Anoxygenic phototroph of the Chloroflexota uses a type I reaction centre.

Scientific exploration of phototrophic bacteria over nearly 200 years has revealed large phylogenetic gaps between known phototrophic groups that limit understanding of how phototrophy evolved and diversified1,2. Here, through Boreal Shield lake water incubations, we cultivated an anoxygenic phototrophic bacterium from a previously unknown order within the Chloroflexota phylum that represents a highly novel transition form in the evolution of photosynthesis. Unlike all other known phototrophs, this bacterium uses a type I reaction centre (RCI) for light energy conversion yet belongs to the same bacterial phylum as organisms that use a type II reaction centre (RCII) for phototrophy. Using physiological, phylogenomic and environmental metatranscriptomic data, we demonstrate active RCI-utilizing metabolism by the strain alongside usage of chlorosomes3 and bacteriochlorophylls4 related to those of RCII-utilizing Chloroflexota members. Despite using different reaction centres, our phylogenomic data provide strong evidence that RCI-utilizing and RCII-utilizing Chloroflexia members inherited phototrophy from a most recent common phototrophic ancestor. The Chloroflexota phylum preserves an evolutionary record of the use of contrasting phototrophic modes among genetically related bacteria, giving new context for exploring the diversification of phototrophy on Earth.

Anoxygenic photosynthesis and iron-sulfur metabolic potential of Chlorobia populations from seasonally anoxic Boreal Shield lakes.

Aquatic environments with high levels of dissolved ferrous iron and low levels of sulfate serve as an important systems for exploring biogeochemical processes relevant to the early Earth. Boreal Shield lakes, which number in the tens of millions globally, commonly develop seasonally anoxic waters that become iron rich and sulfate poor, yet the iron-sulfur microbiology of these systems has been poorly examined. Here we use genome-resolved metagenomics and enrichment cultivation to explore the metabolic diversity and ecology of anoxygenic photosynthesis and iron/sulfur cycling in the anoxic water columns of three Boreal Shield lakes. We recovered four high-completeness and low-contamination draft genome bins assigned to the class Chlorobia (formerly phylum Chlorobi) from environmental metagenome data and enriched two novel sulfide-oxidizing species, also from the Chlorobia. The sequenced genomes of both enriched species, including the novel "Candidatus Chlorobium canadense", encoded the cyc2 gene that is associated with photoferrotrophy among cultured Chlorobia members, along with genes for phototrophic sulfide oxidation. One environmental genome bin also encoded cyc2. Despite the presence of cyc2 in the corresponding draft genome, we were unable to induce photoferrotrophy in "Ca. Chlorobium canadense". Genomic potential for phototrophic sulfide oxidation was more commonly detected than cyc2 among environmental genome bins of Chlorobia, and metagenome and cultivation data suggested the potential for cryptic sulfur cycling to fuel sulfide-based growth. Overall, our results provide an important basis for further probing the functional role of cyc2 and indicate that anoxygenic photoautotrophs in Boreal Shield lakes could have underexplored photophysiology pertinent to understanding Earth's early microbial communities.

Global and local visual processing in autism - a co-twin-control study.

BACKGROUND: Autism Spectrum Disorder (ASD) is associated with altered global and local visual processing. However, the nature of these alterations remains controversial, with contradictory findings and notions ranging from a reduced drive to integrate information into a coherent 'gestalt' ("weak central coherence" = WCC) to an enhanced perceptual functioning (EPF) in local processing. METHODS: This study assessed the association between autism and global/local visual processing, using a large sample of monozygotic (MZ) and dizygotic (DZ) twins (N = 290, 48% females, age = 8-31 years). The Fragmented Pictures Test (FPT) assessed global processing, whereas local processing was estimated with the Embedded Figures Test (EFT) and the Block Design Test (BDT). Autism was assessed both categorically (clinical diagnosis), and dimensionally (autistic traits). Associations between visual tasks and autism were estimated both across the cohort and within-twin pairs where all factors shared between twins are implicitly controlled. RESULTS: Clinical diagnosis and autistic traits predicted a need for more visual information for gestalt processing in the FPT across the cohort. For clinical diagnosis, this association remained within-pairs and at trend-level even within MZ twin pairs alone. ASD and higher autistic traits predicted lower EFT and BDT performance across the cohort, but these associations were lost within-pairs. CONCLUSIONS: In line with the WCC account, our findings indicate an association between autism and reduced global visual processing in children, adolescents and young adults (but no evidence for EPF). Observing a similar association within MZ twins suggests a non-shared environmental contribution.

