Physical Protection Mechanisms Research Articles

De Novo Sequencing and Comparative Analysis of Schima superba Seedlings to Explore the Response to Drought Stress.

Schima superba is an important dominant species in subtropical evergreen broadleaved forests of China, and plays a vital role in community structure and dynamics. However, the survival rate of its seedlings in the field is low, and water shortage could be a factor that limits its regeneration. In order to better understand the response of its seedlings to drought stress on a functional genomics scale, RNA-seq technology was utilized in this study to perform a large-scale transcriptome sequencing of the S. superba seedlings under drought stress. More than 320 million clean reads were generated and 72218 unique transcripts were obtained through de novo assembly. These unigenes were further annotated by blasting with different public databases and a total of 53300 unique transcripts were annotated. A total of 31586 simple sequence repeat (SSR) loci were presented. Through gene expression profiling analysis between drought treatment and control, 11038 genes were found to be significantly enriched in drought-stressed seedlings. Based on these differentially expressed genes (DEGs), Gene Ontology (GO) terms enrichment and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analysis indicated that drought stress caused a number of changes in the types of sugars, enzymes, secondary mechanisms, and light responses, and induced some potential physical protection mechanisms. In addition, the expression patterns of 18 transcripts induced by drought, as determined by quantitative real-time PCR, were consistent with their transcript abundance changes, as identified by RNA-seq. This transcriptome study provides a rapid method for understanding the response of S. superba seedlings to drought stress and provides a number of gene sequences available for further functional genomics studies.

Soil carbon and nitrogen fractions in the soil profile and their response to long-term nitrogen fertilization in a wheat field

Ecosystems receive elevated inputs of nitrogen (N) from anthropogenic sources, and understanding the effects of such N addition on the soil carbon (C) and N cycles are important. Soils contain many different C and N fractions that have diverse physical and chemical compositions, and these fractions can be used as early and sensitive indicators of C and N cycling. In this study, we investigated the composition of different C and N fractions and their sensitivities in the upper 200cm of soils planted with winter wheat in areas that had received different N fertilization rates since 2004. Our results indicate that N enrichment may affect C and N cycling by changing certain fractions of soil organic matter. Light fraction of carbon (LFOC), light fraction of nitrogen (LFON), heavy fraction of carbon (HFOC), and heavy fraction of nitrogen (HFON) were constant among the different N rates. In contrast, dissolved organic carbon (DOC) decreased in the 180, 270 and 360kgha−1 treatments in the 20–200cm soil layer, and easily oxidizable organic C (EOC) was the highest in the 90kgha−1 treatment and decreased in the high-N treatments in the 0–20cm soil layer. Both dissolved organic nitrogen (DON) and inorganic N (NO3− and NH4+) increased as N input increase. Nitrate (NO3−) is the fraction most sensitive to N fertilization. The LFOC, LFON and EOC are more sensitive than other fractions in the surface soil layer, but dissolved organic C and N may be better indicators in the subsurface layers. Our results demonstrate how the C and N fractions respond to different N fertilization rates in the top 200cm of the soil profile and further our understanding of the physical protection mechanisms of soil organic carbon (SOC) and total nitrogen (TN), which will aid in the adoption of appropriate management practices for C and N accumulation and stabilization in the field.

A meta‐analysis on pyrogenic organic matter induced priming effect

AbstractPyrogenic organic matter (PyOM) is considered an important soil carbon (C) sink. However, there are evidences that its addition to soil may induce a priming effect (PE) thus influencing its C abatement potential. The direction, the size and the mechanisms responsible for PyOM induced PE are far from being understood. We collected approximately 650 data points from 18 studies to analyse the characteristics of the PE induced by PyOM. The database was divided between the PE induced on the native soil organic matter and on fresh organic matter. Most of the studies were short‐term incubation therefore the projections of findings on the long term may be critical. Our findings indicate that over 1 year PyOM induces an average positive PE of 0.3 mg C g−1 soil on native soil organic matter and a PE of approximately the same size but opposite direction on fresh organic matter. We studied the correlation of PE with several properties of soil, of the added PyOM, and time after PyOM addition. We found that PyOM primes positively the native soil organic matter in the first 20 days while negative PE appears in a later stage. Negative PE was correlated with the soil C content. PyOM characterized by a low C content induced a higher positive PE on native soil organic carbon. No correlation was found between the factors record in our database and the PE induced on the fresh organic matter. We reviewed the mechanisms proposed in literature to explain PE and discussed them based on findings from our meta‐analysis. We believe that the presence of a labile fraction in PyOM may trigger the activity of soil microorganisms on the short term and therefore induce a positive PE, while on the long term PyOM may induce a negative PE by promoting physical protection mechanisms.

