Contrary to roots and leaves, nodule NO production was stimulated by nitrate and nitrite and inhibited by tungstate, a nitrate reductase inhibitor. Nodules obtained with either plant nitrate reductase RNA interference double knockdown (MtNR1/2) or bacterial nitrate reductase-deficient (napA) and nitrite reductase-deficient (nirK) mutants, or both, exhibited reduced nitrate or nitrite reductase activities and NO production levels. Moreover, NO production in nodules was found to be inhibited by electron transfer chain inhibitors, and nodule energy state (ATP-ADP ratio) was significantly reduced when nodules were incubated in the presence of tungstate. Our data indicate that both plant and bacterial nitrate reductase and electron transfer chains are involved in NO synthesis. We propose the existence of a nitrate-NO respiration process in nodules that could play a role in the maintenance of the energy status required for nitrogen fixation under oxygen-limiting conditions.

  13. Cheating fosters species co-existence in well-mixed bacterial communities.

    Science.gov (United States)

    Leinweber, Anne; Fredrik Inglis, R; Kümmerli, Rolf

    2017-01-06

    Explaining the enormous biodiversity observed in bacterial communities is challenging because ecological theory predicts that competition between species occupying the same niche should lead to the exclusion of less competitive community members. Competitive exclusion should be particularly strong when species compete for a single limiting resource or live in unstructured habitats that offer no refuge for weaker competitors. Here, we describe the 'cheating effect', a form of intra-specific competition that can counterbalance between-species competition, thereby fostering biodiversity in unstructured habitats. Using experimental communities consisting of the strong competitor Pseudomonas aeruginosa (PA) and its weaker counterpart Burkholderia cenocepacia (BC), we show that co-existence is impossible when the two species compete for a single limiting resource, iron. However, when introducing a PA cheating mutant, which specifically exploits the iron-scavenging siderophores produced by the PA wild type, we found that biodiversity was preserved under well-mixed conditions where PA cheats could outcompete the PA wild type. Cheating fosters biodiversity in our system because it creates strong intra-specific competition, which equalizes fitness differences between PA and BC. Our study identifies cheating - typically considered a destructive element - as a constructive force in shaping biodiversity.The ISME Journal advance online publication, 6 January 2017; doi:10.1038/ismej.2016.195.

  14. Dancing for food in the deep sea: bacterial farming by a new species of Yeti crab.

    Directory of Open Access Journals (Sweden)

    Andrew R Thurber

    Full Text Available Vent and seep animals harness chemosynthetic energy to thrive far from the sun's energy. While symbiont-derived energy fuels many taxa, vent crustaceans have remained an enigma; these shrimps, crabs, and barnacles possess a phylogenetically distinct group of chemosynthetic bacterial epibionts, yet the role of these bacteria has remained unclear. We test whether a new species of Yeti crab, which we describe as Kiwa puravida n. sp, farms the epibiotic bacteria that it grows on its chelipeds (claws, chelipeds that the crab waves in fluid escaping from a deep-sea methane seep. Lipid and isotope analyses provide evidence that epibiotic bacteria are the crab's main food source and K. puravida n. sp. has highly-modified setae (hairs on its 3(rd maxilliped (a mouth appendage which it uses to harvest these bacteria. The ε- and γ- proteobacteria that this methane-seep species farms are closely related to hydrothermal-vent decapod epibionts. We hypothesize that this species waves its arm in reducing fluid to increase the productivity of its epibionts by removing boundary layers which may otherwise limit carbon fixation. The discovery of this new species, only the second within a family described in 2005, stresses how much remains undiscovered on our continental margins.

  15. Bacterial community composition associated with freshwater algae: species specificity vs. dependency on environmental conditions and source community.

    Science.gov (United States)

    Eigemann, Falk; Hilt, Sabine; Salka, Ivette; Grossart, Hans-Peter

    2013-03-01

    We studied bacterial associations with the green alga Desmodesmus armatus and the diatom Stephanodiscus minutulus under changing environmental conditions and bacterial source communities, to evaluate whether bacteria-algae associations are species-specific or more generalized and determined by external factors. Axenic and xenic algae were incubated in situ with and without allelopathically active macrophytes, and in the laboratory with sterile and nonsterile lake water and an allelochemical, tannic acid (TA). Bacterial community composition (BCC) of algae-associated bacteria was analyzed by denaturing gradient gel electrophoresis (DGGE), nonmetric multidimensional scaling, cluster analyses, and sequencing of DGGE bands. BCC of xenic algal cultures of both species were not significantly affected by changes in their environment or bacterial source community, except in the case of TA additions. Species-specific interactions therefore appear to overrule the effects of environmental conditions and source communities. The BCC of xenic and axenic D. armatus cultures subjected to in situ bacterial colonization, however, had lower similarities (ca. 55%), indicating that bacterial precolonization is a strong factor for bacteria-algae associations irrespective of environmental conditions and source community. Our findings emphasize the ecological importance of species-specific bacteria-algae associations with important repercussions for other processes, such as the remineralization of nutrients, and organic matter dynamics. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  16. Exploring the bacterial microbiota associated with native South American species of Aphis (Hemiptera: Aphididae).

    Science.gov (United States)

    Arneodo, J D; Ortego, J

    2014-06-01

    Aphids harbor a variety of bacterial endosymbionts, including the obligate symbiont Buchnera aphidicola and diverse facultative symbionts. The former supplies its host with essential amino acids. The latter are not indispensable for insect survival, but often improve their host's fitness. To date, the study of such associations was restricted to aphids of Holarctic origin. The bacterial microbiota of seven Aphis species from Argentina was investigated. The presence of B. aphidicola was assessed by specific PCR. Additional symbionts were identified through PCR with eubacterial universal primers, cloning, and sequencing of nearly complete 16S rRNA gene, intergenic spacer region, and partial 23S rRNA gene and subjected to phylogenetic analysis. Infection with B. aphidicola was confirmed in every species analyzed. The facultative symbiont Serratia symbiotica was detected in Aphis malalhuina Mier Durante, Nieto Nafría & Ortego, 2003, Aphis senecionicoides Blanchard, 1944, and Aphis schinifoliae Blanchard, 1939, while Hamiltonella defensa was identified in Aphis mendocina Mier Durante, Ortego & Nieto Nafría, 2006. Arsenophonus sp. was found infecting Aphis melosae Mier Durante & Ortego, 1999, and a new, undescribed Aphis sp. In Aphis danielae Remaudière, 1994, no facultative symbionts could be recorded. When analyzing the highly conserved 16S rRNA gene, the phylogenetic tree grouped the S. symbiotica, H. defensa, and Arsenophonus isolates into three well-defined clusters showing little variability among clones corresponding to the same aphid host species. This article reports for the first time the endosymbionts associated with aphids native to South America. Despite their geographic origin, the qualitative composition of their microbiota revealed no evident differences from that described for aphids in the Northern Hemisphere.

  17. 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.

  18. Relationship between the Presence of Bartonella Species and Bacterial Loads in Cats and Cat Fleas (Ctenocephalides felis) under Natural Conditions.

    Science.gov (United States)

    Gutiérrez, Ricardo; Nachum-Biala, Yaarit; Harrus, Shimon

    2015-08-15

    Cats are considered the main reservoir of three zoonotic Bartonella species: Bartonella henselae, Bartonella clarridgeiae, and Bartonella koehlerae. Cat fleas (Ctenocephalides felis) have been experimentally demonstrated to be a competent vector of B. henselae and have been proposed as the potential vector of the two other Bartonella species. Previous studies have reported a lack of association between the Bartonella species infection status (infected or uninfected) and/or bacteremia levels of cats and the infection status of the fleas they host. Nevertheless, to date, no study has compared the quantitative distributions of these bacteria in both cats and their fleas under natural conditions. Thus, the present study explored these relationships by identifying and quantifying the different Bartonella species in both cats and their fleas. Therefore, EDTA-blood samples and fleas collected from stray cats were screened for Bartonella bacteria. Bacterial loads were quantified by high-resolution melt real-time quantitative PCR assays. The results indicated a moderate correlation between the Bartonella bacterial loads in the cats and their fleas when both were infected with the same Bartonella species. Moreover, a positive effect of the host infection status on the Bartonella bacterial loads of the fleas was observed. Conversely, the cat bacterial loads were not affected by the infection status of their fleas. Our results suggest that the Bartonella bacterial loads of fleas are positively affected by the presence of the bacteria in their feline host, probably by multiple acquisitions/accumulation and/or multiplication events.

  19. Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer

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    Kaul Rajinder

    2009-11-01

    Full Text Available Abstract Background Phylogeographic reconstruction of some bacterial populations is hindered by low diversity coupled with high levels of lateral gene transfer. A comparison of recombination levels and diversity at seven housekeeping genes for eleven bacterial species, most of which are commonly cited as having high levels of lateral gene transfer shows that the relative contributions of homologous recombination versus mutation for Burkholderia pseudomallei is over two times higher than for Streptococcus pneumoniae and is thus the highest value yet reported in bacteria. Despite the potential for homologous recombination to increase diversity, B. pseudomallei exhibits a relative lack of diversity at these loci. In these situations, whole genome genotyping of orthologous shared single nucleotide polymorphism loci, discovered using next generation sequencing technologies, can provide very large data sets capable of estimating core phylogenetic relationships. We compared and searched 43 whole genome sequences of B. pseudomallei and its closest relatives for single nucleotide polymorphisms in orthologous shared regions to use in phylogenetic reconstruction. Results Bayesian phylogenetic analyses of >14,000 single nucleotide polymorphisms yielded completely resolved trees for these 43 strains with high levels of statistical support. These results enable a better understanding of a separate analysis of population differentiation among >1,700 B. pseudomallei isolates as defined by sequence data from seven housekeeping genes. We analyzed this larger data set for population structure and allele sharing that can be attributed to lateral gene transfer. Our results suggest that despite an almost panmictic population, we can detect two distinct populations of B. pseudomallei that conform to biogeographic patterns found in many plant and animal species. That is, separation along Wallace's Line, a biogeographic boundary between Southeast Asia and Australia

  20. Bacterial species and their associations with acute and chronic mastitis in suckler ewes.

    Science.gov (United States)

    Smith, E M; Willis, Z N; Blakeley, M; Lovatt, F; Purdy, K J; Green, L E

    2015-10-01

    Acute mastitis in suckler ewes is often detected because of systemic signs such as anorexia or lameness, whereas chronic mastitis, characterized by intramammary abscesses with no systemic disease, is typically detected when ewes are inspected before mating. The aims of the current study were to identify the species and strains of culturable bacteria associated with acutely diseased, chronically diseased, and unaffected mammary glands to investigate whether species and strains vary by state. To investigate acute mastitis, 28 milk samples were obtained from both glands of 14 ewes with acute mastitis in one gland only. To investigate chronic mastitis, 16 ovine udders were obtained from 2 abattoirs; milk was aspirated from the 32 glands where possible, and the udders were sectioned to expose intramammary abscesses, which were swab sampled. All milk and swab samples were cultured aerobically. In total, 37 bacterial species were identified, 4 from acute mastitis, 26 from chronic mastitis, and 8 from apparently healthy glands. In chronic mastitis, the overall coincidence index of overlap of species detected in intramammary abscesses and milk was 0.60, reducing to 0.36 within individual glands, indicating a high degree of species overlap in milk and abscesses overall, but less overlap within specific glands. Staphylococcus aureus was detected frequently in all sample types; it was isolated from 10/14 glands with acute mastitis. In 5 ewes, closely related strains were present in both affected and unaffected glands. In chronic mastitis, closely related Staphylococcus aureus strains were detected in milk and abscesses from the same gland. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  1. Efficacy of two sperm preparation techniques in reducing non-specific bacterial species from human semen

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    Prabath K Abeysundara

    2013-01-01

    Full Text Available Context: Artificial reproductive techniques using seminal preparations with bacteria may cause pelvic inflammatory disease and its sequalae. Aims: To assess efficacy of two sperm preparation techniques to clear bacteria and the effect of bacteriospermia on sperm recovery rates. Settings and Design: A descriptive cross-sectional study was carried out among males of subfertile couples. Subjects and Methods: Semen samples were randomly allocated into swim-up method (group S, n = 68 and density gradient method (group D, n = 50 for sperm preparation. Seminal fluid analysis and bacterial cultures were performed in each sample before and after sperm preparation. Statistical Analysis: McNemar′s chi-squared test and independent samples t-test in SPSS version 16.0 were used. Results: Organisms were found in 86 (72.88% out of 118 samples, before sperm preparation; Streptococcus species (n = 40, 46.51% of which 14 were Group D Streptococcus species, Coagulase negative Staphylococcus species (n = 17, 19.76%, Staphylococcus aureus (n = 13, 15.11%, Coliform species (n = 11, 12.79% of which 09 were Escherichia coli and Corynebacterium species (n = 5, 5.81%. There was a statistically significant reduction of culture positive samples in raw vs. processed samples; in group S, 49 (72.05% vs. 16 (23.52% and in group D, 37 (74% vs. 18 (36%. In group S and D, mean (SD recovery rates of culture positive vs. culture negative samples were 39.44% (SD-14.02 vs. 44.22% (SD-22.38, P = 0.39 and 52.50% (SD-37.16 vs. 49.58% (SD-40.32, P = 0.82 respectively. Conclusions: Both sperm preparation methods significantly reduced bacteria in semen, but total clearance was not achieved. Sperm recovery rate was not affected by bacteriospermia.

  2. The cross-species prediction of bacterial promoters using a support vector machine.

    Science.gov (United States)

    Towsey, Michael; Timms, Peter; Hogan, James; Mathews, Sarah A

    2008-10-01

    Due to degeneracy of the observed binding sites, the in silico prediction of bacterial sigma(70)-like promoters remains a challenging problem. A large number of sigma(70)-like promoters has been biologically identified in only two species, Escherichia coli and Bacillus subtilis. In this paper we investigate the issues that arise when searching for promoters in other species using an ensemble of SVM classifiers trained on E. coli promoters. DNA sequences are represented using a tagged mismatch string kernel. The major benefit of our approach is that it does not require a prior definition of the typical -35 and -10 hexamers. This gives the SVM classifiers the freedom to discover other features relevant to the prediction of promoters. We use our approach to predict sigma(A) promoters in B. subtilis and sigma(66) promoters in Chlamydia trachomatis. We extended the analysis to identify specific regulatory features of gene sets in C. trachomatis having different expression profiles. We found a strong -35 hexamer and TGN/-10 associated with a set of early expressed genes. Our analysis highlights the advantage of using TSS-PREDICT as a starting point for predicting promoters in species where few are known.

  3. Forest soil CO2 fluxes as a function of understory removal and N-fixing species addition

    Institute of Scientific and Technical Information of China (English)

    Haifang Li; Shenglei Fu; Hongting Zhao; Hanping Xia

    2011-01-01

    We report on the effects of forest management practices of understory removal and N-fixing species (Cassia alata) addition on soil CO2 fluxes in an Eucalyptus urophylla plantation (EUp), Acacia crassicarpa plantation (ACp), 10-species-mixed plantation (Tp), and 30-species-mixed plantation (THp) using the static chamber method in southern China. Four forest management treatments, including (1) understory removal (UR); (2) C. alata addition (CA); (3) understory removal and replacement with C. alata (UR+CA); and (4)control without any disturbances (CK), were applied in the above four forest plantations with three replications for each treatment.The results showed that soil CO2 fluxes rates remained at a high level during the rainy season (from April to September), followed by a rapid decrease after October reaching a minimum in February. Soil CO2 fluxes were significantly higher (P < 0.01) in EUp (132.6 mg/(m2·hr)) and ACp (139.8 mg/(m2·hr)) than in Tp (94.0 mg/(m2·hr)) and THp (102.9 mg/(m2·hr)). Soil CO2 fluxes in UR and CA were significantly higher (P < 0.01) among the four treatments, with values of 105.7, 120.4, 133.6 and 112.2 mg/(m2·hr) for UR+CA,UR, CA and CK, respectively. Soil CO2 fluxes were positively correlated with soil temperature (P < 0.01), soil moisture (P < 0.01),NO3--N (P < 0.05), and litterfall (P < 0.01), indicating that all these factors might be important controlling variables for soil CO2 fluxes. This study sheds some light on our understanding of soil CO2 flux dynamics in forest plantations under various management practices.

  4. Biomarkers for Tuberculosis Based on Secreted, Species-Specific, Bacterial Small Molecules.

    Science.gov (United States)

    Pan, Shih-Jung; Tapley, Asa; Adamson, John; Little, Tessa; Urbanowski, Michael; Cohen, Keira; Pym, Alexander; Almeida, Deepak; Dorasamy, Afton; Layre, Emilie; Young, David C; Singh, Ravesh; Patel, Vinod B; Wallengren, Kristina; Ndung'u, Thumbi; Wilson, Douglas; Moody, D Branch; Bishai, William

    2015-12-01

    Improved biomarkers are needed for tuberculosis. To develop tests based on products secreted by tubercle bacilli that are strictly associated with viability, we evaluated 3 bacterial-derived, species-specific, small molecules as biomarkers: 2 mycobactin siderophores and tuberculosinyladenosine. Using liquid chromatography-tandem mass spectrometry, we demonstrated the presence of 1 or both mycobactins and/or tuberculosinyladenosine in serum and whole lung tissues from infected mice and sputum, cerebrospinal fluid (CSF), or lymph nodes from infected patients but not uninfected controls. Detection of the target molecules distinguished host infection status in 100% of mice with both serum and lung as the target sample. In human subjects, we evaluated detection of the bacterial small molecules (BSMs) in multiple body compartments in 3 patient cohorts corresponding to different forms of tuberculosis. We detected at least 1 of the 3 molecules in 90%, 71%, and 40% of tuberculosis patients' sputum, CSF, and lymph node samples, respectively. In paucibacillary forms of human tuberculosis, which are difficult to diagnose even with culture, detection of 1 or more BSM was rapid and compared favorably to polymerase chain reaction-based detection. Secreted BSMs, detectable in serum, warrant further investigation as a means for diagnosis and therapeutic monitoring in patients with tuberculosis.

  5. Species Specific Bacterial Spore Detection Using Lateral-Flow Immunoassay with DPA-Triggered Tb Luminescence

    Science.gov (United States)

    Ponce, Adrian

    2003-01-01

    A method of detecting bacterial spores incorporates (1) A method of lateral-flow immunoassay in combination with (2) A method based on the luminescence of Tb3+ ions to which molecules of dipicolinic acid (DPA) released from the spores have become bound. The present combination of lateral-flow immunoassay and DPA-triggered Tb luminescence was developed as a superior alternative to a prior lateral-flow immunoassay method in which detection involves the visual observation and/or measurement of red light scattered from colloidal gold nanoparticles. The advantage of the present combination method is that it affords both (1) High selectivity for spores of the species of bacteria that one seeks to detect (a characteristic of lateral-flow immunoassay in general) and (2) Detection sensitivity much greater (by virtue of the use of DPA-triggered Tb luminescence instead of gold nanoparticles) than that of the prior lateral-flow immunoassay method

  6. Multi-species bacterial biofilm and intracellular infection in otitis media

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    Thornton Ruth B

    2011-10-01

    Full Text Available Abstract Background Bacteria which are metabolically active yet unable to be cultured and eradicated by antibiotic treatment are present in the middle ear effusion of children with chronic otitis media with effusion (COME and recurrent acute otitis media (rAOM. These observations are suggestive of biofilm presence or intracellular sequestration of bacteria and may play a role in OM pathogenesis. The aim of this project is to provide evidence for the presence of otopathogenic bacteria intracellularly or within biofilm in the middle ear mucosa of children with COME or rAOM. Methods Middle ear mucosal biopsies from 20 children with COME or rAOM were examined for otopathogenic bacteria (either in biofilm or located intracellularly using transmission electron microscopy (TEM or species specific fluorescent in situ hybridisation (FISH and confocal laser scanning microscopy (CLSM. One healthy control biopsy from a child undergoing cochlear implant surgery was also examined. Results No bacteria were observed in the healthy control sample. In 2 of the 3 biopsies imaged using TEM, bacteria were observed in mucus containing vacuoles within epithelial cells. Bacterial species within these could not be identified and biofilm was not observed. Using FISH with CLSM, bacteria were seen in 15 of the 17 otitis media mucosal specimens. In this group, 11 (65% of the 17 middle ear mucosal biopsies showed evidence of bacterial biofilm and 12 demonstrated intracellular bacteria. 52% of biopsies were positive for both biofilm and intracellular bacteria. At least one otopathogen was identified in 13 of the 15 samples where bacteria were present. No differences were observed between biopsies from children with COME and those with rAOM. Conclusion Using FISH and CLSM, bacterial biofilm and intracellular infection with known otopathogens are demonstrated on/in the middle ear mucosa of children with COME and/or rAOM. While their role in disease pathogenesis remains to be

  7. Nitrogen Mineralization of Prunings of Six N2-Fixing Hedgerow Species in a Dry Valley of the Jinsha River

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    A litterbag experiment of 12 weeks was conducted to study nitrogen mineralization process of prunings of six nitrogen-fixing hedgerow species in a dry valley of the Jinsha River. Prunings were incorporated into soil or used as mulch. The results indicated that pruning N of the six hedgerow species was mineralized fast in the first week and then decreased slowly in the rest of the study period. When prunings were incorporated into soil, the amount of nitrogen mineralized by the end of the first week accounted for 69.9%, 58.2%, 54.5%,43.0%, 29.6% and 20.6% of the total N in prunings of Desmodium rensonii, Tephrosia candida, Leucaena leucocuphala, Albizia yunnanensis, Acacia dealbata, and Acacia mearnsii, respectively. When prunings of L. leucocephala were used as mulch materials, the amount of nitrogen mineralized in the first week was 16.2% less than that of prunings incorporated into soil. The mineralization pattern of pruning N could be simulated by an exponent model Nt% = N01% (1 - exp(-k1t))+ N02% (1 - exp(-k2t)) where Nt% is cumulative mineralized N in time t, N01% and N02 % are readily and less readily mineralizable N in prunings,respectively, and k1 and k2 are rate constants. A half-life period of pruning nitrogen mineralization could ~ be determined by this model. The nitrogen content in the pruning residues decreased quickly in the first week but fluctuated thereafter. The initial C/N ratio was negatively related to the mineralization rate of prunings.``

  8. Comparative Genomics of Facultative Bacterial Symbionts Isolated from European Orius Species Reveals an Ancestral Symbiotic Association

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    Xiaorui Chen

    2017-10-01

    Full Text Available Pest control in agriculture employs diverse strategies, among which the use of predatory insects has steadily increased. The use of several species within the genus Orius in pest control is widely spread, particularly in Mediterranean Europe. Commercial mass rearing of predatory insects is costly, and research efforts have concentrated on diet manipulation and selective breeding to reduce costs and improve efficacy. The characterisation and contribution of microbial symbionts to Orius sp. fitness, behaviour, and potential impact on human health has been neglected. This paper provides the first genome sequence level description of the predominant culturable facultative bacterial symbionts associated with five Orius species (O. laevigatus, O. niger, O. pallidicornis, O. majusculus, and O. albidipennis from several geographical locations. Two types of symbionts were broadly classified as members of the genera Serratia and Leucobacter, while a third constitutes a new genus within the Erwiniaceae. These symbionts were found to colonise all the insect specimens tested, which evidenced an ancestral symbiotic association between these bacteria and the genus Orius. Pangenome analyses of the Serratia sp. isolates offered clues linking Type VI secretion system effector–immunity proteins from the Tai4 sub-family to the symbiotic lifestyle.

  9. Influences of Plant Species, Season and Location on Leaf Endophytic Bacterial Communities of Non-Cultivated Plants.

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    Tao Ding

    Full Text Available Bacteria are known to be associated endophytically with plants. Research on endophytic bacteria has identified their importance in food safety, agricultural production and phytoremediation. However, the diversity of endophytic bacterial communities and the forces that shape their compositions in non-cultivated plants are largely uncharacterized. In this study, we explored the diversity, community structure, and dynamics of endophytic bacteria in different plant species in the Tallgrass Prairie Preserve of northern Oklahoma, USA. High throughput sequencing of amplified segments of bacterial rDNA from 81 samples collected at four sampling times from five plant species at four locations identified 335 distinct OTUs at 97% sequence similarity, representing 16 phyla. Proteobacteria was the dominant phylum in the communities, followed by the phyla Bacteriodetes and Actinobacteria. Bacteria from four classes of Proteobacteria were detected with Alphaproteobacteria as the dominant class. Analysis of molecular variance revealed that host plant species and collecting date had significant influences on the compositions of the leaf endophytic bacterial communities. The proportion of Alphaproteobacteria was much higher in the communities from Asclepias viridis than from other plant species and differed from month to month. The most dominant bacterial groups identified in LDA Effect Size analysis showed host-specific patterns, indicating mutual selection between host plants and endophytic bacteria and that leaf endophytic bacterial compositions were dynamic, varying with the host plant's growing season in three distinct patterns. In summary, next generation sequencing has revealed variations in the taxonomic compositions of leaf endophytic bacterial communities dependent primarily on the nature of the plant host species.

  10. Influences of Plant Species, Season and Location on Leaf Endophytic Bacterial Communities of Non-Cultivated Plants.

    Science.gov (United States)

    Ding, Tao; Melcher, Ulrich

    2016-01-01

    Bacteria are known to be associated endophytically with plants. Research on endophytic bacteria has identified their importance in food safety, agricultural production and phytoremediation. However, the diversity of endophytic bacterial communities and the forces that shape their compositions in non-cultivated plants are largely uncharacterized. In this study, we explored the diversity, community structure, and dynamics of endophytic bacteria in different plant species in the Tallgrass Prairie Preserve of northern Oklahoma, USA. High throughput sequencing of amplified segments of bacterial rDNA from 81 samples collected at four sampling times from five plant species at four locations identified 335 distinct OTUs at 97% sequence similarity, representing 16 phyla. Proteobacteria was the dominant phylum in the communities, followed by the phyla Bacteriodetes and Actinobacteria. Bacteria from four classes of Proteobacteria were detected with Alphaproteobacteria as the dominant class. Analysis of molecular variance revealed that host plant species and collecting date had significant influences on the compositions of the leaf endophytic bacterial communities. The proportion of Alphaproteobacteria was much higher in the communities from Asclepias viridis than from other plant species and differed from month to month. The most dominant bacterial groups identified in LDA Effect Size analysis showed host-specific patterns, indicating mutual selection between host plants and endophytic bacteria and that leaf endophytic bacterial compositions were dynamic, varying with the host plant's growing season in three distinct patterns. In summary, next generation sequencing has revealed variations in the taxonomic compositions of leaf endophytic bacterial communities dependent primarily on the nature of the plant host species.

  11. MOSAIC: an online database dedicated to the comparative genomics of bacterial strains at the intra-species level.

    Science.gov (United States)

    Chiapello, Hélène; Gendrault, Annie; Caron, Christophe; Blum, Jérome; Petit, Marie-Agnès; El Karoui, Meriem

    2008-11-27

    The recent availability of complete sequences for numerous closely related bacterial genomes opens up new challenges in comparative genomics. Several methods have been developed to align complete genomes at the nucleotide level but their use and the biological interpretation of results are not straightforward. It is therefore necessary to develop new resources to access, analyze, and visualize genome comparisons. Here we present recent developments on MOSAIC, a generalist comparative bacterial genome database. This database provides the bacteriologist community with easy access to comparisons of complete bacterial genomes at the intra-species level. The strategy we developed for comparison allows us to define two types of regions in bacterial genomes: backbone segments (i.e., regions conserved in all compared strains) and variable segments (i.e., regions that are either specific to or variable in one of the aligned genomes). Definition of these segments at the nucleotide level allows precise comparative and evolutionary analyses of both coding and non-coding regions of bacterial genomes. Such work is easily performed using the MOSAIC Web interface, which allows browsing and graphical visualization of genome comparisons. The MOSAIC database now includes 493 pairwise comparisons and 35 multiple maximal comparisons representing 78 bacterial species. Genome conserved regions (backbones) and variable segments are presented in various formats for further analysis. A graphical interface allows visualization of aligned genomes and functional annotations. The MOSAIC database is available online at http://genome.jouy.inra.fr/mosaic.

  12. The pneumococcal serine-rich repeat protein is an intra-species bacterial adhesin that promotes bacterial aggregation in vivo and in biofilms.

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    Carlos J Sanchez

    Full Text Available The Pneumococcal serine-rich repeat protein (PsrP is a pathogenicity island encoded adhesin that has been positively correlated with the ability of Streptococcus pneumoniae to cause invasive disease. Previous studies have shown that PsrP mediates bacterial attachment to Keratin 10 (K10 on the surface of lung cells through amino acids 273-341 located in the Basic Region (BR domain. In this study we determined that the BR domain of PsrP also mediates an intra-species interaction that promotes the formation of large bacterial aggregates in the nasopharynx and lungs of infected mice as well as in continuous flow-through models of mature biofilms. Using numerous methods, including complementation of mutants with BR domain deficient constructs, fluorescent microscopy with Cy3-labeled recombinant (rBR, Far Western blotting of bacterial lysates, co-immunoprecipitation with rBR, and growth of biofilms in the presence of antibodies and competitive peptides, we determined that the BR domain, in particular amino acids 122-166 of PsrP, promoted bacterial aggregation and that antibodies against the BR domain were neutralizing. Using similar methodologies, we also determined that SraP and GspB, the Serine-rich repeat proteins (SRRPs of Staphylococcus aureus and Streptococcus gordonii, respectively, also promoted bacterial aggregation and that their Non-repeat domains bound to their respective SRRPs. This is the first report to show the presence of biofilm-like structures in the lungs of animals infected with S. pneumoniae and show that SRRPs have dual roles as host and bacterial adhesins. These studies suggest that recombinant Non-repeat domains of SRRPs (i.e. BR for S. pneumoniae may be useful as vaccine antigens to protect against Gram-positive bacteria that cause infection.

  13. Diversification of nitrogen fixing bacterial community using nifH gene as a biomarker in different geographical soils of Western Indian Himalayas.

    Science.gov (United States)

    Singh, Chhug; Soni, Ravindra; Jain, Sourabh; Roy, Subhadip; Goel, Reeta

    2010-09-01

    Six soil samples (Pantnagar, Chamoli, Almora, Ranichauri, Pithoragarh and Badrinath) belonging to different geographical locations of Western Himalayas in India, were analyzed to diversify the nitrogen fixing bacterial community using nifH gene biomarker DNA from soil samples were isolated and amplified using nifH gene specific primers. Genomic DNA and PCR amplified products were then individually subjected to restriction digestion with tetra to octacutter enzymes (AluI, MspI, BgIII, XbaI, HindIII, HaeIII, AluI, MspI and PasI. Further restriction pattern was studied by preparing dendograms on the basis of similarity matrix and compared for the nifH community. It was observed that temperate region soils (Ranichauri and Pithoragarh) were negative for nifH marker while subalpine region (Badrinath) and tarai region soils (Pantnagar) documented similar nifH community. Moreover; the direct genomic DNA restriction analysis indicated that subalpine region soil (Badrinath) was most diversified.

  14. Host species and environmental effects on bacterial communities associated with Drosophila in the laboratory and in the natural environment.

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    Fabian Staubach

    Full Text Available The fruit fly Drosophila is a classic model organism to study adaptation as well as the relationship between genetic variation and phenotypes. Although associated bacterial communities might be important for many aspects of Drosophila biology, knowledge about their diversity, composition, and factors shaping them is limited. We used 454-based sequencing of a variable region of the bacterial 16S ribosomal RNA gene to characterize the bacterial communities associated with wild and laboratory Drosophila isolates. In order to specifically investigate effects of food source and host species on bacterial communities, we analyzed samples from wild Drosophila melanogaster and D. simulans collected from a variety of natural substrates, as well as from adults and larvae of nine laboratory-reared Drosophila species. We find no evidence for host species effects in lab-reared flies; instead, lab of origin and stochastic effects, which could influence studies of Drosophila phenotypes, are pronounced. In contrast, the natural Drosophila-associated microbiota appears to be predominantly shaped by food substrate with an additional but smaller effect of host species identity. We identify a core member of this natural microbiota that belongs to the genus Gluconobacter and is common to all wild-caught flies in this study, but absent from the laboratory. This makes it a strong candidate for being part of what could be a natural D. melanogaster and D. simulans core microbiome. Furthermore, we were able to identify candidate pathogens in natural fly isolates.

  15. Evidence of novel plant-species specific ammonia oxidizing bacterial clades in acidic South African fynbos soils

    CSIR Research Space (South Africa)

    Ramond, JB

    2015-02-01

    Full Text Available -1 Journal of Basic Microbiology Evidence of novel plant-species specific ammonia oxidizing bacterial clades in acidic South African fynbos soils Jean-Baptiste Ramond1, Joseph D. W. Lako2, William H. L. Stafford3, Marla I. Tuffin4 and Don A. Cowan1...

  16. Diversity and localization of bacterial symbionts in three whitefly species (Hemiptera: Aleyrodidae) from the east coast of the Adriatic Sea.

    Science.gov (United States)

    Skaljac, M; Zanić, K; Hrnčić, S; Radonjić, S; Perović, T; Ghanim, M

    2013-02-01

    Several whitefly species (Hemiptera: Aleyrodidae) are cosmopolitan phloem-feeders that cause serious damage in numerous agricultural crops. All whitefly species harbor a primary bacterial symbiont and a diverse array of secondary symbionts which may influence several aspects of the insect's biology. We surveyed infections by secondary symbionts in Bemisia tabaci (Gennadius), Trialeurodes vaporariorum (Westwood) and Siphoninus phillyreae (Haliday) from areas in the east cost of the Adriatic Sea. Both the Middle East-Asia Minor 1 (MEAM1) and Mediterranean (MED) B. tabaci genetic groups were detected in Montenegro, whereas only the MED was confirmed in Croatia. Trialeurodes vaporariorum and S. phillyreae were found in all areas surveyed. MEAM1 and MED exhibited similarity to previously reported infections, while populations of T. vaporariorum from Montenegro harbored Rickettsia, Wolbachia and Cardinium in addition to previously reported Hamiltonella and Arsenopnohus. Siphoninus phillyreae harbored Hamiltonella, Wolbachia, Cardinium and Arsenophonus, with the latter appearing in two alleles. Multiple infections of all symbionts were common in the three insect species tested, with some reaching near fixation. Florescent in situ hybridization showed new localization patterns for Hamiltonella in S. phillyreae, and the morphology of the bacteriosome differed from that observed in other whitefly species. Our results show new infections with bacterial symbionts in the whitefly species studied. Infections with the same symbionts in reproductively isolated whitefly species confirm complex relationships between whiteflies and bacterial symbionts, and suggest possible horizontal transfer of some of these bacteria.

  17. Insights into the history of a bacterial group II intron remnant from the genomes of the nitrogen-fixing symbionts Sinorhizobium meliloti and Sinorhizobium medicae.

    Science.gov (United States)

    Toro, N; Martínez-Rodríguez, L; Martínez-Abarca, F

    2014-10-01

    Group II introns are self-splicing catalytic RNAs that act as mobile retroelements. In bacteria, they are thought to be tolerated to some extent because they self-splice and home preferentially to sites outside of functional genes, generally within intergenic regions or in other mobile genetic elements, by mechanisms including the divergence of DNA target specificity to prevent target site saturation. RmInt1 is a mobile group II intron that is widespread in natural populations of Sinorhizobium meliloti and was first described in the GR4 strain. Like other bacterial group II introns, RmInt1 tends to evolve toward an inactive form by fragmentation, with loss of the 3' terminus. We identified genomic evidence of a fragmented intron closely related to RmInt1 buried in the genome of the extant S. meliloti/S. medicae species. By studying this intron, we obtained evidence for the occurrence of intron insertion before the divergence of ancient rhizobial species. This fragmented group II intron has thus existed for a long time and has provided sequence variation, on which selection can act, contributing to diverse genetic rearrangements, and to generate pan-genome divergence after strain differentiation. The data presented here suggest that fragmented group II introns within intergenic regions closed to functionally important neighboring genes may have been microevolutionary forces driving adaptive evolution of these rhizobial species.

  18. Tree phyllosphere bacterial communities: exploring the magnitude of intra- and inter-individual variation among host species

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    Isabelle Laforest-Lapointe

    2016-08-01

    Full Text Available Background The diversity and composition of the microbial community of tree leaves (the phyllosphere varies among trees and host species and along spatial, temporal, and environmental gradients. Phyllosphere community variation within the canopy of an individual tree exists but the importance of this variation relative to among-tree and among-species variation is poorly understood. Sampling techniques employed for phyllosphere studies include picking leaves from one canopy location to mixing randomly selected leaves from throughout the canopy. In this context, our goal was to characterize the relative importance of intra-individual variation in phyllosphere communities across multiple species, and compare this variation to inter-individual and interspecific variation of phyllosphere epiphytic bacterial communities in a natural temperate forest in Quebec, Canada. Methods We targeted five dominant temperate forest tree species including angiosperms and gymnosperms: Acer saccharum, Acer rubrum, Betula papyrifera, Abies balsamea and Picea glauca. For one randomly selected tree of each species, we sampled microbial communities at six distinct canopy locations: bottom-canopy (1–2 m height, the four cardinal points of mid-canopy (2–4 m height, and the top-canopy (4–6 m height. We also collected bottom-canopy leaves from five additional trees from each species. Results Based on an analysis of bacterial community structure measured via Illumina sequencing of the bacterial 16S gene, we demonstrate that 65% of the intra-individual variation in leaf bacterial community structure could be attributed to the effect of inter-individual and inter-specific differences while the effect of canopy location was not significant. In comparison, host species identity explains 47% of inter-individual and inter-specific variation in leaf bacterial community structure followed by individual identity (32% and canopy location (6%. Discussion Our results suggest that

  19. Clostridium algifaecis sp. nov., an anaerobic bacterial species from decomposing algal scum.

    Science.gov (United States)

    Wu, Yu-Fan; Zheng, Hui; Wu, Qing-Long; Yang, Hong; Liu, Shuang-Jiang

    2014-11-01

    Two anaerobic bacterial strains, MB9-7(T) and MB9-9, were isolated from decomposing algal scum and were characterized using a polyphasic approach. Phylogenetic analysis of 16S rRNA gene sequences showed that strains MB9-7(T) and MB9-9 are closely related to each other (99.7% similarity) and they are also closely related to Clostridium tyrobutyricum (96.5%). The two strains were Gram-stain positive and rod-shaped. Growth occurred at 20-45 °C, at pH 4.0-8.0 and at NaCl concentrations of up to 2% (w/v). Acid was produced from glucose, xylose and mannose. Products of fermentation in PYG medium were mainly butyrate, acetate, carbon dioxide and hydrogen. The predominant cellular fatty acids were C(14:0) and C(16:0). The cellular polar lipids comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, two glycolipids, one phospholipid, one aminophospholipid and two aminolipids. The DNA G+C contents of strain MB9-7(T) and MB9-9 were 27.9 and 28.7 mol%, respectively. These results support the assignment of the new isolates to the genus Clostridium and also distinguish them from other species of the genus Clostridium. Hence, it is proposed that strains MB9-7(T) and MB9-9 represent a novel species of the genus Clostridium, with the suggested name Clostridium algifaecis sp. nov. The type strain is MB9-7(T) ( =CGMCC 1.5188(T) =DSM 28783(T)).

  20. Bacterial Profiling Reveals Novel "Ca. Neoehrlichia", Ehrlichia, and Anaplasma Species in Australian Human-Biting Ticks.

    Science.gov (United States)

    Gofton, Alexander W; Doggett, Stephen; Ratchford, Andrew; Oskam, Charlotte L; Paparini, Andrea; Ryan, Una; Irwin, Peter

    2015-01-01

    In Australia, a conclusive aetiology of Lyme disease-like illness in human patients remains elusive, despite growing numbers of people presenting with symptoms attributed to tick bites. In the present study, we surveyed the microbial communities harboured by human-biting ticks from across Australia to identify bacteria that may contribute to this syndrome. Universal PCR primers were used to amplify the V1-2 hyper-variable region of bacterial 16S rRNA genes in DNA samples from individual Ixodes holocyclus (n = 279), Amblyomma triguttatum (n = 167), Haemaphysalis bancrofti (n = 7), and H. longicornis (n = 7) ticks. The 16S amplicons were sequenced on the Illumina MiSeq platform and analysed in USEARCH, QIIME, and BLAST to assign genus and species-level taxonomies. Nested PCR and Sanger sequencing were used to confirm the NGS data and further analyse novel findings. All 460 ticks were negative for Borrelia spp. by both NGS and nested PCR analysis. Two novel "Candidatus Neoehrlichia" spp. were identified in 12.9% of I. holocyclus ticks. A novel Anaplasma sp. was identified in 1.8% of A. triguttatum ticks, and a novel Ehrlichia sp. was identified in both A. triguttatum (1.2%) ticks and a single I. holocyclus (0.6%) tick. Further phylogenetic analysis of novel "Ca. Neoehrlichia", Anaplasma and Ehrlichia based on 1,265 bp 16S rRNA gene sequences suggests that these are new species. Determining whether these newly discovered organisms cause disease in humans and animals, like closely related bacteria do abroad, is of public health importance and requires further investigation.

  1. Bacterial Profiling Reveals Novel "Ca. Neoehrlichia", Ehrlichia, and Anaplasma Species in Australian Human-Biting Ticks.

    Directory of Open Access Journals (Sweden)

    Alexander W Gofton

    Full Text Available In Australia, a conclusive aetiology of Lyme disease-like illness in human patients remains elusive, despite growing numbers of people presenting with symptoms attributed to tick bites. In the present study, we surveyed the microbial communities harboured by human-biting ticks from across Australia to identify bacteria that may contribute to this syndrome. Universal PCR primers were used to amplify the V1-2 hyper-variable region of bacterial 16S rRNA genes in DNA samples from individual Ixodes holocyclus (n = 279, Amblyomma triguttatum (n = 167, Haemaphysalis bancrofti (n = 7, and H. longicornis (n = 7 ticks. The 16S amplicons were sequenced on the Illumina MiSeq platform and analysed in USEARCH, QIIME, and BLAST to assign genus and species-level taxonomies. Nested PCR and Sanger sequencing were used to confirm the NGS data and further analyse novel findings. All 460 ticks were negative for Borrelia spp. by both NGS and nested PCR analysis. Two novel "Candidatus Neoehrlichia" spp. were identified in 12.9% of I. holocyclus ticks. A novel Anaplasma sp. was identified in 1.8% of A. triguttatum ticks, and a novel Ehrlichia sp. was identified in both A. triguttatum (1.2% ticks and a single I. holocyclus (0.6% tick. Further phylogenetic analysis of novel "Ca. Neoehrlichia", Anaplasma and Ehrlichia based on 1,265 bp 16S rRNA gene sequences suggests that these are new species. Determining whether these newly discovered organisms cause disease in humans and animals, like closely related bacteria do abroad, is of public health importance and requires further investigation.

  2. Antibiofilm Activity, Compound Characterization, and Acute Toxicity of Extract from a Novel Bacterial Species of Paenibacillus

    Directory of Open Access Journals (Sweden)

    Saad Musbah Alasil

    2014-01-01

    Full Text Available The effectiveness of many antimicrobial agents is currently decreasing; therefore, it is important to search for alternative therapeutics. Our study was carried out to assess the in vitro antibiofilm activity using microtiter plate assay, to characterize the bioactive compounds using Ultra Performance Liquid Chromatography-Diode Array Detection and Liquid Chromatography-Mass Spectrometry and to test the oral acute toxicity on Sprague Dawley rats of extract derived from a novel bacterial species of Paenibacillus strain 139SI. Our results indicate that the crude extract and its three identified compounds exhibit strong antibiofilm activity against a broad range of clinically important pathogens. Three potential compounds were identified including an amino acid antibiotic C8H20N3O4P (MW 253.237, phospholipase A2 inhibitor C21H36O5 (MW 368.512, and an antibacterial agent C14H11N3O2 (MW 253.260. The acute toxicity test indicates that the mortality rate among all rats was low and that the biochemical parameters, hematological profile, and histopathology examination of liver and kidneys showed no significant differences between experimental groups P>0.05. Overall, our findings suggest that the extract and its purified compounds derived from novel Paenibacillus sp. are nontoxic exhibiting strong antibiofilm activity against Gram-positive and Gram-negative pathogens that can be useful towards new therapeutic management of biofilm-associated infections.

  3. Cooperative role for tetraspanins in adhesin-mediated attachment of bacterial species to human epithelial cells.

    Science.gov (United States)

    Green, Luke R; Monk, Peter N; Partridge, Lynda J; Morris, Paul; Gorringe, Andrew R; Read, Robert C

    2011-06-01

    The tetraspanins are a superfamily of transmembrane proteins with diverse functions and can form extended microdomains within the plasma membrane in conjunction with partner proteins, which probably includes receptors for bacterial adhesins. Neisseria meningitidis, the causative agent of meningococcal disease, attaches to host nasopharyngeal epithelial cells via type IV pili and opacity (Opa) proteins. We examined the role of tetraspanin function in Neisseria meningitidis adherence to epithelial cells. Tetraspanins CD9, CD63, and CD151 were expressed by HEC-1-B and DETROIT 562 cells. Coincubation of cells with antibodies against all three tetraspanin molecules used individually or in combination, with recombinant tetraspanin extracellular domains (EC2), or with small interfering RNAs (siRNAs) significantly reduced adherence of Neisseria meningitidis. In contrast, recombinant CD81, a different tetraspanin, had no effect on meningococcal adherence. Antitetraspanin antibodies reduced the adherence to epithelial cells of Neisseria meningitidis strain derivatives expressing Opa and pili significantly more than isogenic strains lacking these determinants. Adherence to epithelial cells of strains of Staphylococcus aureus, Neisseria lactamica, Escherichia coli, and Streptococcus pneumoniae was also reduced by pretreatment of cells with tetraspanin antibodies and recombinant proteins. These data suggest that tetraspanins are required for optimal function of epithelial adhesion platforms containing specific receptors for Neisseria meningitidis and potentially for multiple species of bacteria.

  4. Burkholderia caballeronis sp. nov., a nitrogen fixing species isolated from tomato (Lycopersicon esculentum) with the ability to effectively nodulate Phaseolus vulgaris.

    Science.gov (United States)

    Martínez-Aguilar, Lourdes; Salazar-Salazar, Corelly; Méndez, Rafael Díaz; Caballero-Mellado, Jesús; Hirsch, Ann M; Vásquez-Murrieta, María Soledad; Estrada-de los Santos, Paulina

    2013-12-01

    During a survey of Burkholderia species with potential use in agrobiotechnology, a group of 12 strains was isolated from the rhizosphere and rhizoplane of tomato plants growing in Mexico (Nepantla, Mexico State). A phylogenetic analysis of 16S rRNA gene sequences showed that the strains are related to Burkholderia kururiensis and Burkholderia mimosarum (97.4 and 97.1 %, respectively). However, they induced effective nitrogen-fixing nodules on roots of Phaseolus vulgaris. Based on polyphasic taxonomy, the group of strains represents a novel species for which the name Burkholderia caballeronis sp. nov. is proposed. The type species is TNe-841(T) (= LMG 26416(T) = CIP 110324(T)).

  5. Influence of fluoride on the bacterial composition of a dual-species biofilm composed of Streptococcus mutans and Streptococcus oralis.

    Science.gov (United States)

    Jung, Ji-Eun; Cai, Jian-Na; Cho, Sung-Dae; Song, Kwang-Yeob; Jeon, Jae-Gyu

    2016-10-01

    Despite the widespread use of fluoride for the prevention of dental caries, few studies have demonstrated the effects of fluoride on the bacterial composition of dental biofilms. This study investigated whether fluoride affects the proportion of Streptococcus mutans and S. oralis in mono- and dual-species biofilm models, via microbiological, biochemical, and confocal fluorescence microscope studies. Fluoride did not affect the bacterial count and bio-volume of S. mutans and S. oralis in mono-species biofilms, except for the 24-h-old S. mutans biofilms. However, fluoride reduced the proportion and bio-volume of S. mutans but did not decrease those of S. oralis during both S. oralis and S. mutans dual-species biofilm formation, which may be related to the decrease in extracellular polysaccharide formation by fluoride. These results suggest that fluoride may prevent the shift in the microbial proportion to cariogenic bacteria in dental biofilms, subsequently inhibiting the cariogenic bacteria dominant biofilm formation.

  6. Composition of the Cutaneous Bacterial Community in Japanese Amphibians: Effects of Captivity, Host Species, and Body Region.

    Science.gov (United States)

    Sabino-Pinto, Joana; Bletz, Molly Catherine; Islam, Mohammed Mafizul; Shimizu, Norio; Bhuju, Sabin; Geffers, Robert; Jarek, Michael; Kurabayashi, Atsushi; Vences, Miguel

    2016-08-01

    The cutaneous microbiota plays a significant role in the biology of their vertebrate hosts, and its composition is known to be influenced both by host and environment, with captive conditions often altering alpha diversity. Here, we compare the cutaneous bacterial communities of 61 amphibians (both wild and captive) from Hiroshima, Japan, using high-throughput amplicon sequencing of a segment of the 16S rRNA gene. The majority of these samples came from a captive breeding facility at Hiroshima University where specimens from six species are maintained under highly standardized conditions for several generations. This allowed to identify host effects on the bacterial communities under near identical environmental conditions in captivity. We found the structure of the cutaneous bacterial community significantly differing between wild and captive individuals of newts, Cynops pyrrhogaster, with a higher alpha diversity found in the wild individuals. Community structure also showed distinct patterns when comparing different species of amphibians kept under highly similar conditions, revealing an intrinsic host effect. Bacterial communities of dorsal vs. ventral skin surfaces did not significantly differ in most species, but a trend of higher alpha diversity on the ventral surface was found in Oriental fire-bellied toads, Bombina orientalis. This study confirms the cutaneous microbiota of amphibians as a highly dynamic system influenced by a complex interplay of numerous factors.

  7. Effect of Initial pH on Sulphate and Phosphate Uptake from Wastewater by Selected Bacterial and Fungal Species

    OpenAIRE

    Oghenerobor Benjamin Akpor; S. O. Dahunsi; R. Aransiola

    2014-01-01

    This study was aimed at investigating the effect of pH on sulphate and phosphate uptake from wastewater by selected bacterial and fungal species. A total of four each of bacterial and fungal isolates were used under shaking flasks conditions. The wastewater was supplemented with sodium acetate to serve as external carbon source at a concentration of 5 g/L. Immediately after inoculation with the respective isolates and at 24 h intervals, for the next 96 h, aliquot wastewater samples were taken...

  8. Microbiological and molecular identification of bacterial species isolated from nasal and oropharyngeal mucosa of fuel workers in Riyadh,

    Directory of Open Access Journals (Sweden)

    Suaad S. AlWakeel

    2017-09-01

    Full Text Available This study aimed to determine the bacterial species colonizing the nasal and oropharyngeal mucosa of fuel workers in Central Riyadh, Saudi Arabia on a microbiological and molecular level. Throat and nasal swab samples were obtained from 29 fuel station attendants in the period of time extending from March to May 2014 in Riyadh, Saudi Arabia. Microbiological identification techniques were utilized to identify the bacterial species isolated. Antibiotic sensitivity was assessed for each of the bacterial isolates. Molecular identification techniques based on PCR analysis of specific genomic sequences was conducted and was the basis on which phylogeny representation was done for 10 randomly selected samples of the isolates. Blood was drawn and a complete blood count was conducted to note the hematological indices for each of the study participants. Nineteen bacterial species were isolated from both the nasal cavity and the oropharynx including Streptococcus thoraltensis, alpha-hemolytic streptococci, Staphylococcus hominis, coagulase-negative staphylococci, Leuconostoc mesenteroides, Erysipelothrix rhusiopathiae and several others. We found 100% sensitivity of the isolates to ciprofloxacin, cefuroxime and gentamicin. Whereas cefotaxime and azithromycin posted sensitivities of 85.7% and 91.4%, respectively. Low sensitivities (<60% sensitivity to the antibiotics ampicillin, erythromycin, clarithromycin and norfloxacin were observed. Ninety-seven percent similarity to the microbial bank species was noted when the isolates were compared to it. Most hematological indices recorded were within the normal range. In conclusion, exposure to toxic fumes and compounds within fuel products may be a contributing factor to bacterial colonization of the respiratory tract in fuel workers.

  9. Characterization of N2-fixing plant growth promoting endophytic and epiphytic bacterial community of Indian cultivated and wild rice (Oryza spp.) genotypes.

