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| 3. |
- Fernandez-Lopez, David, et al.
(författare)
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Bacterial pH-optima for growth track soil pH, but are higher than expected at low pH
- 2011
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Ingår i: Soil Biology & Biochemistry. - : Elsevier BV. - 0038-0717. ; 43:7, s. 1569-1575
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Tidskriftsartikel (refereegranskat)abstract
- One of the most influential factors determining the growth and composition of soil bacterial communities is pH. However, soil pH is often correlated with many other factors, including nutrient availability and plant community, and causality among factors is not easily determined. If soil pH is directly influencing the bacterial community, this must lead to a bacterial community growth optimised for the in situ pH. Using one set of Iberian soils (46 soils covering pH 4.2-7.3) and one set of UK grassland soils (16 soils covering pH 3.3-7.5) we measured the pH-optima for the growth of bacterial communities. Bacterial growth was estimated by the leucine incorporation method. The pH-optima for bacterial growth were positively correlated with soil pH, demonstrating its direct influence on the soil bacterial community. We found that the pH from a water extraction better matched the bacterial growth optimum compared with salt extractions of soil. Furthermore, we also showed a more subtle pattern between bacterial pH growth optima and soil pH. While closely matched at neutral pHs, pH-optima became higher than the in situ pH in more acid soils, resulting in a difference of about one pH-unit at the low-pH end. We propose that an explanation for the pattern is an interaction between increasing overall bacterial growth with higher pHs and the unimodal pH-response for growth of bacterial communities. (C) 2011 Elsevier Ltd. All rights reserved.
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| 4. |
- Rousk, Johannes, et al.
(författare)
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Contrasting Soil pH Effects on Fungal and Bacterial Growth Suggest Functional Redundancy in Carbon Mineralization
- 2009
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Ingår i: Applied and Environmental Microbiology. - 0099-2240. ; 75:6, s. 1589-1596
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Tidskriftsartikel (refereegranskat)abstract
- The influence of pH on the relative importance of the two principal decomposer groups in soil, fungi and bacteria, was investigated along a continuous soil pH gradient at Hoosfield acid strip at Rothamsted Research in the United Kingdom. This experimental location provides a uniform pH gradient, ranging from pH 8.3 to 4.0, within 180 m in a silty loam soil on which barley has been continuously grown for more than 100 years. We estimated the importance of fungi and bacteria directly by measuring acetate incorporation into ergosterol to measure fungal growth and leucine and thymidine incorporation to measure bacterial growth. The growth-based measurements revealed a fivefold decrease in bacterial growth and a fivefold increase in fungal growth with lower pH. This resulted in an approximately 30-fold increase in fungal importance, as indicated by the fungal growth/bacterial growth ratio, from pH 8.3 to pH 4.5. In contrast, corresponding effects on biomass markers for fungi (ergosterol and phospholipid fatty acid [PLFA] 18:2 omega 6,9) and bacteria (bacterial PLFAs) showed only a two- to three-fold difference in fungal importance in the same pH interval. The shift in fungal and bacterial importance along the pH gradient decreased the total carbon mineralization, measured as basal respiration, by only about one-third, possibly suggesting functional redundancy. Below pH 4.5 there was universal inhibition of all microbial variables, probably derived from increased inhibitory effects due to release of free aluminum or decreasing plant productivity. To investigate decomposer group importance, growth measurements provided significantly increased sensitivity compared with biomass-based measurements.
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| 5. |
- Rousk, Johannes, et al.
(författare)
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Fungal and bacterial growth responses to N fertilization and pH in the 150-year 'Park Grass' UK grassland experiment.
- 2011
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Ingår i: FEMS Microbiology Ecology. - : Oxford University Press (OUP). - 1574-6941 .- 0168-6496. ; 76, s. 89-99
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Tidskriftsartikel (refereegranskat)abstract
- The effects of nitrogen (N) fertilization (0-150 kg N ha(-1) year(-1) since 1865) and pH (3.3-7.4) on fungal and bacterial growth, biomass and phospholipid fatty acid (PLFA) composition were investigated in grassland soils from the 'Park Grass Experiment', Rothamsted Research, UK. Bacterial growth decreased and fungal growth increased with lower pH, resulting in a 50-fold increase in the relative importance of fungi between pH 7.4 and 3.3. The PLFA-based fungal : bacterial biomass ratio was unchanged between pH 4.5 and 7.4, and decreased only below pH 4.5. Respiration and substrate-induced respiration biomass both decreased three- to fourfold with lower pH, but biomass concentrations estimated using PLFAs were unaffected by pH. N fertilization did not affect bacterial growth and marginally affected fungal growth while PLFA biomass marker concentrations were all reduced by higher N additions. Respiration decreased with higher N application, suggesting a reduced quality of the soil organic carbon. The PLFA composition was strongly affected by both pH and N. A comparison with a pH gradient in arable soil allowed us to generalize the pH effect between systems. There are 30-50-fold increases in the relative importance of fungi between high (7.4-8.3) and low (3.3-4.5) pH with concomitant reductions of respiration by 30-70%.
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| 6. |
- Rousk, Johannes, et al.
