Characterization of the public transit air microbiome and resistome reveals geographical specificity

BackgroundThe public transit is a built environment with high occupant density across the globe, and identifying factors shaping public transit air microbiomes will help design strategies to minimize the transmission of pathogens. However, the majority of microbiome works dedicated to the public transit air are limited to amplicon sequencing, and our knowledge regarding the functional potentials and the repertoire of resistance genes (i.e. resistome) is limited. Furthermore, current air microbiome investigations on public transit systems are focused on single cities, and a multi-city assessment of the public transit air microbiome will allow a greater understanding of whether and how broad environmental, building, and anthropogenic factors shape the public transit air microbiome in an international scale. Therefore, in this study, the public transit air microbiomes and resistomes of six cities across three continents (Denver, Hong Kong, London, New York City, Oslo, Stockholm) were characterized.ResultsCity was the sole factor associated with public transit air microbiome differences, with diverse taxa identified as drivers for geography-associated functional potentials, concomitant with geographical differences in species- and strain-level inferred growth profiles. Related bacterial strains differed among cities in genes encoding resistance, transposase, and other functions. Sourcetracking estimated that human skin, soil, and wastewater were major presumptive resistome sources of public transit air, and adjacent public transit surfaces may also be considered presumptive sources. Large proportions of detected resistance genes were co-located with mobile genetic elements including plasmids. Biosynthetic gene clusters and city-unique coding sequences were found in the metagenome-assembled genomes.ConclusionsOverall, geographical specificity transcends multiple aspects of the public transit air microbiome, and future efforts on a global scale are warranted to increase our understanding of factors shaping the microbiome of this unique built environment

Migration distance is positively associated with sex-linked genetic diversity in passerine birds

<div><p>A recent comparative analysis of passerine birds found that the frequency of extra-pair paternity was positively associated with neutral genetic diversity. It has been hypothesised that migratory species have more extra-pair paternity than resident species, so we reanalysed the same comparative data set to test whether migration distance could also explain variation in genetic diversity. In this comparative analysis of 19 local populations from 18 passerine species, spanning year-round residents to long-distant migrants, we found that migration distance was positively correlated with sequence diversity at homologous nuclear Z-linked (sex) introns, but not with autosomal intronic diversity. This pattern contrasts with that of extra-pair paternity in the previous study, where extra-pair paternity was positively associated with autosomal diversity and not Z-linked diversity. We discuss several possible explanations for the correlation between Z-linked diversity and migration distance; effects that are specific to sex-linked genetic diversity may occur if migratory behaviour implies different selective regimes in the sexes or affects population structuring. These results suggest that significant amounts of genetic diversity at sex chromosomes and autosomes are shaped by different processes, and should therefore be analysed and interpreted independently in population genetics studies.</p></div

Migrating Lesser Spotted Woodpeckers Dendrocopos minor along the coast of southern Norweay: where do they come from?

The Lesser SpottedWoodpecker (Dendrocopos minor) is a partialmigrant in Fennoscandia, where migratory autumn irruptions outside the regular breeding areas occur in some years. Little is known about themigration of this species along the coast of southern Norway, but such migrants might have an eastern origin. We evaluated this hypothesis, and the possibility that birds come from a more local population, by correlating the numbers ringed at Lista Bird Observatory with breeding-population indices from three regions: Sweden,Møre og Romsdal and Agder. Overall, 99 birds were trapped and ringed at Lista in autumn during 1989–2008 (median = 3.5, range 0–19). We found no correlation between numbers caught at Lista and the population indices fromMøre og Romsdal. There was, however, a significant positive correlation between Lista numbers and the population index from the local Agder region. Breeding-population indices from Sweden were acquired from (1) long-term (1975–2009) summer point counts in observer-chosen routes, and (2) a combination of point counts and line transects along fixed routes systematically distributed across the country (1998–2008). Population trends differed somewhat between these two methods, the latter indicating an increasing population size whereas the former showed a more stable situation. The fixed-routes data were positively correlated with Lista catch numbers, whereas the indices from summer point counts were not. These results suggest that migrating Lesser SpottedWoodpeckers captured in autumn at Lista Bird Observatorymay come from an extensive area in Scandinavia, including more local regions. There was no sex bias in the captured birds, but 98% were in their first year. Hence, migration intensity probably reflects reproductive output in source populations

Sexual selection explains more functional variation in the mammalian major histocompatibility complex than parasitism

Winternitz J, Minchey SG, Garamszegi LZ, Huang S, Stephens PR, Altizer S. Sexual selection explains more functional variation in the mammalian major histocompatibility complex than parasitism. Proceedings of the Royal Society B: Biological Sciences. 2013;280(1769): 20131605.Understanding drivers of genetic diversity at the major histocompatibility complex (MHC) is vitally important for predicting how vertebrate immune defence might respond to future selection pressures and for preserving immunogenetic diversity in declining populations. Parasite-mediated selection is believed to be the major selective force generating MHC polymorphism, and while MHC-based mating preferences also exist for multiple species including humans, the general importance of mate choice is debated. To investigate the contributions of parasitism and sexual selection in explaining among-species variation in MHC diversity, we applied comparative methods and meta-analysis across 112 mammal species, including carnivores, bats, primates, rodents and ungulates. We tested whether MHC diversity increased with parasite richness and relative testes size (as an indicator of the potential for mate choice), while controlling for phylogenetic autocorrelation, neutral mutation rate and confounding ecological variables. We found that MHC nucleotide diversity increased with parasite richness for bats and ungulates but decreased with parasite richness for carnivores. By contrast, nucleotide diversity increased with relative testes size for all taxa. This study provides support for both parasite-mediated and sexual selection in shaping functional MHC polymorphism across mammals, and importantly, suggests that sexual selection could have a more general role than previously thought

Characterization of the public transit air microbiome and resistome reveals geographical specificity

BACKGROUND: The public transit is a built environment with high occupant density across the globe, and identifying factors shaping public transit air microbiomes will help design strategies to minimize the transmission of pathogens. However, the majority of microbiome works dedicated to the public transit air are limited to amplicon sequencing, and our knowledge regarding the functional potentials and the repertoire of resistance genes (i.e. resistome) is limited. Furthermore, current air microbiome investigations on public transit systems are focused on single cities, and a multi-city assessment of the public transit air microbiome will allow a greater understanding of whether and how broad environmental, building, and anthropogenic factors shape the public transit air microbiome in an international scale. Therefore, in this study, the public transit air microbiomes and resistomes of six cities across three continents (Denver, Hong Kong, London, New York City, Oslo, Stockholm) were characterized. RESULTS: City was the sole factor associated with public transit air microbiome differences, with diverse taxa identified as drivers for geography-associated functional potentials, concomitant with geographical differences in species- and strain-level inferred growth profiles. Related bacterial strains differed among cities in genes encoding resistance, transposase, and other functions. Sourcetracking estimated that human skin, soil, and wastewater were major presumptive resistome sources of public transit air, and adjacent public transit surfaces may also be considered presumptive sources. Large proportions of detected resistance genes were co-located with mobile genetic elements including plasmids. Biosynthetic gene clusters and city-unique coding sequences were found in the metagenome-assembled genomes. CONCLUSIONS: Overall, geographical specificity transcends multiple aspects of the public transit air microbiome, and future efforts on a global scale are warranted to increase our understanding of factors shaping the microbiome of this unique built environment