    Science.gov (United States)

    Banik, Avishek; Mukhopadhaya, Subhra Kanti; Dangar, Tushar Kanti

    2016-03-01

    The diversity of endophytic and epiphytic diazotrophs in different parts of rice plants has specificity to the niche (i.e. leaf, stem and root) of different genotypes and nutrient availability of the organ. Inoculation of the indigenous, polyvalent diazotrophs can facilitate and sustain production of non-leguminous crops like rice. Therefore, N2-fixing plant growth promoting bacteria (PGPB) were isolated from different parts of three Indian cultivated [Oryza sativa L. var. Sabita (semi deep/deep water)/Swarna (rain fed shallow lowland)/Swarna-Sub1(submergence tolerant)] and a wild (O. eichingeri) rice genotypes which respond differentially to nitrogenous fertilizers. Thirty-five isolates from four rice genotypes were categorized based on acetylene reduction assay on nitrogenase activity, biochemical tests, BIOLOG and 16S rRNA gene sequencing. The bacteria produced 9.36-155.83 nmole C2H4 mg(-1) dry bacteria h(-1) and among them nitrogenase activity of 11 potent isolates was complemented by nifH-sequence analysis. Phylogenetic analysis based on 16S rDNA sequencing divided them into five groups (shared 95-100 % sequence homology with type strains) belonging to five classes-alpha (Ancylobacter, Azorhizobium, Azospirillum, Rhizobium, Bradyrhizobium, Sinorhizobium, Novosphingobium, spp.), beta (Burkholderia sp.), gamma (Acinetobacter, Aeromonas, Azotobacter, Enterobacter, Klebsiella, Pantoea, Pseudomonas, Stenotrophomonas spp.) Proteobacteria, Bacilli (Bacillus, Paenibacillus spp.) and Actinobacteria (Microbacterium sp.). Besides, all bacterial strains possessed the intrinsic PGP traits of like indole (0.44-7.4 µg ml(-1)), ammonia (0.18-6 mmol ml(-1)), nitrite (0.01-3.4 mol ml(-1)), and siderophore (from 0.16-0.57 μmol ml(-1)) production. Inoculation of rice (cv. Swarna) seedlings with selected isolates had a positive impact on plant growth parameters like shoot and root elongation which was correlated with in vitro PGP attributes. The results indicated that the

  10. Susceptibility of different bacterial species isolated from food animals to copper sulphate, zinc chloride and antimicrobial substances used for disinfection

    DEFF Research Database (Denmark)

    Aarestrup, Frank Møller; Hasman, Henrik

    2004-01-01

    that Danish bacterial isolates from livestock so far have not or have only to a limited degree developed resistance to antimicrobial compounds commonly used for disinfection. Acquired copper resistance was only found in enterococci. There were large differences in the intrinsic susceptibility of the different......A total of 569 different bacterial isolates (156 Salmonella, 202 E. coli, 43 S. aureus, 38 S. hyicus, 52 E. faecalis, 78 E faecium) were tested for susceptibility to copper sulphate, benzalkonium chloride, hydrogen peroxide and chlorhexidine using MIC determinations. A total of 442 isolates were...... of susceptibilities to the different antimicrobial agents. Large variations were observed in the susceptibility of the different bacterial species to the different compounds. Staphylococci were in general very susceptible to all antimicrobial compounds tested. The Salmonella isolates were in general less susceptible...

  11. Comparison of main lactobacillus species between healthy women and women with bacterial vaginosis

    Institute of Scientific and Technical Information of China (English)

    YAN Dong-hui; L(U) Zhi; SU Jian-rong

    2009-01-01

    Background The normal microbial flora of the vagina plays an important role in preventing genital and urinary tract infections in women. Thus an accurate understanding of the composition and ecology of the ecosystem is important to understanding the etiology of these diseases. This study aimed to compare the characteristics of main lactobacillus species between healthy women and women with bacterial vaginosis (BV) by quantitative culture and PCR methods.Main lactobacillus species include L. Crispatus , L. Gassed, L. Jensenii and L. Iners.Methods A total of 150 Women attending Gynecology Outpatient Clinic of Beijing Friendship Hospital, were diagnosed as having BV because three or more of the following criteria were met (standard of Amsel's composite criteria):homogeneous discharge, elevated vaginal pH (pH >4.5), production of amines, and presence of "clue" cells. Those with less than three of the criteria were considered as healthy. Simultaneously, smears were made of vaginal fluid and Gram stained, then were assessed qualitatively as normal (grade Ⅰ), intermediate (grade Ⅱ), or consistent with BV (grade Ⅲ).Gardnerella vaginalis were identified by using Vitek 2 Compact and PCR methods. Lactobacillus species were identified by PCR methods. Gardnerella vaginalis and lactobacilli colony counts were determined by calculating the most number of colonies of each species in the appropriate plates (colonies between 10 and 300), corrected by the dilution of the sample in the plates, and multiplied by 10 (to account for plating 100 μl), in order to get colony forming units per milliliter of vaginal secretion.Results BV was diagnosed in 31% (46/150) patients using the composite criteria, the remainder being regarded as healthy. The majority of patients with BV had a smear assessed as grade Ⅲ (91%, 42/46) and minority of them had a smear assessed as grade Ⅱ (9%, 4/46). The majority of healthy women had a smear assessed as grade Ⅰ (64%, 67/104).Smears assessed as

  12. Symbiotic Burkholderia Species Show Diverse Arrangements of nif/fix and nod Genes and Lack Typical High-Affinity Cytochrome cbb3 Oxidase Genes.

    Science.gov (United States)

    De Meyer, Sofie E; Briscoe, Leah; Martínez-Hidalgo, Pilar; Agapakis, Christina M; de-Los Santos, Paulina Estrada; Seshadri, Rekha; Reeve, Wayne; Weinstock, George; O'Hara, Graham; Howieson, John G; Hirsch, Ann M

    2016-08-01

    Genome analysis of fourteen mimosoid and four papilionoid beta-rhizobia together with fourteen reference alpha-rhizobia for both nodulation (nod) and nitrogen-fixing (nif/fix) genes has shown phylogenetic congruence between 16S rRNA/MLSA (combined 16S rRNA gene sequencing and multilocus sequence analysis) and nif/fix genes, indicating a free-living diazotrophic ancestry of the beta-rhizobia. However, deeper genomic analysis revealed a complex symbiosis acquisition history in the beta-rhizobia that clearly separates the mimosoid and papilionoid nodulating groups. Mimosoid-nodulating beta-rhizobia have nod genes tightly clustered in the nodBCIJHASU operon, whereas papilionoid-nodulating Burkholderia have nodUSDABC and nodIJ genes, although their arrangement is not canonical because the nod genes are subdivided by the insertion of nif and other genes. Furthermore, the papilionoid Burkholderia spp. contain duplications of several nod and nif genes. The Burkholderia nifHDKEN and fixABC genes are very closely related to those found in free-living diazotrophs. In contrast, nifA is highly divergent between both groups, but the papilionoid species nifA is more similar to alpha-rhizobia nifA than to other groups. Surprisingly, for all Burkholderia, the fixNOQP and fixGHIS genes required for cbb3 cytochrome oxidase production and assembly are missing. In contrast, symbiotic Cupriavidus strains have fixNOQPGHIS genes, revealing a divergence in the evolution of two distinct electron transport chains required for nitrogen fixation within the beta-rhizobia.

  13. The effects of micronutrient deficiencies on bacterial species from the human gut microbiota

    Energy Technology Data Exchange (ETDEWEB)

    Hibberd, Matthew C. [Washington Univ. School of Medicine, St. Louis, MO (United States). Center for Genome Sciences and Systems Biology, Center for Gut Microbiome and Nutrition Research; Wu, Meng [Washington Univ. School of Medicine, St. Louis, MO (United States). Center for Genome Sciences and Systems Biology; Rodionov, Dmitry A. [Russian Academy of Sciences (RAS), Moscow (Russian Federation). A.A. Kharkevich Inst. for Information Transmission Problems; Sanford Burnham Prebys Medical Discovery Inst., La Jolla, CA (United States); Li, Xiaoqing [Sanford Burnham Prebys Medical Discovery Inst., La Jolla, CA (United States); Cheng, Jiye [Washington Univ. School of Medicine, St. Louis, MO (United States). Center for Genome Sciences and Systems Biology, Center for Gut Microbiome and Nutrition Researc; Griffin, Nicholas W. [Washington Univ. School of Medicine, St. Louis, MO (United States). Center for Genome Sciences and Systems Biology, Center for Gut Microbiome and Nutrition Researc; Barratt, Michael J. [Washington Univ. School of Medicine, St. Louis, MO (United States). Center for Genome Sciences and Systems Biology, Center for Gut Microbiome and Nutrition Researc; Giannone, Richard J. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Chemical Sciences Division; Hettich, Robert L. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Chemical Sciences Division; Osterman, Andrei L. [Sanford Burnham Prebys Medical Discovery Inst., La Jolla, CA (United States); Gordon, Jeffrey I. [Washington Univ. School of Medicine, St. Louis, MO (United States). Center for Genome Sciences and Systems Biology, Center for Gut Microbiome and Nutrition Researc

    2017-05-17

    Micronutrient deficiencies afflict two billion people. And while the impact of these imbalances on host biology has been studied extensively, much less is known about their effects on the developing or adult gut microbiota. Thus, we established a community of 44 cultured, sequenced human gut-derived bacterial species in gnotobiotic mice and fed the animals a defined, micronutrient-sufficient diet, followed by a derivative diet devoid of vitamin A, folate, iron or zinc, followed by return to the sufficient diet. Acute vitamin A deficiency had the largest effect on community structure and meta-transcriptome, with Bacteroides vulgatus, a prominent responder, increasing its abundance in the absence of vitamin A, and manifesting transcriptional changes involving various metabolic pathways. Applying retinol selection to a library of 30,300 B. vulgatus transposon mutants revealed that disruption of acrR abrogated retinol sensitivity. Genetic complementation studies, microbial RNA-Seq, and transcription factor binding assays disclosed that AcrR functions as a repressor of an adjacent AcrAB-TolC efflux system plus other members of its regulon. Retinol efflux measurements in wild-type, acrR-mutant, and complemented acrR mutant strains, plus treatment with a pharmacologic inhibitor of the efflux system, revealed that AcrAB-TolC is a determinant of retinol and bile acid sensitivity. We associated acute vitamin A deficiency with altered bile acid metabolism in vivo, raising the possibility that retinol, bile acid metabolites, and AcrAB-TolC interact to influence the fitness of B. vulgatus and perhaps other microbiota members. This type of preclinical model can help develop mechanistic insights about and more effective treatment strategies for micronutrient deficiencies.

  14. Growth promotion of Lactuca sativa in response to volatile organic compounds emitted from diverse bacterial species.

    Science.gov (United States)

    Fincheira, Paola; Venthur, Herbert; Mutis, Ana; Parada, Maribel; Quiroz, Andrés

    2016-12-01

    Agrochemicals are currently used in horticulture to increase crop production. Nevertheless, their indiscriminate use is a relevant issue for environmental and legal aspects. Alternative tools for reducing fertilizers and synthetic phytohormones are being investigated, such as the use of volatile organic compounds (VOCs) as growth inducers. Some soil bacteria, such as Pseudomonas and Bacillus, stimulate Arabidopsis and tobacco growth by releasing VOCs, but their effects on vegetables have not been investigated. Lactuca sativa was used as model vegetable to investigate bacterial VOCs as growth inducers. We selected 10 bacteria strains, belonging to Bacillus, Staphylococcus and Serratia genera that are able to produce 3-hydroxy-2-butanone (acetoin), a compound with proven growth promoting activity. Two-day old-seedlings of L. sativa were exposed to VOCs emitted by the selected bacteria grown in different media cultures for 7 days. The results showed that the VOCs released from the bacteria elicited an increase in the number of lateral roots, dry weight, root growth and shoot length, depending on the media used. Three Bacillus strains, BCT53, BCT9 and BCT4, were selected according to its their growth inducing capacity. The BCT9 strain elicited the greatest increases in dry weight and primary root length when L. sativa seedlings were subjected to a 10-day experiment. Finally, because acetoin only stimulated root growth, we suggest that other volatiles could be responsible for the growth promotion of L. sativa. In conclusion, our results strongly suggest that bacteria volatiles can be used as growth-inducers as alternative or complementary strategies for application in horticulture species. Copyright © 2016 Elsevier GmbH. All rights reserved.

  15. Bacterial community structure in the rhizosphere of three cactus species from semi-arid highlands in central Mexico.

    Science.gov (United States)

    Aguirre-Garrido, J Félix; Montiel-Lugo, Daniel; Hernández-Rodríguez, César; Torres-Cortes, Gloria; Millán, Vicenta; Toro, Nicolás; Martínez-Abarca, Francisco; Ramírez-Saad, Hugo C

    2012-05-01

    The nature reserve of Tehuacan-Cuicatlan in central Mexico is known for its diversity and endemism mainly in cactus plants. Although the xerophytic flora is reasonably documented, the bacterial communities associated with these species have been largely neglected. We assessed the diversity and composition of bacterial communities in bulk (non-rhizospheric) soil and the rhizosphere of three cactus plant species: Mammillaria carnea, Opuntia pilifera and Stenocereus stellatus, approached using cultivation and molecular techniques, considering the possible effect of dry and rainy seasons. Cultivation-dependent methods were focused on putative N(2)-fixers and heterotrophic aerobic bacteria, in the two media tested the values obtained for dry season samples grouped together regardless of the sample type (rhizospheric or non-rhizospheric), these groups also included the non-rhizospheric sample for rainy season, on each medium. These CFU values were smaller and significantly different from those obtained on rhizospheric samples from rainy season. Genera composition among isolates of the rhizospheric samples was very similar for each season, the most abundant taxa being α-Proteobacteria, Actinobacteria and Firmicutes. Interestingly, the genus Ochrobactrum was highly represented among rhizospheric samples, when cultured in N-free medium. The structure of the bacterial communities was approached with molecular techniques targeting partial 16S rRNA sequences such as denaturing gradient gel electrophoresis and serial analysis of ribosomal sequence tags. Under these approaches, the most represented bacterial phyla were Actinobacteria, Proteobacteria and Acidobacteria. The first two were also highly represented when using isolation techniques.

  16. Variations in the binding pocket of an inhibitor of the bacterial division protein FtsZ across genotypes and species.

    Directory of Open Access Journals (Sweden)

    Amanda Miguel

    2015-03-01

    Full Text Available The recent increase in antibiotic resistance in pathogenic bacteria calls for new approaches to drug-target selection and drug development. Targeting the mechanisms of action of proteins involved in bacterial cell division bypasses problems associated with increasingly ineffective variants of older antibiotics; to this end, the essential bacterial cytoskeletal protein FtsZ is a promising target. Recent work on its allosteric inhibitor, PC190723, revealed in vitro activity on Staphylococcus aureus FtsZ and in vivo antimicrobial activities. However, the mechanism of drug action and its effect on FtsZ in other bacterial species are unclear. Here, we examine the structural environment of the PC190723 binding pocket using PocketFEATURE, a statistical method that scores the similarity between pairs of small-molecule binding sites based on 3D structure information about the local microenvironment, and molecular dynamics (MD simulations. We observed that species and nucleotide-binding state have significant impacts on the structural properties of the binding site, with substantially disparate microenvironments for bacterial species not from the Staphylococcus genus. Based on PocketFEATURE analysis of MD simulations of S. aureus FtsZ bound to GTP or with mutations that are known to confer PC190723 resistance, we predict that PC190723 strongly prefers to bind Staphylococcus FtsZ in the nucleotide-bound state. Furthermore, MD simulations of an FtsZ dimer indicated that polymerization may enhance PC190723 binding. Taken together, our results demonstrate that a drug-binding pocket can vary significantly across species, genetic perturbations, and in different polymerization states, yielding important information for the further development of FtsZ inhibitors.

  17. Combined chemical and physical transformation method with RbCl and sepiolite for the transformation of various bacterial species.

    Science.gov (United States)

    Ren, Jun; Lee, Haram; Yoo, Seung Min; Yu, Myeong-Sang; Park, Hansoo; Na, Dokyun

    2017-04-01

    DNA transformation that delivers plasmid DNAs into bacterial cells is fundamental in genetic manipulation to engineer and study bacteria. Developed transformation methods to date are optimized to specific bacterial species for high efficiency. Thus, there is always a demand for simple and species-independent transformation methods. We herein describe the development of a chemico-physical transformation method that combines a rubidium chloride (RbCl)-based chemical method and sepiolite-based physical method, and report its use for the simple and efficient delivery of DNA into various bacterial species. Using this method, the best transformation efficiency for Escherichia coli DH5α was 4.3×10(6)CFU/μg of pUC19 plasmid, which is higher than or comparable to the reported transformation efficiencies to date. This method also allowed the introduction of plasmid DNAs into Bacillus subtilis (5.7×10(3)CFU/μg of pSEVA3b67Rb), Bacillus megaterium (2.5×10(3)CFU/μg of pSPAsp-hp), Lactococcus lactis subsp. lactis (1.0×10(2)CFU/μg of pTRKH3-ermGFP), and Lactococcus lactis subsp. cremoris (2.2×10(2)CFU/μg of pMSP3535VA). Remarkably, even when the conventional chemical and physical methods failed to generate transformed cells in Bacillus sp. and Enterococcus faecalis, E. malodoratus and E. mundtii, our combined method showed a significant transformation efficiency (2.4×10(4), 4.5×10(2), 2×10(1), and 0.5×10(1)CFU/μg of plasmid DNA). Based on our results, we anticipate that our simple and efficient transformation method should prove usefulness for introducing DNA into various bacterial species without complicated optimization of parameters affecting DNA entry into the cell.

  18. Reductive dechlorination of methoxychlor by bacterial species of environmental origin: evidence for primary biodegradation of methoxychlor in submerged environments.

    Science.gov (United States)

    Satsuma, Koji; Masuda, Minoru

    2012-02-29

    Methoxychlor [1,1,1-trichloro-2,2-bis(4-methoxyphenyl)ethane] is an organochlorine insecticide that undergoes dechlorination in natural submerged environments. We investigated the ability to dechlorinate this compound in seven environmental bacterial species ( Aeromonas hydrophila , Enterobacter amnigenus , Klebsiella terrigena , Bacillus subtilis , Achromobacter xylosoxidans , Acinetobacter calcoaceticus , and Mycobacterium obuense ) and the enteric bacterium Escherichia coli as a positive control. In R2A broth at 25 °C under aerobic, static culture, all species except Ach. xylosoxidans were observed to convert methoxychlor to dechlorinated methoxychlor [1,1-dichloro-2,2-bis(4-methoxyphenyl)ethane]. The medium was aerobic at first, but bacterial growth resulted in the consumption of oxygen and generated microaerobic and weakly reductive conditions. Replacement of the headspace of the culture tubes with nitrogen gas was found to decrease the dechlorination rate. Our findings suggest that extensive bacterial species ubiquitously inhabiting the subsurface water environment play an important role in the primary dechlorination of methoxychlor.

  19. Nucleoside analogues are activated by bacterial deoxyribonucleoside kinases in a species-specific manner

    DEFF Research Database (Denmark)

    Sandrini, Michael; Clausen, Anders; On, Stephen L. W.

    2007-01-01

    bactericidal activity against several clinical bacterial isolates and type strains. We identified and subcloned the genes coding for putative deoxyribonucleoside kinases in Escherichia coli, Pasteurella multocida, Salmonella enterica, Yersinia enterocolitica, Bacillus cereus, Clostridium perfringens...

  20. Limitations to estimating bacterial cross-species transmission using genetic and genomic markers: inferences from simulation modeling.

    Science.gov (United States)

    Benavides, Julio A; Cross, Paul C; Luikart, Gordon; Creel, Scott

    2014-08-01

    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.

  1. Effects of antibiotic on the bacterial microflora in two commercially important catfish species, Clarias batrachus and Heteropneustes fossilis in Bangladesh

    Directory of Open Access Journals (Sweden)

    Md. Shahdat Hossain

    2014-11-01

    Full Text Available Objective: To assess the effects of a widely used antibiotic, oxytetracycline (OTC on the bacterial microflora in two catfish species under artificial culture conditions in the laboratory. Methods: The experiment was conducted in the Faculty of Fisheries, Bangladesh Agricultural University, Mymensingh-2202. The fish were reared in six aquaria (size 37 cm×30 cm×60 cm where three aquaria served as replicates of the antibiotic treatment groups and the remaining three aquaria served as an untreated control group. Each aquarium was stocked with 25 fish on an average body weight 15 g. OTC was administered to the fish in the treatment groups at the rate of 2 g/kg in-feed twice daily upto ad libitum, whereas fish in the untreated control groups were given the same feed without antibiotics for 20 d. During the experiment, bacterial loads were estimated as colony forming unit (CFU/g by every alternate day in the aquarium water, gills, skin and intestine of fish. Results: The administration of OTC in feed resulted in gradual decrease of bacterial loads in the gills, intestine and skin of the two catfish species tested. In contrast, the bacterial loads remain unchanged or slightly increased in the control groups not fed with OTC. Water quality parameters such as dissolved oxygen, pH and total hardness were found to be within suitable range in the test aquaria but not in control aquarium throughout the experimental period. Conclusions: The results of this experiment showed that in-feed antibiotic OTC for a period of 20 d reduced the bacterial loads in the gills, intestines and skin of treated fish.

  2. Effects of antibiotic on the bacterial microflora in two commercially important catfish species, Clarias batrachus and Heteropneustes fossilis in Bangladesh

    Institute of Scientific and Technical Information of China (English)

    Md Shahdat Hossain; Md Rajib Sharker; Syed Ariful Haque; Md Shaheed Reza; Md Anwar Hossain Mondal

    2014-01-01

    Objective: To assess the effects of a widely used antibiotic, oxytetracycline (OTC) on the bacterial microflora in two catfish species under artificial culture conditions in the laboratory. Methods:The experiment was conducted in the Faculty of Fisheries, Bangladesh Agricultural University, Mymensingh-2202. The fish were reared in six aquaria (size 37 cmí30 cmí60 cm) where three aquaria served as replicates of the antibiotic treatment groups and the remaining three aquaria served as an untreated control group. Each aquarium was stocked with 25 fish on an average body weight 15 g. OTC was administered to the fish in the treatment groups at the rate of 2 g/kg in-feed twice daily upto ad libitum, whereas fish in the untreated control groups were given the same feed without antibiotics for 20 d. During the experiment, bacterial loads were estimated as colony forming unit (CFU/g) by every alternate day in the aquarium water, gills, skin and intestine of fish. Results:The administration of OTC in feed resulted in gradual decrease of bacterial loads in the gills, intestine and skin of the two catfish species tested. In contrast, the bacterial loads remain unchanged or slightly increased in the control groups not fed with OTC. Water quality parameters such as dissolved oxygen, pH and total hardness were found to be within suitable range in the test aquaria but not in control aquarium throughout the experimental period. Conclusions:The results of this experiment showed that in-feed antibiotic OTC for a period of 20d reduced the bacterial loads in the gills, intestines and skin of treated fish.

  3. Evolution in an oncogenic bacterial species with extreme genome plasticity: Helicobacter pylori East Asian genomes

    Directory of Open Access Journals (Sweden)

    Handa Naofumi

    2011-05-01

    Full Text Available Abstract Background The genome of Helicobacter pylori, an oncogenic bacterium in the human stomach, rapidly evolves and shows wide geographical divergence. The high incidence of stomach cancer in East Asia might be related to bacterial genotype. We used newly developed comparative methods to follow the evolution of East Asian H. pylori genomes using 20 complete genome sequences from Japanese, Korean, Amerind, European, and West African strains. Results A phylogenetic tree of concatenated well-defined core genes supported divergence of the East Asian lineage (hspEAsia; Japanese and Korean from the European lineage ancestor, and then from the Amerind lineage ancestor. Phylogenetic profiling revealed a large difference in the repertoire of outer membrane proteins (including oipA, hopMN, babABC, sabAB and vacA-2 through gene loss, gain, and mutation. All known functions associated with molybdenum, a rare element essential to nearly all organisms that catalyzes two-electron-transfer oxidation-reduction reactions, appeared to be inactivated. Two pathways linking acetyl~CoA and acetate appeared intact in some Japanese strains. Phylogenetic analysis revealed greater divergence between the East Asian (hspEAsia and the European (hpEurope genomes in proteins in host interaction, specifically virulence factors (tipα, outer membrane proteins, and lipopolysaccharide synthesis (human Lewis antigen mimicry enzymes. Divergence was also seen in proteins in electron transfer and translation fidelity (miaA, tilS, a DNA recombinase/exonuclease that recognizes genome identity (addA, and DNA/RNA hybrid nucleases (rnhAB. Positively selected amino acid changes between hspEAsia and hpEurope were mapped to products of cagA, vacA, homC (outer membrane protein, sotB (sugar transport, and a translation fidelity factor (miaA. Large divergence was seen in genes related to antibiotics: frxA (metronidazole resistance, def (peptide deformylase, drug target, and ftsA (actin

  4. The bacterial species associated with bacterial vaginosis: research progress%细菌性阴道病的细菌因素研究进展

    Institute of Scientific and Technical Information of China (English)

    马薇; 傅思武

    2012-01-01

    细菌性阴道病是妇科常见疾病,对女性、胎儿和新生儿的健康构成严重威胁.阴道微生物群落中产H2O2的乳酸杆菌与厌氧菌数量发生转换为其主要特征,具体机制不清.本文系统综述了近年来细菌性阴道病的细菌因素研究进展.%Bacterial vaginosis (BV) is a common clinical disease that is associated with a variely of FemAle health problems, fetal and infant outcomes. Although its precise mechanism remains unclear, BV is characterized by a dramatic shift in the vaginal microflora, involving a relative decrease in hydrogen peroxide-producing lactobacilli, and a proliferation of anaerobes. This review summarizes the vaginal bacterial species associated with BV and the progress in recent researches.

  5. Host plant species determines symbiotic bacterial community mediating suppression of plant defenses

    Science.gov (United States)

    Chung, Seung Ho; Scully, Erin D.; Peiffer, Michelle; Geib, Scott M.; Rosa, Cristina; Hoover, Kelli; Felton, Gary W.

    2017-01-01

    Herbivore associated bacteria are vital mediators of plant and insect interactions. Host plants play an important role in shaping the gut bacterial community of insects. Colorado potato beetles (CPB; Leptinotarsa decemlineata) use several Solanum plants as hosts in their natural environment. We previously showed that symbiotic gut bacteria from CPB larvae suppressed jasmonate (JA)-induced defenses in tomato. However, little is known about how changes in the bacterial community may be involved in the manipulation of induced defenses in wild and cultivated Solanum plants of CPB. Here, we examined suppression of JA-mediated defense in wild and cultivated hosts of CPB by chemical elicitors and their symbiotic bacteria. Furthermore, we investigated associations between the gut bacterial community and suppression of plant defenses using 16 S rRNA amplicon sequencing. Symbiotic bacteria decreased plant defenses in all Solanum hosts and there were different gut bacterial communities in CPB fed on different host plants. When larvae were reared on different hosts, defense suppression differed among host plants. These results demonstrate that host plants influence herbivore gut bacterial communities and consequently affect the herbivore’s ability to manipulate JA-mediated plant defenses. Thus, the presence of symbiotic bacteria that suppress plant defenses might help CPB adapt to host plants. PMID:28045052

  6. Complete Genome sequence of Burkholderia phymatum STM815T, a broad host range and efficient nitrogen-fixing symbiont of Mimosa species

    Science.gov (United States)

    Moulin, Lionel; Klonowska, Agnieszka; Caroline, Bournaud; Booth, Kristina; Vriezen, Jan A.C.; Melkonian, Rémy; James, Euan K.; Young, J. Peter W.; Bena, Gilles; Hauser, Loren; Land, Miriam; Kyrpides, Nikos; Bruce, David; Chain, Patrick; Copeland, Alex; Pitluck, Sam; Woyke, Tanja; Lizotte-Waniewski, Michelle; Bristow, Jim; Riley, Margaret

    2014-01-01

    Burkholderia phymatum is a soil bacterium able to develop a nitrogen-fixing symbiosis with species of the legume genus Mimosa, and is frequently found associated specifically with Mimosa pudica. The type strain of the species, STM 815T, was isolated from a root nodule in French Guiana in 2000. The strain is an aerobic, motile, non-spore forming, Gram-negative rod, and is a highly competitive strain for nodulation compared to other Mimosa symbionts, as it also nodulates a broad range of other legume genera and species. The 8,676,562 bp genome is composed of two chromosomes (3,479,187 and 2,697,374 bp), a megaplasmid (1,904,893 bp) and a plasmid hosting the symbiotic functions (595,108 bp). PMID:25197461

  7. Complete Genome sequence of Burkholderia phymatum STM815, a broad host range and efficient nitrogen-fixing symbiont of Mimosa species

    Energy Technology Data Exchange (ETDEWEB)

    Moulin, Lionel [UMR, France; Klonowska, Agnieszka [UMR, France; Caroline, Bournaud [UMR, France; Booth, Kristina [University of Massachusetts; Vriezen, Jan A.C. [University of Massachusetts; Melkonian, Remy [UMR, France; James, Euan [James Hutton Institute, Dundee, United Kingdom; Young, Peter W. [University of York, United Kingdom; Bena, Gilles [UMR, France; Hauser, Loren John [ORNL; Land, Miriam L [ORNL; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Chain, Patrick S. G. [Lawrence Livermore National Laboratory (LLNL); Copeland, A [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Lizotte-Waniewski, Michelle [University of Massachusetts; Bristow, James [U.S. Department of Energy, Joint Genome Institute; Riley, Monica [Woods Hole Oceanographic Institution (WHOI), Woods Hole

    2014-01-01

    Burkholderia phymatum is a soil bacterium able to develop a nitrogen-fixing symbiosis with species of the legume genus Mimosa, and is frequently found associated specifically with Mimosa pudica. The type strain of the species, STM 815T, was isolated from a root nodule in French Guiana in 2000. The strain is an aerobic, motile, non-spore forming, Gram-negative rod, and is a highly competitive strain for nodulation compared to other Mimosa symbionts, as it also nodulates a broad range of other legume genera and species. The 8,676,562 bp genome is composed of two chromosomes (3,479,187 and 2,697,374 bp), a megaplasmid (1,904,893 bp) and a plasmid hosting the symbiotic functions (595,108 bp).

  8. Complete Genome sequence of Burkholderia phymatum STM815(T), a broad host range and efficient nitrogen-fixing symbiont of Mimosa species.

    Science.gov (United States)

    Moulin, Lionel; Klonowska, Agnieszka; Caroline, Bournaud; Booth, Kristina; Vriezen, Jan A C; Melkonian, Rémy; James, Euan K; Young, J Peter W; Bena, Gilles; Hauser, Loren; Land, Miriam; Kyrpides, Nikos; Bruce, David; Chain, Patrick; Copeland, Alex; Pitluck, Sam; Woyke, Tanja; Lizotte-Waniewski, Michelle; Bristow, Jim; Riley, Margaret

    2014-06-15

    Burkholderia phymatum is a soil bacterium able to develop a nitrogen-fixing symbiosis with species of the legume genus Mimosa, and is frequently found associated specifically with Mimosa pudica. The type strain of the species, STM 815(T), was isolated from a root nodule in French Guiana in 2000. The strain is an aerobic, motile, non-spore forming, Gram-negative rod, and is a highly competitive strain for nodulation compared to other Mimosa symbionts, as it also nodulates a broad range of other legume genera and species. The 8,676,562 bp genome is composed of two chromosomes (3,479,187 and 2,697,374 bp), a megaplasmid (1,904,893 bp) and a plasmid hosting the symbiotic functions (595,108 bp).

  9. Responses of Ammonia-Oxidising Bacterial Communities to Nitrogen, Lime, and Plant Species in Upland Grassland Soil

    Directory of Open Access Journals (Sweden)

    Deirdre C. Rooney

    2010-01-01

    Full Text Available Agricultural improvement of seminatural grasslands has been shown to result in changes to plant and microbial diversity, with consequences for ecosystem functioning. A microcosm approach was used to elucidate the effects of two key components of agricultural improvement (nitrogen addition and liming on ammonia-oxidising bacterial (AOB communities in an upland grassland soil. Plant species characteristic of unimproved and improved pastures (A. capillaris and L. perenne were planted in microcosms, and lime, nitrogen (NH4NO3, or lime plus nitrogen added. The AOB community was profiled using terminal restriction fragment length polymorphism (TRFLP of the amoA gene. AOB community structure was largely altered by NH4NO3 addition, rather than liming, although interactions between nitrogen addition and plant species were also evident. Results indicate that nitrogen addition drives shifts in the structure of key microbial communities in upland grassland soils, and that plant species may play a significant role in determining AOB community structure.

  10. Effect of holothurian and zoanthid extracts on growth of some bacterial and diatom species

    Digital Repository Service at National Institute of Oceanography (India)

    Gonsalves, C.

    The antifouling properties of the extracts from two zoanthids, viz. Zoanthus sp, Protopalythoa sp and one holothurian species, viz. Holothuria leucospilota occurring in the coastal waters off Goa were tested against 5 bacteria and 2 diatom species...

  11. Bacterial Species and Antibiotic Sensitivity in Korean Patients Diagnosed with Acute Otitis Media and Otitis Media with Effusion

    Science.gov (United States)

    2017-01-01

    Changes over time in pathogens and their antibiotic sensitivity resulting from the recent overuse and misuse of antibiotics in otitis media (OM) have complicated treatment. This study evaluated changes over 5 years in principal pathogens and their antibiotic sensitivity in patients in Korea diagnosed with acute OM (AOM) and OM with effusion (OME). The study population consisted of 683 patients who visited the outpatient department of otorhinolaryngology in 7 tertiary hospitals in Korea between January 2010 and May 2015 and were diagnosed with acute AOM or OME. Aural discharge or middle ear fluid were collected from patients in the operating room or outpatient department and subjected to tests of bacterial identification and antibiotic sensitivity. The overall bacteria detection rate of AOM was 62.3% and OME was 40.9%. The most frequently isolated Gram-positive bacterial species was coagulase negative Staphylococcus aureus (CNS) followed by methicillin-susceptible S. aureus (MSSA), methicillin-resistant S. aureus (MRSA), and Streptococcus pneumonia (SP), whereas the most frequently isolated Gram-negative bacterium was Pseudomonas aeruginosa (PA). Regardless of OM subtype, ≥ 80% of CNS and MRSA strains were resistant to penicillin (PC) and tetracycline (TC); isolated MRSA strains showed low sensitivity to other antibiotics, with 100% resistant to PC, TC, cefoxitin (CFT), and erythromycin (EM); and isolated PA showed low sensitivity to quinolone antibiotics, including ciprofloxacin (CIP) and levofloxacin (LFX), and to aminoglycosides. Bacterial species and antibiotic sensitivity did not change significantly over 5 years. The rate of detection of MRSA was higher in OME than in previous studies. As bacterial predominance and antibiotic sensitivity could change over time, continuous and periodic surveillance is necessary in guiding appropriate antibacterial therapy. PMID:28244296

  12. Bacterial Species and Antibiotic Sensitivity in Korean Patients Diagnosed with Acute Otitis Media and Otitis Media with Effusion.

    Science.gov (United States)

    Kim, Sang Hoon; Jeon, Eun Ju; Hong, Seok Min; Bae, Chang Hoon; Lee, Ho Yun; Park, Moo Kyun; Byun, Jae Yong; Kim, Myung Gu; Yeo, Seung Geun

    2017-04-01

    Changes over time in pathogens and their antibiotic sensitivity resulting from the recent overuse and misuse of antibiotics in otitis media (OM) have complicated treatment. This study evaluated changes over 5 years in principal pathogens and their antibiotic sensitivity in patients in Korea diagnosed with acute OM (AOM) and OM with effusion (OME). The study population consisted of 683 patients who visited the outpatient department of otorhinolaryngology in 7 tertiary hospitals in Korea between January 2010 and May 2015 and were diagnosed with acute AOM or OME. Aural discharge or middle ear fluid were collected from patients in the operating room or outpatient department and subjected to tests of bacterial identification and antibiotic sensitivity. The overall bacteria detection rate of AOM was 62.3% and OME was 40.9%. The most frequently isolated Gram-positive bacterial species was coagulase negative Staphylococcus aureus (CNS) followed by methicillin-susceptible S. aureus (MSSA), methicillin-resistant S. aureus (MRSA), and Streptococcus pneumonia (SP), whereas the most frequently isolated Gram-negative bacterium was Pseudomonas aeruginosa (PA). Regardless of OM subtype, ≥ 80% of CNS and MRSA strains were resistant to penicillin (PC) and tetracycline (TC); isolated MRSA strains showed low sensitivity to other antibiotics, with 100% resistant to PC, TC, cefoxitin (CFT), and erythromycin (EM); and isolated PA showed low sensitivity to quinolone antibiotics, including ciprofloxacin (CIP) and levofloxacin (LFX), and to aminoglycosides. Bacterial species and antibiotic sensitivity did not change significantly over 5 years. The rate of detection of MRSA was higher in OME than in previous studies. As bacterial predominance and antibiotic sensitivity could change over time, continuous and periodic surveillance is necessary in guiding appropriate antibacterial therapy. © 2017 The Korean Academy of Medical Sciences.

  13. Host plant species determines symbiotic bacterial community mediating suppression of plant defenses

    Science.gov (United States)

    Herbivore associated bacteria are vital mediators of plant and insect interactions. Host plants play an important role in shaping the gut bacterial community of insects. Colorado potato beetles (CPB; Leptinotarsa decemlineata) use several Solanum plants as hosts in their natural environment. We prev...

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

    NARCIS (Netherlands)

    Dols, J.A.M.; Molenaar, D.; Helm, J.J. van der; Caspers, M.P.M.; Kat Angelino-Bart, A. de; Schuren, F.H.J.; Speksnijder, A.G.C.L.; Westerhoff, H.V.; Richardus, J.H.; Boon, M. E.; Reid, G.; Vries, H.J.C de; Kort, R.

    2016-01-01

    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 profiles and evaluate

  15. 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

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

    NARCIS (Netherlands)

    Dols, J.A.M.; Molenaar, D.; van der Helm, J.J.; Caspers, M.P.M.; de Kat Angelino-Bart, A.; Schuren, F.H.J.; Speksnijder, A.G.C.L.; Westerhoff, H.V.; Richardus, J.H.; Boon, M.E.; Reid, G.; de Vries, H.J.C.; Kort, R.

    2016-01-01

    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 profiles and evaluate

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

    NARCIS (Netherlands)

    Dols, J.A.M.; Molenaar, D.; van der Helm, J.J.; Caspers, M.P.M.; de Kat Angelino-Bart, A.; Schuren, F.H.J.; Speksnijder, A.G.C.L.; Westerhoff, H.V.; Richardus, J.H.; Boon, M.E.; Reid, G.; de Vries, H.J.C.; Kort, R.

    2016-01-01

    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 profiles and evaluate ind

  18. 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 profi

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

    NARCIS (Netherlands)

    Dols, J.A.M.; Molenaar, D.; Helm, J.J. van der; Caspers, M.P.M.; Kat Angelino-Bart, A. de; Schuren, F.H.J.; Speksnijder, A.G.C.L.; Westerhoff, H.V.; Richardus, J.H.; Boon, M. E.; Reid, G.; Vries, H.J.C de; Kort, R.

    2016-01-01

    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 profiles and evaluate ind

  20. Reactive oxygen species mediated bacterial biofilm inhibition via zinc oxide nanoparticles and their statistical determination.

    Directory of Open Access Journals (Sweden)

    Sourabh Dwivedi

    Full Text Available The formation of bacterial biofilm is a major challenge in clinical applications. The main aim of this study is to describe the synthesis, characterization and biocidal potential of zinc oxide nanoparticles (NPs against bacterial strain Pseudomonas aeruginosa. These nanoparticles were synthesized via soft chemical solution process in a very short time and their structural properties have been investigated in detail by using X-ray diffraction and transmission electron microscopy measurements. In this work, the potential of synthesized ZnO-NPs (∼ 10-15 nm has been assessed in-vitro inhibition of bacteria and the formation of their biofilms was observed using the tissue culture plate assays. The crystal violet staining on biofilm formation and its optical density revealed the effect on biofilm inhibition. The NPs at a concentration of 100 µg/mL significantly inhibited the growth of bacteria and biofilm formation. The biofilm inhibition by ZnO-NPs was also confirmed via bio-transmission electron microscopy (Bio-TEM. The Bio-TEM analysis of ZnO-NPs treated bacteria confirmed the deformation and damage of cells. The bacterial growth in presence of NPs concluded the bactericidal ability of NPs in a concentration dependent manner. It has been speculated that the antibacterial activity of NPs as a surface coating material, could be a feasible approach for controlling the pathogens. Additionally, the obtained bacterial solution data is also in agreement with the results from statistical analytical methods.

  1. Bacterial and fungal endophthalmitis in Upper Egypt: related species and risk factors

    Directory of Open Access Journals (Sweden)

    AA Gharamah

    2012-08-01

    Conclusions: The ability of bacterial and fungal isolates to produce extracellular enzymes and mycotoxins may be aid in the invasion and destruction of eye tissues. Microbial contamination of operating rooms with air-borne bacteria and fungi in the present work may be a source of postoperative endophthalmitis.

  2. Adsorption and oxidation of SO₂in a fixed-bed reactor using activated carbon produced from oxytetracycline bacterial residue and impregnated with copper.

    Science.gov (United States)

    Zhou, Baohua; Yu, Lei; Song, Hanning; Li, Yaqi; Zhang, Peng; Guo, Bin; Duan, Erhong

    2015-02-01

    The SO₂removal ability (including adsorption and oxidation ability) of activated carbon produced from oxytetracycline bacterial residue and impregnated with copper was investigated. The activated carbon produced from oxytetracycline bacterial residue and modified with copper was characterized by x-ray diffraction, scanning electron microscopy, and energy-dispersive spectroscopy. The effects of the catalysts, SO₂concentration, weight hourly space velocity, and temperature on the SO₂adsorption and oxidation activity were evaluated. Activated carbon produced from oxytetracycline bacterial residue and used as catalyst supports for copper oxide catalysts provided high catalytic activity for the adsorbing and oxidizing of SO₂from flue gases.

  3. Rathayibacter toxicus, Other Rathayibacter Species Inducing Bacterial Head Blight of Grasses, and the Potential for Livestock Poisonings.

    Science.gov (United States)

    Murray, Timothy D; Schroeder, Brenda K; Schneider, William L; Luster, Douglas G; Sechler, Aaron; Rogers, Elizabeth E; Subbotin, Sergei A

    2017-07-01

    Rathayibacter toxicus, a Select Agent in the United States, is one of six recognized species in the genus Rathayibacter and the best known due to its association with annual ryegrass toxicity, which occurs only in parts of Australia. The Rathayibacter species are unusual among phytopathogenic bacteria in that they are transmitted by anguinid seed gall nematodes and produce extracellular polysaccharides in infected plants resulting in bacteriosis diseases with common names such as yellow slime and bacterial head blight. R. toxicus is distinguished from the other species by producing corynetoxins in infected plants; toxin production is associated with infection by a bacteriophage. These toxins cause grazing animals feeding on infected plants to develop convulsions and abnormal gate, which is referred to as "staggers," and often results in death of affected animals. R. toxicus is the only recognized Rathayibacter species to produce toxin, although reports of livestock deaths in the United States suggest a closely related toxigenic species may be present. A closely related but undescribed species, Rathayibacter sp. EV, originally isolated from Ehrharta villosa var. villosa in South Africa, is suspected of producing toxin. Many of the diseases caused by Rathayibacter species occur in arid areas and the extracellular polysaccharide they produce is believed to aid in their survival between crops. For example, R. "agropyri" was isolated from infected plant material after being stored for 50 years in a herbarium. Similarly, the anguinid vectors associated with these bacteria form seed galls in infected plants and are capable of surviving for very long periods of time under dry conditions. The addition of R. toxicus to the list of Select Agents has raised concern over its potential introduction and a realization that current diagnostic methods are inadequate to distinguish among Rathayibacter species. In addition, little is known about the Rathayibacter species and their

  4. Comparative Genomics of the Bacterial Genus Streptococcus Illuminates Evolutionary Implications of Species Groups

    Science.gov (United States)

    Gao, Xiao-Yang; Zhi, Xiao-Yang; Li, Hong-Wei; Klenk, Hans-Peter; Li, Wen-Jun

    2014-01-01

    Members of the genus Streptococcus within the phylum Firmicutes are among the most diverse and significant zoonotic pathogens. This genus has gone through considerable taxonomic revision due to increasing improvements of chemotaxonomic approaches, DNA hybridization and 16S rRNA gene sequencing. It is proposed to place the majority of streptococci into “species groups”. However, the evolutionary implications of species groups are not clear presently. We use comparative genomic approaches to yield a better understanding of the evolution of Streptococcus through genome dynamics, population structure, phylogenies and virulence factor distribution of species groups. Genome dynamics analyses indicate that the pan-genome size increases with the addition of newly sequenced strains, while the core genome size decreases with sequential addition at the genus level and species group level. Population structure analysis reveals two distinct lineages, one including Pyogenic, Bovis, Mutans and Salivarius groups, and the other including Mitis, Anginosus and Unknown groups. Phylogenetic dendrograms show that species within the same species group cluster together, and infer two main clades in accordance with population structure analysis. Distribution of streptococcal virulence factors has no obvious patterns among the species groups; however, the evolution of some common virulence factors is congruous with the evolution of species groups, according to phylogenetic inference. We suggest that the proposed streptococcal species groups are reasonable from the viewpoints of comparative genomics; evolution of the genus is congruent with the individual evolutionary trajectories of different species groups. PMID:24977706

  5. Comparative genomics of the bacterial genus Streptococcus illuminates evolutionary implications of species groups.

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    Xiao-Yang Gao

    Full Text Available Members of the genus Streptococcus within the phylum Firmicutes are among the most diverse and significant zoonotic pathogens. This genus has gone through considerable taxonomic revision due to increasing improvements of chemotaxonomic approaches, DNA hybridization and 16S rRNA gene sequencing. It is proposed to place the majority of streptococci into "species groups". However, the evolutionary implications of species groups are not clear presently. We use comparative genomic approaches to yield a better understanding of the evolution of Streptococcus through genome dynamics, population structure, phylogenies and virulence factor distribution of species groups. Genome dynamics analyses indicate that the pan-genome size increases with the addition of newly sequenced strains, while the core genome size decreases with sequential addition at the genus level and species group level. Population structure analysis reveals two distinct lineages, one including Pyogenic, Bovis, Mutans and Salivarius groups, and the other including Mitis, Anginosus and Unknown groups. Phylogenetic dendrograms show that species within the same species group cluster together, and infer two main clades in accordance with population structure analysis. Distribution of streptococcal virulence factors has no obvious patterns among the species groups; however, the evolution of some common virulence factors is congruous with the evolution of species groups, according to phylogenetic inference. We suggest that the proposed streptococcal species groups are reasonable from the viewpoints of comparative genomics; evolution of the genus is congruent with the individual evolutionary trajectories of different species groups.

  6. Antifouling effect of bioactive compounds from marine sponge Acanthella elongata and different species of bacterial film on larval attachment of Balanus amphitrite (cirripedia, crustacea

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    Viswambaran Ganapiriya

    2012-06-01

    Full Text Available The antifouling activity of bioactive compounds from marine sponge Acanthella elongata (Dendy and five species of bacterial biofilm were studied. Larvae of Balanus amphitrite (Cyprids and nauplii were used to monitor the settlement inhibition and the extent to which inhibition was due to toxicity. The crude extract and partially purified fractions of A.elongata showed significant inhibition over the settlement individually, and with the interaction of bacterial species. No bacterial film stimulated the barnacle settlement. The high but variable levels of antifouling activity in combination with less amount of toxicity showed the potential of these metabolites in environmentally-friendly antifouling preparations.

  7. Bacteroides uniformis is a putative bacterial species associated with the degradation of the isoflavone genistein in human feces.

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    Renouf, Mathieu; Hendrich, Suzanne

    2011-06-01

    Inter-individual variation in isoflavone absorption depends on gut microbial degradation and affects the efficacy of these compounds. We hypothesized that inter-individual variation in fecal isoflavone disappearance coincided with variation in bacterial species. In vitro anaerobic fecal disappearance of isoflavones was measured from 33 participants by HPLC. Fecal microbial 16S rRNA variable region PCR products were obtained from 4 participants with the greatest and least genistein or glycitein degradation and were subjected to denaturing gradient gel electrophoresis. DNA bands with a homology of 90-95% to Bacteroides uniformis and Faecalibacterium prausnitzii were present in greater intensities in fecal samples showing a genistein disappearance rate constant of 1.47 ± 0.14 h(-1) compared with those with a genistein disappearance rate constant of 0.15 ± 0.03 h(-1) (P < 0.05). Human fecal bacterial species with DNA sequences 90-100% homologous to Tannerella forsythensis and 4 other species were present in greater intensities in fecal samples showing a glycitein disappearance rate constant of 0.57 ± 0.30 h(-1) compared with fecal samples with a glycitein disappearance rate constant of 0.08 ± 0.03 h(-1) (P < 0.05). In high degraders, B. uniformis may be a candidate for genistein degradation and T. forsythensis for glycitein degradation, based on fecal isoflavone degradation in the presence of these species. Bacteroides acidifaciens increased isoflavone disappearance in anaerobic human fecal incubations under nutrient-rich and -depleted conditions, suggesting this species as one responsible for the generally high degradation of isoflavones by humans. These fecal microbes are candidate biomarkers for interindividual variation in isoflavone uptake and efficacy.

  8. Discovery of Rickettsia species in Dermacentor niveus Neumann ticks by investigating the diversity of bacterial communities.

    Science.gov (United States)

    Zhuang, Lu; Wang, Cheng-Yan; Tong, Yi-Gang; Tang, Fang; Yang, Hong; Liu, Wei; Cao, Wu-Chun

    2014-09-01

    Ticks (Dermacentor niveus Neumann) were collected from Tacheng, Xinjiang Uygur Autonomous Region, and their bacterial diversity was investigated using the 16S RNA gene library method from one pooled sample. A total of 452 clones was successfully sequenced and assigned to 4 phyla. The dominant phylum was the Proteobacteria, accounting for 62.8% of all the clones of the 16S rRNA gene at the confidence level 80%. The other sequences were assigned to the phyla Bacteroidetes, Firmicutes, Actinobacteria and accounted for 13.5%, 12.4%, and 11.3%, respectively. These results provide an insight into the bacterial diversity associated with D. niveus ticks in the natural environment of Tacheng. They indicate the occurrence of Rickettsia raoultii and Rickettsia slovaca in D. niveus ticks in this area, and as a consequence, cases of TIBOLA/DEBONEL may occur (tick-borne lymphadenopathy/Dermacentor-borne necrosis erythema and lymphadenopathy).

  9. Potential of Some Fungal and Bacterial Species in Bioremediation of Heavy Metals

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    Raman Kumar

    2014-02-01

    Full Text Available Microorganisms including fungi and bacteria have been reported to extract heavy metals from wastewater through bioaccumulation and biosorption. An attempt was, therefore, made to isolate bacteria and fungi from sites contaminated with heavy metals for higher tolerance and removal from wastewater. Bacterial and fungal isolates were obtained from the samples collected from Karnal, Ambala and Yamunanagar districts of Haryana using enrichment culture technique. Bacterial and fungal isolates with tolerant up to 100 ppm concentration of heavy metals (Pb, Cd, Cr were tested for their removal from liquid media containing 50 ppm concentration of Pb, Cd and Cr each. Five fungi (Penicillium chrysogenum, Aspegillus nidulans, Aspergillus flavus, Rhizopus arrhizus, Trichoderma viride were also included in this study. Fungi Aspergillus nidulans, Rhizopus arrhizus and Trichoderma viride showed maximum uptake capacity of 25.67 mg/g for Pb, 13.15 mg/g for Cd and 2.55 mg/g of Cr, respectively. The maximum uptake capacity of tolerant bacterial isolates - BPb12 and BPb16, BCd5 and BCr14 were observed to be ~ 45 mg/g for Pb, 2.12 mg/g for Cd and 3.29 mg/g for Cr, respectively. This indicated the potential of these identified fungi and bacteria as biosorbent for removal of high concentration metals from wastewater and industrial effluents.

  10. A Five Species Cyclically Dominant Evolutionary Game with Fixed Direction: A New Way to Produce Self-Organized Spatial Patterns

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    Yibin Kang

    2016-08-01

    Full Text Available Cyclically dominant systems are hot issues in academia, and they play an important role in explaining biodiversity in Nature. In this paper, we construct a five-strategy cyclically dominant system. Each individual in our system changes its strategy along a fixed direction. The dominant strategy can promote a change in the dominated strategy, and the dominated strategy can block a change in the dominant strategy. We use mean-field theory and cellular automaton simulation to discuss the evolving characters of the system. In the cellular automaton simulation, we find the emergence of spiral waves on spatial patterns without a migration rate, which suggests a new way to produce self-organized spatial patterns.

  11. Honey bees avoid nectar colonized by three bacterial species, but not by a yeast species, isolated from the bee gut.

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    Ashley P Good

    Full Text Available The gut microflora of the honey bee, Apis mellifera, is receiving increasing attention as a potential determinant of the bees' health and their efficacy as pollinators. Studies have focused primarily on the microbial taxa that appear numerically dominant in the bee gut, with the assumption that the dominant status suggests their potential importance to the bees' health. However, numerically minor taxa might also influence the bees' efficacy as pollinators, particularly if they are not only present in the gut, but also capable of growing in floral nectar and altering its chemical properties. Nonetheless, it is not well understood whether honey bees have any feeding preference for or against nectar colonized by specific microbial species. To test whether bees exhibit a preference, we conducted a series of field experiments at an apiary using synthetic nectar inoculated with specific species of bacteria or yeast that had been isolated from the bee gut, but are considered minor components of the gut microflora. These species had also been found in floral nectar. Our results indicated that honey bees avoided nectar colonized by the bacteria Asaia astilbes, Erwinia tasmaniensis, and Lactobacillus kunkeei, whereas the yeast Metschnikowia reukaufii did not affect the feeding preference of the insects. Our results also indicated that avoidance of bacteria-colonized nectar was caused not by the presence of the bacteria per se, but by the chemical changes to nectar made by the bacteria. These findings suggest that gut microbes may not only affect the bees' health as symbionts, but that some of the microbes may possibly affect the efficacy of A. mellifera as pollinators by altering nectar chemistry and influencing their foraging behavior.

  12. Christensenella timonensis, a new bacterial species isolated from the human gut

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    S. Ndongo

    2016-09-01

    Full Text Available We propose a new species, Christensenella timonensis, strain Marseille-P2437T (CSUR P2437T, which was isolated from gut microbiota of a 66-year-old patient as a part of culturomics study. C. timonensis represents the second species isolated within the Christensenella genus.

