Exposure to crop production alters cecal prokaryotic microbiota, inflates virulome and resistome in wild prairie grouse.

Chemically intensive crop production depletes wildlife food resources, hinders animal development, health, survival, and reproduction, and it suppresses wildlife immune systems, facilitating emergence of infectious diseases with excessive mortality rates. Gut microbiota is crucial for wildlife's response to environmental stressors. Its composition and functionality are sensitive to diet changes and environmental pollution associated with modern crop production. In this study we use shotgun metagenomics (median 8,326,092 sequences/sample) to demonstrate that exposure to modern crop production detrimentally affects cecal microbiota of sharp-tailed grouse (Tympanuchus phasianellus: 9 exposed, 18 unexposed and greater prairie chickens (T. cupido; 11, 11). Exposure to crop production had greater effect on microbiota richness (t = 6.675, P < 0.001) and composition (PERMANOVA r2 = 0.212, P = 0.001) than did the host species (t = 4.762, P < 0.001; r2 = 0.070, P = 0.001) or their interaction (t = 3.449; r2 = 0.072, both P = 0.001), whereas sex and age had no effect. Although microbiota richness was greater in exposed (T. cupido chao1 = 152.8 ± 20.5; T. phasianellus 115.3 ± 17.1) than in unexposed (102.9 ± 15.1 and 101.1 ± 17.2, respectively) birds, some beneficial bacteria dropped out of exposed birds' microbiota or declined and were replaced by potential pathogens. Exposed birds also had higher richness and load of virulome (mean ± standard deviation; T. cupido 24.8 ± 10.0 and 10.1 ± 5.5, respectively; T. phasianellus 13.4 ± 6.8/4.9 ± 2.8) and resistome (T. cupido 46.8 ± 11.7/28.9 ± 10.2, T. phasianellus 38.3 ± 16.7/18.9 ± 14.2) than unexposed birds (T. cupido virulome: 14.2 ± 13.5, 4.5 ± 4.2; T. cupido resistome: 31.6 ± 20.2 and 13.1 ± 12.0; T. phasianellus virulome: 5.2 ± 4.7 and 1.4 ± 1.5; T. phasianellus resistome: 13.7 ± 16.1 and 4.0 ± 6.4).

Does solar irradiation drive community assembly of vulture plumage microbiotas?

BACKGROUND: Stereotyped sunning behaviour in birds has been hypothesized to inhibit keratin-degrading bacteria but there is little evidence that solar irradiation affects community assembly and abundance of plumage microbiota. The monophyletic New World vultures (Cathartiformes) are renowned for scavenging vertebrate carrion, spread-wing sunning at roosts, and thermal soaring. Few avian species experience greater exposure to solar irradiation. We used 16S rRNA sequencing to investigate the plumage microbiota of wild individuals of five sympatric species of vultures in Guyana. RESULTS: The exceptionally diverse plumage microbiotas (631 genera of Bacteria and Archaea) were numerically dominated by bacterial genera resistant to ultraviolet (UV) light, desiccation, and high ambient temperatures, and genera known for forming desiccation-resistant endospores (phylum Firmicutes, order Clostridiales). The extremophile genera Deinococcus (phylum Deinococcus-Thermus) and Hymenobacter (phylum, Bacteroidetes), rare in vertebrate gut microbiotas, accounted for 9.1% of 2.7 million sequences (CSS normalized and log2 transformed). Five bacterial genera known to exhibit strong keratinolytic capacities in vitro (Bacillus, Enterococcus, Pseudomonas, Staphylococcus, and Streptomyces) were less abundant (totaling 4%) in vulture plumage. CONCLUSIONS: Bacterial rank-abundance profiles from melanized vulture plumage have no known analog in the integumentary systems of terrestrial vertebrates. The prominence of UV-resistant extremophiles suggests that solar irradiation may play a significant role in the assembly of vulture plumage microbiotas. Our results highlight the need for controlled in vivo experiments to test the effects of UV on microbial communities of avian plumage.

Distinct microbiotas of anatomical gut regions display idiosyncratic seasonal variation in an avian folivore.

BACKGROUND: Current knowledge about seasonal variation in the gut microbiota of vertebrates is limited to a few studies based on mammalian fecal samples. Seasonal changes in the microbiotas of functionally distinct gut regions remain unexplored. We investigated seasonal variation (summer versus winter) and regionalization of the microbiotas of the crop, ventriculus, duodenum, cecum, and colon of the greater sage-grouse (Centrocercus urophasianus), an avian folivore specialized on the toxic foliage of sagebrush (Artemesia spp.) in western North America. RESULTS: We sequenced the V4 region of the 16S rRNA gene on an Illumina MiSeq and obtained 6,639,051 sequences with a median of 50,232 per sample. These sequences were assigned to 457 bacterial and 4 archaeal OTUs. Firmicutes (53.0%), Bacteroidetes (15.2%), Actinobacteria (10.7%), and Proteobacteria (10.1%)were the most abundant and diverse phyla. Microbial composition and richness showed significant differences among gut regions and between summer and winter. Gut region explained almost an order of magnitude more variance in our dataset than did season or the gut region × season interaction. The effect of season was uneven among gut regions. Microbiotas of the crop and cecum showed the greatest seasonal differences. CONCLUSIONS: Our data suggest that seasonal differences in gut microbiota reflect seasonal variation in the microbial communities associated with food and water. Strong differentiation and uneven seasonal changes in the composition and richness of the microbiota among functionally distinct gut regions demonstrate the necessity of wider anatomical sampling for studies of composition and dynamics of the gut microbiota.

