| 1. |
- Affholder, Marie-Cecile, et al.
(författare)
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Cadmium Reduction in Spring Wheat: Root Exudate Composition Affects Cd Partitioning Between Roots and Shoots
- 2023
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Ingår i: Journal of Soil Science and Plant Nutrition. - 0718-9508 .- 0718-9516. ; 23, s. 3537-3547
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Tidskriftsartikel (refereegranskat)abstract
- Cadmium (Cd) in cereals is one of the major sources of Cd intake by human diets, and solutions to reduce Cd concentrations in wheat still need to be developed. Plant breeding, by selecting low-Cd varieties, can be an important tool to reduce Cd in crops. Knowing the genotypic variation in Cd accumulation and furthering our understanding of the impact of root exudates composition on Cd accumulation in crops may provide valuable information for plant breeding. In this study, we selected nine spring wheat varieties and analysed the accumulation and distribution of Cd in shoots, roots, root surfaces and kernels in relation to their qualitative and quantitative composition of root exudates, determined by H-1-NMR (Proton Nuclear Magnetic Resonance). Results showed that the Cd concentration in shoots at an early stage could be used as a predictor for Cd concentration in kernels. Total Cd uptake was not correlated to the mobility of Cd in the rhizosphere, but total Cd was negatively correlated to Cd adsorbed at the root surface. Furthermore, (i) exudation of organic acids (primarily succinate and acetate) increased Cd concentration in shoots, and (ii) exudation of nucleosides, DNA (deoxyribonucleic acid) degradation products, increased Cd adsorption at the root surface. Therefore, root exudates composition should be taken into account when selecting for low-Cd wheat traits.
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| 2. |
- Arrazola Vasquez, Elsa Maria, et al.
(författare)
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Estimating energy costs of earthworm burrowing using calorimetry
- 2024
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Ingår i: European Journal of Soil Biology. - 1164-5563 .- 1778-3615. ; 121
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Tidskriftsartikel (refereegranskat)abstract
- Earthworm burrowing is essential for soil functioning in temperate climates. It is known that soil compaction hampers earthworm burrowing, but there is a lack of knowledge on how it affects the energy costs of earthworms. In the present study, we used respirometry and isothermal calorimetry to quantify earthworm respiration rates and heat dissipation in two endogeic species, Aporrectodea caliginosa and Aporrectodea tuberculata , in compacted and non -compacted soils. We put the measured respiration rates and heat dissipation in relation to the burrow volume and cast volume produced by the earthworms. We found that at higher compaction levels, respiration rates and dissipated heat increased for both studied species. The energy costs associated with burrowing were a significant fraction of the total energy costs. Our results indicate that energy costs per burrow volume increase due to compaction, and that the specific energy costs for burrowing (i.e., per gram earthworm) were lower for A. tuberculata than for A. caliginosa . Further studies are needed to confirm our results. We discuss the potential and current limitations of isothermal calorimetry as a method for direct quantification of energy costs of earthworms. There is a need for further studies that quantify how energy costs of burrowing are affected by various soil conditions, to better predict the implications of land use and soil management on soil processes and functions mediated by earthworm burrowing.
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| 3. |
- Bieroza, Magdalena, et al.
(författare)
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The Cold Region Critical Zone in Transition: Responses to Climate Warming and Land Use Change
- 2021
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Ingår i: Annual Review of Environment and Resources. - : Annual Reviews. - 1543-5938 .- 1545-2050. ; 46, s. 111-134
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Forskningsöversikt (refereegranskat)abstract
- Global climate warming disproportionately affects high-latitude and mountainous terrestrial ecosystems. Warming is accompanied by permafrost thaw, shorter winters, earlier snowmelt, more intense soil freeze-thaw cycles, drier summers, and longer fire seasons. These environmental changes in turn impact surface water and groundwater flow regimes, water quality, greenhouse gas emissions, soil stability, vegetation cover, and soil (micro)biological communities. Warming also facilitates agricultural expansion, urban growth, and natural resource development, adding growing anthropogenic pressures to cold regions' landscapes, soil health, and biodiversity. Further advances in the predictive understanding of how cold regions' critical zone processes, functions, and ecosystem services will continue to respond to climate warming and land use changes require multiscale monitoring technologies coupled with integrated observational and modeling tools. We highlight some of the major challenges, knowledge gaps, and opportunities in cold region critical zone research, with an emphasis on subsurface processes and responses in both natural and agricultural ecosystems.
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| 4. |
- Bölscher, Tobias, et al.
(författare)
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Differences in substrate use efficiency : impacts of microbial community composition, land use management, and substrate complexity
- 2016
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Ingår i: Biology and Fertility of Soils. - : Springer Science and Business Media LLC. - 0178-2762 .- 1432-0789. ; 52:4, s. 547-559
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Tidskriftsartikel (refereegranskat)abstract
- Microbial substrate use efficiency is an important property in process-based soil organic matter models, but is often assumed to be constant in mechanistic models. However, previous studies question if a constant efficiency is appropriate, in particular when evaluating carbon (C) cycling across temperatures and various substrates. In the present study, we evaluated the relation between substrate use efficiency, microbial community composition and substrate complexity in contrasting long-term management regimes (47–49 years of either arable, ley farming, grassland, or forest systems). Microbial community composition was assessed by phospholipid fatty acid analysis and three indices of substrate use efficiencies were considered: (i) thermodynamic efficiency, (ii) calorespirometric ratio, and (iii) metabolic quotient. Three substrates, d-glucose, l-alanine, or glycogen, varying in complexity, were added separately to soils, and heat production as well as C mineralization was determined over a 32-h incubation period at 12.5 °C. Microbial communities from forest systems were most efficient in utilizing substrates, supporting our hypothesis that maturing ecosystems become more efficient. These changes in efficiency were linked to microbial community composition with fungi and Gram-negative bacteria being important biomarkers. Despite our initial hypothesis, complex substrate such as glycogen was utilized most efficiently. Our findings emphasize that differences in land use management systems as well as the composition of soil organic matter need to be considered when modelling C dynamics in soils. Further research is required to establish and evaluate appropriate proxies for substrate use efficiencies in various ecosystems.
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| 5. |
- Bölscher, Tobias, et al.
(författare)
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Land-use alters the temperature response of microbial carbon-use efficiency in soils - a consumption-based approach
- 2020
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Ingår i: Soil Biology and Biochemistry. - : Elsevier BV. - 0038-0717 .- 1879-3428. ; 140
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Tidskriftsartikel (refereegranskat)abstract
- Soil organic carbon (SOC) is a substantial source of atmospheric CO2, but also a large cause of uncertainties in Earth-system models. A principal control on soil CO2 release is the carbon-use efficiency (CUE) of microbial communities, which partitions the carbon (C) allocation between biosynthetic stabilization and CO2 respiration during SOC decomposition. In Earth-system models, CUE is commonly considered as a constant, although it should be susceptible to environmental factors such as temperature. We explored CUE across a set of land-uses and temperatures, and we show the hitherto neglected phenomenon that land-use can alter the temperature response of CUE. In arable soils, CUE was constant over a temperature range between 5 and 20 degrees C, but it decreased with temperature in ley farming, grassland, and forest soils at temperatures above 12.5 degrees C. The decrease in CUE was strongest for forest soils. Implementing our findings into a soil-C model revealed substantial differences in projected SOC losses: Assuming an increase of mean annual temperature of 2 or 4 degrees C, soils were projected to lose up to 6 or 15% of their current SOC, respectively, until they reach a new steady-state. These projections varied among land-uses. Our findings confront the current representation of CUE in global C models and challenges C sequestration strategies based on land-use changes, because land-uses such as e.g. forest ecosystems with current high C storage may lose substantially more C than agricultural soils due to strong declines of CUE.
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| 6. |
- Bölscher, Tobias, et al.