Influence of mechanical loading on static and dynamic CO2 efflux on differently textured and managed Luvisols

Mechanical disturbance of soil structure is commonly related to altered physical changes in pore systems, which control CO2 effluxes e.g. by changes in gas transport properties and in microbial activity. Soil compaction mostly leads to reduced CO2 fluxes. In contrast, structured soils can also release physically entrapped CO2 or give access to protected carbon sources inside aggregates due to aggregate breakdown by disruptive forces. In this study it was investigated how far arable soil management affects structure- and compaction-related CO2-releases using incubation experiments and CO2 gas analysis under standard matric potentials (−6kPa). CO2 efflux was analyzed before, during and after mechanical loading using the alkali trap method (static efflux) and a gas flow compaction device (GaFloCoD, dynamic efflux). Intact soil cores (236 and 471cm3) were collected from a Stagnic Luvisol with loamy sand (conservation and conventional tillage systems) and a Haplic Luvisol with clayey silt (under different fodder crops) from the topsoil (10–15cm) and subsoil (35–45cm). Mechanical stability was reflected by the pre-compression stress value (Pc) and by the tensile strength of aggregates (12–20mm). Changes in pore systems were described by air conductivity as well as air capacity and total porosity. While CO2-releases varied highly during the compaction process (GaFloCoD) for different stress magnitudes, soil depths and management systems, basal respiration rates were generally reduced after mechanical loading by almost half of the initial rates irrespective of soil management. For both methods (dynamic and static efflux) restriction in gas transport functionality was proved to have major influence on inhibition of CO2 efflux due to mechanical loading. GaFloCoD experiments demonstrated that decreases in CO2 efflux were linked to structural degradation of pore systems by exceeding internal soil strength (Pc). Otherwise, re-equilibrating matric potentials to −6kPa and re-incubating offset inhibition of soil respiration suggest a re-enhancement of microbial activity. At this state, physical influences were apparently overlapped by biological effects due to higher energy supply to microbes, which could be offered by spatial distribution changes of microorganisms and organic substrates within a given soil structure. This implies the susceptibility of physical protection mechanism for carbon by disruption of soil structure. In future, special focus should be given on a clear distinction between physical and microbiological effects controlling CO2 fluxes in structured soils.

Aggregate formation and carbon sequestration by earthworms in soil from a temperate forest exposed to elevated atmospheric CO2: A microcosm experiment

The role of soils in mitigating increases in atmospheric carbon dioxide (CO2) levels is uncertain, in part for the complex biotic and abiotic interactions determining soil carbon change. Earthworms, in particular, interact with the physical and chemical protection mechanisms of organic matter, major determinants of carbon storage capacity of soils. Studies of a Liquidambar styraciflua forest plantation located at the Oak Ridge National Laboratory (ORNL), which was exposed to elevated CO2 using free air CO2 enrichment (FACE), show that a key mechanism facilitating soil carbon gain was the protection from rapid decomposition afforded by soil aggregates. To evaluate the effects of site earthworms with different feeding behaviors on soil aggregate formation and the sources of organic matter stabilizing these aggregates, we conducted a 26-day laboratory incubation experiment using plant and soil materials with differential dual isotopic compositions obtained from different CO2 and 15N-labeling treatments at the ORNL-FACE site. We used crushed and sieved (<250 μm) unlabeled soil (δ13C = −25.5‰; δ15N = 5.1‰) to create four treatments: (I) soil only; (II) soil and plant material; (III) soil, plant material, and the native, endogeic earthworm Diplocardia sp.; (IV) soil, plant material, and the European, epi-endogeic earthworm Lumbricus rubellus. Added plant materials consisted of both sweetgum (L. styraciflua) leaf (δ13C = −34.2‰; δ15N = 4755.4‰) and root (δ13C = −38.7‰; δ15N = 44.7‰) litter. Overall, earthworms increased the mass of newly formed soil macroaggregates >250 μm (p < 0.001). Most of the carbon within macroaggregates was soil-derived. Leaf- and root-derived carbon was found only in the treatment with L. rubellus. Hence, the source of carbon within macroaggregates paralleled earthworm feeding ecologies, with endogeic earthworms (Diplocardia sp.) feeding mostly on soil organic matter and epi-endogeic earthworms (L. rubellus) feeding on both plant residues and soil organic matter. Our results suggest that earthworms at the ORNL-FACE site directly contribute to the formation of soil aggregates and, could be an important factor contributing to the soil stabilization of increased recent carbon inputs resulting from atmospheric CO2 enrichment at this site.

