Use of electron microscopy for aiding our understanding of wood biodegradation

Abstract: The use of electron microscopy (EM) has proved to be an invaluable tool for studying structural aspects of lignocellulose degradation by fungi and bacteria and therefore improving our understanding of wood biodegradation. The present review details the application of conventional (SEM, TEM, STEM), analytical (EM X-ray microanalysis, (EDXA)), and immunogold cytochemical EM procedures in the field and gives specific examples of its use for each of the known important types of microbial wood decay including bacterial (tunnelling and erosion), soft rot (cavity and erosion), brown rot and white rot (simultaneous decay and preferential lignin degraders), and discusses important advances made by adopting the techniques. The more recent use of immunogold cytochemistry for studying microbe and fungal enzyme-wood cell wall interactions and its application for localization of specific wood-degrading (laccase, Mn(II) and lignin peroxidases, and cellulases) and H₂O₂ producing (pyranose oxidase) enzymes in situ during white rot decay are also reviewed, as is the application of EM for studying non-enzymatic wood decay. Methods for labelling and detecting wood components (lignin, hemi- and cellulose) in situ by EDXA and enzyme immunogold cytochemistry are also outlined. The use of EM in wood biodegradation research is rapidly expanding and is seen as an important compliment to biochemical and chemical approaches. The future should see even greater advances in our understanding of wood decay as more advanced and recently developed EM techniques are also exploited.     

The resistance of wood chemically modified with isocyanates: the role of moisture content in decay suppression

This paper discusses the moisture content of sound and decayed Corsican pine (Pinus nigra) after modification with isocyanates {n-butyl isocyanate (BuNCO) and 1,6-diisocyanatehexane (HDI)} at specified intervals of weight percent gain (WPG). The main effects of decay fungi (brown and white rot) and levels of modification (WPG) on moisture contents of modified samples are also examined. Corsican pine reacted with isocyanates enhanced the hydrophobic (restrained water) nature of wood. The equilibrium moisture content of chemically modified wood decreases progressively with increasing WPG. Basidiomycete decay tests demonstrated protection by chemical modification. Wood moisture contents after soil block testing are significantly influenced by decay fungi and by the extent of reaction (WPG). Moisture uptake and susceptibility to decay of modified wood are higher when exposed to Coniophora puteana than other decay fungi. Corsican pine cross-linked by reaction with HDI is less susceptible to decay and is more hydrophobic than samples reacted with the single-site reactant BuNCO at comparable WPG.     

The effects of wood decay type on the growth of bryophyte gametophytes

Deadwood is an important habitat for bryophytes in boreal and subalpine forests. The type of decay in wood (white, brown, and soft rot) caused by fungal colonizers has been revealed to affect bryophyte communities. However, little is known about the effects of decay type on the growth of bryophytes. We tested the effect of wood decay type on gametophyte growth for two common bryophyte species, Scapania bolanderi Austin and Pleurozium schreberi (Brid.) Mitt., which dominate the logs in subalpine coniferous forest on Mt. Ontake, in central Honshu, Japan. We used pot culture experiments in an open-sky nursery field. After eight months of cultivation, the growth of S. bolanderi was larger on brown rot wood than white rot wood, but the growth of P. schreberi was not. Mixed cultures of the two species also showed greater growth on brown rot wood. However, growth of S. bolanderi was significantly smaller than P. schreberi in mixed culture. These results suggest that brown rot wood enhances growth of S. bolanderi, but growth may be reduced under competition from P. schreberi. The results are in agreement with the field observation that brown rot wood has a positive association with S. bolanderi coverage on deadwood.     

