A primary aim of microbial ecology is to determine patterns and drivers of community distribution, interaction, and assembly amidst complexity and uncertainty. Microbial community composition has been shown to change across gradients of environment, geographic distance, salinity, temperature, oxygen, nutrients, pH, day length, and biotic factors 1-6 . These patterns have been identified mostly by focusing on one sample type and region at a time, with insights extra polated across environments and geography to produce generalized principles. To assess how microbes are distributed across environments globally-or whether microbial community dynamics follow funda mental ecological 'laws' at a planetary scale-requires either a massive monolithic cross environment survey or a practical methodology for coordinating many independent surveys. New studies of microbial environments are rapidly accumulating; however, our ability to extract meaningful information from across datasets is outstripped by the rate of data generation. Previous meta analyses have suggested robust gen eral trends in community composition, including the importance of salinity 1 and animal association 2 . These findings, although derived from relatively small and uncontrolled sample sets, support the util ity of meta analysis to reveal basic patterns of microbial diversity and suggest that a scalable and accessible analytical framework is needed.The Earth Microbiome Project (EMP, http://www.earthmicrobiome. org) was founded in 2010 to sample the Earth's microbial communities at an unprecedented scale in order to advance our understanding of the organizing biogeographic principles that govern microbial commu nity structure 7,8 . We recognized that open and collaborative science, including scientific crowdsourcing and standardized methods 8 , would help to reduce technical variation among individual studies, which can overwhelm biological variation and make general trends difficult to detect 9 . Comprising around 100 studies, over half of which have yielded peer reviewed publications (Supplementary Table 1), the EMP has now dwarfed by 100 fold the sampling and sequencing depth of earlier meta analysis efforts 1,2 ; concurrently, powerful analysis tools have been developed, opening a new and larger window into the distri bution of microbial diversity on Earth. In establishing a scalable frame work to catalogue microbiota globally, we provide both a resource for the exploration of myriad questions and a starting point for the guided acquisition of new data to answer them. As an example of using this Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of r...

Summary 1.It has been recently showed that one bacterial strain isolated from the uropygial gland of a nestling hoopoe Upupa epops produced antimicrobial peptides active against a broad spectrum of pathogenic bacteria. These bacteria might thus mediate antimicrobial properties of the uropygial secretions as a consequence of the symbiotic association with hoopoes. 2. We study antimicrobial properties of white (from males and non-breeding females) and brown (from nestlings and breeding females) uropygial gland secretions of hoopoes Upupa epops , as well as the association with the presence of bacteria living inside their uropygial gland. 3. We found that brown, but not white secretions contained bacteria and showed antimicrobial activity against the feather degrading bacterium Bacillus licheniformis . The antagonistic activity of bacterial colonies was mediated by antimicrobial peptides because protease inhibited antimicrobial properties. 4. All except one identified bacterium in aerobic cultures were of the genus Enterococcus , and the microscopic study of uropygial secretions and glands confirmed a high density of bacteria within the gland. 5. Furthermore, we studied potential benefits of antimicrobial peptides produced by symbiotic bacteria of hoopoes by adding protease to incubating nests. 6. The experiment increased bacterial growth and hatching failures in hoopoes but not in spotless starlings Sturnus unicolor , a species that does not harbour bacteria in its uropygial gland. 7. Thus, microbiological, anatomical and ecological results suggest a tight symbiotic interaction between bacteria that produce antibiotic substances and the hoopoes.

Animals frequently use metabolites produced by symbiotic bacteria as agents against pathogens and parasites. Secretions from the preen gland of birds are used for this purpose, although its chemicals apparently are produced by the birds themselves. European hoopoes Upupa epops and green woodhoopoes Phoeniculus purpureus harbour symbiotic bacteria in the uropygial gland that might be partly responsible for the chemical composition of secretions. Here we investigate the antimicrobial activity of the volatile fraction of chemicals in hoopoe preen secretions, and, by means of experimental antibiotic injections, test whether symbiotic bacteria living within the uropygial gland are responsible for their production. Hoopoes produce two different kinds of secretions that differ drastically in their chemical composition. While the malodorous dark secretions produced by nestlings included a complex mix of volatiles, these chemicals did not appear in white secretions produced by non-nesting birds. All volatiles detected showed strong antibacterial activity, and a mixture of the chemicals at the concentrations measured in nestling glands inhibited the growth of all bacterial strains assayed. We found support for the hypothesized role of bacteria in the production of such antimicrobial chemicals because experimental clearance of bacteria from glands of nestlings with antibiotics resulted in secretions without most of the volatiles detected in control individuals. Thus, the presence of symbiotic bacteria in the uropygial gland provides hoopoes with potent antimicrobials for topical use.

