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  • Journals
  • Articles  (518)
  • Oxford University Press  (518)
  • American Chemical Society (ACS)
  • Frontiers Media
  • Molecular Diversity Preservation International
  • PeerJ
  • 2015-2019  (518)
  • 1985-1989
  • 2016  (518)
  • FEMS Microbiology Ecology  (262)
  • 62323
  • Biology  (518)
  • Energy, Environment Protection, Nuclear Power Engineering
Collection
  • Journals
  • Articles  (518)
Source
Publisher
  • Oxford University Press  (518)
  • American Chemical Society (ACS)
  • Frontiers Media
  • Molecular Diversity Preservation International
  • PeerJ
Years
  • 2015-2019  (518)
  • 1985-1989
Year
Journal
Topic
  • Biology  (518)
  • Energy, Environment Protection, Nuclear Power Engineering
  • 1
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    Differential utilization patterns of dissolved organic phosphorus compounds by heterotrophic bacteria in two mountain lakes (2016)
    Oxford University Press
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    Publication Date: 2016-07-13
    Description: Although phosphorus limitation is common in freshwaters and bacteria are known to use dissolved organic phosphorus (DOP), little is known about how efficiently DOP compounds are taken up by individual bacterial taxa. Here, we assessed bacterial uptake of three model DOP substrates in two mountain lakes and examined whether DOP uptake followed concentration-dependent patterns. We determined bulk uptake rates by the bacterioplankton and examined bacterial taxon-specific substrate uptake patterns using microautoradiography combined with catalyzed reporter deposition–fluorescence in situ hybridization. Our results show that in the oligotrophic alpine lake, bacteria took up ATP, glucose-6-phosphate and glycerol-3-phosphate to similar extents (mean 29.7 ± 4.3% Bacteria ), whereas in the subalpine mesotrophic lake, ca. 40% of bacteria took up glucose-6-phosphate, but only ~20% took up ATP or glycerol-3-phosphate. In both lakes, the R-BT cluster of Betaproteobacteria (lineage of genus Limnohabitans ) was over-represented in glucose-6-phosphate and glycerol-3-phosphate uptake, whereas AcI Actinobacteria were under-represented in the uptake of those substrates. Alphaproteobacteria and Bacteroidetes contributed to DOP uptake proportionally to their in situ abundance. Our results demonstrate that R-BT Betaproteobacteria are the most active bacteria in DOP acquisition, whereas the abundant AcI Actinobacteria may either lack high affinity DOP uptake systems or have reduced phosphorus requirements.
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    Electronic ISSN: 1574-6941
    Topics: Biology
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  • 2
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    Virus production in phosphorus-limited Micromonas pusilla stimulated by a supply of naturally low concentrations of different phosphorus sources, far into the lytic cycle (2016)
    Oxford University Press
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    Publication Date: 2016-07-13
    Description: Earlier studies show that the proliferation of phytoplankton viruses can be inhibited by depletion of soluble reactive phosphorus (SRP; orthophosphate). In natural marine waters, phytoplankton phosphorus (P) availability is, however, largely determined by the supply rate of SRP (e.g. through remineralization) and potentially by the source of P as well (i.e. the utilization of soluble non-reactive P; SNP). Here we show how a steady low supply of P (mimicking natural P recycling) to virally infected P-limited Micromonas pusilla stimulates virus proliferation. Independent of the degree of P limitation prior to infection (0.32 and 0.97μ max chemostat cultures), SRP supply resulted in 2-fold higher viral burst sizes (viruses lysed per host cell) as compared with no addition (P starvation). Delaying these spikes during the infection cycle showed that the added SRP was utilized for extra M. pusilla virus (MpV) production far into the lytic cycle (18 h post-infection). Moreover, P-limited M. pusilla utilized several SNP compounds with high efficiency and with the same extent of burst size stimulation as for SRP. Finally, addition of virus-free MpV lysate (representing a complex SNP mixture) to newly infected cells enhanced MpV production, implicating host-associated alkaline phosphatase activity, and highlighting its important role in oligotrophic environments.