  13. In vitro inhibitory potentials of crude plant extracts on multidrug resistant bacterial species from infected human wounds

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    Yetunde A Ekanola

    2013-01-01

    Full Text Available Background: Scientific data on usage of plants to promote wound healing is exclusively scare in Nigeria. AIM: The aim of this study was to determine in vitro inhibitory potentials of crude extracts of garlic (Allium sativum and ginger (Zingiber officinale on multiple antibiotic resistant bacteria isolated from deep and superficial human wounds. Materials and Methods: Using agar disc- and modified agar well-diffusion methods, 87 wound-borne bacterial strains, Staphylococcus aureus, Proteus mirabilis and Pseudomonas aeruginosa were screened for in vitro susceptibility to 15 commonly-available antibiotic discs, 18 antibiotic drugs and three plant extracts. Results: Staph. aureus strains exhibited 52.5-97.4% resistance to antibiotic (discs, with multiple antibiotic resistance (MAR of 25.0 -100%. Between 39.1 and 95.7% of Proteus mirabilis strains resisted the antibiotics (discs, while MAR was 37.5-100%. Resistance rates displayed by Ps. aeruginosa strains were 61.5-100% with MAR of 50.0-100%. Overall antibiotic resistance patterns of respective bacterial species recorded for the antibiotic drugs were Staph. aureus (11.1-83.3%, Pr. mirabilis (16.7-77.8% and Ps. aeruginosa (16.7-50.0% and the most-resisted antibiotic drugs were axacef (55.3-82.6%, septrin (84.2-92.3%, primpex (78.3-84.6%, mediphenicol (63.2-73.1% and augmentin 1 (43.2-76.9%. All the multidrug resistant wound-borne bacterial strains exhibited minimal to moderate susceptibility towards crude extracts of garlic (17.4-34.6% and ginger (57.7-60.8%. Conclusion: Human wound-borne bacterial strains, which were multi-resistant to commonly available antibiotics (discs/drugs were minimally or moderately susceptible to crude extracts of garlic (Allium sativum and ginger (Zingiber officinale, which can be of clinical importance as herbal therapy in wound dressings or other forms of wound treatments.

  14. An enhanced vector-free allele exchange (VFAE) mutagenesis protocol for genome editing in a wide range of bacterial species.

    Science.gov (United States)

    Gomaa, Ahmed E; Zhang, Chen; Yang, Zhimin; Shang, Liguo; Jiang, Shijie; Deng, Zhiping; Zhan, Yuhua; Lu, Wei; Lin, Min; Yan, Yongliang

    2017-12-01

    Vector-free allele exchange (VFAE) is a newly developed protocol for genome editing in Pseudomonas species. Although several parameters have been determined to optimize the procedures for obtaining a stable and high-frequency mutation, numerous false-positive clones still appear on the plate, which increases the difficulty of finding the desired mutants. It has also not been established whether this protocol can be used for genome editing in other bacterial species. In the current study, the protocol was modified to dramatically decrease the occurrence of false-positive colonies using Pseudomonas stutzeri A1501 as a model strain. This improvement was reached by increasing the occurrence of circular-DNA cassettes of the correct size. Furthermore, the enhanced protocol was used to construct mutants in both the gram-negative Escherichia coli BL21 and gram-positive Bacillus subtilis 168 strains. The protocol works well in both strains, yielding ideal results with a low percentage of false-positive colonies. In summary, the enhanced VFAE mutagenesis protocol is a potential tool for use in bacterial genome editing.

  15. A survey on species and prevalence rate of bacterial agents isolated from cockroaches in three hospitals.

    Science.gov (United States)

    Zarchi, Ali Akbar Karimi; Vatani, Hadi

    2009-04-01

    The presence of cockroaches has health implications, such as nosocomial infection, as the insects move freely from areas within and around hospitals that may harbor pathogenic organisms. The goals of the present study were to determine species of bacteria isolated from cockroaches found in three Tehran hospitals, and to determine distribution of potential vectors by species and sex. The study is descriptive laboratory research. A total of 305 cockroaches from three species were trapped and identified: Periplaneta americana (65.6%), Blatella germanica (12.1%), and Blatta orientalis (22.3%). From these potential vectors, 19 species of bacteria were isolated and identified. After transportation of cockroaches to the laboratory, separation of the whole-homogenized suspension of each species was carried out. Identification of the isolated bacteria was performed according to Burgey's Manual of Determinative Bacteriology, 9th Edition. The most common species of bacteria isolated from cockroaches were Escherichia coli, Streptococcus Group D, Bacillus spp., Klebsiella pneumoniae, and Proteus vulgaris. No statistical significance was found between sex and species of cockroach carrying bacteria (p > 0.05), but significance was found for sex in Citrobacter freundii, Staphylococcus aureus, and Streptococcus non-group A&B (p < 0.05).

  16. Bacterial colonization of the phyllosphere of mediterranean perennial species as influenced by leaf structural and chemical features.

    Science.gov (United States)

    Yadav, R K P; Karamanoli, K; Vokou, D

    2005-08-01

    In this study, we assessed various leaf structural and chemical features as possible predictors of the size of the phyllosphere bacterial population in the Mediterranean environment. We examined eight perennial species, naturally occurring and coexisting in the same area, in Halkidiki (northern Greece). They are Arbutus unedo, Quercus coccifera, Pistacia lentiscus, and Myrtus communis (evergreen sclerophyllous species), Lavandula stoechas and Cistus incanus (drought semi-deciduous species), and Calamintha nepeta and Melissa officinalis (non-woody perennial species). M. communis, L. stoechas, C. nepeta, and M. officinalis produce essential oil in substantial quantities. We sampled summer leaves from these species and (1) estimated the size of the bacterial population of their phyllosphere, (2) estimated the concentration of different leaf constituents, and (3) studied leaf morphological and anatomical features and expressed them in a quantitative way. The aromatic plants are on average more highly colonized than the other species, whereas the non-woody perennials are more highly colonized than the woody species. The population size of epiphytic bacteria is positively correlated with glandular and non-glandular trichome densities, and with water and phosphorus contents; it is negatively correlated with total phenolics content and the thickness of the leaf, of the mesophyll, and of the abaxial epidermis. No correlation was found with the density of stomata, the nitrogen, and the soluble sugar contents. By regression tree analysis, we found that the leaf-microbe system can be effectively described by three leaf attributes with leaf water content being the primary explanatory attribute. Leaves with water content >73% are the most highly colonized. For leaves with water content 1.34 mg g(-1) d.w.) are more colonized, and leaves with the adaxial epidermis thicker than 20.77 microm are the least colonized. Although these critical attributes and values hold true only within

  17. Culturable bacterial communities associated to Brazilian Oscarella species (Porifera: Homoscleromorpha) and their antagonistic interactions.

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    Laport, Marinella Silva; Bauwens, Mathieu; de Oliveira Nunes, Suzanne; Willenz, Philippe; George, Isabelle; Muricy, Guilherme

    2017-04-01

    Sponges offer an excellent model to investigate invertebrate-microorganism interactions. Furthermore, bacteria associated with marine sponges represent a rich source of bioactive metabolites. The aim of this study was to characterize the bacteria inhabiting a genus of sponges, Oscarella, and their potentiality for antimicrobial production. Bacterial isolates were recovered from different Oscarella specimens, among which 337 were phylogenetically identified. The culturable community was dominated by Proteobacteria and Firmicutes, and Vibrio was the most frequently isolated genus, followed by Shewanella. When tested for antimicrobial production, bacteria of the 12 genera isolated were capable of producing antimicrobial substances. The majority of strains were involved in antagonistic interactions and inhibitory activities were also observed against bacteria of medical importance. It was more pronounced in some isolated genera (Acinetobacter, Bacillus, Photobacterium, Shewanella and Vibrio). These findings suggest that chemical antagonism could play a significant role in shaping bacterial communities within Oscarella, a genus classified as low-microbial abundance sponge. Moreover, the identified strains may contribute to the search for new sources of antimicrobial substances, an important strategy for developing therapies to treat infections caused by multidrug-resistant bacteria. This study was the first to investigate the diversity and antagonistic activity of bacteria isolated from Oscarella spp. It highlights the biotechnological potential of sponge-associated bacteria.

  18. RT-PCR–DGGE Analysis to Elucidate the Dominant Bacterial Species of Industrial Spanish-Style Green Table Olive Fermentations

    Science.gov (United States)

    Benítez-Cabello, Antonio; Bautista-Gallego, Joaquín; Garrido-Fernández, Antonio; Rantsiou, Kalliopi; Cocolin, Luca; Jiménez-Díaz, Rufino; Arroyo-López, Francisco N.

    2016-01-01

    This paper describes the dominant bacterial species metabolically active through the industrial production of Spanish-style Manzanilla and Gordal olives. For this purpose, samples (brines and fruits) obtained at 0, 15, and 90 fermentation days were analyzed by a culture-independent approach to determine viable cells by reverse transcription of RNA and further PCR-DGGE analysis, detecting at least 7 different species. Vibrio vulnificus, Lactobacillus plantarum group, and Lactobacillus parafarraginis were present in samples from both cultivars; Lactobacillus sanfranciscensis and Halolactobacillus halophilus were detected only in Gordal samples, while Staphylococcus sp. was exclusively found at the onset of Manzanilla fermentations. Physicochemical data showed a typical fermentation profile while scanning electron microscopy confirmed the in situ biofilm formation on the olive epidermis. Different Bacillus, Staphylococcus, and Enterococcus species, not detected during the fermentation process, were also found in the solid marine salt used by the industry for preparation of brines. Elucidation of these non-lactic acid bacteria species role during fermentation is then an appealingly challenge, particularly regarding safety issues. PMID:27582739

  19. Effects of Antibiotics on Bacterial Species Composition and Metabolic Activities in Chemostats Containing Defined Populations of Human Gut Microorganisms

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    Newton, Dorothy F.; Macfarlane, George T.

    2013-01-01

    The composition and metabolic activities of the human colonic microbiota are modulated by a number of external factors, including diet and antibiotic therapy. Changes in the structure and metabolism of the gut microbiota may have long-term consequences for host health. The large intestine harbors a complex microbial ecosystem comprising several hundreds of different bacterial species, which complicates investigations on intestinal physiology and ecology. To facilitate such studies, a highly simplified microbiota consisting of 14 anaerobic and facultatively anaerobic organisms (Bacteroides thetaiotaomicron, Bacteroides vulgatus, Bifidobacterium longum, Bifidobacterium infantis, Bifidobacterium pseudolongum, Bifidobacterium adolescentis, Clostridium butyricum, C. perfringens, C. bifermentans, C. innocuum, Escherichia coli, Enterococcus faecalis, Enterococcus faecium, Lactobacillus acidophilus) was used in this investigation. Ampicillin [9.2 μg (ml culture)−1] was added to two chemostats operated at different dilution rates (D; 0.10 h−1 and 0.21 h−1), and metronidazole [76.9 μg (ml culture)−1] was added to a third vessel (D = 0.21 h−1). Perturbations in bacterial physiology and metabolism were sampled over a 48-h period. Lactobacillus acidophilus and C. bifermentans populations did not establish in the fermentors under the imposed growth conditions. Ampicillin resulted in substantial reductions in bacteroides and C. perfringens populations at both dilution rates. Metronidazole strongly affected bacteroides communities but had no effect on bifidobacterial communities. The bacteriostatic effect of ampicillin on bifidobacterial species was growth rate dependent. Several metabolic activities were affected by antibiotic addition, including fermentation product formation and enzyme synthesis. The growth of antibiotic-resistant bifidobacteria in the large bowel may enable them to occupy ecological niches left vacant after antibiotic administration, preventing

  20. Corals form characteristic associations with symbiotic nitrogen-fixing bacteria.

    Science.gov (United States)

    Lema, Kimberley A; Willis, Bette L; Bourne, David G

    2012-05-01

    The complex symbiotic relationship between corals and their dinoflagellate partner Symbiodinium is believed to be sustained through close associations with mutualistic bacterial communities, though little is known about coral associations with bacterial groups able to fix nitrogen (diazotrophs). In this study, we investigated the diversity of diazotrophic bacterial communities associated with three common coral species (Acropora millepora, Acropora muricata, and Pocillopora damicormis) from three midshelf locations of the Great Barrier Reef (GBR) by profiling the conserved subunit of the nifH gene, which encodes the dinitrogenase iron protein. Comparisons of diazotrophic community diversity among coral tissue and mucus microenvironments and the surrounding seawater revealed that corals harbor diverse nifH phylotypes that differ between tissue and mucus microhabitats. Coral mucus nifH sequences displayed high heterogeneity, and many bacterial groups overlapped with those found in seawater. Moreover, coral mucus diazotrophs were specific neither to coral species nor to reef location, reflecting the ephemeral nature of coral mucus. In contrast, the dominant diazotrophic bacteria in tissue samples differed among coral species, with differences remaining consistent at all three reefs, indicating that coral-diazotroph associations are species specific. Notably, dominant diazotrophs for all coral species were closely related to the bacterial group rhizobia, which represented 71% of the total sequences retrieved from tissue samples. The species specificity of coral-diazotroph associations further supports the coral holobiont model that bacterial groups associated with corals are conserved. Our results suggest that, as in terrestrial plants, rhizobia have developed a mutualistic relationship with corals and may contribute fixed nitrogen to Symbiodinium.

  1. Bacterial infections from aquatic species: potential for and prevention of contact zoonoses.

    Science.gov (United States)

    Haenen, O L M; Evans, J J; Berthe, F

    2013-08-01

    As aquaculture production and the consumption of aquaculture products increase, the possibility of contracting zoonotic infections from either handling or ingesting these products also increases. The principal pathogens acquired topically from fish or shellfish through spine/pincer puncture or open wounds are Aeromonas hydrophila, Edwardsiella tarda, Mycobacterium marinum, Streptococcus iniae, Vibrio vulnificus and V. damsela. These pathogens, which are all indigenous to the aquatic environment, have also been associated with disease outbreaks in food fish. Outbreaks are often related to management factors, such as the quality and quantity of nutrients in the water and high stocking density, which can increase bacterial loads on the external surface of the fish. As a result, diseased fish are more likely to transmit infection to humans. This review provides an account of human cases of zoonoses throughout the world from the principal zoonotic pathogens of fish and shellfish.

  2. Nutritional stress induces exchange of cell material and energetic coupling between bacterial species.

    Science.gov (United States)

    Benomar, Saida; Ranava, David; Cárdenas, María Luz; Trably, Eric; Rafrafi, Yan; Ducret, Adrien; Hamelin, Jérôme; Lojou, Elisabeth; Steyer, Jean-Philippe; Giudici-Orticoni, Marie-Thérèse

    2015-02-23

    Knowledge of the behaviour of bacterial communities is crucial for understanding biogeochemical cycles and developing environmental biotechnology. Here we demonstrate the formation of an artificial consortium between two anaerobic bacteria, Clostridium acetobutylicum (Gram-positive) and Desulfovibrio vulgaris Hildenborough (Gram-negative, sulfate-reducing) in which physical interactions between the two partners induce emergent properties. Molecular and cellular approaches show that tight cell-cell interactions are associated with an exchange of molecules, including proteins, which allows the growth of one partner (D. vulgaris) in spite of the shortage of nutrients. This physical interaction induces changes in expression of two genes encoding enzymes at the pyruvate crossroads, with concomitant changes in the distribution of metabolic fluxes, and allows a substantial increase in hydrogen production without requiring genetic engineering. The stress induced by the shortage of nutrients of D. vulgaris appears to trigger the interaction.

  3. Pacaella massiliensis gen. nov., sp. nov., a new bacterial species isolated from the human gut

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    S. Ndongo

    2017-03-01

    Full Text Available Herein, we report the main characteristics of a new species named Pacaella massiliensis gen. nov., sp. nov., strain Marseille-P2670T (CSUR P2670 that was isolated from the gut microbiota of a 45-year-old French patient.

  4. Quantification of bacterial species of the vaginal microbiome in different groups of women, using nucleic acid amplification tests

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    Jespers Vicky

    2012-05-01

    Full Text Available Abstract Background The vaginal microbiome plays an important role in urogenital health. Quantitative real time Polymerase Chain Reaction (qPCR assays for the most prevalent vaginal Lactobacillus species and bacterial vaginosis species G. vaginalis and A. vaginae exist, but qPCR information regarding variation over time is still very limited. We set up qPCR assays for a selection of seven species and defined the temporal variation over three menstrual cycles in a healthy Caucasian population with a normal Nugent score. We also explored differences in qPCR data between these healthy women and an ‘at risk’ clinic population of Caucasian, African and Asian women with and without bacterial vaginosis (BV, as defined by the Nugent score. Results Temporal stability of the Lactobacillus species counts was high with L. crispatus counts of 108 copies/mL and L. vaginalis counts of 106 copies/mL. We identified 2 types of ‘normal flora’ and one ‘BV type flora’ with latent class analysis on the combined data of all women. The first group was particularly common in women with a normal Nugent score and was characterized by a high frequency of L. crispatus, L. iners, L. jensenii, and L. vaginalis and a correspondingly low frequency of L. gasseri and A. vaginae. The second group was characterized by the predominance of L. gasseri and L. vaginalis and was found most commonly in healthy Caucasian women. The third group was commonest in women with a high Nugent score but was also seen in a subset of African and Asian women with a low Nugent score and was characterized by the absence of Lactobacillus species (except for L. iners but the presence of G. vaginalis and A. vaginae. Conclusions We have shown that the quantification of specific bacteria by qPCR contributes to a better description of the non-BV vaginal microbiome, but we also demonstrated that differences in populations such as risk and ethnicity also have to be taken into account. We believe

  5. Detection of reactive oxygen species during the cell cycle under normal culture conditions using a modified fixed-sample staining method.

    Science.gov (United States)

    Hsieh, Chia-Yuan; Chen, Chia-Ling; Yang, Kao-Chi; Ma, Ching-Ting; Choi, Pui-Ching; Lin, Chiou-Feng

    2015-01-01

    We developed an alternative method of simultaneously monitoring the generation of reactive oxygen species (ROS) and cellular oxidative responses using the oxidation-sensitive fluorescent probe dichlorofluorescein (DCF) in fixed samples. In this study, we evaluated the ability of this method to detect ROS generation during the cell cycle under normal culture conditions using flow cytometric analyses. Among the fixatives tested, only acetone and paraformaldehyde did not alter the endogenous oxidation of the responsive dye 5-(and-6)-chloromethyl-2',7'-dichlorodihydrofluorescein diacetate (CM-H2DCFDA), which is a chloromethyl derivative of H2DCFDA. Only acetone fixation followed by staining with propidium iodide was able to detect ROS generation during the cell cycle without altering DCF oxidation. Further thymidine treatment led to cell cycle arrest at the G1 phase followed by the downregulation of total intracellular ROS. Paraformaldehyde-based fixation enabled the evaluation of ROS generation by immunostaining at a different phase of the cell cycle, whereas MPM2 co-staining enabled identification of the specific mitotic phase. This study demonstrates a modified fixed-sample method that can be used to measure intracellular ROS production during the cell cycle using standard immunostaining techniques.

  6. Time-kill behaviour against eight bacterial species and cytotoxicity of antibacterial monomers.

    Science.gov (United States)

    Li, Fang; Weir, Michael D; Fouad, Ashraf F; Xu, Hockin H K

    2013-10-01

    The objectives of this study were to investigate: (1) the antibacterial activity of two antibacterial monomers, dimethylaminododecyl methacrylate (DMADDM) and dimethylammoniumethyl dimethacrylate (DMAEDM), against eight different species of oral pathogens for the first time; (2) the cytotoxicity of DMAEDM and DMADDM. DMAEDM and DMADDM were synthesized by reacting a tertiary amine group with an organo-halide. Minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) against eight species of bacteria were tested. Time-kill determinations were performed to examine the bactericidal kinetics. Cytotoxicity of monomers on human gingival fibroblasts (HGF) was assessed using a methyl thiazolyltetrazolium assay and live/dead viability assay. DMADDM showed strong bactericidal activity against all bacteria, with MIC of 1.2-9.8μg/mL. DMAEDM had MIC of 20-80mg/mL. Time-kill determinations indicated that DMADDM and DMAEDM had rapid killing effects against eight species of bacteria, and eliminated all bacteria in 30min at the concentration of 4-fold MBC. Median lethal concentration for DMADDM and DMAEDM was between 20 and 40μg/mL, which was 20-fold higher than 1-2μg/mL for BisGMA control. DMAEDM and DMADDM were tested in time-kill assay against eight species of oral bacteria for the first time. Both were effective in bacteria-inhibition, but DMADDM had a higher potency than DMAEDM. Different killing efficacy was found against different bacteria species. DMAEDM and DMADDM had much lower cytotoxicity than BisGMA. Therefore, DMADDM and DMAEDM are promising for use in bonding agents and other restorative/preventive materials to combat a variety of oral pathogens. Published by Elsevier Ltd.

  7. Cytotoxic responses to 405nm light exposure in mammalian and bacterial cells: Involvement of reactive oxygen species.

    Science.gov (United States)

    Ramakrishnan, Praveen; Maclean, Michelle; MacGregor, Scott J; Anderson, John G; Grant, M Helen

    2016-06-01

    Light at wavelength 405 nm is an effective bactericide. Previous studies showed that exposing mammalian cells to 405 nm light at 36 J/cm(2) (a bactericidal dose) had no significant effect on normal cell function, although at higher doses (54 J/cm(2)), mammalian cell death became evident. This research demonstrates that mammalian and bacterial cell toxicity induced by 405 nm light exposure is accompanied by reactive oxygen species production, as detected by generation of fluorescence from 6-carboxy-2',7'-dichlorodihydrofluorescein diacetate. As indicators of the resulting oxidative stress in mammalian cells, a decrease in intracellular reduced glutathione content and a corresponding increase in the efflux of oxidised glutathione were observed from 405 nm light treated cells. The mammalian cells were significantly protected from dying at 54 J/cm(2) in the presence of catalase, which detoxifies H2O2. Bacterial cells were significantly protected by sodium pyruvate (H2O2 scavenger) and by a combination of free radical scavengers (sodium pyruvate, dimethyl thiourea (OH scavenger) and catalase) at 162 and 324 J/cm(2). Results therefore suggested that the cytotoxic mechanism of 405 nm light in mammalian cells and bacteria could be oxidative stress involving predominantly H2O2 generation, with other ROS contributing to the damage.

  8. A. actinomycetemcomitans profile and red complex bacterial species of an Afro-Brazilian community: A comparative study.

    Science.gov (United States)

    de Araujo Neris, Murilo; Cortelli, Sheila Cavalca; Aquino, Davi Romeiro; de Miranda, Taís Browne; Costa, Fernando de Oliveira; Cortelli, José Roberto

    2015-05-01

    The primary aim of this cross-sectional study was to compare the levels of red complex bacteria between Afro-Brazilian and non Afro-Brazilian cohort. The secondary aim was to compare the distribution of both Aggregatibacter actinomycetemcomitans serotype b and its JP2 strains among participants who harboured this bacterial species. A total of 84 individuals were included in this study: 42 Afro-descendants (mean age 35.9 ± 13.1 years) and 42 non-Afro-descendants (mean age 36.2 ± 13.1 years) matched (1:1) by periodontal diagnosis, age and gender. All participants received clinical examinations of periodontal pocket depth, clinical attachment level, and plaque and gingival indices. Subgingival samples were taken for microbial analysis. First, genomic DNA (gDNA) was extracted and purified and the quantification of total number of bacterial cells, A. actinomycetemcomitans, Porphyromonas gingivalis, Tannerella forsythia and Treponema denticola was carried out by qPCR. Then, A. actinomycetemcomitans strains were classified according to serotype b and JP2 profiles by conventional PCR. Clinically, mean PD, mean CAL and percentage of CAL ≥ 3 mm differed between groups (Student's t-test pAfro-descendant populations are preferably colonised by A. actinomycetemcomitans serotype b as well as JP2 strains. Copyright © 2015 Elsevier Ltd. All rights reserved.

  9. An empirical strategy for characterizing bacterial proteomes across species in the absence of genomic sequences.

    Directory of Open Access Journals (Sweden)

    Joshua E Turse

    Full Text Available Global protein identification through current proteomics methods typically depends on the availability of sequenced genomes. In spite of increasingly high throughput sequencing technologies, this information is not available for every microorganism and rarely available for entire microbial communities. Nevertheless, the protein-level homology that exists between related bacteria makes it possible to extract biological information from the proteome of an organism or microbial community by using the genomic sequences of a near neighbor organism. Here, we demonstrate a trans-organism search strategy for determining the extent to which near-neighbor genome sequences can be applied to identify proteins in unsequenced environmental isolates. In proof of concept testing, we found that within a CLUSTAL W distance of 0.089, near-neighbor genomes successfully identified a high percentage of proteins within an organism. Application of this strategy to characterize environmental bacterial isolates lacking sequenced genomes, but having 16S rDNA sequence similarity to Shewanella resulted in the identification of 300-500 proteins in each strain. The majority of identified pathways mapped to core processes, as well as to processes unique to the Shewanellae, in particular to the presence of c-type cytochromes. Examples of core functional categories include energy metabolism, protein and nucleotide synthesis and cofactor biosynthesis, allowing classification of bacteria by observation of conserved processes. Additionally, within these core functionalities, we observed proteins involved in the alternative lactate utilization pathway, recently described in Shewanella.

  10. An Empirical Strategy for Characterizing Bacterial Proteomes across Species in the Absence of Genomic Sequences

    Science.gov (United States)

    Turse, Joshua E.; Marshall, Matthew J.; Fredrickson, James K.; Lipton, Mary S.; Callister, Stephen J.

    2010-01-01

    Global protein identification through current proteomics methods typically depends on the availability of sequenced genomes. In spite of increasingly high throughput sequencing technologies, this information is not available for every microorganism and rarely available for entire microbial communities. Nevertheless, the protein-level homology that exists between related bacteria makes it possible to extract biological information from the proteome of an organism or microbial community by using the genomic sequences of a near neighbor organism. Here, we demonstrate a trans-organism search strategy for determining the extent to which near-neighbor genome sequences can be applied to identify proteins in unsequenced environmental isolates. In proof of concept testing, we found that within a CLUSTAL W distance of 0.089, near-neighbor genomes successfully identified a high percentage of proteins within an organism. Application of this strategy to characterize environmental bacterial isolates lacking sequenced genomes, but having 16S rDNA sequence similarity to Shewanella resulted in the identification of 300–500 proteins in each strain. The majority of identified pathways mapped to core processes, as well as to processes unique to the Shewanellae, in particular to the presence of c-type cytochromes. Examples of core functional categories include energy metabolism, protein and nucleotide synthesis and cofactor biosynthesis, allowing classification of bacteria by observation of conserved processes. Additionally, within these core functionalities, we observed proteins involved in the alternative lactate utilization pathway, recently described in Shewanella. PMID:21103051

  11. Characterization of a Single Magnetotactic Bacterial Species from Devil's Bathtub, Mendon Ponds Park, Honeoye Falls, NY

    Science.gov (United States)

    Wagner, C.; Tarduno, J. A.; Stein, A.; Sia, E.

    2015-12-01

    Magnetotactic bacteria (MTB) belong to a lineage of prokaryotic bacteria that synthesize magnetosomes, single domain magnetic particles (typically magnetite or greigite) with an average size of 50 nanometers. MTB utilize magnetosomes through magnetotaxis, the alignment and movement along magnetic field lines to navigate towards preferred environmental conditions. MTB are sensitive to different environments and are thought to exhibit varying magnetosome morphologies, compositions, sizes, and quantities in regards to the environments which they inhabit. These characteristics allow MTB and magnetofossils (preserved magnetosomes) to be used as modern/paleoenvironmental recorders and biomarkers for environmental change(s). Devil's Bathtub (Mendon Ponds Park, Honeoye Falls, NY) is a meromictic glacial kettle pond surrounded by deciduous tree cover. Here we examine one species of MTB based on prominence of this particular morphology at this locale. Magnetotaxis and morphology of this species have been observed using light microscopy. Micrographs have also been taken using Transmission Electron Microscopy (TEM) to verify cell morphology and to determine magnetosome morphology. TEM and magnetic hysteresis measurements were done to find and test the composition of magnetosomes. In this study we also focus on DNA sequencing and characterization of this MTB, as there are few MTB species which have been DNA sequenced successfully. Data from these experiments are directly applicable to this up-and-coming area of research as it will aid in the understanding and correlation of magnetosome and magnetofossils with environmental characteristics.

  12. Biodegradation of free cyanide by bacterial species isolated from cyanide-contaminated artisanal gold mining catchment area in Burkina Faso.

    Science.gov (United States)

    Razanamahandry, Lovasoa Christine; Andrianisa, Harinaivo Anderson; Karoui, Hela; Kouakou, Koffi Marcelin; Yacouba, Hamma

    2016-08-01

    Soil and water samples were collected from a watershed in Burkina Faso where illegal artisanal gold extraction using cyanidation occurs. The samples were used to evaluate cyanide contamination and the presence of cyanide degrading bacteria (CDB). Free cyanide (F-CN) was detected in all samples, with concentrations varying from 0.023 to 0.9 mg kg(-1), and 0.7-23 μg L(-1) in the soil and water samples, respectively. Potential CDB also were present in the samples. To test the effective F-CN degradation capacity of the isolated CDB species, the species were cultivated in growth media containing 40, 60 or 80 mg F-CN L(-1), with or without nutrients, at pH 9.5 and at room temperature. More than 95% of F-CN was degraded within 25 h, and F-CN degradation was associated with bacterial growth and ammonium production. However, initial concentrations of F-CN higher than 100 mg L(-1) inhibited bacterial growth and cyanide degradation. Abiotic tests showed that less than 3% of F-CN was removed by volatilization. Thus, the degradation of F-CN occurred predominately by biological mechanisms, and such mechanisms are recommended for remediation of contaminated soil and water. The bacteria consortium used in the experiment described above exist in a Sahelian climate, which is characterized by a long hot and dry season. Because the bacteria are already adapted to the local climate conditions and show the potential for cyanide biodegradation, further applicability to other contaminated areas in West Africa, where illegal gold cyanidation is widespread, should be explored. Copyright © 2016 Elsevier Ltd. All rights reserved.

  13. Diversity of bacterial species in the nasal cavity of sheep in the highlands of Ethiopia and first report of Histophilus somni in the country.

    Science.gov (United States)

    Tesfaye, Biruk; Sisay Tessema, Tesfaye; Tefera, Genene

    2013-06-01

    A study was conducted to isolate bacterial species/pathogens from the nasal cavity of apparently healthy and pneumonic sheep. Nasal swabs were collected aseptically, transported in tryptose soya broth and incubated for 24 h. Then, each swab was streaked onto chocolate and blood agar for culture. Bacterial species were identified following standard bacteriological procedures. Accordingly, a total of 1,556 bacteria were isolated from 960 nasal swabs collected from three different highland areas of Ethiopia, namely Debre Berhan, Asella, and Gimba. In Debre Berhan, 140 Mannheimia haemolytica, 81 Histophilus somni, 57 Staphylococcus species, and 52 Bibersteinia trehalosi were isolated. While from Gimba M. haemolytica, Staphylococcus, Streptococcus, and H. somni were isolated at rates of 25.2, 15.9, 11.4, and 5.9 %, respectively, of the total 647 bacterial species. In Asella from 352 bacterial species isolated, 93 (26.4 %) were M. haemolytica, 48 (13.6 %) were Staphylococcus species, 26 (7.4 %) were B. trehalosi, and 17 (4.8 %) H. somni were recognized. Further identification and characterization using BIOLOG identification system Enterococcus avium and Sphingomonas sanguinis were identified at 100 % probability, while, H. somni and Actinobacillus lignerisii were suggested by the system. The study showed that a variety of bacterial species colonize the nasal cavity of the Ethiopian highland sheep with variable proportion between healthy and pneumonic ones. To our knowledge, this is the first report on isolation of H. somni, an important pathogen in cattle, from the respiratory tract of a ruminant species in the country.

  14. Diversity and distribution of culturable lactic acid bacterial species in Indonesian Sayur Asin

    Directory of Open Access Journals (Sweden)

    Wibowo Mangunwardoyo

    2016-12-01

    Full Text Available Background and Objectives: Lactic acid bacteria (LAB play important roles in processing of Sayur Asin (spontaneously fermented mustard. Unfortunately, information about LAB in Indonesian Sayur Asin, prepared by traditional manufactures which is important as baseline data for maintenance of food quality and safety, is unclear. The aim of this study was to describe the diversity and distribution of culturable lactic acid bacteria in Sayur Asin of Indonesia.Materials and Methods: Four Sayur Asin samples (fermentation liquor and fermented mustard were collected at harvesting times (3-7 days after fermentation from two traditional manufactures in Tulung Agung (TA and Kediri (KDR, East Java provinces, Indonesia. LAB strains were isolated by using MRS agar method supplemented with 1% CaCO3 and characterized morphologically. Identification of the strains was performed basedon 16S rDNA analysis and the phylogenetic tree was drawn to understand the phylogenetic relationship of the collected strains.Results: Different profiles were detected in total count of the plates, salinity and pH of fermenting liquor of Sayur Asin in TA and KDR provinces. A total of 172 LAB isolates were successfully isolated and identified based on their 16S rDNA sequences. Phylogenetic analysis of 27 representative LAB strains from Sayur Asin showed that these strains belonged to 5 distinct species namely Lactobacilus farciminis (N=32, L. fermentum (N=4, L. namurensis (N=15, L. plantarum (N=118 and L. parafarraginis (N=1. Strains D5-S-2013 and B4-S-2013 showed a close phylogenetic relationship with L. composti and L. paralimentarius, respectively where as the sequence had slightly lower similarity of lower than 99%, suggesting that they may be classified into novel species and need further investigation due to exhibition of significant differences in their nucleotide sequences. Lactobacillus plantarum was found being dominant in all sayur asin samples.Conclusion: Lactobacilli were

  15. Helicobacter species and common gut bacterial DNA in gallbladder with cholecystitis

    Institute of Scientific and Technical Information of China (English)

    Peren; H; Karagin; Unne; Stenram; Torkel; Wadstrm; sa; Ljungh

    2010-01-01

    AIM:To analyze the association between Helicobacter spp. and some common gut bacteria in patients with cholecystitis. METHODS:A nested-polymerase chain reaction (PCR), specif ic to 16S rRNA of Helicobacter spp. was performed on paraff in-embedded gallbladder samples of 100 cholecystitis and 102 control cases. The samples were also analyzed for some common gut bacteria by PCR. Positive samples were sequenced for species identif ication. RESULTS: Helicobacter DNA was found in seven out of 100 cases of acute a...

  16. 三个乡土树种苗期微生物菌肥施肥效应的研究%Fertilization effects of microorganism bacterial fertilizer on seedling stage of three indigenous tree species

    Institute of Scientific and Technical Information of China (English)

    胡彩颜; 康丽华; 江业根; 王胜坤

    2011-01-01

    The fertilization trial of microorganism bacterial fertilizer on seedling stage of three indigenous tree species was conducted in order to study effects of bacteria fertilizer to growth, biomass and nutrient accumulation of seedling for three indigenous tree species. The trial results show that the bacterial fertilizer applied could high markedly increase the growth of seedling with a seedling height of 9.0% ~ 14.5% compared to the contrast (no bacterial fertilizer). The bacterial fertilizer applied could high markedly increase the biomass of seedling, especially in nitrogen-fixing and phosphate-dissolving bacterial fertilizer, which the dry weights of over-ground, underground and whole plant could be increased 89.3%, 50.2% and 67.8% respectively compared with the contrast. The bacterial fertilizer applied also could high markedly increase nutrient accumulation of nitrogen (N) and phosphors (P) for seedling, especially in nitrogen-fixing and phosphate-dissolving bacterial fertilizer applied, which the nutrient accumulations of over-ground, underground and whole plant could be increased 85.0%, 71.0% and 78.8% for N accumulation, 75.5%, 51.7% and 63.5% for P accumulation, respectively compared with the contrast. The effects of bacterial fertilizer applied on height growth, biomass and nutrient accumulation rank from big to small as follows: Cinnamomum camphora, Elaeocarpus apiculatus and Castanopsis hystrix.%对三个乡土树种苗木进行微生物菌肥施肥试验,研究菌肥对不同树种苗木的生长、生物量和养分积累的影响.结果表明:菌肥可显著提高苗木的生长,苗高生长比对照提高了9.0%~14.5%;菌肥可极显著增加苗木生物量,尤其是施固氮溶磷肥处理比对照在地上部分干重、地下干重部分和全株干重分别增加了89.3%、50.2%和67.8%,效果极显著;施用菌肥极显著增加了苗木的N和P养分积累,尤其是施固氮溶磷肥在地上部分、地下部分和全株的N

  17. Helicobacter species and gut bacterial DNA in Meckel's diverticulum and the appendix

    Institute of Scientific and Technical Information of China (English)

    Peren H Karagin; Unne Stenram; Torkel Wadstr(o)m; (A)sa Ljungh

    2011-01-01

    AIM: To analyse the possible association of various Helicobacter species and certain common gut bacteria in patients with Meckel's diverticulum and appendicitis. METHODS: A nested-polymerase chain reaction (PCR), specific to 16S rRNA of the Helicobacter genus, was performed on paraffin embedded samples, 50 with acute appendicitis, 50 normal appendixes, and 33 Meckel's diverticulum with gastric heterotopia and/or ulcer. Helicobacter genus positive samples were sequenced for species identification. All samples were also analysed for certain gut bacteria by PCR. RESULTS: Helicobacter pullorum DNA was found in one out of 33 cases and Enterobacteria in two cases of Meckel's diverticulum. Helicobacter pylori (H. pylori ) was found in three, Enterobacter in 18, and Bacteroides in 19 out of 100 appendix samples by PCR. Enterococcus was not found in any MD or appendix samples. All H. pylori positive cases were from normal appendixes. CONCLUSION: Helicobacter is not an etiological agent in the pathogenesis of symptomatic Meckel's diverticulum or in acute appendicitis.

  18. MLPA diagnostics of complex microbial communities: relative quantification of bacterial species in oral biofilms.

    Science.gov (United States)

    Terefework, Zewdu; Pham, Chi L; Prosperi, Anja C; Entius, Mark M; Errami, Abdellatif; van Spanning, Rob J M; Zaura, Egija; Ten Cate, Jacob M; Crielaard, Wim

    2008-12-01

    A multitude of molecular methods are currently used for identification and characterization of oral biofilms or for community profiling. However, multiplex PCR techniques that are able to routinely identify several species in a single assay are not available. Multiplex Ligation-dependent Probe Amplification (MLPA) identifies up to 45 unique fragments in a single tube PCR. Here we report a novel use of MLPA in the relative quantification of targeted microorganisms in a community of oral microbiota. We designed 9 species specific probes for: Actinomyces gerencseriae, Actinomyces naeslundii, Actinomyces odontolyticus, Candida albicans, Lactobacillus acidophilus, Rothia dentocariosa, Streptococcus mutans, Streptococcus sanguinis and Veillonella parvula; and genus specific probes for selected oral Streptococci and Lactobacilli based on their 16S rDNA sequences. MLPA analysis of DNA pooled from the strains showed the expected specific MLPA products. Relative quantification of a serial dilution of equimolar DNA showed that as little as 10 pg templates can be detected with clearly discernible signals. Moreover, a 2 to 7% divergence in relative signal ratio of amplified probes observed from normalized peak area values suggests MLPA can be a cheaper alternative to using qPCR for quantification. We observed 2 to 6 fold fluctuations in signal intensities of MLPA products in DNAs isolated from multispecies biofilms grown in various media for various culture times. Furthermore, MLPA analyses of DNA isolated from saliva obtained from different donors gave a varying number and intensity of signals. This clearly shows the usefulness of MLPA in a quantitative description of microbial shifts.

  19. PCR-dipstick DNA chromatography for profiling of a subgroup of caries-associated bacterial species in plaque from healthy coronal surfaces and periodontal pockets.

    Science.gov (United States)

    Tian, Lingyang; Sato, Takuichi; Niwa, Kousuke; Kawase, Mitsuo; Mayanagi, Gen; Washio, Jumpei; Takahashi, Nobuhiro

    2016-01-01

    The onset of plaque-mediated disease, including dental caries and periodontal diseases, is highly associated with compositional change of the resident microflora from the ecological perspective. As specific bacterial profiles have been linked to different disease stages, microbial compositional measurements might therefore have great value for clinical diagnosis. Previously we have reported a dry-reagent strip biosensor-PCR-dipstick DNA chromatography, which utilized molecular recognition of oligonucleotides and biotin-streptavidin, and the optical property of colored microspheres, for semiquantifying a five-membered subgroup of caries-associated bacterial species in supragingival plaque from healthy coronal surfaces of teeth. The present study aimed to evaluate this technique's ability to differentiate microflora by comparing the subset profiles. Sixteen subgingival plaque specimens were pooled from periodontal pockets and analyzed for the composition of Streptococcus mutans, Streptococcus sobrinus, Scardovia wiggsiae, Actinomyces sp. and Veillonella parvula. Detection frequencies, relative abundance of each bacterial species, and the five-membered bacterial profiles were compared between supra- and subgingival groups. The supragingival plaque harbored significantly more of the tested species and higher amount of Actinomyces sp. and V. parvula. In subgingival plaque, the predominance was obscured, since several highly overlapped profiles were found at comparable frequencies. Thus, PCR-dipstick DNA chromatography using the same plaque sample enabled simultaneous profiling of multiple species at species level and facilitated discrimination between anticipated different microflora, making this technique a promising chair-side microbiota profiling method.

  20. Analysis of early bacterial communities on volcanic deposits on the island of Miyake (Miyake-jima), Japan: a 6-year study at a fixed site.

    Science.gov (United States)

    Fujimura, Reiko; Sato, Yoshinori; Nishizawa, Tomoyasu; Nanba, Kenji; Oshima, Kenshiro; Hattori, Masahira; Kamijo, Takashi; Ohta, Hiroyuki

    2012-01-01

    Microbial colonization on new terrestrial substrates represents the initiation of new soil ecosystem formation. In this study, we analyzed early bacterial communities growing on volcanic ash deposits derived from the 2000 Mount Oyama eruption on the island of Miyake (Miyake-jima), Japan. A site was established in an unvegetated area near the summit and investigated over a 6-year period from 2003 to 2009. Collected samples were acidic (pH 3.0-3.6), did not utilize any organic substrates in ECO microplate assays (Biolog), and harbored around 106 cells (g dry weight)(-1) of autotrophic Fe(II) oxidizers by most-probable-number (MPN) counts. Acidithiobacillus ferrooxidans, Acidithiobacillus ferrivorans, and the Leptospirillum groups I, II and III were found to be abundant in the deposits by clone library analysis of bacterial 16S rRNA genes. The numerical dominance of Acidithiobacillus ferrooxidans was also supported by analysis of the gene coding for the large subunit of the form I ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO). Comparing the 16S rRNA gene clone libraries from samples differing in age, shifts in Fe(II)-oxidizing populations seemed to occur with deposit aging. The detection of known 16S rRNA gene sequences from Fe(III)-reducing acidophiles promoted us to propose the acidity-driven iron cycle for the early microbial ecosystem on the deposit.

  1. Peracetic acid treatment generates potent inactivated oral vaccines from a broad range of culturable bacterial species

    Directory of Open Access Journals (Sweden)

    Kathrin eMoor

    2016-02-01

    Full Text Available Our mucosal surfaces are the main sites of non-vector-borne pathogen entry, as well as the main interface with our commensal microbiota. We are still only beginning to understand how mucosal adaptive immunity interacts with commensal and pathogenic microbes to influence factors such as infectivity, phenotypic diversity and within-host evolution. This is in part due to difficulties in generating specific mucosal adaptive immune responses without disrupting the mucosal microbial ecosystem itself. Here we present a very simple tool to generate inactivated mucosal vaccines from a broad range of culturable bacteria. Oral gavage of 1010 peracetic acid-inactivated bacteria induces high-titer specific intestinal IgA in the absence of any measurable inflammation or species invasion. As a proof of principal, we demonstrate that this technique is sufficient to provide fully protective immunity in the murine model of invasive non-typhoidal Salmonellosis, even in the face of severe innate immune deficiency.

  2. Helicobacter species and common gut bacterial DNA in gallbladder with cholecystitis

    Science.gov (United States)

    Karagin, Peren H; Stenram, Unne; Wadström, Torkel; Ljungh, Åsa

    2010-01-01

    AIM: To analyze the association between Helicobacter spp. and some common gut bacteria in patients with cholecystitis. METHODS: A nested-polymerase chain reaction (PCR), specific to 16S rRNA of Helicobacter spp. was performed on paraffin-embedded gallbladder samples of 100 cholecystitis and 102 control cases. The samples were also analyzed for some common gut bacteria by PCR. Positive samples were sequenced for species identification. RESULTS: Helicobacter DNA was found in seven out of 100 cases of acute and chronic cholecystitis. Sequence analysis displayed Helicobacter pullorum (H. pullorum) in six cases and Helicobacter pylori in one; H. pullorum was only found in cases with metaplasia. Control samples were negative for Helicobacter spp. and some common gut bacteria. There was a significant difference (P = 0.007) between cholecystitis and control samples for Helicobacter DNA. CONCLUSION: A possible relationship was detected between Helicobacter DNA and cholecystitis. Further serological and immunohistochemical studies are needed to support these data. PMID:20939110

  3. Isolation and characterization of a novel violacein-like pigment producing psychrotrophic bacterial species Janthinobacterium svalbardensis sp. nov.

    Science.gov (United States)

    Ambrožič Avguštin, Jerneja; Žgur Bertok, Darja; Kostanjšek, Rok; Avguštin, Gorazd

    2013-04-01

    A bacterial strain designated JA-1, related to Janthinobacterium lividum, was isolated from glacier ice samples from the island Spitsbergen in the Arctic. The strain was tested for phenotypic traits and the most prominent appeared to be the dark red brown to black pigmentation different from the violet pigment of Janthinobacterium, Chromobacterium and Iodobacter. Phylogenetic analysis based on 16S rRNA gene sequences and DNA-DNA hybridization tests showed that strain JA-1 belongs to the genus Janthinobacterium but represents a novel lineage distinct from the two known species of this genus, J. lividum and Janthinobacterium agaricidamnosum. The DNA G + C content of strain JA-1 was determined to be 62.3 mol %. The isolate is a psychrotrophic Gram negative bacterium, rod-shaped with rounded ends, containing intracellular inclusions and one polar flagellum. On the basis of the presented results strain JA-1 is proposed as the type strain of a novel species of the genus Janthinobacterium, for which the name Janthinobacterium svalbardensis sp. nov. is proposed (JA-1(T) = DSM 25734, ZIM B637).

  4. Parallel Mutations Result in a Wide Range of Cooperation and Community Consequences in a Two-Species Bacterial Consortium.

    Science.gov (United States)

    Douglas, Sarah M; Chubiz, Lon M; Harcombe, William R; Ytreberg, F Marty; Marx, Christopher J

    2016-01-01

    Multi-species microbial communities play a critical role in human health, industry, and waste remediation. Recently, the evolution of synthetic consortia in the laboratory has enabled adaptation to be addressed in the context of interacting species. Using an engineered bacterial consortium, we repeatedly evolved cooperative genotypes and examined both the predictability of evolution and the phenotypes that determine community dynamics. Eight Salmonella enterica serovar Typhimurium strains evolved methionine excretion sufficient to support growth of an Escherichia coli methionine auxotroph, from whom they required excreted growth substrates. Non-synonymous mutations in metA, encoding homoserine trans-succinylase (HTS), were detected in each evolved S. enterica methionine cooperator and were shown to be necessary for cooperative consortia growth. Molecular modeling was used to predict that most of the non-synonymous mutations slightly increase the binding affinity for HTS homodimer formation. Despite this genetic parallelism and trend of increasing protein binding stability, these metA alleles gave rise to a wide range of phenotypic diversity in terms of individual versus group benefit. The cooperators with the highest methionine excretion permitted nearly two-fold faster consortia growth and supported the highest fraction of E. coli, yet also had the slowest individual growth rates compared to less cooperative strains. Thus, although the genetic basis of adaptation was quite similar across independent origins of cooperative phenotypes, quantitative measurements of metabolite production were required to predict either the individual-level growth consequences or how these propagate to community-level behavior.

  5. Impacts of silver nanoparticles on bacterial species B. subtilis and E. coli and the major crop plant Z. mays

    Science.gov (United States)

    Doody, Michael A.

    This thesis examines the impacts of citrate-coated silver nanoparticles (c-AgNPs) on two species of bacteria (Bacillus subtilis and Escherichia coli), the major crop plant Zea mays, and the beneficial plant-microbe relationship between Z. mays and B. subtilis. AgNPs are an increasing component of antimicrobial consumer, industrial, and military products. This has led to widespread scientific concern for the ecological safety outside their intended use. An overview of their history, use, and toxicity was used to inform the design of experiments and resulting data. Growth inhibition and sub-lethal toxic effects were used to assess the effects of c-AgNP exposure to bacteria. Similar analytical methods were used to quantify the response of Z. mays to c-AgNP exposure. Results showed that exposure to c-AgNP significantly reduced the growth of bacterial populations and alters their growth kinetics. Z. mays experienced significant sub-lethal effects due to exposure, including reduced root length and biomass, and hyper-accumulated Ag in root tissues. Beneficial interactions between B. subtilis and Z. mays were reduced as both species suffered sub-lethal effects of exposure to c-AgNPs.

  6. Antarctic bacterial haemoglobin and its role in the protection against nitrogen reactive species.

    Science.gov (United States)

    Coppola, Daniela; Giordano, Daniela; Tinajero-Trejo, Mariana; di Prisco, Guido; Ascenzi, Paolo; Poole, Robert K; Verde, Cinzia

    2013-09-01

    In a cold and oxygen-rich environment such as Antarctica, mechanisms for the defence against reactive oxygen and nitrogen species are needed and represent important components in the evolutionary adaptations. In the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125, the presence of multiple genes encoding 2/2 haemoglobins and a flavohaemoglobin strongly suggests that these proteins fulfil important physiological roles, perhaps associated to the peculiar features of the Antarctic habitat. In this work, the putative role of Ph-2/2HbO, encoded by the PSHAa0030 gene, was investigated by in vivo and in vitro experiments in order to highlight its involvement in NO detoxification mechanisms. The PSHAa0030 gene was cloned and then over-expressed in a flavohaemoglobin-deficient mutant of Escherichia coli, unable to metabolise NO, and the resulting strain was studied analysing its growth properties and oxygen uptake in the presence of NO. We here demonstrate that Ph-2/2HbO protects growth and cellular respiration of the heterologous host from the toxic effect of NO-donors. Unlike in Mycobacterium tuberculosis 2/2 HbN, the deletion of the N-terminal extension of Ph-2/2HbO does not seem to reduce the NO scavenging activity, showing that the N-terminal extension is not a requirement for efficient NO detoxification. Moreover, the ferric form of Ph-2/2HbO was shown to catalyse peroxynitrite isomerisation in vitro, confirming its potential role in the scavenging of reactive nitrogen species. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.

  7. Nosocomial ventilator-associated pneumonia in Cuban intensive care units: bacterial species and antibiotic resistance.

    Science.gov (United States)

    Medell, Manuel; Hart, Marcia; Duquesne, Amílcar; Espinosa, Fidel; Valdés, Rodolfo

    2013-04-01

    Nosocomial pneumonia associated with use of mechanical ventilators is one of the greatest challenges confronted by intensivists worldwide. The literature associates several bacteria with this type of infection; most common in intensive care units are Acinetobacter baumannii, Pseudomonas aeruginosa, methicillin-resistant Staphylococcus aureus and some of the Enterobacteriaceae family. To identify the causal agents of nosocomial ventilator-associated pneumonia in patients receiving mechanical ventilation in the intensive care units of Havana's Hermanos Ameijeiras Clinical-Surgical Teaching Hospital in 2011, and to characterize their antibiotic resistance. A cross-sectional descriptive study was conducted using hospital administrative data of quantitative cultures from positive tracheal aspirates for January through December, 2011. Records were analyzed from 77 intensive care unit patients who developed nosocomial ventilator-associated pneumonia. Variables examined were age and sex, and pathogens identified from culture of tracheal aspirate and related antibiotic susceptibility. RESULTS Species most frequently isolated were: Acinetobacter baumannii in 53 patients (68.8%), Pseudomonas aeruginosa in 34 patients (44.2%), other species of Pseudomonas in 15 patients (19.5%), and Serratia marcescens, Klebsiella pneumoniae, and Escherichia coli in 12 patients each (15.6%). Some patients presented more than one pathogen in concurrent or successive infections. Antimicrobial susceptibility testing found high percentages of resistance to antibiotics in all these pathogens. Least resistance was found to colistin. The prevalence of antibiotic resistance in bacteria causing nosocomial ventilator-associated pneumonia is of concern. Colistin is the drug of choice among the antibiotics reviewed, but sensitivity to other antibiotics should be assessed to search for more appropriate broad-spectrum antibiotics for treating nosocomial ventilator-associated pneumonia. Our results also

  8. Interaction of legionella pneumophila and helicobacter pylori with bacterial species isolated from drinking water biofilms

    Directory of Open Access Journals (Sweden)

    Azevedo Nuno F

    2011-03-01

    Full Text Available Abstract Background It is well established that Legionella pneumophila is a waterborne pathogen; by contrast, the mode of Helicobacter pylori transmission remains unknown but water seems to play an important role. This work aims to study the influence of five microorganisms isolated from drinking water biofilms on the survival and integration of both of these pathogens into biofilms. Results Firstly, both pathogens were studied for auto- and co-aggregation with the species isolated from drinking water; subsequently the formation of mono and dual-species biofilms by L. pneumophila or H. pylori with the same microorganisms was investigated. Neither auto- nor co-aggregation was observed between the microorganisms tested. For biofilm studies, sessile cells were quantified in terms of total cells by SYTO 9 staining, viable L. pneumophila or H. pylori cells were quantified using 16 S rRNA-specific peptide nucleic acid (PNA probes and cultivable cells by standard culture techniques. Acidovorax sp. and Sphingomonas sp. appeared to have an antagonistic effect on L. pneumophila cultivability but not on the viability (as assessed by rRNA content using the PNA probe, possibly leading to the formation of viable but noncultivable (VBNC cells, whereas Mycobacterium chelonae increased the cultivability of this pathogen. The results obtained for H. pylori showed that M. chelonae and Sphingomonas sp. help this pathogen to maintain cultivability for at least 24 hours. Conclusions It appears that M. chelonae may have an important role in the survival of both pathogens in drinking water. This work also suggests that the presence of some microorganisms can decrease the cultivability of L. pneumophila but not the viability which indicates that the presence of autochthonous microorganisms can lead to misleading results when the safety of water is assessed by cultivable methods alone.

