| 1. |
- Börjesson, Gunnar, et al.
(författare)
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Microbial oxidation of CH4 at high partial pressures in an organic landfill cover soil under different moisture regimes
- 1998
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Ingår i: FEMS Microbiology Ecology. - 0168-6496. ; 26:3, s. 207-217
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Tidskriftsartikel (refereegranskat)abstract
- The uptake and utilization of CH4 at high concentrations (5-18% vol.) and different soil moistures were followed for samples from a landfill cover soil with a high organic matter content. Measurements of the utilization of CH4 and O2, and production of CO2 indicated that the activity of methanotrophic organisms accounted for most of the O2 respiration. At water saturation, CH4 oxidation rates decreased with time, probably because NH4/+ accumulated. Denitrification rates, estimated based on both N2 and N2O production, were positively related to soil moisture and only slightly influenced by the extent of CH4 oxidation. Total phospholipid fatty acid concentrations increased, and concentrations of phospholipid fatty acids, typical for obligate methanotrophic bacteria (e.g. 16:1ω8 and 18:1ω8), increased in the CH4-amended samples, indicating growth of both type I and type II methanotrophs.
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| 2. |
- Olsson, Pål Axel, et al.
(författare)
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Interactions between ectomycorrhizal fungi and the bacterial community in soils amended with various primary minerals
- 1998
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Ingår i: FEMS Microbiology Ecology. - 0168-6496. ; 27:2, s. 195-205
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Tidskriftsartikel (refereegranskat)abstract
- The influence of ectomycorrhizal fungi on the soil bacterial community was studied by growing pine seedlings in artificial soils consisting of a peat/sand mixture amended with microcline, biotite or apatite. In the microcline-amended and unamended soils both Suillus variegatus and Paxillus involutus reduced bacterial activity as measured by thymidine incorporation. S. variegatus grew best in the biotite soil, where it increased both bacterial activity and biomass as measured by microscopic counts and specific bacterial fatty acids. Further, the positive influence of S. variegatus on the bacteria in the biotite soil modified the bacterial community, as reflected in the bacteria-specific phospholipid fatty acid composition. The increases in bacterial biomass and activity and changes in the bacterial community induced by S. variegatus may be due to the production of organic substances by this fungus, as indicated by an 10-fold increase in soil-solution citric acid. Two isolates of S. variegatus and an unidentified ectomycorrhizal fungus all tended to stimulate bacterial activity in the apatite-amended soil in compartments isolated from roots by a mesh. We conclude that the same ectomycorrhizal fungus may stimulate bacterial growth under certain conditions and inhibit bacterial growth under other conditions. Copyright (C) 1998 Federation of European Microbiological Societies.
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| 3. |
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| 4. |
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| 5. |
- Langenheder, Silke, et al.
(författare)
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Salinity as a structuring factor for the composition and performance of bacterioplankton degrading riverine DOC
- 2003
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Ingår i: FEMS Microbiology Ecology. - 0168-6496 .- 1574-6941. ; 45:2, s. 189-202
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Tidskriftsartikel (refereegranskat)abstract
- The impact of salinity on the composition and functional performance (biomass production, growth efficiency and growth rates) of bacterial communities was investigated using batch cultures growing on dissolved organic carbon from a river draining into the Northern Baltic Sea. The cultures were adjusted to riverine or estuarine salinity levels and inoculated with bacteria from these two environments. Bacterial growth efficiencies differed in response to salinity and the origin of the inoculum. When salinity was adjusted to correspond to the salinity at the site where the inoculum was retrieved, growth efficiency was relatively high (11.5 +/- 2.6%). However, when bacteria were confronted with a shift in salinity, growth efficiency was lower (7.5 +/- 2.0%) and more of the utilized carbon was respired. In contrast, growth rates were higher when bacteria were exposed to a change in salinity. The composition of the bacterial communities developing in the batch cultures differed, as shown by 16S rDNA DGGE, depending on the origin of the inoculum and salinity. Reverse and direct DNA-DNA hybridization revealed salinity optima in the growth of specific bacterial strains as well as broader phylogenetic groups. Strains belonging to the alpha- and beta-Proteobacteria, Actinobacteria and gamma-Proteobacteria other than the genus Pseudomonas showed higher relative abundance under freshwater conditions, whereas strains of the genus Pseudomonas and the Cytophaga-Flavobacterium-Bacteroides group were favored by estuarine conditions. Generally, our results demonstrate functional changes associated with changes in community composition. We suggest that even moderate changes in salinity affect bacterial community composition, which subsequently leads to altered growth characteristics. (C) 2003 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.
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| 6. |
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| 7. |
- Wikner, Johan, 1961-, et al.
(författare)
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NUCLEIC-ACIDS FROM THE HOST BACTERIUM AS A MAJOR SOURCE OF NUCLEOTIDES FOR 3 MARINE BACTERIOPHAGES
- 1993
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Ingår i: FEMS Microbiology Ecology. - Amsterdam : Elsevier. - 0168-6496 .- 1574-6941. ; 12:4, s. 237-248
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Tidskriftsartikel (refereegranskat)abstract
- The incorporation of P-32-phosphorus into marine bacteriophage nucleic acid was studied in culture experiments to investigate the source of nucleotides used by the phage. We consistently found that the P-32-specific activity in the phage genome increased during the 11 h incubation and was low relative to the specific activity in the medium, averaging 21% (+/- SD 5.9) for the three phage isolates. This was in accordance with a mathematical model where most of the nucleotides for phage DNA synthesis were derived from the host cell nucleic acid rather than de novo synthesis. We propose that this metabolic strategy may be common among marine phages, as an adaptation to a nutrient poor environment. Consequently, the contribution of free DNA to the dissolved fraction through phage lysis of bacteria, may be less that previously thought. Also during radiolabelling of bacteriophages in natural water samples, isotope dilution may be dependent on the specific growth rate of the bacterial host.
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| 8. |
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| 9. |
- Adomas, Aleksandra, et al.
