Microbial Diversity of Wild Bird Feathers Revealed throughCulture-Based and Culture-Independent Techniques

Abstract

Despite recent interest in the interactions between birds and environmental microbes, the identities of the bacteria that inhabit the feathers of wild birds remain largely unknown. We used culture-based and culture-independent surveys of the feathers of eastern bluebirds (Sialis sialis) to examine bacterial flora. When used to analyze feathers taken from the same birds, the two survey techniques produced different results. Species of the poorly defined genus Pseudomonas were most common in the molecular survey, whereas species of the genus Bacillus were predominant in the culture-based survey. This difference may have been caused by biases in both the culture and polymerase chain reaction techniques that we used. The pooled results from both techniques indicate that the overall community is diverse and composed largely of members of the Firmicutes and b-and c-subdivisions of the Proteobacteria. For the most part, bacterial sequences isolated from birds were closely related to sequences of soil-borne and water-borne bacteria in the GenBank database, suggesting that birds may have acquired many of these bacteria from the environment. However, the metabolic properties and optimal growth requirements of several isolates suggest that some of the bacteria may have a specialized association with feathers.

Intraspecific Variation and Interspecific Differences in the Bacterial and Fungal Assemblages of Blue Tit (Cyanistes caeruleus) and Great Tit (Parus major) Nests

“…In all cases, the DNA sequencing analysis matched the original FAME identification, suggesting that the latter was a suitable and reliable identification method for the isolates in this study, as previously found for bird feather microbiota [51].…”

“…dominated the nest samples, since Bacillus spp. has been found to dominate feather samples using similar culture techniques to those used here [51].…”

“…This is seemingly the first time that Pseudomonas isolates from avian nesting environments have been identified to species level. However, P. fluorescens has been isolated from feathers of the Eastern bluebird (Sialia sialis) in America [51], from pharyngeal swabs of alpine accentors (Prunella collaris) in Slovakia [28] and from faeces of wild birds in Wisconsin, USA [7]. It is interesting to note that Pseudomonas spp.…”

“…Culturing was undertaken on nutrient agar to encourage bacterial growth and 3.9% (w/v) potato dextrose agar (PDA) at pH 5.6 to encourage fungal growth. Plates were incubated for 7 days at 28C [51] before colony forming units (CFUs) were counted to ensure that any bias towards fast-growing species was limited. Plates were re-examined after 21 days and any additional CFUs were documented -this occurred in two cases only.…”

“…This process was undertaken through the Sherlock® Microbial Identification System (MIDI Inc., Newark, Delaware) using the Sherlock Rapid Methods® technique and the RTSB50 (environmental isolates) reference library. FAME and Sherlock® systems are validated identification methods have been widely used to successfully identify environmental bacteria [29,44,58], including isolates from bird feathers when the method produced results that were comparable to DNA identifications [51]. Before analysis, isolates were sub-cultured on 4% (w/v) Trypticase Soy Broth agar and incubated at 28°C for 24 hours to ensure a typical FAME profile.…”