TSLR sequencing of landsort deep oxycline. Landsort Deep Oxycline

Microbes in low oxygen layers of the world’s oceans catalyze biogeochemical processes implicated in global climate change and health. Because a predominance of ocean microbes evade cultivation, metagenome sequencing has become a ubiquitous tool for characterizing microbial communities. However, because assembly of individual genomes from metagenomics remains challenging, typical short-read sequencing rarely reveals robust links between taxonomy and function.Here, we show that TruSeq Synthetic Long Read (TSLR) sequencing enables de-novo assembly of genomes for microbes at the oxycline of an estuarine oxygen minimum zone. TSLR metagenomics assembly with subsequent compositional and core gene content analysis resulted in 38 genomes, many near complete and in few scaffolds. Genomes for members of the Candidate Phylum Radiation were recovered from an ocean environment for the first time. The recovered genomes are divergent from existing references and recruited more than half of the metagenomic and metatranscriptomic sequencing reads from multiple size fractions and depths over multiple years. Metabolic reconstructions and transcriptome profiling revealed crowdsourcing: active within-sample sulfur, carbon, and nitrogen cycles catalyzed by multiple diverse genomes for most processes, particularly denitrification, sulfur oxidation, and hydrogen oxidation. Assembled large biosynthetic gene clusters were expressed in the metatranscriptomes, indicating the possible production of siderophores and bacteriostatins. The genomes provide a heretofore-unavailable perspective on the microbial ecology and function of a crucial biome.