Social Cognition in Autism and Other Neurodevelopmental Disorders: A Co-twin Control Study.

Alterations in social cognition (SC) are hypothesized to underlie social communication and interaction challenges in autism spectrum disorder (ASD). The aetiological underpinnings driving this association remain unclear. We examined SC in 196 twins with ASD, other neurodevelopmental disorders or typical development using the naturalistic Movie for the Assessment of Social Cognition. Autism and its severity were assessed with the Autism Diagnostic Observation Schedule-2, and autistic traits with the Social Responsiveness Scale-2. Using within twin-pair regression models, controlling for age, sex, IQ, and unmeasured familial confounders such as genetic background and shared-environment, SC correlated with ASD diagnosis, autism severity, and autistic traits. Our findings highlight the importance of SC alterations in autism and suggest a non-shared environmental impact on the association.

Alterations in resting state connectivity along the autism trait continuum: a twin study.

Autism spectrum disorder (ASD) has been found to be associated with alterations in resting state (RS) functional connectivity, including areas forming the default mode network (DMN) and salience network (SN). However, insufficient control for confounding genetic and environmental influences and other methodological issues limit the generalizability of previous findings. Moreover, it has been hypothesized that ASD might be marked by early hyper-connectivity followed by later hypo-connectivity. To date, only a few studies have explicitly tested age-related influences on RS connectivity alterations in ASD. Using a within-twin pair design (N=150 twins; 8-23 years), we examined altered RS connectivity between core regions of the DMN and SN in relation to autistic trait severity and age in a sample of monozygotic (MZ) and dizygotic (DZ) twins showing typical development, ASD or other neurodevelopmental conditions. Connectivity between core regions of the SN was stronger in twins with higher autistic traits compared to their co-twins. This effect was significant both in the total sample and in MZ twins alone, highlighting the effect of non-shared environmental factors on the link between SN-connectivity and autistic traits. While this link was strongest in children, we did not identify differences between age groups for the SN. In contrast, connectivity between core hubs of the DMN was negatively correlated with autistic traits in adolescents and showed a similar trend in adults but not in children. The results support hypotheses of age-dependent altered RS connectivity in ASD, making altered SN and DMN connectivity promising candidate biomarkers for ASD.

Development of a microbial test suite and data integration method for assessing microbial health of contaminated soil.

There is no standard methodology or guideline for assessing soil microbial health for the purposes of contaminant risk assessments. Here we propose a laboratory-based test suite and novel data integration method for evaluating soil microbial health using site-specific contaminated and reference soil. The test suite encompasses experiments for evaluating microbial biomass, activity, and diversity. The results from the tests are then integrated so that a Soil Microbial Health Score (SMHS) may be assigned. This test suite and data integration method was tested on soils from 3 different contaminated sites in Canada. The soil microbial health of a petroleum hydrocarbon (PHC) contaminated site was found to be 'Mildly Impacted' and 'Moderately Impacted' for two soil horizons at a boreal forest site. The soil microbial health of the mixed metal/PHC and mixed metal sites were both found to be 'Not Impacted'. Continued use of this test suite and data integration method will help create guidelines for assessing soil microbial health in ecological risk assessments.

Millions of Boreal Shield Lakes can be used to Probe Archaean Ocean Biogeochemistry.

Life originated in Archaean oceans, almost 4 billion years ago, in the absence of oxygen and the presence of high dissolved iron concentrations. Early Earth oxidation is marked globally by extensive banded iron formations but the contributing processes and timing remain controversial. Very few aquatic habitats have been discovered that match key physico-chemical parameters of the early Archaean Ocean. All previous whole ecosystem Archaean analogue studies have been confined to rare, low sulfur, and permanently stratified lakes. Here we provide first evidence that millions of Boreal Shield lakes with natural anoxia offer the opportunity to constrain biogeochemical and microbiological aspects of early Archaean life. Specifically, we combined novel isotopic signatures and nucleic acid sequence data to examine processes in the anoxic zone of stratified boreal lakes that are naturally low in sulfur and rich in ferrous iron, hallmark characteristics predicted for the Archaean Ocean. Anoxygenic photosynthesis was prominent in total water column biogeochemistry, marked by distinctive patterns in natural abundance isotopes of carbon, nitrogen, and iron. These processes are robust, returning reproducibly after water column re-oxygenation following lake turnover. Evidence of coupled iron oxidation, iron reduction, and methane oxidation affect current paradigms of both early Earth and modern aquatic ecosystems.

