The carbon-quality temperature hypothesis: Fact or artefact?

Climate warming can reduce global soil carbon stocks by enhancing microbial decomposition. However, the magnitude of this loss remains uncertain because the temperature sensitivity of the decomposition of the major fraction of soil carbon, namely resistant carbon, is not fully known. It is now believed that the resistance of soil carbon mostly depends on microbial accessibility of soil carbon with physical protection being the primary control of the decomposition of protected carbon, which is insensitive to temperature changes. However, it is still unclear whether the temperature sensitivity of the decomposition of unprotected carbon, for example, carbon that is not protected by the soil mineral matrix, may depend on the chemical recalcitrance of carbon compounds. In particular, the carbon-quality temperature (CQT) hypothesis asserts that recalcitrant low-quality carbon is more temperature-sensitive to decomposition than labile high-quality carbon. If the hypothesis is correct, climate warming could amplify the loss of unprotected, but chemically recalcitrant, carbon and the resultant CO2 release from soils to the atmosphere. Previous research has supported this hypothesis based on reported negative relationships between temperature sensitivity and carbon quality, defined as the decomposition rate at a reference temperature. Here we show that negative relationships can arise simply from the arbitrary choice of reference temperature, inherently invalidating those tests. To avoid this artefact, we defined the carbon quality of different compounds as their uncatalysed reaction rates in the absence of enzymes. Taking the uncatalysed rate as the carbon quality index, we found that the CQT hypothesis is not supported for enzyme-catalysed reactions, which showed no relationship between carbon quality and temperature sensitivity. The lack of correlation in enzyme-catalysed reactions implies similar temperature sensitivity for microbial decomposition of soil carbon, regardless of its quality, thereby allaying concerns of acceleration of warming-induced decomposition of recalcitrant carbon.

Livestock exclusion reduces the spillover effects of pastoral agriculture on soil bacterial communities in adjacent forest fragments.

Forest-to-pasture conversion is known to cause global losses in plant and animal diversity, yet impacts of livestock management after such conversion on vital microbial communities in adjoining natural ecosystems remain poorly understood. We examined how pastoral land management practices impact soil microorganisms in adjacent native forest fragments, by comparing bacterial communities sampled along 21 transects bisecting pasture-forest boundaries. Our results revealed greater bacterial taxon richness in grazed pasture soils and the reduced dispersal of pasture-associated taxa into adjacent forest soils when land uses were separated by a boundary fence. Relative abundance distributions of forest-associated taxa (i.e., Proteobacteria and Nitrospirae) and a pasture-associated taxon (i.e., Firmicutes) also suggest a greater impact of pastoral land uses on forest fragment soil bacterial communities when no fence is present. Bacterial community richness and composition were most related to changes in soil physicochemical variables commonly associated with agricultural fertilization, including concentrations of Olsen P, total P, total Cd, delta 15 N and the ratio of C:P and N:P. Overall, our findings demonstrate clear, and potentially detrimental effects of agricultural disturbance on bacterial communities in forest soils adjacent to pastoral land. We provide evidence that simple land management decisions, such as livestock exclusion, can mitigate the effects of agriculture on adjacent soil microbial communities.

Soil microbial sensitivity to temperature remains unchanged despite community compositional shifts along geothermal gradients.

