title: Towards long-read metagenomics: complete assembly of three novel genomes from bacteria dependent on a diazotrophic cyanobacterium in a freshwater lake co-culture.
abstract: 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 cyanobacteriumAphanizomenon 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 asincertae sedis Hyphomonadaceaestrain UKL13-1 (3,501,508 bp and 56.12% GC),incertae sedisBetaproteobacterium strain UKL13-2 (3,387,087 bp and 54.98% GC), andincertae sedis Bacteroidetesstrain 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 bothProteobacteriaare 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 fromA. flos-aquaein the form of ammonium.BacteroidetesUKL13-3 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.
authors.affiliation: Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR 97331 USA.
authors.forename: Connor B
authors.initials: CB
authors.lastname: Driscoll
authors.affiliation: Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR 97331 USA.
authors.forename: Timothy G
authors.initials: TG
authors.lastname: Otten
authors.affiliation: Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR 97331 USA.
authors.forename: Nathan M
authors.initials: NM
authors.lastname: Brown
authors.affiliation: Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR 97331 USA.|Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331 USA.
authors.forename: Theo W
authors.initials: TW
authors.lastname: Dreher
keywords: Aerobic anoxygenic phototroph; Aphanizomenon flos-aquae; Bacteroidetes; Betaproteobacterium; Hyphomonadaceae; PacBio SMRT sequencing