(författare)
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Identification and analysis of differentially expressed cDNAs during nonself-competitive interaction between Phlebiopsis gigantea and Heterobasidion parviporum
- 2006
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Ingår i: FEMS Microbiology Ecology. - : Blackwell Publishing. - 0168-6496 .- 1574-6941. ; 57:1, s. 26-39
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Tidskriftsartikel (refereegranskat)abstract
- The molecular factors regulating interspecific interaction between the saprotrophic biocontrol fungus Phlebiopsis gigantea and the conifer pathogen Heterobasidion parviporum were investigated. We constructed cDNA libraries and used expressed sequence tag analysis for the identification and characterization of genes expressed during the self and nonself-hyphal interaction. cDNA clones from either the pathogen or biocontrol agent were arrayed on nylon membrane filters and differentially screened with cDNA probes made from mycelia forming the barrage zone during nonself-interactions, mycelia growing outside the barrage zones or monocultures. BlastX analysis of the differentially expressed clones led to the identification of genes with diverse functions, including those with potential as virulence factors, such as hydrophobins. Because of the high sequence conservation (r2 = 0.81) between P. gigantea and H. parviporum, a selected number of genes from either fungus were used to monitor the expression profile under varying interaction conditions by virtual northern blot. The results are discussed with respect to the potential role of the induced genes during the nonself-competitive interaction for space and nutrients between P. gigantea and H. parviporum.
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| 10. |
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| 11. |
- Asari, Shashidar, et al.
(författare)
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Multiple effects of Bacillus amyloliquefaciens volatile compounds: plant growth promotion and growth inhibition of phytopathogens
- 2016
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Ingår i: FEMS Microbiology Ecology. - : Oxford University Press (OUP). - 0168-6496 .- 1574-6941. ; 92
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Tidskriftsartikel (refereegranskat)abstract
- Biotic interactions through volatile organic compounds (VOC) are frequent in nature. This investigation aimed to study the role of Bacillus VOC for the beneficial effects on plants observed as improved growth and pathogen control. Four Bacillus amyloliquefaciens subsp. plantarum strains were screened for VOC effects on Arabidopsis thaliana Col-0 seedlings and Brassica fungal phytopathogens. VOC from all four Bacillus strains could promote growth of Arabidopsis plants resulting in increased shoot biomass but the effects were dependent on the growth medium. Dose response studies with UCMB5113 on MS agar with or without root exudates showed significant plant growth promotion even at low levels of bacteria. Bacillus VOC antagonized growth of several fungal pathogens in vitro. However, the plant growth promotion efficacy and fungal inhibition potency varied among the Bacillus strains. VOC inhibition of several phytopathogens indicated efficient microbial antagonism supporting high rhizosphere competence of the Bacillus strains. GC-MS analysis identified several VOC structures where the profiles differed depending on the growth medium. The ability of Bacillus strains to produce both volatile and soluble compounds for plant growth promotion and disease biocontrol provides examples of rhizosphere microbes as an important ecosystem service with high potential to support sustainable crop production.
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| 12. |
- Bagnoud, Alexandre, et al.
(författare)
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A minimalistic microbial food web in an excavated deep subsurface clay rock
- 2016
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Ingår i: FEMS Microbiology Ecology. - : Oxford University Press. - 0168-6496 .- 1574-6941. ; 92:1
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Tidskriftsartikel (refereegranskat)abstract
- Clay rocks are being considered for radioactive waste disposal, but relatively little is known about the impact of microbes on the long-term safety of geological repositories. Thus, a more complete understanding of microbial community structure and function in these environments would provide further detail for the evaluation of the safety of geological disposal of radioactive waste in clay rocks. It would also provide a unique glimpse into a poorly studied deep subsurface microbial ecosystem. Previous studies concluded that microorganisms were present in pristine Opalinus Clay, but inactive. In this work, we describe the microbial community and assess the metabolic activities taking place within borehole water. Metagenomic sequencing and genome-binning of a porewater sample containing suspended clay particles revealed a remarkably simple heterotrophic microbial community, fueled by sedimentary organic carbon, mainly composed of two organisms: a Pseudomonas sp. fermenting bacterium growing on organic macromolecules and releasing organic acids and H-2, and a sulfate-reducing Peptococcaceae able to oxidize organic molecules to CO2. In Opalinus Clay, this microbial system likely thrives where pore space allows it. In a repository, this may occur where the clay rock has been locally damaged by excavation or in engineered backfills.
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| 13. |
- Bahram, Mohammad
(författare)
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Bacterial community dynamics across developmental stages of fungal fruiting bodies
- 2020
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Ingår i: FEMS Microbiology Ecology. - : Oxford University Press (OUP). - 0168-6496 .- 1574-6941. ; 96
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Tidskriftsartikel (refereegranskat)abstract
- Increasing evidence suggest that bacteria form diverse communities in various eukaryotic hosts, including fungi. However, little is known about their succession and the functional potential at different host development stages. Here we examined the effect of fruiting body parts and developmental stages on the structure and potential function of fungus-associated bacterial communities. Using high-throughput sequencing, we characterized bacterial communities and their associated potential functions in fruiting bodies from ten genera belonging to four major mushroom-forming orders and three different developmental stages of a model host species Cantharellus cibarius. Our results demonstrate that bacterial community structure differs between internal and external parts of the fruiting body but not between inner tissues. The structure of the bacterial communities showed significant variation across fruiting body developmental stages. We provide evidence that certain functional groups, such as those related to nitrogen fixation, persist in fruiting bodies during the maturation, but are replaced by putative parasites/pathogens afterwards. These data suggest that bacterial communities inhabiting fungal fruiting bodies may play important roles in their growth and development.
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| 14. |
- Baltar, Federico, et al.
(författare)
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Response of rare, common and abundant bacterioplankton to anthropogenic perturbations in a Mediterranean coastal site
- 2015
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Ingår i: FEMS Microbiology Ecology. - : Oxford University Press (OUP). - 0168-6496 .- 1574-6941. ; 91:6
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Tidskriftsartikel (refereegranskat)abstract
- Bacterioplankton communities are made up of a small set of abundant taxa and a large number of low-abundant organisms (i.e. 'rare biosphere'). Despite the critical role played by bacteria in marine ecosystems, it remains unknown how this large diversity of organisms are affected by human-induced perturbations, or what controls the responsiveness of rare compared to abundant bacteria. We studied the response of a Mediterranean bacterioplankton community to two anthropogenic perturbations (i.e. nutrient enrichment and/or acidification) in two mesocosm experiments (in winter and summer). Nutrient enrichment increased the relative abundance of some operational taxonomic units (OTUs), e.g. Polaribacter, Tenacibaculum, Rhodobacteraceae and caused a relative decrease in others (e.g. Croceibacter). Interestingly, a synergistic effect of acidification and nutrient enrichment was observed on specific OTUs (e.g. SAR86). We analyzed the OTUs that became abundant at the end of the experiments and whether they belonged to the rare (<0.1% of relative abundance), the common (0.1-1.0% of relative abundance) or the abundant (>1% relative abundance) fractions. Most of the abundant OTUs at the end of the experiments were abundant, or at least common, in the original community of both experiments, suggesting that ecosystem alterations do not necessarily call for rare members to grow.