Empathy Modulates the Rewarding Effect of Mimicry.

We tend to like those who mimic us. In this study we formally test if mimicry changes the reward value of the mimicker, using gaze bias as a proxy for reward. Previous research has demonstrated that people show gaze bias towards more rewarding targets, suggesting that gaze bias can be considered a proxy for relative reward value. Forty adults participated in a conditioning task, where they were mimicked by one face and 'anti-mimicked' by another. Subsequently, they were found to show gaze-bias towards faces that mimicked them compared to those that did not, in a preferential looking task. The strength of this effect correlated positively with individual levels of trait empathy. In a separate, similar task, these participants showed a gaze bias for faces paired with high vs low monetary rewards, thus validating the use of gaze bias as a proxy for learnt reward. Together, these results demonstrate that mimicry changes the reward value of social stimuli, and empathy influences the extent of this change. This can potentially inform conditions marked by deficits in forming social bonds, such as Autism.

Increasing Levels of Dietary Hempseed Products Leads to Differential Responses in the Fatty Acid Profiles of Egg Yolk, Liver and Plasma of Laying Hens.

The limited efficiency with which dietary alpha-linolenic acid (ALA) is converted by hens into docosahexaenoic acid (DHA) for egg deposition is not clearly understood. In this study, dietary ALA levels were increased via the inclusion of hempseed (HS) and hempseed oil (HO) in hen diets, with the goal of assessing the effects on the fatty acid (FA) profiles of total lipids and lipid classes in yolk, liver and plasma. Forty-eight hens were individually caged and fed one of six diets containing either HS:10, 20 or 30, HO:4.5 or 9.0 (%, diet) or a control (containing corn oil), providing a range (0.1-1.28 %, diet) of ALA. Fatty acid methyl esters of total lipids and lipid classes, including phosphatidyl choline (PtdCho) and ethanolamine (PtdEtn) in yolk, plasma and liver were then determined. Levels of n-3 FAs in both total lipids and lipid classes increased in all tissues. ALA and eicosapentaenoic acid (EPA) increased linearly, while docosapentaenoic acid and DHA increased quadratically. The FA profiles of yolk closely reflected levels in both plasma and liver. While ALA was highly concentrated in the triacylglycerol, it was low but equally distributed between PtdCho and PtdEtn in all tissues; however, the net accumulation was lower (P < 0.0001) in liver compared to yolk and plasma. Levels of EPA and ALA in yolk-PtdEtn were linearly (P < 0.0001; R (2) = 0.93) associated, and reflected those in liver-PtdEtn (P < 0.0001; R (2) = 0.90). In the liver, a strong inverse correlation (P < 0.0001; r = -0.94) between PL-DHA and ALA-to-EPA ratio in PtdEtn supports theories of low substrate availability, possibly limiting the conversion of ALA into DHA for egg enrichment.

Microbial dynamics and properties of aerobic granules developed in a laboratory-scale sequencing batch reactor with an intermediate filamentous bulking stage.