三江源区高寒草甸退化对土壤水源涵养功能的影响

三江源区是我国重要的水源涵养区,研究草地退化对土壤水源涵养功能的影响,可为三江源区水源涵养功能的科学评估与合理监测提供科学依据。以实地采样与室内测试分析相结合的方法研究了三江源区内不同土壤类型高寒草甸生物量特征、土壤水文物理性质及土壤水源涵养量。结果表明:高寒草甸在重度退化阶段地上生物量、地下生物量、毛管孔隙度、总孔隙度、自然含水量、最大持水量、土壤水源涵养量显著低于未退化和中度退化阶段(P<0.05)。随着高寒草甸退化程度加剧,土壤容重逐渐增大,且非毛管孔隙度规律不显著。未退化、中度退化、重度退化草甸的土壤水源涵养量范围分别为1884.32—1897.44t/hm2、1360.04—1707.79t/hm2、1082.38—1550.10t/hm2。中度退化草甸土壤水源涵养量比未退化草甸低9.37%—10.35%,重度退化草甸低18.31%—27.82%。草甸退化进程中土壤总孔隙度与毛管孔隙度的降低是影响土壤水源涵养量下降的直接原因,而草甸退化进程中地上生物量与地下生物量的减少则是间接原因。度量三江源区高寒草甸土壤水源涵养功能时应着重考虑毛管孔隙度的蓄水作用。研究表明高寒草甸地上生物量与土壤水源涵养量之间存在显著的正相关关系(P<0.05),该结果能够推动水源涵养功能评估向空间化、精细化发展,为探索利用遥感技术监测三江源区水源涵养功能提供参考依据。     

广东白盆珠水库水源林土壤水源涵养能力研究

通过对广东省白盆珠水库水源林土壤类型调查及土壤水分物理性质的测定,结果表明:库区水源林水平地带性土壤属赤红壤,山地土壤垂直带谱明显,分布有赤红壤、山地红壤、山地黄壤和山顶灌丛草甸土4个类型。土壤容重约为1.338g·cm^-3,随海拔升高土壤砂粒含量增加。土壤总孔隙度在45%～50%,非毛管孔隙度在5%～9%之间,毛管孔隙度35%～50%。不同森林类型土壤的最大持水量在30%～50%,即50～60mm,变化不大;蓄水容量有较大区别,范围在500～850t·hm^-2,灌丛草甸土最大,针阔混交林次之,沟谷阔叶林最小;排水能力约在130～180t·hm^-2,并以灌丛草甸土为最大,次生阔叶林为最小。该库区水源林土壤的排水和蓄水容量分别为62.69万t、316.29万t,消洪补枯能力明显。但水源林土壤非毛管孔隙度较小,蓄水量小于广东各种有林地森林类型平均蓄水量,所以该库区的水源林还需加强保育,以提升土壤的水源涵养能力。     

The influence of soil texture on the soil water dynamics and vegetation structure of a shortgrass steppe ecosystem

We analyzed soil water data from three sites with different soil textures in the shortgrass steppe of northeastern Colorado, USA. Our objective was to evaluate the relationship between the occurrence of plant functional types and the effect of soil texture on soil water availability. Soil water availability was greatest in the upper soil layers at all three sites, but the loamy sand site had significantly greater soil water availability than the sandy clay loam and sandy clay sites in wetter years at depths below 60 cm. Calculations of proportional water availability by layer using both field data and fifty-year soil water model simulations, showed that the sandy clay loam and sandy clay soils on average had greater water availability in layers 30 cm and above, but that the loamy sand had the greatest water availability in layers beneath this, particularly at 105 cm. This observation can be linked to the occurrence of a fine textured subsoil at this site. The textural pattern in the loamy sand profile effectively creates two water resources: a shallow pool accessible to all plants; and a deep pool accessible only to deep-rooted plants. This is offered as an explanation for the co-dominance of the two main plant functional types at the loamy sand site. At the other two sites, shallow-rooted shortgrass vegetation dominated, being more consistent with the general pattern for the area. Thus the patterns of vegetation structure at the three sites were consistent with the hypothesis. Aboveground net primary production data for the three sites, along with transpiration estimates from the model simulations, indicated that the additional water availability in the coarse textured soil was associated with higher overall plant productivity.Nomenclature: Taxonomic nomenclature follows R. L. McGregor & T. M. Barkley (1986) Flora of the Great Plains. Great Plains Flora Association. University Press of Kansas, Lawrence.     