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| 15. |
- Barreiro, Ana, et al.
(författare)
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Small-scale agricultural grassland management can affect soil fungal community structure as much as continental scale geographic patterns
- 2021
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Ingår i: FEMS Microbiology Ecology. - : Oxford University Press (OUP). - 0168-6496 .- 1574-6941. ; 97
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Tidskriftsartikel (refereegranskat)abstract
- A European transect was established, ranging from Sweden to the Azores, to determine the relative influence of geographic factors and agricultural small-scale management on the grassland soil microbiome. Within each of five countries (factor ‘Country’), which maximized a range of geographic factors, two differing growth condition regions (factor ‘GCR’) were selected: a favorable region with conditions allowing for high plant biomass production and a contrasting less favorable region with a markedly lower potential. Within each region, grasslands of contrasting management intensities (factor ‘MI’) were defined: intensive and extensive, from which soil samples were collected. Across the transect, ‘MI’ was a strong differentiator of fungal community structure, having a comparable effect to continental scale geographic factors (‘Country’). ‘MI’ was also a highly significant driver of bacterial community structure, but ‘Country’ was clearly the stronger driver. For both, ‘GCR’ was the weakest driver. Also at the regional level, strong effects of MI occurred on various measures of the soil microbiome (i.e. OTU richness, management-associated indicator OTUs), though the effects were largely regional-specific. Our results illustrate the decisive influence of grassland MI on soil microbial community structure, over both regional and continental scales, and, thus, highlight the importance of preserving rare extensive grasslands.
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| 16. |
- Baskaran, Preetisri, et al.
(författare)
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Nitrogen dynamics of decomposing Scots pine needle litter depends on colonizing fungal species
- 2019
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Ingår i: FEMS Microbiology Ecology. - : Oxford University Press. - 0168-6496 .- 1574-6941. ; 95:6
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Tidskriftsartikel (refereegranskat)abstract
- In boreal ecosystems plant production is often limited by low availability of nitrogen. Nitrogen retention in below-ground organic pools plays an important role in restricting recirculation to plants and thereby hampers forest production. Saprotrophic fungi are commonly assigned to different decomposer strategies, but how these relate to nitrogen cycling remains to be understood. Decomposition of Scots pine needle litter was studied in axenic microcosms with the ligninolytic litter decomposing basidiomycete Gymnopus androsaceus or the stress tolerant ascomycete Chalara longipes. Changes in chemical composition were followed by 13C CP/MAS NMR spectroscopy and nitrogen dynamics was assessed by the addition of a 15N tracer. Decomposition by C. longipes resulted in nitrogen retention in non-hydrolysable organic matter, enriched in aromatic and alkylic compounds, whereas the ligninolytic G. androsaceus was able to access this pool, counteracting nitrogen retention. Our observations suggest that differences in decomposing strategies between fungal species play an important role in regulating nitrogen retention and release during litter decomposition, implying that fungal community composition may impact nitrogen cycling at the ecosystem level.
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| 17. |
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| 18. |
- Bengtson, Per, et al.
(författare)
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Bacterial immobilization and remineralization of N at different growth rates and N concentrations
- 2005
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Ingår i: FEMS Microbiology Ecology. - : Oxford University Press (OUP). - 1574-6941 .- 0168-6496. ; 54:1, s. 13-19
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Tidskriftsartikel (refereegranskat)abstract
- An experiment was designed to resolve two largely unaddressed questions about the turnover of N in soils. One is the influence of microbial growth rate on mobilization and remineralization of cellular N. The other is to what extent heterotrophic immobilization of NO3- is controlled by the soil concentration of NH4+. Bacteria were extracted from a deciduous forest soil and inoculated into an aqueous medium. Various N pool dilution/enrichment experiments were carried out to: (1) calculate the gross N immobilization and remineralization rates; (2) investigate their dependence on NH4+ and NO3- concentrations; (3) establish the microbial preference for NH4+ and NO3- depending on the NH4+/NO3- concentration ratio. Remineralization of microbial N occurred mainly at high growth rates and NH4+ concentrations. There was a positive correlation between NH4+ immobilization and remineralization rates, and intracellular recycling of N seemed to be an efficient way for bacteria to withstand low inorganic N concentrations. Thus, extensive remineralization of microbial N is likely to occur only when environmental conditions promote high growth rates. The results support previous observations of high NO3- immobilization rates, especially at low NH4+ concentrations, but NO3- was also immobilized at high NH4 concentrations. The latter can be understood if part of the microbial community has a preference for NO3- over NH4+ (c) 2005 Federation of European Microbiological Societies. Published by Elsevier B.V. All rights reserved.
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| 19. |
- Bengtson, Per, et al.
(författare)
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Links between methanotroph community composition and CH(4) oxidation in a pine forest soil
- 2009
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Ingår i: FEMS Microbiology Ecology. - : Oxford University Press (OUP). - 1574-6941 .- 0168-6496. ; 70:3, s. 356-366
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Tidskriftsartikel (refereegranskat)abstract
- The main gap in our knowledge about what determines the rate of CH(4) oxidation in forest soils is the biology of the microorganisms involved, the identity of which remains unclear. In this study, we used stable-isotope probing (SIP) following (13)CH(4) incorporation into phospholipid fatty acids (PLFAs) and DNA/RNA, and sequencing of methane mono-oxygenase (pmoA) genes, to identify the influence of variation in community composition on CH(4) oxidation rates. The rates of (13)C incorporation into PLFAs differed between horizons, with low (13)C incorporation in the organic soil and relatively high (13)C incorporation into the two mineral horizons. The microbial community composition of the methanotrophs incorporating the (13)C label also differed between horizons, and statistical analyses suggested that the methanotroph community composition was a major cause of variation in CH(4) oxidation rates. Both PLFA and pmoA-based data indicated that CH(4) oxidizers in this soil belong to the uncultivated 'upland soil cluster alpha'. CH(4) oxidation potential exhibited the opposite pattern to (13)C incorporation, suggesting that CH(4) oxidation potential assays may correlate poorly with in situ oxidation rates. The DNA/RNA-SIP assay was not successful, most likely due to insufficient (13)C-incorporation into DNA/RNA. The limitations of the technique are briefly discussed.
