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).

Avian surveys near Camp Lemonnier and Day Forest, Djibouti, Africa

Two brief biodiversity surveys were conducted near Camp Lemonnier, Djibouti, in May 2014 and February 2016,&nbsp;and to the Day Forest (For&ecirc;t du Day) in February 2016. Our complete avian checklist of 143 species, with 96 species&nbsp;preserved as museum specimens is presented here. We document nesting for Spur-winged Lapwing Vanellus spinosus&nbsp;(Linnaeus, 1758), the occurrence of Crimson-rumped Waxbill Estrilda rhodopyga Sundevall, 1850, and confirm&nbsp;Little Tern Sternula albifrons (Pallas, 1764) in Djibouti. We comment on observations for the Critically Endangered&nbsp;Djibouti Spurfowl Pternistis ochropectus (Dorst &amp; Jouanin 1952), and the Endangered Egyptian Vulture Neophron&nbsp;percnopterus (Linnaeus, 1758), and a previously noted Fringillidae (Crithagra sp.) Swainson, 1827 from the Day&nbsp;Forest. Hybridization between Somali Sparrow Passer castanopterus Blythi,1885 and House Sparrow Passer domesticus&nbsp;(Linnaeus, 1758) is documented with voucher specimens. Although these surveys and taxa lists represent brief&nbsp;inventories for the areas visited, they provide a foundation and reference for future work in this understudied region&nbsp;in the Horn of Africa.

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.

Electronic supplementary material

The online version of this article (10.1186/s42523-019-0002-6) contains supplementary material, which is available to authorized users.

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).

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.

Antithrombin III deficiency in neonatal respiratory distress syndrome

Neonatal respiratory distress syndrome (RDS) is an acute lung injury believed to result primarily from surfactant deficiency in the immature lung. Although surfactant replacement therapy has improved the outcome of this disease, RDS remains a major cause of neonatal mortality and morbidity. Preliminary experimental evidence suggests that unopposed intravascular thrombin activity may contribute to the progression of RDS by promoting high permeability pulmonary oedema and pulmonary hypertension. In the extravascular lung compartment, polymerizing fibrin may inhibit surfactant function. In addition, interstitial and alveolar thrombin formation and resulting fibrin deposition may contribute to the development of chronic lung disease through amplification of inflammation and fibrosis. There is good evidence that extravascular coagulation occurs during the course of RDS. Fibrin is a major component of the hyaline membranes, which are a hallmark of acute lung injury, and which can be regarded as locally produced clots. It has been less certain whether neonatal RDS is also associated with intravascular activation of the coagulation system. Although low levels of antithrombin III (AT III) have been reported in infants with RDS, direct evidence of increased intravascular thrombin formation has been lacking. However, recently, plasma concentrations of thrombin-antithrombin III (TAT) complexes have been measured in infants with RDS and correlated with RDS severity. TAT formation was significantly increased in severe neonatal RDS, while free AT III activity was decreased. These data are consistent with increased thrombin generation and resulting AT III consumption. Therefore, to regulate thrombin activity, infants with severe RDS may benefit from replacement therapy with AT III concentrate. This hypothesis has been strengthened by experiments that have demonstrated the efficacy of thrombin inhibition in several animal models of acute lung injury. However, controlled clinical trials will be required to determine whether thrombin is just a coincidental marker of neonatal RDS, or whether unopposed thrombin activity exacerbates the disease process.

Coagulation screening tests in high risk neonates: a prospective cohort study

Forty seven infants in a prospective cohort of 170 high risk neonates without signs of overt bleeding had abnormal coagulation screening tests within 36 hours of birth. Early thrombocytopenia was a better predictor of prolonged prothrombin times and hypofibrinogenemia than very low birth weight, fetal growth retardation, or poor five minute Apgar scores.

An endemic strain of Staphylococcus haemolyticus colonizing and causing bacteremia in neonatal intensive care unit patients

Coagulase-negative staphylococci are now the major cause of bacteremia in neonatal intensive care units. To date, coagulase-negative staphylococci causing neonatal infections have been found to be distinct when typed by standard techniques. To determine whether or not an endemic strain could be identified using more discriminatory techniques, we characterized coagulase-negative staphylococci isolates obtained from a prospective study of coagulase-negative staphylococci bacteremia in a neonatal intensive care unit during 1984 through 1985, by standard techniques supplemented with DNA-DNA hybridization and restriction endonuclease analysis. We typed 58 strains that were isolated from 52 episodes of bacteremia in 38 neonates. There were 46 isolates of Staphylococcus epidermidis. Three pairs of strains were identical, and each strain was from a different patient. There were 12 isolates of Staphylococcus haemolyticus. Ten were identical, referred to as strain TOR-35, and had been isolated from eight different infants. Characterization of strains obtained in 1986 from a prospective study of coagulase-negative staphylococci-colonizing neonates admitted to the same neonatal intensive care unit found the TOR-35 strain had colonized 6 of 17 neonates by day seven. A point prevalence survey of all neonates in the same neonatal intensive care unit in 1990 found 5 of 30 neonates to be colonized with the TOR-35 strain. Therefore, we were able to identify an endemic strain of S haemolyticus that caused multiple episodes of bacteremia during a 6-month period and remained present in the same environment for a 5-year period.

Low antithrombin III in neonatal shock: DIC or non-specific protein depletion?

Low antithrombin III (AT III) levels in shock are usually ascribed to disseminated intravascular coagulation (DIC). However, decreased activities of clotting factors and their inhibitors could reflect a generalised fall in plasma proteins rather than DIC. AT III and albumin were compared in 48 asphyxiated and non-asphyxiated newborn rabbits (pH 6.70-7.30). Both AT III and albumin were markedly decreased in the sickest animals and there was a direct linear relationship between the two proteins (P less than 0.001). Similar results were obtained in ten newborn infants suffering from shock and haemorrhagic diathesis. In all cases AT III and albumin were decreased below the normal range and significantly correlated (P less than 0.01). Our findings suggest that AT III is not a useful diagnostic marker of DIC. Further, a similar fall of clottable and non-clottable proteins in shock questions the general assumption that the ensuing coagulopathy is due to intravascular coagulation.