The impact of rainfall magnitude on the performance of digital soil mapping over low-relief areas using a land surface dynamic feedback method

Previous studies have demonstrated that the pattern of land surface dynamic feedbacks (LSDF) based on remote sensing images after a rainfall event can be used to derive environmental covariates to assist in predicting soil texture variation over low-relief areas. However, the impact of the rainfall magnitude on the performance of these covariates has not been thoroughly investigated. The objective of this study was to investigate this impact during ten observation periods following rainfall events of different magnitudes (0–40 mm). An individual predictive soil mapping method (iPSM) was used to predict soil texture over space based on the environmental covariates derived from land surface dynamic feedbacks. The prediction error showed strong negative correlation with rainfall magnitude (Pearson’s r between root-mean squared error of prediction and rainfall magnitude = −0.943 for percentage of sand and −0.883 for percentage of clay). When the rainfall reaches a certain magnitude, the prediction error becomes stable. The recommended rain magnitude (threshold) using LSDF method in this study area is larger than 20 mm for both sand and clay percentage. The predictive maps based on different observed periods with similar rainfall magnitudes show only slight differences. Rainfall magnitude can thus be said to have a significant impact on the prediction accuracy of soil texture mapping. Greater rainfall magnitude will improve the prediction accuracy when using the LSDF. And high wind speed, high evaporation and low relative humidity during the observed periods also improved the prediction accuracy, all by stimulating differential soil drying.     

Precipitation pulse use by an invasive woody legume: the role of soil texture and pulse size

Plant metabolic activity in arid and semi-arid environments is largely tied to episodic precipitation events or “pulses”. The ability of plants to take up and utilize rain pulses during the growing season in these water-limited ecosystems is determined in part by pulse timing, intensity and amount, and by hydrological properties of the soil that translate precipitation into plant-available soil moisture. We assessed the sensitivity of an invasive woody plant, velvet mesquite (Prosopis velutina Woot.), to large (35 mm) and small (10 mm) isotopically labeled irrigation pulses on two contrasting soil textures (sandy-loam vs. loamy-clay) in semi-desert grassland in southeastern Arizona, USA. Predawn leaf water potential (Ψ_pd), the isotopic abundance of deuterium in stem water (δD), the abundance of ¹³C in soluble leaf sugar (δ¹³C), and percent volumetric soil water content (θ_v) were measured prior to irrigation and repeatedly for 2 weeks following irrigation. Plant water potential and the percent of pulse water present in the stem xylem indicated that although mesquite trees on both coarse- and fine-textured soils quickly responded to the large irrigation pulse, the magnitude and duration of this response substantially differed between soil textures. After reaching a maximum 4 days after the irrigation, the fraction of pulse water in stem xylem decreased more rapidly on the loamy-clay soil than the sandy-loam soil. Similarly, on both soil textures mesquite significantly responded to the 10-mm pulse. However, the magnitude of this response was substantially greater for mesquite on the sandy-loam soil compared to loamy-clay soil. The relationship between Ψ_pd and δ¹³C of leaf-soluble carbohydrates over the pulse period did not differ between plants at the two sites, indicating that differences in photosynthetic response of mesquite trees to the moisture pulses was a function of soil water availability within the rooting zone rather than differences in plant biochemical or physiological constraints. Patterns of resource acquisition by mesquite during the dynamic wetting–drying cycle following rainfall pulses is controlled by a complex interaction between pulse size and soil hydraulic properties. A better understanding of how this interaction affects plant water availability and photosynthetic response is needed to predict how grassland structure and function will respond to climate change.     

The effect of application time and soil factors on the occurrence of Beauveria brongniartii applied as a biological control agent in soil

The effects of abiotic and biotic soil factors on occurrence of the entomopathogenic fungus Beauveria brongniartii after application at different times of the year were examined in Switzerland. Applications made from May to August generally resulted in an increase of 1-5 x 10(3) CFU g(-1) dry soil compared to untreated control plots. Conversely, soils treated in October and November yielded no increase. Soil temperatures between 20 and 25 degrees C, and high clay content of the soil had a positive effect on the occurrence and density of B. brongniartii whereas increased catalase activity and temperatures above 27 degrees C had a negative influence. Laboratory experiments revealed that a higher number of CFUs developed after one month of incubation at 22 degrees C than at 12 degrees C. Differences were not detected after three months of incubation, indicating that growth rate was simply slower at sub-optimal temperatures. The increase was different in three native soils, but was not correlated with different clay contents of the soil. In sterilized soil, though, the differences were not detected, suggesting that biotic factors have a greater influence rather than soil texture.     