Climate warming may be exacerbated if rising temperatures stimulate losses of soil carbon to the atmosphere. The direction and magnitude of this carbon-climate feedback are uncertain, largely due to lack of knowledge of the thermal adaptation of the physiology and composition of soil microbial communities. Here, we applied the macromolecular rate theory (MMRT) to describe the temperature response of the microbial decomposition of soil organic matter (SOM) in a natural long-term warming experiment in a geothermally active area in New Zealand. Our objective was to test whether microbial communities adapt to long-term warming with a shift in their composition and their temperature response that are consistent with evolutionary theory of trade-offs between enzyme structure and function. We characterized the microbial community composition (using metabarcoding) and the temperature response of microbial decomposition of SOM (using MMRT) of soils sampled along transects of increasing distance from a geothermally active zone comprising two biomes (a shrubland and a grassland) and sampled at two depths (0-50 and 50-100 mm), such that ambient soil temperature and soil carbon concentration varied widely and independently. We found that the different environments were hosting microbial communities with distinct compositions, with thermophile and thermotolerant genera increasing in relative abundance with increasing ambient temperature. However, the ambient temperature had no detectable influence on the MMRT parameters or the relative temperature sensitivity of decomposition (Q10 ). MMRT parameters were, however, strongly correlated with soil carbon concentration and carbon:nitrogen ratio. Our findings suggest that, while long-term warming selects for warm-adapted taxa, substrate quality and quantity exert a stronger influence than temperature in selecting for distinct thermal traits. The results have major implications for our understanding of the role of soil microbial processes in the long-term effects of climate warming on soil carbon dynamics and will help increase confidence in carbon-climate feedback projections.

The Inflection Point Hypothesis: The Relationship between the Temperature Dependence of Enzyme-Catalyzed Reaction Rates and Microbial Growth Rates.

The temperature dependence of biological rates at different scales (from individual enzymes to isolated organisms to ecosystem processes such as soil respiration and photosynthesis) is the subject of much historical and contemporary research. The precise relationship between the temperature dependence of enzyme rates and those at larger scales is not well understood. We have developed macromolecular rate theory (MMRT) to describe the temperature dependence of biological processes at all scales. Here we formalize the scaling relationship by investigating MMRT both at the molecular scale (constituent enzymes) and for growth of the parent organism. We demonstrate that the inflection point (Tinf) for the temperature dependence of individual metabolic enzymes coincides with the optimal growth temperature for the parent organism, and we rationalize this concordance in terms of the necessity for linearly correlated rates for metabolic enzymes over fluctuating environmental temperatures to maintain homeostasis. Indeed, Tinf is likely to be under strong selection pressure to maintain coordinated rates across environmental temperature ranges. At temperatures at which rates become uncorrelated, we postulate a regulatory catastrophe and organism growth rates precipitously decline at temperatures where this occurs. We show that the curvature in the plots of the natural log of the rate versus temperature for individual enzymes determines the curvature for the metabolic process overall and the curvature for the temperature dependence of the growth of the organism. We have called this "the inflection point hypothesis", and this hypothesis suggests many avenues for future investigation, including avenues for engineering the thermal tolerance of organisms.

High-frequency, in situ sampling of field woodchip bioreactors reveals sources of sampling error and hydraulic inefficiencies.

Woodchip bioreactors are a practical, low-cost technology for reducing nitrate (NO3) loads discharged from agriculture. Traditional methods of quantifying their performance in the field mostly rely on low-frequency, time-based (weekly to monthly sampling interval) or flow-weighted sample collection at the inlet and outlet, creating uncertainty in their performance and design by providing incomplete information on flow and water chemistry. To address this uncertainty, two field bioreactors were monitored in the US and New Zealand using high-frequency, multipoint sampling for in situ monitoring of NO3-N concentrations. High-frequency monitoring (sub hourly interval) at the inlet and outlet of both bioreactors revealed significant variability in volumetric removal rates and percent reduction, with percent reduction varying by up to 25 percentage points within a single flow event. Time series of inlet and outlet NO3 showed significant lag in peak concentrations of 1-3 days due to high hydraulic residence time, where calculations from instantaneous measurements produced erroneous estimates of performance and misleading relationships between residence time and removal. Internal porewater sampling wells showed differences in NO3 concentration between shallow and deep zones, and "hot spot" zones where peak NO3 removal co-occurred with dissolved oxygen depletion and dissolved organic carbon production. Tracking NO3 movement through the profile showed preferential flow occurring with slower flow in deeper woodchips, and slower flow further from the most direct flowpath from inlet to outlet. High-frequency, in situ data on inlet and outlet time series and internal porewater solute profiles of this initial work highlight several key areas for future research.

Drying-Rewetting Cycles Affect Nitrate Removal Rates in Woodchip Bioreactors.