(författare)
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Temperature sensitivity of substrate-use efficiency can result from altered microbial physiology without change to community composition
- 2017
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Ingår i: Soil Biology and Biochemistry. - : Elsevier BV. - 0038-0717 .- 1879-3428. ; 109, s. 59-69
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Tidskriftsartikel (refereegranskat)abstract
- Mechanisms controlling carbon stabilisation in soil and its feedback to climate change are of considerable importance. Microbial substrate-use ef organic matter. It determines the allocation of substrate towards biosynthetic stabilisation of carbon and for respiratory losses into the atmosphere. Previously, it was observed that substrate-use ef declines with an increase in temperature and that it varies across organic substrates. Yet, our mechanistic understanding of processes causing the temperature sensitivity of substrate-use ef Changes in substrate-use ef communities, (ii) changes in microbial physiology within the same community, or (iii) a combination of both. In the present study, we evaluated the link between microbial community composition and substrate-use ef We found only minor shifts in microbial community composition, despite large differences in substrateuse ef changes in substrate-use ef emphasize that future studies should focus on resolving long-term trade-offs between physiological and community inficiency is an important property during decomposition of soilficiencyficiency is limited.ficiency could be triggered by (i) shifts in the active components of microbialficiency, combining measurements of carbon mineralisation and microbial energetics.ficiencies across incubation temperatures and substrate additions. We conclude that short-termficiency were mainly caused by changes in microbial physiology, butfluences on substrate-use efficiency.
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| 7. |
- Chakrawal, Arjun, et al.
(författare)
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Dynamic upscaling of decomposition kinetics for carbon cycling models
- 2020
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Ingår i: Geoscientific Model Development. - : Copernicus GmbH. - 1991-959X .- 1991-9603. ; 13:3, s. 1399-1429
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Tidskriftsartikel (refereegranskat)abstract
- The distribution of organic substrates and microorganisms in soils is spatially heterogeneous at the microscale. Most soil carbon cycling models do not account for this microscale heterogeneity, which may affect predictions of carbon (C) fluxes and stocks. In this study, we hypothesize that the mean respiration rate (R) over bar at the soil core scale (i) is affected by the microscale spatial heterogeneity of substrate and microorganisms and (ii) depends upon the degree of this heterogeneity. To theoretically assess the effect of spatial heterogeneities on (R) over bar, we contrast heterogeneous conditions with isolated patches of substrate and microorganisms versus spatially homogeneous conditions equivalent to those assumed in most soil C models. Moreover, we distinguish between biophysical heterogeneity, defined as the nonuniform spatial distribution of substrate and microorganisms, and full heterogeneity, defined as the nonuniform spatial distribution of substrate quality (or accessibility) in addition to biophysical heterogeneity. Four common formulations for decomposition kinetics (linear, multiplicative, Michaelis-Menten, and inverse Michaelis-Menten) are considered in a coupled substrate-microbial biomass model valid at the microscale. We start with a 2-D domain characterized by a heterogeneous substrate distribution and numerically simulate organic matter dynamics in each cell in the domain. To interpret the mean behavior of this spatially explicit system, we propose an analytical scale transition approach in which microscale heterogeneities affect (R) over bar through the second-order spatial moments (spatial variances and covariances). The model assuming homogeneous conditions was not able to capture the mean behavior of the heterogeneous system because the second-order moments cause (R) over bar to be higher or lower than in the homogeneous system, depending on the sign of these moments. This effect of spatial heterogeneities appears in the upscaled nonlinear decomposition formulations, whereas the upscaled linear decomposition model deviates from homogeneous conditions only when substrate quality is heterogeneous. Thus, this study highlights the inadequacy of applying at the macroscale the same decomposition formulations valid at the microscale and proposes a scale transition approach as a way forward to capture microscale dynamics in core-scale models.
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| 8. |
- Chakrawal, Arjun, 1992-, et al.
(författare)
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Interacting Bioenergetic and Stoichiometric Controls on Microbial Growth
- 2022
-
Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 13
-
Tidskriftsartikel (refereegranskat)abstract
- Microorganisms function as open systems that exchange matter and energy with their surrounding environment. Even though mass (carbon and nutrients) and energy exchanges are tightly linked, there is a lack of integrated approaches that combine these fluxes and explore how they jointly impact microbial growth. Such links are essential to predicting how the growth rate of microorganisms varies, especially when the stoichiometry of carbon- (C) and nitrogen (N)-uptake is not balanced. Here, we present a theoretical framework to quantify the microbial growth rate for conditions of C-, N-, and energy-(co-) limitations. We use this framework to show how the C:N ratio and the degree of reduction of the organic matter (OM), which is also the electron donor, availability of electron acceptors (EAs), and the different sources of N together control the microbial growth rate under C, nutrient, and energy-limited conditions. We show that the growth rate peaks at intermediate values of the degree of reduction of OM under oxic and C-limited conditions, but not under N-limited conditions. Under oxic conditions and with N-poor OM, the growth rate is higher when the inorganic N (NInorg)-source is ammonium compared to nitrate due to the additional energetic cost involved in nitrate reduction. Under anoxic conditions, when nitrate is both EA and NInorg-source, the growth rates of denitrifiers and microbes performing the dissimilatory nitrate reduction to ammonia (DNRA) are determined by both OM degree of reduction and nitrate-availability. Consistent with the data, DNRA is predicted to foster growth under extreme nitrate-limitation and with a reduced OM, whereas denitrifiers are favored as nitrate becomes more available and in the presence of oxidized OM. Furthermore, the growth rate is reduced when catabolism is coupled to low energy yielding EAs (e.g., sulfate) because of the low carbon use efficiency (CUE). However, the low CUE also decreases the nutrient demand for growth, thereby reducing N-limitation. We conclude that bioenergetics provides a useful conceptual framework for explaining growth rates under different metabolisms and multiple resource-limitations.
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| 9. |
- Chakrawal, Arjun, et al.
(författare)
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Leveraging energy flows to quantify microbial traits in soils
- 2021
-
Ingår i: Soil Biology and Biochemistry. - : Elsevier BV. - 0038-0717 .- 1879-3428. ; 155
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Tidskriftsartikel (refereegranskat)abstract
- Heat dissipation from organic matter decomposition is a well-recognized proxy for microbial activity in soils, but only a few modeling studies have used heat signals to quantify microbial traits such as maximum substrate uptake rate, specific growth rate, mortality rate, and growth efficiency. In this contribution, a hierarchy of coupled mass-energy balance models is proposed to estimate microbial traits encoded in model parameters using heat dissipation and respiration data from glucose induced microbial activity. Moreover, the models are used to explain the observed variability in calorespirometric ratios (CR)-the ratio of heat dissipation to respiration rate. We parametrized four model variants using heat dissipation and respiration rates measured in an isothermal calorimeter during the lag-phase only or during the whole growth-phase. The four variants are referred to as: (i) complex physiological model, (ii) simplified physiological model, (iii) lag-phase model, and (iv) growth-phase model. Model parameters were determined using three combinations of data: A) only the heat dissipation rate, B) only the respiration rate, and C) both heat dissipation and respiration rates. We assumed that the 'best' parameter estimates were those obtained when using all the data (i.e., option C). All model variants were able to fit the observed heat dissipation and respiration rates. The parameters estimated using only heat dissipation data were similar to the 'best' estimates compared to using only respiration rate data, suggesting that the observed heat dissipation rate can be used to constrain microbial models and estimate microbial traits. However, the observed variability in CR was not well captured by some model variants such as the simplified physiological model, in contrast to the lag- and growth-phase model that predicted CR well. This suggests that CR can be used to scrutinize how well metabolic processes are represented in decomposition models.
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| 10. |
- Chakrawal, Arjun, et al.