Assessing humification and organic C compounds by laser-induced fluorescence and FTIR spectroscopies under conventional and no-till management in Brazilian Oxisols

Data on humification is important to assessing the rate and magnitude of soil carbon (C) sequestration. Thus, this study assessed the humification degree (HLIF) of soil organic matter (SOM) and the changes in functional C groups (aromatic-C and aliphatic-C) for contrasting land use and management practices (native vegetation (NV), conventional plow-based tillage (CT) and no-till (NT) systems) in sub-tropical and tropical Brazilian environments. Experiments were conducted at Ponta Grossa (PG) in Paraná State and Lucas do Rio Verde (LRV) in Mato Grosso State of Brazil. Laser-induced fluorescence (LIFS) and Fourier-transform infrared (FTIR) spectroscopies, were used on whole soil samples to 1-m depth, and on seven aggregate size classes (8–19, 4–8, 2–4, 1–2, 0.5–1, 0.25–0.5, 0.053–0.25mm) obtained by wet sieving of 0–5 and 5–10cm layers. Three functional C groups were selected based on FTIR: aliphatic-C1 (1404cm−1), aromatic-C (1632cm−1), and aliphatic-C2 (2852 and 2922cm−1). The HLIF was 3 to 5 times higher at the LRV site than at PG at all soil depths, indicating that selective preservation by aromaticity of SOM is the predominant mechanism in this environment. Relatively lower HFIL was observed in NT soils at both locations because of aggregation which protects most labile moieties. The depletion of C concentration in CT was related to the decrease in functional C groups (i.e., aromatic-C and aliphatic-C) and an overall increase in the humification degree, indicating that physical protection mechanisms are not sufficient to protect the labile fractions of OM. In contrast, the intensity of functional C groups under NT systems was similar to that in the soil under NV at both locations. A discriminant analysis of principal components clearly showed that soils at both locations can be clustered into three groups, corresponding to the three main land-use and management practices. Thus, soils under NV, NT, and CT differed significantly in terms of the composition of organic compounds, and in the interactions between inorganic and organic fractions. Land use changes modify the arrangement of organic compounds necessitating the diversification of agroecosystems and conversion to NT farming. Altogether, our results reveal that LIFS and FTIR are fast, efficient, and precise techniques for analyzing the degree of SOC humification, functional C groups, and hence the efficiency of NT cropping systems in promoting long-term carbon sequestration in soils.

Can minor compaction increase soil carbon sequestration? A case study in a soil under a wheel-track in an orchard

In an organic apple (Malus domestica Borkh., Braeburn on MM.106 rootstock) orchard in New Zealand we observed that the soil's carbon concentration in 0–0.1m depth directly below a wheel-track in the grassed alley-way was significantly higher than under the grassed tree-row. By using a literature review and direct measurements, we systematically exclude two explanations for the possible accumulation of soil carbon under the wheel-track. Firstly, we discard the possibility of higher carbon inputs to the wheel-track compared to the tree-row area. The tree-row received more carbon inputs by the regular application of compost, and the growth of roots was not impeded by compaction. Secondly, we directly measured the monthly dynamics of microbial biomass and respiration rates per unit of soil carbon over a year, and based on 3D X-ray computed tomography (CT) images we modelled the gas exchange close to water saturation. A restricted gas exchange under wet conditions would be an indication that soil carbon mineralization is reduced under wet conditions. We found that both the microbial carbon decomposition dynamics and the gas exchange under wet conditions were similar in the tree-row and under the wheel-track. The most probable explanation for the enhanced carbon sequestration under the wheel-track is a reduction in carbon losses. The water infiltration rates into the wheel-tracks were significantly smaller than in the tree-row. This means that the carbon loss with water flow in the form of dissolved carbon is probably smaller under the wheel-track. Additionally, a reduction in meso- and macro-faunal activities exporting particulate organic matter from the soil volume is probable under minor compaction. We conclude that a minor compaction like under a wheel-track can be a physical protection mechanism for soil carbon.