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  • 3
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    Spatial and taxonomical overlap of fungi on phylloplanes and invasive alien ladybirds with fungal infections in tree crowns of urban green spaces (2016)
    Oxford University Press
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    Publication Date: 2016-07-16
    Description: Occurrence of entomopathogenic fungi on phylloplanes in Tilia x europaea crowns between 1 and 13 m was assessed in urban parks. Prevalence of fungal infections in ladybirds (Coleoptera: Coccinellidae) collected from Tilia x europaea was assessed to determine whether fungi found on phylloplanes also occurred as infections in ladybirds. Isaria spp. was most abundant on phylloplanes (mean colony forming units (CFU) per leaf ± SE, 0.33 ± 0.03) followed by Beauveria spp. (0.22 ± 0.02 CFU per leaf) and Lecanicillium spp. (0.19 ± 0.02 CFU per leaf). Densities of inoculum were higher in inner crowns and decreased with height, although Lecanicillium spp. peaked at 5–7 m. Upper phylloplane surfaces harboured higher densities of Isaria spp. and Beauveria spp. than lower surfaces, whereas Lecanicillium spp. was equally distributed. Most prevalent on ladybirds were Isaria spp. (20.6% Harmonia axyridis ; 4.8% natives), Lecanicillium spp. (13.6% H. axyridis ; 4.8% natives), with fewer Beauveria spp. infections (2.6% H. axyridis ). Molecular identification revealed Beauveria bassiana , B. pseudobassiana , Isaria farinosa and Lecanicillium muscarium among isolates of both tree and ladybird origin. Tilia x europaea phylloplanes support a diverse assemblage of entomopathogenic fungal species with a different prevalence in coccinellids compared to their relative abundance in this habitat.
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  • 4
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    Impacts of human activities on distribution of sulfate-reducing prokaryotes and antibiotic resistance genes in marine coastal sediments of Hong Kong (2016)
    Oxford University Press
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    Publication Date: 2016-07-16
    Description: Sulfate-reducing prokaryotes (SRPs) and antibiotic resistance genes (ARGs) in sediments could be biomarkers for evaluating the environmental impacts of human activities, although factors governing their distribution are not clear yet. By using metagenomic approach, this study investigated the distributions of SRPs and ARGs in marine sediments collected from 12 different coastal locations of Hong Kong, which exhibited different pollution levels and were classified into two groups based on sediment parameters. Our results showed that relative abundances of major SRP genera to total prokaryotes were consistently lower in the more seriously polluted sediments ( P -value 〈 0.05 in 13 of 20 genera), indicating that the relative abundance of SRPs is a negatively correlated biomarker for evaluating human impacts. Moreover, a unimodel distribution pattern for SRPs along with the pollution gradient was observed. Although total ARGs were enriched in sediments from the polluted sites, distribution of single major ARG types could be explained neither by individual sediment parameters nor by corresponding concentration of antibiotics. It supports the hypothesis that the persistence of ARGs in sediments may not need the selection of antibiotics. In summary, our study provided important hints of the niche differentiation of SRPs and behavior of ARGs in marine coastal sediment.
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  • 5
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    The gut microbiome of the sea urchin, Lytechinus variegatus, from its natural habitat demonstrates selective attributes of microbial taxa and predictive metabolic profiles (2016)
    Oxford University Press
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    Publication Date: 2016-07-29
    Description: In this paper, we describe the microbial composition and their predictive metabolic profile in the sea urchin Lytechinus variegatus gut ecosystem along with samples from its habitat by using NextGen amplicon sequencing and downstream bioinformatics analyses. The microbial communities of the gut tissue revealed a near-exclusive abundance of Campylobacteraceae, whereas the pharynx tissue consisted of Tenericutes, followed by Gamma-, Alpha- and Epsilonproteobacteria at approximately equal capacities. The gut digesta and egested fecal pellets exhibited a microbial profile comprised of Gammaproteobacteria, mainly Vibrio , and Bacteroidetes. Both the seagrass and surrounding sea water revealed Alpha- and Betaproteobacteria. Bray–Curtis distances of microbial communities indicated a clustering profile with low intrasample variation. Predictive metagenomics performed on the microbial communities revealed that the gut tissue had high relative abundances of metabolisms assigned to the KEGG-Level-2 designation of energy metabolisms compared to the gut digesta, which had higher carbohydrate, amino acid and lipid metabolisms. Overall, the results of this study elaborate the spatial distribution of microbial communities in the gut ecosystem of L. variegatus , and specifically a selective attribute for Campylobacteraceae in the gut tissue. Also, the predictive functional significance of bacterial communities in uniquely compartmentalized gut ecosystems of L. variegatus has been described.