  9. Bacterial Species-Specific Activity of a Fluoroquinolone against Two Closely Related Pasteurellaceae with Similar MICs: Differential In Vitro Inoculum Effects and In Vivo Efficacies.

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    Guillaume Lhermie

    Full Text Available We investigated the antimicrobial activity of a fluoroquinolone against two genetically close bacterial species belonging to the Pasteurellaceae family. Time-kill experiments were used to measure the in vitro activity of marbofloxacin against two strains of Mannheimia haemolytica and Pasteurella multocida with similar MICs. We observed that marbofloxacin was equally potent against 105 CFU/mL inocula M. haemolytica and P. multocida. However, an inoculum effect was observed with P. multocida, meaning that marbofloxacin activity was decreased against a 108 CFU/mL inoculum, whereas no inoculum effect was observed with M. haemolytica. Marbofloxacin activity was also tested in a lung infection model with immunocompromised mice intratracheally infected with 109 CFU of each bacteria. At the same dose, the clinical and bacteriological outcomes were much better for mice infected with M. haemolytica than for those infected with P. multocida. Moreover, bacteriological eradication was obtained with a lower marbofloxacin dose for mice infected with M. haemolytica. Our results suggest that the differential in vivo marbofloxacin efficacy observed with the two bacterial species of similar MIC could be explained by a differential inoculum effect. Consequently, MICs determined on 105 CFU inocula were not predictive of the differences in antibiotic efficacies against high bacterial inocula of closely related bacterial strains. These results could stimulate further investigations on bacterial species-specific antibiotic doses in a clinical setting.

  10. Bacterial Species-Specific Activity of a Fluoroquinolone against Two Closely Related Pasteurellaceae with Similar MICs: Differential In Vitro Inoculum Effects and In Vivo Efficacies

    Science.gov (United States)

    Lhermie, Guillaume; El Garch, Farid; Toutain, Pierre-Louis; Ferran, Aude A.; Bousquet-Mélou, Alain

    2015-01-01

    We investigated the antimicrobial activity of a fluoroquinolone against two genetically close bacterial species belonging to the Pasteurellaceae family. Time-kill experiments were used to measure the in vitro activity of marbofloxacin against two strains of Mannheimia haemolytica and Pasteurella multocida with similar MICs. We observed that marbofloxacin was equally potent against 105 CFU/mL inocula M. haemolytica and P. multocida. However, an inoculum effect was observed with P. multocida, meaning that marbofloxacin activity was decreased against a 108 CFU/mL inoculum, whereas no inoculum effect was observed with M. haemolytica. Marbofloxacin activity was also tested in a lung infection model with immunocompromised mice intratracheally infected with 109 CFU of each bacteria. At the same dose, the clinical and bacteriological outcomes were much better for mice infected with M. haemolytica than for those infected with P. multocida. Moreover, bacteriological eradication was obtained with a lower marbofloxacin dose for mice infected with M. haemolytica. Our results suggest that the differential in vivo marbofloxacin efficacy observed with the two bacterial species of similar MIC could be explained by a differential inoculum effect. Consequently, MICs determined on 105 CFU inocula were not predictive of the differences in antibiotic efficacies against high bacterial inocula of closely related bacterial strains. These results could stimulate further investigations on bacterial species-specific antibiotic doses in a clinical setting. PMID:26506096

  11. Increasing the dynamic control space of mammalian transcription devices by combinatorial assembly of homologous regulatory elements from different bacterial species.

    Science.gov (United States)

    Bacchus, William; Weber, Wilfried; Fussenegger, Martin

    2013-01-01

    Prokaryotic transcriptional regulatory elements are widely utilized building blocks for constructing regulatory genetic circuits adapted for mammalian cells and have found their way into a broad range of biotechnological applications. Prokaryotic transcriptional repressors, fused to eukaryotic transactivation or repression domains, compose the transcription factor, which binds and adjusts transcription from chimeric promoters containing the repressor-specific operator sequence. Escherichia coli and Chlamydia trachomatis share common features in the regulatory mechanism of the biosynthesis of l-tryptophan. The repressor protein TrpR of C. trachomatis regulates the trpRBA operon and the TrpR of E. coli regulates the trpEDCBA operon, both requiring l-tryptophan as a co-repressor. Fusion of these bacterial repressors to the VP16 transactivation domain of Herpes simplex virus creates synthetic transactivators that could bind and activate chimeric promoters, assembled by placing repressor-specific operator modules adjacent to a minimal promoter, in an l-tryptophan-adjustable manner. Combinations of different transactivator and promoter variants from the same or different bacterial species resulted in a multitude of regulatory systems where l-tryptophan regulation properties, background noise, and maximal gene expression levels were significantly diverse. Different l-tryptophan analogues showed diverse regulatory capacity depending on the promoter/transactivator combination. We believe the systems approach to rationally choose promoters, transactivators and inducer molecules, to obtain desired and predefined genetic expression dynamics and control profiles, will significantly advance the design of new regulatory circuits as well as improving already existing ones. Copyright © 2012 Elsevier Inc. All rights reserved.

  12. Patterns in species persistence and biomass production in soil microcosms recovering from a disturbance reject a neutral hypothesis for bacterial community assembly.

    Science.gov (United States)

    Zhang, Fen-Guo; Zhang, Quan-Guo

    2015-01-01

    The neutral theory of biodiversity has emerged as a major null hypothesis in community ecology. The neutral theory may sufficiently well explain the structuring of microbial communities as the extremely high microbial diversity has led to an expectation of high ecological equivalence among species. To address this possibility, we worked with microcosms of two soils; the microcosms were either exposed, or not, to a dilution disturbance which reduces community sizes and removes some very rare species. After incubation for recovery, changes in bacterial species composition in microcosms compared with the source soils were assessed by pyrosequencing of bacterial 16S rRNA genes. Our assays could detect species with a proportional abundance ≥ 0.0001 in each community, and changes in the abundances of these species should have occurred during the recovery growth, but not be caused by the disturbance per se. The undisturbed microcosms showed slight changes in bacterial species diversity and composition, with a small number of initially low-abundance species going extinct. In microcosms recovering from the disturbance, however, species diversity decreased dramatically (by > 50%); and in most cases there was not a positive relationship between species initial abundance and their chance of persistence. Furthermore, a positive relationship between species richness and community biomass was observed in microcosms of one soil, but not in those of the other soil. The results are not consistent with a neutral hypothesis that predicts a positive abundance-persistence relationship and a null effect of diversity on ecosystem functioning. Adaptation mechanisms, in particular those associated with species interactions including facilitation and predation, may provide better explanations.

  13. Fix 40!

    Index Scriptorium Estoniae

    2008-01-01

    Ansambel Fix peab 13. detsembril Tallinnas Saku Suurhallis oma 40. sünnipäeva. Kontserdi erikülaline on ansambel Apelsin, kaastegevad Jassi Zahharov ja HaleBopp Singers. Õhtut juhib Tarmo Leinatamm

  14. Fix 40!

    Index Scriptorium Estoniae

    2008-01-01

    Ansambel Fix peab 13. detsembril Tallinnas Saku Suurhallis oma 40. sünnipäeva. Kontserdi erikülaline on ansambel Apelsin, kaastegevad Jassi Zahharov ja HaleBopp Singers. Õhtut juhib Tarmo Leinatamm

  15. Is the C-terminal insertional signal in Gram-negative bacterial outer membrane proteins species-specific or not?

    Directory of Open Access Journals (Sweden)

    Paramasivam Nagarajan

    2012-09-01

    heterologous overexpression of almost all OMPs should be feasible in E. coli and other Gram-negative bacterial model organisms. This is relevant especially for biotechnology applications, where recombinant OMPs are used e.g. for the development of vaccines. For the species in which the motif is significantly different, we identify the residues mainly responsible for this difference that can now be changed in heterologous expression experiments to yield functional proteins.

  16. Bacterial intra-species gene loss occurs in a largely clocklike manner mostly within a pool of less conserved and constrained genes.

    Science.gov (United States)

    Bolotin, Evgeni; Hershberg, Ruth

    2016-10-13

    Gene loss is a major contributor to the evolution of bacterial gene content. Gene loss may occur as a result of shifts in environment leading to changes in the intensity and/or directionality of selection applied for the maintenance of specific genes. Gene loss may also occur in a more neutral manner, when gene functions are lost that were not subject to strong selection to be maintained, irrespective of changes to environment. Here, we used a pangenome-based approach to investigate patterns of gene loss across 15 bacterial species. We demonstrate that gene loss tends to occur mostly within a pool of genes that are less constrained within species, even in those strains from which they are not lost, and less conserved across bacterial species. Our results indicate that shifts in selection, resulting from shifts in environment are not required to explain the majority of gene loss events occurring within a diverse collection of bacterial species. Caution should therefore be taken when attributing differences in gene content to differences in environment.

  17. A cross-sectional survey of bacterial species in plaque from client owned dogs with healthy gingiva, gingivitis or mild periodontitis.

    Science.gov (United States)

    Davis, Ian J; Wallis, Corrin; Deusch, Oliver; Colyer, Alison; Milella, Lisa; Loman, Nick; Harris, Stephen

    2013-01-01

    Periodontal disease is the most widespread oral disease in dogs which if left untreated results in significant pain to the pet and loss of dentition. The objective of this study was to identify bacterial species in canine plaque that are significantly associated with health, gingivitis and mild periodontitis (gingivitis and mild periodontitis with 72 to 77 samples per health status. DNA was extracted from the plaque samples and subjected to PCR amplification of the V1-V3 region of the 16S rDNA. Pyrosequencing of the PCR amplicons identified a total of 274 operational taxonomic units after bioinformatic and statistical analysis. Porphyromonas was the most abundant genus in all disease stages, particularly in health along with Moraxella and Bergeyella. Peptostreptococcus, Actinomyces, and Peptostreptococcaceae were the most abundant genera in mild periodontitis. Logistic regression analysis identified species from each of these genera that were significantly associated with health, gingivitis or mild periodontitis. Principal component analysis showed distinct community profiles in health and disease. The species identified show some similarities with health and periodontal disease in humans but also major differences. In contrast to human, healthy canine plaque was found to be dominated by Gram negative bacterial species whereas Gram positive anaerobic species predominate in disease. The scale of this study surpasses previously published research and enhances our understanding of the bacterial species present in canine subgingival plaque and their associations with health and early periodontal disease.

  18. Characterization of a major cluster of nif, fix, and associated genes in a sugarcane endophyte, Acetobacter diazotrophicus.

    Science.gov (United States)

    Lee, S; Reth, A; Meletzus, D; Sevilla, M; Kennedy, C

    2000-12-01

    A major 30.5-kb cluster of nif and associated genes of Acetobacter diazotrophicus (syn. Gluconacetobacter diazotrophicus), a nitrogen-fixing endophyte of sugarcane, was sequenced and analyzed. This cluster represents the largest assembly of contiguous nif-fix and associated genes so far characterized in any diazotrophic bacterial species. Northern blots and promoter sequence analysis indicated that the genes are organized into eight transcriptional units. The overall arrangement of genes is most like that of the nif-fix cluster in Azospirillum brasilense, while the individual gene products are more similar to those in species of Rhizobiaceae or in Rhodobacter capsulatus.

  19. Effect of free and symbiotic nitrogen fixing bacterial co-inoculation on seed and seedling of soybean seeds produced under deficit water condition

    Directory of Open Access Journals (Sweden)

    Hamed Hadi

    2016-04-01

    Full Text Available Effect of free and symbiotic nitrogen fixing bacteria on seed and seedling produced seeds under deficit irrigation was conducted in laboratory and field experiments in 2006. In laboratory of karaj’s Seed and Plant Research and Certificate Institute an experiment was conducted based on factorial in form of completely randomized design with four replications and in field’s of Islamic Azad University, Varamin Branch were split factorial in form of randomized completely block design with three replications. Treatments included water stress [Irrigation after 50 (Normal irrigation, 100 (Middle stress, 150 (Severe stress mm evaporation from pan class A], Cultivar [Manokin & Williams and SRF×T3 Line] and inoculation [Inoculation with Bradyrhizobium japonicum, Bradyrhizobium japonicum co-inoculated with Azotobacter chroococcum, No seed inoculation]. Results showed that drought stress decreased the uniformity and germination speed and seedling emergence. Bacteria increased leaf dry weight, stem dry weight, leaf area and seedling vigor index but had no effect on emergence. In irrigation levels inoculated treatments had higher seedling length, leaf, stem, seedling dry weight and seedling vigor. Severs stress seeds inoculated with Bradyrhizobium japonicum had higher root dry weight than control. Therefore in seeds which were produced under deficit irrigation conditions, bacteria increased seedlings vigor.

  20. The pneumococcal serine-rich repeat protein is an intra-species bacterial adhesin that promotes bacterial aggregation in vivo and in biofilms.

    NARCIS (Netherlands)

    Sanchez, C.J.; Shivshankar, P.; Stol, K.; Trakhtenbroit, S.; Sullam, P.M.; Sauer, K.; Hermans, P.W.M.; Orihuela, C.J.

    2010-01-01

    The Pneumococcal serine-rich repeat protein (PsrP) is a pathogenicity island encoded adhesin that has been positively correlated with the ability of Streptococcus pneumoniae to cause invasive disease. Previous studies have shown that PsrP mediates bacterial attachment to Keratin 10 (K10) on the surf

  1. Antimicrobial activity of plant essential oils against bacterial and fungal species involved in food poisoning and/or food decay.

    Science.gov (United States)

    Lixandru, Brînduşa-Elena; Drăcea, Nicoleta Olguţa; Dragomirescu, Cristiana Cerasella; Drăgulescu, Elena Carmina; Coldea, Ileana Luminiţa; Anton, Liliana; Dobre, Elena; Rovinaru, Camelia; Codiţă, Irina

    2010-01-01

    The currative properties of aromatic and medicinal plants have been recognized since ancient times and, more recently, the antimicrobial activity of plant essential oils has been used in several applications, including food preservation. The purpose of this study was to create directly comparable, quantitative data on the antimicrobial activity of some plant essential oils prepared in the National Institute of Research-Development for Chemistry and Petrochemistry, Bucharest to be used for the further development of food packaging technology, based on their antibacterial and antifungal activity. The essential oils extracted from thyme (Thymus vulgaris L.), basil (Ocimum basilicum L.), coriander (Coriandrum sativum L.), rosemary (Rosmarinus officinalis L.), sage (Salvia officinalis L.), fennel (Foeniculum vulgare L.), spearmint (Mentha spicata L.) and carraway (Carum carvi L.) were investigated for their antimicrobial activity against eleven different bacterial and three fungal strains belonging to species reported to be involved in food poisoning and/or food decay: S. aureus ATCC 25923, S. aureus ATCC 6538, S. aureus ATCC 25913, E. coli ATCC 25922, E. coli ATCC 35218, Salmonella enterica serovar Enteritidis Cantacuzino Institute Culture Collection (CICC) 10878, Listeria monocytogenes ATCC 19112, Bacillus cereus CIP 5127, Bacillus cereus ATCC 11778, Candida albicans ATCC 10231, Aspergillus niger ATCC 16404, Penicillium spp. CICC 251 and two E. coli and Salmonella enterica serovar Enteritidis clinical isolates. The majority of the tested essential oils exibited considerable inhibitory capacity against all the organisms tested, as supported by growth inhibition zone diameters, MICs and MBC's. Thyme, coriander and basil oils proved the best antibacterial activity, while thyme and spearmint oils better inhibited the fungal species.

  2. A Rich Morphological Diversity of Biosaline Drying Patterns Is Generated by Different Bacterial Species, Different Salts and Concentrations: Astrobiological Implications

    Science.gov (United States)

    Gómez Gómez, José María; Medina, Jesús; Rull, Fernando

    2016-07-01

    Biosaline formations (BSFs) are complex self-organized biomineral patterns formed by "hibernating" bacteria as the biofilm that contains them dries out. They were initially described in drying biofilms of Escherichia coli cells + NaCl. Due to their intricate 3-D morphology and anhydrobiosis, these biomineralogical structures are of great interest in astrobiology. Here we report experimental data obtained with various alkali halide salts (NaF, NaCl, NaBr, LiCl, KCl, CsCl) on BSF formation with E. coli and Bacillus subtilis bacteria at two saline concentrations: 9 and 18 mg/mL. Our results indicate that, except for LiCl, which is inactive, all the salts assayed are active during BSF formation and capable of promoting the generation of distinctive drying patterns at each salt concentration. Remarkably, the BSFs produced by these two bacterial species produce characteristic architectural hallmarks as the BSF dries. The potential biogenicity of these biosaline drying patterns is studied, and the astrobiological implications of these findings are discussed.

  3. Cooperative Role for Tetraspanins in Adhesin-Mediated Attachment of Bacterial Species to Human Epithelial Cells ▿ †

    Science.gov (United States)

    Green, Luke R.; Monk, Peter N.; Partridge, Lynda J.; Morris, Paul; Gorringe, Andrew R.; Read, Robert C.

    2011-01-01

    The tetraspanins are a superfamily of transmembrane proteins with diverse functions and can form extended microdomains within the plasma membrane in conjunction with partner proteins, which probably includes receptors for bacterial adhesins. Neisseria meningitidis, the causative agent of meningococcal disease, attaches to host nasopharyngeal epithelial cells via type IV pili and opacity (Opa) proteins. We examined the role of tetraspanin function in Neisseria meningitidis adherence to epithelial cells. Tetraspanins CD9, CD63, and CD151 were expressed by HEC-1-B and DETROIT 562 cells. Coincubation of cells with antibodies against all three tetraspanin molecules used individually or in combination, with recombinant tetraspanin extracellular domains (EC2), or with small interfering RNAs (siRNAs) significantly reduced adherence of Neisseria meningitidis. In contrast, recombinant CD81, a different tetraspanin, had no effect on meningococcal adherence. Antitetraspanin antibodies reduced the adherence to epithelial cells of Neisseria meningitidis strain derivatives expressing Opa and pili significantly more than isogenic strains lacking these determinants. Adherence to epithelial cells of strains of Staphylococcus aureus, Neisseria lactamica, Escherichia coli, and Streptococcus pneumoniae was also reduced by pretreatment of cells with tetraspanin antibodies and recombinant proteins. These data suggest that tetraspanins are required for optimal function of epithelial adhesion platforms containing specific receptors for Neisseria meningitidis and potentially for multiple species of bacteria. PMID:21464080

  4. Hyperoxaluria leads to dysbiosis and drives selective enrichment of oxalate metabolizing bacterial species in recurrent kidney stone endures

    Science.gov (United States)

    Suryavanshi, Mangesh V.; Bhute, Shrikant S.; Jadhav, Swapnil D.; Bhatia, Manish S.; Gune, Rahul P.; Shouche, Yogesh S.

    2016-01-01

    Hyperoxaluria due to endogenously synthesized and exogenously ingested oxalates is a leading cause of recurrent oxalate stone formations. Even though, humans largely rely on gut microbiota for oxalate homeostasis, hyperoxaluria associated gut microbiota features remain largely unknown. Based on 16S rRNA gene amplicons, targeted metagenomic sequencing of formyl-CoA transferase (frc) gene and qPCR assay, we demonstrate a selective enrichment of Oxalate Metabolizing Bacterial Species (OMBS) in hyperoxaluria condition. Interestingly, higher than usual concentration of oxalate was found inhibitory to many gut microbes, including Oxalobacter formigenes, a well-characterized OMBS. In addition a concomitant enrichment of acid tolerant pathobionts in recurrent stone sufferers is observed. Further, specific enzymes participating in oxalate metabolism are found augmented in stone endures. Additionally, hyperoxaluria driven dysbiosis was found to be associated with oxalate content, stone episodes and colonization pattern of Oxalobacter formigenes. Thus, we rationalize the first in-depth surveillance of OMBS in the human gut and their association with hyperoxaluria. Our findings can be utilized in the treatment of hyperoxaluria associated recurrent stone episodes. PMID:27708409

  5. Pseudomonas granadensis sp. nov., a new bacterial species isolated from the Tejeda, Almijara and Alhama Natural Park, Granada, Spain.

    Science.gov (United States)

    Pascual, Javier; García-López, Marina; Bills, Gerald F; Genilloud, Olga

    2015-02-01

    During the course of screening bacterial isolates as sources of as-yet unknown bioactive compounds with pharmaceutical applications, a chemo-organotrophic, Gram-negative bacterium was isolated from a soil sample taken from the Tejeda, Almijara and Alhama Natural Park, Granada, Spain. Strain F-278,770(T) was oxidase- and catalase-positive, aerobic, with a respiratory type of metabolism with oxygen as the terminal electron acceptor, non-spore-forming and motile by one polar flagellum, although some cells had two polar flagella. Phylogenetic analysis of the 16S rRNA, gyrB, rpoB and rpoD genes revealed that strain F-278,770(T) belongs to the Pseudomonas koreensis subgroup (Pseudomonas fluorescens lineage), with Pseudomonas moraviensis, P. koreensis, P. baetica and P. helmanticensis as its closest relatives. Chemotaxonomic traits such as polar lipid and fatty acid compositions and G+C content of genomic DNA corroborated the placement of strain F-278,770(T) in the genus Pseudomonas. DNA-DNA hybridization assays and phenotypic traits confirmed that this strain represents a novel species of the genus Pseudomonas, for which the name Pseudomonas granadensis sp. nov. is proposed. The type strain is F-278,770(T) ( = DSM 28040(T) = LMG 27940(T)).

  6. Comparative proteome analysis of psychrophilic versus mesophilic bacterial species: Insights into the molecular basis of cold adaptation of proteins

    Directory of Open Access Journals (Sweden)

    Reddy Boojala

    2009-01-01

    Full Text Available Abstract Background Cold adapted or psychrophilic organisms grow at low temperatures, where most of other organisms cannot grow. This adaptation requires a vast array of sequence, structural and physiological adjustments. To understand the molecular basis of cold adaptation of proteins, we analyzed proteomes of psychrophilic and mesophilic bacterial species and compared the differences in amino acid composition and substitution patterns to investigate their likely association with growth temperatures. Results In psychrophilic bacteria, serine, aspartic acid, threonine and alanine are overrepresented in the coil regions of secondary structures, whilst glutamic acid and leucine are underrepresented in the helical regions. Compared to mesophiles, psychrophiles comprise a significantly higher proportion of amino acids that contribute to higher protein flexibility in the coil regions of proteins, such as those with tiny/small or neutral side chains. Amino acids with aliphatic, basic, aromatic and hydrophilic side chains are underrepresented in the helical regions of proteins of psychrophiles. The patterns of amino acid substitutions between the orthologous proteins of psychrophiles versus mesophiles are significantly different for several amino acids when compared to their substitutions in orthologous proteins of within the mesophiles or psychrophiles. Conclusion Current results provide quantitative substitution preferences (or avoidance of amino acids that lead to the adaptation of proteins to cold temperatures. These finding would help future efforts in selecting mutations for rational design of proteins with enhanced psychrophilic properties.

  7. 16S-rRNA-based analysis of bacterial diversity in the gut of fungus-cultivating termites (Microtermes and Odontotermes species).

    Science.gov (United States)

    Makonde, Huxley M; Boga, Hamadi I; Osiemo, Zipporah; Mwirichia, Romano; Mackenzie, Lucy M; Göker, Markus; Klenk, Hans-Peter

    2013-11-01

    The interaction between termites and their gut symbionts has continued to attract the curiosity of researchers over time. The aim of this study was to characterize and compare the bacterial diversity and community structure in the guts of three termites (Odontotermes somaliensis, Odontotermes sp. and Microtermes sp.) using 16S rRNA gene sequencing of clone libraries. Clone libraries were screened by restriction fragment length polymorphism and representative clones from O. somaliensis (100 out of 330 clones), Odontotermes sp. (100 out of 359 clones) and Microtermes sp. (96 out 336 clones) were sequenced. Phylogenetic analysis indicated seven bacterial phyla were represented: Bacteroidetes, Spirochaetes, Firmicutes, Proteobacteria, Synergistetes, Planctomycetes and Actinobacteria. Sequences representing the phylum Bacteroidetes (>60 %) were the most abundant group in Odontotermes while those of Spirochaetes (29 %) and Firmicutes (23 %) were the abundant groups in Microtermes. The gut bacterial community structure within the two Odontotermes species investigated here was almost identical at the phylum level, but the Microtermes sp. had a unique bacterial community structure. Bacterial diversity was higher in Odontotermes than in Microtermes. The affiliation and clustering of the sequences, often with those from other termites' guts, indicate a majority of the gut bacteria are autochthonous having mutualistic relationships with their hosts. The findings underscore the presence of termite-specific bacterial lineages, the majority of which are still uncultured.

  8. Bacterial species associated with traditional starter cultures used for fermented bamboo shoot production in Manipur state of India.

    Science.gov (United States)

    Jeyaram, K; Romi, W; Singh, Th Anand; Devi, A Ranjita; Devi, S Soni

    2010-09-30

    Soidon is a non-salted acidic fermented food prepared from the succulent bamboo shoot tip of Schizostachyum capitatum Munro by using a traditional liquid starter called "soidon mahi" in Manipur state of India. In this study, 163 bacterial isolates associated with this starter samples were identified and their population distribution was investigated by amplified ribosomal DNA restriction analysis (ARDRA), 16S rDNA sequencing and randomly amplified polymorphic DNA (RAPD) analysis. This acidic starter (pH 4.5+/-0.15) was dominated by a characteristic association of Bacillus and lactic acid bacteria (LAB) together. The population distribution of dominant species were Bacillus subtilis 29.3%, Bacillus cereus 35.7%, Bacillus pumilus 2.6%, Lactobacillus brevis 9.6%, Lactobacillus plantarum 5.1%, Carnobacterium sp. 11.9%, Enterococcus faecium 1.2% and Pseudomonas fluorescens 4.6%. Alarming population load (10(6)-10(7)cfu/ml) of B. cereus in 87% of starter samples studied should raise concern regarding biosafety of soidon consumption. PCR amplification of 16S-23S rDNA intergenic transcribed spacer (ITS) region and ITS-RFLP profiles revealed a high diversity with eight subgroups in B. subtilis, five subgroups in B. cereus and three subgroups in L. brevis isolates. The most abundant B. subtilis subgroup IB.1 distributed in most of the samples showed very less clonal variability during RAPD analysis. The molecular methods used in this study identified the dominant strains of Bacillus and LAB distributed in most of the starter samples. These dominant strains of B. subtilis, L. brevis and L. plantarum would allow for developing a defined starter culture for the production of quality soidon.

  9. Novel Variants of Streptococcus thermophilus Bacteriophages Are Indicative of Genetic Recombination among Phages from Different Bacterial Species

    Science.gov (United States)

    Szymczak, Paula; Neves, Ana Rute; Kot, Witold; Hansen, Lars H.; Lametsch, René; Neve, Horst; Franz, Charles M. A. P.

    2016-01-01

    ABSTRACT Bacteriophages are the main cause of fermentation failures in dairy plants. The majority of Streptococcus thermophilus phages can be divided into either cos- or pac-type phages and are additionally characterized by examining the V2 region of their antireceptors. We screened a large number of S. thermophilus phages from the Chr. Hansen A/S collection, using PCR specific for the cos- or pac-type phages, as well as for the V2 antireceptor region. Three phages did not produce positive results with the assays. Analysis of phage morphologies indicated that two of these phages, CHPC577 and CHPC926, had shorter tails than the traditional S. thermophilus phages. The third phage, CHPC1151, had a tail size similar to those of the cos- or pac-type phages, but it displayed a different baseplate structure. Sequencing analysis revealed the genetic similarity of CHPC577 and CHPC926 with a subgroup of Lactococcus lactis P335 phages. Phage CHPC1151 was closely related to the atypical S. thermophilus phage 5093, homologous with a nondairy streptococcal prophage. By testing adsorption of the related streptococcal and lactococcal phages to the surface of S. thermophilus and L. lactis strains, we revealed the possibility of cross-interactions. Our data indicated that the use of S. thermophilus together with L. lactis, extensively applied for dairy fermentations, triggered the recombination between phages infecting different bacterial species. A notable diversity among S. thermophilus phage populations requires that a new classification of the group be proposed. IMPORTANCE Streptococcus thermophilus is a component of thermophilic starter cultures commonly used for cheese and yogurt production. Characterizing streptococcal phages, understanding their genetic relationships, and studying their interactions with various hosts are the necessary steps for preventing and controlling phage attacks that occur during dairy fermentations. PMID:28039135

  10. Response in soil of Cupriavidus necator and other copper-resistant bacterial predators of bacteria to addition of water, soluble nutrients, various bacterial species, or Bacillus thuringiensis spores and crystals

    Energy Technology Data Exchange (ETDEWEB)

    Casida, L.E. Jr. (Pennsylvania State Univ., University Park (USA))

    1988-09-01

    Soil was incubated with various species of bacteria, Bacillus subtilis, or Bacillus thuringiensis spores and crystals. These were added to serve as potential prey for indigenous, copper-resistant, nonobligate bacterial predators of bacteria in the soil. Alternatively, the soil was incubated with soluble nutrients or water only to cause potential indigenous prey cells to multiply so the predator cells would multiply. All of these incubation procedures caused excessive multiplication of some gram-negative bacteria in soil. Even greater multiplication, however, often occurred for certain copper-resistant bacterial predators of bacteria that made up a part of the gram-negative response. Incubation of the soil with copper per se did not give these responses. In most cases, the copper-resistant bacteria that responded were Cupriavidus necator, bacterial predator L-2, or previously unknown bacteria that resembled them. The results suggest that, under various conditions of soil incubation, gram-negative bacterial predators of bacteria multiply and that several copper-resistant types among them can be detected, counted, and isolated by plating dilutions of the soil onto media containing excess copper.

  11. The Generalist Inside the Specialist: Gut Bacterial Communities of Two Insect Species Feeding on Toxic Plants Are Dominated by Enterococcus sp.

    Science.gov (United States)

    Vilanova, Cristina; Baixeras, Joaquín; Latorre, Amparo; Porcar, Manuel

    2016-01-01

    Some specialist insects feed on plants rich in secondary compounds, which pose a major selective pressure on both the phytophagous and the gut microbiota. However, microbial communities of toxic plant feeders are still poorly characterized. Here, we show the bacterial communities of the gut of two specialized Lepidoptera, Hyles euphorbiae and Brithys crini, which exclusively feed on latex-rich Euphorbia sp. and alkaloid-rich Pancratium maritimum, respectively. A metagenomic analysis based on high-throughput sequencing of the 16S rRNA gene revealed that the gut microbiota of both insects is dominated by the phylum Firmicutes, and especially by the common gut inhabitant Enterococcus sp. Staphylococcus sp. are also found in H. euphorbiae though to a lesser extent. By scanning electron microscopy, we found a dense ring-shaped bacterial biofilm in the hindgut of H. euphorbiae, and identified the most prominent bacterium in the biofilm as Enterococcus casseliflavus through molecular techniques. Interestingly, this species has previously been reported to contribute to the immobilization of latex-like molecules in the larvae of Spodoptera litura, a highly polyphagous lepidopteran. The E. casseliflavus strain was isolated from the gut and its ability to tolerate natural latex was tested under laboratory conditions. This fact, along with the identification of less frequent bacterial species able to degrade alkaloids and/or latex, suggest a putative role of bacterial communities in the tolerance of specialized insects to their toxic diet.

  12. Oligotyping reveals differences between gut-microbiomes of free-ranging sympatric Namibian carnivores (Acinonyx jubatus, Canis mesomelas on a bacterial species-like level

    Directory of Open Access Journals (Sweden)

    Sebastian eMenke

    2014-10-01

    Full Text Available Recent gut microbiome studies in model organisms emphasize the effects of intrinsic and extrinsic factors on the variation of the bacterial composition and its impact on the overall health status of the host. Species occurring in the same habitat might share a similar microbiome, especially if they overlap in ecological and behavioral traits. So far, the natural variation in microbiomes of free-ranging wildlife species has not been thoroughly investigated. The few existing studies exploring microbiomes through 16S rRNA gene reads clustered sequencing reads into operational taxonomic units (OTUs based on a similarity threshold (e.g. 97%. This approach, in combination with the low resolution of target databases, generally limits the level of taxonomic assignments to the genus level. However, distinguishing natural variation of microbiomes in healthy individuals from abnormal microbial compositions that affect host health requires knowledge of the normal microbial flora at a high taxonomic resolution. This gap can now be addressed using the recently published oligotyping approach, which can resolve closely related organisms into distinct oligotypes by utilizing subtle nucleotide variation. Here, we used Illumina MiSeq to sequence amplicons generated from the V4 region of the 16S rRNA gene to investigate the gut microbiome of two free-ranging sympatric Namibian carnivore species, the cheetah (Acinonyx jubatus and the black-backed jackal (Canis mesomelas. Bacterial phyla with proportions > 0.2 % were identical for both species and included Firmicutes, Fusobacteria, Bacteroidetes, Proteobacteria and Actinobacteria. At a finer taxonomic resolution, black-backed jackals exhibited 69 bacterial taxa with proportions ≥ 0.1 %, whereas cheetahs had only 42. Finally, oligotyping revealed that shared bacterial taxa consisted of distinct oligotype profiles. Thus, in contrast to 3 % OTUs, oligotyping can detect fine-scale taxonomic differences between

  13. Oligotyping reveals differences between gut microbiomes of free-ranging sympatric Namibian carnivores (Acinonyx jubatus, Canis mesomelas) on a bacterial species-like level.

    Science.gov (United States)

    Menke, Sebastian; Wasimuddin; Meier, Matthias; Melzheimer, Jörg; Mfune, John K E; Heinrich, Sonja; Thalwitzer, Susanne; Wachter, Bettina; Sommer, Simone

    2014-01-01

    Recent gut microbiome studies in model organisms emphasize the effects of intrinsic and extrinsic factors on the variation of the bacterial composition and its impact on the overall health status of the host. Species occurring in the same habitat might share a similar microbiome, especially if they overlap in ecological and behavioral traits. So far, the natural variation in microbiomes of free-ranging wildlife species has not been thoroughly investigated. The few existing studies exploring microbiomes through 16S rRNA gene reads clustered sequencing reads into operational taxonomic units (OTUs) based on a similarity threshold (e.g., 97%). This approach, in combination with the low resolution of target databases, generally limits the level of taxonomic assignments to the genus level. However, distinguishing natural variation of microbiomes in healthy individuals from "abnormal" microbial compositions that affect host health requires knowledge of the "normal" microbial flora at a high taxonomic resolution. This gap can now be addressed using the recently published oligotyping approach, which can resolve closely related organisms into distinct oligotypes by utilizing subtle nucleotide variation. Here, we used Illumina MiSeq to sequence amplicons generated from the V4 region of the 16S rRNA gene to investigate the gut microbiome of two free-ranging sympatric Namibian carnivore species, the cheetah (Acinonyx jubatus) and the black-backed jackal (Canis mesomelas). Bacterial phyla with proportions >0.2% were identical for both species and included Firmicutes, Fusobacteria, Bacteroidetes, Proteobacteria and Actinobacteria. At a finer taxonomic resolution, black-backed jackals exhibited 69 bacterial taxa with proportions ≥0.1%, whereas cheetahs had only 42. Finally, oligotyping revealed that shared bacterial taxa consisted of distinct oligotype profiles. Thus, in contrast to 3% OTUs, oligotyping can detect fine-scale taxonomic differences between microbiomes.

  14. A cross-sectional survey of bacterial species in plaque from client owned dogs with healthy gingiva, gingivitis or mild periodontitis.

    Directory of Open Access Journals (Sweden)

    Ian J Davis

    Full Text Available Periodontal disease is the most widespread oral disease in dogs which if left untreated results in significant pain to the pet and loss of dentition. The objective of this study was to identify bacterial species in canine plaque that are significantly associated with health, gingivitis and mild periodontitis (<25% attachment loss. In this survey subgingival plaque samples were collected from 223 dogs with healthy gingiva, gingivitis and mild periodontitis with 72 to 77 samples per health status. DNA was extracted from the plaque samples and subjected to PCR amplification of the V1-V3 region of the 16S rDNA. Pyrosequencing of the PCR amplicons identified a total of 274 operational taxonomic units after bioinformatic and statistical analysis. Porphyromonas was the most abundant genus in all disease stages, particularly in health along with Moraxella and Bergeyella. Peptostreptococcus, Actinomyces, and Peptostreptococcaceae were the most abundant genera in mild periodontitis. Logistic regression analysis identified species from each of these genera that were significantly associated with health, gingivitis or mild periodontitis. Principal component analysis showed distinct community profiles in health and disease. The species identified show some similarities with health and periodontal disease in humans but also major differences. In contrast to human, healthy canine plaque was found to be dominated by Gram negative bacterial species whereas Gram positive anaerobic species predominate in disease. The scale of this study surpasses previously published research and enhances our understanding of the bacterial species present in canine subgingival plaque and their associations with health and early periodontal disease.

  15. Do foliar endophytic bacteria fix nitrogen?

    Science.gov (United States)

    Kueppers, L. M.; Moyes, A. B.; Frank, C.; Pett-Ridge, J.; Carper, D.; Vandehey, N.; O'Neil, J.; Dekas, A.

    2015-12-01

    Endophytic microorganisms - bacteria and fungi that live inside healthy plant tissue - are a relatively unexplored source of functional diversity in natural ecosystems. Prior to modern sequencing technology, detecting uncultured endophytic bacteria and assessing their putative functions was challenging. However, recent work has revealed a remarkable diversity of as yet non-culturable endophytic taxa and is beginning to identify functional roles within plant microbiomes. We recently examined bacterial communities in the foliage of a long-lived, high-elevation conifer species, limber pine (Pinus flexilis), and discovered a community strongly dominated by acetic acid bacteria (Acetobacteraceae), with several taxa closely related to known nitrogen fixers. Given limber pine's status as a pioneer species that is able to grow in low fertility soils, we hypothesized that this bacterial community has a potential functional role in fixing atmospheric nitrogen, providing a source of this limiting nutrient to the host tree. We used the radioisotope 13N2 to confirm that N2 rapidly diffuses into pine needles, where it could potentially be fixed. With an acetylene reduction assay we confirmed nitrogenase enzyme activity inside excised twigs 4 times over a growing season, and estimate potential rates of N2 fixation at 0.1 nmol N2 g needle-1 hr-1. Scaled to the stand level, this N input could be on the order of ~20 mg N m-2 d-1 over a growing season. While these rates are low, the long lifespan of individual trees (~1000 years) makes them biologically meaningful. Still, measured rates of acetylene reduction and bulk 15N2 incorporation are quite variable in space and time. Much work remains to better characterize the plant-microbial interactions in this system, including the rates of nitrogen fixation and their variability over the growing season, across edaphic conditions, among host species, and through plant development; and to determine which community members are responsible

  16. Bacterial diversity assessed by cultivation-based techniques shows predominance of Staphylococccus species on coins collected in Lisbon and Casablanca.

    Science.gov (United States)

    de Carvalho, Carla C C R; Caramujo, Maria José

    2014-04-01

    Money is usually considered a source of infections, yet survival of bacteria on dry metal surfaces is limited. The aim of this work was to assess the bacterial numbers and diversity on coins collected in Casablanca and Lisbon as these two cities, on different continents and only 585 km apart, have diverse cultural habitats, but have similar climate. A cultivation-based characterisation of the bacterial community showed that a relatively low number of cells per area of coin were found on both Moroccan Dirhams and Euros (0.014 and 0.125 colony-forming units (CFU) mm(-2) , respectively). Most of the bacterial isolates were located near the rim of the coins, and coins collected in Europe contained more CFU/area of coin. Coins collected in Europe and transported in pockets presented a higher number of bacterial isolates (maximum 0.125 CFU mm(-2) ) than coins transported in wallets (maximum 0.042 CFU mm(-2) ), regardless of the gender of the person transporting them, suggesting that temperature and moisture might be key parameters for bacterial survival on metallic coins. Bacterial diversity was higher for coins collected in Casablanca relative to coins collected in Lisbon, and there was no evidence that it was dependent on the gender of the person transporting the coins or the place of transport (pockets or wallets). Curiously, the percentage of Staphylococcus strains was 44% of the total isolates on both currencies.

  17. Bacterial lipases

    NARCIS (Netherlands)

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

    1994-01-01

    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, mea

  18. Metacommunity dynamics of bacteria in an arctic lake: the impact of species sorting and mass effects on bacterial production and biogeography

    Directory of Open Access Journals (Sweden)

    Heather E. Adams

    2014-03-01

    Full Text Available To understand mechanisms linking ecosystem processes and microbial diversity in freshwater ecosystems, bacterial productivity and the metacommunity dynamics of species sorting and mass effects were investigated in an 18 ha headwater lake in northern Alaska. On most sampling dates, the phylogenetic composition of bacterial communities in inflowing streams (inlets was strikingly different than that in the lake and the outflowing stream (outlet (16S DGGE fingerprinting, demonstrating the shift in composition that occurs as these communities transit the lake. Outlet and downstream communities were also more productive than inlet and upstream communities (14C-leucine incorporation. Inlet bacteria transplanted to the outlet stream in dialysis bags were equally or less productive than control bacteria, suggesting that the inlet bacteria are capable of growing under lake conditions, but do not remain abundant because of species sorting in the lake. Outlet bacteria (representative of epilimnetic bacteria transplanted to the inlet stream were less productive than control bacteria, suggesting that lake bacteria are not as well adapted to growing under inlet conditions. Based on water density, inlet stream water and bacteria generally entered the lake at the base of the epilimnion. However, during low to medium flow in the inlet stream the residence time of the epilimnion was too long relative to bacterial doubling times for these allochthonous bacteria to have a mass effect on the composition of outlet bacteria. The highest community similarity between inlet and outlet bacteria was detected after a large rain event in 2003, with over 61% similarity (average non-storm similarities were 39% ± 8%. While mass effects may be important during large storm events, species sorting appears to be the predominant mechanism structuring bacterial communities within the lake, leading to the assembly of a lake community that has lost some ability to function in stream

  19. Cohnella capsici sp. nov., a novel nitrogen-fixing species isolated from Capsicum annuum rhizosphere soil, and emended description of Cohnella plantaginis.

    Science.gov (United States)

    Wang, Li-Ying; Wang, Tian-Shu; Chen, San-Feng

    2015-01-01

    A novel bacterial strain designated YN-59(T) was isolated from Capsicum annuum rhizosphere soil in China. The isolate was found to be aerobic, Gram-positive, rod-shaped and to form ellipsoidal or oval spores positioned centrally in swollen sporangia. On the basis of 16S rRNA gene sequence analysis, the isolated strain YN-59 was determined to be related to members of genus Cohnella. High levels of 16S rRNA gene sequence similarity were found between strain YN-59 and Cohnella plantaginis DSM 25424(T) (98.5 %) and Cohnella ginsengisoli DSM18997(T) (97.3 %); the 16S rRNA gene sequence similarities between strain YN-59 and the other strains recognized members of the genus Cohnella were below 97 %. The DNA-DNA hybridization values of strain YN-59 with C. plantaginis DSM 25424(T) and C. ginsengisoli DSM18997(T) were 44.2 ± 8.4 and 28.8 ± 5.8 %, respectively. The DNA G + C content of strain YN-59(T) was determined to be 59.32 mol %. The major isoprenoid quinone was identified as MK-7 and the predominant fatty acids as anteiso-C15:0 (45.32 %), iso-C16:0 (19.19 %), iso-C15:0 (9.65 %) and C16:0 (8.91 %). The polar lipids of strain YN-59(T) were found to consist of diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol; several unidentified phospholipids were also detected. The diagnostic diamino acid in the cell wall was identified as meso-diaminopimelic. On the basis of its phenotypic and genotypic characteristics and levels of DNA-DNA hybridization, strain YN-59(T) is considered to represent a novel species of the genus Cohnella, for which the name Cohnella capsici sp. nov. (type strain YN-59(T) = CGMCC 1.12046(T) = JCM 19168(T)) is proposed.

  20. Impact of in Situ Isolated Bacterial Strains on Nitrogen Fixation in Alfalfa

    OpenAIRE

    Carmen Dragomir; Rodica Schipor; Neculai Dragomir; Nicoleta Moraru; Claudiu Ghiocel; Darius Văcariu

    2013-01-01

    Symbiosis relationships among legumes and nitrogen fixing bacteria play a crucial role in agriculture since they provide the opportunity of converting atmospheric molecular nitrogen into an ammonia form of nitrogen that the plants can use in protein formation. To enhance this process we have selected nitrogen fixing bacterial strains commercialised under different forms depending on the cultivation technologies in legume species. In our research, we have pointed out the efficacy of in situ is...

  1. Isolation and Identification of a New Tetrodotoxin-Producing Bacterial Species, Raoultella terrigena, from Hong Kong Marine Puffer Fish Takifugu niphobles

    Directory of Open Access Journals (Sweden)

    Fred Wang-Fat Lee

    2011-11-01

    Full Text Available Puffer fish, Takifugu niphobles, collected from the Hong Kong coastal waters were screened for tetrodotoxin-producing bacteria. A Gram-negative, non-acid-fast, non-sporing and rod shaped bacterial strain (designated as gutB01 was isolated from the intestine of the puffer fish and was shown to produce tetrodotoxin (TTX. Based on the Microbial Identification (MIDI and 16S-23S rDNA internal transcribed spacer (ITS phylogenetic analysis, the strain was identified as Raoultella terrigena. The TTX production ability of the strain was confirmed by mouse bioassay, ELISA and mass spectrometry (MALDI-TOF. Our results reiterate that the TTX found in puffer fish was likely produced by the associated bacteria and TTX are widely produced amongst a diversity of bacterial species.

  2. Isolation and identification of a new tetrodotoxin-producing bacterial species, Raoultella terrigena, from Hong Kong marine puffer fish Takifugu niphobles.

    Science.gov (United States)

    Yu, Vincent Chung-Him; Yu, Peter Hoi-Fu; Ho, Kin-Chung; Lee, Fred Wang-Fat

    2011-01-01

    Puffer fish, Takifugu niphobles, collected from the Hong Kong coastal waters were screened for tetrodotoxin-producing bacteria. A Gram-negative, non-acid-fast, non-sporing and rod shaped bacterial strain (designated as gutB01) was isolated from the intestine of the puffer fish and was shown to produce tetrodotoxin (TTX). Based on the Microbial Identification (MIDI) and 16S-23S rDNA internal transcribed spacer (ITS) phylogenetic analysis, the strain was identified as Raoultella terrigena. The TTX production ability of the strain was confirmed by mouse bioassay, ELISA and mass spectrometry (MALDI-TOF). Our results reiterate that the TTX found in puffer fish was likely produced by the associated bacteria and TTX are widely produced amongst a diversity of bacterial species.

  3. Quorum signaling mycotoxins: A new risk strategy for bacterial biocontrol of Fusarium verticillioides and other endophytic fungal species?

    Science.gov (United States)

    Bacterial endophytes are used as biocontrol organisms for plant pathogens such as the maize endophyte Fusarium verticillioides and its production of fumonisin mycotoxins. However, such applications are not always predictable and efficient. All bacteria communicate via cell-dependent signals, which...

  4. ‘Lascolabacter vaginalis’ strain KHD1, a new bacterial species cultivated from human female genital tract

    Directory of Open Access Journals (Sweden)

    K. Diop

    2016-09-01

    Full Text Available We present the major characteristics of ‘Lascolabacter vaginalis’ strain KHD1 (= CSUR P0109 = DSM 101752, a new member of the family Prevotellaceae that was cultivated from a vaginal sample of a 33-year-old woman with bacterial vaginosis.

  5. Impact of fluorochrome stains used to study bacterial transport in shallow aquifers on motility and chemotaxis of Pseudomonas species.

    Science.gov (United States)

    Toepfer, J Amanda; Ford, Roseanne M; Metge, David; Harvey, Ronald W

    2012-07-01

    One of the most common methods of tracking movement of bacteria in groundwater environments involves a priori fluorescent staining. A major concern in using these stains to label bacteria in subsurface injection-and-recovery studies is the effect they may have on the bacterium's transport properties. Previous studies investigated the impact of fluorophores on bacterial surface properties (e.g. zeta potential). However, no previous study has looked at the impact of fluorescent staining on swimming speed and chemotaxis. It was found that DAPI lowered the mean population swimming speed of Pseudomonas putida F1 by 46% and Pseudomonas stutzeri by 55%. DAPI also inhibited the chemotaxis in both strains. The swimming speeds of P. putida F1 and P. stutzeri were diminished slightly by CFDA/SE, but not to a statistically significant extent. CFDA/SE had no effect on chemotaxis of either strain to acetate. SYBR(®) Gold had no effect on swimming speed or the chemotactic response to acetate for either strain. This research indicates that although DAPI may not affect sorption to grain surfaces, it adversely affects other potentially important transport properties such as swimming and chemotaxis. Consequently, bacterial transport studies conducted using DAPI are biased to nonchemotactic conditions and do not appear to be suitable for monitoring the effect of chemotaxis on bacterial transport in shallow aquifers.

  6. [Evaluation of mixed biofilm formation between Candida albicans and a variety of bacterial species isolated from peripheral catheters at Tlemcen CHU. First study in Algeria].

    Science.gov (United States)

    Seghir, A; Boucherit-Otmani, Z; Boucherit, K; Sari-Belkharroubi, L; Anselme-Bertrand, I

    2015-06-01

    Mixed-species biofilms constitute a reservoir of infection for a group of bacteria and yeasts that coexist on the same support. Peripheral venous catheters make up a good surface for the attachment of microorganisms that promote biofilm formation and this requires complex strategies for antimicrobial treatments. No such studies on formation mixed biofilms have ever been conducted in Algeria. Therefore, we evaluated the potential for the formation of mixed-species biofilms by Candida albicans and some bacterial species isolated from peripheral vascular catheters at the University Hospital of Tlemcen, in Algeria. The results obtained showed that C. albicans have the potential to form mixed biofilms with three bacteria (Enterobacter cloacae, Bordetella spp. and Serratia liquefaciens) isolated from the same catheter as the yeasts. The amount of biofilms produced varies depending on the species and the composition of the growth medium. Observations by scanning electron microscopy showed that the structure of the mixed biofilm depends on the surface support the biofilm was formed on, and varies with the species. A competition was noted between bacteria and yeasts; it depends on the composition of the medium and its pH, which both play an important role in promoting the dominance of one over the other. Copyright © 2015. Published by Elsevier Masson SAS.

  7. Is Quorum Signaling by Mycotoxins a New Risk-Mitigating Strategy for Bacterial Biocontrol of Fusarium verticillioides and Other Endophytic Fungal Species?

    Science.gov (United States)

    Bacon, Charles W; Hinton, Dorothy M; Mitchell, Trevor R

    2017-08-23

    Bacterial endophytes are used as biocontrol organisms for plant pathogens such as the maize endophyte Fusarium verticillioides and its production of fumonisin mycotoxins. However, such applications are not always predictable and efficient. In this work, we hypothesize and review work that quorum sensing inhibitors are produced either by fungi or by pathogenic bacteria for competitive purposes, altering the efficiency of the biocontrol organisms. Recently, quorum sensing inhibitors have been isolated from several fungi, including Fusarium species, three of which are mycotoxins. Thus, we further postulate that other mycotoxins are inhibitors or quenching metabolites that prevent the protective abilities and activities of endophytic biocontrol bacteria within intercellular spaces. To test the aforementioned suppositions, we review work detailing the use of bioassay bacteria for several mycotoxins for quorum activity. We specifically focus on the quorum use of endophytic bacteria as biocontrols for mycotoxic fungal endophytes, such as the Fusarium species and the fumonisin mycotoxins.

  8. The Effects of Cropping Regimes on Fungal and Bacterial Communities of Wheat and Faba Bean in a Greenhouse Pot Experiment Differ between Plant Species and Compartment

    Directory of Open Access Journals (Sweden)

    Sandra Granzow

    2017-05-01

    Full Text Available Many bacteria and fungi in the plant rhizosphere and endosphere are beneficial to plant nutrient acquisition, health, and growth. Although playing essential roles in ecosystem functioning, our knowledge about the effects of multiple cropping regimes on the plant microbiome and their interactions is still limited. Here, we designed a pot experiment simulating different cropping regimes. For this purpose, wheat and faba bean plants were grown under controlled greenhouse conditions in monocultures and in two intercropping regimes: row and mixed intercropping. Bacterial and fungal communities in bulk and rhizosphere soils as well as in the roots and aerial plant parts were analyzed using large-scale metabarcoding. We detected differences in microbial richness and diversity between the cropping regimes. Generally, observed effects were attributed to differences between mixed and row intercropping or mixed intercropping and monoculture. Bacterial and fungal diversity were significantly higher in bulk soil samples of wheat and faba bean grown in mixed compared to row intercropping. Moreover, microbial communities varied between crop species and plant compartments resulting in different responses of these communities toward cropping regimes. Leaf endophytes were not affected by cropping regime but bacterial and fungal community structures in bulk and rhizosphere soil as well as fungal community structures in roots. We further recorded highly complex changes in microbial interactions. The number of negative inter-domain correlations between fungi and bacteria decreased in bulk and rhizosphere soil in intercropping regimes compared to monocultures due to beneficial effects. In addition, we observed plant species-dependent differences indicating that intra- and interspecific competition between plants had different effects on the plant species and thus on their associated microbial communities. To our knowledge, this is the first study investigating

  9. The Effects of Cropping Regimes on Fungal and Bacterial Communities of Wheat and Faba Bean in a Greenhouse Pot Experiment Differ between Plant Species and Compartment

    Science.gov (United States)

    Granzow, Sandra; Kaiser, Kristin; Wemheuer, Bernd; Pfeiffer, Birgit; Daniel, Rolf; Vidal, Stefan; Wemheuer, Franziska

    2017-01-01

    Many bacteria and fungi in the plant rhizosphere and endosphere are beneficial to plant nutrient acquisition, health, and growth. Although playing essential roles in ecosystem functioning, our knowledge about the effects of multiple cropping regimes on the plant microbiome and their interactions is still limited. Here, we designed a pot experiment simulating different cropping regimes. For this purpose, wheat and faba bean plants were grown under controlled greenhouse conditions in monocultures and in two intercropping regimes: row and mixed intercropping. Bacterial and fungal communities in bulk and rhizosphere soils as well as in the roots and aerial plant parts were analyzed using large-scale metabarcoding. We detected differences in microbial richness and diversity between the cropping regimes. Generally, observed effects were attributed to differences between mixed and row intercropping or mixed intercropping and monoculture. Bacterial and fungal diversity were significantly higher in bulk soil samples of wheat and faba bean grown in mixed compared to row intercropping. Moreover, microbial communities varied between crop species and plant compartments resulting in different responses of these communities toward cropping regimes. Leaf endophytes were not affected by cropping regime but bacterial and fungal community structures in bulk and rhizosphere soil as well as fungal community structures in roots. We further recorded highly complex changes in microbial interactions. The number of negative inter-domain correlations between fungi and bacteria decreased in bulk and rhizosphere soil in intercropping regimes compared to monocultures due to beneficial effects. In addition, we observed plant species-dependent differences indicating that intra- and interspecific competition between plants had different effects on the plant species and thus on their associated microbial communities. To our knowledge, this is the first study investigating microbial communities in

  10. Systematic relationships and cospeciation of bacterial endosymbionts and their carpenter ant host species: proposal of the new taxon Candidatus Blochmannia gen. nov.

