Impact of soil amendments on organic carbon pools under a rice-wheat cropping system

Rice-wheat cropping is the dominant cropping sequence in the Indo-Gangetic plains (IGP) of India. An experiment was conducted to study the impact of continuous application of farmyard manure (FYM) and rice straw (RS), either alone or in conjunction with fertilizer nitrogen (N), under a rice-wheat cropping system on i) total soil organic carbon (SOC) and slow pool C, and ii) stabilization of cumulative input C. Application of FYM, after seven years of rice-wheat cropping cycles, increased total SOC and slow pool C at 0-0.15 m soil depth by 6.7 t/ha and 1.5 t/ha, respectively, with the highest effect when FYM, RS and fertilizer N were applied together. Incorporation of RS increased total SOC by 4.1 t/ha, with an insignificant effect on the slow pool C. There was no significant effect of fertilizer N application on total SOC and slow pool C. The slow pool C was strongly correlated with the total SOC. About 18.5% and 4.2% of the cumulative input C were stabilized as total SOC and slow pool C, respectively, due to application of FYM; values for RS were 17.9% and 3.3%, respectively

Organic amendments influence soil quality and carbon sequestration in the Indo-Gangetic plains of India

Soil organic carbon is considered to be of central importance in maintaining soil quality. We assessed the effects of a range of commonly applied organic and inorganic amendments on soil quality in a rice-wheat cropping system in the Indo-Gangetic plains of eastern India and evaluated the carbon sequestration potential of such management approaches using a 25 year old long-term fertility experiment. Results showed that there were significant increases in soil nutrient availability with the application of farm yard manure (FYM @ 7.5 t ha⁻¹), paddy straw (PS @ 10 t ha⁻¹) and green manure (GM @ 8 t ha⁻¹) along with inorganic fertilizer. Both microbial biomass C and mineralizable C increased following the addition of the organic inputs. Continuous cultivation, without application of organic inputs, significantly depleted total C content (by 39-43%) compared with treatments involving the addition of organic amendments. A significant increase in the non-labile C fraction resulted from both organic and inorganic amendments, but only 26, 18 and 6% of the C applied through FYM, PS and GM, respectively was sequestered in soils. A significant increase in yield of kharif rice was observed as a result of the addition of these organic amendments

Aggregation of rhodopsin mutants in mouse models of autosomal dominant retinitis pigmentosa

Abstract Mutations in rhodopsin can cause it to misfold and lead to retinal degeneration. A distinguishing feature of these mutants in vitro is that they mislocalize and aggregate. It is unclear whether or not these features contribute to retinal degeneration observed in vivo. The effect of P23H and G188R misfolding mutations were examined in a heterologous expression system and knockin mouse models, including a mouse model generated here expressing the G188R rhodopsin mutant. In vitro characterizations demonstrate that both mutants aggregate, with the G188R mutant exhibiting a more severe aggregation profile compared to the P23H mutant. The potential for rhodopsin mutants to aggregate in vivo was assessed by PROTEOSTAT, a dye that labels aggregated proteins. Both mutants mislocalize in photoreceptor cells and PROTEOSTAT staining was detected surrounding the nuclei of photoreceptor cells. The G188R mutant promotes a more severe retinal degeneration phenotype and greater PROTEOSTAT staining compared to that promoted by the P23H mutant. Here, we show that the level of PROTEOSTAT positive cells mirrors the progression and level of photoreceptor cell death, which suggests a potential role for rhodopsin aggregation in retinal degeneration

Simulation of soil organic carbon dynamics under different land use and crop management practices

Soils are the largest reservoir of terrestrial carbon (C) (~1500 Pg organic C in top one meter) and any change in this large soil organic carbon (SOC) stock due to change in land use, management practice or climate change may have significant and long-lived effects on the global C cycle. The SOC turnover models can project the change in SOC storage and turnover rate under future scenarios of land use, management practice, technological improvement and climate change, and investigate hypotheses that are beyond the feasibility of experimental work. In Australia, there is a greater need for modelling such scenarios across a wider range of agro-ecological regions and land uses. In this thesis, SOC dynamics under different land uses and crop management practices in the northern plains and slopes of New South Wales (NSW) was explored using the Rothamsted carbon model (RothC). The specific objectives were (i) to determine turnover times of SOC fractions, separated by a combination of physical and chemical methods, in contrasting land use systems by natural 14C abundance, (ii) to examine whether a combination of physical and chemical laboratory methods of SOC fractionation has the potential to quantify different SOC pools, as required by RothC, (iii) to evaluate the performance of RothC in simulating the effect of land use change (LUC) on SOC dynamics, particularly following a proposed land use change from native vegetation to cropping, using paired-site data sets, (iv) to examine whether initializing RothC with measured SOC pools, rather than using default model equilibrium pools, improves RothC performance in prediction of LUC effects on SOC dynamics, (v) to evaluate RothC performance in simulation of SOC dynamics under a cotton based cropping system on an irrigated Vertosol using long-term field experiment data, (vi) to explore different scenarios of SOC dynamics under different cotton based cropping systems in irrigated Vertosol, (vii) to test whether RothC projections of grassland SOC under climate change were sensitive to the model initialisation method, and (viii) to projected climate change impacts on grassland SOC with three different global climate models (GCMs) forced with four different climate scenarios for the time period 2008-2100, using RothC in the northern slopes and plains of NSW, Australia

