Livestock microbial landscape patterns: Retail poultry microbiomes significantly vary by region and season.

Microbes play key roles in animal welfare and food safety but there is little understanding of whether microbiomes associated with livestock vary in space and time. Here we analysed the bacteria associated with the carcasses of the same breed of 28 poultry broiler flocks at different stages of processing across two climatically similar UK regions over two seasons with 16S metabarcode DNA sequencing. Numbers of taxa types did not differ by region, but did by season (P = 1.2 × 10-19), and numbers increased with factory processing, especially in summer. There was also a significant (P < 1 × 10-4) difference in the presences and abundances of taxa types by season, region and factory processing stage, and the signal for seasonal and regional differences remained highly significant on final retail products. This study therefore revealed that both season and region influence the types and abundances of taxa on retail poultry products. That poultry microbiomes differ in space and time should be considered when testing the efficacy of microbial management interventions designed to increase animal welfare and food safety: these may have differential effects on livestock depending on location and timing.

Separate and combined Hanseniaspora uvarum and Metschnikowia pulcherrima metabolic volatiles are attractive to Drosophila suzukii in the laboratory and field.

Drosophila suzukii flies cause economic losses to fruit crops globally. Previous work shows various Drosophila species are attracted to volatile metabolites produced by individual fruit associated yeast isolates, but fruits naturally harbour a rich diversity of yeast species. Here, we report the relative attractiveness of D. suzukii to yeasts presented individually or in combinations using laboratory preference tests and field trapping data. Laboratory trials revealed four of 12 single yeast isolates were attractive to D. suzukii, of which Metschnikowia pulcherrima and Hanseniaspora uvarum were also attractive in field trials. Four out of 10 yeast combinations involving Candida zemplinina, Pichia pijperi, M. pulcherrima and H. uvarum were attractive in the laboratory. Whilst a combination of M. pulcherrima + H. uvarum trapped the greatest number of D. suzukii in the field, the efficacy of the M. pulcherrima + H. uvarum combination to trap D. suzukii was not significantly greater than traps primed with volatiles from only H. uvarum. While volatiles from isolates of M. pulcherrima and H. uvarum show promise as baits for D. suzukii, further research is needed to ascertain how and why flies are attracted to certain baits to optimise control efficacy.

Outcrossed sex allows a selfish gene to invade yeast populations.

Homing endonuclease genes (HEGs) in eukaryotes are optional genes that have no obvious effect on host phenotype except for causing chromosomes not containing a copy of the gene to be cut, thus causing them to be inherited at a greater than Mendelian rate via gene conversion. These genes are therefore expected to increase in frequency in outcrossed populations, but not in obligately selfed populations. In order to test this idea, we compared the dynamics of the VDE HEG in six replicate outcrossed and inbred populations of yeast (Saccharomyces cerevisiae). VDE increased in frequency from 0.21 to 0.55 in four outcrossed generations, but showed no change in frequency in the inbred populations. The absence of change in the inbred populations indicates that any effect of VDE on mitotic replication rates is less than 1%. The data from the outcrossed populations best fit a model in which 82% of individuals are derived from outcrossing and VDE is inherited by 74% of the meiotic products from heterozygotes (as compared with 50% for Mendelian genes). These results empirically demonstrate how a host mating system plays a key role in determining the population dynamics of a selfish gene.

Recurrent invasion and extinction of a selfish gene.

Homing endonuclease genes show super-Mendelian inheritance, which allows them to spread in populations even when they are of no benefit to the host organism. To test the idea that regular horizontal transmission is necessary for the long-term persistence of these genes, we surveyed 20 species of yeasts for the omega-homing endonuclease gene and associated group I intron. The status of omega could be categorized into three states (functional, nonfunctional, or absent), and status was not clustered on the host phylogeny. Moreover, the phylogeny of omega differed significantly from that of the host, strong evidence of horizontal transmission. Further analyses indicate that horizontal transmission is more common than transposition, and that it occurs preferentially between closely related species. Parsimony analysis and coalescent theory suggest that there have been 15 horizontal transmission events in the ancestry of our yeast species, through simulations indicate that this value is probably an underestimate. Overall, the data support a cyclical model of invasion, degeneration, and loss, followed by reinvasion, and each of these transitions is estimated to occur about once every 2 million years. The data are thus consistent with the idea that frequent horizontal transmission is necessary for the long-term persistence of homing endonuclease genes, and further, that this requirement limits these genes to organisms with easily accessible germ lines. The data also show that mitochondrial DNA sequences are transferred intact between yeast species; if other genes do not show such high levels of horizontal transmission, it would be due to lack of selection, rather than lack of opportunity.

The detection of rotaviruses in products of wastewater treatment.

Rotaviruses present in products of wastewater treatment were assayed in MA104 cells by indirect immunofluorescence. Levels in settled sewage, activated sludge and effluent were greater than 10(3) per litre in March and April but virus was not detected during later months. This pattern correlated with the decline in laboratory reports of human rotavirus infection.

Isolation of indigenous enteroviruses from chemically treated and dewatered sludge samples.

Samples of wastewater sludge were examined for infectious enteroviruses before and after they had been chemically conditioned and dewatered. The least virus was recovered from the cake produced by filter pressing of sludge, which had a greatly increased solids content (39 to 45% [wt/vol]) relative to the untreated sludge (4.2 to 6.2% [wt/vol]) and in one plant was at pH 11 due to the lime conditioner used. Conditioning with a cationic polyelectrolyte before dewatering by centrifugation produced a watery sludge (2.7 to 5.3% [wt/vol]) from which high titers of infectious virus were recovered which were often greater than those isolated from the untreated sludge (0.6 to 1.4% [wt/vol]). This was thought to be due to saturation of virus and sludge floc adsorption sites by the polyelectrolyte, resulting in the liberation of virions from the sludge solids.

Recovery of indigenous enteroviruses from raw and digested sewage sludges.

We examined different types of raw sewage sludge treatment, including consolidation, anaerobic mesophilic digestion with subsequent consolidation, and aerobic-thermophilic digestion. Of these, the most efficient reduction in infectious virus titer was achieved by mesophilic digestion with subsequent consolidation, although a pilot-scale aerobic-thermophilic digester was extremely time effective, producing sludges with similarly low virus titers in a small fraction of the time. Although none of the treatments examined consistently produced a sludge with undetectable virus levels, mesophilic digestion alone was found to be particularly unreliable in reducing the levels of infectious virus present in the raw sludge.