The uropygial gland (preen gland) is a holocrine secretory gland situated at the base of the tail in birds which produces a hydrophobic fatty secretion. In certain birds, such as the hoopoe, Upupa epops, the composition of this secretion is influenced by both seasonal and sexual factors, becoming darker and more malodorous in females and in their nestlings during the nesting phase. The secretion is spread throughout the plumage when the bird preens itself, leaving its feathers flexible and waterproof. It is also thought to play a role in defending the bird against predators and parasites. We have isolated from the uropygial secretion of a nestling a bacterium that grows in monospecific culture which we have identified unambiguously by phenotypic and genotypic means as Enterococcus faecalis. The strain in question produces antibacterial substances that are active against all gram-positive bacteria assayed and also against some gram-negative strains. Its peptide nature identifies it as a bacteriocin within the group known as enterocins. Two peptides were purified to homogeneity (MR10A and MR10B), and matrix-assisted laser desorption ionization-time of flight (mass spectrometry) analysis showed masses of 5201.58 and 5207.7 Da, respectively. Amino acid sequencing of both peptides revealed high similarity with enterocin L50A and L50B (L. M. Cintas, P. Casaus, H. Holo, P. E. Hern�ndez, I. F. Nes, and L. S. H�varstein, J. Bacteriol. 180:1988-1994, 1998). PCR amplification of total DNA from strain MRR10-3 with primers for the L50A/B structural genes and sequencing of the amplified fragment revealed almost identical sequences, except for a single conservative change in residue 38 (Glu→Asp) in MR10A and two changes in residues 9 (Thr→Ala) and 15 (Leu→Phe) in MR10B. This is the first time that the production of bacteriocins by a bacterium isolated from the uropygial gland has been described. The production of these broad-spectrum antibacterial substances by an enterococcal strain living in the uropygial gland may be important to the hygiene of the nest and thus to the health of the eggs and chicks.

The uropygial glands of birds serve multiple functions, and there is great interspecific variability in the composition and properties of their secretions. A special case is the secretion in the hoopoes Upupa epops, and green woodhoopoes Phoeniculus purpureus, which, contrary to the commonly white and odourless secretions, are dark with pungent odour. Recently, bacteria have been isolated from glands of both woodhoopoes and hoopoes and here we test the hypothesis that bacteria are responsible of some of the special properties of glands and secretions of this group of birds. We explore natural seasonal changes and intersexual differences in the properties of hoopoe glands and secretions, check the natural occurrence of bacteria within secretions, and analyse the effect of experimental injection of antibiotics on uropygial gland properties. Male glands underwent no seasonal changes, and their secretions were invariably white and odourless, very similar to female glands outside the breeding season. However, in comparison to the uropygial gland of non-breeding females, those of incubating females showed a marked increase in size and volume of secretion produced, which became dark and pungent. All these parameters increased until the hatching date and returned to values similar to those in the prelaying phase towards the end of the nestling period. Nestling glands produced secretions similar to those of females in colour and odour. Gland size of both females and nestlings predicted the amount of secretion produced. Microscopic techniques confirmed the presence of bacteria at high density and in active division in all dark secretions examined. The antibiotic treatment significantly reduced the load of enterococci in nestling glands, did not affect size of glands, but diminished the volume of secretion, which was lighter in colour than that of control nestlings. In nesting females, the experimental injection of antibiotic affected some measurements of gland size and secretion colour. Because the experiment did not affect general health estimates (immunocompetence, body condition or growing) of nestlings, our results suggest that some of the special properties of hoopoe glands are mediated by the presence of symbiotic bacteria.