Harmonized soil profile data for applications at global and continental scales: updates to the WISE database

Version 3.1 of the ISRIC-WISE database holds selected site and horizon data for some 10 250 soil profiles from 149 countries. Profile data were extracted from a wide range of sources and harmonized with respect to the original (1974) and revised (1988) Legend of the FAO-Unesco Soil Map of the World. Profiles have been described, sampled, and analysed according to methods and standards in use in the originating countries; analytical results for the same property cannot always be compared directly; as a result the amount of measured data available for modelling is sometimes much less than expected. WISE was specifically developed for land-related applications at continental and global scales.     

Testing the accuracy of resistance drilling to assess tree growth rate and the relationship to past climatic conditions

Assessing tree growth trends over time is a central but challenging aspect of urban forest management. The potential damage caused by invasive devices used in dendrochronological analysis is a common concern among urban foresters. Thus, the development of a less-invasive method for assessing tree growth rate faster that provides reliable results is clearly beneficial. In this study, resistance drilling (RD) profiles were compared with stem core assessments (Core) to estimate the growth rate of 78 trees of three species (Quercus robur, Ulmus procera, and Platanus x acerofolia). All studied trees were core-sampled in 2013 and then resistance drilled in 2015 at a stem height of 1–1.3 m in both north (N) and west axes (W). The dependency and accuracy of paired annual ring series (CORE measurements and Resi reading) were tested using ANOVA and regression analysis. In addition, point and event year tests were determined to confirm the accuracy of the RD to assess growth trends at both population and tree level. Growth series from both methods were cross-dated to test the reliability of RD to relate historical tree growth to past climatic conditions. ANOVA analysis confirmed that average ring width values and age of 70 out of 78 trees were statistically similar for both methods and similar for both sampled stem axes. Within each tree, regression analysis indicated significant correlation between cored ring datasets and paired resistance drilled ring datasets (R² = 0.78–0.95, p < 0.05) across species. RD reliably detected pointer years at population level for Q. robur only. For all species, RD could not adequately detect event years at tree level. Regardless of species and drill axes, RD was less accurate in measuring ring width below 1 mm. For all species, RD yielded lower intercorrelation indices and greater number of “A” flagged segments as compared to CORE. Overall, RD can successfully estimate mean annual ring values to a comparable standard as conventional CORE analysis. However, the RD device used in this study did not detect the inter-annual growth pattern to the same standard as stem CORE analysis, RD should not be used to replace dendrochronology in climate-tree growth studies.     

Neotropical mustelids: fecal metabolome diversity and its potential for taxonomic discrimination

Chemical profiles of non-invasive biological material, such as feces, have great potential to study elusive animals or those with low population densities. Here, we use a metabolomic approach to evaluate Neotropical mustelids as a biological model to describe the diversity of the metabolites present in fecal samples, as well as to evaluate the potential of chemical profiles for taxonomic discrimination. We collected fecal samples from captive individuals of 5 species of mustelids occurring in Brazil and analyzed them by liquid chromatography coupled to high-resolution mass spectrometry. Over 200 compounds have been annotated; “bile acids, alcohols and derivatives” was the most expressive class in the metabolome of all the species. We successfully discriminated 3 taxonomic groups: 1—tayra (Eira barbara); 2—otters (Lontra longicaudis and Pteronura brasiliensis; 1); and 3—grisons (Galictis vittata and Galictis cuja). Several compounds seemed to be associated with food intake and the digestive process, while others were found for the first time in Neotropical mustelids. We concluded that mustelids show high metabolome diversity and that species-specific identification through metabolomic profiles is possible, thus contributing to the development and implementation of additional non-invasive approaches in the study of mustelids.     

赤松毛虫质型多角体病毒的引进和利用研究

从日本引进赤松毛虫CPV对我国松毛虫属(Dendrolimus)的七种松毛虫以及棉龄虫有较高的致死效果。根据 RNA 电泳图谱的研究,赤松毛虫 CPV 与在中国松毛虫属上的各复制株是不同的。目前,我国已发现有三种 RNA 类型,日本赤松毛虫CPV 属第一型。JADP-CPV、JYDPW-CPV、CYDPW-CPV 等属于第二型,CGDP-CPV 离心所得的上带多角体属于第三型。类型Ⅱ、Ⅲ属首次报道。和其他CPV一样,JDS-CPV 只侵染中肠上皮细胞。对第一代3龄和5龄虫的 LC_(50) 分别为1.6×10~5CPB/ml 和3.3×10~5CPB/ml,对同代3龄虫的 LD_(60)为2.1×10~3CPB/虫。JDS-CPV 不仅对幼虫防效好,而且也影响幼虫取食、体重以及下代幼虫存活率。此病毒与BT混用可以减少针叶被害72—80％。在油乳剂中于4℃下保存197天,在水悬液中保存 5年,对此病毒活性无明显影响。以林间松毛虫作宿主可进行大量增殖。一头6—7龄幼虫平均可产多角体2亿个。     

