Amplification success of multilocus genotypes from feathers found in the field compared with feathers obtained from shot birds

Effective DNA extraction methods from bird feathers have facilitated non‐invasive sampling, leading to the suggestion that feathers are a great source for genetic studies. However, few studies have assessed whether all feathers can be used or provide equal numbers of useful templates. In this study, feathers collected in various ways from Red Grouse Lagopus lagopus were examined to establish the quality of DNA extracted. Individual samples were classified into two categories according to whether they were collected from shot birds or found in the field. DNA was extracted from all samples and genotyped at 19 microsatellite loci. PCR products were analysed on a MegaBACE 1000. A total of 93% of the ‘shot’ category produced a genotype that was considered successful (i.e. 15 of 18 loci) and 23% of the ‘collected’ category produced successful genotypes under the same criteria. There was a significant difference between shot and collected samples in genotyping success and the observed number of missing loci. Recommendations and best practices are discussed along with the utility of bird feathers as a source of DNA for population and conservation biology.     

Species identification of birds through genetic analysis of naturally shed feathers

Genetic analysis of noninvasively collected bird feathers is of growing importance to avian ecology; however, most genetic studies that utilize feathers make no mention of the need to verify their species of origin. While plumage patterns and collection location often are indicative of species identity, broad‐scale feather collections may require definitive species identification prior to analysis. Genetic species identification has been applied to noninvasively collected samples from a wide range of taxa but, to date, these techniques have not been widely used on bird feathers. Here, we develop and test a polymerase chain reaction (PCR)‐based technique for identifying eastern imperial eagle (Aquila heliaca) samples among a vast number of noninvasively collected feathers. Species identification is accomplished by amplifying a fragment of the mitochondrial cytochrome c oxidase I gene, then digesting that fragment with a restriction enzyme. The resulting species‐specific restriction fragment length polymorphisms (RFLPs) are easily visualized by gel electrophoresis. We tested this PCR‐RFLP assay on over 300 individuals that had been genetically identified from noninvasively collected feathers and demonstrated that the assay is both reliable and robust for DNA of low quality and quantity. The genetic methods of species identification used to develop this assay can readily be applied to other bird assemblages, making them particularly relevant to a broad range of future avian research.     

Generalist dung attraction response in a New Zealand dung beetle that evolved with an absence of mammalian herbivores

1. Dung beetles (Scarabaeidae: Scarabaeinae) are integral parts of many ecosystems because of their role in decomposition of dung; particularly mammal dung, which forms the diet of both larvae and adults. 2. New Zealand dung beetles are unusual as they are flightless and evolved on islands with a highly depauperate mammal fauna and thus without the usual dung resource used by dung beetles elsewhere. The diet of New Zealand dung beetles is unknown. 3. We hypothesised (1) that the endemic dung beetle Saphobius edwardsi would be attracted to a broad range of food types, and (2) that S. edwardsi would be able to survive and reproduce on a range of dung types and puriri (Vitex lucens) humus. 4. Laboratory choice tests identified that S. edwardsi was attracted to a range of mammal, bird, invertebrate, and reptile dung types, but not to non‐dung food sources. Five‐month no‐choice tests found that beetle survival rates were lower for beetles fed with humus compared with those fed on mammal, bird, or invertebrate dung. None of the beetles reproduced. 5. This study suggests S. edwardsi have a strong preference for dung, and are likely to be broad dung generalists in their feeding behaviour.     

Keratinolytic and keratinophilic fungi in the soils of Papua New Guinea

A study was made of soil samples collected during an expedition to the Highlands of Papua New Guinea. Fungi were isolated from the samples by the method of hair baiting (To-Ka-Va). Of the 33 species isolated, about half showed keratinolytic activity. Such activity is previously unreported for Mucor hiemalis f. hiemalis, Myrothecium roridum, Paecilomyces carneus, P. marquandii, Penicillium brevicompactum, Rhinocladiella mansonii and Verticillium lecanii. The species most active keratinolytically were Chrysosporium an. Arthroderma cuniculi, C. an. A. curreyi, C. indicum, Myceliophthora vellerea and Trichophyton ajelloi. The spectrum of fungi with keratinolytic activity isolated from the different sites differed considerably according to the frequency of use by man, heaviest use being correlated with greatest activity. The pH of the soil (varying from 5.8–7.5) had little influence on the type of such fungi isolated.     

