Here we present a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences—the minimum information about a marker gene sequence (MIMARKS). We also introduce a system for describing the environment from which a biological sample originates. The ‘environmental packages’ apply to any genome sequence of known origin and can be used in combination with MIMARKS and other GSC checklists. Finally, to establish a unified standard for describing sequence data and to provide a single point of entry for the scientific community to access and learn about GSC checklists, we present the minimum information about any (x) sequence (MIxS). Adoption of MIxS will enhance our ability to analyze natural genetic diversity documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere.

Microbialites (benthic microbial carbonate deposits) were discovered in a hypersaline alkaline lake on Eleuthera Island (Bahamas). From the edge towards the centre of the lake, four main zones of precipitation could be distinguished: (1) millimetre‐sized clumps of Mg‐calcite on a thin microbial mat; (2) thicker and continuous carbonate crusts with columnar morphologies; (3) isolated patches of carbonate crust separated by a dark non‐calcified gelatinous mat; and (4) a dark microbial mat without precipitation. In thin section, the precipitate displayed a micropeloidal structure characterized by micritic micropeloids (strong autofluorescence) surrounded by microspar and spar cement (no fluorescence). Observations using scanning electron microscopy (SEM) equipped with a cryotransfer system indicate that micrite nucleation is initiated within a polymer biofilm that embeds microbial communities. These extracellular polymeric substances (EPS) are progressively replaced with high‐Mg calcite. Discontinuous EPS calcification generates a micropeloidal structure of the micrite, possibly resulting from the presence of clusters of coccoid or remnants of filamentous bacteria. At high magnification, the microstructure of the initial precipitate consists of 200–500 nm spheres. No precipitation is observed in or on the sheaths of cyanobacteria, and only a negligible amount of precipitation is directly associated with the well‐organized and active filamentous cyanobacteria (in deeper layers of the mat), indicating that carbonate precipitation is not associated with CO2 uptake during photosynthesis. Instead, the precipitation occurs at the uppermost layer of the mat, which is composed of EPS, empty filamentous bacteria and coccoids (Gloeocapsa spp.). Two‐dimensional mapping of sulphate reduction shows high activity in close association with the carbonate precipitate at the top of the microbial mat. In combination, these findings suggest that net precipitation of calcium carbonate results from a temporal and spatial decoupling of the various microbial metabolic processes responsible for CaCO3 precipitation and dissolution. Theoretically, partial degradation of EPS by aerobic heterotrophs or UV fuels sulphate‐reducing activity, which increases alkalinity in microdomains, inducing CaCO3 precipitation. This degradation could also be responsible for EPS decarboxylation, which eliminates Ca2+‐binding capacity of the EPS and releases Ca2+ ions that were originally bound by carboxyl groups. At the end of these processes, the EPS biofilm is calcified and exhibits a micritic micropeloidal structure. The EPS‐free precipitate subsequently serves as a substrate for physico‐chemical precipitation of spar cement from the alkaline water of the lake. The micropeloidal structure has an intimate mixture of micrite and microspar comparable to microstructures of some fossil microbialites.

The environments we humans encounter daily are sources of exposure to diverse microbial communities, some of potential concern to human health. In this study, we used culture-independent technology to investigate the microbial composition of biofilms inside showerheads as ecological assemblages in the human indoor environment. Showers are an important interface for human interaction with microbes through inhalation of aerosols, and showerhead waters have been implicated in disease. Although opportunistic pathogens commonly are cultured from shower facilities, there is little knowledge of either their prevalence or the nature of other microorganisms that may be delivered during shower usage. To determine the composition of showerhead biofilms and waters, we analyzed rRNA gene sequences from 45 showerhead sites around the United States. We find that variable and complex, but specific, microbial assemblages occur inside showerheads. Particularly striking was the finding that sequences representative of non-tuberculous mycobacteria (NTM) and other opportunistic human pathogens are enriched to high levels in many showerhead biofilms, >100-fold above background water contents. We conclude that showerheads may present a significant potential exposure to aerosolized microbes, including documented opportunistic pathogens. The health risk associated with showerhead microbiota needs investigation in persons with compromised immune or pulmonary systems.bioaerosols ͉ Mycobacterium avium complex ͉ Non-tuberculous mycobacteria ͉ public health ͉ rRNA metagenomics

No abstract

The goal of this study was to determine the composition and diversity of microorganisms associated with bioaerosols in a heavily trafficked metropolitan subway environment. We collected bioaerosols by fluid impingement on several New York City subway platforms and associated sites in three sampling sessions over a 1.5-year period. The types and quantities of aerosolized microorganisms were determined by culture-independent phylogenetic analysis of small-subunit rRNA gene sequences by using both Sanger (universal) and pyrosequencing (bacterial) technologies. Overall, the subway bacterial composition was relatively simple; only 26 taxonomic families made up ϳ75% of the sequences determined. The microbiology was more or less similar throughout the system and with time and was most similar to outdoor air, consistent with highly efficient air mixing in the system. Identifiable bacterial sequences indicated that the subway aerosol assemblage was composed of a mixture of genera and species characteristic of soil, environmental water, and human skin commensal bacteria. Eukaryotic diversity was mainly fungal, dominated by organisms of types associated with wood rot. Human skin bacterial species (at 99% rRNA sequence identity) included the Staphylococcus spp. Staphylococcus epidermidis (the most abundant and prevalent commensal of the human integument), S. hominis, S. cohnii, S. caprae, and S. haemolyticus, all well-documented human commensal bacteria. We encountered no organisms of public health concern. This study is the most extensive culture-independent survey of subway microbiota so far and puts in place pre-event information required for any bioterrorism surveillance activities or monitoring of the microbiological impact of recent subway flooding events.