Nutrient profile and availability of co-products from bioethanol processing

Bioethanol production in North America has led to the production of considerable quantities of different co‐products. Variation in nutrient profiles as well as nutrient availability among these co‐products may lead to the formulation of imbalanced diets that may adversely affect animal performance. This study aimed to compare three types of dried distiller’s grains with solubles [100% wheat DDGS (WDDGS); DDGS blend1 (BDDGS1, corn to wheat ratio 30:70); DDGS blend2 (BDDGS2, corn to wheat ratio 50:50)] and their different batches within DDGS type with regard to: (i) protein and carbohydrate sub‐fractions based on Cornell Net Carbohydrate and Protein System (CNCPS); (ii) calculated energy values; and (iii) rumen degradation of dry matter (DDM), organic matter (DOM), crude protein (DCP), neutral detergent fibre (DNDF) and starch (Dstarch) at 36 and 72 h of ruminal incubations. Wheat DDGS had a lower intermediately (PB2, 136.4 vs. 187.4 g/kg DM) and a higher slowly degradable true protein (PB3, 142.2 vs.105.3 g/kg DM) than BDDGS1, but similar to those of BDDGS2. Sugar (CA4) was higher, whereas starch (PB1) and digestible fibre (PB3) were lower in WDDGS than in BDDGS1 and BDDGS2. All carbohydrate sub‐fractions determined differed significantly between the two batches of BDDGS2. The BDDGS2 had the highest calculated energy values (TDN, DE_3×, ME_3×, NEL_3×, NE_m and NE_g) among the three DDGS types. The energy values were slightly different between the batches of the three DDGS types. At all incubation times, wheat DDGS had a significantly higher (p < 0.05) DDM, DOM, DCP and DNDF than both DDGS blends. Differences were observed between different batches within DDGS types with regard to in situ rumen degradation of DM, OM, CP, NDF and starch. In conclusion, differences were observed in protein and carbohydrate sub‐fractions and in situ ruminal degradation of DM, OM, CP, NDF and starch among the three DDGS types and different batches within DDGS type. This indicates that the nutrients supplied to ruminants may not only differ among different types of DDGS but it may also differ among different batches within DDGS type.     

Rapid methodology for antigenic profiling of FMDV field strains and for the control of identity, purity and viral integrity in commercial virus vaccines using monoclonal antibodies

Monoclonal antibodies (MAbs) developed against different foot-and-mouth disease virus (FMDV) vaccine strains were extensively used to study any possible antigenic variations during vaccine production in Argentine facilities. Additionally, a typing ELISA using strain specific MAbs was developed to detect potential cross contaminations among FMDV strains in master and working seeds with high specificity and sensitivity and to confirm strains identity in formulated vaccines. This assay was carried out for the South American strains currently in use in production facilities in Argentina (A24/Cruzeiro, A/Argentina/01, O1/Campos and C3/Indaial) and for the strain O/Taiwan, produced only for export to Asia. These non-cross reactive MAbs were also used to analyze the integrity of viral particles belonging to each one of the individual strains, following isolation of 140S virions by means of sucrose density gradients from the aqueous phase of commercial polyvalent vaccines. Antigenic profiles were defined for FMDV reference strains using panels of MAbs, and a coefficient of correlation of reactivity with these panels was calculated to establish consistent identity upon serial passages of master and production seeds. A comparison of vaccine and field strain antigenic profiles performed using coefficients of correlation allowed the rapid identification of two main groups of serotype A viruses collected during the last FMD epidemic in Argentina, whose reactivity matched closely to A/Argentina/2000 and A/Argentina/2001 strains.     

Plant and soil microbial biomasses in Agrostis capillaris and Lathyrus pratensis monocultures exposed to elevated O3 and CO2 for three growing seasons

Elevated CO₂ usually promotes plant growth, whereas elevated O₃ often has a negative effect, especially on root biomass. Thus both these gases can indirectly affect the soil microbial community. We exposed Agrostis capillaris and Lathyrus pratensis to realistic levels of O₃ (40-50 ppb) and CO₂ (ambient air + 100 ppm) in open-top chambers during 2002-2004. The experiment shows negative effects of both O₃ and CO₂, especially on the bulk soil of L. pratensis, in terms of the decreased biomasses of total (25% and 31%), actinobacterial (29% and 31%), bacterial (26% and 33%) and mycorrhizal (AM fungal) (31% and 35%) indicator subgroups, analysed by the PLFA (phospholipid fatty acid) method. The fungal:bacterial PLFA biomass ratio decreased in the bulk soil of A. capillaris, especially with elevated CO₂ alone (38%). These longer-term changes are considered to arise mainly from differences between the plant functional types (i.e. grass cf. N₂-fixing legume) in litter quality and soil C:N ratio. The results also point to interactions and multi-trophic feedbacks between elevated O₃, plant, parasitic rust fungi and soil readily available P, accompanied by a shift in N balance in favour of plants rather than soil microorganisms.     

