Mammalian mitochondrial DNA (mtDNA) is packaged by mitochondrial transcription factor A (TFAM) into mitochondrial nucleoids that are of key importance in controlling the transmission and expression ...of mtDNA. Nucleoid ultrastructure is poorly defined, and therefore we used a combination of biochemistry, superresolution microscopy, and electron microscopy to show that mitochondrial nucleoids have an irregular ellipsoidal shape and typically contain a single copy of mtDNA. Rotary shadowing electron microscopy revealed that nucleoid formation in vitro is a multistep process initiated by TFAM aggregation and cross-strand binding. Superresolution microscopy of cultivated cells showed that increased mtDNA copy number increases nucleoid numbers without altering their sizes. Electron cryo-tomography visualized nucleoids at high resolution in isolated mammalian mitochondria and confirmed the sizes observed by superresolution microscopy of cell lines. We conclude that the fundamental organizational unit of the mitochondrial nucleoid is a single copy of mtDNA compacted by TFAM, and we suggest a packaging mechanism.
Increasing demand for biofuel has intensified land-use change (LUC) for sugarcane (Saccharum officinarum) expansion in Brazil. Assessments of soil quality (SQ) response to this LUC are essential for ...quantifying and monitoring sustainability of sugarcane production over time. Since there is not a universal methodology for assessing SQ, we conducted a field-study at three sites within the largest sugarcane-producing region of Brazil to develop a SQ index (SQI). The most common LUC scenario (i.e., native vegetation to pasture to sugarcane) was evaluated using six SQI strategies with varying complexities. Thirty eight soil indicators were included in the total dataset. Two minimum datasets were selected: one using principal component analysis (7 indicators) and the other based on expert opinion (5 indicators). Non-linear scoring curves were used to interpret the indicator values. Weighted and non-weighted additive methods were used to combine individual indicator scores into an overall SQI. Long-term conversion from native vegetation to extensive pasture significantly decreased overall SQ. In contrast, conversion from pasture to sugarcane had no significant impact on overall SQ at the regional scale, but site-specific responses were found. In general, sugarcane production improved chemical attributes (i.e., higher macronutrient levels and lower soil acidity); however it has negative effects on physical and biological attributes (i.e., higher soil compaction and structural degradation as well as lower soil organic carbon (SOC), abundance and diversity of macrofauna and microbial activity). Overall, we found that simple, user-friendly strategies were as effective as more complex ones for identifying SQ changes. Therefore, as a protocol for SQ assessments in Brazilian sugarcane areas, we recommend using a small number of indicators (e.g., pH, P, K, Visual Evaluation of Soil Structure -VESS scores and SOC concentration) and proportional weighting to reflect chemical, physical and biological processes within the soil. Our SQ evaluations also suggest that current approaches for expanding Brazilian sugarcane production by converting degraded pasture land to cropland can be a sustainable strategy for meeting increasing biofuel demand. However, management practices that alleviate negative impacts on soil physical and biological indicators must be prioritized within sugarcane producing areas to prevent unintentional SQ degradation over time.
It is clear that the density and porosity of biochar will impact its mobility in the environment, its interaction with the soil hydrologic cycle, and its suitability as an ecological niche for soil ...microorganisms. However, the wide range of biochar pore sizes complicates biochar porosity characterization, making it challenging to find methods appropriate to connect the fundamental physical properties of density and porosity to environmental outcomes. Here, we report the use of two fast, simple density measurement techniques to characterize biochar density and porosity. We measured biochar skeletal density by helium pycnometry and envelope density by displacement of a dry granular suspension. We found that biochar skeletal density ranged from 1.34 g cm−3 to 1.96 g cm−3, and increased with pyrolysis temperature. Biochar envelope density ranged from 0.25 g cm−3 to 0.60 g cm−3, and was higher for wood biochars than grass biochars—a difference we attribute to plant cell structures preserved during pyrolysis. We compared the pore volumes measured by pycnometry with those measured by nitrogen gas sorption and mercury porosimetry. We show that biochar pore volumes measured by pycnometry are comparable to the values obtained by mercury porosimetry, the current benchmark method. We also show that the majority of biochar pore volume is in macropores, and thus, is not measured by gas sorption analysis. These fast, simple techniques can now be used to study the relationship between biochar's physical properties and its environmental behaviors.
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•Biochar's density and porosity relate to its environmental interactions and transport.•Biochar porosity is difficult to characterize due the wide range of pore sizes.•We measured biochar porosity by combining skeletal and envelope density measurements.•Biochar skeletal density increases with pyrolysis temperature.•Biochar envelope density and porosity vary primarily with biomass feedstock.
In the short‐term heterotrophic soil respiration is strongly and positively related to temperature. In the long‐term, its response to temperature is uncertain. One reason for this is because in field ...experiments increases in respiration due to warming are relatively short‐lived. The explanations proposed for this ephemeral response include depletion of fast‐cycling, soil carbon pools and thermal adaptation of microbial respiration. Using a > 15 year soil warming experiment in a mid‐latitude forest, we show that the apparent ‘acclimation’ of soil respiration at the ecosystem scale results from combined effects of reductions in soil carbon pools and microbial biomass, and thermal adaptation of microbial respiration. Mass‐specific respiration rates were lower when seasonal temperatures were higher, suggesting that rate reductions under experimental warming likely occurred through temperature‐induced changes in the microbial community. Our results imply that stimulatory effects of global temperature rise on soil respiration rates may be lower than currently predicted.
