Saskatoon, Canada
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Dai M.,Agriculture and Agri Food Canada | Dai M.,Chongqing Medical University | Hamel C.,Agriculture and Agri Food Canada | Bainard L.D.,Agriculture and Agri Food Canada | And 5 more authors.
Soil Biology and Biochemistry | Year: 2014

Improving technologies and the challenge of producing more bio-products while reducing the environmental footprint of humans are shifting paradigms in agricultural research. Harnessing the microbial resources of arable soils is a new avenue to improve the efficiency of nutrient use in agriculture. The objective of this study was to define how crop management influences the contribution of resident AM fungi to nutrient efficiency and crop productivity. The AM fungal communities of 72 organically and 78 conventionally managed wheat fields of the Canadian prairie were described by 454 pyrosequencing and related to crop productivity and N and P use efficiency. Conventional management reduces soil pH and increases the fluxes of all soil nutrients except S, B, and K. Organic management increased the abundance of Claroideoglomus reads. The efficiency of N and P uptake from soil by organic wheat was 2.3 and 1.8 times higher than that of conventional systems. This high N and P uptake efficiency in organic wheat crops was mainly attributable to the low soil fertility of organic fields, as wheat biomass production was 1.44 times greater in conventional than organic systems. Overall, the amounts of N and P taken up by conventional and organic wheat crops were similar. Plant nutrient balance and the abundance of Paraglomus drove conventional wheat production, whereas organic production depended mainly on soil moisture, plant nutrient balance, and abundance of Glomus, which was associated with reduced and nutrient-inefficient wheat production. The high nutrient concentrations at maturity and the low productivity of organic wheat fit a model of limiting CO2-assimilation. The trade-off between nutrient use efficiency and productivity in low input wheat production could be relieved by reducing the abundance of Glomus species, increasing soil moisture and early N availability, or by improving the inherent CO2 assimilation capacity of wheat. © 2014.


Chaban B.,University of Saskatchewan | Albert A.,Womens Health Research Institute | Links M.G.,University of Saskatchewan | Links M.G.,Saskatoon Research Center | And 4 more authors.
PLoS ONE | Year: 2013

The upper respiratory tract microbiome has an important role in respiratory health. Influenza A is a common viral infection that challenges that health, and a well-recognized sequela is bacterial pneumonia. Given this connection, we sought to characterize the upper respiratory tract microbiota of individuals suffering from the pandemic H1N1 influenza A outbreak of 2009 and determine if microbiome profiles could be correlated with patient characteristics. We determined the microbial profiles of 65 samples from H1N1 patients by cpn60 universal target amplification and sequencing. Profiles were examined at the phylum and nearest neighbor "species" levels using the characteristics of patient gender, age, originating health authority, sample type and designation (STAT/non-STAT). At the phylum level, Actinobacteria-, Firmicutes- and Proteobacteria-dominated microbiomes were observed, with none of the patient characteristics showing significant profile composition differences. At the nearest neighbor "species" level, the upper respiratory tract microbiomes were composed of 13-20 "species" and showed a trend towards increasing diversity with patient age. Interestingly, at an individual level, most patients had one to three organisms dominant in their microbiota. A limited number of discrete microbiome profiles were observed, shared among influenza patients regardless of patient status variables. To assess the validity of analyses derived from sequence read abundance, several bacterial species were quantified by quantitative PCR and compared to the abundance of cpn60 sequence read counts obtained in the study. A strong positive correlation between read abundance and absolute bacterial quantification was observed. This study represents the first examination of the upper respiratory tract microbiome using a target other than the 16S rRNA gene and to our knowledge, the first thorough examination of this microbiome during a viral infection. © 2013 Chaban et al.


Kaddour R.,Tunis el Manar University | Sellami N.,Tunis el Manar University | Chennaoui H.,Tunis el Manar University | Nasri N.,Tunis el Manar University | And 6 more authors.
African Journal of Biotechnology | Year: 2011

Sulla constitutes an important genetic resource contributing to pastoral production, particularly in semi-arid regions. In Tunisia, seedlings of the southern species Sulla carnosa (Desf.) and the northern species Sulla coronaria (L.) were treated with NaCl (0, 100 and 200 mM) for 27 days. Salt treatments decreased leaf dry matter more in S. carnosa than in S. coronaria. S. coronaria accumulated less Na + and greater amounts of K + and showed greater K/Na selectivity, a trait which could be related to the maintenance of higher net K + uptake and transport in the presence of NaCl. Pigments were severely affected by salt stress in leaves of S. carnosa when compared with leaves of S. coronaria. In addition to these physiological characterisations, genetic diversity was measured between the two accessions using inter simple sequence repeat (ISSR) markers. Three ISSR primers generated a total of 63 DNA amplicons for S. carnosa and 64 DNA amplicons for S. coronaria, all of which were polymorphic between the two accessions. Correlations between the molecular and physiological data revealed statistically significant correlations between the salt response of these two Sulla accessions and two molecular markers B340 and B860, in roots and shoots, respectively. S. coronaria showed greater salt tolerance on the basis of growth and K/Na selectivity, making it a good candidate for inclusion in a future breeding programme. © 2011 Academic Journals.


