Many biotic and abiotic processes contribute to nitrous oxide (N2O) production in the biosphere, but N2O consumption in the environment has heretofore been attributed primarily to canonical ...denitrifying microorganisms. The nosZ genes encoding the N2O reductase enzyme, NosZ, responsible for N2O reduction to dinitrogen are now known to include two distinct groups: the well‐studied Clade I which denitrifiers typically possess, and the novel Clade II possessed by diverse groups of microorganisms, most of which are non‐denitrifiers. Clade II N2O reducers could play an important, previously unrecognized role in controlling N2O emissions for several reasons, including: (1) the consumption of N2O produced by processes other than denitrification, (2) hypothesized non‐respiratory functions of NosZ as an electron sink or for N2O detoxification, (3) possible differing enzyme kinetics of Clade II NosZ compared to Clade I NosZ, and (4) greater nosZ gene abundance for Clade II compared to Clade I in soils of many ecosystems. Despite the potential ecological significance of Clade II NosZ, a census of 800 peer‐reviewed original research articles discussing nosZ and published from 2013 to 2019 showed that the percentage of articles evaluating or mentioning Clade II nosZ increased from 5% in 2013 to only 22% in 2019. The census revealed that the slowly spreading awareness of Clade II nosZ may result in part from disciplinary silos, with the percentage of nosZ articles mentioning Clade II nosZ ranging from 0% in Agriculture and Agronomy journals to 32% in Multidisciplinary Sciences journals. In addition, inconsistent nomenclature for Clade I nosZ and Clade II nosZ, with 17 different terminologies used in the literature, may have created confusion about the two distinct groups of N2O reducers. We provide recommendations to accelerate advances in understanding the role of the diversity of N2O reducers in regulating soil N2O emissions.
We present a new paradigm of controls on soil nitrous oxide (N2O) emissions that accounts for N2O reduction beyond the traditional focus on denitrification and Clade I N2O reducers. Based on a synthesis of current knowledge about Clade I N2O reducers and the more recently described Clade II N2O reducers, we propose a conceptual framework for considering how microbial diversity may control N2O emissions. Based on a census of peer‐reviewed articles discussing nosZ and published during 2013–2019, we make recommendations to accelerate progress in understanding the roles of taxonomic and functional diversity in controlling N2O reduction rates and N2O emissions
Quantifying changes in soil organic carbon (SOC) stocks and other soil properties is essential for understanding how soils will respond to land management practices and global change. Although they ...are widely used, comparisons of SOC stocks at fixed depth (FD) intervals are subject to errors when changes in bulk density or soil organic matter occur. The equivalent soil mass (ESM) method has been recommended in lieu of FD for assessing changes in SOC stocks in mineral soils, but ESM remains underutilized for SOC stocks and has rarely been used for other soil properties. In this paper, we draw attention to the limitations of the FD method and demonstrate the advantages of the ESM approach. We provide illustrations to show that the FD approach is susceptible to errors not only for quantifying SOC stocks but also for soil mass‐based properties such as SOC mass percent, C:N mass ratio, and δ13C. We describe the ESM approach and show how it mitigates the FD method limitations. Using bulk density change simulations applied to an empirical dataset from bioenergy cropping systems, we show that the ESM method provides consistently lower errors than FD when quantifying changes in SOC stocks and other soil properties. To simplify the use of ESM, we detail how the method can be integrated into sampling schemes, and we provide an example R computer script that can perform ESM calculations on large datasets. We encourage future studies, whether temporal or comparative, to utilize sampling methods that are amenable to the ESM approach. Overall, we agree with previous recommendations that ESM should be the standard method for evaluating SOC stock changes in mineral soils, but we further suggest that ESM may also be preferred for comparisons of other soil properties including mass percentages, elemental mass ratios, and stable isotope composition.
Bulk density changes can lead to errors when soil mass‐based properties are quantified within fixed depth sampling intervals. We illustrate why these errors occur and show that the equivalent mineral soil mass method usually reduces the errors. In addition to soil organic carbon (SOC) stocks, we recommend that temporal and comparative studies use the equivalent mineral soil mass approach to quantify other soil mass‐based properties such as SOC mass percentages, C:N mass ratios, and δ13C.
Looking back to look ahead Almaraz, Maya; Wong, Michelle Y.; Yang, Wendy H.
Ecology (Durham),
January 2020, Volume:
101, Issue:
1
Journal Article
Peer reviewed
Open access
Denitrification plays a critical role in regulating ecosystem nutrient availability and anthropogenic reactive nitrogen (N) production. Its importance has inspired an increasing number of studies, ...yet it remains the most poorly constrained term in terrestrial ecosystem N budgets. We censused the peer-reviewed soil denitrification literature (1975–2015) to identify opportunities for future studies to advance our understanding despite the inherent challenges in studying the process. We found that only one-third of studies reported estimates of both nitrous oxide (N₂O) and dinitrogen (N₂) production fluxes, often the dominant end products of denitrification, while the majority of studies reported only net N₂O fluxes or denitrification potential. Of the 236 studies that measured complete denitrification to N₂, 49% used the acetylene inhibition method, 84% were conducted in the laboratory, 81% were performed on surface soils (0–20 cm depth), 75% were located in North America and Europe, and 78% performed treatment manipulations, mostly of N, carbon, or water. To improve understanding of soil denitrification, we recommend broadening access to technologies for new methodologies to measure soil N₂ production rates, conducting more studies in the tropics and on subsoils, performing standardized experiments on unmanipulated soils, and using more precise terminology to refer to measured process rates (e.g., net N₂O flux or denitrification potential). To overcome the greater challenges in studying soil denitrification, we envision coordinated research efforts based on standard reporting of metadata for all soil denitrification studies, standard protocols for studies contributing to a Global Denitrification Research Network, and a global consortium of denitrification researchers to facilitate sharing ideas, resources, and to provide mentorship for researchers new to the field.