A study of fungi found in association with Histoplasma capsulatum: three bird roosts in S.E. Missouri,U.S.A.

Summary Soil samples from three bird roosts in SE Missouri were studied in an effort to detect differences in the distribution of microfungi in sites contaminated withHistoplasma capsulatum and presumably favorable, but uncontaminated sites. Seventy-four of 151 species identified were found in conjunction withH. capsulatum; many of the remaining 77 species were isolated only rarely and are probably not important colonizers of these soils. Only minor differences were noted regarding distribution of more commonly occurring species. Fungi known to be parasitic or antagonistic to other microfungi were about evenly distributed among the sites.H. capsulatum was most abundant in the one roost which was still occupied by flocks of birds.     

Potential of endozoochorous seed dispersal by sheep in calcareous grasslands: correlations with seed traits

Questions: What is the potential of sheep to serve as seed dispersers via ingestion and defecation in calcareous grasslands? Is the presence of viable seeds from dung correlated with specific seed traits? Location: Calcareous grasslands, South Limburg, the Netherlands/Belgium. Methods: Dung samples (n=24) from sheep were collected between September 2006 and November 2007 from five sites with Mesobromion plant communities, and communities of Nardo‐Galion saxatilis. Germinability and identity of seeds in the dung samples were ascertained from germination of seedlings under glasshouse conditions. Seed traits of species with viable seeds in dung were compared with those present in the local species pool. Results: Seventy‐two plant species from 23 plant families had viable seeds in sheep dung. The plant families encountered most frequently were Gramineae and Compositae. The most abundant and frequently recorded plant species in dung samples was Urtica dioica, accounting for >80% of the total number of seeds. Mean seed density in sheep dung was 0.8 seeds g^?1 dry matter. Seeds with low seed mass and a high seed longevity index were over‐represented in dung. Viable seeds >2.5 mg were infrequent in the dung samples. Conclusions: We conclude that sheep are potentially important dispersers of plant species in Dutch calcareous grasslands. Although smaller seeds were relatively abundant in sheep dung, it cannot be excluded that this was mainly caused by differences in seed abundance.     

Diversity in soil fungi from undisturbed and disturbed Celtis tala and Scutia buxifolia forests in the eastern Buenos Aires province (Argentina)

The rhizospheric soil microfungi from a native forest (undisturbed and disturbed) were studied using soil dilution plate and soil washing methods. Fungi were isolated using slightly acid and alkaline culture media. 54 taxa were isolated: 49 from undisturbed forest soil and 37 from disturbed forest soil. Acremonium sp., Aspergillus ustus, Coemansia pectinata, Doratomyces stemonitis, Fusarium solani, F. oxysporum, Gliocladium roseum, Humicola fusco-atra, Mortierella sp., Penicillium lilacinum, Trichoderma harzianum, and T. koningii, showed the highest frequency, in both, undisturbed and disturbed forests. In undisturbed soil forest the biodiversity index was 3.97 whereas in disturbed ones was 3.89.     

Cosmetic plumage coloration by iron oxides does not confer protection against feather wear

The active acquisition of plumage cosmetic coloration by iron oxides has been described in several bird species (notably the Bearded Vulture Gypaetus barbatus, but also in cranes, pelicans and other vulture species) but its function remains controversial. We tested the hypothesis that iron oxide acquired through mud bathing protects feathers from wear. We experimentally stained 13 breast feathers collected from two White Storks Ciconia ciconia with mud from a ferruginous pond regularly used by Bearded Vultures, while another 13 feathers (controls) were treated with water. All feathers were exposed to a controlled physical abrasion treatment. We found no differences in wear between control and stained feathers, which is counter to predictions of the wear protection hypothesis for the acquisition of this cosmetic plumage coloration.     