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| 20. |
- Bentzon-Tilia, Mikkel, et al.
(författare)
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Cultivation and isolation of N2-fixing bacteria from suboxic waters in the Baltic Sea
- 2014
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Ingår i: FEMS Microbiology Ecology. - : Oxford University Press (OUP). - 0168-6496 .- 1574-6941. ; 88:2, s. 358-371
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Tidskriftsartikel (refereegranskat)abstract
- Nitrogenase genes (nifH) from heterotrophic dinitrogen (N-2)-fixing bacteria appear ubiquitous in marine bacterioplankton, but the significance of these bacteria for N cycling is unknown. Quantitative data on the N-2-fixation potential of marine and estuarine heterotrophs are scarce, and the shortage of cultivated specimens currently precludes ecophysiological characterization of these bacteria. Through the cultivation of diazotrophs from suboxic (1.79molO(2)L(-1)) Baltic Sea water in an artificial seawater medium devoid of combined N, we report the cultivability of a considerable fraction of the diazotrophic community in the Gotland Deep. Two nifH clades were present both in situ and in enrichment cultures showing gene abundances of up to 4.6x10(5) and 5.8x10(5)nifH gene copies L-1 within two vertical profiles in the Baltic Sea. The distributions of the two clades suggested a relationship with the O-2 concentrations in the water column as abundances increased in the suboxic and anoxic waters. It was possible to cultivate and isolate representatives from one of these prevalent clades, and preliminary analysis of their ecophysiology demonstrated growth optima at 0.5-15molO(2)L(-1) and 186-194molO(2)L(-1) in the absence of combined N.
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| 21. |
- Berckx, Fede
(författare)
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Genome analysis and biogeographic distribution of the earliest divergent Frankia clade in the southern hemisphere
- 2024
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Ingår i: FEMS Microbiology Ecology. - 0168-6496 .- 1574-6941. ; 100
-
Tidskriftsartikel (refereegranskat)abstract
- Coriariaceae are a small plant family of 14-17 species and subspecies that currently have a global but disjunct distribution. All species can form root nodules in symbiosis with diazotrophic Frankia cluster-2 strains, which form the earliest divergent symbiotic clade within this bacterial genus. Studies on Frankia cluster-2 mostly have focused on strains occurring in the northern hemisphere. Except for one strain from Papua New Guinea, namely Candidatus Frankia meridionalis Cppng1, no complete genome of Frankia associated with Coriaria occurring in the southern hemisphere has been published thus far, yet the majority of the Coriariaceae species occur here. We present field sampling data of novel Frankia cluster-2 strains, representing two novel species, which are associated with Coriaria arborea and Coriaria sarmentosa in New Zealand, and with Coriaria ruscifolia in Patagonia (Argentina), in addition to identifying Ca. F. meridionalis present in New Zealand. The novel Frankia species were found to be closely related to both Ca. F. meridionalis, and a Frankia species occurring in the Philippines, Taiwan, and Japan. Our data suggest that the different Frankia cluster-2 species diverged early after becoming symbiotic circa 100 million years ago.
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| 22. |
- Berckx, Fede, 1993-, et al.
(författare)
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Genome analysis and biogeographic distribution of the earliest divergent Frankia clade in the southern hemisphere
- 2024
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Ingår i: FEMS Microbiology Ecology. - 0168-6496 .- 1574-6941. ; 100:5
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Tidskriftsartikel (refereegranskat)abstract
- Coriariaceae are a small plant family of 14–17 species and subspecies that currently have a global but disjunct distribution. All species can form root nodules in symbiosis with diazotrophic Frankia cluster-2 strains, which form the earliest divergent symbiotic clade within this bacterial genus. Studies on Frankia cluster-2 mostly have focused on strains occurring in the northern hemisphere. Except for one strain from Papua New Guinea, namely Candidatus Frankia meridionalis Cppng1, no complete genome of Frankia associated with Coriaria occurring in the southern hemisphere has been published thus far, yet the majority of the Coriariaceae species occur here. We present field sampling data of novel Frankia cluster-2 strains, representing two novel species, which are associated with Coriaria arborea and Coriaria sarmentosa in New Zealand, and with Coriaria ruscifolia in Patagonia (Argentina), in addition to identifying Ca. F. meridionalis present in New Zealand. The novel Frankia species were found to be closely related to both Ca. F. meridionalis, and a Frankia species occurring in the Philippines, Taiwan, and Japan. Our data suggest that the different Frankia cluster-2 species diverged early after becoming symbiotic circa 100 million years ago.
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| 23. |
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| 24. |
- Björk, Robert G., 1974, et al.
(författare)
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Contrasting effects of wood ash application on microbial community structure, biomass and processes in drained forested peatlands
- 2010
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Ingår i: FEMS Microbiology Ecology. - : Oxford University Press (OUP). - 1574-6941 .- 0168-6496. ; 73:3, s. 550-562
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Tidskriftsartikel (refereegranskat)abstract
- The effects of wood ash application on soil microbial processes were investigated in three drained forested peatlands, which differed in nutrient status and time since application. Measured variables included concentrations of soil elements and phospholipid fatty acids (PLFAs), net nitrogen mineralisation, nitrification and denitrification enzyme activity, potential methane oxidation, methane production and microbial respiration kinetics. Wood ash application had a considerable influence on soil element concentrations. This mirrored a decrease in the majority of the microbial biomarkers by more than one-third in the two oligotrophic peatlands, although microbial community composition was not altered. The decreases in PLFAs coincided with reduced net ammonification and net nitrogen mineralisation. Other measured variables did not change systematically as a result of wood ash application. No significant changes in microbial biomass or processes were found in the mesotrophic peatland, possibly because too little time (1 year) had elapsed since the wood ash application. This study suggests that oligotrophic peatlands can be substantially affected by wood ash for a period of at least four years after application. However, within 25 years of the wood ash application, the microbial biomass seemed to have recovered or adapted to enhanced element concentrations in the soil.
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| 25. |
- Brandström Durling, Mikael, et al.
