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Near infrared reflectance spectroscopy (NIRS) holds promise for rapid assessment of soil total N and organic C contents, but its ability to predict soil N supply in soils with contrasting physio-chemical properties needs to be evaluated. The objectives of this study were to: (i) evaluate NIRS predictions of measured soil parameters (total N, organic C, and C/N ratio) and as an indirect indicator of soil N supply, namely corn (Zea mays L.) N uptake and (ii) assess the effect of sample set heterogeneity on NIRS predictions. Soil samples (n = 282 in the total set) were collected between 2000 and 2009 from 52 sites across four Canadian provinces and were allocated to fine-(>350 g clay kg-\ n = 101) and coarse-textured subsets (<350 g clay kg~n = 181). Prediction models were developed using modified partial least squares regression. Prediction precision was assessed using the coefficient of determination {R^) and ratio of prediction to deviation (RPD = ratio of standard error of prediction corrected for bias to standard deviation of the reference data used in the validation). For the total set, predictions were reliable for total N, organic C and C/N ratio (0.7 < R^ < 0.9, 1.75 < RPD < 3), and less reliable for soil N supply {R^ < 0.7, RPD < 1.75). Prediction precision for total N, organic C, C/N ratio, and soil N supply increased with set homogeneity (i.e., better in the texture subsets than the total set), resulting in reliable predictions for soil N supply (RPD > 2.00) in the texture subsets. This study demonstrated the possibility of developing reliable NIRS predictive models for total N, organic C, and C/N ratio for soils with contrasting physiochemical properties, as well as reliable NIRS predictive models for soil N supply within homogeneous texture sets.Abbreviations: CV, coefficient of variation; Math treat, math treatment; n^ number of samples in calibration; n^, number of samples invalidation; NIRS, near infrared reflectance spectroscopy; organic C, organic carbon; R^, coefficient of determination; RPD, ratio of prediction to deviation; SD, standard deviation; SEC, standard error of calibration; SECV, standard error of cross-validation; SEP, standard error of prediction; SEP(C), standard error of prediction corrected for bias; total N, total nitrogen; SNVD, standard normal variate and detrending; T-Outliers, outliers discarded during calibration.

Wheat is among the important crops harnessed by humans whose breeding efforts resulted in a diversity of genotypes with contrasting traits. The goal of this study was to determine whether different old and new cultivars of durum wheat (Triticum turgidum L. var. durum) recruit specific arbuscular mycorrhizal (AM) fungal communities from indigenous AM fungal populations of soil under field conditions. A historical set of five landraces and 26 durum wheat cultivars were field cultivated in a humid climate in Eastern Canada, under phosphorus-limiting conditions. To characterize the community of AMF inhabiting bulk soil, rhizosphere, and roots, MiSeq amplicon sequencing targeting the 18S rRNA gene (SSU) was performed on total DNAs using a nested PCR approach. Mycorrhizal colonization was estimated using root staining and microscope observations. A total of 317 amplicon sequence variants (ASVs) were identified as belonging to Glomeromycota. The core AM fungal community (i.e., ASVs present in > 50% of the samples) in the soil, rhizosphere, and root included 29, 30, and 29 ASVs, respectively. ASVs from the genera Funneliformis, Claroideoglomus, and Rhizophagus represented 37%, 18.6%, and 14.7% of the sequences recovered in the rarefied dataset, respectively. The two most abundant ASVs had sequence homology with the 18S sequences from well-identified herbarium cultures of Funneliformis mosseae BEG12 and Rhizophagus irregularis DAOM 197198, while the third most abundant ASV was assigned to the genus Paraglomus. Cultivars showed no significant difference of the percentage of root colonization ranging from 57.8% in Arnautka to 84.0% in AC Navigator. Cultivars were generally associated with similar soil, rhizosphere, and root communities, but the abundance of F. mosseae, R. irregularis, and Claroideoglomus sp. sequences varied in Eurostar, Golden Ball, and Wakooma. Although these results were obtained in one field trial using a non-restricted pool of durum wheat and at the time of sampling, that

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Arbuscular mycorrhizal fungi (AMF) are obligate plant symbionts that improve the nutrition and health of their host. Most, but not all the crops form a symbiosis with AMF. It is the case for canola (Brassica napus), an important crop in the Canadian Prairies that is known to not form this association. From 2008 to 2018, an experiment was replicated at three locations of the Canadian Prairies and it was used to assess the impact of canola on the community of AMF naturally occurring in three cropping systems, canola monoculture, or canola in two different rotation systems (2-years, canola-wheat and 3-years, barley-pea-canola). We sampled canola rhizosphere and bulk soils to: (i) determine diversity and community structure of AMF, we expected that canola will negatively impact AMF communities in function of its frequency in crop rotations and (ii) wanted to assess how these AMF communities interact with other fungi and bacteria. We detected 49 AMF amplicon sequence variants (ASVs) in canola rhizosphere and bulk soils, confirming the persistence of a diversified AMF community in canola-planted soil, even after 10 years of canola monoculture, which was unexpected considering that canola is among non-mycorrhizal plants. Network analysis revealed a broad range of potential interactions between canola-associated AMF and some fungal and bacterial taxa. We report for the first time that two AMF, Funneliformis mosseae and Rhizophagus iranicus, shared their bacterial cohort almost entirely in bulk soil. Our results suggest the existence of non-species-specific AMF-bacteria or AMF-fungi relationships that could benefit AMF in absence of host plants. The persistence of an AMF community in canola rhizosphere and bulk soils brings a new light on AMF ecology and leads to new perspectives for further studies about AMF and soil microbes interactions and AMF subsistence without mycotrophic host plants.