Sex Determination in 58 Bird Species and Evaluation of CHD Gene as a Universal Molecular Marker in Bird Sexing

The aim of this research was to test the CHD gene (Chromo Helicase DNA‐binding gene) as a universal molecular marker for sexing birds of relatively distant species. The CHD gene corresponds to the aim because of its high degree of conservation and different lengths in Z and W chromosomes due to different intron sizes. DNA was isolated from feathers and the amplification of the CHD gene was performed with the following sets of polymerase chain reaction (PCR) primers: 2550F/2718R and P2/P8. Sex determination was attempted in 284 samples of 58 bird species. It was successful in 50 bird species; in 16 of those (Alopochen aegyptiacus, Ara severus, Aratinga acuticaudata, Bucorvus leadbeateri, Cereopsis novaehollandiae, Columba arquatrix, Corvus corax, C. frugilegus, Cyanoliseus patagonus, Guttera plumifera, Lamprotornis superbus, Milvus milvus, Neophron percnopterus, Ocyphaps lophotes, Podiceps cristatus, and Poicephalus senegalus), it was carried out for the first time using molecular markers and PCR. It is reasonable to assume that extensive research is necessary to define the CHD gene as a universal molecular marker for successful sex determination in all bird species (with exception of ratites). The results of this study may largely contribute to the aim. Zoo Biol 32:269–276, 2013. © 2012 Wiley Periodicals, Inc.     

Disentangling the ‘brown world’ faecal–detritus interaction web: dung beetle effects on soil microbial properties

Many ecosystem services are sustained by the combined action of microscopic and macroscopic organisms, and shaped by interactions between the two. However, studies tend to focus on only one of these two components. We combined the two by investigating the impact of macrofauna on microbial community composition and functioning in the context of a major ecosystem process: the decomposition of dung. We compared bacterial communities of pasture soil and experimental dung pats inhabited by one (Aphodius), two (Aphodius and Geotrupes), or no dung beetle genera. Overall, we found distinct microbial communities in soil and dung samples, and that the communities converged over the course of the experiment. Characterising the soil microbial communities underlying the dung pats revealed a significant interactive effect between the microflora and macrofauna, where the diversity and composition of microbial communities was significantly affected by the presence or absence of dung beetles. The specific identity of the beetles had no detectable impact, but the microbial evenness was lower in the presence of both Aphodius and Geotrupes than in the presence of Aphodius alone. Differences in microbial community composition were associated with differences in substrate usage as measured by Ecoplates. Moreover, microbial communities with similar compositions showed more similar substrate usage. Our study suggests that the presence of macrofauna (dung beetles) will modify the microflora (bacteria) of both dung pats and pasture soil, including community diversity and functioning. In particular, the presence of dung beetles promotes the transfer of bacteria across the soil–dung interface, resulting in increased similarity in community structure and functioning. The results demonstrate that to understand how microbes contribute to the ecosystem process of dung decomposition, there is a need to understand their interactions with larger co‐occurring fauna.     

Impact of cattle dung deposition on the distribution pattern of plant species in an alvar limestone grassland

Abstract. Seed banks in cattle dung, soil under cattle dung and soil under vegetation and growth response of plant species to the changes in soil nitrogen availability were studied in an alvar limestone grassland on Öland, Sweden, in order to analyse the impact of dung deposition and decomposition on the formation of patches of plant species. Results suggest that patches of four plant species could result from cattle dung deposition and decomposition. Impact of dung could proceed in three ways: (1) by changing the relative abundance of species in the soil seed bank under dung, and/or (2) by influencing the deposition of seeds in the dung, and/or (3) by intensifying the growth of some species through nutrient release. Species patches could result from one or more of these aspects. For instance, patches of Arenaria serpyllifolia may be induced by dung deposition because of the dominance of its seeds in dung, while the pattern of Cerastium semidecandrum and Festuca ovina may be due to the abundance of their seeds in the soil seed bank under dung and their positive growth response to increased nitrogen availability.     

