1,721,918 research outputs found
How to link soil C pools with CO<sub>2</sub> fluxes?
No full textDespite the importance of carbon (C) pools and CO2 fluxes in terrestrial ecosystems and especially in soils, as well as many attempts to assign fluxes to specific pools, this challenge remains unsolved. Interestingly, scientists investigating pools are not closely linked with scientists studying fluxes. This review therefore focused on experimental approaches enabling soil C pools to be linked with CO2 flux from the soil. The background, advantages and shortcomings of uncoupled approaches (measuring only pools or fluxes) and of coupled approaches (measuring both pools and fluxes) were evaluated and their prerequisites – steady state of pools and isotopic steady state – described. The uncoupled approaches include: (i) monitoring the decrease of C pools in long-term fallow bare soil lacking C input over decades, (ii) analyzing components of CO2 efflux dynamics by incubating soil without new C input over months or years, and (iii) analyzing turnover rates of C pools based on their 13C and 14C isotopic signature. The uncoupled approaches are applicable for non-steady state conditions only and have limited explanatory power. The more advantageous coupled approaches partition simultaneously pools and fluxes based on one of three types of changes in the isotopic signature of input C compared to soil C: (i) abrupt permanent, (ii) gradual permanent, and (iii) abrupt temporary impacts. I show how the maximal sensitivity of the approaches depends on the differences in the isotopic signature of pools with fast and slow turnover rates. The promising coupled approaches include: (a) δ13C of C pools and CO2 efflux from soil after C3/C4 vegetation changes or in FACE experiments (both corresponding to continuous labeling), (b) addition of 13C or 14C labeled organics (corresponding to pulse labeling), and (c) bomb-14C. I show that physical separation of soil C pools is not a prerequisite to estimate pool size or to link pools with fluxes. Based on simple simulation of C aging in soil after the input, the discordance of MRT of C in pools and of C released in CO2 was demonstrated. This discordance of MRT between pools and fluxes shows that the use of MRT of pools alone underestimates the fluxes at least for two times. The future challenges include combining two or more promising approaches to elucidate more than two C sources for CO2 fluxes, and linking scientific communities investigating the pools with those investigating the fluxes
Active microorganisms in soil: Critical review of estimation criteria and approaches
No full textMicrobial functioning refers to microbial activity because only the active microorganisms drive biogeochemical processes. Despite the importance of active microorganisms, most methods focus on estimating total microbial biomass and fail to evaluate its active fraction. At first, we have described the differences among the active, potentially active, and dormant microbial states in soil and suggested threshold values of parameters for their identification. Secondly, we critically reviewed the ability of a broad range of approaches to estimate and characterize the active and the potentially active microorganisms in soil. Following approaches were evaluated: plate count and microbial cultures; direct microscopy combined with cell staining; ATP, PLFA, DNA and RNA content; microarray analyses; PCR-based approaches: stable isotope probing; soil proteomics, enzymes activity; and various approaches based on respiration and substrate utilization. The "static" approaches, mainly based on the single-stage determination of cell components (ATP, DNA, RNA, and molecular biomarkers), detect well the presence of microorganisms and total biomass, but they fail to evaluate the active part and consequently the functions. In contrast, the dynamic approaches, estimating the changes of these parameters during microbial growth and based on process rates: substrate utilization and product formation, e.g., respiration, help to evaluate active microbial biomass and relate it to specific process rates. Based on a comparison of all approaches for their universality (possibility to analyze active, potentially active and dormant microorganisms), we concluded that 1) direct microscopy with complementary stains, 2) a combination of RNA-based FISH with staining of total microbial biomass, and 3) approaches based on microbial growth were the most advantageous and allowed simultaneous quantitative estimation of active, potentially active, and dormant microorganisms in soil. The active microorganisms compose only about 0.1-2% of the total microbial biomass and very seldom exceed 5% in soils without input of easily available substrates. Nonetheless, the fraction of potentially active microorganisms (ready to start utilization of available substrates within few hours) is much higher, contributing between 10 and 40% (up to 60%) of the total microbial biomass. Therefore, we emphasize the role of potentially active microorganisms with quick response to fluctuating substrate input in soil microhabitats and hotspots. The transition from the potentially active to the active state occurs in minutes to hours, but the shift from dormant to active state takes anywhere from hours to days. Despite very fast activation, the reverse process - fading to the potentially active and dormant stage - requires a much longer period and is very different for individual criteria: ATP, DNA, RNA, enzyme production, respiration rates. This leads to further difficulties in the estimation of the active part of microbial community by methods based on these parameters. Consequently, the standardization, further elaboration, and broad application of approaches focused on the portion of active microorganisms in soil and their functions are urgently needed. We conclude that because active microorganisms are the solely microbial drivers of main biogeochemical processes, analyses of the active and potentially active fractions are necessary in studies focused on soil functions. (C) 2013 Elsevier Ltd. All rights reserved
Sugars in soil and sweets for microorganisms: Review of origin, content, composition and fate