Aerobic granules offer enhanced biological nutrient removal and are compact and dense structures resulting in efficient settling properties. Granule instability, however, is still a challenge as understanding of the drivers of instability is poorly understood. In this study, transient instability of aerobic granules, associated with filamentous outgrowth, was observed in laboratory-scale sequencing batch reactors (SBRs). The transient phase was followed by the formation of stable granules. Loosely bound, dispersed, and pinpoint seed flocs gradually turned into granular flocs within 60 days of SBR operation. In stage 1, the granular flocs were compact in structure and typically 0.2 mm in diameter, with excellent settling properties. Filaments appeared and dominated by stage 2, resulting in poor settleability. By stage 3, the SBRs were selected for larger granules and better settling structures, which included filaments that became enmeshed within the granule, eventually forming structures 2-5 mm in diameter. Corresponding changes in sludge volume index were observed that reflected changes in settleability. The protein-to-polysaccharide ratio in the extracted extracellular polymeric substance (EPS) from stage 1 and stage 3 granules was higher (2.8 and 5.7, respectively), as compared to stage 2 filamentous bulking (1.5). Confocal laser scanning microscopic (CLSM) imaging of the biomass samples, coupled with molecule-specific fluorescent staining, confirmed that protein was predominant in stage 1 and stage 3 granules. During stage 2 bulking, there was a decrease in live cells; dead cells predominated. Denaturing gradient gel electrophoresis (DGGE) fingerprint results indicated a shift in bacterial community composition during granulation, which was confirmed by 16S rRNA gene sequencing. In particular, Janthinobacterium (known denitrifier and producer of antimicrobial pigment) and Auxenochlorella protothecoides (mixotrophic green algae) were predominant during stage 2 bulking. The chitinolytic activity of Chitinophaga is likely antagonistic towards Auxenochlorella and may have contributed to stage 3 stable granule formation. Rhodanobacter, known to support complete denitrification, were predominant in stage 1 and stage 3 granules. The relative abundance of Rhodanobacter coincided with high protein concentrations in EPS, suggesting a role in microbial aggregation and granule formation.

Hempseed Products Fed to Hens Effectively Increased n-3 Polyunsaturated Fatty Acids in Total Lipids, Triacylglycerol and Phospholipid of Egg Yolk.

Hempseed products represent potential alternative feed ingredients for poultry. However, their usage is not currently approved due to a lack of data to support their safety and efficacy. In this regard, the current study was conducted to assess the impact of dietary concentration of hempseed (HS) products and duration of their feeding to hens on the polyunsaturated fatty acid (PUFA) composition of egg yolk lipids. In the current study, 48 Lohmann LSL-Classic hens were individually housed in metabolism cages, in a completely randomized design, and provided one of six diets (wheat-barley-soybean-based) containing either HS (10, 20 and 30 %), hempseed oil (HO; 4.5 and 9.0 %) or no hempseed product (control) over 12 weeks. Increasing alpha-linolenic acid (ALA) intake via increasing dietary hempseed product inclusion, significantly (p < 0.0001) increased the n-3 PUFA contents of yolk total lipid. The values of ALA increased by 12-fold (152 ± 3.56 and 156 ± 2.42 mg/yolk) and docosahexaenoic acid (DHA) by twofold to threefold (41.3 ± 1.57 and 43.6 ± 1.61 mg/yolk) over the control, for the highest levels of HS and HO inclusion, respectively. Increasing levels of hemp products in laying hen diets proved effective in manipulating the fatty acid profile of the total lipid, triacylglycerol (TAG) and total phospholipid (PL) fractions of yolks, enhancing the n-3 fatty acids and reducing the n-6/n-3 ratio. The latter benefit was achieved within 4 weeks of feeding hens either HS- or HO-containing diets.

Performance, egg quality, and blood plasma chemistry of laying hens fed hempseed and hempseed oil.

The aim of this study was to compare the performance of hens (feed intake, rate of lay, egg weight, and BW gain), egg quality and blood biochemistry (enzymes, electrolytes, proteins, and other plasma constituents) of laying hens fed diets containing hemp products. Forty-eight Lohmann LSL-Classic (white-egg layers; 19 wk of age) were individually caged and fed 1 of 6 wheat-barley-soybean-based diets for a period of 12 wk. The diets consisted of hempseed (HS; 10, 20, or 30%), hempseed oil (HO; 4.5 or 9.0%), or a control diet (corn oil-based). All diets were formulated to contain similar levels of crude fat (11%), energy (2,800 kcal/kg), and CP (17%). Data were analyzed as a completely randomized design using the repeated measure analysis of the PROC MIXED procedure of SAS. The results indicated that the inclusion of up to 30 and 9.0% HS and HO, respectively, to diets of laying hens had no significant effects on hen performance, egg quality, or plasma level of metabolites (proteins, glucose, uric acid, and cholesterol) and electrolytes (Na, K, Cl, P, and Ca). Overall plasma enzyme concentrations, particularly gamma-glutamyl transferase, were significantly (P < 0.01) lowest at the 10 and 20% levels of HS inclusion, or at the 4.5% HO level of inclusion of the hempseed products compared with the higher levels or control fed hens. Similar effects were also observed for plasma aspartate aminotransferase levels but with the HS enriched diets only (P < 0.05), particularly being lowest at the inclusion levels of 10 and 20% HS compared with the control. The results may imply a possible protective effect of HS- and HO-containing diets, particularly at 10% HS, 20% HS, and 4.5% HO levels, on liver damage/injury. In summary, both HO and HS appear to be well tolerated by laying hens as judged by markers of plasma clinical chemistry supporting the safety and efficacy of hemp products for use in laying hen rations.