Micro- and nano-environments of carbon sequestration: Multi-element STXM–NEXAFS spectromicroscopy assessment of microbial carbon and mineral associations

Soil represents the largest reservoir of terrestrial organic C, and plays a critical role in global C cycling. In light of predicted climate change and a more unified approach to mitigate greenhouse gas emissions, the soil's ability to sequester C, and thus to act as a sink or a source for atmospheric CO2 has received growing interest. Organomineral assemblages are a unique niche in C cycling, with large capacity for storing anthropogenic C. However, the underlying biogeochemical mechanisms for C sequestration through organomineral associations are not yet well understood. One of the major challenges to study C sequestration in organomineral assemblages is lack of non-invasive analytical tools with a potential to obtain molecular-level information about the interactions between C and mineral components in submicron geochemical environments. In the present study, we have effectively employed synchrotron-based STXM–NEXAFS spectroscopy to access the K- and L-edges of biogeochemically relevant elements (C, N, Ca, Fe, Al, Si) to identify and image micro- and nano-C sequestration environments, and conduct submicron-level investigation of the compositional chemistry and other interactive features of C and minerals present in these hotspots using ultrathin section of intact organomineral assemblage. The C K-edge NEXAFS spectromicroscopy micrographs clearly demonstrated the existence of spatially distinct seemingly terminal micro- and nano-C repository zones, where organic C was sequestered in apparent agglomeration in the investigated organomineral assemblage. These submicron-C repository environments were only a few micrometers apart from each other; yet they were considerably different compositionally from each other. The organic C in the first repository environment was pyrogenic in origin, largely composed of quinone, phenols, ketones and aromatic ring structures. However, the second hotspot was dominated by filament-like structure, with striking similarity to the C 1s NEXAFS spectral signatures of organic C isolated from soil fungal and bacteria, and dominated by resonances from aliphatic-C and CN bonds of imidazol structures, carboxyl/carbonyl-C, amide- and O-alkyl-C functionalities. The composition of organic C in the organomineral interface around the strand-like structure was highly complex and composed of polysaccharides, amino sugars, amino acids, nucleic acids, and phospholipid fatty acid structures with polar and non-polar termini. The chemistry of mineral matter in the organomineral interface was also equally complex, ranging from Ca, Fe and Al ions, Fe and Al oxides, hydroxides and oxyhydroxides to phyllosilicates, which could provide a variety of polyvalent cations, hydroxyl surface functional groups and edge sites that can attract and bind microbial biomolecules. Based on the enormous complexity of the organic C functionalities and the coexistence of various inorganic components in the organomineral interface, it is possible to suggest that no single binding mechanism could be accountable for the organic C stored in the investigated submicron-C repository environment. Our results seem to suggest that the apparent C sequestration in the micro- and nano-C repository environment appear to be the cumulative result of physical protection and heterogeneous binding mechanisms ranging from ion exchange, hydrogen bonding, and hydrophobic bonding on silicate clay–organic complexes to adsorption on external and internal surfaces of clay minerals.

Biochemical changes across a carbon saturation gradient: Lignin, cutin, and suberin decomposition and stabilization in fractionated carbon pools