    Science.gov (United States)

    Sauer, C; Stackebrandt, E; Gadau, J; Hölldobler, B; Gross, R

    2000-09-01

    The systematic relationships of intracellular bacteria of 13 Camponotus species (carpenter ants) from America and Europe were compared to those of their hosts. Phylogenetic trees of the bacteria and the ants were based on 16S rDNA (rrs) gene sequences and mitochondrial cytochrome oxidase subunit I (COI) gene sequences, respectively. The bacterial endosymbionts of Camponotus spp. form a distinct lineage in the y-subclass of the Proteobacteria. The taxa most closely related to these bacteria are endosymbionts of aphids and the tsetse fly. The bacterial and host phylogenies deduced from the sequence data show a high degree of congruence, providing significant evidence for cospeciation of the bacteria and the ants and a maternal transmission route of the symbionts. The cloned rrs genes of the endosymbionts contain putative intervening sequences (IVSs) with a much lower G+C content than the mean of the respective rrs genes. By in situ hybridization specific 16S rDNA oligonucleotide probes verified the presence of the bacteria within tissues of three of the eukaryotic hosts. It is proposed that the endosymbionts of these three carpenter ants be assigned to a new taxon 'Candidatus Blochmannia gen. nov.' with the symbionts of the individual ants being species named according to their host, 'Candidatus Blochmannia floridanus sp. nov.', 'Candidatus Blochmannia herculeanus sp. nov.' and 'Candidatus Blochmannia rufipes sp. nov.'.

  11. Predicting relatedness of bacterial genomes using the chaperonin-60 universal target (cpn60 UT): application to Thermoanaerobacter species.

    Science.gov (United States)

    Verbeke, Tobin J; Sparling, Richard; Hill, Janet E; Links, Matthew G; Levin, David; Dumonceaux, Tim J

    2011-05-01

    D.R. Zeigler determined that the sequence identity of bacterial genomes can be predicted accurately using the sequence identities of a corresponding set of genes that meet certain criteria [32]. This three-gene model for comparing bacterial genome pairs requires the determination of the sequence identities for recN, thdF, and rpoA. This involves the generation of approximately 4.2kb of genomic DNA sequence from each organism to be compared, and also normally requires that oligonucleotide primers be designed for amplification and sequencing based on the sequences of closely related organisms. However, we have developed an analogous mathematical model for predicting the sequence identity of whole genomes based on the sequence identity of the 542-567 base pair chaperonin-60 universal target (cpn60 UT). The cpn60 UT is accessible in nearly all bacterial genomes with a single set of universal primers, and its length is such that it can be completely sequenced in one pair of overlapping sequencing reads via di-deoxy sequencing. These mathematical models were applied to a set of Thermoanaerobacter isolates from a wood chip compost pile and it was shown that both the one-gene cpn60 UT-based model and the three-gene model based on recN, rpoA, and thdF predicted that these isolates could be classified as Thermoanaerobacter thermohydrosulfuricus. Furthermore, it was found that the genomic prediction model using cpn60 UT gave similar results to whole-genome sequence alignments over a broad range of taxa, suggesting that this method may have general utility for screening isolates and predicting their taxonomic affiliations.

  12. Molecular identification of a causative parasite species using formalin-fixed paraffin embedded (FFPE) tissues of a complicated human pulmonary sparganosis case without decisive clinical diagnosis.

    Science.gov (United States)

    Koonmee, Supinda; Intapan, Pewpan M; Yamasaki, Hiroshi; Sugiyama, Hiromu; Muto, Maki; Kuramochi, Toshiaki; Kularbkeaw, Jurairat; Kanpittaya, Jaturat; Maleewong, Wanchai; Nawa, Yukifumi

    2011-12-01

    PCR-based molecular diagnosis was made for the identification of causative agents of the clinically suspected pulmonary proliferative sparganosis case found in Thailand using formalin-fixed paraffin-embedded (FFPE) biopsy specimens. As a reference, FFPE biopsy specimen from a typical cutaneous sparganosis case was examined together. DNA samples were extracted from tissues and two partial fragments of cytochrome c oxidase subunit 1 (cox1) gene were amplified for the detection of Spirometra DNA. Two cox1 fragments were amplified successfully for both specimens. After alignment of nucleotide sequences of the PCR-amplicons, the causative agents of both cases were identified as Spirometra erinaceieuropaei.

  13. Predicting the pathway involved in post-translational modification of Elongation factor P in a subset of bacterial species

    Directory of Open Access Journals (Sweden)

    de Crécy-Lagard Valérie

    2010-01-01

    Full Text Available Abstract Background The bacterial elongation factor P (EF-P is strictly conserved in bacteria and essential for protein synthesis. It is homologous to the eukaryotic translation initiation factor 5A (eIF5A. A highly conserved eIF5A lysine is modified into an unusual amino acid derived from spermidine, hypusine. Hypusine is absolutely required for eIF5A's role in translation in Saccharomyces cerevisiae. The homologous lysine of EF-P is also modified to a spermidine derivative in Escherichia coli. However, the biosynthesis pathway of this modification in the bacterial EF-P is yet to be elucidated. Presentation of the Hypothesis Here we propose a potential mechanism for the post-translational modification of EF-P. By using comparative genomic methods based on physical clustering and phylogenetic pattern analysis, we identified two protein families of unknown function, encoded by yjeA and yjeK genes in E. coli, as candidates for this missing pathway. Based on the analysis of the structural and biochemical properties of both protein families, we propose two potential mechanisms for the modification of EF-P. Testing the hypothesis This hypothesis could be tested genetically by constructing a bacterial strain with a tagged efp gene. The tag would allow the purification of EF-P by affinity chromatography and the analysis of the purified protein by mass spectrometry. yjeA or yjeK could then be deleted in the efp tagged strain and the EF-P protein purified from each mutant analyzed by mass spectrometry for the presence or the absence of the modification. This hypothesis can also be tested by purifying the different components (YjeK, YjeA and EF-P and reconstituting the pathway in vitro. Implication of the hypothesis The requirement for a fully modified EF-P for protein synthesis in certain bacteria implies the presence of specific post-translational modification mechanism in these organisms. All of the 725 bacterial genomes analyzed, possess an efp gene

  14. Association of sexually transmitted infections, Candida species, gram-positive flora and perianal flora with bacterial vaginosis.

    Science.gov (United States)

    Vahidnia, Ali; Tuin, Hellen; Bliekendaal, Harry; Spaargaren, Joke

    2015-10-01

    Bacterial vaginosis (BV) is characterised by depletion of the normal Lactobacillus spp. and overgrowth of commensal anaerobic bacteria. We investigated the composition of vaginal microbiota and their association with BV in women of reproductive age. Vaginal samples from 1197 women were analysed, whereby n=451 patients had normal flora and n=614 were diagnosed with BV, the remaining patients were diagnosed with having either intermediate flora (n=42) or dysbacteriosis (n=90). The reported results show that pathogens are associated with BV. This knowledge will further expand our understanding of events leading to BV, which may lead to more effective prevention and treatment strategies.

  15. The enteric bacterial metabolite propionic acid alters brain and plasma phospholipid molecular species: further development of a rodent model of autism spectrum disorders

    Directory of Open Access Journals (Sweden)

    Thomas Raymond H

    2012-07-01

    Full Text Available Abstract Gastrointestinal symptoms and altered blood phospholipid profiles have been reported in patients with autism spectrum disorders (ASD. Most of the phospholipid analyses have been conducted on the fatty acid composition of isolated phospholipid classes following hydrolysis. A paucity of information exists on how the intact phospholipid molecular species are altered in ASD. We applied ESI/MS to determine how brain and blood intact phospholipid species were altered during the induction of ASD-like behaviors in rats following intraventricular infusions with the enteric bacterial metabolite propionic acid. Animals were infused daily for 8 days, locomotor activity assessed, and animals killed during the induced behaviors. Propionic acid infusions increased locomotor activity. Lipid analysis revealed treatment altered 21 brain and 30 blood phospholipid molecular species. Notable alterations were observed in the composition of brain SM, diacyl mono and polyunsaturated PC, PI, PS, PE, and plasmalogen PC and PE molecular species. These alterations suggest that the propionic acid rat model is a useful tool to study aberrations in lipid metabolism known to affect membrane fluidity, peroxisomal function, gap junction coupling capacity, signaling, and neuroinflammation, all of which may be associated with the pathogenesis of ASD.

  16. Characterization of culturable vaginal Lactobacillus species among women with and without bacterial vaginosis from the United States and India: a cross-sectional study.

    Science.gov (United States)

    Madhivanan, Purnima; Raphael, Eva; Rumphs, Alnecia; Krupp, Karl; Ravi, Kavitha; Srinivas, Vijaya; Arun, Anjali; Reingold, Arthur L; Klausner, Jeffrey D; Riley, Lee W

    2014-07-01

    Lactobacillus species play an integral part in the health of the vaginal microbiota. We compared vaginal Lactobacillus species in women from India and the USA with and without bacterial vaginosis (BV). Between July 2009 and November 2010, a cross-sectional study was conducted among 40 women attending a women's health clinic in Mysore, India, and a sexually transmitted diseases clinic in San Francisco, USA. Women were diagnosed with BV using Amsel's criteria and the Nugent score. Lactobacillus 16S rDNA was sequenced to speciate the cultured isolates. Ten Indian and 10 US women without BV were compared with an equal number of women with BV. Lactobacilli were isolated from all healthy women, but from only 10% of Indian and 50% of US women with BV. 16S rDNA from 164 Lactobacillus colonies was sequenced from healthy women (126 colonies) and women with BV (38 colonies). Seven cultivable Lactobacillus species were isolated from 11 Indian women and nine species from 15 US women. The majority of Lactobacillus species among Indian women were L. crispatus (25.0%), L. jensenii (25.0%) and L. reuteri (16.7%). Among US women, L. crispatus (32.0%), L. jensenii (20.0%) and L. coleohominis (12.0%) predominated. L. jensenii and L. crispatus dominated the vaginal flora of healthy Indian and US women. Indian women appeared to have a higher percentage of obligate heterofermentative species, suggesting the need for a larger degree of metabolic flexibility and a more challenging vaginal environment. © 2014 The Authors.

  17. Architecture and spatial organization in a triple-species bacterial biofilm synergistically degrading the phenylurea herbicide linuron

    DEFF Research Database (Denmark)

    Breugelmans, Philip; Barken, Kim Bundvig; Tolker-Nielsen, Tim;

    2008-01-01

    Members of a triple-species 3-(3,4-dichlorophenyl)-1-methoxy-1-methyl urea (linuron)-mineralizing consortium, i.e. the linuron- and 3,4-dichloroaniline-degrading Variovorax sp. WDL1, the 3,4-dichloroaniline-degrading Comamonas testosteroni WDL7 and the N,O-dimethylhydroxylamine-degrading Hyphomic...

  18. Remarkable impact of PAHs and TPHs on the richness and diversity of bacterial species in surface soils exposed to long-term hydrocarbon pollution.

    Science.gov (United States)

    Benedek, Tibor; Vajna, Balázs; Táncsics, András; Márialigeti, Károly; Lányi, Szabolcs; Máthé, István

    2013-11-01

    Nowadays, because of substantial use of petroleum-derived fuels the number and extension of hydrocarbon polluted terrestrial ecosystems is in growth worldwide. In remediation of aforementioned sites bioremediation still tends to be an innovative, environmentally attractive technology. Although huge amount of information is available concerning the hydrocarbon degradation potential of cultivable hydrocarbonoclastic bacteria little is known about the in situ long-term effects of petroleum derived compounds on the structure of soil microbiota. Therefore, in this study our aim was to determine the long-term impact of total petroleum hydrocarbons (TPHs), volatile petroleum hydrocarbons (VPHs), total alkyl benzenes (TABs) as well as of polycyclic aromatic hydrocarbons (PAHs) on the structure of bacterial communities of four different contaminated soil samples. Our results indicated that a very high amount of TPH affected positively the diversity of hydrocarbonoclastic bacteria. This finding was supported by the occurrence of representatives of the α-, β-, γ-Proteobacteria, Actinobacteria, Flavobacteriia and Bacilli classes. High concentration of VPHs and TABs contributed to the predominance of actinobacterial isolates. In PAH impacted samples the concentration of PAHs negatively correlated with the diversity of bacterial species. Heavily PAH polluted soil samples were mainly inhabited by the representatives of the β-, γ-Proteobacteria (overwhelming dominance of Pseudomonas sp.) and Actinobacteria.

  19. Bacterial Genome Adaptation to Niches: Divergence of the Potential Virulence Genes in Three Burkholderia Species of Different Survival Strategies

    Science.gov (United States)

    2005-12-01

    species For comparative genomic analysis with pathogenic Bm and Bp, we produced finished sequence of the closely related nonpathogenic soil bacterium...1999. 11. Godoy D, Randle G, Simpson AJ, Aanensen DM, Pitt TL, Kinoshita R, Spratt BG: Multilocus sequence typing and evolutionary rela- tionships...5223):496-512. 34. Waterman MS: Computer analysis of nucleic acid sequences . Methods Enzymol 1988, 164:765-793. 35. Bateman A, Birney E, Durbin R, Eddy

  20. Exploiting Bacterial Whole-Genome Sequencing Data for Evaluation of Diagnostic Assays: Campylobacter Species Identification as a Case Study.

    Science.gov (United States)

    Jansen van Rensburg, Melissa J; Swift, Craig; Cody, Alison J; Jenkins, Claire; Maiden, Martin C J

    2016-12-01

    The application of whole-genome sequencing (WGS) to problems in clinical microbiology has had a major impact on the field. Clinical laboratories are now using WGS for pathogen identification, antimicrobial susceptibility testing, and epidemiological typing. WGS data also represent a valuable resource for the development and evaluation of molecular diagnostic assays, which continue to play an important role in clinical microbiology. To demonstrate this application of WGS, this study used publicly available genomic data to evaluate a duplex real-time PCR (RT-PCR) assay that targets mapA and ceuE for the detection of Campylobacter jejuni and Campylobacter coli, leading global causes of bacterial gastroenteritis. In silico analyses of mapA and ceuE primer and probe sequences from 1,713 genetically diverse C. jejuni and C. coli genomes, supported by RT-PCR testing, indicated that the assay was robust, with 1,707 (99.7%) isolates correctly identified. The high specificity of the mapA-ceuE assay was the result of interspecies diversity and intraspecies conservation of the target genes in C. jejuni and C. coli Rare instances of a lack of specificity among C. coli isolates were due to introgression in mapA or sequence diversity in ceuE The results of this study illustrate how WGS can be exploited to evaluate molecular diagnostic assays by using publicly available data, online databases, and open-source software.

  1. Exploiting Bacterial Whole-Genome Sequencing Data for Evaluation of Diagnostic Assays: Campylobacter Species Identification as a Case Study

    Science.gov (United States)

    Jansen van Rensburg, Melissa J.; Swift, Craig; Cody, Alison J.; Jenkins, Claire

    2016-01-01

    The application of whole-genome sequencing (WGS) to problems in clinical microbiology has had a major impact on the field. Clinical laboratories are now using WGS for pathogen identification, antimicrobial susceptibility testing, and epidemiological typing. WGS data also represent a valuable resource for the development and evaluation of molecular diagnostic assays, which continue to play an important role in clinical microbiology. To demonstrate this application of WGS, this study used publicly available genomic data to evaluate a duplex real-time PCR (RT-PCR) assay that targets mapA and ceuE for the detection of Campylobacter jejuni and Campylobacter coli, leading global causes of bacterial gastroenteritis. In silico analyses of mapA and ceuE primer and probe sequences from 1,713 genetically diverse C. jejuni and C. coli genomes, supported by RT-PCR testing, indicated that the assay was robust, with 1,707 (99.7%) isolates correctly identified. The high specificity of the mapA-ceuE assay was the result of interspecies diversity and intraspecies conservation of the target genes in C. jejuni and C. coli. Rare instances of a lack of specificity among C. coli isolates were due to introgression in mapA or sequence diversity in ceuE. The results of this study illustrate how WGS can be exploited to evaluate molecular diagnostic assays by using publicly available data, online databases, and open-source software. PMID:27733632

  2. A screen for bacterial endosymbionts in the model organisms Tribolium castaneum, T. confusum, Callosobruchus maculatus, and related species.

    Science.gov (United States)

    Goodacre, Sara L; Fricke, Claudia; Martin, Oliver Y

    2015-04-01

    Reproductive parasites such as Wolbachia are extremely widespread amongst the arthropods and can have a large influence over the reproduction and fitness of their hosts. Undetected infections could thus confound the results of a wide range of studies that focus on aspects of host behavior, reproduction, fitness, and degrees of reproductive isolation. This potential problem has already been underlined by work investigating the incidence of Wolbachia infections in stocks of the model system Drosophila melanogaster. Here we survey a range of lab stocks of further commonly used model arthropods, focusing especially on the flour beetles Tribolium castaneum and Tribolium confusum, the cowpea weevil Callosobruchus maculatus and related species (Coleoptera: Tenebrionidae and Bruchidae). These species are widespread stored product pests so knowledge of infections with symbionts further has potential use in informing biocontrol measures. Beetles were assessed for infection with 3 known microbial reproductive parasites: Wolbachia, Rickettsia, Spiroplasma. Infections with some of these microbes were found in some of the lab stocks studied, although overall infections were relatively rare. The consequences of finding infections in these or other species and the type of previous studies likely to be affected most are discussed. © 2013 Institute of Zoology, Chinese Academy of Sciences.

  3. Complexation efficiency of differently fixed 8-hydroxyquinoline and salicylic acid ligand groups for labile aluminium species determination in soils--comparison of two methods.

    Science.gov (United States)

    Matús, Peter; Kubová, Jana

    2006-07-28

    Two methods utilizing the complexation of labile Al species by 8-hydroxyquinoline (HQN) and salicylic acid (SA) ligand groups were developed for aluminium operationally defined fractionation in acid soils. First, the solid phase extraction (SPE) procedure by a short-term ion-exchange batch reaction with chelating resins Iontosorb Oxin and Iontosorb Salicyl containing both ligand groups was used previously. Second, the 8-hydroxyquinoline, salicylic acid and ammonium salicylate agents with different concentrations by a single extraction protocol were applied in this paper. The flame atomic absorption spectrometry (FAAS) and optical emission spectrometry with inductively coupled plasma were used for aluminium quantification. The comparison of results from both methods show the possibility to supersede the first laborious method for the second simpler one in Al environmental risk assessment. The use of 1% 8-hydroxyquinoline in 2% acetic acid and 0.2% salicylic acid by a single extraction protocol without a need of sample filtration can supersede the SPE procedure in the Al pollution soil monitoring. Finally, the new scheme usable in a laboratory and moreover, directly in a field was proposed for Al fractionation in solid and liquid environmental samples. The labile Al species in soils and sediments are separated after their single leaching by 8-hydroxyquinoline or salicylic acid without a need of sample filtration. The labile Al species in soil solutions and natural waters are separated after their ultrafiltration followed by the SPE procedure with Iontosorb Oxin or Iontosorb Salicyl.

  4. Complexation efficiency of differently fixed 8-hydroxyquinoline and salicylic acid ligand groups for labile aluminium species determination in soils-comparison of two methods

    Energy Technology Data Exchange (ETDEWEB)

    Matus, Peter [Comenius University in Bratislava, Faculty of Natural Sciences, Mlynska dolina, 842 15 Bratislava (Slovakia)]. E-mail: matus@fns.uniba.sk; Kubova, Jana [Comenius University in Bratislava, Faculty of Natural Sciences, Mlynska dolina, 842 15 Bratislava (Slovakia)

    2006-07-28

    Two methods utilizing the complexation of labile Al species by 8-hydroxyquinoline (HQN) and salicylic acid (SA) ligand groups were developed for aluminium operationally defined fractionation in acid soils. First, the solid phase extraction (SPE) procedure by a short-term ion-exchange batch reaction with chelating resins Iontosorb Oxin and Iontosorb Salicyl containing both ligand groups was used previously. Second, the 8-hydroxyquinoline, salicylic acid and ammonium salicylate agents with different concentrations by a single extraction protocol were applied in this paper. The flame atomic absorption spectrometry (FAAS) and optical emission spectrometry with inductively coupled plasma were used for aluminium quantification. The comparison of results from both methods show the possibility to supersede the first laborious method for the second simpler one in Al environmental risk assessment. The use of 1% 8-hydroxyquinoline in 2% acetic acid and 0.2% salicylic acid by a single extraction protocol without a need of sample filtration can supersede the SPE procedure in the Al pollution soil monitoring. Finally, the new scheme usable in a laboratory and moreover, directly in a field was proposed for Al fractionation in solid and liquid environmental samples. The labile Al species in soils and sediments are separated after their single leaching by 8-hydroxyquinoline or salicylic acid without a need of sample filtration. The labile Al species in soil solutions and natural waters are separated after their ultrafiltration followed by the SPE procedure with Iontosorb Oxin or Iontosorb Salicyl.

  5. Evidence for a high-spin Fe(IV) species in the catalytic cycle of a bacterial phenylalanine hydroxylase.

    Science.gov (United States)

    Panay, Aram Joel; Lee, Michael; Krebs, Carsten; Bollinger, J Martin; Fitzpatrick, Paul F

    2011-03-22

    Phenylalanine hydroxylase is a mononuclear non-heme iron protein that uses tetrahydropterin as the source of the two electrons needed to activate dioxygen for the hydroxylation of phenylalanine to tyrosine. Rapid-quench methods have been used to analyze the mechanism of a bacterial phenylalanine hydroxylase from Chromobacterium violaceum. Mössbauer spectra of samples prepared by freeze-quenching the reaction of the enzyme-(57)Fe(II)-phenylalanine-6-methyltetrahydropterin complex with O(2) reveal the accumulation of an intermediate at short reaction times (20-100 ms). The Mössbauer parameters of the intermediate (δ = 0.28 mm/s, and |ΔE(Q)| = 1.26 mm/s) suggest that it is a high-spin Fe(IV) complex similar to those that have previously been detected in the reactions of other mononuclear Fe(II) hydroxylases, including a tetrahydropterin-dependent tyrosine hydroxylase. Analysis of the tyrosine content of acid-quenched samples from similar reactions establishes that the Fe(IV) intermediate is kinetically competent to be the hydroxylating intermediate. Similar chemical-quench analysis of a reaction allowed to proceed for several turnovers shows a burst of tyrosine formation, consistent with rate-limiting product release. All three data sets can be modeled with a mechanism in which the enzyme-substrate complex reacts with oxygen to form an Fe(IV)═O intermediate with a rate constant of 19 mM(-1) s(-1), the Fe(IV)═O intermediate hydroxylates phenylalanine with a rate constant of 42 s(-1), and rate-limiting product release occurs with a rate constant of 6 s(-1) at 5 °C.

  6. How to improve fertility of African soils? Leguminous fallows (Cameroon), addition of farmyard manure and mineral fertilizer (Kenya), organic residues management and introduction of N2 fixing species in forest plantations (Congo).

    Science.gov (United States)

    Koutika, Lydie-Stella; Mareschal, Louis; Mouanda, Cadeau; Epron, Daniel

    2014-05-01

    Most of African soils are inherently infertile and poor in nutrients mainly nitrogen and phosphorus. Several practices are used to improve soil fertility, increase productivity and ensure their sustainability. Soil fertility in the leguminous fallows was evaluated through particulate organic matter (POM), the more active part of soil organic matter (SOM) in Cameroon. The combination of mineral and organic (manure) fertilizers increased microbial P biomass allowing the release of P along the plant growing period in the Kenyan soils. Organic residues management and introduction of nitrogen fixing species (Acacia) were used to improve soil fertility and sustain forest productivity on the coastal plains of Congo. SOM fractionation was made under Pueraria, Mucuna fallows and natural regrowth mainly Chromolaena and under 3 forest plantation treatments installed in previous savanna: 1) no input, 2) normal input, and 3) double input of organic residues. Microbial P biomass and sequential P fractionation were evaluated in high and low P fixing soils. N, C, available P and pH were determined on soil sampled in acacia (100A), eucalypt (100E) and mixed-species (50A:50E) stands. N and P were determined in aboveground litters and in leaves, bark and wood of trees. The two leguminous fallows increased N content in POM fractions i.e., N >1% for Pueraria and Mucuna against Nmangium in eucalypt plantations increased the soil N concentration under the mixed-species stand (N>0.06%) compared to under the pure eucalypt stand (N1% in the mixed stand and C< 0.9 in the pure Eucalyptus stand).

  7. Pseudomonas argentinensis sp. nov., a novel yellow pigment-producing bacterial species, isolated from rhizospheric soil in Cordoba, Argentina.

    Science.gov (United States)

    Peix, Alvaro; Berge, Odile; Rivas, Raúl; Abril, Adriana; Velázquez, Encarna

    2005-05-01

    During a study in the Argentinian region of Chaco (Cordoba), some strains were isolated from the rhizosphere of grasses growing in semi-desertic arid soils. Two of these strains, one isolated from the rhizospheric soil of Chloris ciliata (strain CH01(T)) and the other from Pappophorum caespitosum (strain PA01), were Gram-negative, strictly aerobic rods, which formed yellow round colonies on nutrient agar. They produced a water-insoluble yellow pigment, and a fluorescent pigment was also detected. A polyphasic taxonomic approach was used to characterize the strains. Comparison of the 16S rRNA gene sequences showed a similarity of 99.3 % between them, and phylogenetic analysis revealed that the strains belong to the genus Pseudomonas, within the gamma-subclass of the Proteobacteria. The closest related species is Pseudomonas straminea IAM 1598(T) (similarity of 99.0 % to strain CH01(T) and 98.8 % to strain PA01), clustering in a separate branch with the various methods of tree building used. Strains CH01(T) and PA01 both had a single polar flagellum, like other yellow pigment-producing pseudomonads related to them. Both strains produced catalase and oxidase. Similar to P. straminea, they did not hydrolyse gelatin or casein. The G+C DNA contents determined were 57.5 mol% for CH01(T) and 58.0 mol% for PA01. DNA-DNA hybridization results showed 81 % relatedness between them, and only 40-44 % relatedness with respect to the type strain of P. straminea. These results, together with other phenotypic characteristics, support the conclusion that both isolates belong to the same species, and should be described as representing a novel species within the genus Pseudomonas, for which the name Pseudomonas argentinensis sp. nov. is proposed. The type strain is CH01(T) (=LMG 22563(T) = CECT 7010(T)).

  8. Species-specificity of the BamA component of the bacterial outer membrane protein-assembly machinery.

    Directory of Open Access Journals (Sweden)

    Elena B Volokhina

    Full Text Available The BamA protein is the key component of the Bam complex, the assembly machinery for outer membrane proteins (OMP in gram-negative bacteria. We previously demonstrated that BamA recognizes its OMP substrates in a species-specific manner in vitro. In this work, we further studied species specificity in vivo by testing the functioning of BamA homologs of the proteobacteria Neisseria meningitidis, Neisseria gonorrhoeae, Bordetella pertussis, Burkholderia mallei, and Escherichia coli in E. coli and in N. meningitidis. We found that no BamA functioned in another species than the authentic one, except for N. gonorrhoeae BamA, which fully complemented a N. meningitidis bamA mutant. E. coli BamA was not assembled into the N. meningitidis outer membrane. In contrast, the N. meningitidis BamA protein was assembled into the outer membrane of E. coli to a significant extent and also associated with BamD, an essential accessory lipoprotein of the Bam complex.Various chimeras comprising swapped N-terminal periplasmic and C-terminal membrane-embedded domains of N. meningitidis and E. coli BamA proteins were also not functional in either host, although some of them were inserted in the OM suggesting that the two domains of BamA need to be compatible in order to function. Furthermore, conformational analysis of chimeric proteins provided evidence for a 16-stranded β-barrel conformation of the membrane-embedded domain of BamA.

  9. Metabolic profiling of two maize (Zea mays L.) inbred lines inoculated with the nitrogen fixing plant-interacting bacteria Herbaspirillum seropedicae and Azospirillum brasilense

    Science.gov (United States)

    Brusamarello-Santos, Liziane Cristina; Gilard, Françoise; Brulé, Lenaïg; Quilleré, Isabelle; Gourion, Benjamin; Ratet, Pascal; Maltempi de Souza, Emanuel; Lea, Peter J.; Hirel, Bertrand

    2017-01-01

    Maize roots can be colonized by free-living atmospheric nitrogen (N2)-fixing bacteria (diazotrophs). However, the agronomic potential of non-symbiotic N2-fixation in such an economically important species as maize, has still not been fully exploited. A preliminary approach to improve our understanding of the mechanisms controlling the establishment of such N2-fixing associations has been developed, using two maize inbred lines exhibiting different physiological characteristics. The bacterial-plant interaction has been characterized by means of a metabolomic approach. Two established model strains of Nif+ diazotrophic bacteria, Herbaspirillum seropedicae and Azospirillum brasilense and their Nif- couterparts defficient in nitrogenase activity, were used to evaluate the impact of the bacterial inoculation and of N2 fixation on the root and leaf metabolic profiles. The two N2-fixing bacteria have been used to inoculate two genetically distant maize lines (FV252 and FV2), already characterized for their contrasting physiological properties. Using a well-controlled gnotobiotic experimental system that allows inoculation of maize plants with the two diazotrophs in a N-free medium, we demonstrated that both maize lines were efficiently colonized by the two bacterial species. We also showed that in the early stages of plant development, both bacterial strains were able to reduce acetylene, suggesting that they contain functional nitrogenase activity and are able to efficiently fix atmospheric N2 (Fix+). The metabolomic approach allowed the identification of metabolites in the two maize lines that were representative of the N2 fixing plant-bacterial interaction, these included mannitol and to a lesser extend trehalose and isocitrate. Whilst other metabolites such as asparagine, although only exhibiting a small increase in maize roots following bacterial infection, were specific for the two Fix+ bacterial strains, in comparison to their Fix- counterparts. Moreover, a number

  10. Metabolic profiling of two maize (Zea mays L.) inbred lines inoculated with the nitrogen fixing plant-interacting bacteria Herbaspirillum seropedicae and Azospirillum brasilense.

    Science.gov (United States)

    Brusamarello-Santos, Liziane Cristina; Gilard, Françoise; Brulé, Lenaïg; Quilleré, Isabelle; Gourion, Benjamin; Ratet, Pascal; Maltempi de Souza, Emanuel; Lea, Peter J; Hirel, Bertrand

    2017-01-01

    Maize roots can be colonized by free-living atmospheric nitrogen (N2)-fixing bacteria (diazotrophs). However, the agronomic potential of non-symbiotic N2-fixation in such an economically important species as maize, has still not been fully exploited. A preliminary approach to improve our understanding of the mechanisms controlling the establishment of such N2-fixing associations has been developed, using two maize inbred lines exhibiting different physiological characteristics. The bacterial-plant interaction has been characterized by means of a metabolomic approach. Two established model strains of Nif+ diazotrophic bacteria, Herbaspirillum seropedicae and Azospirillum brasilense and their Nif- couterparts defficient in nitrogenase activity, were used to evaluate the impact of the bacterial inoculation and of N2 fixation on the root and leaf metabolic profiles. The two N2-fixing bacteria have been used to inoculate two genetically distant maize lines (FV252 and FV2), already characterized for their contrasting physiological properties. Using a well-controlled gnotobiotic experimental system that allows inoculation of maize plants with the two diazotrophs in a N-free medium, we demonstrated that both maize lines were efficiently colonized by the two bacterial species. We also showed that in the early stages of plant development, both bacterial strains were able to reduce acetylene, suggesting that they contain functional nitrogenase activity and are able to efficiently fix atmospheric N2 (Fix+). The metabolomic approach allowed the identification of metabolites in the two maize lines that were representative of the N2 fixing plant-bacterial interaction, these included mannitol and to a lesser extend trehalose and isocitrate. Whilst other metabolites such as asparagine, although only exhibiting a small increase in maize roots following bacterial infection, were specific for the two Fix+ bacterial strains, in comparison to their Fix- counterparts. Moreover, a number

  11. Permanent draft genome sequences of the symbiotic nitrogen fixing Ensifer meliloti strains BO21CC and AK58.

    Science.gov (United States)

    Galardini, Marco; Bazzicalupo, Marco; Biondi, Emanuele; Brambilla, Eveline; Brilli, Matteo; Bruce, David; Chain, Patrick; Chen, Amy; Daligault, Hajnalka; Davenport, Karen Walston; Deshpande, Shweta; Detter, John C; Goodwin, Lynne A; Han, Cliff; Han, James; Huntemann, Marcel; Ivanova, Natalia; Klenk, Hans-Peter; Kyrpides, Nikos C; Markowitz, Victor; Mavrommatis, Kostas; Mocali, Stefano; Nolan, Matt; Pagani, Ioanna; Pati, Amrita; Pini, Francesco; Pitluck, Sam; Spini, Giulia; Szeto, Ernest; Teshima, Hazuki; Woyke, Tanja; Mengoni, Alessio

    2013-12-20

    Ensifer (syn. Sinorhizobium) meliloti is an important symbiotic bacterial species that fixes nitrogen. Strains BO21CC and AK58 were previously investigated for their substrate utilization and their plant-growth promoting abilities showing interesting features. Here, we describe the complete genome sequence and annotation of these strains. BO21CC and AK58 genomes are 6,985,065 and 6,974,333 bp long with 6,746 and 6,992 genes predicted, respectively.

  12. Microencapsulation of a putative probiotic Enterobacter species, C6-6, to protect rainbow trout, Oncorhynchus mykiss (Walbaum), against bacterial coldwater disease.

    Science.gov (United States)

    Ghosh, B; Cain, K D; Nowak, B F; Bridle, A R

    2016-01-01

    Flavobacterium psychrophilum is the causative agent of bacterial coldwater disease (BCWD), which has a major impact on salmonid aquaculture globally. An Enterobacter species, C6-6, isolated from the gut of rainbow trout, Oncorhynchus mykiss (Walbaum), has been identified as a potential probiotic species providing protection against BCWD. This study examined the effects of alginate microencapsulation on the protective efficacy of C6-6 against BCWD in vivo when administered to rainbow trout fry orally or by intraperitoneal (IP) injection. Viable C6-6 bacteria were microencapsulated successfully, and this process (microencapsulation) did not significantly deteriorate its protective properties as compared to the administration of non-microencapsulated C6-6 bacteria. Both oral and IP delivery of C6-6 achieved significantly better protection than control treatments that did not contain C6-6 bacteria. The highest relative percent survival (RPS) resulted from IP delivery (71.4%) and was significantly greater than the highest oral RPS (38.6%). Successful intestinal colonization was not critical to protective effects of C6-6. The study showed that C6-6 administration, with or without encapsulation, was a viable choice for protecting fry from BCWD especially when administered intraperitoneally.

  13. A plasmid RK2-based broad-host-range cloning vector useful for transfer of metagenomic libraries to a variety of bacterial species.

    Science.gov (United States)

    Aakvik, Trine; Degnes, Kristin Fløgstad; Dahlsrud, Rannveig; Schmidt, Frank; Dam, Ragnar; Yu, Lihua; Völker, Uwe; Ellingsen, Trond Erling; Valla, Svein

    2009-06-01

    The majority of microorganisms in natural environments are difficult to cultivate, but their genes can be studied via metagenome libraries. To enhance the chances that these genes become expressed we here report the construction of a broad-host-range plasmid vector (pRS44) for fosmid and bacterial artificial chromosome (BAC) cloning. pRS44 can be efficiently transferred to numerous hosts by conjugation. It replicates in such hosts via the plasmid RK2 origin of replication, while in Escherichia coli it replicates via the plasmid F origin. The vector was found to be remarkably stable due to the insertion of an additional stability element (parDE). The copy number of pRS44 is adjustable, allowing for easy modifications of gene expression levels. A fosmid metagenomic library consisting of 20 000 clones and BAC clones with insert sizes up to 200 kb were constructed. The 16S rRNA gene analysis of the fosmid library DNA confirmed that it represents a variety of microbial species. The entire fosmid library and the selected BAC clones were transferred to Pseudomonas fluorescens and Xanthomonas campestris (fosmids only), and heterologous proteins from the fosmid library were confirmed to be expressed in P. fluorescens. To our knowledge no other reported vector system has a comparable potential for functional screening across species barriers.

  14. Understanding microbial multi-species symbioses

    Directory of Open Access Journals (Sweden)

    Ines Aline Aschenbrenner

    2016-02-01

    Full Text Available Lichens are commonly recognized as a symbiotic association of a fungus and chlorophyll containing partner, either green algae or cyanobacteria, or both. The fungus provides a suitable habitat for the partner, which provides photosynthetically fixed carbon as energy source for the system. The evolutionary result of the self-sustaining partnership is a unique joint structure, the lichen thallus, which is indispensable for fungal sexual reproduction. The classical view of a dual symbiosis has been challenged by recent microbiome research, which revealed host-specific bacterial microbiomes. The recent results about bacterial associations with lichens symbioses corroborate their notion as a multi-species symbiosis. Multi-omics approaches have provided evidence for functional contribution by the bacterial microbiome to the entire lichen meta-organism while various abiotic and biotic factors can additionally influence the bacterial community structure. Results of current research also suggest that neighboring ecological niches influence the composition of the lichen bacterial microbiome. Specificity and functions are here reviewed based on these recent findings, converging to a holistic view of bacterial roles in lichens. Finally we propose that the lichen thallus has also evolved to function as a smart harvester of bacterial symbionts. We suggest that lichens represent an ideal model to study multi-species symbiosis, using the recentily available omics tools and other cutting edge methods.

  15. The Bacterial Species Campylobacter jejuni Induce Diverse Innate Immune Responses in Human and Avian Intestinal Epithelial Cells

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    Daniel A. John

    2017-09-01

    Full Text Available Campylobacter remain the major cause of human gastroenteritis in the Developed World causing a significant burden to health services. Campylobacter are pathogens in humans and chickens, although differences in mechanistic understanding are incomplete, in part because phenotypic strain diversity creates inconsistent findings. Here, we took Campylobacter jejuni isolates (n = 100 from multi-locus sequence typed collections to assess their pathogenic diversity, through their inflammatory, cytotoxicity, adhesion, invasion and signaling responses in a high-throughput model using avian and human intestinal epithelial cells. C. jejuni induced IL-8 and CXCLi1/2 in human and avian epithelial cells, respectively, in a MAP kinase-dependent manner. In contrast, IL-10 responses in both cell types were PI 3-kinase/Akt-dependent. C. jejuni strains showed diverse levels of invasion with high invasion dependent on MAP kinase signaling in both cell lines. C. jejuni induced diverse cytotoxic responses in both cell lines with cdt-positive isolates showing significantly higher toxicity. Blockade of endocytic pathways suggested that invasion by C. jejuni was clathrin- and dynamin-dependent but caveolae- independent in both cells. In contrast, IL-8 (and CXCLi1/2 production was dependent on clathrin, dynamin, and caveolae. This study is important because of its scale, and the data produced, suggesting that avian and human epithelial cells use similar innate immune pathways where the magnitude of the response is determined by the phenotypic diversity of the Campylobacter species.

  16. Microbiota anaeróbia isolada de bovinos com pododermatite Anaerobic bacterial species isolated from bovines with pododermatitis

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    C.A. Silva

    1999-06-01

    Full Text Available O presente trabalho teve como objetivo isolar e identificar espécies bacterianas anaeróbias presentes nos pés de bovinos portadores de vários graus de pododermatite. Foram utilizados 60 bovinos, distribuídos em quatro grupos de 15. O grupo I foi constituído por animais saudáveis e serviu de controle; o grupo II, por bovinos na fase inicial do processo; o grupo III, por animais portadores de pododermatite interdigital vegetativa e o grupo IV, por bovinos portadores de pododermatite necrosante. Foram colhidos fragmentos de tecido interdigital para cultura e as principais espécies bacterianas isoladas foram: Dichelobacter nodosus nos grupos II, III e IV e Fusobacterium necrophorum nos grupos III e IV, com freqüências de 26,7%, 6,7%, 20,0%, 6,7% e de 13,3%, respectivamente. Encontraram-se também Fusobacterium symbiosum em 40,0% no gb>rupo I, 6,7% no grupo II, 13,3% no grupo III e 13,3% no grupo IV, Bacteroides sp. em 6,7% nos grupos I e IV, Bacteroides ruminatus em 33,3% no grupo I, 6,7% no grupo II, 33,3% no grupo III e 13,3% no grupo IV, Bacteroides oralis em 6,7% no grupo III e Fusobacterium mortiferum em 6,7% no grupo IV.The objective of this study was to isolate and identify the anaerobic bacteria species in bovine with different degrees of pododermatitis. Sixty bovines were divided into four groups of 15 as follows: group I included healthy animals, used as control; group II with animals in the initial phase of the process; group III, with animals displaying interdigital skin hyperplasia and group IV with animals with footrot. Interdigital tissue fragments were collected and processed for isolation and identification of anaerobic agents. The bacteria species isolated were: Dichelobacter nodosus in groups II, III and IV and Fusobacterium necrophorum only in groups III and IV, with frequencies of 26.7%, 6.7%, and 20.0% for the former and 6.7% and 13.3% for the latter, respectively. In addition, Fusobacterium symbiosum was present in

  17. High-resolution phylogenetic analysis of residual bacterial species of fouled membranes after NaOCl cleaning.

    Science.gov (United States)

    Navarro, Ronald R; Hori, Tomoyuki; Inaba, Tomohiro; Matsuo, Kazuyuki; Habe, Hiroshi; Ogata, Atsushi

    2016-05-01

    Biofouling is one of the major problems during wastewater treatment using membrane bioreactors (MBRs). In this regard, sodium hypochlorite (NaOCl) has been widely used to wash fouled membranes for maintenance and recovery purposes. Advanced chemical and biological characterization was conducted in this work to evaluate the performance of aqueous NaOCl solutions during washing of polyacrylonitrile membranes. Fouled membranes from MBR operations supplemented with artificial wastewater were washed with 0.1% and 0.5% aqueous NaOCl solutions for 5, 10 and 30 min. The changes in organics composition on the membrane surface were directly monitored by an attenuated total reflection Fourier transform infrared (ATR-FT-IR) spectrometer. In addition, high-throughput Illumina sequencing of 16S rRNA genes was applied to detect any residual microorganisms. Results from ATR-FT-IR analysis indicated the complete disappearance of functional groups representing different fouling compounds after at least 30 min of treatment with 0.1% NaOCl. However, the biomolecular survey revealed the presence of residual bacteria even after 30 min of treatment with 0.5% NaOCl solution. Evaluation of microbial diversity of treated samples using Chao1, Shannon and Simpson reciprocal indices showed an increase in evenness while no significant decline in richness was observed. These implied that only the population of dominant species was mainly affected. The high-resolution phylogenetic analysis revealed the presence of numerous operational taxonomic units (OTUs) whose close relatives exhibit halotolerance. Some OTUs related to thermophilic and acid-resistant strains were also identified. Finally, the taxonomic analysis of recycled membranes that were previously washed with NaOCl also showed the presence of numerous halotolerant-related OTUs in the early stage of fouling. This further suggested the possible contribution of such chemical tolerance on their survival against NaOCl washing, which in turn

  18. Nitrogen-fixing bacteria in Mediterranean seagrass (Posidonia oceanica) roots

    KAUST Repository

    Garcias Bonet, Neus

    2016-03-09

    Biological nitrogen fixation by diazotrophic bacteria in seagrass rhizosphere and leaf epiphytic community is an important source of nitrogen required for plant growth. However, the presence of endophytic diazotrophs remains unclear in seagrass tissues. Here, we assess the presence, diversity and taxonomy of nitrogen-fixing bacteria within surface-sterilized roots of Posidonia oceanica. Moreover, we analyze the nitrogen isotopic signature of seagrass tissues in order to notice atmospheric nitrogen fixation. We detected nitrogen-fixing bacteria by nifH gene amplification in 13 out of the 78 roots sampled, corresponding to 9 locations out of 26 meadows. We detected two different types of bacterial nifH sequences associated with P. oceanica roots, which were closely related to sequences previously isolated from the rhizosphere of a salt marsh cord grass and a putative anaerobe. Nitrogen content of seagrass tissues showed low isotopic signatures in all the sampled meadows, pointing out the atmospheric origin of the assimilated nitrogen by seagrasses. However, this was not related with the presence of endophytic nitrogen fixers, suggesting the nitrogen fixation occurring in rhizosphere and in the epiphytic community could be an important source of nitrogen for P. oceanica. The low diversity of nitrogen-fixing bacteria reported here suggests species-specific relationships between diazotrophs and P. oceanica, revealing possible symbiotic interactions that could play a major role in nitrogen acquisition by seagrasses in oligotrophic environments where they form lush meadows.

  19. The chemical composition of the pharmacologically active Thymus species, its antibacterial activity against Streptococcus mutans and the antiadherent effects of T. vulgaris on the bacterial colonization of the in situ pellicle.

    Science.gov (United States)

    Schött, Gesche; Liesegang, Stefanie; Gaunitz, Franziska; Gleß, Alexandra; Basche, Sabine; Hannig, Christian; Speer, Karl

    2017-09-01

    The pharmacological active genus Thymus L. comprises over 200 species. Besides its traditional pharmacological use, thyme may reduce the risk of caries disease, however, there is very little respective literature. The pharmacological effects can be attributed to the secondary plant metabolites. The composition of the essential oil and the polyphenols is important for the evaluation of the pharmacological activity. Nevertheless, there are no studies regarding a comparative analysis of the different pharmacological thyme species. In the present study, four different pharmacology Thymus species were cultivated under comparable conditions, and the volatile compounds as well as the polyphenols were characterized. In addition, the in vitro antibacterial activity against S. mutans, one of the primary cariogenic bacterial species, as well as of the essential oil and of the polyphenols were investigated. Furthermore, the bacterial viability and its effect on the initial bacterial adhesion under oral conditions were evaluated in situ for the essential oil and the polyphenols. By GC-MS, 69 volatile compounds, and by LC-DAD-MS/MS, 46 polyphenols could be identified. The comprehensive examination of the essential oils and the polyphenols revealed that the main compounds were equal. However, the yield of the essential oil and the polyphenol content differed clearly. The essential oils of the four investigated Thymus species exhibited an antibacterial activity against S. mutans in vitro, in contrast to the polyphenols of T. vulgaris. Rinsing with polyphenol-rich infusions reduced the initial bacterial colonization while the essential oil inhibited the bacterial growth on dental enamel in situ. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. PCR-Independent Detection of Bacterial Species-Specific 16S rRNA at 10 fM by a Pore-Blockage Sensor

    Directory of Open Access Journals (Sweden)

    Leyla Esfandiari

    2016-07-01

    Full Text Available A PCR-free, optics-free device is used for the detection of Escherichia coli (E. coli 16S rRNA at 10 fM, which corresponds to ~100–1000 colony forming units/mL (CFU/mL depending on cellular rRNA levels. The development of a rapid, sensitive, and cost-effective nucleic acid detection platform is sought for the detection of pathogenic microbes in food, water and body fluids. Since 16S rRNA sequences are species specific and are present at high copy number in viable cells, these nucleic acids offer an attractive target for microbial pathogen detection schemes. Here, target 16S rRNA of E. coli at 10 fM concentration was detected against a total RNA background using a conceptually simple approach based on electromechanical signal transduction, whereby a step change reduction in ionic current through a pore indicates blockage by an electrophoretically mobilized bead-peptide nucleic acid probe conjugate hybridized to target nucleic acid. We investigated the concentration detection limit for bacterial species-specific 16S rRNA at 1 pM to 1 fM and found a limit of detection of 10 fM for our device, which is consistent with our previous finding with single-stranded DNA of similar length. In addition, no false positive responses were obtained with control RNA and no false negatives with target 16S rRNA present down to the limit of detection (LOD of 10 fM. Thus, this detection scheme shows promise for integration into portable, low-cost systems for rapid detection of pathogenic microbes in food, water and body fluids.

  1. A 2,4-dichlorophenoxyacetic acid degradation plasmid pM7012 discloses distribution of an unclassified megaplasmid group across bacterial species.

    Science.gov (United States)

    Sakai, Yoriko; Ogawa, Naoto; Shimomura, Yumi; Fujii, Takeshi

    2014-03-01

    Analysis of the complete nucleotide sequence of plasmid pM7012 from 2,4-dichlorophenoxyacetic-acid (2,4-D)-degrading bacterium Burkholderia sp. M701 revealed that the plasmid had 582 142 bp, with 541 putative protein-coding sequences and 39 putative tRNA genes for the transport of the standard 20 aa. pM7012 contains sequences homologous to the regions involved in conjugal transfer and plasmid maintenance found in plasmids byi_2p from Burkholderia sp. YI23 and pBVIE01 from Burkholderia sp. G4. No relaxase gene was found in any of these plasmids, although genes for a type IV secretion system and type IV coupling proteins were identified. Plasmids with no relaxase gene have been classified as non-mobile plasmids. However, nucleotide sequences with a high level of similarity to the genes for plasmid transfer, plasmid maintenance, 2,4-D degradation and arsenic resistance contained on pM7012 were also detected in eight other megaplasmids (~600 or 900 kb) found in seven Burkholderia strains and a strain of Cupriavidus, which were isolated as 2,4-D-degrading bacteria in Japan and the United States. These results suggested that the 2,4-D degradation megaplasmids related to pM7012 are mobile and distributed across various bacterial species worldwide, and that the plasmid group could be distinguished from known mobile plasmid groups.

  2. Native bacterial endophytes promote host growth in a species-specific manner; phytohormone manipulations do not result in common growth responses.

    Directory of Open Access Journals (Sweden)

    Hoang Hoa Long

    Full Text Available BACKGROUND: All plants in nature harbor a diverse community of endophytic bacteria which can positively affect host plant growth. Changes in plant growth frequently reflect alterations in phytohormone homoeostasis by plant-growth-promoting (PGP rhizobacteria which can decrease ethylene (ET levels enzymatically by 1-aminocyclopropane-1-carboxylate (ACC deaminase or produce indole acetic acid (IAA. Whether these common PGP mechanisms work similarly for different plant species has not been rigorously tested. METHODOLOGY/PRINCIPAL FINDINGS: We isolated bacterial endophytes from field-grown Solanum nigrum; characterized PGP traits (ACC deaminase activity, IAA production, phosphate solubilization and seedling colonization; and determined their effects on their host, S. nigrum, as well as on another Solanaceous native plant, Nicotiana attenuata. In S. nigrum, a majority of isolates that promoted root growth were associated with ACC deaminase activity and IAA production. However, in N. attenuata, IAA but not ACC deaminase activity was associated with root growth. Inoculating N. attenuata and S. nigrum with known PGP bacteria from a culture collection (DSMZ reinforced the conclusion that the PGP effects are not highly conserved. CONCLUSIONS/SIGNIFICANCE: We conclude that natural endophytic bacteria with PGP traits do not have general and predictable effects on the growth and fitness of all host plants, although the underlying mechanisms are conserved.

  3. Assessing the resistance and bioremediation ability of selected bacterial and protozoan species to heavy metals in metal-rich industrial wastewater

    Directory of Open Access Journals (Sweden)

    Kamika Ilunga

    2013-02-01

    Full Text Available Abstract Background Heavy-metals exert considerable stress on the environment worldwide. This study assessed the resistance to and bioremediation of heavy-metals by selected protozoan and bacterial species in highly polluted industrial-wastewater. Specific variables (i.e. chemical oxygen demand, pH, dissolved oxygen and the growth/die-off-rates of test organisms were measured using standard methods. Heavy-metal removals were determined in biomass and supernatant by the Inductively Couple Plasma Optical Emission Spectrometer. A parallel experiment was performed with dead microbial cells to assess the biosorption ability of test isolates. Results The results revealed that the industrial-wastewater samples were highly polluted with heavy-metal concentrations exceeding by far the maximum limits (in mg/l of 0.05-Co, 0.2-Ni, 0.1-Mn, 0.1-V, 0.01-Pb, 0.01-Cu, 0.1-Zn and 0.005-Cd, prescribed by the UN-FAO. Industrial-wastewater had no major effects on Pseudomonas putida, Bacillus licheniformis and Peranema sp. (growth rates up to 1.81, 1.45 and 1.43 d-1, respectively compared to other test isolates. This was also revealed with significant COD increases (p Pseudomonas putida demonstrated the highest removal rates of heavy metals (Co-71%, Ni-51%, Mn-45%, V-83%, Pb-96%, Ti-100% and Cu-49% followed by Bacillus licheniformis (Al-23% and Zn-53% and Peranema sp. (Cd-42%. None of the dead cells were able to remove more than 25% of the heavy metals. Bacterial isolates contained the genes copC, chrB, cnrA3 and nccA encoding the resistance to Cu, Cr, Co-Ni and Cd-Ni-Co, respectively. Protozoan isolates contained only the genes encoding Cu and Cr resistance (copC and chrB genes. Peranema sp. was the only protozoan isolate which had an additional resistant gene cnrA3 encoding Co-Ni resistance. Conclusion Significant differences (p Peranema sp. as a potential candidate for the bioremediation of heavy-metals in wastewater treatment, in addition to Pseudomonas

  4. Zirconia in fixed implant prosthodontics.

    Science.gov (United States)

    Guess, Petra Christine; Att, Wael; Strub, Joerg Rudolf

    2012-10-01

    CAD/CAM technology in combination with zirconia ceramic has increasingly gained popularity in implant dentistry. This narrative review presents the current knowledge on zirconia utilized as framework material for implant-borne restorations and implant abutments, laboratory tests and developments, clinical performance, and possible future trends for implant dentistry are addressed. A review of available literature from 1990 through 2010 was conducted with search terms zirconia,"implants,"abutment,"crown," and "fixed dental prosthesis" using electronic databases (PubMed) and manual searching. Latest applications of zirconia in implant dentistry include implant abutments, multiple unit and full-arch frameworks as well as custom-made bars to support fixed and removable prostheses. High biocompatibility, low bacterial surface adhesion as well as favorable chemical properties of zirconia ceramics are reported. Zirconia stabilized with yttrium oxide exhibits high flexural strength and fracture toughness due to a transformation toughening mechanism. Preliminary clinical data confirmed the high stability of zirconia for abutments and as a framework material for implant borne crowns and fixed dental prostheses. Zirconia abutment or framework damage has rarely been encountered. However, veneering porcelain fractures are the most common technical complication in implant-supported zirconia restorations. These porcelain veneer failures have led to concerns regarding differences in coefficient of thermal expansions between core and veneering porcelain and their respective processing techniques. As presently evidence of clinical long-term data is missing, caution with regard to especially extensive implant-borne zirconia frameworks is recommended. © 2010 Wiley Periodicals, Inc.