Woodchip bioreactors are widely used to control nitrogen export from agriculture using denitrification. There is abundant evidence that drying-rewetting (DRW) cycles can promote enhanced metabolic rates in soils. A 287-d experiment investigated the effects of weekly DRW cycles on nitrate (NO) removal in woodchip columns in the laboratory receiving constant flow of nitrated water. Columns were exposed to continuous saturation (SAT) or to weekly, 8-h drying-rewetting (8 h of aerobiosis followed by saturation) cycles (DRW). Nitrate concentrations were measured at the column outlets every 2 h using novel multiplexed sampling methods coupled to spectrophotometric analysis. Drying-rewetting columns showed greater export of total and dissolved organic carbon and increased NO removal rates. Nitrate removal rates in DRW columns increased by up to 80%, relative to SAT columns, although DRW removal rates decreased quickly within 3 d after rewetting. Increased NO removal in DRW columns continued even after 39 DRW cycles, with ∼33% higher total NO mass removed over each weekly DRW cycle. Data collected in this experiment provide strong evidence that DRW cycles can dramatically improve NO removal in woodchip bioreactors, with carbon availability being a likely driver of improved efficiency. These results have implications for hydraulic management of woodchip bioreactors and other denitrification practices.

Macromolecular rate theory (MMRT) provides a thermodynamics rationale to underpin the convergent temperature response in plant leaf respiration.

Temperature is a crucial factor in determining the rates of ecosystem processes, for example, leaf respiration (R) - the flux of plant respired CO2 from leaves to the atmosphere. Generally, R increases exponentially with temperature and formulations such as the Arrhenius equation are widely used in earth system models. However, experimental observations have shown a consequential and consistent departure from an exponential increase in R. What are the principles that underlie these observed patterns? Here, we demonstrate that macromolecular rate theory (MMRT), based on transition state theory (TST) for enzyme-catalyzed kinetics, provides a thermodynamic explanation for the observed departure and the convergent temperature response of R using a global database. Three meaningful parameters emerge from MMRT analysis: the temperature at which the rate of respiration would theoretically reach a maximum (the optimum temperature, Topt ), the temperature at which the respiration rate is most sensitive to changes in temperature (the inflection temperature, Tinf ) and the overall curvature of the log(rate) versus temperature plot (the change in heat capacity for the system, ΔCP‡). On average, the highest potential enzyme-catalyzed rates of respiratory enzymes for R are predicted to occur at 67.0 ± 1.2°C and the maximum temperature sensitivity at 41.4 ± 0.7°C from MMRT. The average curvature (average negative ΔCP‡) was -1.2 ± 0.1 kJ mol-1  K-1 . Interestingly, Topt , Tinf and ΔCP‡ appear insignificantly different across biomes and plant functional types, suggesting that thermal response of respiratory enzymes in leaves could be conserved. The derived parameters from MMRT can serve as thermal traits for plant leaves that represent the collective temperature response of metabolic respiratory enzymes and could be useful to understand regulations of R under a warmer climate. MMRT extends the classic TST to enzyme-catalyzed reactions and provides an accurate and mechanistic model for the short-term temperature response of R around the globe.

Irrigating grazed pasture decreases soil carbon and nitrogen stocks.

The sustainability of using irrigation to produce food depends not only on the availability of sufficient water, but also on the soil's 'response' to irrigation. Stocks of carbon (C) and nitrogen (N) are key components of soil organic matter (SOM), which is important for sustainable agricultural production. While there is some information about the effects of irrigation on soil C stocks in cropping systems, there is a paucity of such studies in pastoral food production systems. For this study, we sampled soils from 34 paired, irrigated and unirrigated pasture sites across New Zealand (NZ) and analysed these for total C and N. On average, irrigated pastures had significantly (P < 0.05) less soil carbon (C) and nitrogen (N) than adjacent unirrigated pastures, with differences of 6.99 t C ha-1 and 0.58 t N ha-1 in the uppermost 0.3 m. Differences in C and N tended to occur throughout the soil profile, so the cumulative differences increased with depth, and the proportion of the soil C lost from deeper horizons was large. There were no relationships between differences in soil C and N stocks and the length of time under irrigation. This study suggests SOM will decrease when pastures under a temperate climate are irrigated. On this basis, increasing the area of temperate pasture land under irrigation would result in more CO2 in the atmosphere and may directly and indirectly increase N leaching to groundwater. Given the large and increasing area of land being irrigated both in NZ and on a global scale, there is an urgent need to determine whether the results found in this study are also applicable in other regions and under different land management systems (e.g. arable).