(författare)
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Quantifying Microbial Metabolism in Soils Using Calorespirometry — A Bioenergetics Perspective
- 2020
-
Ingår i: Soil Biology and Biochemistry. - : Elsevier BV. - 0038-0717 .- 1879-3428. ; 148
-
Tidskriftsartikel (refereegranskat)abstract
- Microbial carbon use efficiency (CUE) measures the partitioning between anabolic and catabolic processes. While most work on CUE has been based on carbon (C) mass flows, the roles of organic C energy contents and microbial energy demand on CUE have been rarely considered. Thus, a bioenergetics perspective could provide new insights on how microorganisms utilize C and ultimately allow evaluating their role in C stabilization in soils. Recently, the calorespirometric ratio (CR)— the ratio of heat dissipation and respiration— has been used to characterize the efficiency of microbial growth in soils. Here, we formulate a coupled mass and energy balance model for microbial growth and provide a generalized relationship between CUE and CR. In the model, we consider two types of organic C in soils: an added substrate (e.g., glucose) and the native soil organic matter (SOM), to also account for priming effects. Furthermore, we consider both aerobic and fermentation metabolic pathways. We use this model as a framework to generalize previous formulations and generate hypotheses on the expected variations in CR as a function of substrate quality, metabolic pathways, and microbial traits (specifically CUE). In turn, the same equations can be used to estimate CUE from measured CR. Our results confirm previous findings on CR and show that without microbial growth, CR depends only on the rates of the different metabolic pathways, while CR is also a function of the growth yields for these metabolic pathways when microbial growth occurs. Under strictly aerobic conditions, CUE increases with increasing CR for substrates with a higher degree of reduction than that of the microbial biomass, while CUE decreases with increasing CR for substrates with a lower degree of reduction than the microbial biomass. When aerobic reactions and fermentation occur simultaneously, the relation between CUE and CR is mediated by (i) the degree of reduction of the substrates, (ii) the rates and growth yields of all metabolic pathways, and (iii) the contribution of SOM priming to microbial growth. Using the proposed framework, calorespirometry can be used to evaluate CUE and the role of different metabolic pathways in soil systems.
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| 11. |
- Christerson, Linus, 1985-, et al.
(författare)
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High-Resolution Genotyping of Chlamydia trachomatis by Use of a Novel Multilocus Typing DNA Microarray
- 2011
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Ingår i: Journal of Clinical Microbiology. - 0095-1137 .- 1098-660X. ; 49:8, s. 2838-2843
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Tidskriftsartikel (refereegranskat)abstract
- Typing of Chlamydia trachomatis is important to understandingits epidemiology. Currently used methods such as DNA sequencingof the ompA gene and multilocus sequence typing (MLST) eitheroffer limited epidemiological resolution or are laborious andexpensive, or both. DNA microarray technology using the ArrayStripformat is an affordable alternative for genotyping. In thisstudy, we developed a new multilocus typing (MLT) DNA microarray,based on the target regions of a high-resolution MLST systemas well as software for easy analysis. Validation of the arraywas done by typing 80 previously MLST-typed clinical specimensfrom unselected adolescents in school. The MLT array showed100% specificity and provided 2.4-times-higher resolution thanompA sequencing, separating the commonly predominating ompAE/Bour genotype into 7 MLT array genotypes. The MLT array reproducedepidemiological findings revealed by the MLST system and showedsufficient sensitivity to work with clinical specimens. Comparedto MLST analysis, the expenses needed for testing a sample withthe MLT array are considerably lower. Moreover, testing canbe completed within 1 working day rather than 3 or 4 days, withdata analysis not requiring highly specialized personnel. Thepresent MLT array represents a powerful alternative in C. trachomatisgenotyping.
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| 12. |
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| 13. |
- Colombi, Tino, et al.
(författare)
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Cortical Cell Diameter Is Key To Energy Costs of Root Growth in Wheat
- 2019
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Ingår i: Plant Physiology. - : Oxford University Press (OUP). - 0032-0889 .- 1532-2548. ; 180, s. 2049-2060
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Tidskriftsartikel (refereegranskat)abstract
- Root growth requires substantial amounts of energy and thus carbohydrates. The energy costs of root growth are particularly high in both dry and compacted soil, due to high soil penetration resistance. Consequently, more carbon must be allocated from aboveground plant tissue to roots, which limits crop productivity. In this study, we tested the utility of root cortical cell diameter as a potential selection target to reduce the energy costs of root growth. Isothermal calorimetry was adopted for in situ quantification of the energy costs of root growth of 16 wheat (Triticum aestivum) genotypes under three levels of penetration resistance. We show that cortical cell diameter is a pivotal and heritable trait, which is strongly related to the energy costs of root growth. Genotypic diversity was found for cortical cell diameter and the energy costs of root growth. A large root cortical cell diameter correlated with reduced energy costs of root growth, particularly under high soil penetration resistance. Moreover, significant correlations were found between the ability to radially enlarge cortical cells upon greater penetration resistance (i.e. phenotypic plasticity) and the responsiveness in the energy costs of root growth. A higher degree of phenotypic plasticity in cortical cell diameter was associated with reduced energy costs of root growth as soil penetration resistance increased. We therefore suggest that genotypic diversity and phenotypic plasticity in cortical cell diameter should be harnessed to adapt crops to dry and compacted soils.
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| 14. |
- Coucheney, Elsa, et al.
(författare)
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Long-term fertilization of a boreal Norway spruce forest increases the temperature sensitivity of soil organic carbon mineralization
- 2013
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Ingår i: Ecology and Evolution. - : Wiley. - 2045-7758. ; 3, s. 5177-5188
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Tidskriftsartikel (refereegranskat)abstract
- Boreal ecosystems store one-third of global soil organic carbon (SOC) and are particularly sensitive to climate warming and higher nutrient inputs. Thus, a better description of how forest managements such as nutrient fertilization impact soil carbon (C) and its temperature sensitivity is needed to better predict feedbacks between C cycling and climate. The temperature sensitivity of in situ soil C respiration was investigated in a boreal forest, which has received long-term nutrient fertilization (22 years), and compared with the temperature sensitivity of C mineralization measured in the laboratory. We found that the fertilization treatment increased both the response of soil in situ CO2 effluxes to a warming treatment and the temperature sensitivity of C mineralization measured in the laboratory (Q10). These results suggested that soil C may be more sensitive to an increase in temperature in long-term fertilized in comparison with nutrient poor boreal ecosystems. Furthermore, the fertilization treatment modified the SOC content and the microbial community composition, but we found no direct relationship between either SOC or microbial changes and the temperature sensitivity of C mineralization. However, the relation between the soil C:N ratio and the fungal/bacterial ratio was changed in the combined warmed and fertilized treatment compared with the other treatments, which suggest that strong interaction mechanisms may occur between nutrient input and warming in boreal soils. Further research is needed to unravel into more details in how far soil organic matter and microbial community composition changes are responsible for the change in the temperature sensitivity of soil C under increasing mineral N inputs. Such research would help to take into account the effect of fertilization managements on soil C storage in C cycling numerical models.
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| 15. |
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| 16. |
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| 17. |
- Coucheney, Elsa, et al.
(författare)
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The thermodynamic efficiency of soil microbial communities subject to long-term stress is lower than those under conventional input regimes
- 2012
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Ingår i: Soil Biology and Biochemistry. - : Elsevier BV. - 0038-0717 .- 1879-3428. ; 47, s. 149-157
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Tidskriftsartikel (refereegranskat)abstract
- Isothermal microcalorimetry measures the thermal flows occurring in systems with very high precision and may be used to quantify carbon (C) assimilation and resource-use efficiencies in soils. We determined the thermodynamic efficiency of soil microbial communities located in soils which had received contrasting long-term management regimes (53 y) with respect to organic matter and nitrogen (N) inputs, viz. farmyard manure, sewage sludge, straw and calcium nitrate, calcium nitrate only, or ammonium sulphate. Two thermodynamic efficiency indices were considered: (i) total thermodynamic efficiency of soil microbial communities (eta(eff)), i.e. general heat production released following substrate addition, per unit heat energy input to the soil system, and (ii) a specific thermodynamic efficiency index of energy retained in the soil system (eta(soil)). The latter index provides quantitative data on how much C is assimilated and energy retained in the soil system. Further, we derived a 'substrate-induced heat production' (SIHP) index, which adjusts for size of the microbial biomass. Optimised concentrations of water or glucose plus water were added to the soil samples and resultant thermal signatures and C mineralisation were determined over a 48-h incubation period at 25 degrees C. The thermal signatures were further related to the microbial community profiles of the soils. The phenotypic structural and functional diversity profiles of the microbial communities in soils were assessed by phospholipid fatty acid and multi-substrate induced respiration methods at the start of the experiment, confirming significant differences between all five treatments in community composition and functional capabilities. Both the total and specific thermodynamic efficiency indices of the soil microbial communities exposed to long-term stress by heavy metal toxicity (sewage sludge) and low pH ((NH4)(2)SO4) were significantly smaller in magnitude than those under the three conventional (i.e. Ca(NO3)(2), Straw + Ca(NO3)(2), farmyard manure) input regimes (P < 0.05). The SIHP index however, was highest in the treatments receiving long-term inorganic inputs, indicating more heat production per unit biomass, than that found in all three organic input regimes. These differences in efficiencies were reflected in both the phenotypic and functional profiles of the communities. These indices may provide quantification of C assimilation and resource-use efficiency under different land-use and management scenarios, and potentially allow evaluation of the role of soils in governing the terrestrial C balance by studying the fate and regulation of C in soil systems. (C) 2011 Elsevier Ltd. All rights reserved.