The sirtuin enzymes are a family of lysine deacylases that regulate gene transcription and metabolism. Sirtuin 5 (SIRT5) hydrolyzes malonyl, succinyl, and glutaryl ϵ‐N‐carboxyacyllysine ...posttranslational modifications and has recently emerged as a vulnerability in certain cancers. However, chemical probes to illuminate its potential as a pharmacological target have been lacking. Here we report the harnessing of aryl fluorosulfate‐based electrophiles as an avenue to furnish covalent inhibitors that target SIRT5. Alkyne‐tagged affinity‐labeling agents recognize and capture overexpressed SIRT5 in cultured HEK293T cells and can label SIRT5 in the hearts of mice upon intravenous injection of the compound. This work demonstrates the utility of aryl fluorosulfate electrophiles for targeting of SIRT5 and suggests this as a means for the development of potential covalent drug candidates. It is our hope that these results will serve as inspiration for future studies investigating SIRT5 and general sirtuin biology in the mitochondria.
SuFEx warheads installed into a previously developed inhibitor scaffold that targets the sirtuin 5 (SIRT5) deacylase, furnish covalently labeling inhibitors that pull down the enzyme from cells and tissue. With further optimization of the compound's potencies, this proof‐of‐concept study may provide the foundation for development of highly efficient covalent chemical probes and/or drug lead compounds targeting SIRT5.
Plant-carbon inputs to soils in the form of dissolved sugars, organic acids and amino acids fuel much of heterotrophic microbial activity belowground. Initial residence times of these compounds in ...the soil solution are on the order of hours, with microbial uptake a primary removal mechanism. Through microbial biosynthesis, the dissolved compounds become dominant precursors for formation of stable soil organic carbon. How the chemical class (e.g. sugar) of a dissolved compound influences stabilization in field soils is unknown and predictions from our understanding of microbial metabolism, turnover and identity are contradictory. We show that soil carbon formation, from chronic amendments of dissolved compounds to fertilized and unfertilized grasslands, is 2.4-times greater from a sugar than an amino acid. Formation rates are negatively correlated with respiration rates of the compounds, and positively correlated with their recovery in microbial biomass. These relationships suggest that the efficiency of microbial growth on a compound is positively related to formation rates of soil organic carbon. Fertilization does not alter these findings, but together nitrogen and phosphorus additions reduce soil carbon formation. Our results highlight the need to consider both nutrient enrichment and global-change induced shifts in the form of dissolved root inputs to soils to predict future soil carbon stocks and hence phenomena such as climate warming and food security to which these stock sizes are intimately tied.
To store substantial amounts of carbon in natural climate solutions the strong interlinkages between carbon and nitrogen cycling must be considered. There are many agricultural management options for ...increasing soil organic carbon stocks but each approach must be evaluated in context of the full, net greenhouse gas balance. This requires a detailed understanding of the implications of increased nitrogen demand to store organic forms of carbon in soil, on potential nitrous oxide emissions in particular.
Manual measurements of nitrous oxide (N2O) emissions with static chambers are commonly practised. However, they generally do not consider the diurnal variability of N2O flux, and little is known ...about the patterns and drivers of such variability. We systematically reviewed and analysed 286 diurnal data sets of N2O fluxes from published literature to (i) assess the prevalence and timing (day or night peaking) of diurnal N2O flux patterns in agricultural and forest soils, (ii) examine the relationship between N2O flux and soil temperature with different diurnal patterns, (iii) identify whether non‐diurnal factors (i.e. land management and soil properties) influence the occurrence of diurnal patterns and (iv) evaluate the accuracy of estimating cumulative N2O emissions with single‐daily flux measurements. Our synthesis demonstrates that diurnal N2O flux variability is a widespread phenomenon in agricultural and forest soils. Of the 286 data sets analysed, ~80% exhibited diurnal N2O patterns, with ~60% peaking during the day and ~20% at night. Contrary to many published observations, our analysis only found strong positive correlations (R > 0.7) between N2O flux and soil temperature in one‐third of the data sets. Soil drainage property, soil water‐filled pore space (WFPS) level and land use were also found to potentially influence the occurrence of certain diurnal patterns. Our work demonstrated that single‐daily flux measurements at mid‐morning yielded daily emission estimates with the smallest average bias compared to measurements made at other times of day, however, it could still lead to significant over‐ or underestimation due to inconsistent diurnal N2O patterns. This inconsistency also reflects the inaccuracy of using soil temperature to predict the time of daily average N2O flux. Future research should investigate the relationship between N2O flux and other diurnal parameters, such as photosynthetically active radiation (PAR) and root exudation, along with the consideration of the effects of soil moisture, drainage and land use on the diurnal patterns of N2O flux. The information could be incorporated in N2O emission prediction models to improve accuracy.