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  • 6
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    Hydrocarbon biodegradation by Arctic sea-ice and sub-ice microbial communities during microcosm experiments, Northwest Passage (Nunavut, Canada) (2016)
    Oxford University Press
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    Publication Date: 2016-08-05
    Description: The increasing accessibility to navigation and offshore oil exploration brings risks of hydrocarbon releases in Arctic waters. Bioremediation of hydrocarbons is a promising mitigation strategy but challenges remain, particularly due to low microbial metabolic rates in cold, ice-covered seas. Hydrocarbon degradation potential of ice-associated microbes collected from the Northwest Passage was investigated. Microcosm incubations were run for 15 days at –1.7°C with and without oil to determine the effects of hydrocarbon exposure on microbial abundance, diversity and activity, and to estimate component-specific hydrocarbon loss. Diversity was assessed with automated ribosomal intergenic spacer analysis and Ion Torrent 16S rRNA gene sequencing. Bacterial activity was measured by 3 H-leucine uptake rates. After incubation, sub-ice and sea-ice communities degraded 94% and 48% of the initial hydrocarbons, respectively. Hydrocarbon exposure changed the composition of sea-ice and sub-ice communities; in sea-ice microcosms, Bacteroidetes (mainly Polaribacter ) dominated whereas in sub-ice microcosms, the contribution of Epsilonproteobacteria increased, and that of Alphaproteobacteria and Bacteroidetes decreased. Sequencing data revealed a decline in diversity and increases in Colwellia and Moritella in oil-treated microcosms. Low concentration of dissolved organic matter (DOM) in sub-ice seawater may explain higher hydrocarbon degradation when compared to sea ice, where DOM was abundant and composed of labile exopolysaccharides.
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  • 7
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    Effects of endophytic fungi on the ash dieback pathogen (2016)
    Oxford University Press
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    Publication Date: 2016-07-16
    Description: While Hymenoscyphus fraxineus causes dieback of the European ash ( Fraxinus excelsior ), flowering ash ( F. ornus ) appears resistant to the pathogen. To date, contributions of endophytic fungi to host resistance are unknown. The following hypotheses were tested: (i) endophytic fungi enhance the resistance of F. excelsior to the pathogen; (ii) resistance of F. ornus relies on its community of endophytic fungi. Two experiments were performed. (i) The effect of exudates of ash endophytes on the germination rate of H. fraxineus ascospores was studied in vitro . Isolates of abundant Fraxinus leaf endophytes, such as Venturia fraxini, Paraconiothyrium sp., Boeremia exigua, Kretzschmaria deusta and Neofabraea alba inhibited ascospore germination. (ii) Ash seedlings inoculated in a climate chamber, with fungi sporulating on the previous year's leaf litter, were exposed to natural infections by the pathogen present in the forest. Non-inoculated seedlings were used as controls. Venturia spp. dominated the inoculated endophyte ‘communities’. Subsequent exposure to H. fraxineus led to infection of F. excelsior leaves by the pathogen, but no differences in health status between pre-inoculated and non-inoculated seedlings were detected. Fraxinus ornus leaves experienced a low infection rate, independent of their colonization by endophytic fungi. These results did not support either hypothesis.