Soils that exhibit soil organic carbon (SOC) saturation provide an opportunity to examine mechanisms of C storage in soils with increasingly limited C-stabilization potential. A manure rate experiment in Lethbridge, Alberta, in which SOC responded asymptotically to long-term manure C additions, allowed us to assess changes in SOC biochemical composition in response to soil C saturation. By quantifying the cupric oxide oxidation products of lignin, cutin, and suberin in fractionated SOC pools that are characterized by chemical (i.e., mineral-associated), physical (i.e., microaggregate-associated), or no protection (i.e., free particulate organic matter), we evaluated the interaction between C saturation and the biochemical characteristics of SOC.We tested the specific responses of soil fraction lignin, cutin, and suberin to C saturation level by using the bulk soil to approximate C-input composition across manure input treatments. Carbon-normalized lignin (lignin-VSC/OC) in the chemically protected fractions did not differ, while in the non-protected and physically protected soil fractions, it decreased with C saturation level. Neither the stabilization of cutin and suberin, nor the lignin:cutin + suberin ratio, differed in any of the measured soil fractions in response to C saturation level.These results indicate that with C saturation and decreased C stabilization potential, lignin, cutin, or suberin were not preferentially stabilized or depleted in mineral protected soil C pools. The lack of evidence for biochemical preference in mineral associations with C saturation supports the existence of an outer kinetic zone of organomineral associations, in which partitioning of organic compounds, rather than sorption, controls mineral SOC accumulation at high SOC loadings. Furthermore, despite theories of inherent lignin recalcitrance, depleted lignin concentrations with C saturation in the non-protected and aggregate protected fractions indicate that lignin was, in this study, preferentially decomposed when not protected by association with mineral phases in the soil. In conclusion, C-input quantity, and not quality, combined with physical and chemical protection mechanisms that govern long-term C storage, appeared to control C saturation and stabilization at this site.

Review of researches on soil aggregate and soil organic carbon

增加土壤有机碳有助于农业可持续发展, 同时对缓解温室气体增加造成的全球气候变暖等具有重要意义。土壤团聚体是土壤的重要组成部分, 影响土壤的各种物理化学性质。土壤团聚体和有机碳是不可分割的, 前者是后者存在的场所, 后者是前者存在的胶结物质。本文在综合各方面研究的基础上, 阐述了土壤团聚体和有机碳的依存关系, 影响团聚体固碳的几大因素, 团聚体对有机碳的物理保护机制以及目前应用比较广泛的团聚体内有机碳的研究方法, 为以后的研究提供理论和方法上的支持。

A Review of Dissolved Organic Matter Transport Processes Affecting Soil and Environmental Quality

Dissolved organic matter (DOM) affects several processes in soil and water including nutrient cycling, soil and water pollution and CO2 flux between the soil and atmosphere. The aim of this review is to collate and synthesize the literature on the transport processes of DOM in soil. The DOM normally comprises of only a small fraction of soil organic matter (SOM) and originates mainly from the decomposition and solubilization of SOM, which is accumulated on soil surface or soil profile from plant residues and additions of organic amendments such as animal and poultry manures and other biosolids. The DOM is one of the most reactive and mobile SOM fractions and has a major influence on biogeochemical processes in both terrestrial and aquatic environments. Terrestrially borne DOM is subjected to microbial decomposition, photodegradation and adsorption on soil mineral surfaces. It is sorbed on mineral surfaces and high adsorption capacities of clay minerals and oxides for DOM sorption are demonstrated in laboratory studies. However, these high sorption values are not reproduced in limited field studies. Similarly, a few data available on the transport of DOM through macropores also demonstrate the limited control of sorption on DOM retention in soil profile. Thus, there is a need to further investigate the physical and chemical protection mechanisms, as well as the biodegradability of DOM shown in laboratory studies. There is an increasing need to clearly understand the formation, fate and transport of DOM at field scales. The environmental factors such as precipitation and temperature, land use change, land management, and biological factors have profound and discrete influences on DOM dynamics in soil profile. Future research efforts must focus on the assessment of the influences of these factors by conducting field studies in different climatic zones, soils, and land use and management systems.

Dps proteins, an efficient detoxification and DNA protection machinery in the bacterial response to oxidative stress

The proteins belonging to the Dps (DNA-binding proteins from starved cells) family play an important role within the bacterial defence system against oxidative stress. They act on Fe(II) and hydrogen peroxide that are potentially toxic in the presence of air. Fe(II) forms spontaneously insoluble Fe(III) and reacts with molecular oxygen or its reduced forms to yield the highly damaging hydroxyl radicals. All Dps proteins have the distinctive capacity to annul the toxic combination of iron and hydrogen peroxide as they use the latter compound to oxidise Fe(II). In addition to this intrinsic DNA protection capacity, several members of the family, including the archetypical Escherichia coli Dps, protect DNA physically by shielding it in large Dps-DNA complexes. The structural and functional characteristics that endow Dps proteins with the chemical and physical protection mechanism are presented and discussed also in the framework of the varied situations that may be encountered in different bacterial species.

