In-depth assessment of microbial communities in the full-scale vertical flow treatment wetlands fed with raw domestic wastewater.

A multiphase study was proposed to examine microbial communities linked to the nitrogen cycle in the first stage of four full-scale French vertical flow treatment systems. To this end, denaturing gradient gel electrophoresis (DGGE) was performed for structural assessment and quantitative PCR (qPCR) to enumerate the abundance of ammonia-oxidizing (AOB). 16S rRNA sequencing was used to assess the taxonomic profile followed by putative assessment of functional genes. The samples were collected under different conditions, such as operational time (presence/absence of sludge layer on the surface of the filters), season (winter and summer), sampling depth (0, 15 and 30 cm) and operation cycle (rest and feed periods). A structural disparity was noted in the upper layers, whereas higher similarity at 30 cm was observed highlighting the effect of organic matter on bacterial diversity. The 7th rest day was highlighted by an apparent decline in the microbial community abundance. Additionally, qPCR indicated that the largest amount of AOB was found at 30 cm depth and during the feeding period. From the taxonomic profile, Mycobacterium, Acinetobacter, Flavobacterium, and Nitrospira were the most abundant genre found in all systems. The functional prediction results showed predicted genes linked to the denitrification process. The results suggested that operating time and season were responsible for the pattern of the microbial community behavior. This study allowed us to further understand the bacterial dynamics and to advance the idea of design modifications made in the first stage of the classical French system to improve nitrogen removal are promising.

Whole transcriptome analysis of the pectoralis major muscle reveals molecular mechanisms involved with white striping in broiler chickens.

White striping (WS) is one of the most common myopathies identified in broiler chickens leading to substantial production losses, where the incidence reaches 12% in commercial chickens. It occurs primarily in heavier chickens being a modification of the breast muscle characterized by the presence of pale parallel streaks in the same orientation of the muscle fibers. Since the WS etiology remains unclear, we aimed to identify the biological and genetic mechanisms involved in its occurrence through the whole transcriptome analysis of WS in affected and unaffected chicken breast muscles. A total of 11,177 genes were expressed in the pectoralis major muscle. Out of those, 1,441 genes were differentially expressed (FDR ≤ 0.01) between the two analyzed groups, being, respectively, 772 genes upregulated and 669 downregulated in the WS affected group. A total of 36 significantly overrepresented GO terms related to WS myopathy were enriched, and the most relevant biological processes were activation of immune system, angiogenesis, hypoxia, cell death, and striated muscle contraction. The unbalance of those biological processes may trigger the occurrence of the WS phenotype in broilers. The possible lack of capillary blood supply homogeneously in the muscle triggers the hypoxia, following the activation of glycolysis, calcium signaling and apoptosis related genes facilitating the tissue damage and WS incidence.

Bacterial community diversity in a full scale biofilter treating wastewater odor.

Constantly, the odors coming from sewage plants are considered a problem by the population. The purpose of this study was to evaluate the microbial community present in a full scale biofilter used for odor treatment. The filter was packed with peat. The main gas treated was hydrogen sulphide (H2S). The removal efficiency reached 99%, with an empty bed residence time of 30 seconds. Molecular analysis can enhance our understanding of the microbial communities in biofilters treating wastewater odor. The analysis made to characterize microbial community was High-throughput 16S rRNA sequencing analysis MiSeq® Illumina. The sampling, carried out in the year 2015, was seasonal (summer and winter) and spatial (depth and position in the biofilter). In this study, a total of 206,174 raw sequence reads for six samples were analyzed using Mothur software (v 1.33.3) based on MiSeq SOP protocol. After Mothur analysis, the results of the bacterial community were explored at the Phylum and Genus levels. In this study, the efficiency removal of hydrogen sulfide reached values greater than 99% during the monitoring, and the main bacterial genera found were Acidotermus, Telmatobacter, Methylovirgula and Bryobacter representing the bacterial community active in the transformation of H2S into a system with long operating time.

Relationship of runs of homozygosity with adaptive and production traits in a paternal broiler line.

Genomic regions under high selective pressure present specific runs of homozygosity (ROH), which provide valuable information on the genetic mechanisms underlying the adaptation to environment imposed challenges. In broiler chickens, the adaptation to conventional production systems in tropical environments lead the animals with favorable genotypes to be naturally selected, increasing the frequency of these alleles in the next generations. In this study, ~1400 chickens from a paternal broiler line were genotyped with the 600 K Affymetrix® Axiom® high-density (HD) genotyping array for estimation of linkage disequilibrium (LD), effective population size (N e ), inbreeding and ROH. The average LD between adjacent single nucleotide polymorphisms (SNPs) in all autosomes was 0.37, and the LD decay was higher in microchromosomes followed by intermediate and macrochromosomes. The N e of the ancestral population was high and declined over time maintaining a sufficient number of animals to keep the inbreeding coefficient of this population at low levels. The ROH analysis revealed genomic regions that harbor genes associated with homeostasis maintenance and immune system mechanisms, which may have been selected in response to heat stress. Our results give a comprehensive insight into the relationship between shared ROH regions and putative regions related to survival and production traits in a paternal broiler line selected for over 20 years. These findings contribute to the understanding of the effects of environmental and artificial selection in shaping the distribution of functional variants in the chicken genome.