Isotope Tracing of Long-Term Cadmium Fluxes in an Agricultural Soil.

Globally widespread phosphate fertilizer applications have resulted in long-term increases in the concentration of cadmium (Cd) in soils. The accumulation of this biotoxic, and bioaccumulative metal presents problems for the management of soil-plant-animal systems, because the magnitude and direction of removal fluxes (e.g., crop uptake, leaching) have been difficult to estimate. Here, Cd isotopic compositions (δ114/110Cd) of archived fertilizer and soil samples from a 66 year-long agricultural field trial in Winchmore, New Zealand, were used to constrain the Cd soil mass balance between 1959 and 2015 AD, informing future soil Cd accumulation trajectories. The isotopic partitioning of soil Cd sources in this system was aided by a change in phosphate source rocks in 1998 AD, and a corresponding shift in fertilizer isotope composition. The dominant influence of mixing between isotopically distinct Cd end-members was confirmed by a Bayesian modeling approach. Furthermore, isotope mass balance modeling revealed that Cd removal processes most likely increased in magnitude substantially between 2000 and 2015 AD, implying an increase in Cd bioaccumulation and/or leaching over that interval. Natural-abundance stable isotopes are introduced here as a powerful tool for tracing the fate of Cd in agricultural soils, and potentially the wider environment.

On the Temperature Dependence of Enzyme-Catalyzed Rates.

One of the critical variables that determine the rate of any reaction is temperature. For biological systems, the effects of temperature are convoluted with myriad (and often opposing) contributions from enzyme catalysis, protein stability, and temperature-dependent regulation, for example. We have coined the phrase "macromolecular rate theory (MMRT)" to describe the temperature dependence of enzyme-catalyzed rates independent of stability or regulatory processes. Central to MMRT is the observation that enzyme-catalyzed reactions occur with significant values of ΔCp(‡) that are in general negative. That is, the heat capacity (Cp) for the enzyme-substrate complex is generally larger than the Cp for the enzyme-transition state complex. Consistent with a classical description of enzyme catalysis, a negative value for ΔCp(‡) is the result of the enzyme binding relatively weakly to the substrate and very tightly to the transition state. This observation of negative ΔCp(‡) has important implications for the temperature dependence of enzyme-catalyzed rates. Here, we lay out the fundamentals of MMRT. We present a number of hypotheses that arise directly from MMRT including a theoretical justification for the large size of enzymes and the basis for their optimum temperatures. We rationalize the behavior of psychrophilic enzymes and describe a "psychrophilic trap" which places limits on the evolution of enzymes in low temperature environments. One of the defining characteristics of biology is catalysis of chemical reactions by enzymes, and enzymes drive much of metabolism. Therefore, we also expect to see characteristics of MMRT at the level of cells, whole organisms, and even ecosystems.

Moving Denitrifying Bioreactors beyond Proof of Concept: Introduction to the Special Section.

