Draft Genome Sequences of 10 Environmental Pseudomonas aeruginosa Strains Isolated from Soils, Sediments, and Waters

Evolutionary Genomics of Niche-Specific Adaptation to the Cystic Fibrosis Lung in Pseudomonas aeruginosa

The comparative genomics of the transition of the opportunistic pathogen Pseudomonas aeruginosa from a free-living environmental strain to one that causes chronic infection in the airways of cystic fibrosis (CF) patients remain poorly studied. Chronic infections are thought to originate from colonization by a single strain sampled from a diverse, globally distributed population, followed by adaptive evolution to the novel, stressful conditions of the CF lung. However, we do not know whether certain clades are more likely to form chronic infections than others and we lack a comprehensive view of the suite of genes under positive selection in the CF lung. We analyzed whole-genome sequence data from 1,000 P. aeruginosa strains with diverse ecological provenances including the CF lung. CF isolates were distributed across the phylogeny, indicating little genetic predisposition for any one clade to cause chronic infection. Isolates from the CF niche experienced stronger positive selection on core genes than those derived from environmental or acute infection sources, consistent with recent adaptation to the lung environment. Genes with the greatest differential positive selection in the CF niche include those involved in core cellular processes such as metabolism, energy production, and stress response as well as those linked to patho-adaptive processes such as antibiotic resistance, cell wall and membrane modification, quorum sensing, biofilms, mucoidy, motility, and iron homeostasis. Many genes under CF-specific differential positive selection had regulatory functions, consistent with the idea that regulatory mutations play an important role in rapid adaptation to novel environments.

Draft Genome Sequences of Bacillus subtilis Strains TNC1(2019), TNC3(2019), and TNW1(2019), as Well as Bacillus velezensis Strains TNC2(2019) and TNW2(2019), Isolated from Cabbage Kimchee

We report the draft genome sequences of five novel Bacillus strains isolated from five different batches of fermented Napa cabbage kimchee. Strains TNC1(2019), TNC3(2019), and TNW1(2019) were identified as Bacillus subtilis, while TNC2(2019) and TNW2(2019) were identified as Bacillus velezensis.

We report the draft genome sequences of five novel Bacillus strains isolated from five different batches of fermented Napa cabbage kimchee. Strains TNC1(2019), TNC3(2019), and TNW1(2019) were identified as Bacillus subtilis, while TNC2(2019) and TNW2(2019) were identified as Bacillus velezensis.

Draft Genome Sequences of Bacillus sp. Strains RM1(2019), RM2(2019), RM9(2019), RM11(2019), and RM15(2019), Isolated from Temperate Soils in the Hudson River Valley of New York

We report the draft genome sequences of five novel Bacillus strains isolated from temperate soils in Annandale-on-Hudson, NY. Strains RM1(2019), RM9(2019), and RM15(2019) were identified as Bacillus toyonensis, while RM11(2019) was identified as Bacillus thuringiensis. The draft genome of strain RM2(2019) was unclassified and likely represents a new species.

We report the draft genome sequences of five novel Bacillus strains isolated from temperate soils in Annandale-on-Hudson, NY. Strains RM1(2019), RM9(2019), and RM15(2019) were identified as Bacillus toyonensis, while RM11(2019) was identified as Bacillus thuringiensis. The draft genome of strain RM2(2019) was unclassified and likely represents a new species.

Draft Genome Sequences of Phenotypically Distinct Janthinobacterium sp. Isolates Cultured from the Hudson Valley Watershed

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.

Draft Genome Sequence of a Violacein-Producing Iodobacter sp. from the Hudson Valley Watershed

Iodobacter species are among a number of freshwater Gram-negative violacein-producing bacteria. Janthinobacterium lividum and Chromobacterium violaceum have had their whole genomes sequenced and annotated. This is the first report of a draft whole-genome sequence of a violacein-producing Iodobacter strain that was isolated from the Hudson Valley watershed.

Draft Genome Sequence of a Red-Pigmented Janthinobacterium sp. Native to the Hudson Valley Watershed

Water samples from the Hudson Valley watershed indicate that the area is host to many violacein-producing bacterial isolates. Here, we report the draft whole-genome sequence of Janthinobacterium sp. strain BJB412, an isolate lacking violacein production yet containing genes responsible for prodigiosin, biofilm production, and quorum sensing, like its purple-pigmented counterparts.