Mitochondrial dysfunction is associated with a spectrum of human conditions, ranging from rare, inborn errors of metabolism to the aging process. To identify pathways that modify mitochondrial ...dysfunction, we performed genome-wide CRISPR screens in the presence of small-molecule mitochondrial inhibitors. We report a compendium of chemical-genetic interactions involving 191 distinct genetic modifiers, including 38 that are synthetic sick/lethal and 63 that are suppressors. Genes involved in glycolysis (PFKP), pentose phosphate pathway (G6PD), and defense against lipid peroxidation (GPX4) scored high as synthetic sick/lethal. A surprisingly large fraction of suppressors are pathway intrinsic and encode mitochondrial proteins. A striking example of such “intra-organelle” buffering is the alleviation of a chemical defect in complex V by simultaneous inhibition of complex I, which benefits cells by rebalancing redox cofactors, increasing reductive carboxylation, and promoting glycolysis. Perhaps paradoxically, certain forms of mitochondrial dysfunction may best be buffered with “second site” inhibitors to the organelle.
Display omitted
•Genome-wide CRISPR screens were performed with multiple mitochondrial inhibitors•Loss of G6PD, PFKP, or GPX4 is synthetic lethal with mitochondrial dysfunction•“Intra-mitochondrial” interactions are pervasive•Fitness defect from CV inhibition is alleviated by simultaneous loss of CI activity
A chemical-genetic map of the mitochondrion provides insights into the pathways that modulate its function.
Specifications in the U.S. Code of Federal Regulations for the color additive D&C Red No. 17 (R17, Colour Index No. 26100) limit the levels of the dye's intermediates, aniline (AN), 2-naphthol ...(β-naphthol, BN), and 4-aminoazobenzene (4AAB), to 0.2, 0.2, and 0.1%, respectively. The present work reports the development and application of an ultra-HPLC method for the quantitative determination of these impurities in R17. A 1.7 μm particle size C-18 column was used with 0.2 M ammonium acetate and acetonitrile as the eluents. AN, BN, and 4AAB were quantified by using six-point calibration curves with data points (w/w) ranging from 0.01 to 0.25% for AN, 0.01 to 0.24% for BN, and 0.01 to 0.19% for 4AAB. The correlation coefficients ranged from 0.9992 to 0.9999. Limits of detection for the analytes ranged from 0.002 to 0.01%. Recoveries of the analytes ranged from 99.5 to 102%. Relative standard deviations ranged from 0.482 to 1.262%. The new method was applied to analyze portions from 22 batches of R17 submitted to the U.S. Food and Drug Administration for certification. It was found to be simpler to implement, faster, and more sensitive than the older gravity-elution column chromatography method, which it has replaced.
Slower leaf litter decomposition rates for trees associated with ectomycorrhizal (ECM) fungi compared to arbuscular mycorrhizal (AM) fungi may lead to the development of conservative nitrogen cycling ...and accumulation of soil organic matter in surface soils of ECM-dominated forests. Slower decomposition is hypothesized to occur via two often-confounded mechanisms: production of lower quality litter by ECM-associated trees compared to AM-associated trees and competition for nitrogen between ECM and saprotrophic decomposers in ECM-dominated stands. To disentangle the effects of litter quality and stand mycorrhizal type on decomposition, we measured litter mass loss rates of two AM species higher and two AM species similar in chemical quality to two ECM species. Leaf litter was decomposed for two years in neighboring ECM- and AM-dominated stands of a wet tropical montane forest. Litter phosphorus (P) was the strongest predictor of decomposition rates across all species, with no effect of litter mycorrhizal type on decomposition rates. Only one species, which exhibited intermediate litter chemical quality and decomposition rate, decomposed significantly faster in AM- compared to ECM-dominated stands. Leaf litter decomposition rates cannot be predicted directly from litter mycorrhizal type or stand mycorrhizal type because litter chemical quality and environmental conditions mediate the manifestation of slower decomposition in ECM stands.
