| 1. |
- Baltar, Federico, et al.
(författare)
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Bacterial Versus Archaeal Origin of Extracellular Enzymatic Activity in the Northeast Atlantic Deep Waters
- 2013
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Ingår i: Microbial Ecology. - Springer-Verlag : Springer Science and Business Media LLC. - 0095-3628 .- 1432-184X. ; 65:2, s. 277-288
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Tidskriftsartikel (refereegranskat)abstract
- We determined the total and dissolved extracellularenzymatic activity (EEA) of α-glucosidase and β-glucosidase(AGase and BGase), alkaline phosphatase (APase) and leucineaminopeptidase (LAPase) activities in the epi-, meso- andbathypelagic waters of the subtropical Northeast Atlantic.EEA was also determined in treatments in which bacterialEEAwas inhibited by erythromycin. Additionally, EEA decayexperiments were performed with surface and deep waters todetermine EEA lifetimes in both water masses. The proportionof dissolved to total EEA (66–89 %, 44–88 %, 57–82 % and86–100 % for AGase, BGase, APase and LAPase, respectively)was generally higher than the cell-associated (i.e.,particulate) EEA. The percentage of dissolved to total EEAwas inversely proportional to the percentage of erythromycininhibitedto total EEA. Since erythromycin-inhibited plusdissolved EEA equaled total EEA, this tentatively suggeststhat cell-associated EEA in the open oceanic water column isalmost exclusively of bacterial origin. The decay constants ofdissolved EEAwere in the range of 0.002–0.048 h−1 dependingon the type of extracellular enzyme, temperature and depthin the water column. Although dissolved EEA can have differentorigins, the major contribution of Bacteria to cellassociatedEEA and the long life-time of dissolved EEAsuggest that Bacteria—and not mesophilic Archaea—areessentially the main producers of EEA in the open subtropicalNortheast Atlantic down to bathypelagic layers.
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| 2. |
- Bapiri, Azadeh, et al.
(författare)
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Drying-Rewetting Cycles Affect Fungal and Bacterial Growth Differently in an Arable Soil
- 2010
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Ingår i: Microbial Ecology. - : Springer Science and Business Media LLC. - 1432-184X .- 0095-3628. ; 60:2, s. 419-428
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Tidskriftsartikel (refereegranskat)abstract
- Drying and rewetting is a frequent physiological stress for soil microbial communities; a stress that is predicted to grow more influential with future climate change. We investigated the effect of repeated drying-rewetting cycles on bacterial (leucine incorporation) and fungal (acetate in ergosterol incorporation) growth, on the biomass concentration and composition (PLFA), and on the soil respiration. Using different plant material amendments, we generated soils with different initial fungal:bacterial compositions that we exposed to 6-10 repetitions of a drying-rewetting cycle. Drying-rewetting decreased bacterial growth while fungal growth remained unaffected, resulting in an elevated fungal:bacterial growth ratio. This effect was found irrespective of the initial fungal:bacterial biomass ratio. Many drying-rewetting cycles did not, however, affect the fungal:bacterial growth ratio compared to few cycles. The biomass response of the microbial community differed from the growth response, with fungal and total biomass only being slightly negatively affected by the repeated drying-rewetting. The discrepancy between growth- and biomass-based assessments underscores that microbial responses to perturbations might previously have been misrepresented with biomass-based assessments. In light of this, many aspects of environmental microbial ecology may need to be revisited with attention to what measure of the microbial community is relevant to study.
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| 3. |
- Bengtsson, Göran, et al.
(författare)
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Microbial Diversity and PAH Catabolic Genes Tracking Spatial Heterogeneity of PAH Concentrations.
- 2012
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Ingår i: Microbial Ecology. - : Springer Science and Business Media LLC. - 1432-184X .- 0095-3628.