Desert vegetation patterns at the northern foot of Tianshan Mountains: The role of soil conditions

Vegetation patterns along environmental gradients in the typical temperate desert from the northern slope of Tianshan Mountains to the southern edge of Dungaree Basin were quantitatively investigated. The results implied that the soil mechanical composition in the study area affects the vegetation distribution remarkably. With concern to the preference to fine grain, the order is Tamarix ramosissima community>Reaumuria soongorica community>Haloxylon ammodendron community. An opposite order exists for the preference to coarse grain. R. soongorica community has higher resistance to saline soil than H. ammodendron community, and occurs in habitats of higher salinity. T. ramosissima community does not show an obvious preference to salinity or water table depth, but a quite remarkable preference to a high soil moisture content.     

The cytokine storm in COVID-19: Further advances in our understanding the role of specific chemokines involved

SARS-COV-2 infection represents the greatest pandemic of the world, counting daily increasing number of subjects positive to the virus and, sadly, increasing number of deaths. Current studies reported that the cytokine/chemokine network is crucial in the onset and maintenance of the “cytokine storm”, the event occurring in those patients in whom the progression of COVID-19 will progress, in most cases, to a very severe and potentially threatening disease. Detecting a possible “immune signature” in patients, as assessed by chemokines status in patients with COVID-19, could be helpful for individual risk stratification for developing a more or less severe clinical course of the disease. The present review is specifically aimed at overviewing current evidences provided by in vitro and in vivo studies addressing the issue of which chemokines seems to be involved, at least at present, in COVID-19. Currently available experimental and clinical studies regarding those chemokines more deeply studied in COVID-19, with a specific focus on their role in the cytokine storm and ultimately with their ability to predict the clinical course of the disease, will be taken into account. Moreover, similarities and differences between chemokines and cytokines, which both contribute to the onset of the pro-inflammatory loop characterizing SARS-COV-2 infection, will be briefly discussed. Future studies will rapidly accumulate in the next months and their results will hopefully provide more insights as to the complex physiopathology of COVID-19-related cytokine storm. This will likely make the present review somehow “dated” in a short time, but still the present review provides an overview of the scenario of the current knowledge on this topic.     

Evaluation of a soil test method and plant analysis for determing the sulphur status of alluvial soils

Summary In a pot experiment with soils of Alfisol, Entisol, and Inceptisol orders, the relative yield of Egyptian clover (Trifolium alexandrinum L.) was significantly correlated with Morgan's reagent (N NaOAc+HOAc, pH 4.8)—extractable soil S (r=0.88), plant S (r=0.82), and plant N/S ratio (r=−0.77) suggesting suitability of these tests for diagnosing S deficiency. Total plant S lower than 0.21 per cent, plant N/S ratio wider than 17, and extractable soil S lower than 10 ppm were indicative of S deficiency, and were suggested therefore to be critical limits for these tests. Nitrogen and S in plant proteins were in near constant ratio of 16 and were significantly correlated (r=0.99). Sixty one per cent of 250 surface soil samples had less than 10 ppm extractable S and hence were deficient in S, suggesting a widespread S deficiency in soils under study. Extractable soil S in all soil series was significantly correlated with electrical conductivity and alkaline KMnO₄-extractable N, but not with pH, organic C, and CaCO₃.     

Phosphorus Transformations in an Oxisol under contrasting land-use systems: The role of the soil microbial biomass