Multisubstrate isotope labeling and metagenomic analysis of active soil bacterial communities.

Soil microbial diversity represents the largest global reservoir of novel microorganisms and enzymes. In this study, we coupled functional metagenomics and DNA stable-isotope probing (DNA-SIP) using multiple plant-derived carbon substrates and diverse soils to characterize active soil bacterial communities and their glycoside hydrolase genes, which have value for industrial applications. We incubated samples from three disparate Canadian soils (tundra, temperate rainforest, and agricultural) with five native carbon ((12)C) or stable-isotope-labeled ((13)C) carbohydrates (glucose, cellobiose, xylose, arabinose, and cellulose). Indicator species analysis revealed high specificity and fidelity for many uncultured and unclassified bacterial taxa in the heavy DNA for all soils and substrates. Among characterized taxa, Actinomycetales (Salinibacterium), Rhizobiales (Devosia), Rhodospirillales (Telmatospirillum), and Caulobacterales (Phenylobacterium and Asticcacaulis) were bacterial indicator species for the heavy substrates and soils tested. Both Actinomycetales and Caulobacterales (Phenylobacterium) were associated with metabolism of cellulose, and Alphaproteobacteria were associated with the metabolism of arabinose; members of the order Rhizobiales were strongly associated with the metabolism of xylose. Annotated metagenomic data suggested diverse glycoside hydrolase gene representation within the pooled heavy DNA. By screening 2,876 cloned fragments derived from the (13)C-labeled DNA isolated from soils incubated with cellulose, we demonstrate the power of combining DNA-SIP, multiple-displacement amplification (MDA), and functional metagenomics by efficiently isolating multiple clones with activity on carboxymethyl cellulose and fluorogenic proxy substrates for carbohydrate-active enzymes. Importance: The ability to identify genes based on function, instead of sequence homology, allows the discovery of genes that would not be identified through sequence alone. This is arguably the most powerful application of metagenomics for the recovery of novel genes and a natural partner of the stable-isotope-probing approach for targeting active-yet-uncultured microorganisms. We expanded on previous efforts to combine stable-isotope probing and metagenomics, enriching microorganisms from multiple soils that were active in degrading plant-derived carbohydrates, followed by construction of a cellulose-based metagenomic library and recovery of glycoside hydrolases through functional metagenomics. The major advance of our study was the discovery of active-yet-uncultivated soil microorganisms and enrichment of their glycoside hydrolases. We recovered positive cosmid clones in a higher frequency than would be expected with direct metagenomic analysis of soil DNA. This study has generated an invaluable metagenomic resource that future research will exploit for genetic and enzymatic potential.

Inside a synesthete's head: a functional connectivity analysis with grapheme-color synesthetes.

