Rapid decrease of soil carbon after abandonment of subtropical paddy fields

Aims

This study is aimed to investigate the efficiency of plant growth-promoting (PGP) strategies of Enterobacter sp. strain EG16 under metal stress and its potential application in phytoremediation.

Methods

Production of siderophores and indole-3-acetic acid (IAA) by EG16 were assessed in a hydroponic system in which Hibiscus cannabinus was grown with different concentrations of Cd and Fe. A pot experiment was also carried out to evaluate the practical effect of EG16 on H. cannabinus growth and remediation efficiency.

Results

Inoculation with EG16 significantly improved plant growth, probably as a result of increased plant uptake of Fe and immobilization of Cd²⁺, which resulted in decreased plant accumulation of Cd. Increased production of siderophores by EG16 in response to Cd exposure appeared to be the PGP strategy functioning in the EG16–H. cannabinus association. The bacterial Cd response system promoted plant and bacterial uptake of Fe, alleviated Cd-induced inhibition of bacterial IAA production, and potentially assisted in metal immobilization in the rhizosphere.

Conclusions

The EG16–H. cannabinus association may be useful for phytostabilization, as it exhibits good plant growth, low plant accumulation of metals, and reduced metal bioavailability in soil.

     

Respiration costs associated with nitrate reduction as estimated by 14CO2 pulse labeling of corn at various growth stages

Utilization of nitrogen in the form of either nitrate (NO ₃ ^? ) or ammonium (NH ₄ ⁺ ) ions may affect the carbohydrate metabolism and energy budget of plants. Recent studies showed that greater expenses of NO ₃ ^? to NH ₄ ⁺ reduction mostly occur in the roots and during darkness. Fertilization of corn with ¹⁵N-labeled nitrate and ammonium, combined with pulse labeling of plants in a ¹⁴CO₂ atmosphere at the V6 and V8 growth stages, allowed us to evaluate the effect of N form on the CO₂ efflux from soil. NH ₄ ⁺ oxidation was inhibited by adding dicyandiamide. In respect to ammonium, nitrate addition increased root-derived CO₂ efflux from corn by 2.6 times at stage V6 and by 1.8 times at stage V8. The time of peak ¹⁴CO₂ efflux from soil also differed between two growing stages: at V6, efflux peaked only on the second day after pulse labeling, while at V8 this occurred within the first 6 h. The strong effect of NO ₃ ^? and NH ₄ ⁺ on root respiration requires considering the N form in the soil and the nitrate reduction site location in a plant when modeling soil respiration changes and when separately estimating individual CO₂ sources that contribute to the total soil CO₂ efflux.     

Direct chemiluminescence detection of nitric oxide in aqueous solutions using the natural nitric oxide target soluble guanylyl cyclase

Nitric oxide (NO) is a free radical involved in many physiological processes including regulation of blood pressure, immune response, and neurotransmission. However, the measurement of extremely low, in some cases subnanomolar, physiological concentrations of nitric oxide presents an analytical challenge. The purpose of this methods article is to introduce a new highly sensitive chemiluminescence approach to direct NO detection in aqueous solutions using a natural nitric oxide target, soluble guanylyl cyclase (sGC), which catalyzes the conversion of guanosine triphosphate to guanosine 3′,5′-cyclic monophosphate and inorganic pyrophosphate. The suggested enzymatic assay uses the fact that the rate of the reaction increases by about 200 times when NO binds with sGC and, in so doing, provides a sensor for nitric oxide. Luminescence detection of the above reaction is accomplished by converting inorganic pyrophosphate into ATP with the help of ATP sulfurylase followed by light emission from the ATP-dependent luciferin–luciferase reaction. Detailed protocols for NO quantification in aqueous samples are provided. The examples of applications include measurement of NO generated by a nitric oxide donor (PAPA-NONOate), nitric oxide synthase, and NO gas dissolved in buffer. The method allows for the measurement of NO concentrations in the nanomolar range and NO generation rates as low as 100 pM/min.     

Losses of soil carbon by converting tropical forest to plantations: erosion and decomposition estimated by δ13C

Indonesia lost more tropical forest than all of Brazil in 2012, mainly driven by the rubber, oil palm, and timber industries. Nonetheless, the effects of converting forest to oil palm and rubber plantations on soil organic carbon (SOC) stocks remain unclear. We analyzed SOC losses after lowland rainforest conversion to oil palm, intensive rubber, and extensive rubber plantations in Jambi Province on Sumatra Island. The focus was on two processes: (1) erosion and (2) decomposition of soil organic matter. Carbon contents in the Ah horizon under oil palm and rubber plantations were strongly reduced up to 70% and 62%, respectively. The decrease was lower under extensive rubber plantations (41%). On average, converting forest to plantations led to a loss of 10 Mg C ha^?1 after about 15 years of conversion. The C content in the subsoil was similar under the forest and the plantations. We therefore assumed that a shift to higher δ¹³C values in plantation subsoil corresponds to the losses from the upper soil layer by erosion. Erosion was estimated by comparing the δ¹³C profiles in the soils under forest and under plantations. The estimated erosion was the strongest in oil palm (35 ± 8 cm) and rubber (33 ± 10 cm) plantations. The ¹³C enrichment of SOC used as a proxy of its turnover indicates a decrease of SOC decomposition rate in the Ah horizon under oil palm plantations after forest conversion. Nonetheless, based on the lack of C input from litter, we expect further losses of SOC in oil palm plantations, which are a less sustainable land use compared to rubber plantations. We conclude that δ¹³C depth profiles may be a powerful tool to disentangle soil erosion and SOC mineralization after the conversion of natural ecosystems conversion to intensive plantations when soils show gradual increase of δ¹³C values with depth.     