Combined description (morphology with DNA barcode data) of a new quill mite Torotrogla paenae n. sp. (Acariformes: Syringophilidae) parasitising the Kalahari scrub-robin Cercotrichas paena (Smith) (Passeriformes: Muscicapidae) in Namibia.

A new quill mite species Torotrogla paenae n. sp. (Acariformes: Syringophilidae) parasitising the Kalahari scrub-robin Cercotrichas paena (Smith) (Passeriformes: Muscicapidae) in Namibia is described based on the external morphology and DNA barcode data (the mitochondrial cytochrome c oxidase subunit 1 sequences, cox1). Females of T. paenae n. sp. morphologically differ from the most similar species T. lusciniae Skoracki, 2004 by the total body length (780-830 vs 645-715 µm in T. lusciniae) and the presence of hysteronotal shields (vs absence), apunctate propodonotal and pygidial shields (vs punctate), apunctate coxal fields (vs punctate), the fan-like setae p' and p" of legs III-IV provided with c.10 tines (vs 14-15) and the length of setae si (140-180 vs 190-210 µm) and se (160-185 vs 210-225 µm). The male of T. paenae n. sp. morphologically differs from T. lusciniae by the lateral branch of peritremes composed of 4 chambers (vs 7-8 chambers) and lengths of setae ve (45 vs 70-75 µm) and se (120 vs 165 µm).

New taxa of the subfamily Picobiinae (Cheyletoidea: Syringophilidae) parasitizing antbirds and gnateaters (Passeriformes: Thamnophilidae, Conopophagidae) in Guyana.

A new genus and three new species of the picobiin quill mites (Cheyletoidea: Syringophilidae) are described from passeriform birds in Guyana, Phipicobia pygiptilae gen. nov. and sp. nov. parasitizing Pygiptila stellaris (Spix) (Thamnophilidae), Rafapicobia thamnophili sp. nov. from Thamnophilus insignis Salvin et Godman (type host), Myrmoborus leucophrys (Tschudi), Myrmeciza ferruginea (St. Müller), Myrmotherula longipennis Pelzeln, and Hypocnemis cantator (Boddaert) (Thamnophilidae), and Rafapicobia milenskyi sp. nov. from Conopophaga aurita (Gmelin) (Conopophagidae).

New quill mites (Cheyletoidea: Syringophilidae) parasitizing the black-headed paradise-flycatcher Terpsiphone rufiventer (Passeriformes: Monarchidae) in Gabon.

A new genus of quill mites (Cheyletoidea: Syringophilidae) and two new species Pipicobia terpsiphoni gen. nov. and sp. nov. and Syringophiloidus furthi sp. nov. parasitizing the black-headed paradise-flycatcher Terpsiphone rufiventer (Swainson) (Passeriformes: Monarchidae) in Gabon are described. Three species of the Neopicobia Skoracki, 2011 are moved to the newly established genus: Pipicobia locustella (Skoracki, Bochkov and Wauthy, 2004) comb. nov., Pipicobia pyrrholaemus (Skoracki and Glowska, 2008) comb.nov., and Pipicobia glossopsitta (Skoracki, Glowska and Sikora, 2008) comb.nov. Syringophilids are recorded on hosts of the family Monarchidae and in Gabon for the first time. A key to the genera of the subfamily Picobiinae is proposed.

Ecomorphology of eye shape and retinal topography in waterfowl (Aves: Anseriformes: Anatidae) with different foraging modes.

Despite the large body of literature on ecomorphological adaptations to foraging in waterfowl, little attention has been paid to their sensory systems, especially vision. Here, we compare eye shape and retinal topography across 12 species representing 4 different foraging modes. Eye shape was significantly different among foraging modes, with diving and pursuit-diving species having relatively smaller corneal diameters compared to non-diving species. This may be associated with differences in ambient light intensity while foraging or an ability to tightly constrict the pupil in divers in order to facilitate underwater vision. Retinal topography was similar across all species, consisting of an oblique visual streak, a central area of peak cell density, and no discernible fovea. Because the bill faces downwards when the head is held in the normal posture in waterfowl, the visual streak will be held horizontally, allowing the horizon to be sampled with higher visual acuity. Estimates of spatial resolving power were similar among species with only the Canada goose having a higher spatial resolution. Overall, we found no evidence of ecomorphological adaptations to different foraging modes in the retinal ganglion cell layer in waterfowl. Rather, retinal topography in these birds seems to reflect the 'openness' of their habitats.

Host associations and evolutionary relationships of avian blood parasites from West Africa.

The host specificity of blood parasites recovered from a survey of 527 birds in Cameroon and Gabon was examined at several levels within an evolutionary framework. Unique mitochondrial lineages of Haemoproteus were recovered from an average of 1.3 host species (maximum=3) and 1.2 host families (maximum=3) while lineages of Plasmodium were recovered from an average of 2.5 species (maximum=27) and 1.6 families (maximum=9). Averaged within genera, lineages of both Plasmodium and Haemoproteus were constrained in their host distribution relative to random expectations. However, while several individual lineages within both genera exhibited significant host constraint, host breadth varied widely among related lineages, particularly within the genus Plasmodium. Several lineages of Plasmodium exhibited extreme generalist host-parasitism strategies while other lineages appeared to have been constrained to certain host families over recent evolutionary history. Sequence data from two nuclear genes recovered from a limited sample of Plasmodium parasites indicated that, at the resolution of this study, inferences regarding host breadth were unlikely to be grossly affected by the use of parasite mitochondrial lineages as a proxy for biological species. The use of divergent host-parasitism strategies among closely related parasite lineages suggests that host range is a relatively labile character. Since host specificity may also influence parasite virulence, these results argue for considering the impact of haematozoa on avian hosts on a lineage-specific basis.