ISME communications最新文献

While the air microbiome and its diversity are essential for human health and ecosystem resilience, comprehensive air microbial diversity monitoring has remained rare, so that little is known about the air microbiome's composition, distribution, or functionality. Here we show that nanopore sequencing-based metagenomics can robustly assess the air microbiome in combination with active air sampling through liquid impingement and tailored computational analysis. We provide fast and portable laboratory and computational approaches for air microbiome profiling, which we leverage to robustly assess the taxonomic composition of the core air microbiome of a controlled greenhouse environment and of a natural outdoor environment. We show that long-read sequencing can resolve species-level annotations and specific ecosystem functions through de novo metagenomic assemblies despite the low amount of fragmented DNA used as an input for nanopore sequencing. We then apply our pipeline to assess the diversity and variability of an urban air microbiome, using Barcelona, Spain, as an example; this randomized experiment gives first insights into the presence of highly stable location-specific air microbiomes within the city's boundaries, and showcases the robust microbial assessments that can be achieved through automatable, fast, and portable nanopore sequencing technology.

Harmful algal blooms (HABs) have had significant adverse impacts on the seafood industry along the Tasmanian east coast over the past 4 decades. To investigate the history of regional HABs, we performed analyses of sedimentary ancient DNA (sedaDNA) in coastal sediments up to ~9000 years old collected inshore and offshore of Maria Island, Tasmania. We used metagenomic shotgun sequencing and a hybridisation capture array ("HABbaits1") to target three harmful dinoflagellate genera, Alexandrium, Gymnodinium, and Noctiluca. Bioinformatic and DNA damage analyses verified the authenticity of the sedaDNA sequences. Our results show that dinoflagellates of Alexandrium genera have been present off eastern Tasmania during the last ~8300 years, and we sporadically detected and unambiguously verified sequences of Gymnodinium catenatum that were present offshore up to ~7600 years ago. We also recovered sedaDNA of the fragile, soft-bodied Noctiluca scintillans with increased relative abundance since 2010, consistent with plankton surveys. This study enabled us to identify challenges of sedaDNA sequence validation (in particular for G. catenatum, a microreticulate gymnodinoid species) and provided guidance for the development of tools to monitor past and present HAB species and improvement of future HAB event predictions.

Microbial genomes produced by standard single-cell amplification methods are largely incomplete. Here, we show that primary template-directed amplification (PTA), a novel single-cell amplification technique, generated nearly complete genomes from three bacterial isolate species. Furthermore, taxonomically diverse genomes recovered from aquatic and soil microbiomes using PTA had a median completeness of 81%, whereas genomes from standard multiple displacement amplification-based approaches were usually <30% complete. PTA-derived genomes also included more associated viruses and biosynthetic gene clusters.

Emissions of microbially produced methane (CH₄) from lake sediments are a major source of this potent greenhouse gas to the atmosphere. The rates of CH₄ production and emission are believed to be influenced by electron acceptor distributions and organic carbon contents, which in turn are affected by anthropogenic inputs of nutrients leading to eutrophication. Here, we investigate how eutrophication influences the abundance and community structure of CH₄ producing Archaea and methanogenesis pathways across time-resolved sedimentary records of five Swiss lakes with well-characterized trophic histories. Despite higher CH₄ concentrations which suggest higher methanogenic activity in sediments of eutrophic lakes, abundances of methanogens were highest in oligotrophic lake sediments. Moreover, while the methanogenic community composition differed significantly at the lowest taxonomic levels (OTU), depending on whether sediment layers had been deposited under oligotrophic or eutrophic conditions, it showed no clear trend in relation to in situ distributions of electron acceptors. Remarkably, even though methanogenesis from CO₂-reduction was the dominant pathway in all sediments based on carbon isotope fractionation values, taxonomic identities, and genomes of resident methanogens, CO₂-reduction with hydrogen (H₂) was thermodynamically unfavorable based on measured reactant and product concentrations. Instead, strong correlations between genomic abundances of CO₂-reducing methanogens and anaerobic bacteria with potential for extracellular electron transfer suggest that methanogenic CO₂-reduction in lake sediments is largely powered by direct electron transfer from syntrophic bacteria without involvement of H₂ as an electron shuttle.