| 1. |
- Székely, Anna J., et al.
(författare)
-
The importance of species sorting in bacterial communities differs between habitat generalists and specialists
- 2014
-
Ingår i: FEMS Microbiology Ecology. - : Oxford University Press (OUP). - 0168-6496 .- 1574-6941. ; 87:1, s. 102-112
-
Tidskriftsartikel (refereegranskat)abstract
- Recent studies have shown that the spatial turnover of bacterial communities, that is, beta-diversity, is determined by a combination of different assembly mechanisms, such as species sorting, that is, environmental filtering, and dispersal-related mechanisms. However, it is currently unclear to what extent the importance of the different mechanisms depends on community traits. Here, we implemented a study using a rock pool metacommunity to test whether habitat specialization of bacterial taxa and groups or their phylogenetic identity influenced by which mechanisms communities were assembled. Ingeneral, our results show that species sorting was the most important assembly mechanism. However, we found that a larger fraction of the variation in bacterial community composition between pools could be explained by environmental factors in case of habitat generalists, that is, taxa that were widespread and abundant in the metacommunity, compared with habitat specialists, that is, taxa that had a more restricted distribution range and tended to be rare. Differences in assembly mechanisms were observedbetween different major phyla and classes. However, also here, a larger fraction of the variation incommunity composition among pools could be explained for taxonomic groups that contained on average more habitat generalists. In summary, our results show that species sorting is stronger for themost common taxa, indicating that beta-diversity along environmental gradients can be adequately described without considering rare taxa.
|
|
| 2. |
- Bengtson, Per, et al.
(författare)
-
Links between methanotroph community composition and CH(4) oxidation in a pine forest soil
- 2009
-
Ingår i: FEMS Microbiology Ecology. - : Oxford University Press (OUP). - 1574-6941 .- 0168-6496. ; 70:3, s. 356-366
-
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.
|
|
| 3. |
|
|
| 4. |
- de Vries, Franciska T., et al.
(författare)
-
High turnover of fungal hyphae in incubation experiments
- 2009
-
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.
|
|
| 5. |
- Fernandez-Calvino, David, et al.
(författare)
-
Growth response of the bacterial community to pH in soils differing in pH
- 2010
-
Ingår i: FEMS Microbiology Ecology. - : Oxford University Press (OUP). - 1574-6941 .- 0168-6496. ; 73:1, s. 149-156
-
Tidskriftsartikel (refereegranskat)abstract
- The effect of pH on the instantaneous growth of soil bacterial communities was studied in five soils with different pH (4.5-7.8) using leucine (Leu) and thymidine (TdR) incorporation. The pH dependency of bacterial growth was modelled using three different unimodal functions, and the pH(opt) for growth and the pH range in which growth was > 50% of the optimal growth were compared. Leu and TdR incorporation yielded very similar results. The best fits were obtained using a third-degree polynomial function and the cardinal pH model. However, a simple second-degree function was adequate in most cases, yielding very similar pH(opt) values to the other two models. Bacterial growth was highly influenced by pH, showing optimum growth at a pH related to the soil pH. The lowest pH(opt) was found in the most acidic soil and the highest pH(opt) in the soil with the highest pH. The pH(opt) for bacterial growth was close to the soil pH measured in water, but higher (0.7-2.1 units) than the pH measured with 0.1 M KCl. The pH range in which bacterial growth was > 50% of that at optimum was, on average, 1.7 units below and above the optimum pH.
|
|
| 6. |
- Hallbeck, Lotta, 1957, et al.
(författare)
-
Culture-dependent comparison of microbial diversity in deep granitic groundwater from two sites considered for a Swedish final repository of spent nuclear fuel
- 2012
-
Ingår i: FEMS Microbiology Ecology. - : Oxford University Press (OUP). - 1574-6941 .- 0168-6496. ; 81:1, s. 66-77
-
Tidskriftsartikel (refereegranskat)abstract
- Site selection for a spent nuclear fuel (SNF) repository required analysis of microbial abundance and diversity at two Swedish sites, Forsmark and Laxemar-Simpevarp. Information about sulphate-reducing bacteria (SRB) was required, as sulphide could corrode copper SNF canisters. Total number of cells (TNC) and ATP were analysed, and plate counts and most probable number (MPN) analyses were conducted using eight media based on different electron donors and acceptors for specific microorganism physiological groups. Groundwater chemical composition and Eh were analysed; sampling depths were 112-978 m below sea level. TNC was 5.5 × 103 to 4.7 × 105 cells mL-1, correlating with ATP concentrations. Culturability in TNC percentage was 0.01-35.9, averaging 5.12. Culturable numbers varied greatly between sample positions and uncorrelated with depth. SRB were found in 29 samples and were below detection in three; the MPN of SRB correlated negatively with Eh, as did the MPN of acetogens. Data indicated that microbial sulphate reduction was ongoing in many sampled aquifers; published stable isotope data and modelling results supported this observation. The sites did not differ significantly, but the large data range suggested that analysis of more samples would enable detailed evaluation of microbial processes and their relationship with geochemical information. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.
|
|
| 7. |
- Hammer, Edith, et al.