Plant species influence microbial diversity and carbon allocation in the rhizosphere

Plant species effects on microbial communities are attributed to changes in microbial community composition and biomass, and may depend on plant species specific differences in the quality of resources (carbon) inputs. We examined the idea that plant-soil feedbacks can be explained by a chance effect, which is the probability of a highly productive or keystone plant species is present in the community and will influence the functions more than the number of species per se. A ¹³C pulse labelling technique was applied to three plant species and a species mixture in a greenhouse experiment to examine the carbon flow from plants to soil microbial communities. The ¹³C label was given as CO₂ to shoots of a legume (Lotus corniculatus), a forb (Plantago lanceolata), a grass (Holcus lanatus) and a mixture of the three species. Microbial phospholipid fatty acids (PLFA) was analysed in order to determine the biomass and composition of the soil microbial community. The incorporation of the stable isotope into soil microorganisms was determined through GC-IRMS analyses of the microbial PLFAs. Plant species identity did not influence the microbial biomass when determined as total carbon of microbial phospholipid fatty acids. However, the labelled carbon showed that the grass monoculture (H. lanatus) and the plant mixture allocated more ¹³C into bacteria and actinomycete biomass than the other plant species. H. lanatus monocultures had also the highest amounts of ¹³C allocated to AM-fungi and saprophytic fungi. The carbon allocation from plants to soil microorganisms in a plant species mixture can thus be explained by the presence of a highly productive species that influence soil functions.     

Phosphorus limitation in a Ferralsol: Impact on microbial activity and cell internal P pools

Soil microorganisms are key regulators of the biogeochemical phosphorus (P) cycle. Microbial P limitation in highly weathered tropical soils has been reported, but whether it affects the cellular P content of indigenous soil microorganisms and its biochemical composition is unknown. We investigated the effect of microbial P limitation by measuring respiration, microbial growth, community composition and P content of microbial cells in a Ferralsol with low amounts of available P as affected by amendments with C substrates with ample nitrogen (CN) with and without extra phosphate (P). Microbial biomass and community composition were quantified by phospholipid fatty acid (PLFA) analyses. Cellular P content and P pools (PLFA, DNA and RNA per cell) were determined after extraction of microbial cells from soil by density gradient centrifugation. The apparent microbial growth rate during exponential increase in respiration rates in response to CNP addition was 0.072 h⁻¹, compared to 0.017 h⁻¹ for the CN amendment (no extra P added). This suggests that the microbial growth after a combined C and N addition was retarded by P limitation in the native soil (without added P). The net increase in microbial biomass, however, reached similar levels for both the CN and CNP treatment (measured at the point in time when respiration rates peaked). This outcome was unexpected since maximum respiration rates were about three times higher in the CNP compared to the CN treatment. Total P in extracted cells ranged from 2.1 to 8.9 fg P cell⁻¹ (microscopic counts), with a tendency for lower values for treatments without C amendments. Only 10-25% of the measured total P in extracted cells was accounted for by the measured RNA, DNA and PLFA. This low percentage could partly be due to underestimation of the RNA pool (degradation during extraction). PLFA analyses showed that substrate induced growth, regardless of P addition, led to a change in microbial community composition and was dominated by fungi. The extraction of microbial cells from soil by density gradient centrifugation, however, discriminates against fungi. Accordingly, the extracted cells were not fully representative for the entire soil microbiota regarding the community composition and metabolic state. Nevertheless, for the first time microbial cell P content and P pools are reported for microorganisms that actually grew in soil and not in chemostat or batch cultures.     

Acidification of a sandy grassland favours bacteria and disfavours fungal saprotrophs as estimated by fatty acid profiling

We have investigated the structure of a microbial community in semi-natural sandy grassland in southeast Sweden. The sand is rich in lime, but in most places the soil is decalcified in the upper layers, and therefore this site shows a large variation in pH within short distances. We collected samples at three different soil depths (0-10 cm, 10-20 cm and 20-30 cm) and found the pH to range from 5 to 8 in the topsoil and from 4.5 to 9.5 in the deepest layer. The abundance of saprophytic fungi and bacteria was investigated using signature phospholipid fatty acids and arbuscular mycorrhizal fungi (AMF) using the neutral lipid fatty acid 16:1ω5. The PLFA pattern of the topsoil was different from that in the other two layers, as indicated by principal component analysis. The saprotrophic fungi were associated with high pH, and bacteria with low pH in these sandy soils. No relation was found between pH and AMF in the topsoil, while a positive relation was found in the deepest soil layer. The saprophytic fungi-to-bacteria ratio was constant with depth, while the AMF-to-bacteria ratio increased with soil depth. The results showed that high soil pH favoured fungal saprophytes in sandy grasslands and that AMF are relatively more abundant than the other two groups in deeper soil layers; particularly so when the pH is high.