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| 18. |
- Dufour, Louis, et al.
(författare)
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Potential energetic return on investment positively correlated with overall soil microbial activity
- 2022
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Ingår i: Soil Biology and Biochemistry. - : Elsevier BV. - 0038-0717 .- 1879-3428. ; 173
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Tidskriftsartikel (refereegranskat)abstract
- Microbial communities are a critical component of the soil carbon (C) cycle as they are responsible for the decomposition of both organic inputs from plants and of soil organic C. However, there is still no consensus about how to explicitly represent their role in terrestrial C cycling. The objective of the study was to determine how the molecular and energetic properties of readily available organic matter affect the metabolic activity of the resident microbial communities in soils. This was achieved by cross-amending six soils, taken from woodland and grassland sites along an urban pressure gradient, with organic matter extracted from the same six soils and measuring heat dissipated due to the increase in microbial metabolic activity. The energetic properties of the organic matter were used to estimate a potential energetic return on investment (ROI) that microbial communities could obtain from the transformation of the organic matter. Specifically, the ROI was calculated as the ratio between the total net energy available (ΔE) and the weighted average standard state Gibbs energies of oxidation half reactions of organic C (ΔG°Cox). ΔE was measured as the heat of combustion using bomb calorimetry. ΔG°Cox was estimated using the average nominal oxidation state of C (NOSC) of the molecular species in the organic matter. The overall metabolic activity of microbial communities was positively related to the potential energetic return on investment but no significant relationship was found with the molecular diversity of organic matter. The temporal differences in metabolism across soils indicate that bacterial communities do not exploit the potential energetic return on investment in the same way: the suburban grassland communities responded more rapidly and the suburban woodland communities more slowly to the organic matter additions than the other communities. The urban gradient did not affect the properties of the molecular or energetic properties of the organic matter nor the response of the microbial communities to the organic matter additions. However, the organic matter from the grassland soils caused soils to dissipate 36.4% more heat than organic matter from the woodland soils. The metabolic response was also more rapid after the addition of grassland organic matter: the time taken for half the heat to be dissipated was 6.4 h after the addition of grassland organic matter and 6.1 h after the addition of woodland organic matter. Overall, our results suggest that microbial communities preferentially use organic matter with a high potential energetic return on investment, i.e. organic molecules that do not require high cost associated with catalysis whilst yielding a high net energetic benefit.
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| 19. |
- Garcia, Armando Hernández, et al.
(författare)
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Isothermal microcalorimetry for rapid viability assessment of freeze-dried Lactobacillus reuteri
- 2017
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Ingår i: Process Biochemistry. - : Elsevier BV. - 1359-5113. ; 55, s. 49-54
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Tidskriftsartikel (refereegranskat)abstract
- The rapid assessment of viable cells in freeze-dried formulations of probiotic Lactobacilli is an important issue in the probiotic industry. The probiotic Lactobacillus reuteri DSM 17938 is the active ingredient of BioGaia Protectis whose viable cell concentrations are currently determined using the classical and time-consuming viable count technique. In this paper we present a rapid method based on Isothermal microcalorimetry (IMC) for viability assessment of freeze-dried DSM 17938. Fresh and rehydrated freeze-dried cells were incubated in MRS medium at different cell concentration and the thermal power (mu W) at 37 degrees C was measured over time. A linear dependence between the time to reach a certain thermal power value and the decimal logarithm of viable cells was found. This allowed rapid viability assessment of rehydrated cells, reducing the detection time from 48 h (viable count) to 10 h (microcalorimetry) in samples with 3 x 10(3) cfu/mL, and to 4 h in samples with 4 x 10(6) cfu/mL. No significant differences were found between the two methods when freeze-dried rehydrated cells were analysed (p > 0.05). Therefore, IMC is a promising tool to be used in the quality control of freeze-dried DSM 17938 as well as other bacteria-based products. (C) 2017 Elsevier Ltd. All rights reserved.
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| 20. |
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| 21. |
- Herrmann, Anke
(författare)
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Discerning Microbially Mediated Processes During Redox Transitions in Flooded Soils Using Carbon and Energy Balances
- 2018
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Ingår i: Frontiers in Environmental Science. - : Frontiers Media SA. - 2296-665X. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- Recurring dry-wet cycles of soils, such as in rice paddies and on floodplains, have a dramatic impact on biogeochemical processes. The rates and trajectories of microbial metabolic functions during transition periods from drained to flooded conditions affect the transformation rates and phase partitioning of carbon, nutrients, and contaminants. However, the regulating mechanisms responsible for diverging functional metabolisms during such transitions are poorly resolved. The chemistry of organic carbon within the microbially available pool likely holds key information regarding carbon cycling and redox transformation rates. In this study, we used mesocosms to examine the influence of different carbon sources (glucose, straw, manure, char) on microbial energetics, respiration rates, and carbon balances in rice paddy soils during the transition from drained to flooded conditions following inundation. We found that variability in carbon solubility (1.6-400 mg g(-1)) and chemical composition of the amendments led to non-uniform stimulation of carbon dioxide production per unit carbon added (0.4-32.9 mmol CO2 mol(-1) added C). However, there was a clear linear correlation between energy release and net CO2 production rate (R-2 = 0.85), between CO2 and initial soluble C (R-2 = 0.91, excluding glucose treatment) and between heat output and Gibbs free energy of initial soluble C (R-2 = 0.78 and 0.69, with/without glucose respectively). Our results further indicated that the chemical composition of the soluble C from amendments initiated divergent anaerobic respiration behavior, impacting methane production and the partitioning of elements between soil solid phase and solution. This study shows the benefit of monitoring energy and element mass balances for elucidating the contribution of various microbial metabolic functions in complex systems. Further, our results highlight the importance of organic carbon composition within the water soluble pool as a key driver of microbially mediated redox transformations with major impacts on greenhouse gas emissions, contaminant fate, and nutrient cycling in paddy soils and similar ecosystems.
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| 22. |
- Herrmann, Anke
(författare)
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Editorial: Environmental Bioenergetics
- 2019
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Ingår i: Frontiers in Environmental Science. - : Frontiers Media SA. - 2296-665X. ; 7
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Tidskriftsartikel (refereegranskat)
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| 23. |
- Herrmann, Anke, et al.
(författare)
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Energy use efficiency of root growth - a theoretical bioenergetics framework
- 2019
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Ingår i: Plant Signaling and Behavior. - : Informa UK Limited. - 1559-2316 .- 1559-2324. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- Metabolic efficiency of root growth is a crucial physiological parameter, contributing to the amount of photosynthate that plants need to invest into soil exploration. Common measurements of metabolic efficiency usually rely on CO2 respiration measurements with the underlying assumption that all metabolic processes are taking place under aerobic conditions. In this conceptual paper, we introduce energy use efficiency based on the quantification of heat dissipation and energy fluxes as an alternative metric to quantify the metabolic efficiency of root growth. In a theoretical framework, we adopted recently published heat dissipation data from wheat seedlings and show that energy use efficiency decreases in response to (i) soil hypoxia and (ii) increased soil penetration resistance. In contrast to traditional CO2 respiration measurements, heat dissipation measurements account for both aerobic as well as anaerobic respiration in growing roots. Hence, we advocate that the quantification of heat dissipation provides a more complete picture of the metabolic efficiency of root growth than CO2 respiration measurements alone. We therefore propose that energy use efficiency should be included in future studies assessing the metabolic efficiency of root growth.