It is generally assumed that phosphorus (P) availability for plant growth on highly weathered and P-deficient tropical soils may depend more on biologically mediated organic P (P_o) turnover processes than on the release of adsorbed inorganic P (P_i). However, experimental evidence showing the linkages between P_o, microbial activity, P cycling and soil P availability is scarce. To test whether land-use systems with higher soil P_o are characterized by greater soil biological activity and increased P mineralization, we analyzed the partitioning of P among various organic and inorganic P fractions in soils of contrasting agricultural land-use systems and related it to biological soil properties. Isotopic labeling was used to obtain information on the turnover of P held in the microbial biomass. Soil samples were taken from grass–legume pasture (GL), continuous rice (CR) and native savanna (SAV) which served as reference. In agreement with estimated P budgets (+277, +70 and 0 kg P ha^–1 for CR, GL and SAV, respectively), available P estimated using Bray-2 and resin extraction declined in the order CR > GL > SAV. Increases in Bray-2 and resin P_i were greater in CR than GL relative to total soil P increase. Organic P fractions were significantly less affected by P inputs than inorganic fractions, but were a more important sink in GL than CR soils. Extractable microbial P (P_chl) was slightly higher in GL (6.6 mg P kg^–1) than SAV soils (5.4 mg P kg^–1), and significantly lowest in CR (2.6 mg P kg^–1). Two days after labeling the soil with carrier free ³³P, 25, 10 and 2% of the added ³³P were found in P_chl in GL, SAV and CR soils, respectively, suggesting a high and rapid microbial P turnover that was highest in GL soils. Indicators of P mineralization were higher in GL than CR soils, suggesting a greater transformation potential to render P_o available. Legume-based pastures (GL) can be considered as an important land-use option as they stimulate P cycling. However, it remains to be investigated whether crops planted in pasture–crop rotations could benefit from the enhanced P_o cycling in grass–legume soils. Furthermore, there is need to develop and test a direct method to quantify P_o mineralization in these systems.     

The population genetics of adaptation on correlated fitness landscapes: the block model

Several recent theoretical studies of the genetics of adaptation have focused on the mutational landscape model, which considers evolution on rugged fitness landscapes (i.e., ones having many local optima). Adaptation in this model is characterized by several simple results. Here I ask whether these results also hold on correlated fitness landscapes, which are smoother than those considered in the mutational landscape model. In particular, I study the genetics of adaptation in the block model, a tunably rugged model of fitness landscapes. Considering the scenario in which adaptation begins from a high fitness wild-type DNA sequence, I use extreme value theory and computer simulations to study both single adaptive steps and entire adaptive walks. I show that all previous results characterizing single steps in adaptation in the mutational landscape model hold at least approximately on correlated landscapes in the block model; many entire-walk results, however, do not.     

The influence of competing-risks setting on the choice of hypothesis test for treatment effect

There is considerable debate regarding the choice of test for treatment difference in a randomized clinical trial in the presence of competing risks. This question arose in the study of standard and new antiepileptic drugs (SANAD) trial comparing new and standard antiepileptic drugs. This paper provides simulation results for the log-rank test comparing cause-specific hazard rates and Gray's test comparing cause-specific cumulative incidence curves. To inform the analysis of the SANAD trial, competing-risks settings were considered where both events are of interest, events may be negatively correlated, and the degree of correlation may differ in the 2 treatment groups. In settings where there are effects in opposite directions for the 2 event types, a likely situation for the SANAD trial, Gray's test has greater power to detect treatment differences than log-rank analysis. For the epilepsy application, conclusions were qualitatively similar for both log-rank and Gray's tests.     

The role of inter-ploidy block for reproductive isolation of the diploid Leucanthemum pluriflorum Pau (Compositae,Anthemideae) and its tetra- and hexaploid relatives

Theory suggests that post-zygotic reproductive isolation of polyploids from their diploid progenitors is often caused by developmental disorder in the endosperm of hybrid seeds. Yet, this so-called triploid block is increasingly recognized to be less strong than initially assumed, indicating that other isolation mechanisms are needed to explain reproductive isolation of polyploids and diploids. In the present study, the extent of inter-ploidy block was quantified based on crossing experiments between closely related diploid, tetraploid, and hexaploid species from the genus Leucanthemum Mill. (Compositae, Anthemideae). Seed set and viability of seeds obtained from inter-cytotype crosses were measured and compared to fertilities of intra-cytotype crosses. Although inter-ploidy block was observed when diploids acted as pollen donors, the main observation was that all inter-ploidy crosses were capable of producing viable offspring. By contrast, flow cytometrical analysis of 233 individuals from natural populations did not reveal the presence of any unambiguous cross-ploidy offspring in the field. Hence, the results of the present study demonstrate that inter-cytotype mating may be rare even though inter-ploidy block is weak. Consequently, it can be assumed that pre-zygotic barriers and reduced fitness of inter-cytotype hybrids play a decisive role in the reproductive isolation of polyploid Leucanthemum species.     