Denitrifying bioreactors are organic carbon-filled excavations designed to enhance the natural process of denitrification for the simple, passive treatment of nitrate-nitrogen. Research on and installation of these bioreactors has accelerated within the past 10 years, particularly in watersheds concerned about high nonpoint-source nitrate loads and also for tertiary wastewater treatment. This special section, inspired by the meeting of the Managing Denitrification in Agronomic Systems Community at the 2014 Annual Meeting of the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, aims to firmly establish that denitrifying bioreactors for treatment of nitrate in drainage waters, groundwater, and some wastewaters have moved beyond the proof of concept. This collection of 14 papers expands the peer-reviewed literature of denitrifying bioreactors into new locations, applications, and environmental conditions. There is momentum behind the pairing of wood-based bioreactors with other media (biochar, corn cobs) and in novel designs (e.g., use within treatment trains or use of baffles) to broaden applicability into new kinds of waters and pollutants and to improve performance under challenging field conditions such as cool early season agricultural drainage. Concerns about negative bioreactor by-products (nitrous oxide and hydrogen sulfide emissions, start-up nutrient flushing) are ongoing, but this translates into a significant research opportunity to develop more advanced designs and to fine tune management strategies. Future research must think more broadly to address bioreactor impacts on holistic watershed health and greenhouse gas balances and to facilitate collaborations that allow investigation of mechanisms within the bioreactor "black box."

Fecal Bacteria, Bacteriophage, and Nutrient Reductions in a Full-Scale Denitrifying Woodchip Bioreactor.

Denitrifying bioreactors using woodchips or other slow-release carbon sources can be an effective method for removing nitrate (NO) from wastewater and tile drainage. However, the ability of these systems to remove fecal microbes from wastewater has been largely uninvestigated. In this study, reductions in fecal indicator bacteria () and viruses (F-specific RNA bacteriophage [FRNA phage]) were analyzed by monthly sampling along a longitudinal transect within a full-scale denitrifying woodchip bioreactor receiving secondary-treated septic tank effluent. Nitrogen, phosphorus, 5-d carbonaceous biochemical oxygen demand (CBOD), and total suspended solids (TSS) reduction were also assessed. The bioreactor demonstrated consistent and substantial reduction of (2.9 log reduction) and FRNA phage (3.9 log reduction) despite receiving highly fluctuating inflow concentrations [up to 3.5 × 10 MPN (100 mL) and 1.1 × 10 plaque-forming units (100 mL) , respectively]. Most of the removal of fecal microbial contaminants occurred within the first meter of the system (1.4 log reduction for ; 1.8 log reduction for FRNA phage). The system was also efficient at removing NO (>99.9% reduction) and TSS (89% reduction). There was no evidence of consistent removal of ammonium, organic nitrogen, or phosphorus. Leaching of CBOD occurred during initial operation but decreased and stabilized at lower values (14 g O m) after 9 mo. We present strong evidence for reliable microbial contaminant removal in denitrifying bioreactors, demonstrating their broader versatility for wastewater treatment. Research on the removal mechanisms of microbial contaminants in these systems, together with the assessment of longevity of removal, is warranted.

Denitrifying Bioreactors for Nitrate Removal: A Meta-Analysis.

Meta-analysis approaches were used in this first quantitative synthesis of denitrifying woodchip bioreactors. Nitrate removal across environmental and design conditions was assessed from 26 published studies, representing 57 separate bioreactor units (i.e., walls, beds, and laboratory columns). Effect size calculations weighted the data based on variance and number of measurements for each bioreactor unit. Nitrate removal rates in bed and column studies were not significantly different, but both were significantly higher than wall studies. In denitrifying beds, wood source did not significantly affect nitrate removal rates. Nitrate removal (mass per volume) was significantly lower in beds with <6-h hydraulic retention times, which argues for ensuring that bed designs incorporate sufficient time for nitrate removal. Rates significantly declined after the first year of bed operation but then stabilized. Nitrogen limitation significantly affected bed nitrate removal. Categorical and linear assessments found significant nitrate removal effects with bed temperature; a of 2.15 was quite similar to other studies. Lessons from this meta-analysis can be incorporated into bed designs, especially extending hydraulic retention times to increase nitrate removal under low temperature and high flow conditions. Additional column studies are warranted for comparative assessments, as are field-based studies for assessing in situ conditions, especially in aging beds, with careful collection and reporting of design and environmental data. Future assessment of these systems might take a holistic view, reviewing nitrate removal in conjunction with other processes, including greenhouse gas and other unfavorable by-product production.