  5. A one-month study of the zooplankton community at a fixed station in the Ligurian Sea: the potential impact of the species composition on the mineralization of organic matter

    Directory of Open Access Journals (Sweden)

    L. Mousseau

    2009-01-01

    scales. The aim of the work presented here was to estimate, at a fixed station in the Ligurian Sea (NW Mediterranean Sea,the impact of zooplankton on organic matter fluxes. We determined the species composition and then for the dominant species of the community, we estimated rates of, oxygen consumption, carbon dioxide production and ammonium excretion. Our sampling period, the summer-autumn transition featuring strong wind events, offered contrasting situations for primary and export production (Marty et al., 2008. We thus have the opportunity to estimate how the zooplankton, from a species-specific point of view, react to these changes.

  6. Symbiosis within Symbiosis: Evolving Nitrogen-Fixing Legume Symbionts.

    Science.gov (United States)

    Remigi, Philippe; Zhu, Jun; Young, J Peter W; Masson-Boivin, Catherine

    2016-01-01

    Bacterial accessory genes are genomic symbionts with an evolutionary history and future that is different from that of their hosts. Packages of accessory genes move from strain to strain and confer important adaptations, such as interaction with eukaryotes. The ability to fix nitrogen with legumes is a remarkable example of a complex trait spread by horizontal transfer of a few key symbiotic genes, converting soil bacteria into legume symbionts. Rhizobia belong to hundreds of species restricted to a dozen genera of the Alphaproteobacteria and Betaproteobacteria, suggesting infrequent successful transfer between genera but frequent successful transfer within genera. Here we review the genetic and environmental conditions and selective forces that have shaped evolution of this complex symbiotic trait. Copyright © 2015 Elsevier Ltd. All rights reserved.

  7. Enriching vermicompost by nitrogen fixing and phosphate solubilizing bacteria.

    Science.gov (United States)

    Kumar, V; Singh, K P

    2001-01-01

    The effect of inoculation of vermicompost with nitrogen-fixing Azotobacter chroococcum strains, Azospirillum lipoferum and the phosphate solubilizing Pseudomonas striata on N and P contents of the vermicompost was assessed. Inoculation of N2 fixing bacteria into vermicompost increased contents of N and P. Enriching vermicompost with rock phosphate improved significantly the available P when inoculated with P. striata. During the incubation period, the inoculated bacterial strains proliferated rapidly, fixed N and solubilized added and native phosphate.

  8. Detection of Bacterial and Yeast Species with the Bactec 9120 Automated System with Routine Use of Aerobic, Anaerobic, and Fungal Media▿

    Science.gov (United States)

    Chiarini, Alfredo; Palmeri, Angelo; Amato, Teresa; Immordino, Rita; Distefano, Salvatore; Giammanco, Anna

    2008-01-01

    During the period 2006 and 2007, all blood cultures required by four units at high infective risk and most of those required by other units of the University Hospital of Palermo, Palermo, Italy were performed using a Bactec 9120 automated blood culture system with a complete set of Plus Aerobic/F, Plus Anaerobic/F, and Mycosis IC/F bottles. The aim of the study was to enable the authors to gain firsthand experience of the culture potentialities of the three different media, to obtain information regarding the overall and specific recovery of bacteria and yeasts from blood cultures in the hospital, and to reach a decision as to whether and when to utilize anaerobic and fungal bottles. Although very few bloodstream infections (1.8%) were associated with obligate anaerobes, the traditional routine use of anaerobic bottles was confirmed because of their usefulness, not only in the detection of anaerobes, but also in that of gram-positive cocci and fermentative gram-negative bacilli. In this study, Mycosis IC/F bottles detected 77.4% of all the yeast isolates, 87.0% of yeasts belonging to the species Candida albicans, and 45.7% of nonfermentative gram-negative bacilli resistant to chloramphenicol and tobramycin. In order to improve the diagnosis of fungemia in high-risk patients, the additional routine use of fungal bottles was suggested when, as occurred in the intensive-care unit and in the hematology unit of the University Hospital of Palermo, high percentages of bloodstream infections are associated with yeasts, and/or antibiotic-resistant bacteria and/or multiple bacterial isolates capable of inhibiting yeast growth in aerobic bottles. PMID:18923011

  9. QCD at Fixed Topology

    CERN Document Server

    Brower, Richard C; Negele, John W; Wiese, U J

    2003-01-01

    Since present Monte Carlo algorithms for lattice QCD may become trapped in a fixed topological charge sector, it is important to understand the effect of calculating at fixed topology. In this work, we show that although the restriction to a fixed topological sector becomes irrelevant in the infinite volume limit, it gives rise to characteristic finite size effects due to contributions from all $\\theta$-vacua. We calculate these effects and show how to extract physical results from numerical data obtained at fixed topology.

  10. Bacterial Vaginosis

    Science.gov (United States)

    ... Form Controls Cancel Submit Search the CDC Bacterial Vaginosis (BV) Note: Javascript is disabled or is not ... STD on Facebook Sexually Transmitted Diseases (STDs) Bacterial Vaginosis – CDC Fact Sheet Language: English (US) Españ ...

  11. Bacterial Vaginosis

    Science.gov (United States)

    ... Issues > Conditions > Sexually Transmitted > Bacterial Vaginosis Health Issues Listen Español Text Size Email Print Share Bacterial Vaginosis Page Content Bacterial vaginosis (BV) is the most common vaginal infection in sexually active teenaged girls . It appears to be caused by ...

  12. A canonical FtsZ protein in Verrucomicrobium spinosum, a member of the Bacterial phylum Verrucomicrobia that also includes tubulin-producing Prosthecobacter species

    Directory of Open Access Journals (Sweden)

    Staley James T

    2007-03-01

    Full Text Available Abstract Background The origin and evolution of the homologous GTP-binding cytoskeletal proteins FtsZ typical of Bacteria and tubulin characteristic of eukaryotes is a major question in molecular evolutionary biology. Both FtsZ and tubulin are central to key cell biology processes – bacterial septation and cell division in the case of FtsZ and in the case of tubulins the function of microtubules necessary for mitosis and other key cytoskeleton-dependent processes in eukaryotes. The origin of tubulin in particular is of significance to models for eukaryote origins. Most members of domain Bacteria possess FtsZ, but bacteria in genus Prosthecobacter of the phylum Verrucomicrobia form a key exception, possessing tubulin homologs BtubA and BtubB. It is therefore of interest to know whether other members of phylum Verrucomicrobia possess FtsZ or tubulin as their FtsZ-tubulin gene family representative. Results Verrucomicrobium spinosum, a member of Phylum Verrucomicrobia of domain Bacteria, has been found to possess a gene for a protein homologous to the cytoskeletal protein FtsZ. The deduced amino acid sequence has sequence signatures and predicted secondary structure characteristic for FtsZ rather than tubulin, but phylogenetic trees and sequence analysis indicate that it is divergent from all other known FtsZ sequences in members of domain Bacteria. The FtsZ gene of V. spinosum is located within a dcw gene cluster exhibiting gene order conservation known to contribute to the divisome in other Bacteria and comparable to these clusters in other Bacteria, suggesting a similar functional role. Conclusion Verrucomicrobium spinosum has been found to possess a gene for a protein homologous to the cytoskeletal protein FtsZ. The results suggest the functional as well as structural homology of the V. spinosum FtsZ to the FtsZs of other Bacteria implying its involvement in cell septum formation during division. Thus, both bacteria-like FtsZ and eukaryote

  13. Bacterial Sialidase

    Science.gov (United States)

    2004-01-01

    Data shows that elevated sialidase in bacterial vaginosis patients correlates to premature births in women. Bacterial sialidase also plays a significant role in the unusual colonization of Pseudomonas aeruginosa in cystic fibrosis patients. Crystals of Salmonella sialidase have been reproduced and are used for studying the inhibitor-enzyme complexes. These inhibitors may also be used to inhibit a trans-sialidase of Trypanosome cruzi, a very similar enzyme to bacterial sialidase, therefore preventing T. cruzi infection, the causitive agent of Chagas' disease. The Center for Macromolecular Crystallography suggests that inhibitors of bacterial sialidases can be used as prophylactic drugs to prevent bacterial infections in these critical cases.

  14. Targeting of a Fixed Bacterial Immunogen to Fc Receptors Reverses the Anti-Inflammatory Properties of the Gram-Negative Bacterium, Francisella tularensis, during the Early Stages of Infection.

    Directory of Open Access Journals (Sweden)

    Zulfia Babadjanova

    Full Text Available Production of pro-inflammatory cytokines by innate immune cells at the early stages of bacterial infection is important for host protection against the pathogen. Many intracellular bacteria, including Francisella tularensis, the agent of tularemia, utilize the anti-inflammatory cytokine IL-10, to evade the host immune response. It is well established that IL-10 has the ability to inhibit robust antigen presentation by dendritic cells and macrophages, thus suppressing the generation of protective immunity. The pathogenesis of F. tularensis is not fully understood, and research has failed to develop an effective vaccine to this date. In the current study, we hypothesized that F. tularensis polarizes antigen presenting cells during the early stages of infection towards an anti-inflammatory status characterized by increased synthesis of IL-10 and decreased production of IL-12p70 and TNF-α in an IFN-ɣ-dependent fashion. In addition, F. tularensis drives an alternative activation of alveolar macrophages within the first 48 hours post-infection, thus allowing the bacterium to avoid protective immunity. Furthermore, we demonstrate that targeting inactivated F. tularensis (iFt to Fcγ receptors (FcɣRs via intranasal immunization with mAb-iFt complexes, a proven vaccine strategy in our laboratories, reverses the anti-inflammatory effects of the bacterium on macrophages by down-regulating production of IL-10. More specifically, we observed that targeting of iFt to FcγRs enhances the classical activation of macrophages not only within the respiratory mucosa, but also systemically, at the early stages of infection. These results provide important insight for further understanding the protective immune mechanisms generated when targeting immunogens to Fc receptors.

  15. 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.

  16. Fixed mobile convergence handbook

    CERN Document Server

    Ahson, Syed A

    2010-01-01

    From basic concepts to future directions, this handbook provides technical information on all aspects of fixed-mobile convergence (FMC). The book examines such topics as integrated management architecture, business trends and strategic implications for service providers, personal area networks, mobile controlled handover methods, SIP-based session mobility, and supervisory and notification aggregator service. Case studies are used to illustrate technical and systematic implementation of unified and rationalized internet access by fixed-mobile network convergence. The text examines the technolo

  17. Optically fixed photorefractive correlator

    Institute of Scientific and Technical Information of China (English)

    刘友文; 刘立人; 周常河; 徐良瑛

    2002-01-01

    An optically fixed photorefractive correlator is presented, where two-centre non-volatile holographic recording isemployed to write and fix the matched filter in doubly doped LiNbO3 crystals. This correlator shows good correlationcharacteristics and insensitivity to the writing beam during readout. It can be used in cases requiring stability and notrequiring modification for a long period, and it is refreshed optically when new information needs to be registered.

  18. Species-specific engagement of human nucleotide oligomerization domain 2 (NOD)2 and Toll-like receptor (TLR) signalling upon intracellular bacterial infection

    DEFF Research Database (Denmark)

    Salem, M; Seidelin, J B; Eickhardt-Dalbøge, Steffen Robert

    2015-01-01

    Recognition of bacterial peptidoglycan-derived muramyl-dipeptide (MDP) by nucleotide oligomerization domain 2 (NOD2) induces crucial innate immune responses. Most bacteria carry the N-acetylated form of MDP (A-MDP) in their cell membranes, whereas N-glycolyl MDP (G-MDP) is typical for mycobacteri...

  19. Gram-negative bacterial isolates from fresh-cut processing plants enhance the presence of Escherichia Coli O157:H7 in dual-species biofilms

    Science.gov (United States)

    Biofilms formed by resident microflora may provide a microenvironment for foodborne bacterial pathogens to survive and cause cross-contamination in fresh-cut processing and handling facilities. The objective of this study is to determine the impact of individual bacteria strains isolated from two l...

  20. Use of Amplified Ribosomal DNA Restriction Analysis for Identification of Ralstonia and Pandoraea Species: Interest in Determination of the Respiratory Bacterial Flora in Patients with Cystic Fibrosis

    Science.gov (United States)

    Segonds, Christine; Paute, Sandrine; Chabanon, Gérard

    2003-01-01

    The recovery of Ralstonia and Pandoraea species from respiratory tract cultures of patients with cystic fibrosis has recently been reported. These species are difficult to identify, and especially to differentiate from Burkholderia cepacia complex organisms, with classical methods. The discriminatory power of amplified ribosomal DNA restriction analysis (ARDRA) within the two genera was assessed by comparing the restriction profiles of reference strains of each species by using a panel of six enzymes already proven suitable for the identification of Burkholderia species. ARDRA provided differentiation of all the Ralstonia species tested and of Pandoraea norimbergensis. Pandoraea species P. pnomenusa, P. sputorum, P. pulmonicola, and P. apista were not discriminated to the species level. This method allowed the identification of five clinical isolates recovered from French cystic fibrosis patients as Ralstonia mannitolilytica. PMID:12843108

  1. The response to nitric oxide of the nitrogen-fixing symbiont Sinorhizobium meliloti.

    Science.gov (United States)

    Meilhoc, Eliane; Cam, Yvan; Skapski, Agnès; Bruand, Claude

    2010-06-01

    Nitric oxide (NO) is crucial in animal- and plant-pathogen interactions, during which it participates in host defense response and resistance. Indications for the presence of NO during the symbiotic interaction between the model legume Medicago truncatula and its symbiont Sinorhizobium meliloti have been reported but the role of NO in symbiosis is far from being elucidated. Our objective was to understand the role or roles played by NO in symbiosis. As a first step toward this goal, we analyzed the bacterial response to NO in culture, using a transcriptomic approach. We identified approximately 100 bacterial genes whose expression is upregulated in the presence of NO. Surprisingly, most of these genes are regulated by the two-component system FixLJ, known to control the majority of rhizobial genes expressed in planta in mature nodules, or the NO-dedicated regulator NnrR. Among the genes responding to NO is hmp, encoding a putative flavohemoglobin. We report that an hmp mutant displays a higher sensitivity toward NO in culture and leads to a reduced nitrogen fixation efficiency in planta. Because flavohemoglobins are known to detoxify NO in numerous bacterial species, this result is the first indication of the importance of the bacterial NO response in symbiosis.

  2. [Diagnosis of bacterial vaginosis].

    Science.gov (United States)

    Djukić, Slobodanka; Ćirković, Ivana; Arsić, Biljana; Garalejić, Eliana

    2013-01-01

    Bacterial vaginosis is a common, complex clinical syndrome characterized by alterations in the normal vaginal flora. When symptomatic, it is associated with a malodorous vaginal discharge and on occasion vaginal burning or itching. Under normal conditions, lactobacilli constitute 95% of the bacteria in the vagina. Bacterial vaginosis is associated with severe reduction or absence of the normal H2O2-producing lactobacilli and overgrowth of anaerobic bacteria and Gardnerella vaginalis, Atopobium vaginae, Mycoplasma hominis and Mobiluncus species. Most types of infectious disease are diagnosed by culture, by isolating an antigen or RNA/DNA from the microbe, or by serodiagnosis to determine the presence of antibodies to the microbe. Therefore, demonstration of the presence of an infectious agent is often a necessary criterion for the diagnosis of the disease. This is not the case for bacterial vaginosis, since the ultimate cause of the disease is not yet known. There are a variety of methods for the diagnosis of bacterial vaginosis but no method can at present be regarded as the best. Diagnosing bacterial vaginosis has long been based on the clinical criteria of Amsel, whereby three of four defined criteria must be satisfied. Nugent's scoring system has been further developed and includes validation of the categories of observable bacteria structures. Up-to-date molecular tests are introduced, and better understanding of vaginal microbiome, a clear definition for bacterial vaginosis, and short-term and long-term fluctuations in vaginal microflora will help to better define molecular tests within the broader clinical context.

  3. Ectopic expression of Hrf1 enhances bacterial resistance via regulation of diterpene phytoalexins, silicon and reactive oxygen species burst in rice.

    Directory of Open Access Journals (Sweden)

    Wenqi Li

    Full Text Available Harpin proteins as elicitor derived from plant gram negative bacteria such as Xanthomonas oryzae pv. oryzae (Xoo, Erwinia amylovora induce disease resistance in plants by activating multiple defense responses. However, it is unclear whether phytoalexin production and ROS burst are involved in the disease resistance conferred by the expression of the harpin(Xoo protein in rice. In this article, ectopic expression of hrf1 in rice enhanced resistance to bacterial blight. Accompanying with the activation of genes related to the phytoalexin biosynthesis pathway in hrf1-transformed rice, phytoalexins quickly and consistently accumulated concurrent with the limitation of bacterial growth rate. Moreover, the hrf1-transformed rice showed an increased ability for ROS scavenging and decreased hydrogen peroxide (H(2O(2 concentration. Furthermore, the localization and relative quantification of silicon deposition in rice leaves was detected by scanning electron microscopy (SEM and energy-dispersive X-ray spectrometer (EDS. Finally, the transcript levels of defense response genes increased in transformed rice. These results show a correlation between Xoo resistance and phytoalexin production, H(2O(2, silicon deposition and defense gene expression in hrf1-transformed rice. These data are significant because they provide evidence for a better understanding the role of defense responses in the incompatible interaction between bacterial disease and hrf1-transformed plants. These data also supply an opportunity for generating nonspecific resistance to pathogens.

  4. Infectious prosthetic hip joint loosening: bacterial species involved in its aetiology and their antibiotic resistance profiles against antibiotics recommended for the therapy of implant-associated infections.

    Science.gov (United States)

    Bogut, Agnieszka; Niedźwiadek, Justyna; Strzelec-Nowak, Dagmara; Blacha, Jan; Mazurkiewicz, Tomasz; Marczyński, Wojciech; Kozioł-Montewka, Maria

    2014-04-01

    Reliable microbiological diagnosis along with surgery and prolonged antibiotic therapy are key elements in the management of prosthetic-joint infections (PJIs). The purpose of this study was to characterize antibiotic resistance profiles of bacteria involved in the aetiology of PJIs. A total of 33 bacterial isolates cultured from 31 patients undergoing exchange of total hip prostheses were analyzed. The diagnostic approach toward isolation of prosthesis- associated microorganisms included sonication of retrieved implants and conventional cultures of periprosthetic tissues and synovial fluid. The in vitro resistance profiles of bacterial isolates were determined in relation to antibiotics recommended for the therapy of PJIs using the disc diffusion method, E-tests(®) and broth microdilution system. Coagulase-negative staphylococci (CNS) were predominant microorganisms followed by Staphylococcus aureus, Enterobacter cloacae, Streptococcus mitis, and Propionibacterium acnes. Twenty out of 30 and 12 out of 30 staphylococcal isolates were methicillin- and multi-drug resistant, respectively. Only two isolates were rifampicinresistant. All staphylococci were susceptible to glycopeptides and linezolid. This paper stresses the pathogenic role of staphylococci in patients suffering from implant loosening and reports high methicillin- and multidrug-resistance rates in these bacteria. Hence, antimicrobial susceptibility tests of individual bacterial isolates must always be performed to guide selection of the optimal therapeutic option.

  5. Ectopic Expression of Hrf1 Enhances Bacterial Resistance via Regulation of Diterpene Phytoalexins, Silicon and Reactive Oxygen Species Burst in Rice

    Science.gov (United States)

    Zhong, Weigong; Yang, Jie; Okada, Kazunori; Yamane, Hisakazu; Zhang, Lei; Wang, Guang; Wang, Dong; Xiao, Shanshan; Chang, Shanshan; Qian, Guoliang; Liu, Fengquan

    2012-01-01

    Harpin proteins as elicitor derived from plant gram negative bacteria such as Xanthomonas oryzae pv. oryzae (Xoo), Erwinia amylovora induce disease resistance in plants by activating multiple defense responses. However, it is unclear whether phytoalexin production and ROS burst are involved in the disease resistance conferred by the expression of the harpinXoo protein in rice. In this article, ectopic expression of hrf1 in rice enhanced resistance to bacterial blight. Accompanying with the activation of genes related to the phytoalexin biosynthesis pathway in hrf1-transformed rice, phytoalexins quickly and consistently accumulated concurrent with the limitation of bacterial growth rate. Moreover, the hrf1-transformed rice showed an increased ability for ROS scavenging and decreased hydrogen peroxide (H2O2) concentration. Furthermore, the localization and relative quantification of silicon deposition in rice leaves was detected by scanning electron microscopy (SEM) and energy-dispersive X-ray spectrometer (EDS). Finally, the transcript levels of defense response genes increased in transformed rice. These results show a correlation between Xoo resistance and phytoalexin production, H2O2, silicon deposition and defense gene expression in hrf1-transformed rice. These data are significant because they provide evidence for a better understanding the role of defense responses in the incompatible interaction between bacterial disease and hrf1-transformed plants. These data also supply an opportunity for generating nonspecific resistance to pathogens. PMID:22970151

  6. Stress tolerant crops from nitrogen fixing trees

    Energy Technology Data Exchange (ETDEWEB)

    Becker, R.; Saunders, R.M.

    1983-01-01

    Notes are given on the nutritional quality and uses of: pods of Geoffroea decorticans, a species tolerant of saline and limed soils and saline water; seeds of Olneya tesota which nodulates readily and fixes nitrogen and photosynthesizes at low water potential; and pods of Prosopis chilensis and P. tamarugo which tolerate long periods without rain. 3 references.

  7. Bacterial glycosyltransferase toxins.

    Science.gov (United States)

    Jank, Thomas; Belyi, Yury; Aktories, Klaus

    2015-12-01

    Mono-glycosylation of host proteins is a common mechanism by which bacterial protein toxins manipulate cellular functions of eukaryotic target host cells. Prototypic for this group of glycosyltransferase toxins are Clostridium difficile toxins A and B, which modify guanine nucleotide-binding proteins of the Rho family. However, toxin-induced glycosylation is not restricted to the Clostridia. Various types of bacterial pathogens including Escherichia coli, Yersinia, Photorhabdus and Legionella species produce glycosyltransferase toxins. Recent studies discovered novel unexpected variations in host protein targets and amino acid acceptors of toxin-catalysed glycosylation. These findings open new perspectives in toxin as well as in carbohydrate research.

  8. Analysis and exploitation of bacterial population from natural uranium-rich soils: selection of a model specie; Analyse et exploitation des populations bacteriennes de sols riches en uranium: selection d'une espece modele

    Energy Technology Data Exchange (ETDEWEB)

    Mondani, L.

    2010-11-23

    It is well known that soils play a key role in controlling the mobility of toxic metals and this property is greatly influenced by indigenous bacterial communities. This study has been conducted on radioactive and controls soils, collected in natural uraniferous areas (Limousin). A physico-chemical and mineralogical analysis of soils samples was carried out.The structure of bacterial communities was estimated by Denaturing Gradient Gel Electrophoresis (DGGE). The community structure is remarkably more stable in the uranium-rich soils than in the control ones, indicating that uranium exerts a high selection from the soils was constructed and screened for uranium resistance in order to study bacteria-uranium interactions. Scanning electron microscopy revealed that a phylo-genetically diverse set of uranium-resistant species ware able to chelate uranium at the cell surface. (author) [French] On sait que les sols et les populations bacteriennes indigenes ont une influence sur la mobilite des metaux, donc sur leur toxicite. Cette etude a ete menee sur des sols uraniferes et controles collectes dans le Limousin (regions naturellement riches en uranium ). Une analyse physico-chimique et mineralogique des echantillons de sol a ete realisee. La structure des communautes bacteriennes a ete etudiee par electrophorese en gradient de denaturant (DGGE). La structure des communautes est remarquablement stable dans les sols uraniferes, ce qui indique que l'uranium exerce une forte pression de selection. D'autre part, une collection de bacteries cultivables a ete realisee a partir des sols, puis criblee pour la resistance a l'uranium, dans le but d'etudier les interactions entre bacteries et uranium. Des observations en Microscopie electronique a Balayage ont mis en evidence differents mecanismes de chelation de l'uranium a la surface cellulaire

  9. Fixing Dataset Search

    Science.gov (United States)

    Lynnes, Chris

    2014-01-01

    Three current search engines are queried for ozone data at the GES DISC. The results range from sub-optimal to counter-intuitive. We propose a method to fix dataset search by implementing a robust relevancy ranking scheme. The relevancy ranking scheme is based on several heuristics culled from more than 20 years of helping users select datasets.

  10. Temporal dynamics of abundance and composition of nitrogen-fixing communities across agricultural soils.

    Directory of Open Access Journals (Sweden)

    Michele C Pereira E Silva

    Full Text Available BACKGROUND: Despite the fact that the fixation of nitrogen is one of the most significant nutrient processes in the terrestrial ecosystem, a thorough study of the spatial and temporal patterns in the abundance and distribution of N-fixing communities has been missing so far. METHODOLOGY/PRINCIPAL FINDINGS: In order to understand the dynamics of diazotrophic communities and their resilience to external changes, we quantified the abundance and characterized the bacterial community structures based on the nifH gene, using real-time PCR, PCR-DGGE and 454-pyrosequencing, across four representative Dutch soils during one growing season. In general, higher nifH gene copy numbers were observed in soils with higher pH than in those with lower pH, but lower numbers were related to increased nitrate and ammonium levels. Results from nifH gene pyrosequencing confirmed the observed PCR-DGGE patterns, which indicated that the N fixers are highly dynamic across time, shifting around 60%. Forward selection on CCA analysis identified N availability as the main driver of these variations, as well as of the evenness of the communities, leading to very unequal communities. Moreover, deep sequencing of the nifH gene revealed that sandy soils (B and D had the lowest percentage of shared OTUs across time, compared with clayey soils (G and K, indicating the presence of a community under constant change. Cosmopolitan nifH species (present throughout the season were affiliated with Bradyrhizobium, Azospirillum and Methylocistis, whereas other species increased their abundances progressively over time, when appropriate conditions were met, as was notably the case for Paenibacilus and Burkholderia. CONCLUSIONS: Our study provides the first in-depth pyrosequencing analysis of the N-fixing community at both spatial and temporal scales, providing insights into the cosmopolitan and specific portions of the nitrogen fixing bacterial communities in soil.

  11. Bacterial gastroenteritis

    Science.gov (United States)

    ... most common types of bacterial gastroenteritis in a couple of days. The goal is to make you feel better and avoid dehydration. Drinking enough fluids and learning what to eat will help ease symptoms. You ...

  12. Bacterial vaginosis

    National Research Council Canada - National Science Library

    Islam, Aliya; Safdar, Anjum; Malik, Ayesha

    2009-01-01

    To estimate the frequency of bacterial vaginosis in women with preterm labour. Descriptive cross sectional study carried out in department of Obstetrics and Gynaecology, Military Hospital and Army Medical College Laboratory, Rawalpindi...

  13. Nitrogen Fixing Legumes in the Plant Communities

    Directory of Open Access Journals (Sweden)

    M. A.A. Al-Fredan

    2011-01-01

    Full Text Available Problems statement: Numerous authors have used energetic to explain the ecological success of N-fixing plants. Legume biodiversity assessment, species dynamics, nitrogen fixation monitoring and environment impact assessment of these ecological events in Al-Hassa Oasis, Saudi Arabia are rare and need to be continuous and more frequent. Approach: Thus the objectives of this study were to analyze legume abundance within and outside Al-Hassa Oasis and relate it to the distribution of the different genera. Results: Thirty two legume plant species from 20 genera have been recorded within and outside the Oasis. The largest genera were Cassia (4 species, Indigofera (4 and Acacia (3. Annual herbs were the dominant growth form (34% of species recorded, followed by shrubs (28%, perennial herbs (19% and trees (19%. Eighteen alien plant species were recorded (maybe an underestimated number. The nitrogen fixation of the legume plant species in Al-Hassa Oasis was estimated/analyzing the fixing potentiality of these species and nonfixing reference species (Panicum turgidum using the 15N natural abundance method. Species with great nitrogen fixing capacity in Al-Hassa include: Medicago sativa, Vicia faba, Vicia sativa, Melitotus indicus, Dolicus lablab, Melitotus alba and Cliforia ternate. The mean biological fixation contribution of most of the recorded legume plants were high, varying from 3.9% (Indigofera argentea to 64.6% (Medicago sativa. Conclusion: Al-Hassa Oasis is richer than expected based on its location within the desert zone. This study confirms the importance of the Oasis for national flora conservation in the Kingdom. results showed a good potential for use of the 15N natural abundance methodology for evaluating the nitrogen fixation ability of the legume plants under field conditions as well as for the estimation of %Ndfa.

  14. Fixed textile shutters

    Directory of Open Access Journals (Sweden)

    K.A. Chernova

    2010-06-01

    Full Text Available One of the main socio-economic problems in Russia is the high cost and the poor condition of housing.Such goals as cost reduction, reducing installation time and increasing the service life of structures are accomplishing by creating new technologies of erecting buildings and developing ways ofquickconstruction, using different types of fixed formwork. One of themis textstone.Textstone is an artificial construction stone, containing on the outer surface the reinforcing fine-mesh shell with multifunctional properties, formed by the interwoven threads of a vigorous fixed formwork textile material (basalt, linen, silica and other glass yarns adhered by binding material. The innovative construction technology of production and installation of a new generation of textstone buildings has been registered as a brand TextStone. The fundamental difference between texstone and reinforced concrete and all known building materials is that the whole outer surface of solidified light binders is protected by strong, vigorous and fixed formwork made from inexpensive textile materials. Manufacturing textile shells allows using it as an internal finishing material, reducing or eliminating the cost of finishing work.The use of fixed textile construction shutters during the construction of buildings has obvious technical, economic, operational, sanitary and environmental benefits: short construction time (from 3 to 10 days, compact packaging and light weight of fabric shells, high fire resistance, frost resistance, ease of engineering services installation in the hollow communicating shells; minimal amount of finishing, roofing, heat and noise insulation works. Texstone is a durable solid monolithic construction that provides high viability and earthquakes, hurricanes wind, solar sultriness and frost resistance. Material complies with all sanitary and environmental requirements. Due to such physical, mechanical, operational, sanitary and ecological characteristics

  15. Fixed Sagittal Plane Imbalance

    OpenAIRE

    Savage, Jason W.; Patel, Alpesh A.

    2014-01-01

    Study Design Literature review. Objective To discuss the evaluation and management of fixed sagittal plane imbalance. Methods A comprehensive literature review was performed on the preoperative evaluation of patients with sagittal plane malalignment, as well as the surgical strategies to address sagittal plane deformity. Results Sagittal plane imbalance is often caused by de novo scoliosis or iatrogenic flat back deformity. Understanding the etiology and magnitude of sagittal malalignment is ...

  16. Targeting bacterial toxins.

    Science.gov (United States)

    Ivarsson, Mattias E; Leroux, Jean-Christophe; Castagner, Bastien

    2012-04-23

    Protein toxins constitute the main virulence factors of several species of bacteria and have proven to be attractive targets for drug development. Lead candidates that target bacterial toxins range from small molecules to polymeric binders, and act at each of the multiple steps in the process of toxin-mediated pathogenicity. Despite recent and significant advances in the field, a rationally designed drug that targets toxins has yet to reach the market. This Review presents the state of the art in bacterial toxin targeted drug development with a critical consideration of achieved breakthroughs and withstanding challenges. The discussion focuses on A-B-type protein toxins secreted by four species of bacteria, namely Clostridium difficile (toxins A and B), Vibrio cholerae (cholera toxin), enterohemorrhagic Escherichia coli (Shiga toxin), and Bacillus anthracis (anthrax toxin), which are the causative agents of diseases for which treatments need to be improved. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. A composite microbial agent containing bacterial and fungal species: Optimization of the preparation process, analysis of characteristics, and use in the purification for volatile organic compounds.

    Science.gov (United States)

    Cheng, Zhuowei; Lu, Lichao; Kennes, Christian; Ye, Jiexu; Yu, Jianming; Chen, Dongzhi; Chen, Jianmeng

    2016-10-01

    Proper preservation of microbial activity over long periods poses a considerable challenge for pollutant biopurification. A composite microbial agent, mainly composed of bacteria and fungi isolated by the current research team, was constructed in this study and its performance in the removal of mixed waste gases (containing α-pinene, n-butyl acetate and o-xylene) was investigated. According to the removal efficiency in the first 24h and the response to starvation, the optimal ratio of selected carriers (activated carbon, wheat bran and sawdust) was found to be 1:2:1. In some cases of storages, the removal capability of the microbial agent was more than twice that of the suspension. Microbial analysis showed that the inoculated bacterial and fungal strains dominated the agent preparation and utilization. These results indicated that the agent has potential for use in biopurification of mixed waste gas, favoring the reduction of environmental passives and longer retention of microbial activity.

  18. Biodiversity of aerobic endospore-forming bacterial species occurring in Yanyanku and Ikpiru, fermented seeds of Hibiscus sabdariffa used to produce food condiments in Benin

    DEFF Research Database (Denmark)

    Agbobatinkpo, Pélagie B.; Thorsen, Line; Nielsen, Dennis Sandris

    2013-01-01

    toxin encoding genes cytK-1, cytK-2, hblA, hblC, and hblD were present in 0%, 91% 15%, 34% and 35% of B. cereus isolates, respectively. 9% of them harbored the emetic toxin genetic determinant, cesB. This study is the first to identify the AEFB of Yanyanku and Ikpiru to species level and perform...... a safety evaluation based on toxin gene detections. We further suggest, that the gyrA gene can be used for differentiating the closely related species Bacillus pumilus and B. safensis....

  19. ‘Arthrobacter saudimassiliensis’ sp. nov. a new bacterial species isolated from air samples in the urban environment of Makkah, Saudi Arabia

    Directory of Open Access Journals (Sweden)

    A. Papadioti

    2017-03-01

    Full Text Available We report here the main characteristics of ‘Arthrobacter saudimassiliensis’ strain 11W110_airT (CSUR P1223, a new species of the Arthrobacter genus that was isolated from air samples in the city environment of Makkah, Saudi Arabia, during the pilgrim period of Hajj 2012.

  20. ‘Pseudomonas saudiphocaensis’ sp. nov., a new bacterial species isolated from currency notes collected during the Hajj pilgrimage in 2012 at Makkah, Saudi Arabia

    Directory of Open Access Journals (Sweden)

    E.I. Azhar

    2017-01-01

    Full Text Available We report here the main characteristics of ‘Pseudomonas saudiphocaensis’ strain 20_BNT (CSUR P1224, a new species of the Pseudomonas genus that was isolated from currency notes collected during the Hajj pilgrimage in 2012 at Makkah, Saudi Arabia.

  1. ‘Lysinibacillus saudimassiliensis’ sp. nov., a new bacterial species isolated from air samples in the urban environment of Makkah, Saudi Arabia

    Directory of Open Access Journals (Sweden)

    A. Papadioti

    2017-03-01

    Full Text Available We report here the main characteristics of ‘Lysinibacillus saudimassiliensis’ strain 13S34_airτ (CSUR=P1222, a new species of the Lysinibacillus genus that was isolated from air samples in the city environment of Makkah, Saudi Arabia, during the pilgrim period of Hajj 2012.

  2. Biodiversity of aerobic endospore-forming bacterial species occurring in Yanyanku and Ikpiru, fermented seeds of Hibiscus sabdariffa used to produce food condiments in Benin.

    Science.gov (United States)

    Agbobatinkpo, Pélagie B; Thorsen, Line; Nielsen, Dennis S; Azokpota, Paulin; Akissoe, Noèl; Hounhouigan, Joseph D; Jakobsen, Mogens

    2013-05-15

    Yanyanku and Ikpiru made by the fermentation of Malcavene bean (Hibiscus sabdariffa) are used as functional additives for Parkia biglobosa seed fermentations in Benin. A total of 355 aerobic endospore-forming bacteria (AEFB) isolated from Yanyanku and Ikpiru produced in northern and southern Benin were identified using phenotypic and genotypic methods, including GTG5-PCR, M13-PCR, 16S rRNA, gyrA and gyrB gene sequencing. Generally, the same 5-6 species of the genus Bacillus predominated: Bacillus subtilis (17-41% of isolates), Bacillus cereus (8-39%), Bacillus amyloliquefaciens (9-22%), Bacillus licheniformis (3-26%), Bacillus safensis (8-19%) and Bacillus altitudinis (0-19%). Bacillus aryabhattai, Bacillus flexus, and Bacillus circulans (0-2%), and species of the genera Lysinibacillus (0-14%), Paenibacillus (0-13%), Brevibacillus (0-4%), and Aneurinibacillus (0-3%) occurred sporadically. The diarrheal toxin encoding genes cytK-1, cytK-2, hblA, hblC, and hblD were present in 0%, 91% 15%, 34% and 35% of B. cereus isolates, respectively. 9% of them harbored the emetic toxin genetic determinant, cesB. This study is the first to identify the AEFB of Yanyanku and Ikpiru to species level and perform a safety evaluation based on toxin gene detections. We further suggest, that the gyrA gene can be used for differentiating the closely related species Bacillus pumilus and B. safensis.

  3. Identification of symbiotic nitrogen-fixing bacteria from three African leguminous trees in Gorongosa National Park.

    Science.gov (United States)

    Teixeira, Helena; Rodríguez-Echeverría, Susana

    2016-07-01

    The symbiosis between leguminous plants and symbiotic nitrogen-fixing bacteria is a key component of terrestrial ecosystems. Woody legumes are well represented in tropical African forests but despite their ecological and socio-economic importance, they have been little studied for this symbiosis. In this study, we examined the identity and diversity of symbiotic-nitrogen fixing bacteria associated with Acacia xanthophloea, Faidherbia albida and Albizia versicolor in the Gorongosa National Park (GNP) in Mozambique. To the best of our knowledge, this is the first report on the identity of symbiotic-nitrogen fixing bacteria in this region. 166 isolates were obtained and subjected to molecular identification. BOX-A1R PCR was used to discriminate different bacterial isolates and PCR-sequencing of 16S rDNA, and two housekeeping genes, glnII and recA, was used to identify the obtained bacteria. The gene nifH was also analyzed to assess the symbiotic capacity of the obtained bacteria. All isolates from F. albida and Al. versicolor belonged to the Bradyrhizobium genus whereas isolates from Ac. xanthophloea clustered with Mesorhizobium, Rhizobium or Ensifer strains. Soil chemical analysis revealed significant differences between the soils occupied by the three studied species. Thus, we found a clear delimitation in the rhizobial communities and soils associated with Ac. xanthophloea, F. albida and Al. versicolor, and higher rhizobial diversity for Ac. xanthophloea than previously reported.

  4. Low diversity bacterial community and the trapping activity of metabolites from cultivable bacteria species in the female reproductive system of the Oriental fruit fly, Bactrocera dorsalis Hendel (Diptera: Tephritidae).

    Science.gov (United States)

    Shi, Zhanghong; Wang, Lili; Zhang, Hongyu

    2012-01-01

    Our goal was to identify the bacteria inhabiting the reproductive system of the female oriental fruit fly, Bactrocera dorsalis (Hendel), and evaluate the chemotaxis of B. dorsalis to the metabolites produced by the bacteria. Based on 16S rRNA-based polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), 18 operational taxonomic units (OTUs) were assigned to the five bacterial classes Betaproteobacteria, Alphaproteobacteria, Gammaproteobacteria, Bacilli and Actinobacteria. Nine OTUs were assigned to Gammaproteobacteria, which was the most highly represented class. Enterobacteriaceae constituted the dominant family, and within this family, three genera and five species were identified, including Enterobacter sakazakii, Klebsiella oxytoca, Klebsiella pneumoniae, Raoultella terrigena and Enterobacter amnigenus. In this set, the first two species were the dominant components, and the latter three species were the minor ones. Finally, we found that the metabolites produced by R. terrigena, K. oxytoca and K. pneumoniae were attractive to the B. dorsalis adults, and in field studies, B. dorsalis adults were most attracted to K. oxytoca. Collectively, our results suggest that the female reproductive system plays an important role in the transfer of enterobacteria from the gut to fruit. Our data may prompt the development of a female-targeted population control strategy for this fly.

  5. Low Diversity Bacterial Community and the Trapping Activity of Metabolites from Cultivable Bacteria Species in the Female Reproductive System of the Oriental Fruit Fly, Bactrocera dorsalis Hendel (Diptera: Tephritidae)

    Science.gov (United States)

    Shi, Zhanghong; Wang, Lili; Zhang, Hongyu

    2012-01-01

    Our goal was to identify the bacteria inhabiting the reproductive system of the female oriental fruit fly, Bactrocera dorsalis (Hendel), and evaluate the chemotaxis of B. dorsalis to the metabolites produced by the bacteria. Based on 16S rRNA-based polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), 18 operational taxonomic units (OTUs) were assigned to the five bacterial classes Betaproteobacteria, Alphaproteobacteria, Gammaproteobacteria, Bacilli and Actinobacteria. Nine OTUs were assigned to Gammaproteobacteria, which was the most highly represented class. Enterobacteriaceae constituted the dominant family, and within this family, three genera and five species were identified, including Enterobacter sakazakii, Klebsiella oxytoca, Klebsiella pneumoniae, Raoultella terrigena and Enterobacter amnigenus. In this set, the first two species were the dominant components, and the latter three species were the minor ones. Finally, we found that the metabolites produced by R. terrigena, K. oxytoca and K. pneumoniae were attractive to the B. dorsalis adults, and in field studies, B. dorsalis adults were most attracted to K. oxytoca. Collectively, our results suggest that the female reproductive system plays an important role in the transfer of enterobacteria from the gut to fruit. Our data may prompt the development of a female-targeted population control strategy for this fly. PMID:22754363

  6. Fixed-Term Homotopy

    Directory of Open Access Journals (Sweden)

    Hector Vazquez-Leal

    2013-01-01

    Full Text Available A new tool for the solution of nonlinear differential equations is presented. The Fixed-Term Homotopy (FTH delivers a high precision representation of the nonlinear differential equation using only a few linear algebraic terms. In addition to this tool, a procedure based on Laplace-Padé to deal with the truncate power series resulting from the FTH method is also proposed. In order to assess the benefits of this proposal, two nonlinear problems are solved and compared against other semianalytic methods. The obtained results show that FTH is a power tool capable of generating highly accurate solutions compared with other methods of literature.

  7. Diagnosis of bacterial vaginosis

    Directory of Open Access Journals (Sweden)

    Đukić Slobodanka

    2013-01-01

    Full Text Available Bacterial vaginosis is a common, complex clinical syndrome characterized by alterations in the normal vaginal flora. When symptomatic, it is associated with a malodorous vaginal discharge and on occasion vaginal burning or itching. Under normal conditions, lactobacilli constitute 95% of the bacteria in the vagina. Bacterial vaginosis is associated with severe reduction or absence of the normal H2O2­producing lactobacilli and overgrowth of anaerobic bacteria and Gardnerella vaginalis, Atopobium vaginae, Mycoplasma hominis and Mobiluncus species. Most types of infectious disease are diagnosed by culture, by isolating an antigen or RNA/DNA from the microbe, or by serodiagnosis to determine the presence of antibodies to the microbe. Therefore, demonstration of the presence of an infectious agent is often a necessary criterion for the diagnosis of the disease. This is not the case for bacterial vaginosis, since the ultimate cause of the disease is not yet known. There are a variety of methods for the diagnosis of bacterial vaginosis but no method can at present be regarded as the best. Diagnosing bacterial vaginosis has long been based on the clinical criteria of Amsel, whereby three of four defined criteria must be satisfied. Nugent’s scoring system has been further developed and includes validation of the categories of observable bacteria structures. Up­to­date molecular tests are introduced, and better understanding of vaginal microbiome, a clear definition for bacterial vaginosis, and short­term and long­term fluctuations in vaginal microflora will help to better define molecular tests within the broader clinical context.

  8. Bacterial Ecology

    DEFF Research Database (Denmark)

    Fenchel, Tom

    2011-01-01

    Bacterial ecology is concerned with the interactions between bacteria and their biological and nonbiological environments and with the role of bacteria in biogeochemical element cycling. Many fundamental properties of bacteria are consequences of their small size. Thus, they can efficiently exploit...

  9. Fixed and Sunk Costs Revisited.

    Science.gov (United States)

    Wang, X. Henry; Yang, Bill Z.

    2001-01-01

    Attempts to clarify the concepts of, and the link between, fixed costs and sunk costs. Argues that the root of confusion is the inconsistency in defining the term fixed costs. Consistently defines fixed and sunk costs, and describes how instructors must teach under these definitions. (RLH)

  10. Bacterial Adhesion & Blocking Bacterial Adhesion

    DEFF Research Database (Denmark)

    Vejborg, Rebecca Munk

    2008-01-01

    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......, 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...

  11. Fixed sagittal plane imbalance.

    Science.gov (United States)

    Savage, Jason W; Patel, Alpesh A

    2014-12-01

    Study Design Literature review. Objective To discuss the evaluation and management of fixed sagittal plane imbalance. Methods A comprehensive literature review was performed on the preoperative evaluation of patients with sagittal plane malalignment, as well as the surgical strategies to address sagittal plane deformity. Results Sagittal plane imbalance is often caused by de novo scoliosis or iatrogenic flat back deformity. Understanding the etiology and magnitude of sagittal malalignment is crucial in realignment planning. Objective parameters have been developed to guide surgeons in determining how much correction is needed to achieve favorable outcomes. Currently, the goals of surgery are to restore a sagittal vertical axis Sagittal plane malalignment is an increasingly recognized cause of pain and disability. Treatment of sagittal plane imbalance varies according to the etiology, location, and severity of the deformity. Fixed sagittal malalignment often requires complex reconstructive procedures that include osteotomy correction. Reestablishing harmonious spinopelvic alignment is associated with significant improvement in health-related quality-of-life outcome measures and patient satisfaction.

  12. Comparison of the bacterial species diversity of spontaneous cocoa bean fermentations carried out at selected farms in Ivory Coast and Brazil.

    Science.gov (United States)

    Papalexandratou, Zoi; Camu, Nicholas; Falony, Gwen; De Vuyst, Luc

    2011-08-01

    To compare the spontaneous cocoa bean fermentation process carried out in different cocoa-producing regions, heap and box (one Ivorian farm) and box (two Brazilian farms) fermentations were carried out. All fermentations were studied through a multiphasic approach. In general, the temperature inside the fermenting mass increased throughout all fermentations and reached end-values of 42-48 °C. The main end-products of pulp carbohydrate catabolism were ethanol, lactic acid, acetic acid, and/or mannitol. In the case of the fermentations on the selected Ivorian farm, the species diversity of lactic acid bacteria (LAB) and acetic acid bacteria (AAB) was restricted. Lactobacillus fermentum and Leuconostoc pseudomesenteroides were the predominant LAB species, due to their ethanol and acid tolerance and citrate consumption. The levels of mannitol, ascribed to growth of L. fermentum, were fermentation-dependent. Also, enterobacterial species, such as Erwinia soli and Pantoea sp., were among the predominating microbiota during the early stages of both heap and box fermentations in Ivory Coast, which could be responsible for gluconic acid production. Consumption of gluconic acid at the initial phases of the Ivorian fermentations could be due to yeast growth. A wider microbial species diversity throughout the fermentation process was seen in the case of the box fermentations on the selected Brazilian farms, which differed, amongst other factors, regarding pod/bean selection on these farms as compared to fermentations on the selected Ivorian farm. This microbiota included Lactobacillus plantarum, Lactobacillus durianis, L. fermentum, Lactobacillus mali, Lactobacillus nagelii, L. pseudomesenteroides, and Pediococcus acidilactici, as well as Bacillus subtilis that was present at late fermentation, when the temperature inside the fermenting mass reached values higher than 50 °C. Moreover, AAB seemed to dominate the Brazilian box fermentations studied, explaining higher acetic

  13. Influence of initial glycerol concentration upon bacterial cells ...

    African Journals Online (AJOL)

    user

    submerged aerated fixed bed reactor using Biocell®. (PE05) packing ... nitrogen, phosphorus and some oligo-elements with different initial chemical oxygen demand (COD) of: ... (Reaction 2) is related to multiplication of bacterial cells.

  14. 42种攀援植物固碳释氧和降温增湿效应研究初探%Preliminary Study on Carbon-fixing, Oxygen-releasing, Cooling and Humidifying Effects of 42 Species of Climbing Plants

    Institute of Scientific and Technical Information of China (English)

    徐冬云; 周媛; 童俊; 董艳芳; 姚中华

    2015-01-01

    In order to screen out good climbing plants , the author tested the carbon-fixing, oxygen-releasing, cooling and hu-midifying effects of 42 species of climbing plants , quantitatively evaluated their ecological benefits , and carried out grade classifica-tion of them.%为了筛选出优良攀援植物,通过对42种攀援植物的固碳释氧和降温增湿能力进行了测定,定量评价了42种攀援植物的生态效益,并进行了等级分类。

  15. Bioremediation of polycyclic aromatic hydrocarbon (PAH) compounds: (acenaphthene and fluorene) in water using indigenous bacterial species isolated from the Diep and Plankenburg rivers, Western Cape, South Africa.

    Science.gov (United States)

    Alegbeleye, Oluwadara Oluwaseun; Opeolu, Beatrice Olutoyin; Jackson, Vanessa

    2016-11-24

    This study was conducted to investigate the occurrence of PAH degrading microorganisms in two river systems in the Western Cape, South Africa and their ability to degrade two PAH compounds: acenaphthene and fluorene. A total of 19 bacterial isolates were obtained from the Diep and Plankenburg rivers among which four were identified as acenaphthene and fluorene degrading isolates. In simulated batch scale experiments, the optimum temperature for efficient degradation of both compounds was determined in a shaking incubator after 14 days, testing at 25°C, 30°C, 35°C, 37°C, 38°C, 40°C and 45°C followed by experiments in a Stirred Tank Bioreactor using optimum temperature profiles from the batch experiment results. All experiments were run without the addition of supplements, bulking agents, biosurfactants or any other form of biostimulants. Results showed that Raoultella ornithinolytica, Serratia marcescens, Bacillus megaterium and Aeromonas hydrophila efficiently degraded both compounds at 37°C, 37°C, 30°C and 35°C respectively. The degradation of fluorene was more efficient and rapid compared to that of acenaphthene and degradation at Stirred Tank Bioreactor scale was more efficient for all treatments. Raoultella ornithinolytica, Serratia marcescens, Bacillus megaterium and Aeromonas hydrophila degraded a mean total of 98.60%, 95.70%, 90.20% and 99.90% acenaphthene, respectively and 99.90%, 97.90%, 98.40% and 99.50% fluorene, respectively. The PAH degrading microorganisms isolated during this study significantly reduced the concentrations of acenaphthene and fluorene and may be used on a larger, commercial scale to bioremediate PAH contaminated river systems.

  16. An electron microscope survey of the surface structures and hydrophobicity of oral and non-oral species of the bacterial genus Bacteroides.

    Science.gov (United States)

    Handley, P S; Tipler, L S

    1986-01-01

    Seventeen strains of Bacteroides representing 10 species were examined by negative staining; the majority were from the mouth but a few non-oral strains were included. Seven species had peritrichously-arranged, non-flagellar appendages which could be divided by morphology and ultrastructure into two subgroups, fibrils and fimbriae. Bacteroides asaccharolyticus strains B536 and B537 and Bacteroides gingivalis strains W50, W83, WPH15 and WPH35 had fimbriae with mean width of 4.4 nm and 0.5 to 6.0 microns long depending on the strain. The fimbrial length within each strain also varied. Fibrils were present on two fresh oral isolates of Bacteroides melaninogenicus, Bacteroides intermedius strains T588 and W09, Bacteroides corporis ATCC 33547, Bacteroides oralis ATCC 33269 and Bacteroides buccae ATCC 33574. Fibrils consistently clumped into bundles of variable thickness and formed a fringe around the cell periphery, ranging from 0.27 to 1.2 microns long depending on the strain. Fibril lengths of each strain were uniform. Fibrils had no measurable width and the clumps tapered towards the free ends. Bacteroides loeschii VPI 9085, Bacteroides pentosaceus strains NP333 and J1 and Bacteroides capillosus 29799 had no detectable surface appendages. Fimbriate strains had a layer outside the outer membrane, with a mean thickness of between 17.8 and 28.6 nm. Both fibrillar and fimbriate strains produced many small membranous vesicles budding from the outer membrane. There were two morphological forms of vesicles, ones with either fimbriae or fibrils (species-dependent) and ones with no attached appendages. Of eleven strains tested for cell-surface hydrophobicity by partitioning between hexadecane and buffer, all but one was non-hydrophobic.