Background
Assessments of the soil microbiome provide valuable insight to ecosystem function due to the integral role microorganisms play in biogeochemical cycling of carbon and nutrients. For ...example, treatment effects on nitrogen cycling functional groups are often presented alongside one another to demonstrate how agricultural management practices affect various nitrogen cycling processes. However, the functional groups commonly evaluated in nitrogen cycling microbiome studies range from phylogenetically narrow (e.g., N-fixation, nitrification) to broad e.g., denitrification, dissimilatory nitrate reduction to ammonium (DNRA). The bioinformatics methods used in such studies were developed for 16S rRNA gene sequence data, and how these tools perform across functional genes of different phylogenetic diversity has not been established. For example, an OTU clustering method that can accurately characterize sequences harboring comparatively little diversity may not accurately resolve the diversity within a gene comprised of a large number of clades. This study uses two nitrogen cycling genes,
nifH
, a gene which segregates into only three distinct clades, and
nrfA
, a gene which is comprised of at least eighteen clades, to investigate differences which may arise when using heuristic OTU clustering (abundance-based greedy clustering, AGC) vs. true hierarchical OTU clustering (Matthews Correlation Coefficient optimizing algorithm, Opti-MCC). Detection of treatment differences for each gene were evaluated to demonstrate how conclusions drawn from a given dataset may differ depending on clustering method used.
Results
The heuristic and hierarchical methods performed comparably for the more conserved gene,
nifH
. The hierarchical method outperformed the heuristic method for the more diverse gene,
nrfA
; this included both the ability to detect treatment differences using PERMANOVA, as well as higher resolution in taxonomic classification. The difference in performance between the two methods may be traced to the AGC method’s preferential assignment of sequences to the most abundant OTUs: when analysis was limited to only the largest 100 OTUs, results from the AGC-assembled OTU table more closely resembled those of the Opti-MCC OTU table. Additionally, both AGC and Opti-MCC OTU tables detected comparable treatment differences using the rank-based ANOSIM test. This demonstrates that treatment differences were preserved using both clustering methods but were structured differently within the OTU tables produced using each method.
Conclusion
For questions which can be answered using tests agnostic to clustering method (e.g., ANOSIM), or for genes of relatively low phylogenetic diversity (e.g.,
nifH
), most upstream processing methods should lead to similar conclusions from downstream analyses. For studies involving more diverse genes, however, care should be exercised to choose methods that ensure accurate clustering for all genes. This will mitigate the risk of introducing Type II errors by allowing for detection of comparable treatment differences for all genes assessed, rather than disproportionately detecting treatment differences in only low-diversity genes.
Litter decomposition represents one of the largest annual fluxes of carbon (C) from terrestrial ecosystems, particularly for tropical forests, which are generally characterized by high net primary ...productivity and litter turnover. We used data from the Long-Term Intersite Decomposition Experiment (LIDET) to (1) determine the relative importance of climate and litter quality as predictors of decomposition rates, (2) compare patterns in root and leaf litter decomposition, (3) identify controls on net nitrogen (N) release during decay, and (4) compare LIDET rates with native species studies across five bioclimatically diverse neotropical forests. Leaf and root litter decomposed fastest in the lower montane rain and moist forests and slowest in the seasonally dry forest. The single best predictor of leaf litter decomposition was the climate decomposition index (CDI), explaining 51% of the variability across all sites. The strongest models for predicting leaf decomposition combined climate and litter chemistry, and included CDI and lignin (R²=0.69), or CDI, N and nonpolar extractives (R²=0.69). While we found no significant differences in decomposition rates between leaf and root litter, drivers of decomposition differed for the two tissue types. Initial stages of decomposition, determined as the time to 50% mass remaining, were driven primarily by precipitation for leaf litter (R²=0.93) and by temperature for root litter (R²=0.86). The rate of N release from leaf litter was positively correlated with initial N concentrations; net N immobilization increased with decreasing initial N concentrations. This study demonstrates that decomposition is sensitive to climate within and across tropical forests. Our results suggest that climate change and increasing N deposition in tropical forests are likely to result in significant changes to decomposition rates in this biome.
Precipitation events are increasing in intensity in the Midwestern US due to climate change. This is resulting in flooding of poorly-drained upland soils, which can feed back on climate change by ...altering greenhouse gas (GHG) emissions, including nitrous oxide (N₂O) and carbon dioxide (CO₂). The objective of this study was to determine if soil drainage history affects the response of soil GHG emissions to rain events. To do this, we measured N₂O and CO₂ fluxes from poorly-drained (PD) and well-drained (WD) soils in an agricultural field in Urbana, Illinois before and after large rain events. We also performed a lab experiment to separate effects of soil drainage history from contemporary effects of ponding. Finally, we utilized stable isotope techniques to measure gross N₂O dynamics and to determine the contributions of nitrifiers and denitrifiers to net N₂O fluxes. We found that ponding of WD soils led to pulses of net N₂O efflux caused by stimulation of gross N₂O production by denitrifiers. In contrast, PD soils had high net N₂O effluxes only between large rain events, and gross N₂O production was inhibited following ponding. Soil CO₂ efflux was greater from PD soils under lab conditions, but autotrophic respiration obscured this trend in the field. Soil GHG emissions were a result of different contemporary ponding status as well as historical soil drainage, suggesting that historical soil redox regimes regulate soil GHG dynamics in response to precipitation. These soil drainage legacy effects are likely important in predicting soil GHG feedback effects on climate change.
PDF