Thermodynamic theory explains the temperature optima of soil microbial processes and high Q10 values at low temperatures.

Our current understanding of the temperature response of biological processes in soil is based on the Arrhenius equation. This predicts an exponential increase in rate as temperature rises, whereas in the laboratory and in the field, there is always a clearly identifiable temperature optimum for all microbial processes. In the laboratory, this has been explained by denaturation of enzymes at higher temperatures, and in the field, the availability of substrates and water is often cited as critical factors. Recently, we have shown that temperature optima for enzymes and microbial growth occur in the absence of denaturation and that this is a consequence of the unusual heat capacity changes associated with enzymes. We have called this macromolecular rate theory - MMRT (Hobbs et al., , ACS Chem. Biol. 8:2388). Here, we apply MMRT to a wide range of literature data on the response of soil microbial processes to temperature with a focus on respiration but also including different soil enzyme activities, nitrogen and methane cycling. Our theory agrees closely with a wide range of experimental data and predicts temperature optima for these microbial processes. MMRT also predicted high relative temperature sensitivity (as assessed by Q10 calculations) at low temperatures and that Q10 declined as temperature increases in agreement with data synthesis from the literature. Declining Q10 and temperature optima in soils are coherently explained by MMRT which is based on thermodynamics and heat capacity changes for enzyme-catalysed rates. MMRT also provides a new perspective, and makes new predictions, regarding the absolute temperature sensitivity of ecosystems - a fundamental component of models for climate change.

Subsidence Rates of Drained Agricultural Peatlands in New Zealand and the Relationship with Time since Drainage.

The drainage and conversion of peatlands to productive agro-ecosystems leads to ongoing surface subsidence because of densification (shrinkage and consolidation) and oxidation of the peat substrate. Knowing the ra0te of this surface subsidence is important for future land-use planning, carbon accounting, and economic analysis of drainage and pumping costs. We measured subsidence rates over the past decade at 119 sites across three large, agriculturally managed peatlands in the Waikato region, New Zealand. The average contemporary (2000s-2012) subsidence rate for Waikato peatlands was 19 ± 2 mm yr (± SE) and was significantly less ( = 0.01) than the historic rate of 26 ± 1 mm yr between the 1920s and 2000s. A reduction in the rate of subsidence through time was attributed to the transition from rapid initial consolidation and shrinkage to slower, long-term, ongoing oxidation. These subsidence rates agree well with a literature synthesis of temperate zone subsidence rates reported for similar lengths of time since drainage. A strong nonlinear relationship was found between temperate zone subsidence rates and time since initial peatland drainage: Subsidence (mm yr) = 226 × (years since drained) ( = 0.88). This relationship suggests that time since drainage exerts strong control over the rate of peatland subsidence and that ongoing peatland subsidence rates can be predicted to gradually decline with time in the absence of major land disturbance.

Elucidating phosphorus removal dynamics in a denitrifying woodchip bioreactor.

Denitrifying woodchip bioreactors (DBRs) are an established nitrate mitigation technology, but uncertainty remains on their viability for phosphorus (P) removal due to inconsistent source-sink behaviour in field trials. We investigated whether iron (Fe) redox cycling could be the missing link needed to explain P dynamics in these systems. A pilot-scale DBR (Aotearoa New Zealand) was monitored for the first two drainage seasons (2017-2018), with supplemental in-field measurements of reduced solutes (Fe2+, HS-/H2S) and their conjugate oxidised species (Fe3+/SO42-) made in 2021 to constrain within-reactor redox gradients. Consistent with thermodynamics, the dissolution of Fe3+(s) to Fe2+(aq) within the DBR sequentially followed O2, NO3- and MnO2(s) reduction, but occurred before SO42- reduction. Monitoring of inlet and outlet chemistry revealed tight coupling between Fe and P (inlet R2 0.94, outlet R2 0.85), but distinct dynamics between drainage seasons. In season one, outlet P exceeded inlet P (net P source), and coincided with elevated outlet Fe2+, but at ⁓50 % lower P concentrations relative to inlet Fe:P ratios. In season 2 the reactor became a net P sink, coinciding with declining outlet Fe2+ concentrations (indicating exhaustion of Fe3+(s) hydroxides and associated P). In order to characterize P removal under varying source dynamics (i.e. inflows vs in-situ P releases), we used the inlet Fe vs P relationship to estimate P binding to colloidal Fe (hydr)oxide surfaces under oxic conditions, and the outlet Fe2+ concentration to estimate in-situ P releases associated with Fe (hydr)oxide reduction. Inferred P-removal rates were highest early in season 1 (k = 0.60 g P m3 d-1; 75-100 % removal), declining significantly thereafter (k = 0.01 ± 0.02 g P m3 d-1; ca. 3-67 % removal). These calculations suggest that microbiological P removal in DBRs can occur at comparable magnitudes to nitrate removal by denitrification, depending mainly on P availability and hydraulic retention efficiency.

