A physical map of the 1-gigabase bread wheat chromosome 3B

As the staple food for 35% of the world's population, wheat is one of the most important crop species. To date, sequence-based tools to accelerate wheat improvement are lacking. As part of the international effort to sequence the 17-billion-base-pair hexaploid bread wheat genome (2n = 6x = 42 chromosomes), we constructed a bacterial artificial chromosome (BAC)-based integrated physical map of the largest chromosome, 3B, that alone is 995 megabases. A chromosome-specific BAC library was used to assemble 82% of the chromosome into 1036 contigs that were anchored with 1443 molecular markers, providing a major resource for genetic and genomic studies. This physical map establishes a template for the remaining wheat chromosomes and demonstrates the feasibility of constructing physical maps in large, complex, polyploid genomes with a chromosome-based approach.     

High colonization by native arbuscular mycorrhizal fungi (AMF) of rubber trees in small-holder plantations on low fertility soils in North East Thailand

Rubber tree is a very important crop in Thailand, representing an essential source of income for farmers. In the past two decades, rubber tree plantations have been greatly expanding in unfavorable areas, where climate conditions are difficult and soil fertility is very poor. To optimize latex yields, mineral fertilizers have been widely used. A better understanding of the roles of the biological compartment in soil fertility is essential to determine alternative management practices to sustain soil fertility and optimize latex yields. Arbuscular mycorrhizal fungi (AMF) are widely recognized as beneficial for plants, mainly through their role in improving plant nutrient uptake. The objective of this study was to assess the AMF populations in rubber tree plantations and the impact of both soil characteristics and plantation age on these communities. Our results showed that all rubber trees were highly colonized, regardless of the soil structure and nutrient contents. AMF colonization was not affected by the age of the trees, suggesting that maintaining the symbiosis is likely to be beneficial at all stages. A better understanding and management of the microbial communities would contribute to maintaining or restoring soil fertility, leading to a better tree growth and optimized latex yield.     

Fine earth soil bulk density at 0.2 m depth from Land Use and Coverage Area Frame Survey (LUCAS) soil 2018

Soil Bulk Density (BD) is an extremely important variable because it is an important site characterization parameter, and it is highly relevant for policy development because it is mandatory for calculating soil nutrient stocks. BD can influence soil chemical properties, land-use planning and agronomic management. The 2018 Land Use and Coverage Area Frame Survey (LUCAS) saw the unprecedented collection of BD core analysis in a subset of the locations in Europe and the United Kingdom where soil physical and chemical properties were analysed in the 2009 and the 2015 sampling campaigns. Here, we integrated the LUCAS 2018 BD sampling campaign with the mass fraction of coarse fragments previously determined in LUCAS 2009–2015 in order to provide a dataset of the volume fraction of coarse fragments and the BD of the fine earth and improve soil organic carbon (SOC) stock estimation accuracy for topsoil. BD data sampled at 0–10 and 10–20 cm were averaged to harmonize the BD with the mass fraction of coarse fragments measured in 2009, 2012 and 2015. Samples were from cropland, grassland and woodland soils, which accounted for 41%, 21% and 30%, respectively, of the total number of selected sites (n = 6059); ‘bareland’, and ‘shrubland’ accounted for 3% of the sites each, whereas ‘artificial land’ accounted for <1%. Only six samples were classified as ‘wetland’. The dataset was produced assuming the mass density of the coarse fraction to be constant across all LUCAS soil samples. We also estimated the SOC stocks associated with LUCAS 2018 BD and SOC content measurements and showed that correcting the BD by the coarse mass fraction instead of the coarse volume fraction generates SOC stock underestimation. We found the highest deviations in woodlands and shrublands. We showed that, when SOC stock is computed with coarse mass fraction, the error compared with the computation by volume may vary depending on the SOC and coarse mass fraction. This may imply a SOC stock underestimation for European soils. This dataset fits into the big framework of LUCAS soil properties monitoring and contributes both to soil awareness and soil research and assessments, which are two important objectives of the Soil Strategy and the European Soil Observatory (EUSO).     