(författare)
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Deciphering the genome and secondary metabolome of the plant pathogen Fusarium culmorum
- 2018
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Ingår i: FEMS Microbiology Ecology. - : Oxford University Press (OUP). - 0168-6496 .- 1574-6941. ; 94
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Tidskriftsartikel (refereegranskat)abstract
- Fusarium culmorum is one of the most important fungal plant pathogens that causes diseases on a wide diversity of cereal and non-cereal crops. We report herein for the first time the genome sequence of F. culmorum strain PV and its associated secondary metabolome that plays a role in the interaction with other microorganisms and contributes to its pathogenicity on plants. The genome revealed the presence of two terpene synthases, trichodiene and longiborneol synthase, which generate an array of volatile terpenes. Furthermore, we identified two gene clusters, deoxynivalenol and zearalenone, which encode for the production of mycotoxins. Linking the production of mycotoxins with in vitro bioassays, we found high virulence of F. culmorum PV on maize, barley and wheat. By using ultra-performance liquid chromatography-mass spectrometry, we confirmed several compounds important for the behaviour and lifestyle of F. culmorum. This research sets the basis for future studies in microbe-plant interactions.
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| 26. |
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| 27. |
- Bugge Harder, Christoffer, et al.
(författare)
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Successional trophic complexity and biogeographical structure of eukaryotic communities in waterworks' rapid sand filters
- 2019
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Ingår i: FEMS Microbiology Ecology. - : Oxford University Press (OUP). - 0168-6496 .- 1574-6941. ; 95:11
-
Tidskriftsartikel (refereegranskat)abstract
- As groundwater-fed waterworks clean their raw inlet water with sand filters, a variety of pro-and eukaryotic microbial communities develop on these filters. While several studies have targeted the prokaryotic sand filter communities, little is known about the eukaryotic communities, despite the obvious need for knowledge of microorganisms that get in contact with human drinking water. With a new general eukaryotic primer set (18S, V1-V3 region), we performed FLX-454 sequencing of material from 21 waterworks' sand filters varying in age (3-40 years) and geographical location on a 250 km east-west axis in Denmark, and put the data in context of their previously published prokaryotic communities. We find that filters vary highly in trophic complexity depending on age, from simple systems with bacteria and protozoa (3-6 years) to complex, mature systems with nematodes, rotifers and turbellarians as apex predators (40 years). Unlike the bacterial communities, the eukaryotic communities display a clear distance-decay relationship that predominates over environmental variations, indicating that the underlying aquifers feeding the filters harbor distinct eukaryotic communities with limited dispersal in between. Our findings have implications for waterworks' filter management, and offer a window down to the largely unexplored eukaryotic microbiology of groundwater aquifers.
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| 28. |
- Börjesson, Gunnar, et al.
(författare)
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Microbial oxidation of CH4 at different temperatures in landfill cover soils
- 2004
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Ingår i: FEMS Microbiology Ecology. - : Oxford University Press (OUP). - 0168-6496 .- 1574-6941. ; 48:3, s. 305-312
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Tidskriftsartikel (refereegranskat)abstract
- Biological oxidation of CH4 is an important constraint on the emission of this gas from areas, such as landfills to the atmosphere. We studied the effect of temperature on methanotrophic bacteria in three different landfill cover soils, incubated in the laboratory. In samples of a young cover, consisting of wood chips and sewage sludge, the phospholipid fatty acids (PLFAs), regarded as biomarkers for type I methanotrophs (16:1?5t, 16:1?6c, 16:1?8c), primarily increased at low temperatures (5-10°C). On the other hand, the PLFA marker for type II methanotrophs (18:1?8c) was highly elevated only at 20°C. These results suggest that temperature can determine the selection of methanotroph populations. © 2004 Federation of European Microbiological Societies. Published by Elsevier B.V. All rights reserved.
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| 29. |
- Camenzind, Tessa, et al.
(författare)
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Arbuscular mycorrhizal fungal and soil microbial communities in African Dark Earths
- 2018
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Ingår i: FEMS Microbiology Ecology. - : Oxford University Press (OUP). - 0168-6496 .- 1574-6941. ; 94:4
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Tidskriftsartikel (refereegranskat)abstract
- The socio-economic values of fertile and carbon-rich Dark Earth soils are well described from the Amazon region. Very recently, Dark Earth soils were also identified in tropical West Africa, with comparable beneficial soil properties and plant growth-promoting effects. The impact of this management technique on soil microbial communities, however, is less well understood, especially with respect to the ecologically relevant group of arbuscular mycorrhizal (AM) fungi. Thus, we tested the hypotheses that (1) improved soil quality in African Dark Earth (AfDE) will increase soil microbial biomass and shift community composition and (2) concurrently increased nutrient availability will negatively affect AM fungal communities. Microbial communities were distinct in AfDE in comparison to adjacent sites, with an increased fungal:bacterial ratio of 71%, a pattern mainly related to shifts in pH. AM fungal abundance and diversity, however, did not differ despite clearly increased soil fertility in AfDE, with 3.7 and 1.7 times greater extractable P and total N content, respectively. The absence of detrimental effects on AM fungi, often seen following applications of inorganic fertilizers, and the enhanced role of saprobic fungi relevant for mineralization and C sequestration support previous assertions of this management type as a sustainable alternative agricultural practice.
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| 30. |
- Cantoran, Anahi, et al.
(författare)
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Defining a core microbial necrobiome associated with decomposing fungal necromass
- 2023
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Ingår i: FEMS Microbiology Ecology. - 0168-6496. ; 99:9
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Tidskriftsartikel (refereegranskat)abstract
- Despite growing interest in fungal necromass decomposition due to its importance in soil carbon retention, whether a consistent group of microorganisms is associated with decomposing necromass remains unresolved. Here, we synthesize knowledge on the composition of the bacterial and fungal communities present on decomposing fungal necromass from a variety of fungal species, geographic locations, habitats, and incubation times. We found that there is a core group of both bacterial and fungal genera (i.e. a core fungal necrobiome), although the specific size of the core depended on definition. Based on a metric that included both microbial frequency and abundance, we demonstrate that the core is taxonomically and functionally diverse, including bacterial copiotrophs and oligotrophs as well as fungal saprotrophs, ectomycorrhizal fungi, and both fungal and animal parasites. We also show that the composition of the core necrobiome is notably dynamic over time, with many core bacterial and fungal genera having specific associations with the early, middle, or late stages of necromass decomposition. While this study establishes the existence of a core fungal necrobiome, we advocate that profiling the composition of fungal necromass decomposer communities in tropical environments and other terrestrial biomes beyond forests is needed to fill key knowledge gaps regarding the global nature of the fungal necrobiome.