Physical carbon‐sequestration mechanisms under special consideration of soil wettability

AbstractThe protective impact of aggregation on microbial degradation through separation has been described frequently, especially for biotically formed aggregates. However, to date little information exists on the effects of organic‐matter (OM) quantity and OM quality on physical protection, i.e., reduced degradability by microorganisms caused by physical factors. In the present paper, we hypothesize that soil wettability, which is significantly influenced by OM, may act as a key factor for OM stabilization as it controls the microbial accessibility for water, nutrients, and oxygen in three‐phase systems like soil. Based on this hypothesis, the first objective is to evaluate new findings on the organization of organo‐mineral complexes at the nanoscale as one of the processes creating water‐repellent coatings on mineral surfaces. The second objective is to quantify the degree of alteration of coated surfaces with regard to water repellence. We introduce a recently developed trial that combines FTIR spectra with contact‐angle data as the link between chemical composition of OM and the physical wetting behavior of soil particles. In addition to characterizing the wetting properties of OM coatings, we discuss the implications of water‐repellent surfaces for different physical protection mechanisms of OM. For typical minerals, the OM loading on mineral surfaces is patchy, whereas OM forms nanoscaled micro‐aggregates together with metal oxides and hydroxides and with layered clay minerals. Such small aggregates may efficiently stabilize OM against microbial decomposition. However, despite the patchy structure of OM coating, we observed a relation between the chemical composition of OM and wettability. A higher hydrophobicity of the OM appears to stabilize the organic C in soil, either caused by a specific reduced biodegradability of OM or indirectly caused by increased aggregate stability. In partly saturated nonaggregated soil, the specific distribution of the pore water appears to further affect the mineralization of OM as a function of wettability. We conclude that the wettability of OM, quantified by the contact angle, links the chemical structure of OM with a bundle of physical soil properties and that reduced wettability results in the stabilization of OM in soils.

Platform independent overall security architecture in multi-processor system-on-chip integrated circuits for use in mobile phones and handheld devices

A platform independent security architecture for use in Multi-Processor System-on-Chip integrated circuits, primarily oriented for mobile phones and handheld devices, is presented. The suggested architecture provides an enhanced security protection scheme for use in smartphones, PDA’s, as well as other similar systems. Sensitive data storage facilities, cryptographic engines, and physical protection mechanisms such as debug port access control are presented and described in detail. The proposed secure architecture has been incorporated as a part of an application processor which in turn is embedded in a number of smartphone and handheld products. System operation is discussed and hardware realization and experimental results of the proposed architecture are described.

Acid hydrolysis of easily dispersed and microaggregate‐derived silt‐ and clay‐sized fractions to isolate resistant soil organic matter

SummaryThe current paradigm in soil organic matter (SOM) dynamics is that the proportion of biologically resistant SOM will increase when total SOM decreases. Recently, several studies have focused on identifying functional pools of resistant SOM consistent with expected behaviours. Our objective was to combine physical and chemical approaches to isolate and quantify biologically resistant SOM by applying acid hydrolysis treatments to physically isolated silt‐ and clay‐sized soil fractions. Microaggegrate‐derived and easily dispersed silt‐ and clay‐sized fractions were isolated from surface soil samples collected from six long‐term agricultural experiment sites across North America. These fractions were hydrolysed to quantify the non‐hydrolysable fraction, which was hypothesized to represent a functional pool of resistant SOM. Organic C and total N concentrations in the four isolated fractions decreased in the order: native &gt; no‐till &gt; conventional‐till at all sites. Concentrations of non‐hydrolysable C (NHC) and N (NHN) were strongly correlated with initial concentrations, and C hydrolysability was found to be invariant with management treatment. Organic C was less hydrolysable than N, and overall, resistance to acid hydrolysis was greater in the silt‐sized fractions compared with the clay‐sized fractions. The acid hydrolysis results are inconsistent with the current behaviour of increasing recalcitrance with decreasing SOM content: while %NHN was greater in cultivated soils compared with their native analogues, %NHC did not increase with decreasing total organic C concentrations. The analyses revealed an interaction between biochemical and physical protection mechanisms that acts to preserve SOM in fine mineral fractions, but the inconsistency of the pool size with expected behaviour remains to be fully explained.