A Three-Arm Scaffold Carrying Affinity Molecules for Multiplex Recognition Imaging by Atomic Force Microscopy: The Synthesis, Attachment to Silicon Tips, and Detection of Proteins

We have developed a multiplex imaging method for detection of proteins using atomic force microscopy (AFM), which we call multiplex recognition imaging (mRI). AFM has been harnessed to identify protein using a tip functionalized with an affinity molecule at a single molecule level. However, many events in biochemistry require identification of colocated factors simultaneously, and this is not possible with only one type of affinity molecule on an AFM tip. To enable AFM detection of multiple analytes, we designed a recognition head made from conjugating two different affinity molecules to a three-arm linker. When it is attached to an AFM tip, the recognition head would allow the affinity molecules to function in concert. In the present study, we synthesized two recognition heads: one was composed of two nucleic acid aptamers, and the other one composed of an aptamer and a cyclic peptide. They were attached to AFM tips through a catalyst-free click reaction. Our imaging results show that each affinity unit in the recognition head can recognize its respective cognate in an AFM scanning process independently and specifically. The AFM method was sensitive, only requiring 2 to 3 μL of protein solution with a concentration of ∼2 ng/mL for the detection with our current setup. When a mixed sample was deposited on a surface, the ratio of proteins could be determined by counting numbers of the analytes. Thus, this mRI approach has the potential to be used as a label-free system for detection of low-abundance protein biomarkers

Rhodopsin Forms Nanodomains in Rod Outer Segment Disc Membranes of the Cold-Blooded Xenopus laevis.

Rhodopsin forms nanoscale domains (i.e., nanodomains) in rod outer segment disc membranes from mammalian species. It is unclear whether rhodopsin arranges in a similar manner in amphibian species, which are often used as a model system to investigate the function of rhodopsin and the structure of photoreceptor cells. Moreover, since samples are routinely prepared at low temperatures, it is unclear whether lipid phase separation effects in the membrane promote the observed nanodomain organization of rhodopsin from mammalian species. Rod outer segment disc membranes prepared from the cold-blooded frog Xenopus laevis were investigated by atomic force microscopy to visualize the organization of rhodopsin in the absence of lipid phase separation effects. Atomic force microscopy revealed that rhodopsin nanodomains form similarly as that observed previously in mammalian membranes. Formation of nanodomains in ROS disc membranes is independent of lipid phase separation and conserved among vertebrates

Application of Catalyst-Free Click Reactions in Attaching Affinity Molecules to Tips of Atomic Force Microscopy for Detection of Protein Biomarkers

Atomic force microscopy (AFM) has been extensively used in studies of biological interactions. Particularly, AFM based force spectroscopy and recognition imaging can sense biomolecules on a single molecule level, having great potential to become a tool for molecular diagnostics in clinics. These techniques, however, require affinity molecules to be attached to AFM tips in order to specifically detect their targets. The attachment chemistry currently used on silicon tips involves multiple steps of reactions and moisture sensitive chemicals, such as (3-aminopropyl)­triethoxysilane (APTES) and <i>N</i>-hydroxysuccinimide (NHS) ester, making the process difficult to operate in aqueous solutions. In the present study, we have developed a user-friendly protocol to functionalize the AFM tips with affinity molecules. A key feature of it is that all reactions are carried out in aqueous solutions. In summary, we first synthesized a molecular anchor composed of cyclooctyne and silatrane for introduction of a chemically reactive function to AFM tips and a bifunctional polyethylene glycol linker that harnesses two orthogonal click reactions, copper free alkyne–azide cycloaddition and thiol-vinylsulfone Michael addition, for attaching affinity molecules to AFM tips. The attachment chemistry was then validated by attaching antithrombin DNA aptamers and cyclo-RGD peptides to silicon nitride (SiN) tips, respectively, and measuring forces of unbinding these affinity molecules from their protein cognates human α-thrombin and human α₅β₁-integrin immobilized on mica surfaces. In turn, we used the same attachment chemistry to functionalize silicon tips with the same affinity molecules for AFM based recognition imaging, showing that the disease-relevant biomarkers such as α-thrombin and α₅β₁-integrin can be detected with high sensitivity and specificity by the single molecule technique. These studies demonstrate the feasibility of our attachment chemistry for the use in functionalization of AFM tips with affinity molecules