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| 31. |
- Carrier, Tyler J., et al.
(författare)
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Geographic location and food availability offer differing levels of influence on the bacterial communities associated with larval sea urchins
- 2019
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Ingår i: FEMS Microbiology Ecology. - : Oxford University Press (OUP). - 0168-6496 .- 1574-6941. ; 95:8
-
Tidskriftsartikel (refereegranskat)abstract
- © 2019 FEMS. Determining the factors underlying the assembly, structure, and diversity of symbiont communities remains a focal point of animal-microbiome research. Much of these efforts focus on taxonomic variation of microbiota within or between animal populations, but rarely test the proportional impacts of ecological components that may affect animal-associated microbiota. Using larvae from the sea urchin Strongylocentrotus droebachiensis from the Atlantic and Pacific Oceans, we test the hypothesis that, under natural conditions, inter-population differences in the composition of larval-associated bacterial communities are larger than intra-population variation due to a heterogeneous feeding environment. Despite significant differences in bacterial community structure within each S. droebachiensis larval population based on food availability, development, phenotype, and time, variation in OTU membership and community composition correlated more strongly with geographic location. Moreover, 20-30% of OTUs associated with larvae were specific to a single location while less than 10% were shared. Taken together, these results suggest that inter-populational variation in symbiont communities may be more pronounced than intra-populational variation, and that this difference may suggest that broad-scale ecological variables (e.g., across ocean basins) may mask smaller scale ecological variables (e.g., food availability).
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| 32. |
- Collin, Betty, 1976, et al.
(författare)
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Characteristics of potentially pathogenic vibrios from subtropical Mozambique compared with isolates from tropical India and boreal Sweden
- 2013
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Ingår i: Fems Microbiology Ecology. - : Oxford University Press (OUP). - 0168-6496 .- 1574-6941. ; 83:2, s. 255-264
-
Tidskriftsartikel (refereegranskat)abstract
- Reported outbreaks of Vibrio parahaemolyticus have increased worldwide, particularly in regions of high seafood consumption. In Mozambique, seafood constitutes an important food resource and diarrheal diseases are common among its inhabitants. Edible clams were collected in Maputo Bay during both the dry and rainy seasons, with the results showing the number of viable counts of vibrios in clams to peak during the latter. Vibrio parahaemolyticus was the predominant species identified among the isolated strains. Although only one of 109 total strains carried the tdh virulence gene, 69% of isolates showed evidence of hemolytic capacity when subjected to a functional test. Similar virulence patterns and biochemical properties were found in strains isolated from Indian and Swedish marine waters. Antibiotic resistance was, however, more pronounced in strains isolated from these latter two environments.
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| 33. |
- Collin, Betty, 1976-, et al.
(författare)
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Occurrence and potential pathogenesis of Vibrio cholerae, Vibrio parahaemolyticus and Vibrio vulnificus on the South Coast of Sweden
- 2011
-
Ingår i: FEMS Microbiology Ecology. - 0168-6496 .- 1574-6941. ; 78:2, s. 306-313
-
Tidskriftsartikel (refereegranskat)abstract
- During the summer of 2006, several wound infections - of which three were fatal caused by Vibrio cholerae were reported from patients who had been exposed to water from the Baltic Sea. Before these reports, we initiated a sampling project investigating the occurrence of potential human pathogenic V. cholerae, Vibrio vulnificus and Vibrio parahaemolyticus in The Sound between Sweden and Denmark. The Blue mussel (Mytilus edulis) was used as an indicator to follow the occurrence of vibrios over time. Molecular analyses showed high frequencies of the most potent human pathogenic Vibrio spp.; 53% of mussel samples were positive for V. cholerae (although none were positive for the cholera toxin gene), 63% for V. vulnificus and 79% for V. parahaemolyticus (of which 47% were tdh(+) and/or trh(+)). Viable vibrios were also isolated from the mussel meat and screened for virulence by PCR. The mortality of eukaryotic cells when exposed to bacteria was tested in vivo, with results showing that the Vibrio strains, independent of species and origin, were harmful to the cells. Despite severe infections and several deaths, no report on potential human pathogenic vibrios in this area had been published before this study.
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| 34. |
- Collin, Betty, 1976, et al.
(författare)
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Occurrence and potential pathogenesis of Vibrio cholerae, Vibrio parahaemolyticus and Vibrio vulnificus on the South Coast of Sweden
- 2011
-
Ingår i: FEMS MICROBIOLOGY ECOLOGY. - : Oxford University Press. - 0168-6496 .- 1574-6941. ; 78:2, s. 306-313
-
Tidskriftsartikel (refereegranskat)abstract
- During the summer of 2006, several wound infections - of which three were fatal - caused by Vibrio cholerae were reported from patients who had been exposed to water from the Baltic Sea. Before these reports, we initiated a sampling project investigating the occurrence of potential human pathogenic V. cholerae, Vibrio vulnificus and Vibrio parahaemolyticus in The Sound between Sweden and Denmark. The Blue mussel (Mytilus edulis) was used as an indicator to follow the occurrence of vibrios over time. Molecular analyses showed high frequencies of the most potent human pathogenic Vibrio spp.; 53% of mussel samples were positive for V. cholerae (although none were positive for the cholera toxin gene), 63% for V. vulnificus and 79% for V. parahaemolyticus (of which 47% were tdh(+) and/or trh(+)). Viable vibrios were also isolated from the mussel meat and screened for virulence by PCR. The mortality of eukaryotic cells when exposed to bacteria was tested in vivo, with results showing that the Vibrio strains, independent of species and origin, were harmful to the cells. Despite severe infections and several deaths, no report on potential human pathogenic vibrios in this area had been published before this study.
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| 35. |
- Costa, JL, et al.
(författare)
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Cyanobiont diversity within coralloid roots of selected cycad species
- 1999
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Ingår i: FEMS MICROBIOLOGY ECOLOGY. - : ELSEVIER SCIENCE BV. - 0168-6496. ; 28:1, s. 85-91
-
Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- The diversity and host specificity of the cyanobionts of several cycad species (Cycas circinalis L., C. rumphii Miq., Encephalartos lebomboensis I. Verd., E. villosus Lem., and Zamia pumila L.) collected in a botanical garden were examined using the tRNA(
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| 36. |
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| 37. |
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| 38. |
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| 39. |
- Daga-Quisbert, Jeanett, et al.
