Microbiome profiling by Illumina sequencing of combinatorial sequence-tagged PCR products

We developed a low-cost, high-throughput microbiome profiling method that uses combinatorial sequence tags attached to PCR primers that amplify the rRNA V6 region. Amplified PCR products are sequenced using an Illumina paired-end protocol to generate millions of overlapping reads. Combinatorial sequence tagging can be used to examine hundreds of samples with far fewer primers than is required when sequence tags are incorporated at only a single end. The number of reads generated permitted saturating or near-saturating analysis of samples of the vaginal microbiome. The large number of reads al- lowed an in-depth analysis of errors, and we found that PCR-induced errors composed the vast majority of non-organism derived species variants, an ob- servation that has significant implications for sequence clustering of similar high-throughput data. We show that the short reads are sufficient to assign organisms to the genus or species level in most cases. We suggest that this method will be useful for the deep sequencing of any short nucleotide region that is taxonomically informative; these include the V3, V5 regions of the bac- terial 16S rRNA genes and the eukaryotic V9 region that is gaining popularity for sampling protist diversity.Comment: 28 pages, 13 figure

The role of open-air inhalatoria in the air quality improvement in spa towns

Objectives: The present study was aimed at evaluating microbiological contamination of air in Ciechocinek and Ino­wro­cław – Polish lowland spa towns. Additionally, the impact of open-air inhalatoria on the quality of air was evaluated. Material and Methods: Air samples were collected seasonally in the urban areas, in the recreation areas and in the vicinity of inhalatoria in both towns using impaction. The numbers of mesophilic bacteria, staphylococci, hemolytic bacteria and actinomycetes were determined on media according to the Polish Standard PN-86/Z-04111/02. The number of moulds was determined on media according to the Polish Standard PN-86/Z-04111/03. Results: While the highest numbers of microorganisms were noted at the sites located in the urban areas, the lowest numbers were noted in the vicinity of the open-air inhalatoria. In all the investigated air samples the values of bioaerosol concentrations were below the recommended TLVs (≤ 5000 CFU×m–3 for both bacteria and fungi in outdoor environments). Location of the sampling site was invariably a decisive factor in determining the number of microorganisms in the air. Conclusions: The aerosol which is formed in the open-air inhalatoria has a positive influence on microbiological air quality. Owing to a unique microclimate and low air contamination, Ciechocinek and Inowrocław comply with all necessary requirements set for health resorts specializing in treating upper respiratory tract infections

Long-range transport of airborne microbes over the global tropical and subtropical ocean

The atmosphere plays a fundamental role in the transport of microbes across the planet but it is often neglected as a microbial habitat. Although the ocean represents two thirds of the Earth’s surface, there is little information on the atmospheric microbial load over the open ocean. Here we provide a global estimate of microbial loads and air-sea exchanges over the tropical and subtropical oceans based on the data collected along the Malaspina 2010 Circumnavigation Expedition. Total loads of airborne prokaryotes and eukaryotes were estimated at 2.2 × 1021 and 2.1 × 1021 cells, respectively. Overall 33–68% of these microorganisms could be traced to a marine origin, being transported thousands of kilometres before re-entering the ocean. Moreover, our results show a substantial load of terrestrial microbes transported over the oceans, with abundances declining exponentially with distance from land and indicate that islands may act as stepping stones facilitating the transoceanic transport of terrestrial microbes.En prens

Bluetongue Virus Serotype 1 Outbreak in the Basque Country (Northern Spain) 2007–2008. Data Support a Primary Vector Windborne Transport

BACKGROUND: Bluetongue (BT) is a vector-borne disease of ruminants that has expanded its traditional global distribution in the last decade. Recently, BTV-1 emerged in Southern Spain and caused several outbreaks in livestock reaching the north of the country. The aim of this paper was to review the emergence of BTV-1 in the Basque Country (Northern Spain) during 2007 and 2008 analyzing the possibility that infected Culicoides were introduced into Basque Country by winds from the infected areas of Southern Spain. METHODOLOGY/PRINCIPAL FINDINGS: We use a complex HYSPLIT (Hybrid Single-Particle Lagrangian Integrated Trajectory) model to draw wind roses and backward wind trajectories. The analysis of winds showed September 28 to October 2 as the only period for the introduction of infected midges in the Basque Country. These wind trajectories crossed through the areas affected by serotype 1 on those dates in the South of the Iberian Peninsula. Additionally meteorological data, including wind speed and humidity, and altitude along the trajectories showed suitable conditions for Culicoides survival and dispersion. CONCLUSIONS/SIGNIFICANCE: An active infection in medium-long distance regions, wind with suitable speed, altitude and trajectory, and appropriate weather can lead to outbreaks of BTV-1 by transport of Culicoides imicola, not only over the sea (as reported previously) but also over the land. This shows that an additional factor has to be taken into account for the control of the disease which is currently essentially based on the assumption that midges will only spread the virus in a series of short hops. Moreover, the epidemiological and serological data cannot rule out the involvement of other Culicoides species in the spread of the infection, especially at a local level