Chaban B.,University of Saskatchewan | Links M.G.,University of Saskatchewan | Links M.G.,Saskatoon Research Center | Hill J.E.,University of Saskatchewan
Microbial Ecology | Year: 2012

Members of the rare microbiome can be important components of complex microbial communities. For example, pet dog ownership is a known risk factor for human campylobacteriosis, and Campylobacter is commonly detected in dog feces by targeted assays. However, these organisms have not been detected by metagenomic methods. The goal of this study was to characterize fecal microbiota from healthy and diarrheic pet dogs using two different levels of molecular detection. PCR amplification and pyrosequencing of the universal cpn60 gene target was used to obtain microbial profiles from each dog. To investigate the relatively rare epsilon-proteobacteria component of the microbiome, a molecular enrichment was carried out using a PCR that first amplified the cpn10-cpn60 region from epsilon-proteobacteria, followed by universal cpn60 target amplification and pyrosequencing. From the non-enriched survey, the major finding was a significantly higher proportion of Bacteroidetes, notably Bacteroides vulgatus, in healthy dogs compared to diarrheic dogs. Epsilon-proteobacteria from the genera Helicobacter and Campylobacter were also detected at a low level in the non-enriched profiles of some dogs. Molecular enrichment increased the proportion of epsilon-proteobacteria sequences detected from each dog, as well as identified novel, presumably rare sequences not seen in the non-enriched profiles. Enriched profiles contained known species of Arcobacter, Campylobacter, Flexispira, and Helicobacter and identified two possibly novel species. These findings add to our understanding of the canine fecal microbiome in general, the epsilon-proteobacteria component specifically, and present a novel modification to traditional metagenomic approaches for study of the rare microbiome. © 2011 Springer Science+Business Media, LLC.


Olfert O.,Saskatoon Research Center | Weiss R.M.,Saskatoon Research Center | Elliott R.H.,Saskatoon Research Center
Canadian Entomologist | Year: 2015

Wheat midge, Sitodiplosis mosellana (Géhin) (Diptera: Cecidomyiidae), Palaearctic in origin, is thought to have been introduced into North America in the early 1800s. It is a major pest of spring wheat (Triticum aestivum Linnaeus (Poaceae)), durum wheat (T. durum Desfontaines), triticale (X-Triticosecale), and, to a lesser extent, spring rye (Secale cereale Linnaeus (Poaceae)) throughout the northern Great Plains. Climate is the principal factor regulating the distribution and abundance of most insects. A bioclimate simulation model was developed to explain the current distribution and abundance of S. mosellana. The current distribution for North America, Europe, and Asia was consistent with model projections. General circulation model scenarios (CSIRO-MK 3.0 and MIROC-H) for the 2030 and 2070 time periods were applied to the bioclimate simulation model of S. mosellana to assess the potential impact of changing climates on their distribution and relative abundance. Potential changes to relative abundance and distribution were most sensitive to time period, as opposed to climate change scenario. Differences between the MIROC-H and CSIRO-MK 3.0 models were restricted to particular regions in North America. The study found that the range and abundance of S. mosellana, and associated crop risk, was predicted to expand in a northerly direction and contract across the present southern limits. © Entomological Society of Canada 2015


Desai A.R.,University of Saskatchewan | Links M.G.,University of Saskatchewan | Links M.G.,Saskatoon Research Center | Collins S.A.,University of Saskatchewan | And 4 more authors.
Aquaculture | Year: 2012

Replacement of fish meal in aquaculture diets with plant proteins is economically desirable, but the effects of alternative protein sources on the intestinal microbiota and fish health are poorly understood. We examined the intestinal microbiome of 108 rainbow trout (. Oncorhynchus mykiss) fed with diets including plant ingredients (peas, soybean, canola) at two processing levels (meal, concentrate), or a fish meal (FM) control diet. Microbial community profiles were determined using pyrosequencing of . cpn60 PCR products and 16S rRNA DGGE. Microbial profiles of fish fed the FM diet changed over the course of the study with reduction in species richness and diversity and therefore evaluation of the effects of experimental diets was accomplished through comparison of each diet with its concurrent FM control. Plant ingredient diets were associated with higher Firmicutes:Proteobacteria ratios than controls. Both DGGE and pyrosequencing data showed that microbiomes of fish fed meal-based diets were more distinguishable from the FM control microbiomes than were the microbiomes of fish fed protein concentrate diets. Changes in the FM diet associated profiles could be the result of age-related physiological changes in these fish or a long-term effect of the change in environment from outdoor aquaculture facility to an indoor re-circulating facility. Regardless of the reason, these observations have significant implications for future evaluations of diets and ingredients. We also demonstrated changes in the intestinal microbiome that may contribute to negative health outcomes when diets contain plant meal proteins. These changes in microbiome structure can be minimized with additional processing of plant ingredients. © 2012 Elsevier B.V.