Our systematic review extracted and analysed data from 46 studies with sub‐daily soil nitrous oxide (N2O) flux measurements and revealed diurnal variability in soil N2O emissions in agricultural and forest ecosystems. Most datasets exhibited either daytime or night‐time peaking diurnal patterns, which are found to associate with non‐diurnal soil factors and land managements.
Land use changes (LUC) from pasture to sugarcane (Saccharum spp.) crop are expected to add 6.4Mha of new sugarcane land by 2021 in the Brazilian Cerrado and Atlantic Forest biomes. We assessed the ...effects of these LUC on the abundance and community structure of animals that inhabit soils belowground through a field survey using chronosequences of land uses comprising native vegetation, pasture, and sugarcane along a 1000-km-long transect across these two major tropical biomes in Brazil. Macrofauna community composition differed among land uses. While most groups were associated with samples taken in native vegetation, high abundance of termites and earthworms appeared associated with pasture soils. Linear mixed effects analysis showed that LUC affected total abundance (X2(1)=6.79, p=0.03) and taxa richness (X2(1)=6.08, p=0.04) of soil macrofauna. Abundance increased from 411±70individualsm−2 in native vegetation to 1111±202individualsm−2 in pasture, but decreased sharply to 106±24individualsm−2 in sugarcane soils. Diversity decreased 24% from native vegetation to pasture, and 39% from pasture to sugarcane. Thus, a reduction of ~90% in soil macrofauna abundance, besides a loss of ~40% in the diversity of macrofauna groups, can be expected when sugarcane crops replace pasture in Brazilian tropical soils. In general, higher abundances of major macrofauna groups (ants, coleopterans, earthworms, and termites) were associated with higher acidity and low contents of macronutrients and organic matter in soil. This study draws attention for a significant biodiversity loss belowground due to tropical LUC in sugarcane expansion areas. Given that many groups of soil macrofauna are recognized as key mediators of ecosystem processes such as soil aggregation, nutrients cycling and soil carbon storage, our results warrant further efforts to understand the impacts of altering belowground biodiversity and composition on soil functioning and agriculture performance across LUC in the tropics.
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•We examined the soil macrofaunal community responses to sugarcane expansion from pasturelands.•Macrofaunal abundance decreases 89% and diversity of macrofauna groups deceases 39% when sugarcane replaces pasture.•Termites and earthworms largely dominate the macrofaunal community in PA soils.•Ants and coleopteran insects become the most abundant groups when land use is changed to SC.•This study draws attention for a significant biodiversity loss belowground due to bioenergy crop expansion in the tropics.
Globally, the rate of land-use change (LUC) is increasing rapidly to support biofuel feedstock production. In Brazil, sugarcane (Saccharum officinarum) expansion to produce ethanol is displacing ...degraded pastures. Intensive mechanization for sugarcane production, could impact soil physical quality in these areas. We evaluated a typical LUC sequence (i.e., native vegetation–pasture–sugarcane) on soil physical quality at three sites in the central-southern region of Brazil. The soil physical properties evaluated through on-farm and laboratory soil analyses were: bulk density, degree of compactness, macroporosity, microporosity and total porosity, water-filled pore space, indexes of soil water storage and aeration capacity, soil resistance to penetration, field-saturated hydraulic conductivity and stability structural index. Calculations of mean weight diameter for the soil aggregates and soil physical quality ratings from a visual evaluation of soil structure (VESS) were also included in this study. From those data we defined a minimum dataset for calculating an additive soil physical quality index (SPQI). Long-term conversion from native ecosystems to pasture increased soil compaction (i.e., higher bulk density, degree of compactness and resistance to penetration values), decreased aeration porosity and water hydraulic conductivity, and consequently, created an unbalanced ratio between water- and air-filled pore space in the soil. Based on our SPQI, the soil's capacity to perform its physical functions decreased from 90% under native vegetation to 73% under pasture. Land-use change from pasture to sugarcane induced slight soil physical quality degradation, in which soil function was 68 and 56% of capacity. Overall, soil physical quality decreased under sugarcane fields, due to decreases in soil porosity, aeration and water hydraulic conductivity as well as increases in soil penetration resistance, structural degradation and erosion risk. Tillage operations performed during the sugarcane replanting (~5years) had a short-term positive effect on soil physical quality, although over time it further decreased the resistance to erosion and structural degradation. Therefore, to convert degraded pasture to sugarcane in a sustainable manner, the soils should be managed in ways that increase the soil organic matter and minimize compaction. These actions are needed to prevent further soil physical quality degradation and to improve both economic and environmental sustainability of sugarcane ethanol production.
•We assessed soil physical changes due to land use change for sugarcane production in Brazil.•Soil physical quality decreased from native vegetation (90%) to pasture (70%) to sugarcane (56 to 68%).•Soil compaction limits soil aeration and water availability under pasture and sugarcane.•Soil tillage in sugarcane fields had short-term positive effects over soil compaction.•Sugarcane soils are more susceptive to degradation by erosion process.
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