Identification of rumen microbial biomarkers linked to methane emission in Holstein dairy cows

Mitigation of greenhouse gas emissions is relevant for reducing the environmental impact of ruminant production. In this study, the rumen microbiome from Holstein cows was characterized through a combination of 16S rRNA gene and shotgun metagenomic sequencing. Methane production (CH₄) and dry matter intake (DMI) were individually measured over 4–6 weeks to calculate the CH₄ yield (CH₄y = CH₄/DMI) per cow. We implemented a combination of clustering, multivariate and mixed model analyses to identify a set of operational taxonomic unit (OTU) jointly associated with CH₄y and the structure of ruminal microbial communities. Three ruminotype clusters (R1, R2 and R3) were identified, and R2 was associated with higher CH₄y. The taxonomic composition on R2 had lower abundance of Succinivibrionaceae and Methanosphaera, and higher abundance of Ruminococcaceae, Christensenellaceae and Lachnospiraceae. Metagenomic data confirmed the lower abundance of Succinivibrionaceae and Methanosphaera in R2 and identified genera (Fibrobacter and unclassified Bacteroidales) not highlighted by metataxonomic analysis. In addition, the functional metagenomic analysis revealed that samples classified in cluster R2 were overrepresented by genes coding for KEGG modules associated with methanogenesis, including a significant relative abundance of the methyl-coenzyme M reductase enzyme. Based on the cluster assignment, we applied a sparse partial least-squares discriminant analysis at the taxonomic and functional levels. In addition, we implemented a sPLS regression model using the phenotypic variation of CH₄y. By combining these two approaches, we identified 86 discriminant bacterial OTUs, notably including families linked to CH₄ emission such as Succinivibrionaceae, Ruminococcaceae, Christensenellaceae, Lachnospiraceae and Rikenellaceae. These selected OTUs explained 24% of the CH₄y phenotypic variance, whereas the host genome contribution was ~14%. In summary, we identified rumen microbial biomarkers associated with the methane production of dairy cows; these biomarkers could be used for targeted methane-reduction selection programmes in the dairy cattle industry provided they are heritable.     

Seasonal water stress and the resistance of Pinus yunnanensis to a bark-beetle-associated fungus

We examined the influence of seasonal water stress on the resistance of Pinus yunnanensis (Franch.) to inoculation with Leptographium yunnanense, a pathogenic fungus associated with the aggressive bark beetle, Tomicus n. sp. Experiments took place between October 1997 and November 1999 in two plots located at the top and at the foot of a hill in Shaogiu, China, a region characterized by dry winters and wet summers. Following isolated and mass fungal inoculations, we observed the reaction zone length, fungal growth in the phloem, and the occlusion, blue-staining and specific hydraulic conductivity of the sapwood. Measurements of soil and needle water contents and predawn needle water potentials confirmed that trees were subject to mild water stress during winter, especially at the drier hilltop site. Measures of tree resistance to fungal infection of phloem and sapwood were congruent and indicated that trees were most susceptible to inoculation during the wet summer, especially at the lower-elevation plot. Specific hydraulic conductivity decreased after inoculation in summer. The results indicate that mild seasonal water stress is not likely responsible for the recent extensive damage to young P. yunnanensis stands by Tomicus n. sp. in the vicinity of our study plots. Rather, the results suggest that mild water stress enhances tree resistance to fungal pathogens associated with Tomicus n. sp.     

Survey of mussel (Mytilus) species at Scottish shellfish farms

Mytilus trossulus and its hybrids with the native species Mytilus edulis and also Mytilus galloprovincialis have been recently detected in both farmed and natural populations of mussels in Scotland, adding complexity to the known M. edulis × M. galloprovincialis hybrid zone in Europe. Mytilus trossulus was first found in Scotland at aquaculture sites, where it was associated with significant losses in production and reductions in profitability. Mytilus trossulus and its hybrids have been identified at higher frequencies in farm stock than in natural intertidal populations, raising concerns about the potential wider impact of M. trossulus genotypes at mussel aquaculture sites in Scotland. The present study clarifies the composition of Mytilus species in cultivation at Scottish mussel aquaculture farms, by screening samples from 41 mussel aquaculture sites using a high-throughput real-time PCR methodology. Mytilus edulis alleles were detected at all sites. Mytilus galloprovincialis alleles were detected from samples collected at 39 sites, and M. trossulus alleles were found at five sites. Overall, M. trossulus genotypes were restricted in their geographical distribution. It is suggested that, in order to support the sustainability of the Scottish shellfish cultivation industry, the economic impact arising from the presence of M. trossulus could be limited through good management practice.     

Analysis of patulin in pear- and apple-based foodstuffs by liquid chromatography electrospray ionization tandem mass spectrometry

A liquid chromatography electrospray ionization tandem mass spectrometry method for the determination of patulin in apple- and pear-based foodstuffs was developed. The sample preparation is based on the QuEChERS procedure involving an initial extraction step with water and acetonitrile, followed by a partitioning step after the addition of magnesium sulfate and sodium chloride. The cleanup was performed by using dispersive solid-phase extraction with a mixture of magnesium sulfate, primary secondary amine sorbent, and n-octadecylsiloxane sorbent added together to the extract. The cleaned extract was finally evaporated and reconstituted in water prior to injection. Quantitation was performed by isotope dilution using ((13)C(7))-patulin as internal standard. The method was first fully validated in three different baby food products including apple-pear juice, apple-pear puree, and infant cereals. Then the scope of application of the method was extended to pear concentrate, raw apples, apple flakes (naturally contaminated), dried apples, and yogurt. The sensitivity achieved by the method in all matrices gave limits of detection (LOD) and quantitation (LOQ) of ≤0.5 and ≤10 μg/kg, respectively, which was compliant with maximum levels settled in Commission Regulation (EC) No. 1881/2006. Method performances for all matrices also fulfilled the criteria established in the CEN/TR 16059:2010 document. Indeed, recoveries were within the 94-104% range; relative standard deviations of repeatability (RSD(r)) and intermediate reproducibility (RSD(IR)) were ≤7.5 and ≤13.0%, respectively, and trueness in an infant apple drink (FAPAS 1642) was measured at 99%.