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  • 8
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    The role of plant-microbiome interactions in weed establishment and control (2016)
    Oxford University Press
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    Publication Date: 2016-08-03
    Description: The soil microbiome plays an important role in the establishment of weeds and invasive plants. They associate with microorganisms supporting their growth and health. Weed management strategies, like tillage and herbicide treatments, to control weeds generally alter soil structure going alongside with changes in the microbial community. Once a weed population establishes in the field, the plants build up a close relationship with the available microorganisms. Seeds or vegetative organs overwinter in soil and select early in the season their own microbiome before crop plants start to vegetate. Weed and crop plants compete for light, nutrition and water, but may differently interact with soil microorganisms. The development of new sequencing technologies for analyzing soil microbiomes has opened up the possibility for in depth analysis of the interaction between ‘undesired’ plants and crop plants under different management systems. These findings will help us to understand the functions of microorganisms involved in crop productivity and plant health, weed establishment and weed prevention. Exploitation of the knowledge offers the possibility to search for new biocontrol methods against weeds based on soil and plant-associated microorganisms. This review discusses the recent advances in understanding the functions of microbial communities for weed/invasive plant establishment and shows new ways to use plant-associated microorganisms to control weeds and invasive plants in different land management systems.
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  • 9
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    Methane and carbon dioxide flux in the profile of wood ant (Formica aquilonia) nests and the surrounding forest floor during a laboratory incubation (2016)
    Oxford University Press
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    Publication Date: 2016-08-03
    Description: We compared methane (CH 4 ) and carbon dioxide (CO 2 ) fluxes in samples collected from the aboveground parts of wood ant nests and in the organic and mineral layer of the surrounding forest floor. Gas fluxes were measured during a laboratory incubation, and microbial properties (abundance of fungi, bacteria and methanotrophic bacteria) and nutrient contents (total and available carbon and nitrogen) were also determined. Both CO 2 and CH 4 were produced from ant nest samples, indicating that the aboveground parts of wood ant nests act as sources of both gases; in comparison, the forest floor produced about four times less CO 2 and consumed rather than produced CH 4 . Fluxes of CH 4 and CO 2 were positively correlated with contents of available carbon and nitrogen. The methanotrophic community was represented by type II methanotrophic bacteria, but their abundance did not explain CH 4 flux. Fungal abundance was greater in ant nest samples than in forest floor samples, but bacterial abundance was similar in both kinds of samples, suggesting that the organic materials in the nests may have been too recalcitrant for bacteria to decompose. The results indicate that the aboveground parts of wood ant nests are hot spots of CO 2 and CH 4 production in the forest floor.
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  • 10
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    Plant growth promotion, metabolite production and metal tolerance of dark septate endophytes isolated from metal-polluted poplar phytomanagement sites (2016)
    Oxford University Press
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    Publication Date: 2016-08-03
    Description: Numerous studies address the distribution and the diversity of dark septate endophytes (DSEs) in the literature, but little is known about their ecological role and their effect on host plants, especially in metal-polluted soils. Seven DSE strains belonging to Cadophora , Leptodontidium , Phialophora and Phialocephala were isolated from roots of poplar trees from metal-polluted sites. All strains developed on a wide range of carbohydrates, including cell-wall-related compounds. The strains evenly colonized birch, eucalyptus and ryegrass roots in re-synthesis experiments. Root and shoot growth promotion was observed and was both plant and strain dependent. Two Phialophora and Leptodontidium strains particularly improved plant growth. However, there was no correlation between the level of root colonization by DSEs and the intensity of growth promotion. All strains produced auxin and six also stimulated plant growth through the release of volatile organic compounds (VOCs). SPME-GC/MS analyses revealed four major VOCs emitted by Cadophora and Leptodontidium . The strains exhibited growth at high concentrations of several metals. The ability of metal-resistant DSE strains to produce both soluble and volatile compounds for plant growth promotion indicates interesting microbial resources with high potential to support sustainable production of bioenergy crops within the context of the phytomanagement of metal-contaminated sites.
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