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Tidskriftsartikel (refereegranskat)abstract
- We analyzed the within-site spatial heterogeneity of microbial community diversity, polyaromatic hydrocarbon (PAH) catabolic genotypes, and physiochemical soil properties at a creosote contaminated site. Genetic diversity and community structure were evaluated from an analysis of denaturant gradient gel electrophoresis (DGGE) of polymerase chain reaction (PCR)-amplified sequences of 16S rRNA gene. The potential PAH degradation capability was determined from PCR amplification of a suit of aromatic dioxygenase genes. Microbial diversity, evenness, and PAH genotypes were patchily distributed, and hot and cold spots of their distribution coincided with hot and cold spots of the PAH distribution. The analyses revealed a positive covariation between microbial diversity, biomass, evenness, and PAH concentration, implying that the creosote contamination at this site promotes diversity and abundance. Three patchily distributed PAH-degrading genotypes, NAH, phnA, and pdo1, were identified, and their abundances were positively correlated with the PAH concentration and the fraction of soil organic carbon. The covariation of the PAH concentration with the number and spatial distribution of catabolic genotypes suggests that a field site capacity to degrade PAHs may vary with the extent of contamination.
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| 4. |
- Berggren, Martin, 1981-, et al.
(författare)
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Nutrient constraints on metabolism affect the temperature regulation of aquatic bacterial growth efficiency
- 2010
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Ingår i: Microbial Ecology. - : Springer. - 0095-3628 .- 1432-184X. ; 60:4, s. 894-902
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Tidskriftsartikel (refereegranskat)abstract
- Inorganic nutrient availability and temperature are recognized as major regulators of organic carbon processing by aquatic bacteria, but little is known about how these two factors interact to control bacterial metabolic processes. We manipulated the temperature of boreal humic stream water samples within 0–25°C and measured bacterial production (BP) and respiration (BR) with and without inorganic nitrogen + phosphorus addition. Both BP and BR increased exponentially with temperature in all experiments, with Q 10 values varying between 1.2 and 2.4. The bacterial growth efficiency (BGE) showed strong negative relationships with temperature in nutrient-enriched samples and in natural stream water where community-level BP and BR were not limited by nutrients. However, there were no relationships between BGE and temperature in samples where BP and BR were significantly constrained by the inorganic nutrient availability. The results suggest that metabolic responses of aquatic bacterial communities to temperature variations can be strongly dependent on whether the bacterial metabolism is limited by inorganic nutrients or not. Such responses can have consequences for both the carbon flux through aquatic food webs and for the flux of CO2 from aquatic systems to the atmosphere.
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| 5. |
- Damiani, Claudia, et al.
(författare)
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Mosquito-Bacteria Symbiosis : The Case of Anopheles gambiae and Asaia
- 2010
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Ingår i: Microbial Ecology. - : Springer Science and Business Media LLC. - 0095-3628 .- 1432-184X. ; 60:3, s. 644-654
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Tidskriftsartikel (refereegranskat)abstract
- The symbiotic relationship between Asaia, an alpha-proteobacterium belonging to the family Acetobacteriaceae, and mosquitoes has been studied mainly in the Asian malaria vector Anopheles stephensi. Thus, we have investigated the nature of the association between Asaia and the major Afro-tropical malaria vector Anopheles gambiae. We have isolated Asaia from different wild and laboratory reared colonies of A. gambiae, and it was detected by PCR in all the developmental stages of the mosquito and in all the specimens analyzed. Additionally, we have shown that it localizes in the midgut, salivary glands and reproductive organs. Using recombinant strains of Asaia expressing fluorescent proteins, we have demonstrated the ability of the bacterium to colonize A. gambiae mosquitoes with a pattern similar to that described for A. stephensi. Finally, fluorescent in situ hybridization on the reproductive tract of females of A. gambiae showed a concentration of Asaia at the very periphery of the eggs, suggesting that transmission of Asaia from mother to offspring is likely mediated by a mechanism of egg-smearing. We suggest that Asaia has potential for use in the paratransgenic control of malaria transmitted by A. gambiae.
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| 6. |
- Edberg, Frida, et al.