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| 24. |
- Herrmann, Anke, et al.
(författare)
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Isothermal Microcalorimetry Provides New Insight into Terrestrial Carbon Cycling
- 2014
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Ingår i: Environmental Science and Technology. - : American Chemical Society (ACS). - 0013-936X .- 1520-5851. ; 48, s. 4344-4352
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Tidskriftsartikel (refereegranskat)abstract
- Energy is continuously transformed in environmental systems through the metabolic activities of living organisms, but little is known about the relationship between the two. In this study, we tested the hypothesis that microbial energetics are controlled by microbial community composition in terrestrial ecosystems. We determined the functional diversity profiles of the soil biota (i.e., multiple substrate-induced respiration and microbial energetics) in soils from an arable ecosystem with contrasting long-term management regimes (54 years). These two functional profiling methods were then related to the soils' microbial community composition. Using isothermal microcalorimetry, we show that direct measures of energetics provide a functional link between energy flows and the composition of below-ground microbial communities at a high taxonomic level (Mantel R = 0.4602, P = 0.006). In contrast, this link was not apparent when carbon dioxide (CO2) was used as an aggregate measure of microbial metabolism (Mantel R = 0.2291, P = 0.11). Our work advocates that the microbial energetics approach provides complementary information to soil respiration for investigating the involvement of microbial communities in below-ground carbon dynamics. Empirical data of our proposed microbial energetics approach can feed into carbon-climate based ecosystem feedback modeling with the suggested conceptual ecological model as a base.
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| 25. |
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| 26. |
- Herrmann, Anke
(författare)
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Monitoring soil microbial communities using molecular tools:DNAextraction methods may offset long-term management effects
- 2021
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Ingår i: European Journal of Soil Science. - : Wiley. - 1351-0754 .- 1365-2389. ; 72, s. 1026-1041
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Tidskriftsartikel (refereegranskat)abstract
- Despite recent technological advances in molecular ecology, DNA extraction from soil remains a crucial step when quantifying and characterizing soil microbial communities. Potential biases could hamper fundamental understanding of the dynamic relationships between soil properties and microorganisms under different agricultural practices. In this study, we compared four different DNA extraction methods for their ability to discriminate microbial communities of an arable soil subjected to different fertilization managements for more than 50 years (Ultuna, Sweden). The abundance and the diversity of bacteria, archaea and fungi were studied using qPCR and molecular fingerprints, respectively. Overall, the choice of DNA extraction method had a more pronounced effect on the fungal and archaeal communities in comparison to bacterial ones. The assessment of the microbial diversity was more sensitive to DNA extraction methods in comparison with the quantification of the abundances. The DNA extraction method clearly affects the intensity of the correlations between the abundance and/or diversity of microbial communities and environmental variables (C, N and pH) according to the targeted taxon. This study highlights that long-term effects can be offset by biases in DNA extraction methods. HighlightsUsing different DNA extraction methods may alter soil microbial survey. Average DNA concentrations vary from 1 to 3 mu g.g(-1)according to the extraction method. Gene copies numbers vary up to 2 orders of magnitude among DNA extraction methods. Fungal communities diversity descriptors were the most affected by DNA extraction
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| 27. |
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| 28. |
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| 29. |
- Herrmann, Anke
(författare)
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Ryegrass-derived pyrogenic organic matter changes organic carbon and nitrogen mineralization in a temperate forest soil
- 2014
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Ingår i: Soil Biology and Biochemistry. - : Elsevier BV. - 0038-0717 .- 1879-3428. ; 69, s. 291-301
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Tidskriftsartikel (refereegranskat)abstract
- Pyrogenic organic matter (PyOM) is considered as a technique to improve soil fertility and store carbon (C) in soil. However, little is known regarding soil organic C and nitrogen (N) mineralization in PyOM-amended soils. To investigate the relationship between the C and N mineralization rates and the possible consequences in terms of C storage and N availability, we incubated ryegrass-derived PyOM (pyrolyzed at 450 degrees C) enriched in C-13 (4.33 atom %) in a forest Cambisol for 158 days with and without mineral N addition. We determined PyOM and native soil organic C mineralization, NH4+ and NO3- contents in the soil, gross N mineralization, phenol-oxidase and protease activities, and microbial biomass throughout the incubation experiment and the incorporation of PyOM in microbial biomass at the end of the experiment (158 days). We determined that 4.3% of the initial PyOM-C was mineralized after 158 days. Moreover, PyOM induced a strongly positive priming effect within the first 18 days; a negative priming effect was observed from Days 18 to 158. The initial increase in organic matter mineralization corresponded to a higher gross N mineralization and NH4+ content in the PyOM-treated soil than in the untreated soil. Ammonium was rapidly transformed into nitrate and stored in this form until the end of the experiment. We conclude that the presence of PyOM affected the mineralization pattern of native soil organic matter mineralization and increased mineral N content, while N addition did not influence PyOM or soil organic matter mineralization. (C) 2013 Elsevier Ltd. All rights reserved.
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| 30. |
- Herrmann, Anke, et al.
(författare)
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Simultaneous screening of microbial energetics and CO2 respiration in soil samples from different ecosystems
- 2015
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Ingår i: Soil Biology and Biochemistry. - : Elsevier BV. - 0038-0717 .- 1879-3428. ; 83, s. 88-92
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Tidskriftsartikel (refereegranskat)abstract
- The calorespirometric ratio, i.e. the ratio of heat production-to-CO2 production has been used to evaluate metabolism and microbial carbon use efficiency in soil systems. But limited sample throughput and high variability when evaluating microbial energetics and CO2 respiration separately hampered its applicability in soil science. In this study we tested if heat flows and CO2 respiration can be determined simultaneously in the same soil sample without any measurable experimental biases. Heat outputs were not significantly different when CO2 respiration was determined concurrently by means of a colorimetric method. Our method provides a simple, cheap and rapid screening of the calorespirometric ratio, and in comparison with previous studies, the reproducibility of the ratios was improved. Its non-destructive nature allows combination with the characterization of the chemical and biological composition in soil systems. Used together these methods have the potential to improve our understanding of microbial communities, their processes and activities below-ground. (C) 2015 Elsevier Ltd. All rights reserved.
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| 31. |
- Herrmann, Anke
(författare)
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Submicron scale imaging of soil organic matter dynamics using NanoSIMS - From single particles to intact aggregates
- 2012
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Ingår i: Organic Geochemistry. - : Elsevier BV. - 0146-6380. ; 42, s. 1476-1488
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Tidskriftsartikel (refereegranskat)abstract
- The specific features of the nano-scale secondary ion mass spectrometry (NanoSIMS) technology with the simultaneous analysis of up to seven ion species with high mass and lateral resolution enables us to perform multi-element and stable isotope measurements at the submicron scale. To elucidate the power of this technique, we performed an incubation experiment with soil particles of the fine silt and clay fractions (from an Albic Luvisol), with occluded particulate organic material and intact soil aggregates (from a Haplic Chernozem), using a C-13 and N-15 labelled amino acid mixture as tracer. Before and during 6-day incubation after the addition of the label, samples were consecutively prepared for NanoSIMS analysis. For this purpose, two different sample preparation techniques were developed: (i) wet deposition and (ii) the sectioning of epoxy resin embedded samples. Single soil particles (fine silt/clay fraction) showed an enrichment of C-13 and N-15 after label addition that decreased over time. On aggregates of particulate organic matter, re-aggregated during the 6-day incubation experiment, we could show a spatially heterogeneous enrichment of C-13 and N-15 on the particle surface. The enrichment in N-15 demonstrated the diffusion of dissolved organic matter into intact soil aggregate interiors. The prospects of NanoSIMS for three dimensional studies of stable C and N isotopes in organo-mineral associations is demonstrated by the recorded depth profiles of the organic matter distribution on mineral particles. (C) 2011 Elsevier Ltd. All rights reserved.
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| 32. |
- Herrmann, Anke, et al.