Protein Identification Using Top-Down Spectra

In the last two years, because of advances in protein separation and mass spectrometry, top-down mass spectrometry moved from analyzing single proteins to analyzing complex samples and identifying hundreds and even thousands of proteins. However, computational tools for database search of top-down spectra against protein databases are still in their infancy. We describe MS-Align+, a fast algorithm for top-down protein identification based on spectral alignment that enables searches for unexpected post-translational modifications. We also propose a method for evaluating statistical significance of top-down protein identifications and further benchmark various software tools on two top-down data sets from Saccharomyces cerevisiae and Salmonella typhimurium. We demonstrate that MS-Align+ significantly increases the number of identified spectra as compared with MASCOT and OMSSA on both data sets. Although MS-Align+ and ProSightPC have similar performance on the Salmonella typhimurium data set, MS-Align+ outperforms ProSightPC on the (more complex) Saccharomyces cerevisiae data set.In the past two decades, proteomics was dominated by bottom-up mass spectrometry that analyzes digested peptides rather than intact proteins. Bottom-up approaches, although powerful, do have limitations in analyzing protein species, e.g. various proteolytic forms of the same protein or various protein isoforms resulting from alternative splicing. Top-down mass spectrometry focuses on analyzing intact proteins and large peptides (1–10) and has advantages in localizing multiple post-translational modifications (PTMs)¹ in a coordinated fashion (e.g. combinatorial PTM code) and identifying multiple protein species (e.g. proteolytically processed protein species) (11). Until recently, most top-down studies were limited to single purified proteins (12–15). Top-down studies of protein mixtures were restricted by difficulties in separating and fragmenting intact proteins and a shortage of robust computational tools.In the last two years, because of advances in protein separation and top-down instrumentation, top-down mass spectrometry moved from analyzing single proteins to analyzing complex samples containing hundreds and even thousands of proteins (16–21). Because algorithms for interpreting top-down spectra are still in their infancy, many recent developments include computational innovations in protein identification.Because top-down spectra are complex, the first step in top-down spectral interpretation is usually spectral deconvolution, which converts a complex top-down spectrum to a list of monoisotopic masses (a deconvolved spectrum). Every protein (possibly with modifications) can be scored against a top-down deconvoluted spectrum, resulting in a Protein-Spectrum-Match (PrSM). The top-down protein identification problem is finding a protein in a database with the highest scoring PrSM for a top-down spectrum and further output the PrSM if it is statistically significant. There are several software tools for top-down protein identification (

Carbon cost of collective farming collapse in Russia

The collapse of collective farming in Russia after 1990 and the subsequent economic crisis led to the abandonment of more than 45 million ha of arable lands (23% of the agricultural area). This was the most widespread and abrupt land use change in the 20th century in the northern hemisphere. The withdrawal of land area from cultivation led to several benefits including carbon (C) sequestration. Here, we provide a geographically complete and spatially detailed analysis of C sequestered in these abandoned lands. The average C accumulation rate in the upper 20 cm of mineral soil was 0.96 ± 0.08 Mg C ha^?1 yr^?1 for the first 20 years after abandonment and 0.19 ± 0.10 Mg C ha^?1 yr^?1 during the next 30 years of postagrogenic evolution and natural vegetation establishment. The amount of C sequestered over the period 1990–2009 accounts to 42.6 ± 3.8 Tg C per year. This C sequestration rate is equivalent to ca. 10% of the annual C sink in all Russian forests. Furthermore, it compensates all fire and postfire CO₂ emissions in Russia and covers about 4% of the global CO₂ release due to deforestation and other land use changes. Our assessment shows a significant mitigation of increasing atmospheric CO₂ by prolonged C accumulation in Russian soils caused by collective farming collapse.     

Morphological variation of Juniperus oxycedrus subsp. oxycedrus (Cupressaceae) in the Mediterranean region

The intra- and inter-population variation of Juniperus oxycedrus subsp. oxycedrus were examined biometrically on the basis of morphological characters of needles, seeds and cones. Cluster analysis of Euclidean distances and discriminant analysis were performed to verify the hypothesis of geographic differentiation and origin from the West- and East-Mediterranean Pleistocene refugial regions. The West-Mediterranean populations of J. oxycedrus subsp. oxycedrus differed from the eastern ones. The intra-populational differentiation of three of the West-Mediterranean populations was significantly higher than within the other West- and all the East-Mediterranean ones.Results confirm the hypothesis of probable different origins of the East- and West-Mediterranean populations of the taxon.