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Here we report three complete bacterial genome assemblies from a PacBio shotgun metagenome of a co-culture from Upper Klamath Lake, OR. Genome annotations and culture conditions indicate these bacteria are dependent on carbon and nitrogen fixation from the cyanobacterium  Aphanizomenon flos-aquae,  whose genome was assembled to draft-quality .  Due to their taxonomic novelty relative to previously sequenced bacteria, we have temporarily designated these bacteria as  incertae sedis Hyphomonadaceae  strain UKL13-1 (3,501,508 bp and 56.12% GC),  incertae sedis  Betaproteobacterium strain UKL13-2 (3,387,087 bp and 54.98% GC), and  incertae sedis Bacteroidetes  strain UKL13-3 (3,236,529 bp and 37.33% GC). Each genome consists of a single circular chromosome with no identified plasmids. When compared with binned Illumina assemblies of the same three genomes, there was ~7% discrepancy in total genome length. Gaps where Illumina assemblies broke were often due to repetitive elements. Within these missing sequences were essential genes and genes associated with a variety of functional categories. Annotated gene content reveals that both  Proteobacteria  are aerobic anoxygenic phototrophs, with Betaproteobacterium UKL13-2 potentially capable of phototrophic oxidation of sulfur compounds. Both proteobacterial genomes contain transporters suggesting they are scavenging fixed nitrogen from  A. flos-aquae  in the form of ammonium.  Bacteroidetes  UKL13-3 has few completely annotated biosynthetic pathways, and has a comparatively higher proportion of unannotated genes. The genomes were detected in only a few other freshwater metagenomes, suggesting that these bacteria are not ubiquitous in freshwater systems. Our results indicate that long-read sequencing is a viable method for sequencing dominant members from low-diversity microbial communities, and should be considered for environmental metagenomics when conditions meet these requirements.   Electronic supplementary material  The online version of this article (doi:10.1186/s40793-017-0224-8) contains supplementary material, which is available to authorized users.

standards in genomic sciences

Towards long-read metagenomics: complete assembly of three novel genomes from bacteria dependent on a diazotrophic cyanobacterium in a freshwater lake co-culture