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Background Mastitis caused by different pathogens including Streptococcus uberis (S. uberis) is responsible for huge economic losses to the dairy industry. In order to investigate the potential genetic and epigenetic regulatory mechanisms of subclinical mastitis due to S. uberis, the DNA methylome (whole genome DNA methylation sequencing) and transcriptome (RNA sequencing) of milk somatic cells from cows with naturally occurring S. uberis subclinical mastitis and healthy control cows (N = 3/group) were studied. Results Globally, the DNA methylation levels of CpG sites were low in the promoters and first exons but high in inner exons and introns. The DNA methylation levels at the promoter, first exon and first intron regions were negatively correlated with the expression level of genes at a whole-genome-wide scale. In general, DNA methylation level was lower in S. uberis-positive group (SUG) than in the control group (CTG). A total of 174342 differentially methylated cytosines (DMCs) (FDR < 0.05) were identified between SUG and CTG, including 132237, 7412 and 34693 in the context of CpG, CHG and CHH (H = A or T or C), respectively. Besides, 101612 methylation haplotype blocks (MHBs) were identified, including 451 MHBs that were significantly different (dMHB) between the two groups. A total of 2130 differentially expressed (DE) genes (1378 with up-regulated and 752 with down-regulated expression) were found in SUG. Integration of methylome and transcriptome data with MethGET program revealed 1623 genes with significant changes in their methylation levels and/or gene expression changes (MetGDE genes, MethGET p-value < 0.001). Functional enrichment of genes harboring ≥ 15 DMCs, DE genes and MetGDE genes suggest significant involvement of DNA methylation changes in the regulation of the host immune response to S. uberis infection, especially cytokine activities. Furthermore, discriminant correlation analysis with DIABLO method identified 26 candidate biomarkers, including 6 DE genes, 15 CpG-DMCs and 5 dMHBs that discriminated between SUG and CTG. Conclusion Finally, the integration of methylome and transcriptome of milk somatic cells suggests the possible involvement of DNA methylation changes in the regulation of host immune response to subclinical mastitis due to S. uberis. The presented genetic and epigenetic biomarkers could contribute to the design of management strategies of subclinical mastitis and breeding for mastitis resistance.

Staphylococcus aureus (S. aureus) is one of the most prevalent pathogens of bovine subclinical mastitis and a challenging pathogen in dairy production. DNA methylation involvement in regulating mammary gland inflammatory defense has been documented. This study adopted whole genome bisulfite sequencing and RNA-sequencing technologies to profile the genome-wide DNA methylation and transcriptome landscapes, respectively, of milk somatic cells (MSCs) from 15 cows with S. aureus-induced subclinical mastitis (SACs) and 13 healthy cows (HCs). Bioinformatics processing of data with standard tools indicated that the global DNA methylation patterns of MSCs demonstrated inverse correlations between gene expression and DNA methylation levels at promoter, first exon and first intron regions, suggesting potential regulatory roles of DNA methylation in transcriptional activities. Totally, 26,289 differential methylation regions (DMRs) were identified between SACs and HCs (1,000 bp window, 1,000 bp step, q-value &lt; 0.05, &gt;20% methylation difference and ≥3 differentially methylated cytosines). A total of 887, 334 and 3,414 DMRs were overlapped with promoter, first exon, and first intron regions, respectively, including 363 DMRs harboring transcription start sites. Among them, the methylation levels of 956 DMRs were strongly correlated with the expression levels of their overlapped genes (|Spearman’s correlation coefficient| &gt;0.5, adjusted-p-value&lt; 0.05). Functional annotation of the overlapped genes indicated significant (adjusted-p-value &lt; 0.05) enrichment in 18 GO terms and 1 KEGG pathway related to cellular activities, notably in cell migration, epithelial cell differentiation and tight junction, among others (Figure 1). These results suggest the involvement of DNA methylation in mammary gland defense against S. aureus-invasion. Applying DIABLO method to integrate correlated DMRs and genes, a total of 20 DMR and 10 gene candidate markers were found to discriminate SACs from HCs. The identified candidate markers could serve as reference for enhancing breeding for mastitis resistance and for developing new mastitis management strategies.