(författare)
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Analysis of the microbiome of the Bolivian high-altitude Lake Pastos Grandes
- 2023
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Ingår i: FEMS Microbiology Ecology. - : Oxford University Press (OUP). - 0168-6496 .- 1574-6941. ; 99:8
-
Tidskriftsartikel (refereegranskat)abstract
- Lake Pastos Grandes in Bolivia is mainly composed of salt flats, which are sporadically and only partially submerged during the wet season. In the present study, the chemical composition of water samples of the lake and some influent rivers was determined. We found that it is likely that the lake was influenced by the dilution of metals from ancient evaporites. We performed the first metagenomic studies of this lake. Analyses of shotgun metagenomics revealed that the relative abundances of Burkholderiales and Pseudomonadales were noteworthy in the water samples, whereas the archaea belonging to the Halobacteriales and Cyanobacteria from subsection III had high abundances in the salt flat. The eukaryotes Crustacea and Diatomea exhibited the highest abundances in the water samples. We investigated further the potential effect of human activities on the nitrogen cycle mobilization in the lake and the propagation of antimicrobial resistance genes. This is the first report about the cycle in the lake. Additionally, rifamycin resistance genes and genes related to efflux pumps, which are not considered a hazard when identified in metagenomes, had the uppermost relative abundances in all sampling points. We found that Lake Pastos Grandes hitherto does not show an appreciable influence by anthropogenic actions. The microbiome of Lake Pastos Grandes, including microbial distribution, the nitrogen cycle and antibiotic resistance genes, was analyzed.
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| 40. |
- de Vries, Franciska T., et al.
(författare)
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High turnover of fungal hyphae in incubation experiments
- 2009
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Ingår i: FEMS Microbiology Ecology. - : Oxford University Press (OUP). - 1574-6941 .- 0168-6496. ; 67:3, s. 389-396
-
Tidskriftsartikel (refereegranskat)abstract
- Soil biological studies are often conducted on sieved soils without the presence of plants. However, soil fungi build delicate mycelial networks, often symbiotically associated with plant roots (mycorrhizal fungi). We hypothesized that as a result of sieving and incubating without plants, the total fungal biomass decreases. To test this, we conducted three incubation experiments. We expected total and arbuscular mycorrhizal (AM) fungal biomass to be higher in less fertilized soils than in fertilized soils, and thus to decrease more during incubation. Indeed, we found that fungal biomass decreased rapidly in the less fertilized soils. A shift towards thicker hyphae occurred, and the fraction of septate hyphae increased. However, analyses of phospholipid fatty acids (PLFAs) and neutral lipid fatty acids could not clarify which fungal groups were decreasing. We propose that in our soils, there was a fraction of fungal biomass that was sensitive to fertilization and disturbance (sieving, followed by incubation without plants) with a very high turnover (possibly composed of fine hyphae of AM and saprotrophic fungi), and a fraction that was much less vulnerable with a low turnover (composed of saprotrophic fungi and runner hyphae of AMF). Furthermore, PLFAs might not be as sensitive in detecting changes in fungal biomass as previously thought.
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| 41. |
- Degerholm, Jenny, et al.
(författare)
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Phosphorus-limited growth dynamics in two Baltic Sea cyanobacteria, Nodularia sp and Aphanizomenon sp.
- 2006
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Ingår i: FEMS Microbiology Ecology. - : Oxford University Press (OUP). - 0168-6496 .- 1574-6941. ; 58:3, s. 323-332
-
Tidskriftsartikel (refereegranskat)abstract
- Rates of carbon (C) specific growth and nitrogen (N(2)) fixation were monitored in cultures of Baltic Sea Nodularia and Aphanizomenon exposed to gradual limitation by inorganic phosphorus (P). Both cyanobacteria responded by decreased cellular P content followed by lowered rates of growth and N(2) fixation. C-specific growth and cellular N content changed faster in Aphanizomenon both when inorganic P was lowered as well as during reintroduction of P. Aphanizomenon also showed a more rapid increase in N-specific N(2) fixation associated with increased C-specific growth. When ambient concentrations of inorganic P declined, both cyanobacteria displayed higher rates of alkaline phosphatase (APase) activity. Lower substrate half-saturation constants (K(M)) and higher V(max) : K(M) ratio of the APase enzyme associated with Nodularia suggest a higher affinity for dissolved organic P (DOP) substrate than Aphanizomenon. Aphanizomenon, which appears more sensitive to changes in ambient dissolved inorganic P, may be adapted to environments with elevated concentrations of P or repeated intrusions of nutrient-rich water. Nodularia on the other hand, with its higher tolerance to increased P starvation may have an ecological advantage in stratified surface waters of the Baltic Sea during periods of low P availability.
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| 42. |
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| 43. |
- Edlund, Anna, et al.
(författare)
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Use of bromodeoxyuridine immunocapture to identify psychrotolerant phenanthrene-degrading bacteria in phenanthrene-enriched polluted Baltic Sea sediments
- 2008
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Ingår i: FEMS Microbiology Ecology. - : Oxford University Press (OUP). - 0168-6496 .- 1574-6941. ; 65:3, s. 513-525
-
Tidskriftsartikel (refereegranskat)abstract
- The aim of this study was to enrich and identify psychrotolerant phenanthrene-degrading bacteria from polluted Baltic Sea sediments. Polyaromatic hydrocarbon (PAH)-contaminated sediments were spiked with phenanthrene and incubated for 2 months in the presence of bromodeoxyuridine that is incorporated into the DNA of replicating cells. The bromodeoxyuridine-incorporated DNA was extracted by immunocapture and analyzed by terminal-restriction fragment length polymorphism and 16S rRNA gene cloning and sequencing to identify bacterial populations that were growing. In addition, degradation genes were quantified in the bromodeoxyuridine-incorporated DNA by real-time PCR. Phenanthrene concentrations decreased after 2 months of incubation in the phenanthrene-enriched sediments and this reduction correlated to increases in copy numbers of xylE and phnAc dioxygenase genes. Representatives of Exiguobacterium, Schewanella, Methylomonas, Pseudomonas, Bacteroides and an uncultured Deltaproteobacterium and a Gammaproteobacterium dominated the growing community in the phenanthrene-spiked sediments. Isolates that were closely related to three of these bacteria (two pseudomonads and an Exiguobacterium sp.) could reduce phenanthrene concentrations in pure cultures and they all harbored phnAc dioxygenase genes. These results confirm that this combination of culture-based and molecular approaches was useful for identification of actively growing bacterial species with a high potential for phenanthrene degradation.