(författare)
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Bacterial Community Composition in the Water Column of a Lake Formed by a Former Uranium Open Pit Mine
- 2012
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Ingår i: Microbial Ecology. - : Springer Science and Business Media LLC. - 0095-3628 .- 1432-184X. ; 64:4, s. 870-880
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Tidskriftsartikel (refereegranskat)abstract
- Mining of pyrite minerals is a major environmental issue involving both biological and geochemical processes. Here we present a study of an artificial lake of a former uranium open pit mine with the aim to connect the chemistry and bacterial community composition (454-pyrosequencing of 16S rRNA genes) in the stratified water column. A shift in the water chemistry from oxic conditions in the epilimnion to anoxic, alkaline, and metal and sulfide-rich conditions in the hypolimnion was corresponded by a strong shift in the bacterial community, with few shared operational taxonomic units (OTU) between the water layers. The epilimnetic bacterial community of the lake (~20 years old) showed similarities to other temperate freshwater lakes, while the hypolimnetic bacterial community showed similarity to extreme chemical environments. The epilimnetic bacterial community had dominance of Actinobacteria and Betaproteobacteria. The hypolimnion displayed a higher bacterial diversity and was dominated by the phototrophic green sulphur bacterium of the genus Chlorobium (ca. 40 % of the total community). Deltaproteobacteria were only represented in the hypolimnion and the most abundant OTUs were affiliated with ferric iron and sulfate reducers of the genus Geobacter and Desulfobulbus, respectively. The chemistry is clearly controlling, especially the hypolimnetic, bacterial community but the community composition also indicates that the bacteria are involved in metal cycling in the lake.
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| 7. |
- Fernandez, D. A., et al.
(författare)
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Effects of Water Stress, Organic Amendment and Mycorrhizal Inoculation on Soil Microbial Community Structure and Activity During the Establishment of Two Heavy Metal-Tolerant Native Plant Species
- 2012
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Ingår i: Microbial Ecology. - : Springer Science and Business Media LLC. - 1432-184X .- 0095-3628. ; 63:4, s. 794-803
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Tidskriftsartikel (refereegranskat)abstract
- Our aim was to examine the effect of water stress on plant growth and development of two native plant species (Tetraclinis articulata and Crithmum maritimum) and on microbial community composition and activity in the rhizosphere soil, following the addition of an organic amendment, namely sugar beet residue (SBR), and/or the inoculation with an arbuscular mycorrhizal (AM) fungus, namely Glomus mosseae, in a non-sterile heavy metal-polluted soil. The AM inoculation did not have any significant effect on plant growth of both species. In T. articulata, SBR increased shoot growth, foliar P, total phospholipid fatty acids (PLFA), fungi-related PLFA, AM fungi-related neutral lipid fatty acid, bacterial gram-positive/gram-negative PLFA ratio and the beta-glucosidase and dehydrogenase activities. SBR and AM inoculation increased phosphatase activity in T. articulata plants grown under drought conditions. In both plants, there was a synergistic effect between AM inoculation and SBR on mycorrhizal colonisation under drought conditions. In C. maritimum, the increase produced by the SBR on total amounts of PLFA, bacterial gram-positive-related PLFA and bacterial gram-negative-related PLFA was considerably higher under drought conditions. Our results suggest that the effectiveness of the amendment with regard to stimulating microbial communities and plant growth was largely limited by drought, particularly for plant species with a low degree of mycorrhizal colonisation.
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| 8. |
- Holmfeldt, Karin, 1980-, et al.
(författare)
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Virus Production and Lysate Recycling in Different Sub-basins of the Northern Baltic Sea
- 2010
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Ingår i: Microbial Ecology. - : Springer Science and Business Media LLC. - 0095-3628 .- 1432-184X. ; 60:3, s. 572-580
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Tidskriftsartikel (refereegranskat)abstract
- In the Gulf of Bothnia, northern Baltic Sea, a large freshwater inflow creates north-southerly gradients in physico-chemical and biological factors across the two sub-basins, the Bothnian Bay (BB) and the Bothnian Sea. In particular, the sub-basins differ in nutrient limitation (nitrogen vs. phosphorus; P). Since viruses are rich in P, and virus production is commonly connected with bacterial abundance and growth, we hypothesized that the role of viral lysis differs between the sub-basins. Thus, we examined virus production and the potential importance of lysate recycling in surface waters along a transect in the Gulf of Bothnia. Surprisingly, virus production and total P were negatively correlated. In the BB, virus production rates were double those elsewhere in the system, although bacterial abundance and production were the lowest. In the BB, virus-mediated cell lysates could account for 70-180% and 100-250% of the bacterial carbon and P demand, respectively, while only 4-15% and 8-21% at the other stations. Low concentrations of dissolved DNA (D-DNA) with a high proportion of encapsulated DNA (viruses) in the BB suggested rapid turnover and high uptake of free DNA. The correlation of D-DNA and total P indicates that D-DNA is a particularly important nutrient source in the P-limited BB. Our study demonstrates large and counterintuitive differences in virus-mediated recycling of carbon and nutrients in two basins of the Gulf of Bothnia, which differ in microbial community composition and nutrient limitation.
