Draft Genome Sequences of Two Pseudoalteromonas Strains Isolated from Roots and Leaf Blades of the Seagrass Zostera marina.

Here, we present the draft genome sequences for Pseudoalteromonas sp. strain UCD-33C and Pseudoalteromonas lipolytica UCD-48B. Pseudoalteromonas sp. UCD-33C was isolated from Zostera marina roots and P. lipolytica UCD-48B from Z. marina leaf blades, both collected in Woods Hole, MA. These assemblies contain 4,479,285 bp and 4,592,435 bp, respectively.

GENOME ANNOUNCEMENT

Pseudoalteromonas lipolytica was first isolated from Yangtze River estuary seawater. It is Gram-negative, motile, and strictly aerobic, has rod-shaped cells, and produces exopolysaccharides (1). Some Pseudoalteromonas strains exhibit antimicrobial abilities that are inhibitory to cystic fibrosis-associated opportunistic pathogens (2). Pseudoalteromonas sp. strain UCD-33C and P. lipolytica UCD-48B were both isolated from seagrass (Zostera marina) collected in Woods Hole, MA. Pseudoalteromonas sp. UCD-33C came from roots, whereas strain UCD-48B was isolated from leaf blades. This culturing project was done as part of a collaboration between researchers at the University of California, Davis, CA, and University of Oregon, Eugene, OR, called The Seagrass Microbiome Project (http://www.seagrassmicrobiome.org). The project seeks to characterize and analyze the microbial communities living in and on seagrasses.

Bacterial isolates were grown and double-dilution struck on Luria broth (LB) agar (Difco), seawater agar (SWA), 10% diluted seawater agar (SW10), and Azotobacter isolation medium agar (NFM). The isolates were incubated at 25°C for 1 to 21 days. Scrapings were then frozen in 25% glycerol for long-term storage. The isolates were later thawed and grown in seawater nutrient agar medium (ATCC medium 2205, using Instant Ocean instead of synthetic seawater). DNA was subsequently extracted from a fresh overnight culture using the Wizard genomic DNA purification kit (Promega).

A paired-end library was produced using a Nextera DNA sample prep kit (Illumina) and sequenced on an Illumina HiSeq (250 bp paired-end reads). Sequencing of Pseudoalteromonas sp. UCD-33C resulted in 807,945 reads and approximately 90× coverage. The genome size was 4,479,285 bp, and the G+C content was 41.3%. Sequencing of P. lipolytica UCD-48B yielded 885,488 reads and approximately 96× coverage. Its genome size was 4,592,435 bp and had 41.4% G+C content. The sequences were processed using the A5-miseq assembly pipeline (3, 4), which automates error correction, data cleaning, contig assembly, scaffolding, and quality control. The completeness of the genome was assessed using PhyloSift (5), which utilizes a list of 37 highly conserved single-copy marker genes (6). One copy of each marker gene was found in the sequences. Automated annotation was done using the RAST annotation server (7). A combination of BLAST and phylogenetic trees using the full-length assembled 16S rRNA sequences revealed strain UCD-48B to belong to P. lipolytica. However, the placement of the UCD-33C strain was ambiguous, falling into a polyphyletic and poorly resolved group, making it impossible to determine a species without further work.

Nucleotide sequence accession numbers.

The genome sequence for Pseudoalteromonas sp. UCD-33C has been deposited at DDBJ/EMBL/GenBank under the accession no. LJTB00000000. The version described in this paper is no. LJTB00000000.1. The genome sequence for P. lipolytica UCD-48B has been deposited at DDBJ/EMBL/GenBank under the accession no. LJTC00000000. The version described in this paper is no. LJTC00000000.1.