Larval traits of the Caribbean amphidromous goby Sicydium punctatum (Gobioidei: Sicydiinae) in Guadeloupe

Amphidromous fish are the biggest contributor to the diversity of fish communities in river systems of Caribbean islands. Among them, Sicydium punctatum Perugia, 1896, which is endemic to the West Indies, represents the vast majority of fish in these rivers. The otolith microstructure and the biometry of S. punctatum postlarvae from Guadeloupe were investigated to explore the dispersal modalities of this species through an appreciation of the growth pattern, the pelagic larval duration (PLD) and the size‐at‐recruitment. The study was made on one cohort of 83 recruited postlarvae, fished at the Capesterre River's mouth on 2 November 2011. The mean (±SD) size‐at‐recruitment of the postlarvae was 24.6 ± 1.3 mm (range of 20.5–28.1 mm, n = 83). We found a mean (±SD) PLD of 72.2 ± 10.5 days (range of 54–101.5 days, n = 67). The growth rate estimated from the otolith increments showed a globally decreasing pattern during the marine larval phase. Growth rates at the beginning of the larval stage were significantly different between hatching periods, suggesting a relation between the hatching period and the growth rate in S. punctatum. This study adds on to the general understanding of the life cycle of S. punctatum in Guadeloupe that will help implement strategies to manage amphidromous fish populations in the Caribbean region.     

Thigmomorphogenesis versus light in biomechanical growth strategies of saplings of two tropical rain forest tree species

? In the dense tropical rainforest understorey, saplings exhibit different growth strategies aiming at reaching light levels better fitting their ecology. Investing mainly in height growth, at the expense of their width, a lot are close to mechanical instability. Tachigali melinonii, a long living heliophilic tree species, is frequently observed to be extremely slender and supported by neighbours. Such observations suggest an active growth control through the perception of mechanical environment.

? Mechanical environment or light availability, which one is the most influent on growth and slenderness (H/D)? To test this question, we recorded growth of control and staked saplings of two species with contrasting habits and ecology: T. melinonii, and Dicorynia guianensis, along a natural light gradient.

? Dicorynia, the more stable, responded more clearly to the staking treatment, showing slenderness increase when light is available, whereas for Tachigali, only light availability governed growth.

? For Tachigali, growth allocation is mainly governed by light availability and ontogeny, whereas Dicorynia is probably similar to the average tree strategy, using the thigmomorphogenetic physiological process to control its stability.

     

Seasonal and phenological variations of the essential oil from the narrow endemic species Artemisia molinieri and its biological activities

The volatile components of the aerial parts of Artemisia molinieri, an endemic wormwood of southern France, were analyzed by GC and GC-MS. Among the 69 compounds identified, major components were ascaridole (19-76%), alpha-terpinene (traces-36%), p-cymene (1-17%), 1,8-cineole (0.3-8%), and germacrene D (0.6-15%). Quantitative variations have been characterized following the season, the phenological cycle, and the aging of the plants. Bioassays have been performed on a sample of essential oil, which has shown a strong inhibition of the growth of both tested yeasts (Candida albicans and Saccharomyces cerevisiae var. chevalieri) and minor activity on both tested Gram-negative bacteria (Escherichia coli and Enterococcus hirae). The oils have shown interesting antioxidant activities on the basis of alpha-tocopherol as reference compound, up to 400-1200%.     

A minimum data set for evaluating the ecological soil functions in remediation projects

Purpose

Soil functioning becomes a matter of growing concern in soil remediation projects as, apart from preparing contaminated land for construction purposes, some parts of the sites are usually transformed into green spaces for recreation and inspiration. The objective of this paper is to develop and apply a minimum data set (MDS) for evaluating the ecological soil functions for green areas in remediation projects.

Materials and methods

The MDS was chosen from the previous applications in literature. Using a nonlinear scoring algorithm to transform observed data into sub-scores for evaluating ecological soil functions, the MDS was applied on the Kvillebäcken site in Sweden. The mean sub-scores of the individual soil quality indicators (SQIs) were integrated into a soil quality index to classify the soil into one of the five soil classes. Monte Carlo simulations were used to treat the uncertainties in the predicted soil class resulting from spatial heterogeneity of SQIs, a limited sampling size, and analytical errors.