(författare)
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Investigating the mechanisms for the opposing pH relationships of fungal and bacterial growth in soil
- 2010
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Ingår i: Soil Biology & Biochemistry. - : Elsevier BV. - 0038-0717. ; 42:6, s. 926-934
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Tidskriftsartikel (refereegranskat)abstract
- Soil pH is one of the most influential variables in soil, and is a powerful factor in influencing the size, activity and community structure of the soil microbial community. It was previously shown in a century old artificial pH gradient in an arable soil (pH 4.0-8.3) that bacterial growth is positively related to pH, while fungal growth increases with decreasing pH. In an attempt to elucidate some of the mechanisms for this, plant material that especially promotes fungal growth (straw) or bacterial growth (alfalfa) was added to soil samples of the pH gradient in 5-day laboratory incubation experiments. Also, bacterial growth was specifically inhibited by applying a selective bacterial growth inhibitor (bronopol) along the entire pH gradient to investigate if competitive interaction caused the shift in the decomposer community along the gradient. Straw benefited fungal growth relatively more than bacterial, and vice versa for alfalfa. The general pattern of a shift in fungal:bacterial growth with pH was, however, unaffected by substrate additions, indicating that lack of a suitable substrate was not the cause of the pH effect on the microbial community. In response to the bacterial growth inhibition by bronopol, there was stimulation of fungal growth up to pH 7, but not beyond, both for alfalfa and straw addition. However, the accumulation of ergosterol (an indicator of fungal biomass) during the incubation period after adding alfalfa increased at all pHs, indicating that fungal growth had been high at some time during the 5-day incubation following joint addition of alfalfa and bronopol. This was corroborated in a time-series experiment. In conclusion, the low fungal growth at high pH in an arable soil was caused to a large extent by bacterial competition, and not substrate limitation. (C) 2010 Elsevier Ltd. All rights reserved.
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| 7. |
- Rousk, Johannes, et al.
(författare)
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Soil bacterial and fungal communities across a pH gradient in an arable soil.
- 2010
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Ingår i: The Isme Journal. - : Springer Science and Business Media LLC. - 1751-7362 .- 1751-7370. ; 4, s. 1340-1351
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Tidskriftsartikel (refereegranskat)abstract
- Soils collected across a long-term liming experiment (pH 4.0-8.3), in which variation in factors other than pH have been minimized, were used to investigate the direct influence of pH on the abundance and composition of the two major soil microbial taxa, fungi and bacteria. We hypothesized that bacterial communities would be more strongly influenced by pH than fungal communities. To determine the relative abundance of bacteria and fungi, we used quantitative PCR (qPCR), and to analyze the composition and diversity of the bacterial and fungal communities, we used a bar-coded pyrosequencing technique. Both the relative abundance and diversity of bacteria were positively related to pH, the latter nearly doubling between pH 4 and 8. In contrast, the relative abundance of fungi was unaffected by pH and fungal diversity was only weakly related with pH. The composition of the bacterial communities was closely defined by soil pH; there was as much variability in bacterial community composition across the 180-m distance of this liming experiment as across soils collected from a wide range of biomes in North and South America, emphasizing the dominance of pH in structuring bacterial communities. The apparent direct influence of pH on bacterial community composition is probably due to the narrow pH ranges for optimal growth of bacteria. Fungal community composition was less strongly affected by pH, which is consistent with pure culture studies, demonstrating that fungi generally exhibit wider pH ranges for optimal growth.
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| 8. |
- Rousk, Johannes, et al.
(författare)
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The microbial PLFA composition as affected by pH in an arable soil
- 2010
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Ingår i: Soil Biology & Biochemistry. - : Elsevier BV. - 0038-0717. ; 42:3, s. 516-520
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Tidskriftsartikel (refereegranskat)abstract
- The influence of soil pH on the phospholipid fatty acid (PLFA) composition of the microbial community was investigated along the Hoosfield acid strip, Rothamsted Research, UK - a uniform pH gradient between pH 8.3 and 4.5. The influence of soil pH on the total concentration of PLFAs was not significant, while biomass estimated using substrate induced respiration decreased by about 25%. However, the PLFA composition clearly changed along the soil pH gradient. About 40% of the variation in PLFA composition along the gradient was explained by a first principal component, and the sample scores were highly correlated to pH (R-2 = 0.97). Many PLFAs responded to pH similarly in the Hoosfield arable soil compared with previous assessments in forest soils, including, e.g. monounsaturated PLFAs 16:1 omega 5, 16:1 omega 7c and 18:1 omega 7, which increased in relative concentrations with pH, and i16:0 and cy19:0, both of which decreased with pH. Some PLFAs responded differently to pH between the soil types, e.g. br18:0. We conclude that soil pH has a profound influence on the microbial PLFA composition, which must be considered in all applications of this method to detect changes in the microbial community. (C) 2009 Elsevier Ltd. All rights reserved.
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| 9. |
- Wilkinson, Mark D., et al.
(författare)
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Comment : The FAIR Guiding Principles for scientific data management and stewardship
- 2016
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Ingår i: Scientific Data. - : Springer Science and Business Media LLC. - 2052-4463. ; 3
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Tidskriftsartikel (refereegranskat)abstract
- There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders-representing academia, industry, funding agencies, and scholarly publishers-have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.
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