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Soil microbial communities are involved in most biogeochemical processes creating hotspots for nutrient cycling. The spatial visualization of such soil hotspots via microscopic techniques is still challenging caused by the intrinsic fluorescence and opacity of the soil. One way to differentiate microbial cells from the heterogeneous soil matrix is a fluorescence lifetime-based technique (FLIM) with subsequent phasor plot separation; it separates and visualizes the distinctly different photon arrival times of all photons per pixel. FLIM delivers additional independent information behind intensity-based image processing and image analysis which is often hampered by, e.g., autofluorescence, resolution issues, and photobleaching artifacts caused by the prevailing minerals and organic substances. We determined characteristic fluorescence lifetime profiles of BacLight™ Green for Rhodotorula mucilaginosa and Bacillus subtilits in phosphate-buffered saline (PBS) solution and water as well as in natural, autoclaved, glucose-activated, and soil mineral particles by FLIM measurements via confocal laser scanning fluorescence microscopy. Rhodotorula mucilaginosa and Bacillus subtilits from pure cultures measured in water and PBS accounted for 1.20 (± 0.2) ns and 1.3 (± 0.1) ns respectively. The lifetime profile within the cells was rather homogeneous for both microbial species tested. This suggests stable photon arrival times for microbial strains with minor effects of matrix components as tested in PBS and water. We identified a clear difference in fluorescence lifetime profiles between microorganisms (around 1 ns) and the surrounding soil matrix (0.2 to 0.7 ns, > 3.6 ns) via phasor plot separation. The results presented raise the feasibility to extend the applicability of FLIM to other soils and their accompanying microbiota. [ABSTRACT FROM AUTHOR]

The transformation and turnover time of medium- to long-chain dicarboxylic acids (DCA) in soil is regulated by microbial uptake and mineralization. However, the chain length of n-alkyl lipids may have a remarkable influence on its microbial utilization and mineralization and therefore on the formation of stable soil organic carbon from e.g. leave- needle- and root-derived organic matter during decomposition. To investigate their size dependent mineralization and microbial incorporation, four DCA of different chain lengths (12–30 carbon atoms), that were 13C labeled at each of their terminal carboxylic groups, were applied to the Ah horizon of a Fluvic Gleysol. Incorporation of 13C into CO2 and in distinct microbial groups classified by phospholipid fatty acid (PLFA) analysis was investigated. Mineralization of DCA and incorporation into PLFA decreased with increasing chain length, and the mineralization rate was highest during the first days of incubation. Half-life time of DCA carbon in soil increased from 7.6 days for C12 DCA to 86.6 days for C18 DCA and decreased again to 46.2 days for C22 DCA, whereas C30 DCA had the longest half-life time. Rapid and efficient uptake of C12 DCA as an intact molecule was observable. Gram-negative bacteria incorporated higher amounts of DCA-derived 13C compared to other microbial groups, especially compared to actinomycetes and fungi during the first phase of incubation. However, the incorporation of C12 DCA derived 13C into the PLFA of actinomycetes, and fungi increased steadily during the entire incubation time, suggesting that those groups take up the 13C label from necromass of bacteria that used the C12 DCA for formation of their lipids before. [ABSTRACT FROM AUTHOR]

Aims: Microbial turnover processes are typically restricted by low substrate availability in the subsoil. We hypothesized that SOM decomposition increases with plant density and decreases with N fertilization: We expected a greater rate of C allocation to the rhizosphere in the topsoil than in the subsoil treatments. Methods: In order to simulate different degrees of rhizodeposition, wheat was planted in pots at four different densities. The plants were continuously labeled with 13C-depleted CO2. Soil CO2 efflux was partitioned for root- and SOM-derived CO2. Moreover, we determined the enzyme kinetics by measuring catalytic efficiency and enzyme stoichiometry in both topsoil and subsoil. Results: Shoot biomass and the shoot to root ratio were significantly higher for plants grown in the topsoil compared with the subsoil, which demonstrated higher relative C allocation to root biomass in the subsoil treatment. Despite the similar size of the rhizosphere, root-derived CO2 was always higher in the topsoil compared with the subsoil treatment, indicating enhanced root exudation. Effect sizes of all enzyme activities showed stronger magnitudes for the subsoil treatments. This was in line with a two-times increase of the effect size of SOM decomposition in the subsoil relative to topsoil. Conclusions: Overall, the plants in the subsoil treatments allocated more C to root biomass, less C to shoot biomass, and substantially less C to root exudates. However, the effect sizes of both SOM decomposition and enzyme activities were higher in the subsoil than in the topsoil, reflecting a stronger sensitivity to C inputs. [ABSTRACT FROM AUTHOR]

Responsible editor: Edward Brzostek, Ph.D. B Correction to: Biogeochemistry (2022) 162:79-95 b https://doi.org/10.1007/s10533-022-00990-0 The paper was updated as the phrase: "Furthermore, actinobacteria with the alkB gene were shown to be able to grow on n-alkanes with lengths ranging from C10 to C19 as their sole source of carbon and energy (Ratajczak et al. 1998; Gibu et al. 2019)." Should be corrected to: "Furthermore, actinobacteria and proteobacteria with the alkB gene were shown to be able to grow on n-alkanes with lengths ranging from C10 to C19 as their sole source of carbon and energy (Ratajczak et al. 1998; Gibu et al. 2019)". [Extracted from the article]