Evaluation and application of aquatic toxicity tests: use of the Microtox test for the prediction of toxicity based upon concentrations of contaminants in soil

The quality control for the reuse of cleaned soil from a contaminated site consisted in the determination of the main contaminants by analytical chemical methods such as GC and HPLC. Since it is not possible to analyze for all contaminants a toxicity test should be used to detect large concentrations of not routinely analyzed chemicals. The aim of the study was to develop a system for toxicity testing, which should be able to predict the toxicity of soil samples based on the concentration of chemicals in the soil and to detect toxic chemicals not analyzed by the routinely conducted soil analysis.Based upon the relative sensitivity to various contaminants as well as practical aspects such as test duration and costs the Microtox® test was favoured over the bioassays with Daphnia magna and Scenedesmus subspicatus. The Microtox® test was used to measure the toxicity of various pesticides and their major metabolites. The toxicity data of the pure compounds were used to predict the toxicity (EC₅₀ and % inhibition of the bioluminescence reaction) of defined mixtures of chemicals in water by applying two different mathematical appriaches which are based on the additivity of the effects of the single chemicals. The predicted values were compared with the experimental data and showed good agreement.In order to be able to predict the toxicity of soil samples using the Microtox® test the soil/water partition coefficient (K _d) was measured for the main contaminants. The toxicity of soil samples was predicted by calculating the concentration of the contaminants in the leachate by using the corresponding concentration in the soil and applying the K _d values determined. From the calculated composition of the leachate the expected toxicity was estimated. This value was compared with the toxicity experimentally determined in the Microtox® test.     

Locomotor activity of mice divergently selected for basal metabolic rate: a test of hypotheses on the evolution of endothermy

The aerobic capacity model postulates that high basal metabolic rates (BMR) underlying endothermy evolved as a correlated response to the selection on maximal levels of oxygen consumption () associated with locomotor activity. The recent assimilation capacity model specifically assumes that high BMR evolved as a by‐product of the selection for effective parental care, which required long‐term locomotor activity fuelled by energy assimilated from food. To test both models, we compared metabolic and behavioural correlates in males of laboratory mice divergently selected on body mass‐corrected BMR. elicited by running on the treadmill did not differ between selection lines, which points to the lack of genetic correlation between BMR and . In contrast, there was a positive, genetic correlation between spontaneous long‐term locomotor activity, food intake and BMR. Our results therefore corroborate predictions of the assimilation capacity model of endothermy evolution.     

The impact of confounders on the test performance of natriuretic peptides for cardiac dysfunction in subjects aged 80 and older

The hypothesis that natriuretic peptides could be used to identify ‘pancardiac’ damage has been proposed. However, multiple factors are known to influence circulating levels of natriuretic peptides, especially in the very old. Therefore, the impact of confounders on the association between natriuretic peptide levels and cardiac dysfunction was further explored in subjects aged 80 and older. A diagnostic cross-sectional study embedded within the BELFRAIL study (n = 567) was performed. Baseline BNP and NT-proBNP levels were measured and echocardiograms were performed at the subject's home. Cardiac dysfunction was defined as systolic dysfunction, valvular heart disease or isolated severe diastolic dysfunction. Several functional and structural echocardiographic parameters were independently related to circulating levels of natriuretic peptides. Cystatin C, BMI, β blockers, diabetes, heart frequency, usCRP, age and sex were identified as confounders. The prevalence of cardiac dysfunction was 17.1% in the subjects without and 30.8% in the subjects with chronic atrial fibrillation (CAF) or pacemaker (PM). Only in subjects with CAF or PM the C statistic for cardiac dysfunction improved after correcting for confounders. The post-test probability for a negative test (PTP−) ranged from 3.7% to 12.2% and the PTP+ ranged from 21.9% to 62.2% in different strata of confounders. According to these data adjusting for identified confounders does not improve the diagnostic accuracy of the natriuretic peptides for cardiac dysfunction, except in subjects with CAF or PM. Stratifying for individual confounders showed that different cut-off values could be used to optimize the diagnostic characteristics of natriuretic peptides.