Genome-wide association study of periweaning failure-to-thrive syndrome (PFTS) in pigs.

Porcine periweaning-failure-to-thrive syndrome (PFTS) is a condition that affects newly weaned piglets. It is characterised by a progressive debilitation leading to death, in the absence of infectious, nutritional, management or environmental factors. In this study, we present the first report of PFTS in South America and the results of a genome-wide association study to identify the genetic markers associated with the appearance of this condition in a crossbred swine population. Four chromosomal regions were associated with PFTS predisposition, one located on SSCX, one on SSC8, and the two other regions on SSC14. Regions on SSC8 and SSC14 harbour important functional candidate genes involved in human depression and might have an important role in PFTS. Our findings contribute to the increasing knowledge about this syndrome, which has been investigated since 2007, and to the identification of the aetiology of this disease.

Comparison of iterated single-step and Bayesian regressions on genomic evaluations for age at 100 kg in swine.

The effects of modified single-step genomic best linear unbiased prediction (ssGBLUP) iterations on GEBV and SNP were investigated using 85,388 age at 100 kg phenotypes from the BRF SA breeding program Landrace pure line animals, off-tested between 2002 and 2013. Pedigree data comprised animals born between 1999 and 2013. A total of 1,068 animals were assigned to the training population, in which all of them had genotypes, original and corrected age at 100 kg phenotypes, and weighted deregressed proof records. A total of 100 genotyped animals, with high accuracy age at 100 kg estimated breeding values, were assigned to the validation population. After applying the quality control workflow, a set of 41,042 SNP was used for the analysis. Standard and modified ssGBLUP, BayesCπ, and Bayesian Lasso were compared, and their predictive abilities were accessed by approximate true and GEBV correlations. Modified ssGBLUP iteration effects on SNP estimates and GEBV were relevant, in which assigned differential weights and shrinkage caused important losses on ssGBLUP predictive ability for age at 100 kg GEBV. Even though ssGBLUP accuracy can be equal or better than the compared Bayesian methods, additional gains can be obtained by correctly identifying the number of iterations required for best ssGBLUP performance.

Optimal clone identifier for genomic shotgun libraries: "OC Identifier tool".

In DNA microarray experiments, the gene fragments that are spotted on the slides are usually obtained by the synthesis of specific oligonucleotides that are able to amplify genes through PCR. Shotgun library sequences are an alternative to synthesis of primers for the study of each gene in the genome. The possibility of putting thousands of gene sequences into a single slide allows the use of shotgun clones in order to proceed with microarray analysis without a completely sequenced genome. We developed an OC Identifier tool (optimal clone identifier for genomic shotgun libraries) for the identification of unique genes in shotgun libraries based on a partially sequenced genome; this allows simultaneous use of clones in projects such as transcriptome and phylogeny studies, using comparative genomic hybridization and genome assembly. The OC Identifier tool allows comparative genome analysis, biological databases, query language in relational databases, and provides bioinformatics tools to identify clones that contain unique genes as alternatives to primer synthesis. The OC Identifier allows analysis of clones during the sequencing phase, making it possible to select genes of interest for construction of a DNA microarray.

Optimal clone identifier for genomic shotgun libraries: "OC Identifier tool"

In DNA microarray experiments, the gene fragments that are spotted on the slides are usually obtained by the synthesis of specific oligonucleotides that are able to amplify genes through PCR. Shotgun library sequences are an alternative to synthesis of primers for the study of each gene in the genome. The possibility of putting thousands of gene sequences into a single slide allows the use of shotgun clones in order to proceed with microarray analysis without a completely sequenced genome. We developed an OC Identifier tool (optimal clone identifier for genomic shotgun libraries) for the identification of unique genes in shotgun libraries based on a partially sequenced genome; this allows simultaneous use of clones in projects such as transcriptome and phylogeny studies, using comparative genomic hybridization and genome assembly. The OC Identifier tool allows comparative genome analysis, biological databases, query language in relational databases, and provides bioinformatics tools to identify clones that contain unique genes as alternatives to primer synthesis. The OC Identifier allows analysis of clones during the sequencing phase, making it possible to select genes of interest for construction of a DNA microarray.