Results and discussion

The suggested MDS consists of soil texture, content of coarse material, available water capacity, organic matter content, potentially mineralizable nitrogen, pH, and available phosphorus. The high mean sub-score for organic matter at Kvillebäcken indicated that the soil was rich on organic matter thus having a good water storage and nutrient cycling potential. However, the low mean sub-score for potentially mineralizable nitrogen indicated limited biological activity in the soil. The low mean sub-score for the content of coarse fragments indicated plant rooting limitations. Further, the soil quality index (that integrates the sub-scores for SQIs) corresponded to soil class 3 and a medium soil performance with a high certainty.

Conclusions

The suggested MDS can provide practitioners with relevant basic information on soil’s ability to carry out its ecological functions. The suggested scoring method helps to interpret and integrate information from different SQIs into a decision-making process in remediation projects.     

Linking the abundance of aspen with soil faunal communities and rates of belowground processes within single stands of mixed aspen–black spruce

The occurrence of aspen (Populus tremuloides Michx.) patches within stands dominated by black spruce (Picea mariana Mill. BSP) has been shown to increase litter decomposition and nutrient cycling rates by improving soil physical and chemical properties. It is well known, however, that these processes are also influenced by the structure of the soil biota, but this factor has received less attention. In this study, relationships between forest floor properties and soil invertebrates were studied along black spruce–trembling aspen gradients in three stands of the eastern boreal forest of Canada. The forest floor layer of 36 plots differing in aspen basal area was sampled and analyzed to determine physical and chemical properties, the rates of decomposition of standard substrates, net N mineralization, as well as microbial basal respiration and metabolic quotient. Soil invertebrates were also collected using funnel-extraction and pitfall trapping methods. Based on redundancy analyses, we found that forest floor properties, the abundance and composition of soil invertebrates, and the rates of belowground processes changed along the spruce–aspen gradient. The increase in aspen basal area was associated with a reduction in forest floor thickness, moisture content and microbial biomass, and with an increase in the concentration of nutrients. It was also accompanied by changes in soil faunal communities, as soil invertebrates were associated with specific soil properties. In general, macroinvertebrates (i.e., Lumbricidae, Formicidae, Carabidae, Staphylinidae and Gastropoda) were related to the nutrient-rich forest floor associated with aspen, whereas microarthropods and Enchytraeidae tended to be negatively related to aspen basal area. According to mixed linear models, decomposition rates of standard substrates and net ammonification significantly increased along the spruce–aspen gradient. Given the functional significance of macroinvertebrates in soils, these results suggest that aspen favours the elaboration of a macrofaunal community, which in turn accelerates the rate of soil processes by having either direct or indirect influence on microbial activity. Moreover, this study shows that the changes in soil processes and in the biodiversity of soil organisms related to the presence of mixed stands can operate only in the immediate surroundings of a given tree species. Therefore, coarse-scale tree species mixing in a forest stand may have a different effect on soil biodiversity and soil processes than fine-scale mixing.     

Evaluation of Natural Chemical Compounds Against Root-lesion and Root-knot Nematodes and Side-effects on the Infectivity of Arbuscular Mycorrhizal Fungi

The survival of two species of plant parasitic nematodes: the root-lesion nematode Pratylenchus brachyurus, and the root-knot nematode Meloidogyne javanica, was evaluated in saturated atmospheres of 12 natural chemical compounds. The infectivity of two isolates of arbuscular mycorrhizal fungi: Glomus mosseae and Glomus intraradices, under identical experimental conditions, was also determined. All the compounds tested exerted a highly significant control against M. javanica and among them, benzaldehyde, salicilaldehyde, borneol, p-anisaldehyde and cinnamaldehyde caused a mortality rate above 50% over P. brachyurus. The infectivity of G. intraradices was inhibited by cinnamaldehyde, salicilaldehyde, thymol, carvacrol, p-anisaldehyde, and benzaldehyde, while only cinnamaldehyde and thymol significantly inhibited mycorrhizal colonization by G. mosseae.