Projections of changes in grassland soil organic carbon under climate change are relatively insensitive to methods of model initialization

Model initialization in soil organic carbon (SOC) turnover models has often been described as a crucial step in making future projections. Model initialization by the spin-up of pools of SOC (model equilibrium run) has been questioned, because equilibrium has to be assumed. Measured SOC pools are independent of model assumptions and are thought to reflect better real site conditions. It has been suggested that model initialization with measured SOC fractions could provide an advantage over model spin-up of SOC pools. In this study we tested this suggestion in relatively undisturbed native grasslands in Australia. We tested the Rothamsted SOC turnover model (RothC) under climate change at 12 sites with three different initialization methods, viz. model initialization with (i) spin-up of model pools with inert organic matter (IOM) pool size calculated from a regression equation, (ii) spin-up of model pools with measured IOM and (iii) all pools estimated from measured fractions. Averaged over the sites and initialization methods, maximum absolute variations (absolute differences in projected SOC stocks expressed as a percentage of initial 2008 SOC stocks) as well as averaged absolute variations throughout the projection period were very small (2.2 and 1.6%, respectively). Averaged across the sites, there were no significant differences in projected grassland SOC stocks under climate change after 93 years of simulation with model initialization by different methods and averaged absolute variation was only 1.6% across initialization methods. These findings suggest that in a relatively undisturbed land-use system such as native grassland, projections of SOC under climate change are relatively insensitive to the model initialization method

Response to Letter to the Editor "Comments on "Modelling soil organic carbon storage with RothC in irrigated Vertisols under cotton cropping systems in the sub-tropics" (Nimai Senapati, Nilantha R. Hulugalle, Pete Smith, Brian R. Wilson, Jagadeesh B. Yeluripati, Heiko Daniel, Subhadip Ghosh, Peter Lockwood. Soil &amp; Tillage Research 143 (2014) 38-49)"

Irrigation water was not included in our original publication (Senapati et al., 2014) but should have been. Though there is no irrigation water module in the Rothamsted Carbon Model (RothC) (Coleman and Jenkinson, 1996, 2008), irrigation water can be added to the precipitation input file. In this Response to Letter to the Editor, we have addressed this issue by adding irrigation water to the precipitation, and accounted to deep drainage and runoff, in simulation of soil organic carbon (SOC) storage with RothC in irrigated Vertisols under cotton cropping systems

Modelling soil organic carbon storage with RothC in irrigated Vertisols under cotton cropping systems in the sub-tropics

The performance of the Rothamsted Carbon Model (RothC) in simulating soil carbon (SOC) storage in cotton based cropping systems under different tillage management practices on an irrigated Vertisol in semi-arid, subtropics was evaluated using data from a long-term (1994-2012) cotton cropping systems experiment near Narrabri in north-western New South Wales, Australia. The experimental treatments were continuous cotton/conventional tillage (CC/CT), continuous cotton/minimum tillage (CC/MT), and cotton-wheat (Triticum aestivum L.) rotation/minimum tillage (CW/MT). Soil carbon (C) input was calculated by published functions that relate crop yield to soil C input. Measured values showed a loss in SOC of 34%, 24% and 31% of the initial SOC storages within 19 years (1994-2012) under CC/CT, CC/MT, and CW/MT, respectively. RothC satisfactorily simulated the dynamics of SOC in cotton based cropping systems under minimum tillage (CC/MT and CW/MT), whereas the model performance was poor under intensive conventional tillage (CC/CT). The model RothC overestimated SOC storage in cotton cropping under conventional intensive tillage management system. This over estimation could not be attributed to the overestimation of soil C inputs, or errors in initial quantification of SOC pools for model initialization, or the ratio of incoming decomposable plant materials to resistant plant materials. Among other different factors affecting SOC dynamics and its modelling under intensive tillage in tropics and sub-tropics, we conclude that factors for tillage and soil erosion might be needed when modelling SOC dynamics using RothC under intensive tillage management system in the tropics and the sub-tropics