  17. Diversity, relative abundance and metabolic potential of bacterial endosymbionts in three Bathymodiolus mussel species from cold seeps in the Gulf of Mexico.

    Science.gov (United States)

    Duperron, Sébastien; Sibuet, Myriam; MacGregor, Barbara J; Kuypers, Marcel M M; Fisher, Chuck R; Dubilier, Nicole

    2007-06-01

    Cold seeps in the Gulf of Mexico are often dominated by mussels of the genus Bathymodiolus that harbour symbiotic bacteria in their gills. In this study, we analysed symbiont diversity, abundance and metabolic potential in three mussel species from the northern Gulf of Mexico: Bathymodiolus heckerae from the West Florida Escarpment, Bathymodiolus brooksi from Atwater Valley and Alaminos Canyon, and 'Bathymodiolus' childressi, which co-occurs with B. brooksi in Alaminos Canyon. Comparative 16S rRNA sequence analysis confirmed a single methanotroph-related symbiont in 'B.' childressi and a dual symbiosis with a methanotroph- and thiotroph-related symbiont in B. brooksi. A previously unknown diversity of four co-occurring symbionts was discovered in B. heckerae: a methanotroph, two phylogenetically distinct thiotrophs and a methylotroph-related phylotype not previously described from any marine invertebrate symbiosis. A gene characteristic of methane-oxidzing bacteria, pmoA, was identified in all three mussel species confirming the methanotrophic potential of their symbionts. Stable isotope analyses of lipids and whole tissue also confirmed the importance of methanotrophy in the carbon nutrition of all of the mussels. Analyses of absolute and relative symbiont abundance in B. heckerae and B. brooksi using fluorescence in situ hybridization (FISH) and rRNA slot blot hybridization indicated a clear dominance of methanotrophic over thiotrophic symbionts in their gill tissues. A site-dependent variability in total symbiont abundance was observed in B. brooksi, with specimens from Alaminos Canyon harbouring much lower densities than those from Atwater Valley. This shows that symbiont abundance is not species-specific but can vary considerably between populations.

  18. Nitrogen fixing bacteria in the family Acetobacteraceae and their role in agriculture.

    Science.gov (United States)

    Reis, Veronica Massena; Teixeira, Kátia Regina dos Santos

    2015-08-01

    For centuries, the Acetobacteraceae is known as a family that harbors many species of organisms of biotechnological importance for industry. Nonetheless, since 1988 representatives of this family have also been described as nitrogen fixing bacteria able to plant growth promotion by a variety of mechanisms. Nitrogen fixation is a biological process that guarantees that the atmospheric N2 is incorporated into organic matter by several bacterial groups. Most representatives of this group, also known as diazotrophic, are generally associated with soil rhizosphere of many plants and also establishing a more specific association living inside roots, leaves, and others plants tissues as endophyte. Their roles as plant growth-promoting microorganisms are generally related to increase in plant biomass, phosphate and other mineral solubilization, and plant pathogen control. Here, we report many of these plant growth-promoting processes related to nitrogen fixing species already described in Acetobacteraceae family, especially Gluconacetobacter diazotrophicus and their importance to agriculture. In addition, a brief review of the state of art of the phylogenetics, main physiological and biochemical characteristics, molecular and functional genomic data of this group of Acetobacteraceae is presented.

  19. Recombination and the nature of bacterial speciation

    OpenAIRE

    2007-01-01

    Genetic surveys are uncovering the diversity of bacteria, and are causing the species concepts used to categorize these to be questioned. One difficulty in defining bacterial species arises from the high rates of recombination that results in the transfer of DNA between relatively distantly related bacteria. Barriers to this process, which could be used to define species naturally, are not apparent. Here, we have reviewed conceptual models of bacterial speciation and simulate speciation in si...

  20. Fixed Access Network Sharing

    Science.gov (United States)

    Cornaglia, Bruno; Young, Gavin; Marchetta, Antonio

    2015-12-01

    Fixed broadband network deployments are moving inexorably to the use of Next Generation Access (NGA) technologies and architectures. These NGA deployments involve building fiber infrastructure increasingly closer to the customer in order to increase the proportion of fiber on the customer's access connection (Fibre-To-The-Home/Building/Door/Cabinet… i.e. FTTx). This increases the speed of services that can be sold and will be increasingly required to meet the demands of new generations of video services as we evolve from HDTV to "Ultra-HD TV" with 4k and 8k lines of video resolution. However, building fiber access networks is a costly endeavor. It requires significant capital in order to cover any significant geographic coverage. Hence many companies are forming partnerships and joint-ventures in order to share the NGA network construction costs. One form of such a partnership involves two companies agreeing to each build to cover a certain geographic area and then "cross-selling" NGA products to each other in order to access customers within their partner's footprint (NGA coverage area). This is tantamount to a bi-lateral wholesale partnership. The concept of Fixed Access Network Sharing (FANS) is to address the possibility of sharing infrastructure with a high degree of flexibility for all network operators involved. By providing greater configuration control over the NGA network infrastructure, the service provider has a greater ability to define the network and hence to define their product capabilities at the active layer. This gives the service provider partners greater product development autonomy plus the ability to differentiate from each other at the active network layer.

  1. A method for the determination of bacterial spore DNA content based on isotopic labelling, spore germination and diphenylamine assay; ploidy of spores of several Bacillus species.

    Science.gov (United States)

    Hauser, P M; Karamata, D

    1992-01-01

    A reliable method for measuring the spore DNA content, based on radioactive DNA labelling, spore germination in absence of DNA replication and diphenylamine assay, was developed. The accuracy of the method, within 10-15%, is adequate for determining the number of chromosomes per spore, provided that the genome size is known. B subtilis spores were shown to be invariably monogenomic, while those of larger bacilli Bacillus megaterium, Bacillus cereus and Bacillus thuringiensis, often, if not invariably, contain two genomes. Attempts to modify the spore DNA content of B subtilis by altering the richness of the sporulation medium, the sporulation conditions (liquid or solid medium), or by mutation, were apparently unsuccessful. An increase of spore size with medium richness, not accompanied by an increase in DNA content, was observed. The implication of the apparently species-specific spore ploidy and the influence of the sporulation conditions on spore size and shape are discussed.

  2. [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.

  3. Comparisons of host mitochondrial, nuclear and endosymbiont bacterial genes reveal cryptic fig wasp species and the effects of Wolbachia on host mtDNA evolution and diversity

    Directory of Open Access Journals (Sweden)

    Feng Gui

    2011-04-01

    Full Text Available Abstract Background Figs and fig-pollinating wasp species usually display a highly specific one-to-one association. However, more and more studies have revealed that the "one-to-one" rule has been broken. Co-pollinators have been reported, but we do not yet know how they evolve. They may evolve from insect speciation induced or facilitated by Wolbachia which can manipulate host reproduction and induce reproductive isolation. In addition, Wolbachia can affect host mitochondrial DNA evolution, because of the linkage between Wolbachia and associated mitochondrial haplotypes, and thus confound host phylogeny based on mtDNA. Previous research has shown that fig wasps have the highest incidence of Wolbachia infection in all insect taxa, and Wolbachia may have great influence on fig wasp biology. Therefore, we look forward to understanding the influence of Wolbachia on mitochondrial DNA evolution and speciation in fig wasps. Results We surveyed 76 pollinator wasp specimens from nine Ficus microcarpa trees each growing at a different location in Hainan and Fujian Provinces, China. We found that all wasps were morphologically identified as Eupristina verticillata, but diverged into three clades with 4.22-5.28% mtDNA divergence and 2.29-20.72% nuclear gene divergence. We also found very strong concordance between E. verticillata clades and Wolbachia infection status, and the predicted effects of Wolbachia on both mtDNA diversity and evolution by decreasing mitochondrial haplotypes. Conclusions Our study reveals that the pollinating wasp E. verticillata on F. microcarpa has diverged into three cryptic species, and Wolbachia may have a role in this divergence. The results also indicate that Wolbachia strains infecting E. verticillata have likely resulted in selective sweeps on host mitochondrial DNA.

  4. Studies of iron-uptake mechanisms in two bacterial species of the shewanella genus adapted to middle-range (Shewanella putrefaciens) or antarctic (Shewanella gelidimarina) temperatures.

    Science.gov (United States)

    Pakchung, Amalie A H; Soe, Cho Z; Codd, Rachel

    2008-10-01

    Iron(III)-uptake mechanisms in bacteria indigenous to the Antarctic, which is the most Fe-deficient continent on Earth, have not been extensively studied. The cold-adapted, Antarctic bacterium, Shewanella gelidimarina, does not produce detectable levels of the siderophore, putrebactin, in the supernatant of Fe(III)-deprived cultures. This is distinct from the putrebactin-producing bacterium from the same genus, Shewanella putrefaciens, which is adapted to middle-range temperatures. The production of putrebactin by S. putrefaciens is optimal, when the pH value of the medium is 7.0. According to the strong positive response from whole cells in the Chrome Azurol S (CAS) agar diffusion assay, Shewanella gelidimarina appears to produce cell-associated siderophores. In the RP-HPLC trace of an Fe(III)-loaded extract from the cell-associated components of S. gelidimarina cultured in media with [Fe(III)] ca. 0 microM, a peak appears at [MeCN] ca. 77%, which decreases in intensity in a parallel experiment in which [Fe(III)] ca. 5 microM, and is barely detectable in Fe(III)-replete media ([Fe(III)] ca. 20 microM). The Fe(III)-dependence of this peak suggests that the attendant species, which is significantly more hydrophobic than putrebactin (RP-HPLC elution: [MeCN] ca. 14%), is associated with Fe(III)-management in S. gelidimarina. This study highlights the diversity in Fe(III)-uptake mechanisms in Shewanella species adapted to different environmental and thermal niches.

  5. Epiphytic bacterial communities on two common submerged macrophytes in Taihu Lake: diversity and host-specificity

    Institute of Scientific and Technical Information of China (English)

    HE Dan; REN Lijuan; WU Qinglong

    2012-01-01

    Leaves of terrestrial and aquatic plants are home to a wide diversity of bacterial species.However,the diversity and variability of epiphytic bacteria on their submerged plant hosts remains poorly understood.We investigated the diversity and composition of epiphytic bacteria from two common submerged macrophytes:Vallisneria natans and Hydrilla verticillata in Taihu Lake,Jiangsu,China,using methods of terminal restriction fragment length polymorphisms (T-RFLP) and clone library analyses targeted at bacterial 16S rRNA genes.The results show that:(1) the libraries of the two waterweeds contain wide phylogenetic distribution of bacteria,and that the sequences of the two libraries can be separated into 93 OTUs (at 97% similar value); (2) Betaproteobacteria,including Burkholderiales,was the most abundant bacterial group on both plants.Cyanobacteria and Gammaproteobacteria were the second largest groups on V.natans and H.verticillata,respectively.Both clone libraries included some sequences related to those of methanotrophs and nitrogen-fixing bacteria; (3) Cluster analysis of the T-RFLP profiles showed two distinct clusters corresponding to the two plant populations.Both ANOSIM of the T-RFLPdata and Libshuff analysis of the two clone libraries indicated a significant difference in epiphytic bacterial communities between the two plants.Therefore,the epiphytic bacterial communities on submerged macrophytes appear to be diverse and host-specific,which may aid in understanding the ecological functions of submerged macrophytes in general.

  6. Low Diversity Bacterial Community and the Trapping Activity of Metabolites from Cultivable Bacteria Species in the Female Reproductive System of the Oriental Fruit Fly, Bactrocera dorsalis Hendel (Diptera: Tephritidae

    Directory of Open Access Journals (Sweden)

    Hongyu Zhang

    2012-05-01

    Full Text Available Our goal was to identify the bacteria inhabiting the reproductive system of the female oriental fruit fly, Bactrocera dorsalis (Hendel, and evaluate the chemotaxis of B. dorsalis to the metabolites produced by the bacteria. Based on 16S rRNA-based polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE, 18 operational taxonomic units (OTUs were assigned to the five bacterial classes Betaproteobacteria, Alphaproteobacteria, Gammaproteobacteria, Bacilli and Actinobacteria. Nine OTUs were assigned to Gammaproteobacteria, which was the most highly represented class. Enterobacteriaceae constituted the dominant family, and within this family, three genera and five species were identified, including Enterobacter sakazakii, Klebsiella oxytoca, Klebsiella pneumoniae, Raoultella terrigena and Enterobacter amnigenus. In this set, the first two species were the dominant components, and the latter three species were the minor ones. Finally, we found that the metabolites produced by R. terrigena, K. oxytoca and K. pneumoniae were attractive to the B. dorsalis adults, and in field studies, B. dorsalis adults were most attracted to K. oxytoca. Collectively, our results suggest that the female reproductive system plays an important role in the transfer of enterobacteria from the gut to fruit. Our data may prompt the development of a female-targeted population control strategy for this fly.

  7. Bacterial fucose-rich polysaccharide stabilizes MAPK-mediated Nrf2/Keap1 signaling by directly scavenging reactive oxygen species during hydrogen peroxide-induced apoptosis of human lung fibroblast cells.

    Science.gov (United States)

    Roy Chowdhury, Sougata; Sengupta, Suman; Biswas, Subir; Sinha, Tridib Kumar; Sen, Ramkrishna; Basak, Ratan Kumar; Adhikari, Basudam; Bhattacharyya, Arindam

    2014-01-01

    Continuous free radical assault upsets cellular homeostasis and dysregulates associated signaling pathways to promote stress-induced cell death. In spite of the continuous development and implementation of effective therapeutic strategies, limitations in treatments for stress-induced toxicities remain. The purpose of the present study was to determine the potential therapeutic efficacy of bacterial fucose polysaccharides against hydrogen peroxide (H2O2)-induced stress in human lung fibroblast (WI38) cells and to understand the associated molecular mechanisms. In two different fermentation processes, Bacillus megaterium RB-05 biosynthesized two non-identical fucose polysaccharides; of these, the polysaccharide having a high-fucose content (∼ 42%) conferred the maximum free radical scavenging efficiency in vitro. Structural characterizations of the purified polysaccharides were performed using HPLC, GC-MS, and (1)H/(13)C/2D-COSY NMR. H2O2 (300 µM) insult to WI38 cells showed anti-proliferative effects by inducing intracellular reactive oxygen species (ROS) and by disrupting mitochondrial membrane permeability, followed by apoptosis. The polysaccharide (250 µg/mL) attenuated the cell death process by directly scavenging intracellular ROS rather than activating endogenous antioxidant enzymes. This process encompasses inhibition of caspase-9/3/7, a decrease in the ratio of Bax/Bcl2, relocalization of translocated Bax and cytochrome c, upregulation of anti-apoptotic members of the Bcl2 family and a decrease in the phosphorylation of MAPKs (mitogen activated protein kinases). Furthermore, cellular homeostasis was re-established via stabilization of MAPK-mediated Nrf2/Keap1 signaling and transcription of downstream cytoprotective genes. This molecular study uniquely introduces a fucose-rich bacterial polysaccharide as a potential inhibitor of H2O2-induced stress and toxicities.

  8. Bacterial fucose-rich polysaccharide stabilizes MAPK-mediated Nrf2/Keap1 signaling by directly scavenging reactive oxygen species during hydrogen peroxide-induced apoptosis of human lung fibroblast cells.

    Directory of Open Access Journals (Sweden)

    Sougata Roy Chowdhury

    Full Text Available Continuous free radical assault upsets cellular homeostasis and dysregulates associated signaling pathways to promote stress-induced cell death. In spite of the continuous development and implementation of effective therapeutic strategies, limitations in treatments for stress-induced toxicities remain. The purpose of the present study was to determine the potential therapeutic efficacy of bacterial fucose polysaccharides against hydrogen peroxide (H2O2-induced stress in human lung fibroblast (WI38 cells and to understand the associated molecular mechanisms. In two different fermentation processes, Bacillus megaterium RB-05 biosynthesized two non-identical fucose polysaccharides; of these, the polysaccharide having a high-fucose content (∼ 42% conferred the maximum free radical scavenging efficiency in vitro. Structural characterizations of the purified polysaccharides were performed using HPLC, GC-MS, and (1H/(13C/2D-COSY NMR. H2O2 (300 µM insult to WI38 cells showed anti-proliferative effects by inducing intracellular reactive oxygen species (ROS and by disrupting mitochondrial membrane permeability, followed by apoptosis. The polysaccharide (250 µg/mL attenuated the cell death process by directly scavenging intracellular ROS rather than activating endogenous antioxidant enzymes. This process encompasses inhibition of caspase-9/3/7, a decrease in the ratio of Bax/Bcl2, relocalization of translocated Bax and cytochrome c, upregulation of anti-apoptotic members of the Bcl2 family and a decrease in the phosphorylation of MAPKs (mitogen activated protein kinases. Furthermore, cellular homeostasis was re-established via stabilization of MAPK-mediated Nrf2/Keap1 signaling and transcription of downstream cytoprotective genes. This molecular study uniquely introduces a fucose-rich bacterial polysaccharide as a potential inhibitor of H2O2-induced stress and toxicities.

  9. Comparative study on bacterial species in conjunctival sac between Qiang minority and Han nationality%羌族与汉族结膜囊细菌状况对照研究

    Institute of Scientific and Technical Information of China (English)

    董万江; 张悦; 刘治容; 陈辉; 曹奎; 喻华; 王光进; 李玉婵

    2011-01-01

    背景 羌族是中国的少数民族,有特定的生活习惯和居住环境,羌族人群的疾病谱以及结膜囊细菌状况是否与汉族有差别是一个值得关注的问题.目的 了解羌族与汉族中老年人结膜囊细菌状况的异同.方法研究遵循统一的调查流程及方法.由经过培训的眼科医师整群抽取四川北川县2个羌族聚居点的中老年人106人212眼及居住地地域近似的2个汉族聚居地160人320眼进行眼科检查、问卷调查并睑结膜囊分泌物接种于血琼脂培养基上,培养48 h后进行细菌分离鉴定,并对2组受检人群的结果进行比较.结果 羌族和汉族受检者的人口基线特征比较差异无统计学意义(χ2=0.32,P=0.57).羌族中老年人结膜囊细菌培养阳性率为59.43%,汉族为66.30%,差异无统计学意义(χ2=2.27,P=0.13).羌族结膜囊多种细菌共存者占26.20%,汉族为11.80%;羌族人群中多种细菌共存的构成比明显高于汉族(χ2=106.40,P=0.00).羌族结膜囊中棒状杆菌培养的阳性率为20.70%,汉族的为45.00%,差异有统计学意义(χ2=31.75,P=0.00);羌族结膜囊中表皮葡萄球菌培养的阳性率为21.70%,汉族人群为16.6%,差异无统计学意义(χ2=1.89,P=0.17).结论 羌族中老年人结膜囊细菌培养阳性率与汉族中老年人基本相似,羌族和汉族中老年人结膜囊的细菌大多为单一菌株,但羌族人多种菌株共存的现象比汉族更为多见.羌族人与汉族人结膜囊细菌属有一定的区别.%Background Qiang minority is minority groups of China with the special habits and customs and living condition. So whether the spectrum of disease and bacteria spectrum in conjunctiva are similar with Han nationality is worth paying attention. Objective Present survey was to obtain the data about bacterial species in conjunctival sac in Qiang minority population with the age 40 years old and more and the compare with matched Han nationality population. Methods This survey

  10. Multiple Genome Comparison within a Bacterial Species Reveals a Unit of Evolution Spanning Two Adjacent Genes in a Tandem Paralog Cluster

    Science.gov (United States)

    Tsuru, Takeshi

    2008-01-01

    It has been assumed that an open reading frame (ORF) represents a unit of gene evolution as well as a unit of gene expression and function. In the present work, we report a case in which a unit comprising the 3′ region of an ORF linked to a downstream intergenic region that is in turn linked to the 5′ region of a downstream ORF has been conserved, and has served as the unit of gene evolution. The genes are tandem paralogous genes from the bacterium Staphylococcus aureus, for which more than ten entire genomes have been sequenced. We compared these multiple genome sequences at a locus for the lpl (lipoprotein-like) cluster (encoding lipoprotein homologs presumably related to their host interaction) in the genomic island termed νSaα. A highly conserved nucleotide sequence found within every lpl ORF is likely to provide a site for homologous recombination. Comparison of phylogenies of the 5′-variable region and the 3′-variable region within the same ORF revealed significant incongruence. In contrast, pairs of the 3′-variable region of an ORF and the 5′-variable region of the next downstream ORF gave more congruent phylogenies, with distinct groups of conserved pairs. The intergenic region seemed to have coevolved with the flanking variable regions. Multiple recombination events at the central conserved region appear to have caused various types of rearrangements among strains, shuffling the two variable regions in one ORF, but maintaining a conserved unit comprising the 3′-variable region, the intergenic region, and the 5′-variable region spanning adjacent ORFs. This result has strong impact on our understanding of gene evolution because most gene lineages underwent tandem duplication and then diversified. This work also illustrates the use of multiple genome sequences for high-resolution evolutionary analysis within the same species. PMID:18765438

  11. Bacterial Communities: Interactions to Scale

    Directory of Open Access Journals (Sweden)

    Reed M. Stubbendieck

    2016-08-01

    Full Text Available In the environment, bacteria live in complex multispecies communities. These communities span in scale from small, multicellular aggregates to billions or trillions of cells within the gastrointestinal tract of animals. The dynamics of bacterial communities are determined by pairwise interactions that occur between different species in the community. Though interactions occur between a few cells at a time, the outcomes of these interchanges have ramifications that ripple through many orders of magnitude, and ultimately affect the macroscopic world including the health of host organisms. In this review we cover how bacterial competition influences the structures of bacterial communities. We also emphasize methods and insights garnered from culture-dependent pairwise interaction studies, metagenomic analyses, and modeling experiments. Finally, we argue that the integration of multiple approaches will be instrumental to future understanding of the underlying dynamics of bacterial communities.

  12. Structural Diversity of Bacterial Communities Associated with Bloom-Forming Freshwater Cyanobacteria Differs According to the Cyanobacterial Genus.

    Directory of Open Access Journals (Sweden)

    Imen Louati

    Full Text Available The factors and processes driving cyanobacterial blooms in eutrophic freshwater ecosystems have been extensively studied in the past decade. A growing number of these studies concern the direct or indirect interactions between cyanobacteria and heterotrophic bacteria. The presence of bacteria that are directly attached or immediately adjacent to cyanobacterial cells suggests that intense nutrient exchanges occur between these microorganisms. In order to determine if there is a specific association between cyanobacteria and bacteria, we compared the bacterial community composition during two cyanobacteria blooms of Anabaena (filamentous and N2-fixing and Microcystis (colonial and non-N2 fixing that occurred successively within the same lake. Using high-throughput sequencing, we revealed a clear distinction between associated and free-living communities and between cyanobacterial genera. The interactions between cyanobacteria and bacteria appeared to be based on dissolved organic matter degradation and on N recycling, both for N2-fixing and non N2-fixing cyanobacteria. Thus, the genus and potentially the species of cyanobacteria and its metabolic capacities appeared to select for the bacterial community in the phycosphere.

  13. Bacterial cell division proteins as antibiotic targets

    NARCIS (Netherlands)

    den Blaauwen, T.; Andreu, J.M.; Monasterio, O.

    2014-01-01

    Proteins involved in bacterial cell division often do not have a counterpart in eukaryotic cells and they are essential for the survival of the bacteria. The genetic accessibility of many bacterial species in combination with the Green Fluorescence Protein revolution to study localization of

  14. Definition and evolution of a new symbiovar, sv. rigiduloides, among Ensifer meliloti efficiently nodulating Medicago species.

    Science.gov (United States)

    Gubry-Rangin, Cécile; Béna, Gilles; Cleyet-Marel, Jean-Claude; Brunel, Brigitte

    2013-10-01

    Understanding functional diversity is one of the main goals of microbial ecology, and definition of new bacterial ecotypes contributes significantly to this objective. Nitrogen-fixing bacteria provide a good system for investigation of ecotypes/biovars/symbiovars, as they present different specific associations with several host plants. This specific symbiosis is reflected both in the nodulation and fixation efficiency and in genetic characters of the bacteria, and several biovars have already been described in the bacterial species Ensifer meliloti. In the present study, the species affiliation of E. meliloti strains trapped from nodules sampled from Medicago rigiduloïdes roots was analyzed using housekeeping recA genes and DNA-DNA hybridization. The genetic diversity of these isolates was also investigated using several symbiotic markers: nodulation (nodA, nodB, nodC) and nitrogen fixation (nifH) genes, as well as the performance of phenotypic tests of nodulation capacity and nitrogen fixation efficiency. These analyses led to the proposal of a new bacterial symbiovar, E. meliloti sv. rigiduloides, that fixed nitrogen efficiently on M. rigiduloïdes, but not on Medicago truncatula. Using phylogenetic reconstructions, including the different described symbiovars, several hypotheses of lateral gene transfer and gene loss are proposed to explain the emergence of symbiovars within this species. The widespread geographical distribution of this symbiovar around the Mediterranean Basin, in contrast to restriction of M. rigiduloïdes to Eastern European countries, suggests that these isolates might also be associated with other plant species. The description of a new symbiovar within E. meliloti confirms the need for accurate bacterial ecological classification, especially for analysis of bacterial populations.

  15. Bacterial Adhesion & Blocking Bacterial Adhesion

    DEFF Research Database (Denmark)

    Vejborg, Rebecca Munk

    2008-01-01

    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...... in the formation of highly complex sessile communities, referred to as biofilms. Such microbial communities are often highly dynamic and heterogeneous in nature. Microbial biofilms are of great importance in a wide range of natural processes and industrial settings, from the commensal flora of the gastrointestinal...

  16. Recovery of symbiotic nitrogen fixing acacia rhizobia from Merzouga Desert sand dunes in South East Morocco--Identification of a probable new species of Ensifer adapted to stressed environments.

    Science.gov (United States)

    Sakrouhi, Ilham; Belfquih, Meryem; Sbabou, Laïla; Moulin, Patricia; Bena, Gilles; Filali-Maltouf, Abdelkarim; Le Quéré, Antoine

    2016-03-01

    Bacteria capable of nodulating Acacia tortilis and A. gummifera could be recovered from sand dunes collected in the Moroccan Merzouga desert. The trapping approach enabled the recovery of 17 desert rhizobia that all clustered within the Ensifer (Sinorhizobium) genus. Four isolates of the dominant genotype comprising 15 strains as well as 2 divergent strains were further characterized by MLSA. Phylogenetic analyzes indicated that the dominant genetic type was belonging to a new and yet undefined species within the Ensifer genus. Interestingly, housekeeping gene phylogenies showed that this possibly new species is also present in another desert but in India. Phylogenetic analyses of nifH and nodC sequences showed high sequence conservation among the Moroccan strains belonging to the dominant genotype but high divergence with sequences from Indian isolates suggesting acquisition of symbiotic genes through Horizontal Gene Transfer. These desert rhizobia were capable of growing in media containing high salt concentrations, under high pH and most of the strains showed growth at 45°C. Only recovered from desert type of Biome, yet, this new taxon appears particularly adapted to such harsh environment.

  17. Bacterial hydrodynamics

    CERN Document Server

    Lauga, Eric

    2015-01-01

    Bacteria predate plants and animals by billions of years. Today, they are the world's smallest cells yet they represent the bulk of the world's biomass, and the main reservoir of nutrients for higher organisms. Most bacteria can move on their own, and the majority of motile bacteria are able to swim in viscous fluids using slender helical appendages called flagella. Low-Reynolds-number hydrodynamics is at the heart of the ability of flagella to generate propulsion at the micron scale. In fact, fluid dynamic forces impact many aspects of bacteriology, ranging from the ability of cells to reorient and search their surroundings to their interactions within mechanically and chemically-complex environments. Using hydrodynamics as an organizing framework, we review the biomechanics of bacterial motility and look ahead to future challenges.

  18. Diversity of Bacterial Photosymbionts in Lubomirskiidae Sponges from Lake Baikal

    National Research Council Canada - National Science Library

    Nina V. Kulakova; Natalia N. Denikina; Sergei I. Belikov

    2014-01-01

    ... of bacterial phototrophs associated with four species of Lubomirskiidae in Lake Baikal. The phylogeny inferred from both genes showed three main clusters of Synechococcus associated with Baikalian sponges...

  19. Bacterial contamination of hospital physicians' stethoscopes.

    Science.gov (United States)

    Bernard, L; Kereveur, A; Durand, D; Gonot, J; Goldstein, F; Mainardi, J L; Acar, J; Carlet, J

    1999-09-01

    Because stethoscopes might be potential vectors of nosocomial infections, this study, conducted in a 450-bed general hospital, was devised to evaluate the bacterial contamination of stethoscopes; bacterial survival on stethoscope membranes; the kinetics of the bacterial load on stethoscope membranes during clinical use; and the efficacy of 70% alcohol or liquid soap for membrane disinfection. Among the 355 stethoscopes tested, 234 carried > or =2 different bacterial species; 31 carried potentially pathogenic bacteria. Although some bacteria deposited onto membranes could survive 6 to 18 hours, none survived after disinfection.

  20. Bacterial Nanocellulose as a Microbiological Derived Nanomaterial

    Directory of Open Access Journals (Sweden)

    Stanisławska A.

    2016-12-01

    Full Text Available Bacterial nanocellulose (BNC is a nanofibrilar polymer produced by strains such as Gluconacetobacter xylinus, one of the best bacterial species which given the highest efficiency in cellulose production. Bacterial cellulose is a biomaterial having unique properties such as: chemical purity, good mechanical strength, high flexibility, high absorbency, possibility of forming any shape and size and many others. Such a large number of advantages contributes to the widespread use of the BNC in food technology, paper, electronic industry, but also the architecture in use. However, the greatest hopes are using the BNC in medicine. This text contains information about bacterial nanocellulose, its specific mechanical and biological properties and current applications.

  1. The genetic diversity of culturable nitrogen-fixing bacteria in the rhizosphere of wheat.

    Science.gov (United States)

    Venieraki, Anastasia; Dimou, Maria; Pergalis, Panagiotis; Kefalogianni, Io; Chatzipavlidis, Iordanis; Katinakis, Panagiotis

    2011-02-01

    A total of 17 culturable nitrogen-fixing bacterial strains associated with the roots of wheat growing in different regions of Greece were isolated and characterized for plant-growth-promoting traits such as auxin production and phosphate solubilization. The phylogenetic position of the isolates was first assessed by the analysis of the PCR-amplified 16S rRNA gene. The comparative sequence analysis and phylogenetic analysis based on 16S rRNA gene sequences show that the isolates recovered in this study are grouped with Azospirillum brasilense, Azospirillum zeae, and Pseudomonas stutzeri. The diazotrophic nature of all isolates was confirmed by amplification of partial nifH gene sequences. The phylogenetic tree based on nifH gene sequences is consistent with 16S rRNA gene phylogeny. The isolates belonging to Azospirillum species were further characterized by examining the partial dnaK gene phylogenetic tree. Furthermore, it was demonstrated that the ipdC gene was present in all Azospirillum isolates, suggesting that auxin is mainly synthesized via the indole-3-pyruvate pathway. Although members of P. stutzeri and A. zeae are known diazotrophic bacteria, to the best of our knowledge, this is the first report of isolation and characterization of strains belonging to these bacterial genera associated with wheat.

  2. Lattice Chiral Fermions Through Gauge Fixing

    CERN Document Server

    Bock, W; Shamir, Y; Bock, Wolfgang; Golterman, Maarten; Shamir, Yigal

    1998-01-01

    We study a concrete lattice regularization of a U(1) chiral gauge theory. We use Wilson fermions, and include a Lorentz gauge-fixing term and a gauge-boson mass counterterm. For a reduced version of the model, in which the gauge fields are constrained to the trivial orbit, we show that there are no species doublers, and that the fermion spectrum contains only the desired states in the continuum limit, namely charged left-handed (LH) fermions and neutral right-handed (RH) fermions.

  3. CERN's Fixed Target Primary Ion Programme

    CERN Document Server

    Manglunki, Django; Axensalva, Jerome; Bellodi, Giulia; Blas, Alfred; Bodendorfer, Michael; Bohl, Thomas; Cettour-Cave, Stephane; Cornelis, Karel; Damerau, Heiko; Efthymiopoulos, Ilias; Fabich, Adrian; Ferreira Somoza, Jose; Findlay, Alan; Freyermuth, Pierre; Gilardoni, Simone; Hancock, Steven; Holzer, Eva Barbara; Jensen, Steen; Kain, Verena; Küchler, Detlef; Lombardi, Alessandra; Michet, Alice; O'Neil, Michael; Pasinelli, Sergio; Scrivens, Richard; Steerenberg, Rende; Tranquille, Gerard

    2016-01-01

    The renewed availability of heavy ions at CERN for the needs of the LHC programme has triggered the interest of the fixed-target community. The project, which involves sending several species of primary ions at various energies to the North Area of the Super Proton Synchrotron, has now entered its operational phase. The first argon run, with momenta ranging from 13 AGeV/c to 150 AGeV/c, took place from February 2015 to April 2015. This paper presents the status of the project, the performance achieved thus far and an outlook on future plans.

  4. 下呼吸道感染革兰阴性杆菌的种类及耐药性探讨%Bacterial species and drug resistance of gram-negative bacilli causing lower respiratory tract infections

    Institute of Scientific and Technical Information of China (English)

    孙杨

    2011-01-01

    OBJECTIVE To investigate the bacterial species and drug resistance in lower respiratory tract infections with gram-negative bacilli and to provide the scientific reference for clinically reasonable application of antibiotics.METHODS Referring to National Clinical Laboratory Procedures, the strains were cultured and identified. The antibiotic susceptibility testing was performed by K-B method. RESULTS Among 243 strains of Gram-negative bacilli, the top one of isolating rates was Pseudomonas aeruginosa (85.5%), followed by Klebsiella pneunmoniae (22.6%), Escherichia coli (ECO) and Acinetobacter baumannii (8. 6%). The total detection rate of extensivespectrum beta-lactamases producing strains was 37.4%. The drug resistance rates of PAE and ABA carbapenems were 4.8%-9.5%. CONCLUSION The drug resistance status of Gram-negative bacilli causing lower respiratory tract infections is serious. The monitoring to bacterial drug resistance should be strengthened.%目的:了解医院下呼吸道感染患者革兰阴性杆菌的种类及耐药现状,为临床医师合理用药提供试验依据.方法:细菌培养鉴定按照进行;药物敏感试验采用K-B法.结果:243株革兰阴性杆菌中,分离率居第1位的为铜绿假单胞菌(25.5%),其余依次为肺炎克雷伯菌(22.6%)、大肠埃希菌(18.2%)和鲍氏不动杆菌(8.6%);产超广谱β-内酰酞胺酶菌株总检出率为37.4%;铜绿假单胞菌和鲍氏不动杆菌对碳青霉烯类抗菌药物已产生了4.8%~9.5%的耐药率.结论:下呼吸道感染革兰阴性杆菌的耐药现状已十分严重,临床微生物室应加强细菌耐药性的监测工作.

  5. Pregnancy Complications: Bacterial Vaginosis

    Science.gov (United States)

    ... Complications & Loss > Pregnancy complications > Bacterial vaginosis and pregnancy Bacterial vaginosis and pregnancy E-mail to a friend Please ... this page It's been added to your dashboard . Bacterial vaginosis (also called BV or vaginitis) is an infection ...

  6. Pregnancy Complications: Bacterial Vaginosis

    Science.gov (United States)

    ... Loss > Pregnancy complications > Bacterial vaginosis and pregnancy Bacterial vaginosis and pregnancy E-mail to a friend Please ... page It's been added to your dashboard . Bacterial vaginosis (also called BV or vaginitis) is an infection ...

  7. Bacterial vaginosis -- aftercare

    Science.gov (United States)

    ... page: //medlineplus.gov/ency/patientinstructions/000687.htm Bacterial vaginosis - aftercare To use the sharing features on this ... back after you use the bathroom. Preventing Bacterial Vaginosis You can help prevent bacterial vaginosis by: Not ...

  8. Bacterial pericarditis (image)

    Science.gov (United States)

    Bacterial pericarditis is an inflammation of the pericardium, the sac-like covering of the heart, caused by a bacterial infection. The bacterial infection causes inflammation and swelling of the pericardium. Pain ...

  9. Food-Borne Bacterial Toxins

    Science.gov (United States)

    Thatcher, F. S.

    1966-01-01

    Food poisoning caused by the ingestion of preformed bacterial toxins is considered in relation to comparative symptoms, procedures for extraction and purification of the causal toxins, their chemistry, serology, assay procedures and pharmacology, in so far as these are known. The bacteria discussed in this context are Clostridium botulinum, C. perfringens, Staphylococcus aureus, Bacillus cereus, and Vibrio parahemolyticus. The possible roles of the enterococci, Proteus, E. coli and of unknown species, in relation to production of non-antigenic toxic substances, are discussed briefly. Requirements for prevention of the various forms of bacterial food poisoning are outlined. PMID:5905949

  10. Combinations of bacterial species in endodontic infections

    NARCIS (Netherlands)

    Peters, LB; Wesselink, P.R.; van Winkelhoff, AJ

    2002-01-01

    Aim This study was undertaken to investigate combinations of bacteria found in root-canal infections of teeth with periapical bone destruction without clinical signs and symptoms. Methodology Endodontic samples from 58 root canals were cultured anaerobically and microorganisms were counted and ident

  11. National Radiological Fixed Lab Data

    Data.gov (United States)

    U.S. Environmental Protection Agency — The National Radiological Fixed Laboratory Data Asset includes data produced in support of various clients such as other EPA offices, EPA Regional programs, DOE,...

  12. Elevated Fixed Platform Test Facility

    Data.gov (United States)

    Federal Laboratory Consortium — The Elevated Fixed Platform (EFP) is a helicopter recovery test facility located at Lakehurst, NJ. It consists of a 60 by 85 foot steel and concrete deck built atop...

  13. Fixed Exchange Rates and Trade

    OpenAIRE

    Michael W. Klein; Jay C. Shambaugh

    2004-01-01

    A classic argument for a fixed exchange rate is its promotion of trade. Empirical support for this, however, is mixed. While one branch of research consistently shows a small negative effect of exchange rate volatility on trade, another, more recent, branch presents evidence of a large positive impact of currency unions on trade. This paper helps resolve this disconnect. Our results, which use a new data-based classification of fixed exchange rate regimes, show a large, significant effect of ...

  14. The Human Vaginal Bacterial Biota and Bacterial Vaginosis

    Directory of Open Access Journals (Sweden)

    Sujatha Srinivasan

    2008-01-01

    Full Text Available The bacterial biota of the human vagina can have a profound impact on the health of women and their neonates. Changes in the vaginal microbiota have been associated with several adverse health outcomes including premature birth, pelvic inflammatory disease, and acquisition of HIV infection. Cultivation-independent molecular methods have provided new insights regarding bacterial diversity in this important niche, particularly in women with the common condition bacterial vaginosis (BV. PCR methods have shown that women with BV have complex communities of vaginal bacteria that include many fastidious species, particularly from the phyla Bacteroidetes and Actinobacteria. Healthy women are mostly colonized with lactobacilli such as Lactobacillus crispatus, Lactobacillus jensenii, and Lactobacillus iners, though a variety of other bacteria may be present. The microbiology of BV is heterogeneous. The presence of Gardnerella vaginalis and Atopobium vaginae coating the vaginal epithelium in some subjects with BV suggests that biofilms may contribute to this condition.

  15. Bacterial endophytes enhance competition by invasive plants.

    Science.gov (United States)

    Rout, Marnie E; Chrzanowski, Thomas H; Westlie, Tara K; DeLuca, Thomas H; Callaway, Ragan M; Holben, William E

    2013-09-01

    Invasive plants can alter soil microbial communities and profoundly alter ecosystem processes. In the invasive grass Sorghum halepense, these disruptions are consequences of rhizome-associated bacterial endophytes. We describe the effects of N2-fixing bacterial strains from S. halepense (Rout and Chrzanowski, 2009) on plant growth and show that bacteria interact with the plant to alter soil nutrient cycles, enabling persistence of the invasive. • We assessed fluxes in soil nutrients for ∼4 yr across a site invaded by S. halepense. We assayed the N2-fixing bacteria in vitro for phosphate solubilization, iron chelation, and production of the plant-growth hormone indole-3-acetic acid (IAA). We assessed the plant's ability to recruit bacterial partners from substrates and vertically transmit endophytes to seeds and used an antibiotic approach to inhibit bacterial activity in planta and assess microbial contributions to plant growth. • We found persistent alterations to eight biogeochemical cycles (including nitrogen, phosphorus, and iron) in soils invaded by S. halepense. In this context, three bacterial isolates solubilized phosphate, and all produced iron siderophores and IAA in vitro. In growth chamber experiments, bacteria were transmitted vertically, and molecular analysis of bacterial community fingerprints from rhizomes indicated that endophytes are also horizontally recruited. Inhibiting bacterial activity with antibiotics resulted in significant declines in plant growth rate and biomass, with pronounced rhizome reductions. • This work suggests a major role of endophytes on growth and resource allocation of an invasive plant. Indeed, bacterial isolate physiology is correlated with invader effects on biogeochemical cycles of nitrogen, phosphate, and iron.

  16. 藏族与汉族中老年人结膜囊细菌状况对照研究%Comparative study on bacterial species in conjunctival sac between the Tibetan minority and Han nationality

    Institute of Scientific and Technical Information of China (English)

    多吉; 张悦; 郑红; 刘治容; 嘉初丹巴; 泽旺格玛; 王光进; 李玉婵

    2012-01-01

    背景 流行病学调查结果显示,不同民族结膜囊的菌种分布有所不同,可能与其居住环境有关.了解不同民族结膜囊菌种的分布特点对感染性眼病的防治具有重要意义.目的 了解藏族与汉族中老年人结膜囊细菌状况的异同.方法 整群抽取四川甘孜州康定县、九龙县各1个藏族聚居地40岁以上藏族人群145人,九龙县1个及康定县2个汉族聚居地汉族人群173人,共计346眼进行调查,取结膜囊分泌物进行细菌培养及分离鉴定,比较藏族与汉族人群的检查结果.结果 受试的藏族和汉族人群的性别及年龄的差异均无统计学意义(x2=0.987,P=0.320;t=1.142,P=0.254),两组人群农牧民和非农业人口构成比的差异有统计学意义(x2=8.557,p=0.000).藏族人群结膜囊细菌培养阳性率为50.7%,汉族为60.4%,藏族人群结膜囊细菌培养阳性率低于汉族,差异有统计学意义(x2 =6.042,P=0.014).藏族结膜囊多种细菌共存者占11.6%,汉族为11.0%,差异无统计学意义(x2=0.027,P=0.869);藏族人群结膜囊中表皮葡萄球菌培养的阳性率为26.6%,汉族人群为33.2%,差异无统计学意义(x2=3.350,P=0.060);藏族人群结膜囊内棒状杆菌培养的阳性率为15.9%,汉族人群为17.3%;差异无统计学意义(x2=0.248,P=0.618).结论 四川甘孜州藏区藏族中老年人结膜囊细菌培养阳性率较汉族中老年人低,藏族和汉族中老年人结膜囊的细菌的种类及分布相似.%Background Epidemiological surveys showed that the types of bacteria are different in the conjunvical sac from different nationalities,which possibly is associated with living environment.To characterize the types of conjunctival bacteria involved is important for the prevention and treatment of infectious eye diseases.Objective The present survey was to obtain data about bacterial species in the conjunctival sac in the Tibetan minority population aged over 40 years old and compared

  17. A Comparison Simulation of Fixed-fixed Type MEMS Switches

    Science.gov (United States)

    Rezazadeh, G.; Sadeghian, H.; Malekpour, E.

    2006-04-01

    In the present work pull-in voltage of fixed-fixed end type MEMS switches with variative electrostatic area has been calculated using a distributed model and applying a full nonlinear finite difference discretizing method. The governing nonlinear differential equation has been derived using of the variational principle for multi domain electromechanical coupled system. The numerical results of the beam with variative electrostatic area with the results of Coupled-Domain Finite Element method have been compared and very good agreement has been achieved.

  18. Diclofenac Induced Fixed Drug Eruption

    Directory of Open Access Journals (Sweden)

    Dr. Umeshchandra C Honnaddi

    2016-02-01

    Full Text Available Background: Diclofenac is the most commonly used non-steroidal anti-inflammatory drug (NSAID for treating various inflammatory and painful conditions. It is generally well tolerated; gastric upset is the most common adverse effect. However very few cases of fixed drug eruptions were reported. Here we present a case of Diclofenac Induced Fixed Drug Eruption. A 62 year old male patient developed fixed drug eruptions with plaques on left thigh two days after receiving diclofenac for osteoarthritic pain. Other etiologies including insect bite, infections were ruled out. One week later after stopping the drug, the lesions were subsided. Diclofenac was strongly suspected as the casual drug. CD8+ effector T-cells have shown to play an important role. However it seems to be a reversible and drug related event. Although it is not life-threatening, fixed drug eruption can have significant effect on the quality of life of patients.Conclusion: Diclofenac is one of the most commonly prescribed NSAIDs by the Physicians. It is usually well tolerated, gastric upset is the most common adverse effect noted with this drug. This case is being reported to highlight a drug as safe as Diclofenac may also be associated with Fixed Drug Eruptions.

  19. Explaining coexistence of nitrogen fixing and non-fixing rhizobia in legume-rhizobia mutualism using mathematical modeling.

    Science.gov (United States)

    Moyano, G; Marco, D; Knopoff, D; Torres, G; Turner, C

    2017-10-01

    In the mutualism established between legumes and soil bacteria known as rhizobia, bacteria from soil infect plants roots and reproduce inside root nodules where they fix atmospheric N2 for plant nutrition, receiving carbohydrates in exchange. Host-plant sanctions against non N2 fixing, cheating bacterial symbionts have been proposed to act in the legume-Rhizobium symbiosis, to preserve the mutualistic relationship. Sanctions include decreased rhizobial survival in nodules occupied by cheating rhizobia. Previously, a simple population model experimentally based showed that the coexistence of fixing and cheating rhizobia strains commonly found in field conditions is possible, and that the inclusion of sanctions leads to the extinction of cheating strains in soil. Here, we extend the previous model to include other factors that could complicate the sanction scenario, like horizontal transmission of symbiotic plasmids, turning non-nodulating strains into nodulating rhizobia, and competition between fixing and cheating strains for nodulation. In agreement with previous results, we show that plant populations persist even in the presence of cheating rhizobia without incorporating any sanction against the cheater populations in the model, under the realistic assumption that plants can at least get some amount of fixed N2 from the effectively mutualistic rhizobia occupying some nodules. Inclusion of plant sanctions leads to the unrealistic extinction of cheater strains in soil. Our results agree with increasing experimental evidence and theoretical work showing that mutualisms can persist in presence of cheating partners. Copyright © 2017 Elsevier Inc. All rights reserved.

  20. Binding and entry of DNA in bacterial transformation

    Energy Technology Data Exchange (ETDEWEB)

    Lacks, S.A.

    1976-01-01

    Bacterial transformation in relation to DNA transport and competence in Streptococcus pneumoniae (also called Diplococcus pneumoniae) is discussed. This species will serve as a model with which to compare transformation in other bacterial species, particularly Bacillus subtilis and Haemophilus influenzae, with emphasis on the many similarities as well as differences.

  1. Evidence of the Big Fix

    CERN Document Server

    Hamada, Yuta; Kawana, Kiyoharu

    2014-01-01

    We give an evidence of the Big Fix. The theory of wormholes and multiverse suggests that the parameters of the Standard Model are fixed in such a way that the total entropy at the late stage of the universe is maximized, which we call the maximum entropy principle. In this paper, we discuss how it can be confirmed by the experimental data, and we show that it is indeed true for the Higgs vacuum expectation value $v_{h}$. We assume that the baryon number is produced by the sphaleron process, and that the current quark masses, the gauge couplings and the Higgs self coupling are fixed when we vary $v_{h}$. It turns out that the existence of the atomic nuclei plays a crucial role to maximize the entropy. This is reminiscent of the anthropic principle, however it is required by the fundamental low in our case.

  2. Evidence of the big fix

    Science.gov (United States)

    Hamada, Yuta; Kawai, Hikaru; Kawana, Kiyoharu

    2014-06-01

    We give an evidence of the Big Fix. The theory of wormholes and multiverse suggests that the parameters of the Standard Model are fixed in such a way that the total entropy at the late stage of the universe is maximized, which we call the maximum entropy principle. In this paper, we discuss how it can be confirmed by the experimental data, and we show that it is indeed true for the Higgs vacuum expectation value vh. We assume that the baryon number is produced by the sphaleron process, and that the current quark masses, the gauge couplings and the Higgs self-coupling are fixed when we vary vh. It turns out that the existence of the atomic nuclei plays a crucial role to maximize the entropy. This is reminiscent of the anthropic principle, however it is required by the fundamental law in our case.

  3. Fourier transform infrared spectroscopic study of intact cells of the nitrogen-fixing bacterium Azospirillum brasilense

    Science.gov (United States)

    Kamnev, A. A.; Ristić, M.; Antonyuk, L. P.; Chernyshev, A. V.; Ignatov, V. V.

    1997-06-01

    The data of Fourier transform infrared (FTIR) spectroscopic measurements performed on intact cells of the soil nitrogen-fixing bacterium Azospirillum brasilense grown in a standard medium and under the conditions of an increased metal uptake are compared and discussed. The structural FTIR information obtained is considered together with atomic absorption spectrometry (AAS) data on the content of metal cations in the bacterial cells. Some methodological aspects concerning preparation of bacterial cell samples for FTIR measurements are also discussed.

  4. [DNA homology in various strains of nitrogen-fixing bacteria].

    Science.gov (United States)

    Vardevanian, P O; Minasbekian, L A; Parsadanian, M A

    2000-01-01

    Melting temperature and GC content were evaluated for DNA of some nitrogen-fixing bacteria of Rhizobium leguminosarum and Onobrychis spp. (Adans). The degree of homology between strains of the same species was determined. A combination of thermal denaturing and molecular hybridization can serve as a rapid test for evaluating the genome homology of the organisms compared.

  5. Fixed-point signal processing

    CERN Document Server

    Padgett, Wayne T

    2009-01-01

    This book is intended to fill the gap between the ""ideal precision"" digital signal processing (DSP) that is widely taught, and the limited precision implementation skills that are commonly required in fixed-point processors and field programmable gate arrays (FPGAs). These skills are often neglected at the university level, particularly for undergraduates. We have attempted to create a resource both for a DSP elective course and for the practicing engineer with a need to understand fixed-point implementation. Although we assume a background in DSP, Chapter 2 contains a review of basic theory

  6. Perfect and Imperfect Gauge Fixing

    CERN Document Server

    Shirzad, A

    2006-01-01

    Gauge fixing may be done in different ways. We show that using the chain structure to describe a constrained system, enables us to use either a perfect gauge, in which all gauged degrees of freedom are determined; or an imperfect gauge, in which some first class constraints remain as subsidiary conditions to be imposed on the solutions of the equations of motion. We also show that the number of constants of motion depends on the level in a constraint chain in which the gauge fixing condition is imposed. The relativistic point particle, electromagnetism and the Polyakov string are discussed as examples and perfect or imperfect gauges are distinguished.

  7. Fixed effects analysis of variance

    CERN Document Server

    Fisher, Lloyd; Birnbaum, Z W; Lukacs, E

    1978-01-01

    Fixed Effects Analysis of Variance covers the mathematical theory of the fixed effects analysis of variance. The book discusses the theoretical ideas and some applications of the analysis of variance. The text then describes topics such as the t-test; two-sample t-test; the k-sample comparison of means (one-way analysis of variance); the balanced two-way factorial design without interaction; estimation and factorial designs; and the Latin square. Confidence sets, simultaneous confidence intervals, and multiple comparisons; orthogonal and nonorthologonal designs; and multiple regression analysi

  8. Dynamic of functional microbial groups during mesophilic composting of agro-industrial wastes and free-living (N2)-fixing bacteria application.

    Science.gov (United States)

    Pepe, Olimpia; Ventorino, Valeria; Blaiotta, Giuseppe

    2013-07-01

    Although several reports are available concerning the composition and dynamics of the microflora during the composting of municipal solid wastes, little is known about the microbial diversity during the composting of agro-industrial refuse. For this reason, the first parts of this study included the quantification of microbial generic groups and of the main functional groups of C and N cycle during composting of agro-industrial refuse. After a generalized decrease observed during the initial phases, a new bacterial growth was observed in the final phase of the process. Ammonifiers and (N2)-fixing aerobic groups predominated outside of the piles whereas, nitrate-reducing group increased inside the piles during the first 23days of composting. Ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB), showed an opposite trend of growth since ammonia oxidation decreased with the increase of the nitrite oxidation activity. Pectinolytics, amylolytics and aerobic cellulolytic were present in greater quantities and showed an upward trend in both the internal and external part of the heaps. Several free-living (N2)-fixing bacteria were molecularly identify as belonging especially to uncommon genera of nitrogen-fixing bacteria as Stenotrophomonas, Xanthomonas, Pseudomonas, Klebsiella, Alcaligenes, Achromobacter and Caulobacter. They were investigated for their ability to fix atmospheric nitrogen to employ as improvers of quality of compost. Some strains of Azotobacter chrococcum and Azotobacter salinestris were also tested. When different diazotrophic bacterial species were added in compost, the increase of total N ranged from 16% to 27% depending on the selected microbial strain being used. Such microorganisms may be used alone or in mixtures to provide an allocation of plant growth promoting rhizobacteria in soil. Copyright © 2013 Elsevier Ltd. All rights reserved.