Grapheme-color synesthesia is a condition in which letters are perceived with an additional color dimension. To identify brain regions involved in this type of synesthesia and to analyze functional connectivity of these areas, 18 grapheme-color synesthetes and 18 matched controls were stimulated with letters and pseudo-letters presented in black and color in an event-related fMRI experiment. Based on the activation-differences between synesthetes and non-synesthetic controls regions of interest were defined. In a second analysis step functional connectivity was calculated using beta series correlation analysis for these seed regions. First we identified one seed region in the left inferior parietal (IPL) cortex (BA7) showing activation differences between grapheme-color synesthetes and controls. Furthermore, we found activation differences in brain areas involved in processing of letters and pseudo-letters, in particular the right IPL cortex (BA7), but also two more clusters in the right hemispheric BA 18 and BA 40. Functional connectivity analysis revealed an increased connectivity between the left IPL seed region and primary/secondary visual areas (BA 18) in synesthetes. Also the right BA 7 showed a stronger connectivity with primary/secondary visual areas (BA 18) in grapheme-color synesthetes. The results of this study support the idea that the parietal lobe plays an important role in synesthetic experience. The data suggest furthermore that the information flow in grapheme-color synesthetes was already modulated at the level of the primary visual cortex which is different than previously thought. Therefore, the current models of grapheme-color synesthesia have to be refined as the unusual communication flow in synesthetes is not restricted to V4, fusiform cortex and the parietal lobe but rather involves a more extended network.

Disinhibited feedback as a cause of synesthesia: evidence from a functional connectivity study on auditory-visual synesthetes.

In synesthesia, certain stimuli to one sensory modality lead to sensory perception in another unstimulated modality. In addition to other models, a two-stage model is discussed to explain this phenomenon, which combines two previously formulated hypotheses regarding synesthesia: direct cross-activation and hyperbinding. The direct cross-activation model postulates that direct connections between sensory-specific areas are responsible for co-activation and synesthetic perception. The hyperbinding hypothesis suggests that the inducing stimulus and the synesthetic sensation are coupled by a sensory nexus area, which may be located in the parietal cortex. This latter hypothesis is compatible with the disinhibited feedback model, which suggests unusual feedback from multimodal convergence areas as the cause of synesthesia. In this study, the relevance of these models was tested in a group (n=14) of auditory-visual synesthetes by performing a functional connectivity analysis on functional magnetic resonance imaging (fMRI) data. Different simple and complex sounds were used as stimuli, and functionally defined seed areas in the bilateral auditory cortex (AC) and the left inferior parietal cortex (IPC) were used for the connectivity calculations. We found no differences in the connectivity of the AC and the visual areas between synesthetes and controls. The main finding of the study was stronger connectivity of the left IPC with the left primary auditory and right primary visual cortex in the group of auditory-visual synesthetes. The results support the model of disinhibited feedback as a cause of synesthetic perception but do not suggest direct cross-activation.

The neural correlates of coloured music: a functional MRI investigation of auditory-visual synaesthesia.

In auditory-visual synaesthesia, all kinds of sound can induce additional visual experiences. To identify the brain regions mainly involved in this form of synaesthesia, functional magnetic resonance imaging (fMRI) has been used during non-linguistic sound perception (chords and pure tones) in synaesthetes and non-synaesthetes. Synaesthetes showed increased activation in the left inferior parietal cortex (IPC), an area involved in multimodal integration, feature binding and attention guidance. No significant group-differences could be detected in area V4, which is known to be related to colour vision and form processing. The results support the idea of the parietal cortex acting as sensory nexus area in auditory-visual synaesthesia, and as a common neural correlate for different types of synaesthesia.

Natural attenuation of septic system nitrogen by anammox.

On-site disposal of sewage in septic systems can lead to groundwater plumes with NO(3)(-)-N concentrations exceeding the common drinking water limit of 10 mg/L. Currently, denitrification is considered as the principal natural attenuation process. However, at a large seasonal-use septic system in Ontario (256 campsites), a suboxic zone exists where nitrogen removal of up to 80% occurs including removal of NH(4)(+)-N. This zone has both NO(3)(-)-N and NH(4)(+)-N at >5 mg/L each. In the distal NH(4)(+)-rich zone, NH(4)(+)-N concentrations (8.1 ± 8.0 mg/L) are lower than in the proximal zone (48 ± 36 mg/L) and NH(4)(+)-N is isotopically enriched (concentration-weighted mean δ(15)N of +15.7‰) compared to the proximal zone (+7.8‰). Furthermore, δ(15)N-NH(4)(+) isotopic enrichment increases with depth in the distal zone, which is opposite to what would result if nitrification along the water table zone was the mechanism causing NH(4)(+) depletion. Bacterial community composition was assessed with molecular (DNA-based) analysis and demonstrated that groundwater bacterial populations were predominantly composed of bacteria from two Candidatus genera of the Planctomycetales (Brocadia and Jettenia). Together, these data provide strong evidence that anaerobic ammonium oxidation (anammox) plays an important role in nitrogen attenuation at this site.