Cooperative Conformational Transitions Underpin the Activation Heat Capacity in the Temperature Dependence of Enzyme Catalysis.

Many enzymes display non-Arrhenius behavior with curved Arrhenius plots in the absence of denaturation. There has been significant debate about the origin of this behavior and recently the role of the activation heat capacity (ΔCP⧧) has been widely discussed. If enzyme-catalyzed reactions occur with appreciable negative values of ΔCP⧧ (arising from narrowing of the conformational space along the reaction coordinate), then curved Arrhenius plots are a consequence. To investigate these phenomena in detail, we have collected high precision temperature-rate data over a wide temperature interval for a model glycosidase enzyme MalL, and a series of mutants that change the temperature-dependence of the enzyme-catalyzed rate. We use these data to test a range of models including macromolecular rate theory (MMRT) and an equilibrium model. In addition, we have performed extensive molecular dynamics (MD) simulations to characterize the conformational landscape traversed by MalL in the enzyme-substrate complex and an enzyme-transition state complex. We have crystallized the enzyme in a transition state-like conformation in the absence of a ligand and determined an X-ray crystal structure at very high resolution (1.10 Å). We show (using simulation) that this enzyme-transition state conformation has a more restricted conformational landscape than the wildtype enzyme. We coin the term "transition state-like conformation (TLC)" to apply to this state of the enzyme. Together, these results imply a cooperative conformational transition between an enzyme-substrate conformation (ES) and a transition-state-like conformation (TLC) that precedes the chemical step. We present a two-state model as an extension of MMRT (MMRT-2S) that describes the data along with a convenient approximation with linear temperature dependence of the activation heat capacity (MMRT-1L) that can be used where fewer data points are available. Our model rationalizes disparate behavior seen for MalL and previous results for a thermophilic alcohol dehydrogenase and is consistent with a raft of data for other enzymes. Our model can be used to characterize the conformational changes required for enzyme catalysis and provides insights into the role of cooperative conformational changes in transition state stabilization that are accompanied by changes in heat capacity for the system along the reaction coordinate. TLCs are likely to be of wide importance in understanding the temperature dependence of enzyme activity and other aspects of enzyme catalysis.

Quantifying thermal adaptation of soil microbial respiration.

Quantifying the rate of thermal adaptation of soil microbial respiration is essential in determining potential for carbon cycle feedbacks under a warming climate. Uncertainty surrounding this topic stems in part from persistent methodological issues and difficulties isolating the interacting effects of changes in microbial community responses from changes in soil carbon availability. Here, we constructed a series of temperature response curves of microbial respiration (given unlimited substrate) using soils sampled from around New Zealand, including from a natural geothermal gradient, as a proxy for global warming. We estimated the temperature optima ([Formula: see text]) and inflection point ([Formula: see text]) of each curve and found that adaptation of microbial respiration occurred at a rate of 0.29 °C ± 0.04 1SE for [Formula: see text] and 0.27 °C ± 0.05 1SE for [Formula: see text] per degree of warming. Our results bolster previous findings indicating thermal adaptation is demonstrably offset from warming, and may help quantifying the potential for both limitation and acceleration of soil C losses depending on specific soil temperatures.