High Diversity among Feather-Degrading Bacteria from a Dry Meadow Soil

The aim of this study was to determine the diversity of cultivable bacteria able to degrade feathers and present in soil under temperate climate. We obtained 33 isolates from soil samples, which clustered in 13 ARDRA groups. These isolates were able to grow on solid medium with pigeon feathers as sole carbon and nitrogen source. One representative isolate of each ARDRA group was selected for identification and feather degradation tests. The phylogenetic analysis of 16S rDNA gene fragments revealed that only 4 isolates were gram positives. Two other isolates belonged to the Cytophaga–Flavobacterium group, and the remaining to Proteobacteria. High keratinolysis activity was found for strains related to Bacillus, Cytophagales, Actinomycetales, and Proteobacteria. The 13 selected strains showed variable efficiency in degrading whole feathers and 5 strains were able to degrade maximum 40% to 98% of the whole feathers. After 4 weeks incubation, five strains grown on milled feathers produced more than 0.5 U keratinase per mL. Keratinase activities across the 13 strains were positively correlated with the percentage of feather fragmentation and protein concentration.     

A survey to determine the occurrence of Histoplasma capsulatum and Cryptococcus neoformans in air-conditioners

Summary A survey of 84 dust samples from 42 air-conditioners and controls was conducted at Kansas State University, Manhattan. Isolations ofC. neoformans andH. capsulatum were attemped using various mycological procedures. H. capsulatum was not recovered in this survey. One isolate ofC. neoformans was obtained. The contaminated air-conditioner yielding the organism contained considerable bird feces, feathers, and dust.Contribution No. 102, Department of Infectious Diseases, Kansas Agricultural Experiment Station, Manhattan, Kansas.     

Exserohilum israeli, a new species isolated from soil from Timna Park (Israel), and its physiological properties

Fungi isolated from soil in Timna Park (Israel) were found to belong to a new species of Exserohilum for which the name Exserohilum israeli sp. nov. is proposed. The main physiological properties of members of this species are discussed and the influence of temperature and copper concentrations on the growth and morphology of the fungus were investigated.     

Comparison of methods for isolation of dematiaceous fungi from nature

Direct plating and animal inoculation techniques were compared for effectiveness in isolating dematiaceous fungi from nature. The direct plating technique involved comparison of aqueous and mineral oil extraction of the samples with subsequent plating on Mycobiotic and Sabhi agar. Twenty four different organisms were recovered from 19 samples using both extraction procedures and both media. Dematiaceous fungi isolated by direct plating were Alternaria alternata, Cladosporium spp., Exophiala jeanselmei, Wangiella dermatitidis and 6 unidentified organisms. Direct plating resulted in more isolations of dematiaceous fungi partly because of the frequent isolations of A. alternata and W. dermatitidis. Both more and a larger variety of organisms were recovered on Mycobiotic than on Sabhi agar. The aqueous extraction of samples resulted in more direct plating isolations of fungi than oil extraction.Only dematiaceous fungi were isolated with the animal inoculation techniques. Fungi isolated from hamsters included Cladosporium spp., Exophiala spinifera, Phialophora verrucosa, Rhinocladiella sp. and 3 unidentified organisms. Fungi isolated by the mouse inoculation technique included Bispora betulina, Cladosporium spp., W. dermatitidis and 1 unidentified organism. In general there was variation in the types of organisms isolated from the same samples depending on the isolation procedure used.     

Melanosome diversity and convergence in the evolution of iridescent avian feathers—Implications for paleocolor reconstruction

Some of the most varied colors in the natural world are created by iridescent nanostructures in bird feathers, formed by layers of melanin‐containing melanosomes. The morphology of melanosomes in iridescent feathers is known to vary, but the extent of this diversity, and when it evolved, is unknown. We use scanning electron microscopy to quantify the diversity of melanosome morphology in iridescent feathers from 97 extant bird species, covering 11 orders. In addition, we assess melanosome morphology in two Eocene birds, which are the stem lineages of groups that respectively exhibit hollow and flat melanosomes today. We find that iridescent feathers contain the most varied melanosome morphologies of all types of bird coloration sampled to date. Using our extended dataset, we predict iridescence in an early Eocene trogon (cf. Primotrogon) but not in the early Eocene swift Scaniacypselus, and neither exhibit the derived melanosome morphologies seen in their modern relatives. Our findings confirm that iridescence is a labile trait that has evolved convergently in several lineages extending down to paravian theropods. The dataset provides a framework to detect iridescence with more confidence in fossil taxa based on melanosome morphology.     