No full textSugars are the most abundant organic compounds in the biosphere because they are monomers of all polysaccharides. We summarize the results of the last 40 years on the sources, content, composition and fate of sugars in soil and discuss their main functions. We especially focus on sugar uptake, utilization and recycling by microorganisms as this is by far the dominating process of sugar transformation in soil compared to sorption, leaching or plant uptake. Moreover, sugars are the most important carbon (C) and energy source for soil microorganisms. Two databases have been created. The 1st database focused on the contents of cellulose, non-cellulose, hot-water and cold-water extractable sugars in soils (348 data, 32 studies). This enabled determining the primary (plant-derived) and secondary (microbially and soil organic matter (SUM) derived) sources of carbohydrates in soil based on the galactose + mannose/arabinose + xylose (GM/AX) ratio. The 2nd database focused on the fate of sugar C in soils (734 data pairs, 32 studies using C-13 or C-14 labeled sugars). C-13 and C-14 dynamics enabled calculating the: 1) initial rate of sugar mineralization, 2) mean residence time (MRT) of C of the applied sugars, and 3) MRT of sugar C incorporated into 3a) microbial biomass and 3b) SOM. The content of hexoses was 3-4 times higher than pentoses, because hexoses originate from plants and microorganisms. The GM/AX ratio of non-cellulose sugars revealed a lower contribution of hexoses in cropland and grassland (ratio 0.7-1) compare to forest (ratio 1.5) soils. C-13 and C-14 studies showed very high initial rate of glucose mineralization (1.1% min(-1)) and much higher rate of sugars uptake by microorganisms from the soil solution. Considering this rate along with the glucose input from plants and its content in soil solution, we estimate that only about 20% of all sugars in soil originate from the primary source - decomposition of plant litter and rhizodeposits. The remaining 80% originates from the secondary source - microorganisms and their residues. The estimated MRT of sugar C in microbial biomass was about 230 days, showing intense and efficient internal recycling within microorganisms. The assessed MRT of sugar C in SUM was about 360 days, reflecting the considerable accumulation of sugar C in microbial residues and its comparatively slow external recycling. The very rapid uptake of sugars by microorganisms and intensive recycling clearly demonstrate the importance of sugars for microbes in soil. We speculate that the most important functions of sugars in soil are to maintain and stimulate microbial activities in the rhizosphere and detritusphere leading to mobilization of nutrients by accelerated SUM decomposition - priming effects. We conclude that the actual contribution of sugar C (not only whole sugar molecules, which are usually determined) to SOM is much higher than the 10 +/- 5% commonly measured based on their content. (C) 2015 Elsevier Ltd. All rights reserved
Distribution of microbial- and root-derived phosphatase activities in the rhizosphere depending on P availability and C allocation - Coupling soil zymography with C-14 imaging
No full textDespite its importance for terrestrial nutrient and carbon cycling, the spatial organization of microbial activity in soil and in the rhizosphere is poorly understood. We related carbon allocation by roots to distribution of acid and alkaline phosphatase activity in the rhizosphere of Lupinus albus L To do so, we further developed soil zymography - an in situ method for the analysis of the two-dimensional distribution of enzyme activity in soil - integrating fluorescent substrates. Soil zymography was combined with C-14 imaging, a technique that gives insights into the distribution of photosynthates after labeling plants with C-14. Both acid and alkaline phosphatase activity were up to 5.4-times larger in the rhizosphere than in the bulk soil. While acid phosphatase activity (produced by roots and microorganisms) was closely associated with roots, alkaline phosphatase activity (produced only by microorganisms) was more widely distributed, leading to a 2.5-times larger area of activity of alkaline than of acid phosphatase. These results indicate a spatial differentiation of different ecophysiological groups of organic P mineralizing organisms. The spatial differentiation could be either between microorganisms and L albus or between microorganisms that produce exclusively alkaline phosphatases on the one hand, and L albus and root associated microorganisms that produce acid phosphatases on the other hand. The spatial separation of different organic P mineralizing organisms might alleviate a potential competition between them. While alkaline phosphatase activity strongly decreased with P fertilization, acid phosphatase activity was not affected by fertilization, suggesting that alkaline phosphatase-producing microorganisms react more strongly to it than other organic P mineralizing organisms. Alkaline phosphatase activity was high in parts of the rhizosphere where relatively little recent photosynthates were allocated, indicating that rhizodeposition and the activity of alkaline phosphatase-producing microorganisms are not directly related. Our study indicates, first, a spatial differentiation of organic P mineralization by various ecophysiological groups that react differently to inorganic P fertilization and second, that rhizodeposition and alkaline phosphatase-producing microorganisms were not directly related. Finally, we conclude that soil zymography with fluorescent substrates is a very promising approach for studying the distribution of a broad range of extracellular enzymes at microscales. (C) 2013 Elsevier Ltd. All rights reserved.German Research Foundation [SP-1389, SPP 1685
Soil organic matter priming: The pH effects
No full textAbstract Priming of soil organic matter (SOM) decomposition by microorganisms is a key phenomenon of global carbon (C) cycling. Soil pH is a main factor defining priming effects (PEs) because it (i) controls microbial community composition and activities, including enzyme activities, (ii) defines SOM stabilization and destabilization mechanisms, and (iii) regulates intensities of many biogeochemical processes. In this critical review, we focus on prerequisites and mechanisms of PE depending on pH and assess the global change consequences for PE. The highest PEs were common in soils with pH between 5.5 and 7.5, whereas low molecular weight organic compounds triggered PE mainly in slightly acidic soils. Positive PEs up to 20 times of SOM decomposition before C input were common at pH around 6.5. Negative PEs were common at soil pH below 4.5 or above 7 reflecting a suboptimal environment for microorganisms and specific SOM stabilization mechanisms at low and high pH. Short‐term soil acidification (in rhizosphere, after fertilizer application) affects PE by: mineral‐SOM complexation, SOM oxidation by iron reduction, enzymatic depolymerization, and pH‐dependent changes in nutrient availability. Biological processes of microbial metabolism shift over the short‐term, whereas long‐term microbial community adaptations to slow acidification are common. The nitrogen fertilization induced soil acidification and land use intensification strongly decrease pH and thus boost the PE. Concluding, soil pH is one of the strongest but up to now disregarded factors of PE, defining SOM decomposition through short‐term metabolic adaptation of microbial groups and long‐term shift of microbial communities
Reviews and syntheses: Agropedogenesis – humankind as the sixth soil-forming factor and attractors of agricultural soil degradation
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