Species-specific DNA markers for identification of two root-knot nematodes of coffee: Meloidogyne arabicida and M. izalcoensis

Seven root-knot nematodes (RKN), including Meloidogyne exigua, M. incognita, M. paranaensis, M. enterolobii, M. arabicida, M. izalcoensis and M. arenaria are major pathogens of coffee crop in the Americas. Species-specific primers for their identification have been developed for five of them and constitute a fast and reliable method of identification. Here we report a PCR-based assay for specific detection of M. arabicida and M. izalcoensis. Random Amplified Polymorphic DNA fragments specific for these two species were converted into sequence characterized amplified region (SCAR) markers. PCR amplification using the SCAR primers produced a specific fragment of 300 bp and 670 bp for M. arabicida and M. izalcoensis, respectively, which were absent in other coffee-associated Meloidogyne spp. tested. SCAR primers also allowed successful amplification of DNA from single second-stage juveniles (J2), males and females. In addition, these primers were able to unambiguously detect the target species in nematode suspensions extracted from soil and roots samples, in different isolates of the same species or when used in multiplex PCR reactions containing mixtures of species. These results demonstrated the effectiveness of these SCAR markers and their multiplex use with those previously developed for M. exigua, M. incognita, M. paranaensis, M. enterolobii and M. arenaria constitute an essential detection tool. This diagnostic kit will contribute for specific J2 identification of the major RKN infecting coffee from field samples in the Americas.     

Ruminal and morphometric parameters of the rumen and intestines of sheep fed with increasing levels of spineless cactus (Nopalea cochenillifera Salm-Dyck)

Tropical Animal Health and Production - The objective of this study was to evaluate the ruminal parameters (pH, N-NH3, and microbial protein) and morphometry of the rumen and intestine of sheep fed...     

Laser-based spectroscopic methods to evaluate the humification degree of soil organic matter in whole soils: a review

Purpose

The objective of this review is to survey critically the results obtained by the application of laser-induced fluorescence spectroscopy (LIFS) and laser-induced breakdown spectroscopy (LIBS) to the evaluation of the humification degree (HD) of soil organic matter (SOM) directly in untreated, intact whole soils.

Materials and methods

A large number of soils of various origin and nature, either native or under various cultivations, land use, and management, at various depths, have been studied to evaluate the HD of their SOM directly in intact whole samples. The LIFS spectra were obtained by either a bench or a portable argon laser apparatus that emits UV-VIS light of high power, whereas the LIBS spectra were obtained using a Q-switched Nd:YAG laser at 1064 nm.

Results and discussion

The close correlations found by comparing H_LIF values of whole soil samples with values of earlier proposed humification indexes confirmed the applicability of LIFS to assess the HD of SOM in whole soils. The high correlation found between HD_LIBS values and H_LIF values showed the promising potential of LIBS for the evaluation HD of SOM.

Conclusions

The LIFS technique shows to be a valuable alternative to evaluate the HD of SOM by probing directly the whole solid soil sample, thus avoiding the use of any previous chemical and/or physical treatments or separation procedures of SOM from the mineral soil matrix. The emerging application of LIBS to evaluate the HD of SOM in whole soils appears promising and appealing due to its sensitivity, selectivity, accuracy, and precision.

     

Surface liming effects on soil radiation attenuation properties

Purpose

This study investigates the effects of surface liming on soil attenuation radiation properties. For this, measurements of soil chemical attributes (pH, organic carbon, H+Al, Al³⁺, Ca²⁺, and Mg²⁺) and attenuation radiation parameters (mass attenuation coefficient, μ_m, atomic and electronic cross sections, σ_a and σ_e, effective atomic number and electron density, Z_eff and N_el) were carried out. This aim was motivated by the fact that possible μ_m variation might cause as well variation in the determination of soil physical properties.

Materials and methods

The studied soil, classified as a Dystrudept sity-clay, is located in South Brazil. The trial consisted of five stripes, one of them under pasture and the remaining under no-till system (NTS). Lime rates of 0, 10, 15, and 20 t ha^?1 were broadcast on the NTS soil surface. Disturbed soil samples were collected 30 months after liming at the top (0–10 cm) and subsoil (10–20 cm) layers. Soil chemical attributes were characterized following standard experimental procedures. The soil oxide composition, obtained by EDXRF analysis, was used to calculate μ_m for ²⁴¹Am and ¹³⁷Cs photon energies with XCOM computer code. μ_m values were employed to calculate σ_a, σ_e, Z_eff, and N_el and to predict variations in soil bulk density (ρ) and total porosity (φ).

Results and discussion

Surface liming notably increased contents of soil pH, Ca²⁺, and Mg²⁺ while reduced H+Al and Al³⁺ at the top soil layer, where μ_m, σ_a, σ_e, and Z_eff were also increased with the lime rates. However, at the subsoil layer, liming neither lessened soil acidity nor induced remarkable changes in the attenuation parameters. When using ¹³⁷Cs photon energy, incoherent scattering totally dominated over the radiation interaction processes whereas photoelectric absorption and coherent scattering substantially contributed when ²⁴¹Am photon energy was used. Therefore, the increasing in soil attenuation parameters at the top soil layer was more accentuated considering ²⁴¹Am than ¹³⁷Cs photon energy. Variation in μ_m caused considerable variation in ρ and φ only for ²⁴¹Am photon energy.

Conclusions

The findings regarding the effect of μ_m variation induced by liming on the determination of soil physical properties are extremely relevant because traditionally, in the soil science area, μ_m values are calculated without considering any chemical modification to which the soil can be submitted. Bearing in mind that ρ and φ are important parameters from the agricultural and environmental points of view, not representative measurements of μ_m can lead to biased values of ρ and φ.

     

Ex‐post facto analysis of diseases of the Gulf of Mexico′s white shrimp Litopenaeus setiferus

This study presents an Ex‐Post Facto analysis of diseases of wild juvenile and adults of Litopenaeus setiferus collected from a field survey at the Natural Protected Area of Terminos lagoon, southern Mexico. The objective of the present approach was to determine if sampling site and/or shrimp age were contributing risk factors for disease between juvenile and adult shrimp; if there was a determined period of time in a year cycle when diseases were more critical, and if the analysis would help to decision‐ making considering what population would pose less risk of disease‐carrying when withdrawn for experimental purposes; all under an after‐the‐fact (ex‐post facto) approach. We identified that juvenile shrimp were at more risk of contracting some diseases in the estuarine environment and June, July and August months, were found to be a critical period when colonizing and parasitic diseases maintained a significant high prevalence in the shrimp population. These assumptions may help for decision‐making when wild shrimp have to be withdrawn from their natural environment for research purposes.