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| 9. |
- Jägevall, Sara, 1973, et al.
(författare)
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Abundance and Diversity of Biofilms in Natural and Artificial Aquifers of the Äspö Hard Rock Laboratory, Sweden
- 2011
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Ingår i: Microbial Ecology. - : Springer Science and Business Media LLC. - 0095-3628 .- 1432-184X. ; 61, s. 410-422
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Tidskriftsartikel (refereegranskat)abstract
- Six cores were drilled and retrieved from 186-m12 depth in the Äspö Hard Rock Laboratory (HRL) tunnel to13 investigate whether indigenous biofilms develop on fracture14 surfaces in groundwater-conducting aquifers in granitic15 rock. A clone library was constructed from fracture surface16 material (FSM), for community composition analysis.17 Quantitative polymerase chain reaction (qPCR) was appliedQ1 18 to quantify gene copies using the 16S rRNA gene for19 domain Bacteria and the adenosine-phosphosulfate reduc-Q1 20 tase gene (apsA) for sulfate-reducing bacteria (SRB).21 Results were compared with three groundwater systems22 with biofilms in laminar flow reactors (LFRs) at 450-m23 depth in the Äspö HRL. The total number of cells, counted24 microscopically, was approximately 2×105 cells·cm–2 in the25 LFR systems, consistent with the obtained qPCR 16S rRNA26 gene copies. qPCR analysis reported ∼1×102 up to ∼1×10427 gene copies·cm–2 on the FSM from the drill cores. In the28 FSM biofilms, 33% of the sequenced clones were related to29 the iron-reducing bacterium Stenotrophomonas maltophilia,30 while in the LFR biofilms, 41% of the sequenced clones31 were affiliated with the genera Desulfovibrio, Desulforho-32 palus, Desulfomicrobium, and Desulfobulbus. The commu-33 nity composition of the FSM biofilms differed from thedrill water community, excluding drill water contamination. 34This work reports significant numbers of microorganisms 35on natural hard rock aquifer fracture surfaces with site- 36specific community compositions. The probability that 37biofilms are generally present in groundwater-conducting 38aquifers in deep granitic rock is consequently great.
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| 10. |
- Karlsson, Fredrik, 1984, et al.
(författare)
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A Closer Look at Bacteroides: Phylogenetic Relationship and Genomic Implications of a Life in the Human Gut
- 2011
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Ingår i: Microbial Ecology. - : Springer Science and Business Media LLC. - 0095-3628 .- 1432-184X. ; 61:3, s. 473-485
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Tidskriftsartikel (refereegranskat)abstract
- The human gut is extremely densely inhabited by bacteria mainly from two phyla, Bacteroidetes and Firmicutes, and there is a great interest in analyzing whole-genome sequences for these species because of their relation to human health and disease. Here, we do whole-genome comparison of 105 Bacteroidetes/Chlorobi genomes to elucidate their phylogenetic relationship and to gain insight into what is separating the gut living Bacteroides and Parabacteroides genera from other Bacteroidetes/Chlorobi species. A comprehensive analysis shows that Bacteroides species have a higher number of extracytoplasmic function sigma factors (ECF sigma factors) and two component systems for extracellular signal transduction compared to other Bacteroidetes/Chlorobi species. A whole-genome phylogenetic analysis shows a very little difference between the Parabacteroides and Bacteroides genera. Further analysis shows that Bacteroides and Parabacteroides species share a large common core of 1,085 protein families. Genome atlases illustrate that there are few and only small unique areas on the chromosomes of four Bacteroides/Parabacteroides genomes. Functional classification to clusters of othologus groups show that Bacteroides species are enriched in carbohydrate transport and metabolism proteins. Classification of proteins in KEGG metabolic pathways gives a detailed view of the genome's metabolic capabilities that can be linked to its habitat. Bacteroides pectinophilus and Bacteroides capillosus do not cluster together with other Bacteroides species, based on analysis of 16S rRNA sequence, whole-genome protein families and functional content, 16S rRNA sequences of the two species suggest that they belong to the Firmicutes phylum. We have presented a more detailed and precise description of the phylogenetic relationships of members of the Bacteroidetes/Chlorobi phylum by whole genome comparison. Gut living Bacteroides have an enriched set of glycan, vitamin, and cofactor enzymes important for diet digestion.
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