Open resource metagenomics: a model for sharing metagenomic libraries.

Both sequence-based and activity-based exploitation of environmental DNA have provided unprecedented access to the genomic content of cultivated and uncultivated microorganisms. Although researchers deposit microbial strains in culture collections and DNA sequences in databases, activity-based metagenomic studies typically only publish sequences from the hits retrieved from specific screens. Physical metagenomic libraries, conceptually similar to entire sequence datasets, are usually not straightforward to obtain by interested parties subsequent to publication. In order to facilitate unrestricted distribution of metagenomic libraries, we propose the adoption of open resource metagenomics, in line with the trend towards open access publishing, and similar to culture- and mutant-strain collections that have been the backbone of traditional microbiology and microbial genetics. The concept of open resource metagenomics includes preparation of physical DNA libraries, preferably in versatile vectors that facilitate screening in a diversity of host organisms, and pooling of clones so that single aliquots containing complete libraries can be easily distributed upon request. Database deposition of associated metadata and sequence data for each library provides researchers with information to select the most appropriate libraries for further research projects. As a starting point, we have established the Canadian MetaMicroBiome Library (CM(2)BL [1]). The CM(2)BL is a publicly accessible collection of cosmid libraries containing environmental DNA from soils collected from across Canada, spanning multiple biomes. The libraries were constructed such that the cloned DNA can be easily transferred to Gateway® compliant vectors, facilitating functional screening in virtually any surrogate microbial host for which there are available plasmid vectors. The libraries, which we are placing in the public domain, will be distributed upon request without restriction to members of both the academic research community and industry. This article invites the scientific community to adopt this philosophy of open resource metagenomics to extend the utility of functional metagenomics beyond initial publication, circumventing the need to start from scratch with each new research project.

Diagnostic test results and pathology associated with the 2007 Canadian H7N3 highly pathogenic avian influenza outbreak.

In September 2007, an H7N3 highly pathogenic avian influenza outbreak (HPAI) occurred on a multiple-age broiler breeder operation near Regina Beach, Saskatchewan, Canada. Mortality was initially observed in a barn that housed 24-wk-old roosters, with later involvement of 32-wk-old breeders. All birds on the affected premises were destroyed, and surveillance of surrounding farms demonstrated no further spread. The use of water from a dugout pond during periods of high demand, and the proximity of the farm to Last Mountain Lake, the northern end of which is a bird sanctuary, implicated wild aquatic birds as a possible source of the virus. Of particular note, the H7-specific real-time reverse transcription polymerase chain reaction assay that was in use at the time did not detect the virus associated with this outbreak. A Canadian national influenza A virus survey of wild aquatic birds detected no H7 subtype viruses in 2005 and 2006; however, H7 subtype viruses were detected in the fall of 2007. Phylogenetic analysis of a number of these H7 isolates demonstrated an evolutionary relationship with each other, as well as with the H7N3 HPAI virus that was isolated from the Saskatchewan broiler breeder farm.

Studying possible cross-protection of Canada geese preexposed to North American low pathogenicity avian influenza virus strains (H3N8, H4N6, and H5N2) against an H5N1 highly pathogenic avian influenza challenge.

Highly pathogenic avian influenza (HPAI) H5N1 virus infections have caused unprecedented morbidity and mortality in different species of domestic and wild birds in Asia, Europe, and Africa. In our previous study, we demonstrated the susceptibility and potential epidemiologic importance of H5N1 HPAI virus infections in Canada geese. In this study, we investigated the potential of preexposure with North American lineage H3N8, H4N6, and H5N2 low pathogenicity avian influenza (LPAI) viruses to cross-protect Canada geese against a lethal H5N1 HPAI virus challenge. Based on our results, birds that were primed and boosted with an H5N2 LPAI virus survived a lethal H5N1 challenge. In contrast, only two of five birds from the H3N8 group and none of the birds preexposed to H4N6 survived a lethal H5N1 challenge. In vitro cell proliferation assays demonstrated that peripheral blood mononuclear cells collected from each group were no better stimulated by homologous vs. heterologous antigens.