(författare)
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Temperature responses of nitrogen processes cannot be inferred from carbon turnover in a boreal Norway spruce forest
- 2019
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Ingår i: Journal of Plant Nutrition and Soil Science. - : Wiley. - 1436-8730 .- 1522-2624. ; 182, s. 934-944
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Tidskriftsartikel (refereegranskat)abstract
- Cold season processes contribute substantially to annual carbon (C) and nitrogen (N) budgets in boreal forest ecosystems, but little is known about how decomposition processes are affected at temperatures prevalent during wintertime. The aim of this study was to evaluate temperature responses of soil C and N processes and to test the hypothesis that there is a switch towards decomposing N-rich material when soil temperatures drop to near 0 degrees C. In the laboratory, soils from a boreal forest long-term nutrient fertilization experiment were exposed to different temperatures varying from +2 to +15 degrees C, and C mineralization, gross as well as net N mineralization/immobilization were estimated. Carbon mineralization declined exponentially as temperature decreased, whereas the response of N processes to temperature varied, with some indication that soil C and N processes are decoupled at low temperatures. We could only partially confirm that the decoupling between C and N processes at low temperature was due to a switch to N-rich material, i.e., a change in the material undergoing decomposition. Overall, our results clearly showed that temperature responses of N processes cannot be inferred from C processes in boreal forest ecosystems, and that there is a need to improve our understanding of the relationship between the two across the range of temperatures experienced throughout the year. In particular, further research is required to establish and evaluate appropriate proxies for modelling the relationship of C and N processes at temperatures close to the freezing point.
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| 33. |
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| 34. |
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| 35. |
- Hudson, Lawrence N, et al.
(författare)
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The database of the PREDICTS (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems) project
- 2017
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Ingår i: Ecology and Evolution. - : John Wiley & Sons. - 2045-7758. ; 7:1, s. 145-188
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Tidskriftsartikel (refereegranskat)abstract
- The PREDICTS project-Projecting Responses of Ecological Diversity In Changing Terrestrial Systems (www.predicts.org.uk)-has collated from published studies a large, reasonably representative database of comparable samples of biodiversity from multiple sites that differ in the nature or intensity of human impacts relating to land use. We have used this evidence base to develop global and regional statistical models of how local biodiversity responds to these measures. We describe and make freely available this 2016 release of the database, containing more than 3.2 million records sampled at over 26,000 locations and representing over 47,000 species. We outline how the database can help in answering a range of questions in ecology and conservation biology. To our knowledge, this is the largest and most geographically and taxonomically representative database of spatial comparisons of biodiversity that has been collated to date; it will be useful to researchers and international efforts wishing to model and understand the global status of biodiversity.
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| 36. |
- Isaksson, Jenny, et al.
(författare)
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Comparison of multilocus sequence typing and multilocus typing microarray of Chlamydia trachomatis strains from Argentina and Chile
- 2016
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Ingår i: Journal of Microbiological Methods. - : Elsevier BV. - 0167-7012 .- 1872-8359. ; 127, s. 214-218
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Tidskriftsartikel (refereegranskat)abstract
- This study compared conventional ompA genotyping of Chlamydia trachomatis with multilocus sequence typing (MLST) and multilocus typing (MLT) DNA microarray. DNA extracts of 104 C trachomatis positive specimens were analyzed by ompA sequencing and MIST and of these 76 by MLT array. Obtained MIST sequence types (STs) were compared to sequences in the database http://mIstdb.uu.se. The resolution obtained for MIST (35 STs) was 2.1 higher than for ompA sequencing (17 variants) and 13 higher than MLT array (27 MLT groups). Among the 104 samples the predominant genotype E could be divided into 5 ompA variants and 23 STs of which 16 had not been reported in previous studies. The most common STs, ST3 and ST56, were identified as founders and are common in several countries on a global scale. The MIST and the MLT array provided similar strain discrimination capacity and showed considerably higher resolution than conventional ompA sequencing.
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| 37. |
- Koestel, Johannes, et al.
(författare)
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Potential of combined neutron and X-ray imaging to quantify local carbon contents in soil
- 2022
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Ingår i: European Journal of Soil Science. - : Wiley. - 1351-0754 .- 1365-2389. ; 73
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Tidskriftsartikel (refereegranskat)abstract
- In this study, we investigated the potential and limitations of using joint X-ray and time-of-flight (TOF) neutron imaging for mapping the 3-dimensional organic carbon distribution in soil. This approach is viable because neutron and X-ray beams have complementary attenuation properties. Soil minerals consist to a large part of silicon and aluminium, and elements that are relatively translucent to neutrons but attenuate X-rays. In contrast, attenuation of neutrons is strong for hydrogen, which is abundant in soil organic matter (SOM), while hydrogen barely attenuates X-rays. In theory, TOF neutron imaging does further more allow the imaging of Bragg edges, which correspond to d-spacings in minerals. This could help to distinguish between SOM and clay minerals, the mineral group in soil that is most strongly associated with hydrogen atoms. We collected TOF neutron image data at the IMAT beamline at the ISIS facility and synchrotron X-ray image data at the I12 beamline at the Diamond Light source, both located within the Rutherford Appleton Laboratory, Harwell, UK. The white beam (the full energy spectrum) neutron image clearly showed variations in neutron attenuation within soil aggregates at approximately constant X-ray attenuations. This indicates a constant bulk density with varying organic matter and/or clay content. Unfortunately, the combination of TOF neutron and X-ray imaging was not suited to allow for a distinction between SOM and clay minerals at the voxel scale. While such a distinction is possible in theory, it is prevented by technical limitations. One of the main reasons is that the neutron frequencies available at modern neutron sources are too large to capture the main d-spacings of clay minerals. As a result, inference to voxel scale SOM concentrations is presently not feasible. Future improved neutron sources and advanced detector designs will eventually overcome the technical problems encountered here. On the positive side, combined X-ray and TOF neutron imaging demonstrated abilities to identify quartz grains and to distinguish between plastics and plant seeds. Highlights Full understanding of biogeochemical processes requires three-dimensional (3-D) maps of organic matter in soil (SOM). This study investigates a novel method to map voxel-scale SOM contents with 3-D resolution. The method is based a combination of X-ray and time-of-flight neutron tomography. At present, technical limitations prevent distinguishing between SOM and clay mineral contents. More advanced neutron sources are required to overcome the encountered technical obstacles.
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| 38. |
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| 39. |
- Lerch, Thomas, et al.
(författare)
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Sensitivity of soil microbial catabolic profiles to a gradient of carbon inputs: Does the soil organic matter Matter?
- 2013
-
Ingår i: Soil Biology and Biochemistry. - : Elsevier BV. - 0038-0717 .- 1879-3428. ; 57, s. 911-915
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Tidskriftsartikel (refereegranskat)abstract
- The development of the MicroResp (TM) approach (Campbell et al., 2003) has allowed large-scale monitoring of community-level physiological profiles (CLPP). Here, we tested the sensitivity of this method to a carbon (C) substrate concentration gradient on 12 arable soils which had received contrasting long-term (53 years) managements. Irrespectively to the soil organic carbon (SOC), total activity and catabolic evenness were similar for C substrate addition above 10% C added of SOC, suggesting microbial respiratory metabolism saturation. Below this threshold. CLPP were significantly altered, especially when the amount of SOC was low. This threshold corresponded to 4 up to 10 mgC mL(-1) soil water which is 66-87% lower than used in the original approach. Such C concentrations could be used in future MicroResp (TM) assaying when determining CLPP via multi-substrate induced respiration of the microbial biomass. (C) 2012 Elsevier Ltd. All rights reserved.
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| 40. |
- Manzoni, Stefano, et al.