Wang X.,Agriculture and Agri Food Canada | Gan Y.,Agriculture and Agri Food Canada | Hamel C.,Agriculture and Agri Food Canada | Lemke R.,Saskatoon Research Center | McDonald C.,Agriculture and Agri Food Canada
Field Crops Research | Year: 2012

Knowledge of crop water use at various soil depths is key to improving water use efficiency (WUE) for cropping systems in semiarid areas. The objective of this study was to characterize soil water extraction profiles across rooting zones for various pulse crops in a semiarid environment. We tested the hypothesis that water use profiles across the rooting zone vary between pulse species and among individual cultivars. Six dry pea (Pisum sativum L.), six chickpea (Cicer arietinum L.), 11 lentil (Lens culinaris Medik.) cultivars, along with fababean (Vicia faha L.), dry bean (Phaseolus vulgaris L.) and lupin (Sundial lupine L.) were grown in southwest Saskatchewan, 2008-2010. In the low-rainfall year, pulse plants extracted water mainly from the top 60cm soil layer, and no water was extracted from the soil below 90cm. In the moderate-rainfall year, pulses extracted an average of 9mm water from the top 15cm layer, 10mm from the 15-30cm layer, and <5mm from each of the 30-60, 60-90, and 90-120cm layers. In the high-rainfall year, pulse plants extracted about 4mm of water from the top 30cm layer, and extracted little to none below 30cm soil depth; in the 30-120cm layers, the soil under dry pea stored >85mm of water and the soil under kabuli chickpea and fababean stored about 20mm. Dry pea had the highest WUE among the pulses evaluated, averaging 8.3kgha -1mm -1, and chickpea the lowest WUE especially in the wet year. No difference was found in water use profile or WUE among individual cultivars in dry pea or chickpea and only small differences existed among lentil cultivars. In semiarid areas, pulse plants extract soil water mostly from shallow depths, and the water in the deeper soil layers is left unused which could benefit deep-rooting crops the following year. Alternatively, improved pulse cultivars should be bred to utilize soil water that is available in the deeper rooting zones. © 2012.


Sakiyan O.,Selcuk University | Sumnu G.,Middle East Technical University | Sahin S.,Middle East Technical University | Meda V.,University of Saskatchewan | And 2 more authors.
Food and Bioprocess Technology | Year: 2011

The main objective of the study was to determine the effects of different baking ovens and different cake formulations on the degree of starch gelatinization during cake baking. Baking was performed in microwave, infrared-microwave combination, and conventional ovens. Starch gelatinization levels of fat free, 25% fat, and 25% Simplesse™-containing cake samples were examined using differential scanning calorimeter (DSC) and rapid visco analyzer (RVA). Both DSC and RVA results showed that increasing baking time increased gelatinization level for all baking types significantly. It was also found that the effect of fat content on starch gelatinization was different depending on the type of baking. Addition of fat reduced the degree of starch gelatinization in conventional baking. However, fat enhanced the gelatinization in microwave and infrared-microwave combination ovens. Usage of Simplesse™ as a fat replacer decreased the starch gelatinization in all types of baking significantly. There was insufficient starch gelatinization in microwave-baked cakes in which the degree of gelatinization ranged from 55% to 78% depending on formulation. On the other hand, it ranged from 85% to 93% in conventionally baked cakes. Combining infrared with microwaves increased degree of starch gelatinization (70-90%). © 2009 Springer Science + Business Media, LLC.


PubMed | Saskatoon Research Center
Type: Journal Article | Journal: Phytopathology | Year: 2013

This study investigated how the timing of application of the biofungicide Serenade (Bacillus subtilis QST713) or it components (product filtrate and bacterial cell suspension) influenced infection of canola by Plasmodiophora brassicae under controlled conditions. The biofungicide and its components were applied as a soil drench at 5% concentration (vol/vol or equivalent CFU) to a planting mix infested with P. brassicae at seeding or at transplanting 7 or 14 days after seeding (DAS) to target primary and secondary zoospores of P. brassicae. Quantitative polymerase chain reaction (qPCR) was used to assess root colonization by B. subtilis as well as P. brassicae. The biofungicide was consistently more effective than the individual components in reducing infection by P. brassicae. Two applications were more effective than one, with the biofungicide suppressing infection completely and the individual components reducing clubroot severity by 62 to 83%. The biofungicide also reduced genomic DNA of P. brassicae in canola roots by 26 to 99% at 7 and 14 DAS, and the qPCR results were strongly correlated with root hair infection (%) assessed at the same time (r = 0.84 to 0.95). qPCR was also used to quantify the transcript activity of nine host-defense-related genes in inoculated plants treated with Serenade at 14 DAS for potential induced resistance. Genes encoding the jasmonic acid (BnOPR2), ethylene (BnACO), and phenylpropanoid (BnOPCL and BnCCR) pathways were upregulated by 2.2- to 23-fold in plants treated with the biofungicide relative to control plants. This induced defense response was translocated to the foliage (determined based on the inhibition of infection by Leptosphaeria maculans). It is possible that antibiosis and induced resistance are involved in clubroot suppression by Serenade. Activity against the infection from both primary and secondary zoospores of P. brassicae may be required for maximum efficacy against clubroot.

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