No abstract

We present QIIME 2, an open-source microbiome data science platform accessible to users spanning the microbiome research ecosystem, from scientists and engineers to clinicians and policy makers. QIIME 2 provides new features that will drive the next generation of microbiome research. These include interactive spatial and temporal analysis and visualization tools, support for metabolomics and shotgun metagenomics analysis, and automated data provenance tracking to ensure reproducible, transparent microbiome data science.

We applied nucleic acid-based molecular methods, combined with estimates of biomass (ATP), pigments, and microelectrode measurements of chemical gradients, to map microbial diversity vertically on a millimeter scale in a hypersaline microbial mat from Guerrero Negro, Baja California Sur, Mexico. To identify the constituents of the mat, small-subunit rRNA genes were amplified by PCR from community genomic DNA extracted from layers, cloned, and sequenced. Bacteria dominated the mat and displayed unexpected and unprecedented diversity. The majority (1,336) of the 1,586 bacterial 16S rRNA sequences generated were unique, representing 752 species (>97% rRNA sequence identity) in 42 of the main bacterial phyla, including 15 novel candidate phyla. The diversity of the mat samples differentiated according to the chemical milieu defined by concentrations of O 2 and H 2 S. Bacteria of the phylum Chloroflexi formed the majority of the biomass by percentage of bulk rRNA and of clones in rRNA gene libraries. This result contradicts the general belief that cyanobacteria dominate these communities. Although cyanobacteria constituted a large fraction of the biomass in the upper few millimeters (>80% of the total rRNA and photosynthetic pigments), Chloroflexi sequences were conspicuous throughout the mat. Filamentous Chloroflexi bacteria were identified by fluorescence in situ hybridization within the polysaccharide sheaths of the prominent cyanobacterium Microcoleus chthonoplastes, in addition to free living in the mat. The biological complexity of the mat far exceeds that observed in other polysaccharide-rich microbial ecosystems, such as the human and mouse distal guts, and suggests that positive feedbacks exist between chemical complexity and biological diversity.

The geochemical energy budgets for high-temperature microbial ecosystems such as occur at Yellowstone National Park have been unclear. To address the relative contributions of different geochemistries to the energy demands of these ecosystems, we draw together three lines of inference. We studied the phylogenetic compositions of high-temperature (>70°C) communities in Yellowstone hot springs with distinct chemistries, conducted parallel chemical analyses, and carried out thermodynamic modeling. Results of extensive molecular analyses, taken with previous results, show that most microbial biomass in these systems, as reflected by rRNA gene abundance, is comprised of organisms of the kinds that derive energy for primary productivity from the oxidation of molecular hydrogen, H 2. The apparent dominance by H2-metabolizing organisms indicates that H 2 is the main source of energy for primary production in the Yellowstone high-temperature ecosystem. Hydrogen concentrations in the hot springs were measured and found to range up to >300 nM, consistent with this hypothesis. Thermodynamic modeling with environmental concentrations of potential energy sources also is consistent with the proposed microaerophilic, hydrogen-based energy economy for this geothermal ecosystem, even in the presence of high concentrations of sulfide.geothermal springs ͉ phylogenetic study ͉ primary productivity ͉ Yellowstone National Park ͉ hydrogen metabolism M icrobial communities associated with volcanic hot springs have attracted broad interest because of the unique thermophilic properties of the constituent organisms. However, little attention has been given to hot spring communities as whole microbial ecosystems. One fundamental consideration in understanding any ecosystem is the energy budget: the relative contributions of different energy sources that fuel primary productivity, the conversion of carbon dioxide into biomass. Most of Earth's biomass is considered to be the product of photosynthesis. However, at temperatures higher than Ϸ70°C, photosynthesis is not known to occur, § but thermophilic microbial communities develop well beyond that temperature (1-5). Consequently, high-temperature primary productivity must derive from chemosynthesis based on the oxidation of reduced inorganic or organic sources. A variety of lithotrophic microorganisms (which use inorganic energy sources) and heterotrophic organisms (which use reduced carbon) have been cultured from hot spring communities (6-11). However, the relative contributions of different potential energy sources to particular communities have not been systematically addressed.Previous chemical analyses of Yellowstone hot springs have not provided satisfactory explanations of the energy sources that fuel the communities. Potential energy sources detected in different hot springs included sulfide, CH 4 and other short-chain hydrocarbons, and reduced metals such as As [III], Fe [II], and Mn[II] (12, 13). However, none of these chemicals is ubiquitous in the hot springs, and robust microbial...