The energy–diversity relationship of complex bacterial communities in Arctic deep-sea sediments

The availability of nutrients and energy is a main driver of biodiversity for plant and animal communities in terrestrial and marine ecosystems, but we are only beginning to understand whether and how energy–diversity relationships may be extended to complex natural bacterial communities. Here, we analyzed the link between phytodetritus input, diversity and activity of bacterial communities of the Siberian continental margin (37–3427 m water depth). Community structure and functions, such as enzymatic activity, oxygen consumption and carbon remineralization rates, were highly related to each other, and with energy availability. Bacterial richness substantially increased with increasing sediment pigment content, suggesting a positive energy–diversity relationship in oligotrophic regions. Richness leveled off, forming a plateau, when mesotrophic sites were included, suggesting that bacterial communities and other benthic fauna may be structured by similar mechanisms. Dominant bacterial taxa showed strong positive or negative relationships with phytodetritus input and allowed us to identify candidate bioindicator taxa. Contrasting responses of individual taxa to changes in phytodetritus input also suggest varying ecological strategies among bacterial groups along the energy gradient. Our results imply that environmental changes affecting primary productivity and particle export from the surface ocean will not only affect bacterial community structure but also bacterial functions in Arctic deep-sea sediment, and that sediment bacterial communities can record shifts in the whole ocean ecosystem functioning

Temporal variability and effect of environmental variables on airborne bacterial communities in an urban area of Northern Italy

Despite airborne microorganisms representing a relevant fraction of atmospheric suspended particles, only a small amount of information is currently available on their abundance and diversity and very few studies have investigated the environmental factors influencing the structure of airborne bacterial communities. In this work, we used quantitative PCR and Illumina technology to provide a thorough description of airborne bacterial communities in the urban area of Milan (Italy). Forty samples were collected in 10-day sampling sessions, with one sessionper season.Themeanbacterialabundancewasabout104 ribosomal operons perm3 of air andwas lower inwinter than in the other seasons. Communitieswere dominated by Actinobacteridae, Clostridiales, Sphingobacteriales and fewproteobacterial orders (Burkholderiales, Rhizobiales, Sphingomonadales andPseudomonadales).Chloroplastswere abundant in all samples. Ahigher abundanceof Actinobacteridae,which are typical soil-inhabiting bacteria, and a lower abundance of chloroplasts in samples collected on cold days were observed. The variation in community composition observed within seasons was comparable to that observed between seasons, thus suggesting that airborne bacterial communities showlarge temporal variability, even between consecutive days. The structure of airborne bacterial communities therefore suggests that soil and plants are the sources which contribute most to the airborne communities of Milan atmosphere, but the structure of the bacterial community seems to depend mainly on the source of bacteria that predominates in a given period of time

The santorini volcanic complex as a valuable source of enzymes for bioenergy

Marine microbial communities are an untapped reservoir of genetic and metabolic diversity and a valuable source for the discovery of new natural products of biotechnological interest. The newly discovered hydrothermal vent field of Santorini volcanic complex located in the Aegean Sea is gaining increasing interest for potential biotechnological exploitation. The conditions in these environments, i.e., high temperatures, low pH values and high concentration of heavy metals, often resemble harsh industrial settings. Thus, these environments may serve as pools of enzymes of enhanced catalytic properties that may provide benefits to biotechnology. Here, we screened 11 metagenomic libraries previously constructed from microbial mat samples covering the seafloor and the polymetallic chimneys of Kolumbo volcano as well as mat samples from Santorini caldera, to mine, in silico, genes associated with bioenergy applications. We particularly focused on genes encoding biomass hydrolysis enzymes such as cellulases, hemicellulases and lignin-degrading enzymes. A total of 10,417 genes were found for three specific groups of enzymes—i.e., the endoglucanases, the three different beta-glucosidases BGL, bglX and bglB, and the alpha-galactosidases melA, and rafA. Overall, we concluded that the Santorini–Kolumbo volcanic ecosystems constitute a significant resource of novel genes with potential applications in bioenergy that deserve further investigation

The effects of the 2009 dust storm on emergency admissions to a hospital in Brisbane, Australia

In September 2009 an enormous dust storm swept across eastern Australia. Dust is potentially hazardous to health as it interferes with breathing, and previous dust storms have been linked to increased risks of asthma and even death. We examined whether the 2009 Australian dust storm changed the volume or characteristics of emergency admissions to hospital. We used an observational study design, using time series analyses to examine changes in the number of admissions, and case-only analyses to examine changes in the characteristics of admissions. The admission data were from the Prince Charles Hospital, Brisbane, between 1 January 2009 and 31 October 2009. There was a 39% increase in emergency admissions associated with the storm (95% confidence interval: 5, 81%), which lasted for just one day. The health effects of the storm could not be detected using particulate matter levels. We found no significant change in the characteristics of admissions during the storm, specifically there was no increase in respiratory admissions. The dust storm had a short-lived impact on emergency hospital admissions. This may be because the public took effective avoidance measures, or because the dust was simply not toxic, being mainly composed of soil. Emergency departments should be prepared for a short-term increase in admissions during dust storms