Cross-biome microbial networks reveal functional redundancy and suggest genome reduction through functional complementarity.

The structure of microbial communities arises from a multitude of factors, including the interactions of microorganisms with each other and with the environment. In this work, we sought to disentangle those drivers by performing a cross-study, cross-biome meta-analysis of microbial occurrence data in more than 5000 samples, applying a novel network clustering algorithm aimed to capture conditional taxa co-occurrences. We then examined the phylogenetic and functional composition of the resulting clusters, and searched for global patterns of assembly both at the community level and in the presence/absence of individual metabolic pathways.

Bacterioplankton taxa compete for iron along the early spring-summer transition in the Arctic Ocean.

Microbial assemblages under the sea ice of the Dease Strait, Canadian Arctic, were sequenced for metagenomes of a small size fraction (0.2-3 μm). The community from early March was typical for this season, with - and Gammaproteobacteria as the dominant taxa, followed by Thaumarchaeota and Bacteroidetes.

Quantifying microbial guilds.

The ecological role of microorganisms is of utmost importance due to their multiple interactions with the environment. However, assessing the contribution of individual taxonomic groups has proven difficult despite the availability of high throughput data, hindering our understanding of such complex systems. Here, we propose a quantitative definition of guild that is readily applicable to metagenomic data.

In situ metagenomics: A platform for rapid sequencing and analysis of metagenomes in less than one day.

We present here a complete system for metagenomic analysis that allows performing the sequencing and analysis of a medium-size metagenome in less than one day. This unprecedented development was possible due to the conjunction of state-of-the-art experimental and computational advances: a portable laboratory suitable for DNA extraction and sequencing with nanopore technology; the powerful metagenomic analysis pipeline SqueezeMeta, capable to provide a complete analysis in a few hours and using scarce computational resources; and tools for the automatic inspection of the results via a graphical user interface, that can be coupled to a web server to allow remote visualization of data (SQMtools and SQMxplore). We have tested the feasibility of our approach in the sequencing of the microbiota associated to volcanic rocks in La Palma, Canary Islands.