(författare)
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Reviews and syntheses : Carbon use efficiency from organisms to ecosystems - definitions, theories, and empirical evidence
- 2018
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Ingår i: Biogeosciences. - : COPERNICUS GESELLSCHAFT MBH. - 1726-4170 .- 1726-4189. ; 15:19, s. 5929-5949
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Forskningsöversikt (refereegranskat)abstract
- The cycling of carbon (C) between the Earth surface and the atmosphere is controlled by biological and abiotic processes that regulate C storage in biogeochemical compartments and release to the atmosphere. This partitioning is quantified using various forms of C-use efficiency (CUE) - the ratio of C remaining in a system to C entering that system. Biological CUE is the fraction of C taken up allocated to biosynthesis. In soils and sediments, C storage depends also on abiotic processes, so the term C-storage efficiency (CSE) can be used. Here we first review and reconcile CUE and CSE definitions proposed for autotrophic and heterotrophic organisms and communities, food webs, whole ecosystems and watersheds, and soils and sediments using a common mathematical framework. Second, we identify general CUE patterns; for example, the actual CUE increases with improving growth conditions, and apparent CUE decreases with increasing turnover. We then synthesize > 5000CUE estimates showing that CUE decreases with increasing biological and ecological organization - from uni-cellular to multicellular organisms and from individuals to ecosystems. We conclude that CUE is an emergent property of coupled biological-abiotic systems, and it should be regarded as a flexible and scale-dependent index of the capacity of a given system to effectively retain C.
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| 41. |
- Meurer, Katharina, et al.
(författare)
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A framework for modelling soil structure dynamics induced by biological activity
- 2020
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Ingår i: Global Change Biology. - : Wiley. - 1354-1013 .- 1365-2486. ; 26, s. 5382-5403
-
Tidskriftsartikel (refereegranskat)abstract
- Soil degradation is a worsening global phenomenon driven by socio-economic pressures, poor land management practices and climate change. A deterioration of soil structure at timescales ranging from seconds to centuries is implicated in most forms of soil degradation including the depletion of nutrients and organic matter, erosion and compaction. New soil-crop models that could account for soil structure dynamics at decadal to centennial timescales would provide insights into the relative importance of the various underlying physical (e.g. tillage, traffic compaction, swell/shrink and freeze/thaw) and biological (e.g. plant root growth, soil microbial and faunal activity) mechanisms, their impacts on soil hydrological processes and plant growth, as well as the relevant timescales of soil degradation and recovery. However, the development of such a model remains a challenge due to the enormous complexity of the interactions in the soil-plant system. In this paper, we focus on the impacts of biological processes on soil structure dynamics, especially the growth of plant roots and the activity of soil fauna and microorganisms. We first define what we mean by soil structure and then review current understanding of how these biological agents impact soil structure. We then develop a new framework for modelling soil structure dynamics, which is designed to be compatible with soil-crop models that operate at the soil profile scale and for long temporal scales (i.e. decades, centuries). We illustrate the modelling concept with a case study on the role of root growth and earthworm bioturbation in restoring the structure of a severely compacted soil.
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| 42. |
- Meurer, Katharina, et al.
(författare)
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Beyond growth: The significance of non-growth anabolism for microbial carbon-use efficiency in the light of soil carbon stabilisation
- 2024
-
Ingår i: Soil Biology and Biochemistry. - 0038-0717 .- 1879-3428. ; 193
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Tidskriftsartikel (refereegranskat)abstract
- Microbial carbon-use efficiency (CUE) in soils captures carbon (C) partitioning between anabolic biosynthesis of microbial metabolites and catabolic C emissions (i.e. respiratory C waste). The use of C for biosynthesis provides a potential for the accumulation of microbial metabolic residues in soil. Recognised as a crucial control in C cycling, microbial CUE is implemented in the majority of soil C models. Due to the models' high sensitivity to CUE, reliable soil C projections demand accurate CUE quantifications. Current measurements of CUE neglect microbial non-growth metabolites, such as extracellular polymeric substances (EPS) or exoenzymes, although they remain in soil and could be quantitatively important. Here, we highlight that disregarding non-growth anabolism can lead to severe underestimations of CUE. Based on two case studies, we demonstrate that neglecting exoenzyme and EPS production underestimates CUE by more than 100% and up to 30%, respectively. By incorporating these case-specific values in model simulations, we observed that the model projects up to 34% larger SOC stocks over a period of 64 years when non-growth metabolites are considered for estimating CUE, highlighting the crucial importance of accurate CUE quantification. Our considerations outlined here challenge the current ways how CUE is measured and we suggest improvements concerning the quantification of nongrowth metabolites. Research efforts should focus on (i) advancing CUE estimations by capturing the multitude of microbial C uses, (ii) improving techniques to quantify non-growth metabolic products in soil, and (iii) providing an understanding of dynamic metabolic C uses under different environmental conditions and over time. In the light of current discussion on soil C stabilisation mechanisms, we call for efforts to open the 'black box' of microbial physiology in soil and to incorporate all quantitative important C uses in CUE measurements.
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| 43. |
- Meurer, Katharina, et al.
(författare)
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Modelling dynamic interactions between soil structure and the storage and turnover of soil organic matter
- 2020
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Ingår i: Biogeosciences. - : Copernicus GmbH. - 1726-4170 .- 1726-4189. ; 17, s. 5025-5042
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Tidskriftsartikel (refereegranskat)abstract
- Models of soil organic carbon (SOC) storage and turnover can be useful tools to analyse the effects of soil and crop management practices and climate change on soil organic carbon stocks. The aggregated structure of soil is known to protect SOC from decomposition and, thus, influence the potential for long-term sequestration. In turn, the turnover and storage of SOC affects soil aggregation, physical and hydraulic properties and the productive capacity of soil. These two-way interactions have not yet been explicitly considered in modelling approaches. In this study, we present and describe a new model of the dynamic feedbacks between soil organic matter (SOM) storage and soil physical properties (porosity, pore size distribution, bulk density and layer thickness). A sensitivity analysis was first performed to understand the behaviour of the model. The identifiability of model parameters was then investigated by calibrating the model against a synthetic data set. This analysis revealed that it would not be possible to unequivocally estimate all of the model parameters from the kind of data usually available in field trials. Based on this information, the model was tested against measurements of bulk density, SOC concentration and limited data on soil water retention and soil surface elevation made during 63 years in a field trial located near Uppsala (Sweden) in three treatments with different organic matter (OM) inputs (bare fallow, animal and green manure). The model was able to accurately reproduce the changes in SOC, soil bulk density and surface elevation observed in the field as well as soil water retention curves measured at the end of the experimental period in 2019 in two of the treatments. Treatment-specific variations in SOC dynamics caused by differences in OM input quality could be simulated very well by modifying the value for the OM retention coefficient epsilon (0.37 for animal manure and 0.14 for green manure). The model approach presented here may prove useful for management purposes, for example, in an analysis of carbon sequestration or soil degradation under land use and climate change.
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| 44. |
- Nunan, Naoise, et al.
(författare)
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Catching change in microbial diversity indicators under different soil organic matter managements: Higher taxonomic resolution, better discrimination?
- 2022
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Ingår i: Ecological Indicators. - : Elsevier BV. - 1470-160X .- 1872-7034. ; 139
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Tidskriftsartikel (refereegranskat)abstract
- Recent advances in molecular ecology have dramatically improved our knowledge of soil microbial diversity and offers new indicators of soil quality. The usefulness of diversity indices has never been greater as the astronomical amounts of data generated in the literature needs to be synthesized. Despite technical guidelines have been proposed to characterize soil microbiomes using high throughput sequencing, the effect of taxonomic resolution on diversity indices is still largely unknown. Here, we explored how downscaling to higher taxonomic resolution levels may affect alpha-and beta-diversity indices of bacterial communities exposed to different soil organic matter management. To this aim, we collected soil samples in a long-term experimental site (Ultuna, Sweden) where different mineral and organic fertilizers have been applied for since 1956. We used both massive amplicon sequencing from phylum to species (OTU) and molecular fingerprints (PLFA, DGGE and T-RFLP). Our results showed that the discrimination potential increased at finer taxonomic resolution for beta-diversity but not for alpha-diversity indices such as richness and evenness. Also, the relative importance of hierarchical drivers of soil microbial communities such as C, N and pH varied depending on the taxonomic resolution. This study also demonstrated that indicators generated by molecular fingerprints such as PLFA, DGGE and T-RFLP are still consistent to monitor the effect of agricultural management on beta-diversity but not on alpha-diversity, which is useful information as it allows for a better use of results in past literature. We encourage performing such comparative studies on wider surveys, including different contexts and other indicators, in order to increase the efficiency and the robustness of the use of sequencing data in soil biodiversity monitoring.
