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

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 whose genome was assembled t...

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Veröffentlicht in:Environmental microbiome 2017-01, Vol.12 (1), p.9, Article 9
Hauptverfasser: Driscoll, Connor B, Otten, Timothy G, Brown, Nathan M, Dreher, Theo W
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Sprache:eng
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Zusammenfassung: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 whose genome was assembled to draft-quality Due to their taxonomic novelty relative to previously sequenced bacteria, we have temporarily designated these bacteria as strain UKL13-1 (3,501,508 bp and 56.12% GC), Betaproteobacterium strain UKL13-2 (3,387,087 bp and 54.98% GC), and 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 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 in the form of ammonium. 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.
ISSN:1944-3277
1944-3277
2524-6372
DOI:10.1186/s40793-017-0224-8