Draft Genome Sequence of Novosphingobium nitrogenifigens Y88T

Abstract

Novosphingobium nitrogenifigens was originally isolated from pulp and paper mill wastewater, a low-nitrogen, high-carbon environment. N. nitrogenifigens is the first known nitrogen-fixing, polyhydroxyalkanoate-accumulating sphingomonad, and we report the annotated draft genome sequence of the type strain Y88 T here. Sphingomonad bacteria are often found in high-carbon, lownitrogen, environmentally degraded habitats and/or are capable of metabolizing various industrial pollutants as carbon sources (1,5,6,9). Several of these species have also been found to produce polyhydroxyalkanoate (PHA) (1, 4, 6), which represents a class of polymers with properties comparable to those of petroleum-derived plastics (2). The potential of diazotrophic bacteria that can use waste-derived feedstocks to help lower the cost of PHA production is an active area of research (8). Sphingomonads can potentially serve as PHA production strains in nitrogen-poor waste stream substrates, based on their abilities to thrive in such environments.Novosphingobium nitrogenifigens Y88 T is a Gram-negative, obligate aerobe sphingomonad that was originally isolated from nickel-enriched pulp and paper mill wastewater (1). N. nitrogenifigens is capable of nitrogen fixation and production of poly-3-hydroxybutyrate (PHB). N. nitrogenifigens has also proven effective in the removal of Mn and Zn from model biorefinery effluent (A. Palumbo et al., submitted for publication). These metabolic properties led us to further explore the characteristics of this organism aided by its genome sequence.The draft genome of N. nitrogenifigens Y88 T (ICMP 16470 T , DSM 19370 T ) was obtained via Roche 454 pyrosequencing (454 Life Sciences, Branford CT) combining 454 GS 20 and 454 GS FLX Titanium paired-end sequencing (1,151,296 quality reads). Using Newbler 2.3 (454 Life Sciences), these reads were assembled into 19 scaffolds comprising 77 contigs at 60-fold coverage, totaling 4.14 Mbp. GϩC content was 63%. Annotation of predicted coding sequences (CDS) was performed using Glimmer version 3.02 (3), which identified 3,801 putative protein-coding genes. Of these CDS, 1,056 were identified as hypothetical/unknown function predicted proteins. Additionally, 49 tRNA genes were identified using the stand-alone version of tRNAscan-SE, v1.23 (7).Two small, related plasmids named py8 (5,911 bp) and py157 (5,720 bp) were also identified and independently confirmed (Quanfeng Liang and Gareth Lloyd-Jones, unpublished results). In contrast to the genome sequence, 363-fold (py8) and 465-fold (py157) coverage of the plasmids was achieved. The GϩC content of both plasmids was 58%. Neither of the plasmids harbored any CDS similar to known genes other than rep, mob, and traA genes, involved in plasmid conjugation and replication functions. Interestingly, these genes and a number of hypothetical CDS possess the greatest similarity to CDS in Sphingobium japonicum UT26S plasmid pUT2 (GenBank accession no. AP010807), a molecule with a molecular weight similar to those of py8 and py157.As expec...

Proteomic Phenotyping of Novosphingobium nitrogenifigens Reveals a Robust Capacity for Simultaneous Nitrogen Fixation, Polyhydroxyalkanoate Production, and Resistance to Reactive Oxygen Species

“…The identification of constitutively abundant proteins in both the EM and ED pathways, the latter of which produces additional NADPH relative to the former and has been shown to be associated with PHA production in other species (19), indicates the potential for continuous supply of carbon and reducing equivalents for PHB production. Examination of the Y88 genome (46) confirms that all genes in the ED pathway are present in Y88, which supports the proteomic data.…”

“…MS/MS data were interpreted using Mascot, version 2.2.00 (Matrix Science, London, United Kingdom) and an in-house Y88 genome database containing 3,801 predicted protein sequences as well as a concatenated database containing 456,037 sequences from translated Y88 genome sequences, a proprietary in-house translated sphingomonad genome database, and Swiss-Prot. The genome sequence data (46) were subsequently deposited in GenBank/EMBL/DDBJ and assigned the accession number AEWJ00000000. Locus tag numbers (format Y88_XXXX) discussed in the text are derived from this accession.…”

Comparative genomic analysis of six bacteria belonging to the genus Novosphingobium: insights into marine adaptation, cell-cell signaling and bioremediation

“…The six bacteria are as follows; Novosphingobium aromaticivorans DSM12444 (NC_007794, NC_009426, NC_009427), Novosphingobium pentaromaticivorans US6-1 (AGFM010000000), Novosphingobium nitrogenifigens Y88 (AEWJ010000000), Novosphingobium sp. PP1Y (NC_015579, NC_015582, NC_015583, NC_015580), Novosphingobium sp Rr 2–17 (AKFJ010000000) and Novosphingobium sp AP12 (AKKE010000000) [12-16]. The diverse isolation source and metabolic property of these strains provides an excellent opportunity to apply comparative genomics to identify the genetic features that differentiate each bacterium within this genus.…”

Variation in resource competition traits among Microcystis strains is affected by their microbiomes

“…Since N requirements are higher, it is logical that impacts on N acquisition were more noticeable. Another factor that helps explain the differences between microbiome impacts on growth under N versus P limitation is the fact that new inputs of N can be provided by associated N‐fixing bacteria, while this is not the case for P. We do not know whether any of the associated bacteria were N fixers, although some species of the abundantly present genus Novosphingobium have been found to do so 67 . In addition, bacterial N metabolism may have converted the supplied nitrate to the more preferred ammonium, which may explain enhanced Microcystis growth in presence of a microbiome.…”