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| 45. |
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| 46. |
- Nykyri, Johanna, et al.
(författare)
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Isothermal microcalorimetry for thermal viable count of microorganisms in pure cultures and stabilized formulations
- 2019
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Ingår i: Journal of Applied Toxicology. - : Springer Science and Business Media LLC. - 0260-437X .- 1099-1263. ; 19
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundQuantification of viable microorganisms is an important step in microbiological research as well as in microbial product formulation to develop biological control products or probiotics. Often, the efficiency of the resulting product is dependent on the microbial cell density and their viability, which may decrease over time. Commonly, the number of viable cells is determined by serial dilution and plating techniques or flow cytometry. In 2017, we developed a mathematical model for isothermal microcalorimetry (IMC) data analysis and showed that the new method allows for a more rapid quantification of viable fresh and freeze-dried anaerobic Lactobacillus reuteri cells than traditional viable count methods.ResultsThis study developed the new method further by applying it to well-known aerophilic plant-beneficial microbial species (Pseudomonas brassicacearum, Bacillus amyloliquefaciens subsp. plantarum and Clonostachys rosea) used in biological control products. We utilized IMC to quantify viable cells in microbial pure cultures as well as when coated onto wheat seeds. The results from this study confirmed that thermal viable count methods are more rapid and sensitive than traditional viable count techniques. Most interestingly, a thermal viable count method was able to quantify microbes coated on seeds despite the presence of the natural microbiota of the seeds. Our results also showed that, in contrast to plating techniques for which clustered cells skew the results, IMC does not require single cells for accurate viable counts.ConclusionsThermal viable count methods are novel methods for the rapid quantification of divergent bacterial and fungal species and enhance the speed, sensitivity, and accuracy of routine viable counts of pure cultures and controlled microbiomes such as plant seed coatings.
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| 47. |
- Poeplau, Christopher, et al.
(författare)
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Opposing effects of nitrogen and phosphorus on soil microbial metabolism and the implications for soil carbon storage
- 2016
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Ingår i: Soil Biology and Biochemistry. - : Elsevier BV. - 0038-0717 .- 1879-3428. ; 100, s. 83-91
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Tidskriftsartikel (refereegranskat)abstract
- Nitrogen (N) and phosphorus (P) availability plays a crucial role for carbon cycling in terrestrial ecosystems. However, the effect of nutrient supply on soil organic matter decomposition and microbial metabolism is generally not well understood. In this study, we incubated soils with three contrasting nutrient regimes from each of three Swedish long-term agricultural experiments (>45 years, 7-30% clay), namely an unfertilised control (0NPK), high P but no N fertilisation (PK0N) and high N but no P fertilisation (N-0pk). In the laboratory, we amended all soils with no fertiliser or with N, P and N P, with and without glucose, and monitored CO2 and heat production over five hours. Significant effects of the treatments were observed when nutrients were added in combination with glucose. Averaged over all field treatments, Glucose + N addition reduced CO2 and heat production by 14% and 14%, respectively, compared with glucose addition alone, while glucose + P addition increased CO2 and heat production by 17% and 9%, respectively. Similar results were found comparing the contrasting long-term field-treatments: PK0N showed higher glucose-induced CO2 and heat production per unit SOC than 0NPK, while both variables were suppressed in N-0pk-fertilised soils. Basal respiration per unit soil organic carbon (SOC) proved to be linked to long-term losses in SOC stocks, which were highest in the PK0N-fertilised plots at all three sites. Combined analyses of field and laboratory treatments revealed that the suppressing effect of laboratory N-addition on respiration only occurred in N-deficient soils, which clearly indicates that long-term N-addition alleviated N-mining. In conclusion, N and P showed opposing effects on the microbial metabolic processes, including respiration. The observed effects were similar in the short- and long-term and across different sites, which suggests that direct physiological controls of nutrients on microbial metabolism strongly regulate SOC turnover. Short-term nutrient effects were only observed in combination with a labile C source and the N-effect was restricted to N-deficient soils. Therefore, we conclude that those findings might be more important for nutrient-poor but carbon-rich ecosystems exposed to sudden nutrient inputs in comparison with nutrient rich and relatively carbon poor agricultural systems. (C) 2016 Elsevier Ltd. All rights reserved.
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| 48. |
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| 49. |
- Ruettger, Anke, et al.
(författare)
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Genotyping of Chlamydia trachomatis strains from culture and clinical samples using an ompA-based DNA microarray assay
- 2011
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Ingår i: Molecular and Cellular Probes. - : Elsevier BV. - 0890-8508 .- 1096-1194. ; 25:1, s. 19-27
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Tidskriftsartikel (refereegranskat)abstract
- Current typing methods of Chlamydia (C) trachomatis are mainly based on the diversity of the ompA gene, which is coding for the major outer membrane protein A. The present study aimed at facilitating genotyping of strains of this obligate intracellular human pathogen by developing a DNA microarray assay using the ArrayTube (TM) format for individual samples and the ArrayStrip (TM) format for higher throughput. The new test is exploiting multiple discriminatory sites by involving a total of 61 oligonucleotide probes representing genotype-specific polymorphisms in variable domains 1, 2 and 4 of the ompA gene. After multiplex amplification of these domains using biotinylated primers, the sample is hybridized in the microarray vessel under highly stringent conditions. The resulting binding pattern is genotype specific, thus allowing direct identification. We were able to show that DNA from each of the currently accepted genotypes (serovars) yielded a unique, theoretically expected and distinct hybridization pattern. The assay was also shown to be highly sensitive as a dilution containing the equivalent of 1 inclusion-forming unit was still correctly genotyped. In addition, when 62 clinical samples were examined and compared to PCR-RFLP typing results, the genotype was correctly identified by the DNA microarray in all cases. The present test is easy to handle and economically affordable, and it allows genotyping of C. trachomatis to be accomplished within a working day, thus lending itself for epidemiological studies and routine diagnosis.
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- Rönnberg Wästljung, Ann-Christin, et al.
(författare)
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Optimized utilization of Salix—Perspectives for the genetic improvement toward sustainable biofuel value chains
- 2022
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Ingår i: Global Change Biology Bioenergy. - : John Wiley and Sons Inc. - 1757-1693 .- 1757-1707. ; 14:10, s. 1128-144
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Tidskriftsartikel (refereegranskat)abstract
- Bioenergy will be one of the most important renewable energy sources in the conversion from fossil fuels to bio-based products. Short rotation coppice Salix could be a key player in this conversion since Salix has rapid growth, positive energy balance, easy to manage cultivation system with vegetative propagation of plant material and multiple harvests from the same plantation. The aim of the present paper is to provide an overview of the main challenges and key issues in willow genetic improvement toward sustainable biofuel value chains. Primarily based on results from the research project “Optimized Utilization of Salix” (OPTUS), the influence of Salix wood quality on the potential for biofuel use is discussed, followed by issues related to the conversion of Salix biomass into liquid and gaseous transportation fuels. Thereafter, the studies address genotypic influence on soil carbon sequestration in Salix plantations, as well as on soil carbon dynamics and climate change impacts. Finally, the opportunities for plant breeding are discussed using willow as a resource for sustainable biofuel production. Substantial phenotypic and genotypic variation was reported for different wood quality traits important in biological (i.e., enzymatic and anaerobic) and thermochemical conversion processes, which is a prerequisite for plant breeding. Furthermore, different Salix genotypes can affect soil carbon sequestration variably, and life cycle assessment illustrates that these differences can result in different climate mitigation potential depending on genotype. Thus, the potential of Salix plantations for sustainable biomass production and its conversion into biofuels is shown. Large genetic variation in various wood and biomass traits, important for different conversion processes and carbon sequestration, provides opportunities to enhance the sustainability of the production system via plant breeding. This includes new breeding targets in addition to traditional targets for high yield to improve biomass quality and carbon sequestration potential. © 2022 The Authors.
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