ABSTRACT
Investigation of the Hudson Valley watershed reveals many violacein-producing bacteria. These are of interest for their biotherapeutic potential in treating chytrid infections of amphibians. The draft whole-genome sequences for seven Janthinobacterium isolates with a variety of phenotypes are provided in this study.
GENOME ANNOUNCEMENT
The Hudson Valley watershed is home to a large number of vibrantly colored bacterial isolates (1). Many of these Gram-negative Bacillus species produce violacein. Production is mediated via a five-gene operon, vioA–E (2). Violacein production was first described in Chromobacterium violaceum in 1927 (3), and violacein has been widely investigated for its potential biotherapeutic properties; studies have demonstrated bacterial killing (4), fungal killing (5, 6), antiviral activity (7), tumoral cytotoxicity (8, 9), and antinematodal action (10).
Strains BJB1, BJB301, BJB303, BJB304, BJB312, BJB426, and BJB446 were obtained by plating Hudson Valley freshwater sources on R2A agar and incubating at 22 to 25°C for 48 h. All strains initially presented as violet-pigmented colonies and were cultured on R2A, LB, and 1% tryptone agar media. All strains have been characterized for phenotypic behaviors related to growth, motility, quorum sensing, biofilm production, and violacein expression (our unpublished data). Density-dependent phenotypes, including biofilm production and violacein expression, may provide the microorganism with the ability to persist and thrive in a freshwater environment (11).
Genomic DNA extraction was completed with the Qiagen Gentra Puregene Yeast/Bact. kit according to the manufacturer’s protocol. Paired-end Illumina libraries (150 bp) were prepared and HiSeq sequencing was completed using the Illumina HiSeq 4000 instrument (Wright Labs, Huntington, PA). Reads were assembled with a modified version of a previously published local pipeline (12). Adapters and contaminants were scanned for and removed when present. Reads were subsequently quality filtered using BBDuk from the BBMap package version 37.50, keeping to a Q score cutoff of 10 (https://sourceforge.net/projects/bbmap). A draft whole-genome assembly was built using SPAdes version 3.11.0 (13) using k-mer sizes of 21, 33, 55, 77, 99, and 127. Contigs shorter than 500 bp or those composed of fewer than four reads were subsequently filtered out of the assembly.
The draft whole-genome assemblies ranged from a high of 70 contigs for BJB426 to a low of 22 contigs for BJB446 (Table 1). The average N50 value for all seven optimal assemblies was 940,382 bp, with two genomes, those of BJB301 and BJB446, resulting in high N50 values of 1,349,355 bp and 3,551,037 bp, respectively (Table 1). The average genome size is predicted to be 6.36 Mbp in length, with an average G+C content of 62.85%, comparable to those of published Janthinobacterium species (Table 1) (14, 15).
TABLE 1 .
Characteristics of the isolates in this study
| Isolate | Origin | Location | No. of contigs |
Genome size (bp) |
G+C content (%) |
N50 (bp) | Median read depth (×) |
Avg no. of CDSs |
GenBank accession no. |
|---|---|---|---|---|---|---|---|---|---|
| BJB1 | Water | Esopus, Hudson Valley, NY | 56 | 6,353,752 | 63.35 | 369,198 | 730 | 5,718 | PDZO00000000 |
| BJB301 | Water | Fishkill Creek, Hudson Valley, NY | 24 | 6,386,165 | 62.78 | 1,349,355 | 504 | 5,665 | PDZJ00000000 |
| BJB303 | Water | North Tivoli Bay, Red Hook, NY | 48 | 6,275,771 | 63.36 | 319,682 | 577 | 5,680 | PDZI00000000 |
| BJB304 | Water | Norrie Pond, Hudson Valley, NY | 62 | 6,466,089 | 62.72 | 218,724 | 67 | 5,773 | PDZN00000000 |
| BJB312 | Water | Dutchess County, NY (vernal pool) | 38 | 6,224,897 | 62.61 | 488,122 | 864 | 5,559 | PDZM00000000 |
| BJB426 | Water | Staatsburg, NY | 70 | 6,413,115 | 62.47 | 286,558 | 156 | 5,711 | PDZL00000000 |
| BJB446 | Water | Echo Valley, Hudson Valley, NY | 22 | 6,403,346 | 62.67 | 3,551,037 | 316 | 5,701 | PDZK00000000 |
The assembled contigs were annotated using three methods, a local pipeline running the Prokka genome annotation software (16), the RASTtk annotation software, via the PATRIC pipeline (17, 18), and the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (19). The 16S rRNA BLAST results for all seven strains aligned most closely with other Janthinobacterium species. Annotations across platforms yielded an average of 5,686 coding sequences (CDSs). As expected, a violacein biosynthesis operon (vioA–E) was present in all strains. Additionally, all genomes contained genes involved in the bacterial quorum sensing cascade, jqsA, qseC, and qseS (10, 15), as well as twitching motility (pilT, pilJ, pilH, and pilG), correlating with the phenotypes observed on media.
Further investigation of this large population of related strains may lead to insights into the therapeutic potential of violacein-producing strains.
Accession number(s).
The whole-genome assemblies have been deposited at DDBJ/ENA/GenBank under the accession numbers listed in Table 1.
ACKNOWLEDGMENTS
Many thanks go to Veronica Steckler and Liza Miller for collection water and initial growth of strains.
B.A.J. was provided funding by the New York State Water Resources Institute. Support for training was provided by GCAT-SEEK. GCAT-SEEK has been supported by U.S. National Science Foundation award DBI-1248096: RCN-UBE—GCAT-SEEK: the Genome Consortium for Active Undergraduate Research and Teaching Using Next-Generation Sequencing. K.O. and G.D. were provided summer research support by the Bard Summer Research Institute.
Footnotes
Citation Bettina AM, Doing G, O’Brien K, Perron GG, Jude BA. 2018. Draft genome sequences of phenotypically distinct Janthinobacterium sp. isolates cultured from the Hudson Valley watershed. Genome Announc 6:e01426-17. https://doi.org/10.1128/genomeA.01426-17.
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