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| 44. |
- Edman, Mattias, et al.
(författare)
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Competitive outcomes between wood-decaying fungi are altered in burnt wood
- 2016
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Ingår i: FEMS Microbiology Ecology. - : Oxford University Press (OUP). - 0168-6496 .- 1574-6941. ; 92:6, s. 1-7
-
Tidskriftsartikel (refereegranskat)abstract
- Fire is an important disturbance agent in boreal forests where it creates a wide variety of charred and other types of heat-modified dead wood substrates, yet how these substrates affect fungal community structure and development within wood is poorly understood. We allowed six species of wood-decaying basidiomycetes to compete in pairs in wood-discs that were experimentally burnt before fungal inoculation. The outcomes of interactions in burnt wood differed from those in unburnt control wood for two species:Antrodia sinuosanever lost on burnt wood and won over its competitor in 67% of the trials compared to 40% losses and 20% wins on unburnt wood. In contrast, Ischnoderma benzoinumwon all interactions on unburnt wood compared to 33% on burnt wood. However, the responses differed depending on the identity of the competing species, suggesting an interaction between competitor and substrate type. The observed shift in competitive balance between fungal species probably results from chemical changes in burnt wood, but the underlying mechanism needs further investigation. Nevertheless, the results indicate that forest fires indirectly structure fungal communities by modifying dead wood, and highlight the importance of fire-affected dead wood substrates in boreal forests.
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| 45. |
- Eiler, Alexander, et al.
(författare)
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Growth response of Vibrio cholerae and other Vibrio spp. to cyanobacterial dissolved organic matter and temperature in Brackish Water
- 2007
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Ingår i: FEMS Microbiology Ecology. - : Oxford University Press (OUP). - 0168-6496 .- 1574-6941. ; 60:3, s. 411-418
-
Tidskriftsartikel (refereegranskat)abstract
- Environmental control of growth and persistence of vibrios in aquatic environments is poorly understood even though members of the genus Vibrio are globally important pathogens. To study how algal-derived organic matter and temperature influenced the abundance of different Vibrio spp., Baltic Sea microcosms inoculated with Vibrio cholerae, Vibrio vulnificus, Vibrio parahaemolyticus, Vibrio alginolyticus and native bacterioplankton, were exposed to different temperatures (12–25°C) and amended with dissolved organic matter from Nodularia spumigena (0–4.2 mg C L−1). Vibrio abundance was monitored by culture-dependent and molecular methods. Results suggested that Vibrio populations entered a viable but nonculturable state during the incubations. Abundance of Vibrio spp. and total bacterioplankton were orders of magnitude higher in microcosms amended with organic matter compared with reference microcosms. Vibrio cholerae abundances ranged from 0.9 to 1.9 × 105 cells mL−1 in treatments amended with 4.2 mg C L−1. Vibrio cholerae abundance relative to total bacterioplankton and other Vibrio spp. also increased >10-fold. In addition, V. vulnificus abundance increased in mesocosms with the highest organic matter addition (0.9–1.8 × 104 cells mL−1). Temperature alone did not significantly affect abundances of total bacterioplankton, total Vibrio spp. or individual Vibrio populations. By contrast, cyanobacterial-derived organic matter represented an important factor regulating growth and abundance of V. cholerae and V. vulnificus in brackish waters.
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| 46. |
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| 47. |
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| 48. |
- Eriksson, M., et al.
(författare)
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Bacterial growth and biofilm production on pyrene
- 2002
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Ingår i: FEMS Microbiology Ecology. - : Oxford University Press (OUP). - 0168-6496 .- 1574-6941. ; 40:1, s. 21-27
-
Tidskriftsartikel (refereegranskat)abstract
- Enrichment cultures inoculated with Arctic soil yielded a biofilm that grew on pyrene and phenanthrene. In a 60-day period, the biofilm degraded 20 mug ml(-1) pyrene or 39 mug ml(-1) phenanthrene. Single colonized pyrene crystals (approximately 1.5 x 0.75 X 0.35 mm) yielded 10(11) culturable heterotrophs and 10(5) biofilm propagules. Analysis of ribosomal intergenic spacers identified six phylotypes in a clone library from the pyrene biofilm. Analysis of 16S rRNA gene sequences indicated that the phylotypes. in order of decreasing abundance, are most closely related to members of the genera Polaromonas, Sphingomonas, Alcaligenes, Caulobacter and Variovorax. Two isolates capable of growth on pyrene. both Pseudomonas spp., were obtained from the pyrene enrichment culture. Growth of microbial biofilms on polycyclic aromatic hydrocarbons has not been reported previously, and this mode of growth may have important effects on substrate uptake.
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| 49. |
- Feng, Xin Mei, et al.
(författare)
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Impact of trace element addition on biogas production from food industrial waste - linking process to microbial communities
- 2010
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Ingår i: FEMS Microbiology Ecology. - : Oxford University Press (OUP). - 0168-6496 .- 1574-6941. ; 74:1, s. 226-240
-
Tidskriftsartikel (refereegranskat)abstract
- Laboratory-scale reactors treating food industry waste were used to investigate the effects of additions of cobalt (Co), nickel/molybdenum/boron (Ni/Mo/B) and selenium/tungsten (Se/W) on the biogas process and the associated microbial community. The highest methane production (predicted value: 860 mL g-1 VS) was linked to high Se/W concentrations in combination with a low level of Co. A combination of quantitative real-time PCR of 16S rRNA genes, terminal restriction fragment length polymorphism (T-RFLP) and clone library sequencing was used for the community analysis. The T-RFLP data show a higher diversity for bacteria than for archaea in all the treatments. The most abundant bacterial population (31-55% of the total T-RFLP fragments' intensity) was most closely related to Actinomyces europaeus (94% homology). Two dominant archaeal populations shared 98-99% sequence homology with Methanosarcina siciliae and Methanoculleus bourgensis, respectively. Only limited influence of the trace metal additions was found on the bacterial community composition, with two bacterial populations responding to the addition of a combination of Ni/Mo/B, while the dominant archaeal populations were influenced by the addition of Ni/Mo/B and/or Se/W. The maintenance of methanogenic activity was largely independent of archaeal community composition, suggesting a high degree of functional redundancy in the methanogens of the biogas reactors.
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| 50. |
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