The morphology of neoptile feathers: Ancestral state reconstruction and its phylogenetic implications

Avian neoptile feathers are defined as the first feather generation, which covers the chick after hatching, and usually described as simple structures consisting of numerous downy barbs which are radially symmetrically arranged and come together in a short calamus. In contrast, in some birds (e.g., Anas platyrhynchos, Dromaius novaehollandiae) the neoptile feathers have a prominent rhachis, and therefore display clear bilateral symmetry. Because the symmetrical variety found in neoptile feathers is poorly understood, their morphology was studied in a more comprehensive and phylogenetic approach. Neoptile body feathers from over 22 bird species were investigated using light microscopy, SEM, and MicroCT. Characters such as an anterior–posterior axis, a central rhachis, medullary cells, and structure of the calamus wall were defined and mapped onto recent phylogenetic hypotheses for extant birds. It can be shown that bilaterally symmetric neoptile feathers (with a solid calamus wall) were already present in the stem lineage of crown‐group birds (Neornithes). In contrast, simple radially symmetric neoptile feathers (with a fragile calamus wall) are an apomorphic character complex for the clade Neoaves. The simple morphology of this feather type may be the result of a reduced period of development during embryogenesis. To date, embryogenesis of neoptile feathers from only a few bird species was used as a model to reconstruct feather evolution. Because this study shows that the morphology of neoptile feathers is more diverse and even shows a clear phylogenetic signal, it is necessary to expand the spectrum of “model organisms” to species with bilaterally symmetric neoptile feathers and compare differences in the frequency of feather development from a phylogenetic point of view. J. Morphol., 2011. © 2011 Wiley‐Liss, Inc.     

Isolation and characterization of microsatellites in the kakerori (<Emphasis Type="Italic">Pomarea dimidiata</Emphasis>) using feathers as source of DNA

The kakerori (Pomarea dimidiata) is an endangered forest bird in the Cook Islands, South Pacific. We have developed 10 microsatellite markers using kakerori feathers as the DNA source. Seven of these loci were found to be polymorphic in 42 individuals examined. The number of alleles per locus in the polymorphic loci varied from 3 to 5. Observed and expected heterozygosity ranges were 0.57–0.74 and 0.50–0.74, respectively. All loci isolated conformed to Hardy–Weinberg equilibrium expectations. We believe these loci will be useful in studying kakerori conservation genetics, and our success in developing microsatellite markers from feather samples will encourage the use of less invasive sample sources in microsatellite isolation studies.     

Ecological study of soil fungi of an agricultural field in Allahabad

Summary The soil fungi from an agricultural field in Allahabad where sugarcane is being grown for many years, have been isolated from various depths during different seasons and were identified. The inter-relations of chemical composition of soil and distribution of fungi is also being shown here.The techniques for the isolation and the study of the fungus flora was that ofGoddard modified bySaksena &Mehrotra. Soil samples were examined from 1–6 depths in three seasons of the year and were mechanically and chemically analysed.For the isolation, soil dilution plate method, a modification ofMenzies' method, direct method ofWaksman, Rossi Cholodny Burried slide technique, and screened immersion plate method, were followed Fifty five different species of microfungi belonging to Phycomycetes, Ascomycetes and Fungi — Imperfecti were isolated and identified. The moisture contents, hydrogen-ion concentrations, carbon, nitrogen, phosphorus, calcium, magnesium and iron, etc., of the soil samples from 1–6 inches depths, were also studied.Out of these 12 species covering 9 genera belonged to the Phycomycetes, nine genera of Ascomycetes and nine genera of Fungi Imperfecti were recorded.P. multicolor Grigorieva-Monoilova &Poradielova, andP. roqueforti Thom.,Gliocladium vermoesoni (Biourge)Thom. andMasoniella grisea (Smith)Smith were recorded for the first time from Indian Soil. A new varietyChaetominum nigricolor Ames var.simplex was also isolated.