Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Nitrogen-Induced Changes in Soil Environmental Factors Are More Important Than Nitrification and Denitrification Gene Abundance in Regulating N2O Emissions in Subtropical Forest Soils

Subtropical regions are currently experiencing a dramatic increase in nitrogen (N) deposition; however, the contributions of nitrification and denitrification processes to soil N2O emissions and the underlying mechanisms under increasing N deposition remain unclear. Therefore, a 15N-tracing laboratory experiment with four N application rates (0, 12.5, 25, and 50 μg 15N g–1 soil) was conducted to investigate the response of nitrification- and denitrification-derived N2O to N additions in an evergreen broad-leaved forest (BF) and a Pinus forest (PF) in the Wuyi Mountains in southeastern China. Moreover, the abundance of functional genes related to nitrification (amoA), denitrification (nirK, nirS, and nosZ), and soil properties were measured to clarify the underlying mechanisms. Results showed that nitrification-derived N2O emissions were generally decreased with increasing N input. However, denitrification-derived N2O emissions were a non-linear response to N additions, with maximum N2O emissions at the middle N application rate. Denitrification-derived N2O was the dominant pathway of N2O production, accounting for 64 to 100% of the total N2O fluxes. Soil NH4+-N content and pH were the predominant factors in regulating nitrification-derived N2O emissions in BF and PF, respectively. Soil pH and the nirS abundance contributed the most to the variations of denitrification-derived N2O emissions in BF and PF, respectively. Our results suggest that N application has the potential to increase the contribution of denitrification to N2O production in subtropical forest soils. Changes in soil chemical properties induced by N addition are more important than the abundance of nitrification and denitrification functional genes in regulating soil nitrification- and denitrification-derived N2O emissions.</jats:p

Arbuscular mycorrhizal fungi mitigate soil nitrogen and phosphorus losses: A meta-analysis

Nutrient loss from terrestrial ecosystems via leaching and gaseous emissions is increasingly threatening global environmental and human health. Although arbuscular mycorrhizal fungi (AMF) have been shown to regulate soil N and P losses, a comprehensive quantitative overviewof their influences on the losses of these soil nutrients across global scales is currently lacking. This study used a meta-analysis of 322 observations from 36 studies to assess the effect of AMF inoculum on 11 variables related to the loss of soil N and P.We found that the presence of AMF significantly reduced soil N and P losses, with the most pronounced reduction occurring in soil NO3 –N (−32%), followed by total P (−21%), available P (−16%) and N2O (−10%). However, the mitigation effects of AMF on soil N and P loss were dependent on the identity of AMF inoculum, plant type and soil biotic and abiotic factors. Generally, the mitigation effects of AMF increased with increasing AMF root colonization rate, microbial diversity of inoculants, soil organic carbon (SOC) content and experimental duration as well as with decreasing soil sand contents and soil N and P availability. Overall, this meta-analysis highlights the importance of AMF inoculation inmitigating N and P nutrient loss and environmental pollution for terrestrial ecosystem sustainability

Different effects of plant-derived dissolved organic matter (DOM) and urea on the priming of soil organic carbon

Plant-derived dissolved organic matter, a complex labile substrate, was used to investigate its effect on SOC priming and sequestration.</p

Changes in Soil Properties and Enzyme Stoichiometry in Three Different Forest Types Changed to Tea Plantations

Understanding the characteristics and driving factors of soil carbon, nitrogen, phosphorus, and enzyme stoichiometry during land use/cover change is of great significance for assessing microbial nutrient restriction and sustainable land development during the process. China, the world&rsquo;s largest tea producer, is witnessing a significant expansion of tea plantations into previously forested areas. We performed field sampling in three forest types with the area partially converted to tea plantations in Wuyishan National Park. We examined the changes in soil carbon (TC), nitrogen (TN), phosphorus (TP), and three kinds of extracellular enzyme activities, &beta;-glucosidase (BG), &beta;-n-acetylglucosidase (NAG), and acid phosphatase (ACP). By analyzing the enzyme stoichiometric ratio, vector length (VL), and vector angle (VA), the relative nutrient limitations of soil microorganisms were explored. The results showed that soil TC and TN decreased significantly (p &lt; 0.05), TP increased significantly, and soil carbon (C):nitrogen (N), carbon (C):phosphorus (P), and nitrogen (N):phosphorus (P) ratios decreased significantly after the conversion of forest land to tea plantation. Soil BG, NAG, and ACP contents decreased significantly (p &lt; 0.05). There were no significant differences in enzyme carbon:nitrogen ratios (EC/N), enzyme carbon:phosphorus ratios (EC/P), enzyme nitrogen:phosphorus ratios (EN/P), VL, or VA (p &gt; 0.05). Through the analysis of soil enzyme stoichiometry, it was found that forest soil was generally limited by P, which was, to some extent, relieved after the conversion to tea plantation. Redundancy analysis showed that TC, TN, and the C:N ratio were the main factors influencing enzyme activity and stoichiometry. These results indicated that land use/cover change had significant effects on soil nutrient status, enzyme activity, and stoichiometry. Soil enzyme activity is very sensitive to the changes in soil nutrients and can reflect the restriction of soil nutrients more accurately

Effects of different forms of plant-derived organic matter on nitrous oxide emissions

To investigate the impact of different forms of plant-derived organic matter on nitrous oxide (N2O) emissions, an incubation experiment with the same rate of total nitrogen (N) application was carried out at 25 degrees C for 250 days. Soils were incorporated with maize-derived organic matter (i. e., maize residuederived dissolved organic matter and maize residues with different C/N ratios) and an inorganic N fertilizer (urea). The pattern and magnitude of nitrous oxide (N2O) emissions were affected by the form of N applied. Single application of maize-derived organic matter resulted in a higher N2O emission than single application of the inorganic N fertilizer or combined application of the inorganic N fertilizer and maize-derived organic matter. The positive effect of maize residue-derived dissolved organic matter (DOM) addition on N2O emissions was relatively short-lived and mainly occurred at the early stage following DOM addition. In contrast, the positive effect induced by maize residue addition was more pronounced and lasted for a longer period. Single application of maize residues resulted in a substantial decrease in soil nitric nitrogen (NO3- -N), but it did not affect the production of N2O. No significant relationship between N2O emission and NO3--N and ammonium nitrogen (NH4+-N) suggested that the availability of soil N was not limiting the production of N2O in our study. The key factors affecting soil N2O emission were the soil dissolved organic carbon (DOC) content and metabolism quotient (qCO(2)). Both of them could explain 87% of the variation in cumulative N2O emission. The C/N ratio of maizederived organic matter was a poor predictor of N2O emission when the soil was not limited by easily available C and the available N content met the microbial N demands for nitrification and denitrification. The results suggested that the magnitude of N2O emission was determined by the impact of organic amendments on soil C availability and microbial activity rather than on soil N availability. In agricultural management practices, if the N inputs from organic and inorganic N fertilizers are equivalent, addition of organic N fertilizers that contain high amounts of available C will result in a higher N2O emission