(författare)
-
Tit for tat? A mycorrhizal fungus accumulates phosphorus under low plant carbon availability.
- 2011
-
Ingår i: FEMS Microbiology Ecology. - : Oxford University Press (OUP). - 1574-6941 .- 0168-6496. ; 76, s. 236-244
-
Tidskriftsartikel (refereegranskat)abstract
- The exchange of carbohydrates and mineral nutrients in the arbuscular mycorrhizal symbiosis must be controlled by both partners in order to sustain an evolutionarily stable mutualism. Plants down-regulate their carbon flow to the fungus when nutrient levels are sufficient, while the mechanism controlling fungal nutrient transfer is unknown. Here we show that the fungus accumulates nutrients when connected to a host that is of less benefit to the fungus, indicating a potential of the fungus to control the transfer of nutrients. We used a monoxenic in vitro model of root organ cultures associated with G. intraradices, in which we manipulated the carbon availability to the plant. We found that G. intraradices accumulated up to 7 times more nutrients in its spores, and up to 9 times more in its hyphae, when the carbon pool available to the associated roots was halved. The strongest effect was found for phosphorus, considered to be the most important nutrient in the arbuscular mycorrhizal symbiosis. Other elements such as potassium and chorine were also accumulated, but to a lesser extent, while no accumulation of iron or manganese was found. Our results suggest a functional linkage between carbon and phosphorus exchange.
|
|
| 8. |
|
|
| 9. |
- Iovieno, Paola, et al.
(författare)
-
Effect of drying and rewetting on bacterial growth rates in soil.
- 2008
-
Ingår i: FEMS Microbiology Ecology. - : Oxford University Press (OUP). - 1574-6941 .- 0168-6496. ; 65:3, s. 400-407
-
Tidskriftsartikel (refereegranskat)abstract
- The effect of soil moisture on bacterial growth was investigated, and the effects of rewetting were compared with glucose addition because both treatments increase substrate availability. Bacterial growth was estimated as thymidine and leucine incorporation, and was compared with respiration. Low growth rates were found in air-dried soil, increasing rapidly to high stable values in moist soils. Respiration and bacterial growth at different soil moisture contents were correlated. Rewetting air-dried soil resulted in a linear increase in bacterial growth with time, reaching the levels in moist soil (10 times higher) after about 7 h. Respiration rates increased within 1 h to a level >10 times higher than that in moist soil. After the initial flush, there was a gradual decrease in respiration rate, while bacterial growth increased to levels twice that of moist soil 24 h after rewetting, and decreased to levels similar to those in moist soil after 2 days. Adding glucose resulted in no positive effect on bacterial growth during the first 9 h, despite resulting in more than five times higher respiration. This indicated that the initial increase in bacterial growth after rewetting was not due to increased substrate availability.
|
|
| 10. |
- Javelle, Arnaud, et al.
(författare)
-
Ammonium and methylamine transport by the ectomycorrhizal fungus Paxillus involutus and ectomycorrhizas
- 1999
-
Ingår i: FEMS Microbiology Ecology. - : Oxford University Press (OUP). - 1574-6941 .- 0168-6496. ; 30:4, s. 355-366
-
Tidskriftsartikel (refereegranskat)abstract
- Using [C-14]methylamine as an analogue of ammonium, the kinetics and the energetics of NH: transport were studied in the ectomycorrhizal fungus, Paxillus involutus (Batsch) Fr. The apparent half-saturation constant (K-m) and the maximum uptake rate (V-max) for the carrier-mediated transport derived from the Eadie-Hofstee transformation were 180 mu M and 380 nmol (mg dry wt)(-1) min(-1,) respectively. Both pH dependence and inhibition by protonophores indicate that methylamine transport in P. involutus was dependent on the electrochemical H+ gradient. Both long-term and short-term uptake experiments were consistent with regulation of ammonium/methylamine transport processes by the presence of an organic nitrogen source. Analysis of methylamine uptake by different P. involutus isolates revealed no obvious trend in the uptake capacities in relation to N deposition at the collection site. Kinetic parameters were determined in P. involutus/Betula pendula (Roth.) axenic association and in detached mycorrhizal roots isolated from forest sites. Enhanced methylamine uptake in the presence of the fungal symbiont was demonstrated. Homogeneous V-max values were found for axenic and detached mycorrhizas, whereas K-m values showed greater variations. (C) 1999 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.
|
|