The temperature and flow dependence of nitrate concentration and load estimates based on diffusive gradients in thin films.

Concentrations determined using diffusive gradients in thin films (DGT) have been used to derive time-averaged loads in streams and rivers. However, DGT provide time-weighted average concentrations that assume the independence of concentration and flow. Additionally, dynamic and coordinated changes in temperature, flow, and concentration are potential sources of bias in concentration and load calculations. We modeled scenarios in which temperature and flow were correlated to varying degrees with concentration and evaluated the consequences for DGT concentration and load calculations. As the correlation between solution flow and concentration moved toward 1 and -1, the load determined by DGT either overestimated or underestimated the actual load by as much as 30%. In DGT-based load estimates, the degree of potential bias should be assessed, and the concentration-flow relation should be characterized. As the correlation of analyte concentration and temperature approached 1 and -1, the deviation of the concentration determined by DGT from the actual concentration increased. In most cases, this bias was < 2%; however, if the changes in concentration and temperature were large (∼10 mg L-1 and ∼10 °C), the bias exceeded 5%. Concentration and temperature are unlikely to be perfectly or strongly correlated or anti-correlated in natural systems and thus should not affect the accuracy of DGT concentration calculations in most circumstances. The more solution temperature, flow, and concentration were uncorrelated, the closer DGT-derived concentration and load were to the actual solution concentration and load.

Toward In-Field Determination of Nitrate Concentrations Via Diffusive Gradients in Thin Films-Incorporation of Reductants and Color Reagents.

Diffusive gradients in thin films (DGTs) have been established as useful tools for the determination of nitrate, phosphate, trace metals, and organic concentrations. General use of DGTs, however, is limited by the subsequent requirement for laboratory analysis. To increase the uptake of DGT as a tool for routine monitoring by nonspecialists, not researchers alone, methods for in-field analysis are required. Incorporation of color reagents into the binding layer, or as the binding layer, could enable the easy and accurate determination of analyte concentrations in-field. Here, we sought to develop a chitosan-stabilized silver nanoparticle (AuNP) suspension liquid-binding layer which developed color on exposure to nitrite, combined with an Fe(0)-impregnated poly-2-acrylamido-2-methyl-1-propanesulfonic acid/acrylamide copolymer hydrogel [Fe(0)-p(AMPS/AMA)] for the reduction of nitrate. The AuNP-chitosan suspension was housed in a 3D designed and printed DGT base, with a volume of 2 mL, for use with the standard DGT solution probe caps. A dialysis membrane with a molecular weight cutoff of <15 kDa was used, as part of the material diffusion layer, to ensure that the AuNP-chitosan did not diffuse through to the bulk solution. This synthesized AuNP-chitosan provided quantitative nitrite concentrations (0 to 1000 mg L-1) and masses (145 µg) in laboratory-based color development studies. An Fe(III)-impregnated poly-2-acrylamido-2-methyl-1-propanesulfonic acid/acrylamide copolymer hydrogel [Fe(III)-p(AMPS/AMA)] was developed (10% AMPS, and 90% AMA), which was treated with NaBH4 to form an Fe(0)-p(AMPS/AMA) hydrogel. The Fe(0)-p(AMPS/AMA) hydrogel quantitatively reduced nitrate to nitrite. The total nitrite mass produced was ∼110 µg, from nitrate. The diffusional characteristics of nitrite and nitrate through the Fe(III)-p(AMPS/AMA) and dialysis membrane were 1.40 × 10-5 and 1.40 × 10-5 and 5.05 × 10-6 and 5.15 × 10-6 cm2 s-1 at 25 °C respectively. The Fe(0)-hydrogel and AuNP-chitosan suspension operated successfully in laboratory tests individually; however, the combined AuNP-chitosan suspension and Fe(0)-hydrogel DGT did not provide quantitative nitrate concentrations. Further research is required to improve the reaction rate of the AuNP-chitosan nitrite-binding layer, to meet the requirement of rapid binding to operate as a DGT.