  9. Bacterial Associations: Antagonism to Symbiosis

    Digital Repository Service at National Institute of Oceanography (India)

    Nair, S.

    with the faeces and then are present in relatively large numbers (Schulz, 1987). Negative Relationship ? Antagonism Microbial populations have a resilient dynamic stability produced by biological buffering from competition. Microorganisms compete for nutrients... Assisted Molecular Breeding (PAMB), wherein, under selective environmental pressure, plasmid transfer and natural recombinants could be derived among bacterial species to enhance their competence and degradation efficiency. It has been able to demonstrate...

  10. In-situ effects of eutrophication and overfishing on physiology and bacterial diversity of the red sea coral Acropora hemprichii.

    Science.gov (United States)

    Jessen, Christian; Villa Lizcano, Javier Felipe; Bayer, Till; Roder, Cornelia; Aranda, Manuel; Wild, Christian; Voolstra, Christian R

    2013-01-01

    Coral reefs of the Central Red Sea display a high degree of endemism, and are increasingly threatened by anthropogenic effects due to intense local coastal development measures. Overfishing and eutrophication are among the most significant local pressures on these reefs, but there is no information available about their potential effects on the associated microbial community. Therefore, we compared holobiont physiology and 16S-based bacterial communities of tissue and mucus of the hard coral Acropora hemprichii after 1 and 16 weeks of in-situ inorganic nutrient enrichment (via fertilizer diffusion) and/or herbivore exclusion (via caging) in an offshore reef of the Central Red Sea. Simulated eutrophication and/or overfishing treatments did not affect coral physiology with respect to coral respiration rates, chlorophyll a content, zooxanthellae abundance, or δ (15)N isotopic signatures. The bacterial community of A. hemprichii was rich and uneven, and diversity increased over time in all treatments. While distinct bacterial species were identified as a consequence of eutrophication, overfishing, or both, two bacterial species that could be classified to the genus Endozoicomonas were consistently abundant and constituted two thirds of bacteria in the coral. Several nitrogen-fixing and denitrifying bacteria were found in the coral specimens that were exposed to experimentally increased nutrients. However, no particular bacterial species was consistently associated with the coral under a given treatment and the single effects of manipulated eutrophication and overfishing could not predict the combined effect. Our data underlines the importance of conducting field studies in a holobiont framework, taking both, physiological and molecular measures into account.

  11. In-situ effects of eutrophication and overfishing on physiology and bacterial diversity of the red sea coral Acropora hemprichii.

    KAUST Repository

    Jessen, Christian

    2013-04-22

    Coral reefs of the Central Red Sea display a high degree of endemism, and are increasingly threatened by anthropogenic effects due to intense local coastal development measures. Overfishing and eutrophication are among the most significant local pressures on these reefs, but there is no information available about their potential effects on the associated microbial community. Therefore, we compared holobiont physiology and 16S-based bacterial communities of tissue and mucus of the hard coral Acropora hemprichii after 1 and 16 weeks of in-situ inorganic nutrient enrichment (via fertilizer diffusion) and/or herbivore exclusion (via caging) in an offshore reef of the Central Red Sea. Simulated eutrophication and/or overfishing treatments did not affect coral physiology with respect to coral respiration rates, chlorophyll a content, zooxanthellae abundance, or δ (15)N isotopic signatures. The bacterial community of A. hemprichii was rich and uneven, and diversity increased over time in all treatments. While distinct bacterial species were identified as a consequence of eutrophication, overfishing, or both, two bacterial species that could be classified to the genus Endozoicomonas were consistently abundant and constituted two thirds of bacteria in the coral. Several nitrogen-fixing and denitrifying bacteria were found in the coral specimens that were exposed to experimentally increased nutrients. However, no particular bacterial species was consistently associated with the coral under a given treatment and the single effects of manipulated eutrophication and overfishing could not predict the combined effect. Our data underlines the importance of conducting field studies in a holobiont framework, taking both, physiological and molecular measures into account.

  12. Flat coalgebraic fixed point logics

    CERN Document Server

    Schröder, Lutz

    2010-01-01

    Fixed point logics have a wide range of applications in computer science, in particular in artificial intelligence and concurrency. The most expressive logics of this type are the mu-calculus and its relatives. However, popular fixed point logics tend to trade expressivity for simplicity and readability, and in fact often live within the single variable fragment of the mu-calculus. The family of such flat fixed point logics includes, e.g., CTL, the *-nesting-free fragment of PDL, and the logic of common knowledge. Here, we extend this notion to the generic semantic framework of coalgebraic logic, thus covering a wide range of logics beyond the standard mu-calculus including, e.g., flat fragments of the graded mu-calculus and the alternating-time mu-calculus (such as ATL), as well as probabilistic and monotone fixed point logics. Our main results are completeness of the Kozen-Park axiomatization and a timed-out tableaux method that matches EXPTIME upper bounds inherited from the coalgebraic mu-calculus but avo...

  13. Landau Gauge Fixing on GPUs

    CERN Document Server

    Cardoso, Nuno; Bicudo, Pedro; Oliveira, Orlando

    2012-01-01

    In this paper we present and explore the performance of Landau gauge fixing in GPUs using CUDA. We consider the steepest descent algorithm with Fourier acceleration, and compare the GPU performance with a parallel CPU implementation. Using $32^4$ lattice volumes, we find that the computational power of a single Tesla C2070 GPU is equivalent to approximately 256 CPU cores.

  14. Fixed drug eruption to tartrazine.

    Science.gov (United States)

    Orchard, D C; Varigos, G A

    1997-11-01

    An 11-year-old girl with a recurrent fixed drug eruption to tartrazine on the dorsum of the left hand is presented. Oral provocation tests to both the suspected food, an artificially coloured cheese crisp, and to tartrazine were positive. This case highlights fire need to consider artificial flavours, colours and preservatives as potential culprits in classic drug eruptions.

  15. 儿童烧伤创面感染细菌种类分布及耐药情况%INVESTIGATION OF BACTERIAL SPECIES DISTRIBUTION AND DRUG RESISTANCE OF CHILDREN WITH BURN WOUND INFECTION

    Institute of Scientific and Technical Information of China (English)

    戴昆琦; 奕利娟; 陈群英

    2012-01-01

    目的 研究医院病房儿童烧(烫)伤患者创面感染细菌分布和耐药情况.方法 采用细菌分离培养和药敏试验方法,对住院儿童烧伤创面分泌物标本进行了检测.结果 从1 698份标本中检出致病菌379株,检出率为22.32%.烧伤感染致病菌中,革兰阳性球菌占65.17%,革兰阴性杆菌占32.98%,真菌占1.85%.检出的铜绿假单胞菌对氨苄西林、头孢曲松、复方新诺明耐药率均高达100%,鲍曼不动杆菌对氨曲南、环丙沙星和复方新诺明耐药率均高达80%以上.结论 该医院住院儿童烧伤感染致病菌以革兰阳性球菌为主,但革兰阴性杆菌耐药率高.%Objective To investigate the bacterial species distribution and drug resistance of children with bum wound infection. Methods The bacteria isolated culturing and the medicine sensitive test were used to detect secretion specimen from burn wound of children. Results From 1 698 specimen there were 379 strains pathogenic bacteria detected and the positive rate was 22. 32%. Of the burn infection pathogenic bacteria the gram positive coccus accounted for 63. 17% , the gram negative bacillus accounted for 32. 98% and the fungus accounted for 1.85%. The resistance rates of Pseudomonas aeruginosa detected to Amicillin, Ceftriaxone, Trimethoprim - sulfamethoxazole reached 100% , while the resistance rates of Acinetobacter buumannii detected to Aztreonam, Ciprofloxacin and Trimethoprim - sulfamethoxazole were above 80%. Conclusion The main infection pathogenic bacteria of children bum wound are the gram positive coccus and the drug resistance rate of negative bacillus is high.

  16. Adhesives for fixed orthodontic bands.

    Science.gov (United States)

    Millett, Declan T; Glenny, Anne-Marie; Mattick, Rye Cr; Hickman, Joy; Mandall, Nicky A

    2016-10-25

    Orthodontic treatment involves using fixed or removable appliances (dental braces) to correct the positions of teeth. It has been shown that the quality of treatment result obtained with fixed appliances is much better than with removable appliances. Fixed appliances are, therefore, favoured by most orthodontists for treatment. The success of a fixed orthodontic appliance depends on the metal attachments (brackets and bands) being attached securely to the teeth so that they do not become loose during treatment. Brackets are usually attached to the front and side teeth, whereas bands (metal rings that go round the teeth) are more commonly used on the back teeth (molars). A number of adhesives are available to attach bands to teeth and it is important to understand which group of adhesives bond most reliably, as well as reducing or preventing dental decay during the treatment period. To evaluate the effectiveness of the adhesives used to attach bands to teeth during fixed appliance treatment, in terms of:(1) how often the bands come off during treatment; and(2) whether they protect the banded teeth against decay during fixed appliance treatment. The following electronic databases were searched: Cochrane Oral Health's Trials Register (searched 2 June 2016), Cochrane Central Register of Controlled Trials (CENTRAL; 2016, Issue 5) in the Cochrane Library (searched 2 June 2016), MEDLINE Ovid (1946 to 2 June 2016) and EMBASE Ovid (1980 to 2 June 2016). We searched ClinicalTrials.gov and the World Health Organization International Clinical Trials Registry Platform for ongoing trials. No restrictions were placed on the language or date of publication when searching the electronic databases. Randomised and controlled clinical trials (RCTs and CCTs) (including split-mouth studies) of adhesives used to attach orthodontic bands to molar teeth were selected. Patients with full arch fixed orthodontic appliance(s) who had bands attached to molars were included. All review authors

  17. Can mushrooms fix atmospheric nitrogen?

    Indian Academy of Sciences (India)

    H S Jayasinghearachchi; Gamini Seneviratne

    2004-09-01

    It is generally reported that fungi like Pleurotus spp. can fix nitrogen (N2). The way they do it is still not clear. The present study hypothesized that only associations of fungi and diazotrophs can fix N2. This was tested in vitro. Pleurotus ostreatus was inoculated with a bradyrhizobial strain nodulating soybean and P. ostreatus with no inoculation was maintained as a control. At maximum mycelial colonization by the bradyrhizobial strain and biofilm formation, the cultures were subjected to acetylene reduction assay (ARA). Another set of the cultures was evaluated for growth and nitrogen accumulation. Nitrogenase activity was present in the biofilm, but not when the fungus or the bradyrhizobial strain was alone. A significant reduction in mycelial dry weight and a significant increase in nitrogen concentration were observed in the inoculated cultures compared to the controls. The mycelial weight reduction could be attributed to C transfer from the fungus to the bradyrhizobial strain, because of high C cost of biological N2 fixation. This needs further investigations using 14C isotopic tracers. It is clear from the present study that mushrooms alone cannot fix atmospheric N2. But when they are in association with diazotrophs, nitrogenase activity is detected because of the diazotrophic N2 fixation. It is not the fungus that fixes N2 as reported earlier. Effective N2 fixing systems, such as the present one, may be used to increase protein content of mushrooms. Our study has implications for future identification of as yet unidentified N2 systems occurring in the environment.

  18. Biofilms of Clostridium species.

    Science.gov (United States)

    Pantaléon, Véronique; Bouttier, Sylvie; Soavelomandroso, Anna Philibertine; Janoir, Claire; Candela, Thomas

    2014-12-01

    The biofilm is a microbial community embedded in a synthesized matrix and is the main bacterial way of life. A biofilm adheres on surfaces or is found on interfaces. It protects bacteria from the environment, toxic molecules and may have a role in virulence. Clostridium species are spread throughout both environments and hosts, but their biofilms have not been extensively described in comparison with other bacterial species. In this review we describe all biofilms formed by Clostridium species during both industrial processes and in mammals where biofilms may be formed either during infections or associated to microbiota in the gut. We have specifically focussed on Clostridium difficile and Clostridium perfringens biofilms, which have been studied in vitro. Regulatory processes including sporulation and germination highlight how these Clostridium species live in biofilms. Furthermore, biofilms may have a role in the survival and spreading of Clostridium species. Copyright © 2014 Elsevier Ltd. All rights reserved.

  19. Influence of Bacterial Quantitiy in Mycorrhizosphere on Species Diversity of Arbuscular Mycorrhizal Fungi in an Alpine Grassland on the Tibetan Plateau%高寒草原菌根围细菌数量对丛枝茵根真菌物种多样性的影响

    Institute of Scientific and Technical Information of China (English)

    蔡晓布; 彭岳林

    2011-01-01

    Based on spore identification, the influence of bacterial quantity in mycorrhizosphere of dominant grasses on species diversity of arbuscular mycorrhizal fungi (AMF) was investigated in an alpine grassland on North Tibetan Plateau. The results indicated that: 1) When the bacterial number was in the range of 1.02×106 to 2.96 × 106 and 3.01 × 106 to 6.06 × 106 g-1, Glomus and Acaulospora were the dominant genera and Scutellospora was the common genera. The spore density, isolation frequency, relative abundance, importance value and species richness (SN, SR) of AMF showed the similar trend of Glomus > Acaulospora > Scutellospora. 2) When the bacterial number was below 3.0 × 106 g-1, spore density of each AMF genus and species richness (SR) were relatively high. The Shannon-Weiner index and species evenness index were 1.774 and 0.127, respectively. 3) The spore density of AMF declined slightly with the increase of bacterial number, whereas the root infection rate, infection intensity and arbuscule richness of AMF tended to increase. The effect was remarkable when the bacterial number was over 3.0 × 106 g-1.4) Regardless of bacterial number, the species of AMF was mainly composed of common species and dominant species (Glomus was the main genus), and rare species and unique species were less reported. Spore density, relative abundance and importance value differed greatly among different genera of AMF. Fig 6, Tab 3, Ref 25%基于从枝菌根真菌(Arbuscular mycorrhizas fungi,AMF)孢子形态学鉴定,研究了藏北高寒草原主要建群植物菌根围细菌数量对AMF物种多样性的影响.结果表明:1)细菌数量1.02×106~2.96×106、3.01×106~6.06×106个/g范围内,Glomus、Acaulospor均为优势属,Scutellospora则均为最常见属;AMF孢子密度、分离频度、相对多度、重要值和种的丰度(SN、SR)均呈Glomus>Acaulospora> Scutellospora属的趋势.2)细菌数量较低时(<3.0×106个/g),AMF各属孢子密度、种的丰

  20. Exploring the plant-associated bacterial communities in Medicago sativa L

    Directory of Open Access Journals (Sweden)

    Pini Francesco

    2012-05-01

    Full Text Available Abstract Background Plant-associated bacterial communities caught the attention of several investigators which study the relationships between plants and soil and the potential application of selected bacterial species in crop improvement and protection. Medicago sativa L. is a legume crop of high economic importance as forage in temperate areas and one of the most popular model plants for investigations on the symbiosis with nitrogen fixing rhizobia (mainly belonging to the alphaproteobacterial species Sinorhizobium meliloti. However, despite its importance, no studies have been carried out looking at the total bacterial community associated with the plant. In this work we explored for the first time the total bacterial community associated with M. sativa plants grown in mesocosms conditions, looking at a wide taxonomic spectrum, from the class to the single species (S. meliloti level. Results Results, obtained by using Terminal-Restriction Fragment Length Polymorphism (T-RFLP analysis, quantitative PCR and sequencing of 16 S rRNA gene libraries, showed a high taxonomic diversity as well as a dominance by members of the class Alphaproteobacteria in plant tissues. Within Alphaproteobacteria the families Sphingomonadaceae and Methylobacteriaceae were abundant inside plant tissues, while soil Alphaproteobacteria were represented by the families of Hyphomicrobiaceae, Methylocystaceae, Bradyirhizobiaceae and Caulobacteraceae. At the single species level, we were able to detect the presence of S. meliloti populations in aerial tissues, nodules and soil. An analysis of population diversity on nodules and soil showed a relatively low sharing of haplotypes (30-40% between the two environments and between replicate mesocosms, suggesting drift as main force shaping S. meliloti population at least in this system. Conclusions In this work we shed some light on the bacterial communities associated with M. sativa plants, showing that Alphaproteobacteria may

  1. On Fixing number of Functigraphs

    OpenAIRE

    Fazil, Muhammad; Javaid, Imran; Murtaza, Muhammad

    2016-01-01

    The fixing number of a graph $G$ is the order of the smallest subset $S$ of its vertex set $V(G)$ such that stabilizer of $S$ in $G$, $\\Gamma_{S}(G)$ is trivial. Let $G_{1}$ and $G_{2}$ be disjoint copies of a graph $G$, and let $g:V(G_{1})\\rightarrow V(G_{2})$ be a function. A functigraph $F_{G}$ consists of the vertex set $V(G_{1})\\cup V(G_{2})$ and the edge set $E(G_{1})\\cup E(G_{2})\\cup \\{uv:v=g(u)\\}$. In this paper, we study the behavior of the fixing number in passing from $G$ to $F_{G}...

  2. Comprehensive characterization of indoor airborne bacterial profile

    Institute of Scientific and Technical Information of China (English)

    P.L.Chan; P.H.F.Yu; Y.W.Cheng; C.Y.Chan; P.K.Wong

    2009-01-01

    This is the first detailed characterization of the air-borne bacterial profiles in indoor environments and two restaurants were selected for this study.Fifteen genera of bacteria were isolated from each restaurant and identified by three different bacterial identification systems including MIDI, Biolog and Riboprinter?.The dominant bacteria of both restaurants were Gram-positive bacteria in which Micrococcus and Bacillus species were the most abundant species.Most bacteria identified were representative species of skin and respiratory tract of human, and soil.Although the bacterial levels in these restaurants were below the limit of the Hong Kong Indoor Air Quality Objective (HKIAQO) Level 1 standard (i.e., < 500 cfu/m3), the majority of these bacteria were opportunistic pathogens.These results suggested that the identity of airborne bacteria should also be included in the IAQ to ensure there is a safety guideline for the public.

  3. Bacterial communities in the rhizosphere of Vitis vinifera L. cultivated under distinct agricultural practices in Argentina.

    Science.gov (United States)

    Vega-Avila, A D; Gumiere, T; Andrade, P A M; Lima-Perim, J E; Durrer, A; Baigori, M; Vazquez, F; Andreote, F D

    2015-02-01

    Plants interact with a myriad of microbial cells in the rhizosphere, an environment that is considered to be important for plant development. However, the differential structuring of rhizosphere microbial communities due to plant cultivation under differential agricultural practices remains to be described for most plant species. Here we describe the rhizosphere microbiome of grapevine cultivated under conventional and organic practices, using a combination of cultivation-independent approaches. The quantification of bacterial 16S rRNA and nifH genes, by quantitative PCR (qPCR), revealed similar amounts of these genes in the rhizosphere in both vineyards. PCR-DGGE was used to detect differences in the structure of bacterial communities, including both the complete whole communities and specific fractions, such as Alphaproteobacteria, Betaproteobacteria, Actinobacteria, and those harboring the nitrogen-fixing related gene nifH. When analyzed by a multivariate approach (redundancy analysis), the shifts observed in the bacterial communities were poorly explained by variations in the physical and chemical characteristics of the rhizosphere. These approaches were complemented by high-throughput sequencing (67,830 sequences) based on the V6 region of the 16S rRNA gene, identifying the major bacterial groups present in the rhizosphere of grapevines: Proteobacteria, Actinobacteria, Firmicutes, Bacteriodetes, Acidobacteria, Cloroflexi, Verrucomicrobia and Planctomycetes, which occur in distinct proportions in the rhizosphere from each vineyard. The differences might be related to the selection of plant metabolism upon distinct reservoirs of microbial cells found in each vineyard. The results fill a gap in the knowledge of the rhizosphere of grapevines and also show distinctions in these bacterial communities due to agricultural practices.

  4. Oral rehabilitation with fixed prosthesis

    OpenAIRE

    Watanabe Velásquez, Romel; Dpto. Académico Estomatología Rehabilitadora. Facultad Odontología. UNMSM. Lima, Perú.; Salcedo Moncada, Doris; Dpto. Académico Estomatología Rehabilitadora. Facultad Odontología. UNMSM. Lima, Perú.; Ochoa Tataje, Julio; Dpto. Académico Estomatología Rehabilitadora. Facultad Odontología. UNMSM. Lima, Perú; Horna Palomino, Hernán; Dpto. Académico Estomatología Rehabilitadora. Facultad Odontología. UNMSM. Lima, Perú.; Herrera Cisneros, Marco; Dpto. Académico Estomatología Rehabilitadora. Facultad Odontología. UNMSM. Lima, Perú.; Paz Fernández, Juan José; Dpto. Académico Estomatología Rehabilitadora. Facultad Odontología. UNMSM. Lima, Perú.

    2014-01-01

    This treatment was carried out in a 58 years old male patient, who has had the antecedent of a car crash accident two years before; he loosed several teeth and fractured others. Pulp necrosis and alteration of occlusal plane occurred. Because of the pathologies presented, it was installed a multidisciplinary treatment phase having periodontal, endodontic, surgical and orthodontic procedures, tehe installation of posts, crowns and fixed bridges. Treatment was carried out for five months. El...

  5. A fixed-point farrago

    CERN Document Server

    Shapiro, Joel H

    2016-01-01

    This text provides an introduction to some of the best-known fixed-point theorems, with an emphasis on their interactions with topics in analysis. The level of exposition increases gradually throughout the book, building from a basic requirement of undergraduate proficiency to graduate-level sophistication. Appendices provide an introduction to (or refresher on) some of the prerequisite material and exercises are integrated into the text, contributing to the volume’s ability to be used as a self-contained text. Readers will find the presentation especially useful for independent study or as a supplement to a graduate course in fixed-point theory. The material is split into four parts: the first introduces the Banach Contraction-Mapping Principle and the Brouwer Fixed-Point Theorem, along with a selection of interesting applications; the second focuses on Brouwer’s theorem and its application to John Nash’s work; the third applies Brouwer’s theorem to spaces of infinite dimension; and the fourth rests ...

  6. DesinFix TM 135 in fermentation process for bioethanol production

    Directory of Open Access Journals (Sweden)

    Dorothee Barth

    2014-01-01

    Full Text Available Brazil has the world's largest ethanol production from sugarcane, but bacterial contamination decreases the ethanol yields. It was shown that the biocide DesinFixTM 135 can reduce the contamination without decreasing the yeasts' viability or negatively affecting the ethanol production.

  7. Influence of Cervitec gel on periodontal health of patients wearing fixed orthodontic appliances

    Directory of Open Access Journals (Sweden)

    Burcu Özdemir

    2014-09-01

    Conclusion: The present data suggested that brushing with Cervitec gel once a day has the potential to reduce bacterial accumulation around teeth and fixed appliances in patients undergoing orthodontic treatment. However, within the limits of this study, Cervitec seems to have no significant effect on total bacteria, P.g., and T.d. levels of subgingival dental plaque.

  8. Bacterial communities associated with the lichen symbiosis.

    Science.gov (United States)

    Bates, Scott T; Cropsey, Garrett W G; Caporaso, J Gregory; Knight, Rob; Fierer, Noah

    2011-02-01

    Lichens are commonly described as a mutualistic symbiosis between fungi and "algae" (Chlorophyta or Cyanobacteria); however, they also have internal bacterial communities. Recent research suggests that lichen-associated microbes are an integral component of lichen thalli and that the classical view of this symbiotic relationship should be expanded to include bacteria. However, we still have a limited understanding of the phylogenetic structure of these communities and their variability across lichen species. To address these knowledge gaps, we used bar-coded pyrosequencing to survey the bacterial communities associated with lichens. Bacterial sequences obtained from four lichen species at multiple locations on rock outcrops suggested that each lichen species harbored a distinct community and that all communities were dominated by Alphaproteobacteria. Across all samples, we recovered numerous bacterial phylotypes that were closely related to sequences isolated from lichens in prior investigations, including those from a lichen-associated Rhizobiales lineage (LAR1; putative N(2) fixers). LAR1-related phylotypes were relatively abundant and were found in all four lichen species, and many sequences closely related to other known N(2) fixers (e.g., Azospirillum, Bradyrhizobium, and Frankia) were recovered. Our findings confirm the presence of highly structured bacterial communities within lichens and provide additional evidence that these bacteria may serve distinct functional roles within lichen symbioses.

  9. Isolation and characterization of culturable seed-associated bacterial endophytes from gnotobiotically grown Marama bean seedlings.

    Science.gov (United States)

    Chimwamurombe, Percy Maruwa; Grönemeyer, Jann Lasse; Reinhold-Hurek, Barbara

    2016-06-01

    Marama bean (Tylosema esculentum) is an indigenous non-nodulating legume to the arid agro-ecological parts of Southern Africa. It is a staple food for the Khoisan and Bantu people from these areas. It is intriguing how it is able to synthesize the high-protein content in the seeds since its natural habitat is nitrogen deficient. The aim of the study was to determine the presence of seed transmittable bacterial endophytes that may have growth promoting effects, which may be particularly important for the harsh conditions. Marama bean seeds were surface sterilized and gnotobiotically grown to 2 weeks old seedlings. From surface-sterilized shoots and roots, 123 distinct bacterial isolates were cultured using three media, and identified by BOX-PCR fingerprinting and sequence analyses of the 16S rRNA and nifH genes. Phylogenetic analyses of 73 putative endophytes assigned them to bacterial species from 14 genera including Proteobacteria (Rhizobium, Massilia, Kosakonia, Pseudorhodoferax, Caulobacter, Pantoea, Sphingomonas, Burkholderia, Methylobacterium), Firmicutes (Bacillus), Actinobacteria (Curtobacterium, Microbacterium) and Bacteroidetes (Mucilaginibacter, Chitinophaga). Screening for plant growth-promoting activities revealed that the isolates showed production of IAA, ACC deaminase, siderophores, endoglucanase, protease, AHLs and capacities to solubilize phosphate and fix nitrogen. This is the first report that marama bean seeds may harbor endophytes that can be cultivated from seedlings; in this community of bacteria, physiological characteristics that are potentially plant growth promoting are widespread.

  10. Jellyfish modulate bacterial dynamic and community structure.

    Science.gov (United States)

    Tinta, Tinkara; Kogovšek, Tjaša; Malej, Alenka; Turk, Valentina

    2012-01-01

    Jellyfish blooms have increased in coastal areas around the world and the outbreaks have become longer and more frequent over the past few decades. The Mediterranean Sea is among the heavily affected regions and the common bloom-forming taxa are scyphozoans Aurelia aurita s.l., Pelagia noctiluca, and Rhizostoma pulmo. Jellyfish have few natural predators, therefore their carcasses at the termination of a bloom represent an organic-rich substrate that supports rapid bacterial growth, and may have a large impact on the surrounding environment. The focus of this study was to explore whether jellyfish substrate have an impact on bacterial community phylotype selection. We conducted in situ jellyfish-enrichment experiment with three different jellyfish species. Bacterial dynamic together with nutrients were monitored to assess decaying jellyfish-bacteria dynamics. Our results show that jellyfish biomass is characterized by protein rich organic matter, which is highly bioavailable to 'jellyfish-associated' and 'free-living' bacteria, and triggers rapid shifts in bacterial population dynamics and composition. Based on 16S rRNA clone libraries and denaturing gradient gel electrophoresis (DGGE) analysis, we observed a rapid shift in community composition from unculturable Alphaproteobacteria to culturable species of Gammaproteobacteria and Flavobacteria. The results of sequence analyses of bacterial isolates and of total bacterial community determined by culture independent genetic analysis showed the dominance of the Pseudoalteromonadaceae and the Vibrionaceae families. Elevated levels of dissolved proteins, dissolved organic and inorganic nutrient release, bacterial abundance and carbon production as well as ammonium concentrations characterized the degradation process. The biochemical composition of jellyfish species may influence changes in the amount of accumulated dissolved organic and inorganic nutrients. Our results can contribute insights into possible changes in

  11. Jellyfish modulate bacterial dynamic and community structure.

    Directory of Open Access Journals (Sweden)

    Tinkara Tinta

    Full Text Available Jellyfish blooms have increased in coastal areas around the world and the outbreaks have become longer and more frequent over the past few decades. The Mediterranean Sea is among the heavily affected regions and the common bloom-forming taxa are scyphozoans Aurelia aurita s.l., Pelagia noctiluca, and Rhizostoma pulmo. Jellyfish have few natural predators, therefore their carcasses at the termination of a bloom represent an organic-rich substrate that supports rapid bacterial growth, and may have a large impact on the surrounding environment. The focus of this study was to explore whether jellyfish substrate have an impact on bacterial community phylotype selection. We conducted in situ jellyfish-enrichment experiment with three different jellyfish species. Bacterial dynamic together with nutrients were monitored to assess decaying jellyfish-bacteria dynamics. Our results show that jellyfish biomass is characterized by protein rich organic matter, which is highly bioavailable to 'jellyfish-associated' and 'free-living' bacteria, and triggers rapid shifts in bacterial population dynamics and composition. Based on 16S rRNA clone libraries and denaturing gradient gel electrophoresis (DGGE analysis, we observed a rapid shift in community composition from unculturable Alphaproteobacteria to culturable species of Gammaproteobacteria and Flavobacteria. The results of sequence analyses of bacterial isolates and of total bacterial community determined by culture independent genetic analysis showed the dominance of the Pseudoalteromonadaceae and the Vibrionaceae families. Elevated levels of dissolved proteins, dissolved organic and inorganic nutrient release, bacterial abundance and carbon production as well as ammonium concentrations characterized the degradation process. The biochemical composition of jellyfish species may influence changes in the amount of accumulated dissolved organic and inorganic nutrients. Our results can contribute insights into

  12. Differentiation of bacterial versus viral otitis media using a combined Raman scattering spectroscopy and low coherence interferometry probe (Conference Presentation)

    Science.gov (United States)

    Zhao, Youbo; Shelton, Ryan L.; Tu, Haohua; Nolan, Ryan M.; Monroy, Guillermo L.; Chaney, Eric J.; Boppart, Stephen A.

    2016-02-01

    Otitis media (OM) is a highly prevalent disease that can be caused by either a bacterial or viral infection. Because antibiotics are only effective against bacterial infections, blind use of antibiotics without definitive knowledge of the infectious agent, though commonly practiced, can lead to the problems of potential harmful side effects, wasteful misuse of medical resources, and the development of antimicrobial resistance. In this work, we investigate the feasibility of using a combined Raman scattering spectroscopy and low coherence interferometry (LCI) device to differentiate OM infections caused by viruses and bacteria and improve our diagnostic ability of OM. Raman spectroscopy, an established tool for molecular analysis of biological tissue, has been shown capable of identifying different bacterial species, although mostly based on fixed or dried sample cultures. LCI has been demonstrated recently as a promising tool for determining tympanic membrane (TM) thickness and the presence and thickness of middle-ear biofilm located behind the TM. We have developed a fiber-based ear insert that incorporates spatially-aligned Raman and LCI probes for point-of-care diagnosis of OM. As shown in human studies, the Raman probe provides molecular signatures of bacterial- and viral-infected OM and normal middle-ear cavities, and LCI helps to identify depth-resolved structural information as well as guide and monitor positioning of the Raman spectroscopy beam for relatively longer signal acquisition time. Differentiation of OM infections is determined by correlating in vivo Raman data collected from human subjects with the Raman features of different bacterial and viral species obtained from cultured samples.

  13. Prevention of bacterial adhesion

    DEFF Research Database (Denmark)

    Klemm, Per; Vejborg, Rebecca Munk; Hancock, Viktoria

    2010-01-01

    Management of bacterial infections is becoming increasingly difficult due to the emergence and increasing prevalence of bacterial pathogens that are resistant to available antibiotics. Conventional antibiotics generally kill bacteria by interfering with vital cellular functions, an approach...... that imposes selection pressure for resistant bacteria. New approaches are urgently needed. Targeting bacterial virulence functions directly is an attractive alternative. An obvious target is bacterial adhesion. Bacterial adhesion to surfaces is the first step in colonization, invasion, and biofilm formation....... 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...

  14. Bacterial community reconstruction using compressed sensing.

    Science.gov (United States)

    Amir, Amnon; Zuk, Or

    2011-11-01

    Bacteria are the unseen majority on our planet, with millions of species and comprising most of the living protoplasm. We propose a novel approach for reconstruction of the composition of an unknown mixture of bacteria using a single Sanger-sequencing reaction of the mixture. Our method is based on compressive sensing theory, which deals with reconstruction of a sparse signal using a small number of measurements. Utilizing the fact that in many cases each bacterial community is comprised of a small subset of all known bacterial species, we show the feasibility of this approach for determining the composition of a bacterial mixture. Using simulations, we show that sequencing a few hundred base-pairs of the 16S rRNA gene sequence may provide enough information for reconstruction of mixtures containing tens of species, out of tens of thousands, even in the presence of realistic measurement noise. Finally, we show initial promising results when applying our method for the reconstruction of a toy experimental mixture with five species. Our approach may have a potential for a simple and efficient way for identifying bacterial species compositions in biological samples. All supplementary data and the MATLAB code are available at www.broadinstitute.org/?orzuk/publications/BCS/.

  15. GOLD and the fixed ratio

    Directory of Open Access Journals (Sweden)

    Vestbo J

    2012-09-01

    Full Text Available Jørgen VestboUniversity of Manchester, Manchester, UKI read with interest the paper entitled "Diagnosis of airway obstruction in the elderly: contribution of the SARA study" by Sorino et al in a recent issue of this journal.1 Being involved in the Global Initiative for Obstructive Lung Diseases (GOLD, it is nice to see the interest sparked by the GOLD strategy document. However, in the paper by Sorino et al, there are a few misunderstandings around GOLD and the fixed ratio (forced expiratory volume in 1 second/forced volume vital capacity < 0.70 that need clarification.View original paper by Sorino and colleagues.

  16. Homotopies and the Universal Fixed Point Property

    DEFF Research Database (Denmark)

    Szymik, Markus

    2015-01-01

    A topological space has the fixed point property if every continuous self-map of that space has at least one fixed point. We demonstrate that there are serious restraints imposed by the requirement that there be a choice of fixed points that is continuous whenever the self-map varies continuously...

  17. Fixed Target Collisions at STAR

    Science.gov (United States)

    Meehan, Kathryn C.

    2016-12-01

    The RHIC Beam Energy Scan (BES) program was proposed to look for the turn-off of signatures of the quark gluon plasma (QGP), search for a possible QCD critical point, and study the nature of the phase transition between hadronic and partonic matter. Previous results have been used to claim that the onset of deconfinement occurs at a center-of-mass energy of 7 GeV. Data from lower energies are needed to test if this onset occurs. The goal of the STAR Fixed-Target Program is to extend the collision energy range in BES II to energies that are likely below the onset of deconfinement. Currently, STAR has inserted a gold target into the beam pipe and conducted test runs at center-of-mass energies of 3.9 and 4.5 GeV. Tests have been done with both Au and Al beams. First physics results from a Coulomb potential analysis of Au + Au fixed-target collisions are presented and are found to be consistent with results from previous experiments. Furthermore, the Coulomb potential, which is sensitive to the Z of the projectile and degree of baryonic stopping, will be compared to published results from the AGS.

  18. Utilization of nitrogen fixing trees

    Energy Technology Data Exchange (ETDEWEB)

    Brewbaker, J.L.; Beldt, R. van den; MacDicken, K.; Budowski, G.; Kass, D.C.L.; Russo, R.O.; Escalante, G.; Herrera, R.; Aranguren, J.; Arkcoll, D.B.; Doebereinger, J. (cord.)

    1983-01-01

    Six papers from the symposium are noted. Brewbaker, J.L., Beldt, R. van den, MacDicken, K. Fuelwood uses and properties of nitrogen-fixing trees, pp 193-204, (Refs. 15). Includes a list of 35 nitrogen-fixing trees of high fuelwood value. Budowski, G.; Kass, D.C.L.; Russo, R.O. Leguminous trees for shade, pp 205-222, (Refs. 68). Escalante, G., Herrera, R., Aranguren, J.; Nitrogen fixation in shade trees (Erythrina poeppigiana) in cocoa plantations in northern Venezuela, pp 223-230, (Refs. 13). Arkcoll, D.B.; Some leguminous trees providing useful fruits in the North of Brazil, pp 235-239, (Refs. 13). This paper deals with Parkia platycephala, Pentaclethra macroloba, Swartzia sp., Cassia leiandra, Hymenaea courbaril, dipteryz odorata, Inga edulis, I. macrophylla, and I. cinnamonea. Baggio, A.J.; Possibilities of the use of Gliricidia sepium in agroforestry systems in Brazil, pp 241-243; (Refs. 15). Seiffert, N.F.; Biological nitrogen and protein production of Leucaena cultivars grown to supplement the nutrition of ruminants, pp 245-249, (Refs. 14). Leucaena leucocephala cv. Peru, L. campina grande (L. leucocephala), and L. cunningham (L. leucocephalae) were promising for use as browse by beef cattle in central Brazil.

  19. Bacterial degradation of aminopyrine.

    Science.gov (United States)

    Blecher, H; Blecher, R; Wegst, W; Eberspaecher, J; Lingens, F

    1981-11-01

    1. Four strains of bacteria growing with aminopyrine as sole source of carbon were isolated from soil and were identified as strains of Phenylobacterium immobilis. 2. Strain M13 and strain E, the type species of Phenylobacterium immobilis (DSM 1986), which had been isolated by enrichment with chloridazon (5-amino-4-chloro-2-phenyl-2H-pyridazin-3-one) were used to investigate the bacterial degradation of aminopyrine. 3. Three metabolites were isolated and identified as: 4-(dimethylamino)-1,2-dihydro-1,5-dimethyl-2-(2,3-dihydro-2,3-dihydroxy-4,6-cyc lohexadien-1-yl)-3H-pyrazol-3-one, 4-(dimethylamino)-1,2-dihydro-1,5-dimethyl-2-(2,3-dihydroxyphenyl)-3H-pyrazol-3 -one and 4-(dimethylamino)-1,2-dihydro-1,5-dimethyl-3H-pyrazol-3-one. 4. An enzyme extract from cells of strain m13 was shown to further metabolize the catechol derivative of aminopyrine, with the formation of 2-pyrone-6-carboxylic acid. 5. Results indicate that the benzene ring of aminopyrine is the principal site of microbial metabolism.

  20. Bacterial Profiles of Root Caries in Elderly Patients▿ †

    OpenAIRE

    Preza, Dorita; Olsen, Ingar; Aas, Jørn A.; Willumsen, Tiril; Grinde, Bjørn; Paster, Bruce J.

    2008-01-01

    Culture-based studies have shown that Streptococcus mutans and lactobacilli are associated with root caries (RC). The purpose of the present study was to assess the bacterial diversity of RC in elderly patients by use of culture-independent molecular techniques and to determine the associations of specific bacterial species or bacterial communities with healthy and carious roots. Plaque was collected from root surfaces of 10 control subjects with no RC and from 11 subjects with RC. The bacter...

  1. PyBact: an algorithm for bacterial identification.

    Science.gov (United States)

    Nantasenamat, Chanin; Preeyanon, Likit; Isarankura-Na-Ayudhya, Chartchalerm; Prachayasittikul, Virapong

    2011-01-01

    PyBact is a software written in Python for bacterial identification. The code simulates the predefined behavior of bacterial species by generating a simulated data set based on the frequency table of biochemical tests from diagnostic microbiology textbook. The generated data was used for predictive model construction by machine learning approaches and results indicated that the classifiers could accurately predict its respective bacterial class with accuracy in excess of 99 %.

  2. Sialidases (neuraminidases) in bacterial vaginosis and bacterial vaginosis-associated microflora.

    OpenAIRE

    Briselden, A M; Moncla, B J; Stevens, C E; Hillier, S L

    1992-01-01

    Bacterial vaginosis, Prevotella species, and Bacteroides species have been associated with prematurity and upper genital tract infection. Prevotella (Bacteroides) species and Bacteroides fragilis have also been associated with preterm birth. However, the mechanism by which lower genital tract infection causes upper genital tract disease remains poorly understood. Sialidases (neuraminidases) are enzymes which enhance the ability of microorganisms to invade and destroy tissue. Elevated levels o...

  3. An Alternative Approach to "Identification of Unknowns": Designing a Protocol to Verify the Identities of Nitrogen Fixing Bacteria.

    Science.gov (United States)

    Martinez-Vaz, Betsy M; Denny, Roxanne; Young, Nevin D; Sadowsky, Michael J

    2015-12-01

    Microbiology courses often include a laboratory activity on the identification of unknown microbes. This activity consists of providing students with microbial cultures and running biochemical assays to identify the organisms. This approach lacks molecular techniques such as sequencing of genes encoding 16S rRNA, which is currently the method of choice for identification of unknown bacteria. A laboratory activity was developed to teach students how to identify microorganisms using 16S rRNA polymerase chain reaction (PCR) and validate microbial identities using biochemical techniques. We hypothesized that designing an experimental protocol to confirm the identity of a bacterium would improve students' knowledge of microbial identification techniques and the physiological characteristics of bacterial species. Nitrogen-fixing bacteria were isolated from the root nodules of Medicago truncatula and prepared for 16S rRNA PCR analysis. Once DNA sequencing revealed the identity of the organisms, the students designed experimental protocols to verify the identity of rhizobia. An assessment was conducted by analyzing pre- and posttest scores and by grading students' verification protocols and presentations. Posttest scores were higher than pretest scores at or below p = 0.001. Normalized learning gains (G) showed an improvement of students' knowledge of microbial identification methods (LO4, G = 0.46), biochemical properties of nitrogen-fixing bacteria (LO3, G = 0.45), and the events leading to the establishment of nitrogen-fixing symbioses (LO1&2, G = 0.51, G = 0.37). An evaluation of verification protocols also showed significant improvement with a p value of less than 0.001.

  4. The bacterial lux reporter system: applications in bacterial localisation studies.

    Science.gov (United States)

    Gahan, Cormac G M

    2012-02-01

    Bacterial production of visible light is a natural phenomenon occurring in marine (Vibrio and Photobacterium) and terrestrial (Photorhabdus) species. The mechanism underpinning light production in these organisms is similar and involves the oxidation of an aldehyde substrate in a reaction catalysed by the bacterial luciferase enzyme. The genes encoding the luciferase and a fatty acid reductase complex which synthesizes the substrate are contained in a single operon (the lux operon). This provides a useful reporter system as cloning the operon into a recipient host bacterium will generate visible light without the requirement to add exogenous substrate. The light can be detected in vivo in the living animal using a sensitive detection system and is therefore ideally suited to bioluminescence imaging protocols. The system has therefore been widely used to track bacteria during infection or colonisation of the host. As bacteria are currently being examined as bactofection vectors for gene delivery, particularly to tumour tissue, the use of bioluminescence imaging offers a powerful means to investigate vector amplification in situ. The implications of this technology for bacterial localization, tumour targeting and gene transfer (bactofection) studies are discussed.

  5. Effect of bacterial inoculation in some mixtures of grassland legumes and gramineae

    Directory of Open Access Journals (Sweden)

    Claudiu Ghiocel

    2014-05-01

    Full Text Available Normal 0 false false false EN-US X-NONE X-NONE MicrosoftInternetExplorer4 The paper presents the influence of bacterial inoculation of perennial legumes (alfalfa, bird’s-foot trefoil in pure culture and cultivated in association with perennial gramineae on fodder yield, fodder quality, and atmospheric nitrogen-fixing ability. Results point out an increase of 10-12% of the yield of dry matter in the variants inoculated. Bacterial inoculation with specific bacterial stems (Sinorhizobium meliloti and Mezorhizobium loti has a positive influence on fodder quality too, materialised in the raw protein content and the amount of nitrogen fixed biologically.

  6. Complex issues in accounting for fixed assets

    Directory of Open Access Journals (Sweden)

    Mykhaylo Luchko

    2013-11-01

    Full Text Available This paper considers the mentioned complex issues of business fixed assets accounting. The main emphasis in this case refers to the change in value of fixed assets over time. Author studied problems of the regulatory revaluation of fixed assets in accordance with the applicable accounting standards (regulations. Particular attention is paid to the revaluation and impairment of the business fixed assets objects and their recording on accounts. Author analyzed the complex issues in establishing the fair value of fixed assets. Attention is focused on the harmonization of accounting information with tax calculations and reporting provided by the Ukrainian Tax Code. In considering the matter referred to the tax differences (temporary and permanent. Established tax differences in depreciation of fixed assets, impairment amounts and revaluation of fixed assets and accounting entries to them.

  7. 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 ...

  8. Z-DNA immunoreactivity in fixed metaphase chromosomes of primates.

    Science.gov (United States)

    Viegas-Péquignot, E; Derbin, C; Malfoy, B; Taillandier, E; Leng, M; Dutrillaux, B

    1983-10-01

    Antibodies against Z-DNA bind to fixed metaphase chromosomes of man and Cebus albifrons (Platyrrhini, Primate). By indirect immunofluorescence and indirect immunoperoxidase techniques, a heavy staining is detected in some segments of chromosomes of C. albifrons. These segments correspond to R-band-positive heterochromatin, which has a high G + C-base content. Euchromatin of human and Cebus chromosomes show a weak and heterogeneous staining that consistently reproduces an R- and T-banding pattern in both species. Because chromosome homologies previously were demonstrated between these distantly related species by chromosome banding, our results suggest that Z-DNA has been conserved during the course of primate evolution.

  9. Simple fixed functional space maintainer.

    Science.gov (United States)

    Goenka, Puneet; Sarawgi, Aditi; Marwah, Nikhil; Gumber, Parvind; Dutta, Samir

    2014-01-01

    Premature loss of a primary tooth is one of the most common etiology for malocclusion. Space maintainers are employed to prevent this complication. In anterior region, esthetics is an important concern along with function and space management. Fiber-reinforced composite (FRC) retained space maintainer solves all these purposes ef ficiently and ef fectively. In addition, the technique is simple and the appliance is very comfortable inside the oral cavity. Here is a case of premature loss of anterior primary tooth which was replaced by FRC retained esthetic functional space maintainer. The appliance was found to be functioning satisfactorily inside the oral cavity till the last visit (1 Year). How to cite this article: Goenka P, Sarawgi A, Marwah N, Gumber P, Dutta S. Simple Fixed Functional Space Maintainer. Int J Clin Pediatr Dent 2014;7(3):225-228.

  10. Fixed Point and Aperiodic Tilings

    CERN Document Server

    Durand, Bruno; Shen, Alexander

    2008-01-01

    An aperiodic tile set was first constructed by R.Berger while proving the undecidability of the domino problem. It turned out that aperiodic tile sets appear in many topics ranging from logic (the Entscheidungsproblem) to physics (quasicrystals) We present a new construction of an aperiodic tile set that is based on Kleene's fixed-point construction instead of geometric arguments. This construction is similar to J. von Neumann self-reproducing automata; similar ideas were also used by P. Gacs in the context of error-correcting computations. The flexibility of this construction allows us to construct a ``robust'' aperiodic tile set that does not have periodic (or close to periodic) tilings even if we allow some (sparse enough) tiling errors. This property was not known for any of the existing aperiodic tile sets.

  11. Kinetics of Colonization of Adult Queensland Fruit Flies (Bactrocera tryoni) by Dinitrogen-Fixing Alimentary Tract Bacteria.

    Science.gov (United States)

    Murphy, K M; Teakle, D S; Macrae, I C

    1994-07-01

    The average total population of bacteria remained constant in the alimentary tracts of adult laboratory-raised Queensland fruit flies (Bactrocera tryoni) although the insects had ingested large numbers of live bacteria as part of their diet. The mean number of bacteria (about 13 million) present in the gut of the insects from 12 to 55 days after emergence was not significantly modified when, at 5 days after emergence, the flies were fed antibiotic-resistant bacteria belonging to two species commonly isolated from the gut of field-collected B. tryoni. Flies were fed one marked dinitrogen-fixing strain each of either Klebsiella oxytoca or Enterobacter cloacae, and the gastrointestinal tracts of fed flies were shown to be colonized within 7 days by antibiotic-resistant isolates of K. oxytoca but not E. cloacae. The composition of the microbial population also appeared to be stable in that the distribution and frequency of bacterial taxa among individual flies exhibited similar patterns whether or not the flies had been bacteria fed. Isolates of either E. cloacae or K. oxytoca, constituting 70% of the total numbers, were usually dominant, with oxidative species including pseudomonads forming the balance of the population. Antibiotic-resistant bacteria could be spread from one cage of flies to the adjacent surfaces of a second cage within a few days and had reached a control group several meters distant by 3 weeks. Restriction of marked bacteria to the population of one in five flies sampled from the control group over the next 30 days suggested that the bacterial population in the gut of the insect was susceptible to alteration in the first week after emergence but that thereafter it entered a steady state and was less likely to be perturbed by the introduction of newly encountered strains. All populations sampled, including controls, included at least one isolate of the dinitrogen-fixing family Enterobacteriaceae; many were distinct from the marked strains fed to the

  12. Plant Growth-Promoting Nitrogen-Fixing Enterobacteria Are in Association with Sugarcane Plants Growing in Guangxi, China

    OpenAIRE

    2012-01-01

    The current nitrogen fertilization for sugarcane production in Guangxi, the major sugarcane-producing area in China, is very high. We aim to reduce nitrogen fertilization and improve sugarcane production in Guangxi with the help of indigenous sugarcane-associated nitrogen-fixing bacteria. We initially obtained 196 fast-growing bacterial isolates associated with the main sugarcane cultivar ROC22 plants in fields using a nitrogen-deficient minimal medium and screened out 43 nitrogen-fixing isol...

  13. Bacterial associates of arboreal ants and their putative functions in an obligate ant-plant mutualism.

    Science.gov (United States)

    Eilmus, Sascha; Heil, Martin

    2009-07-01

    Bacterial communities are highly diverse and have great ecological importance. In the present study, we used an in silico analysis of terminal restriction fragments (tRF) to characterize the bacterial community of the plant ant Pseudomyrmex ferrugineus. This species is an obligate inhabitant of Acacia myrmecophytes and feeds exclusively on plant-derived food sources. Ants are the dominant insect group in tropical rain forests. Associations of ants with microbes, which contribute particularly to the ants' nitrogen nutrition, could allow these insects to live on mostly or entirely plant-based diets and could thus contribute to the explanation of the high abundances that are reached by tropical ants. We found tRF patterns representing at least 30 prokaryotic taxa, of which the Acidobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Planctomycetes, Proteobacteria, and Spirochaetes comprised 93%. Because most bacterial taxa were found in all ant-derived samples studied and because the bacteria detected on the ants' host plant revealed little overlap with this community, we regard our results as reliably representing the bacterial community that is associated with P. ferrugineus. Genera with a likely function as ant symbionts were Burkholderia, Pantoea, Weissella, and several members of the Enterobacteriaceae. The presence of these and various other groups was confirmed via independent PCR and cultivation approaches. Many of the bacteria that we detected belong to purportedly N-fixing taxa. Bacteria may represent important further partners in ant-plant mutualisms, and their influences on ant nutrition can contribute to the extraordinary abundance and evolutionary success of tropical arboreal ants.

  14. Prevention of bacterial adhesion

    DEFF Research Database (Denmark)

    Klemm, Per; Vejborg, Rebecca Munk; Hancock, Viktoria

    2010-01-01

    Management of bacterial infections is becoming increasingly difficult due to the emergence and increasing prevalence of bacterial pathogens that are resistant to available antibiotics. Conventional antibiotics generally kill bacteria by interfering with vital cellular functions, an approach that ...... valuable weapons for preventing pathogen contamination and fighting infectious diseases in the future....

  15. Bacterial diseases affecting apple

    Science.gov (United States)

    Bacterial diseases of plants are usually difficult to control and often require a combination of control measures to successfully manage the disease. There are often stark differences between the means available to control bacterial diseases in annual crops versus a woody tree crop, such as apple. ...

  16. Recent advances in nitrogen-fixing acetic acid bacteria.

    Science.gov (United States)

    Pedraza, Raúl O

    2008-06-30

    Nitrogen is an essential plant nutrient, widely applied as N-fertilizer to improve yield of agriculturally important crops. An interesting alternative to avoid or reduce the use of N-fertilizers could be the exploitation of plant growth-promoting bacteria (PGPB), capable of enhancing growth and yield of many plant species, several of agronomic and ecological significance. PGPB belong to diverse genera, including Azospirillum, Azotobacter, Herbaspirillum, Bacillus, Burkholderia, Pseudomonas, Rhizobium, and Gluconacetobacter, among others. They are capable of promoting plant growth through different mechanisms including (in some cases), the biological nitrogen fixation (BNF), the enzymatic reduction of the atmospheric dinitrogen (N(2)) to ammonia, catalyzed by nitrogenase. Aerobic bacteria able to oxidize ethanol to acetic acid in neutral or acid media are candidates of belonging to the family Acetobacteraceae. At present, this family has been divided into ten genera: Acetobacter, Gluconacetobacter, Gluconobacter, Acidomonas, Asaia, Kozakia, Saccharibacter, Swaminathania, Neoasaia, and Granulibacter. Among them, only three genera include N(2)-fixing species: Gluconacetobacter, Swaminathania and Acetobacter. The first N(2)-fixing acetic acid bacterium (AAB) was described in Brazil. It was found inside tissues of the sugarcane plant, and first named as Acetobacter diazotrophicus, but then renamed as Gluconacetobacter diazotrophicus. Later, two new species within the genus Gluconacetobacter, associated to coffee plants, were described in Mexico: G. johannae and G. azotocaptans. A salt-tolerant bacterium named Swaminathania salitolerans was found associated to wild rice plants. Recently, N(2)-fixing Acetobacter peroxydans and Acetobacter nitrogenifigens, associated with rice plants and Kombucha tea, respectively, were described in India. In this paper, recent advances involving nitrogen-fixing AAB are presented. Their natural habitats, physiological and genetic aspects

  17. Microbial Changes in Subgingival Plaque and Polymicrobial Intracellular Flora in Buccal Cells after Fixed Orthodontic Appliance Therapy: A Preliminary Study

    Directory of Open Access Journals (Sweden)

    Caterina Montaldo

    2013-01-01

    Full Text Available The oral ecosystem is strictly related to a balance maintained by specific niches recognized as sites, where oral bacteria can metabolize avoiding the immune system response. The oral bacteria species that colonize the ecological niches vary during fixed orthodontic treatment, with a prevalence of periodontal bacterial species. Qualitative analysis of five periodontal pathogens was used to in