Dataset Information

Pseudomonas Diversity Within Urban Freshwaters.

ABSTRACT: Freshwater lakes are home to bacterial communities with 1000s of interdependent species. Numerous high-throughput 16S rRNA gene sequence surveys have provided insight into the microbial taxa found within these waters. Prior surveys of Lake Michigan waters have identified bacterial species common to freshwater lakes as well as species likely introduced from the urban environment. We cultured bacterial isolates from samples taken from the Chicago nearshore waters of Lake Michigan in an effort to look more closely at the genetic diversity of species found there within. The most abundant genus detected was Pseudomonas, whose presence in freshwaters is often attributed to storm water or runoff. Whole genome sequencing was conducted for 15 Lake Michigan Pseudomonas strains, representative of eight species and three isolates that could not be resolved with named species. These genomes were examined specifically for genes encoding functionality which may be advantageous in their urban environment. Antibiotic resistance, amidst other known virulence factors and defense mechanisms, were identified in the genome annotations and verified in the lab. We also tested the Lake Michigan Pseudomonas strains for siderophore production and resistance to the heavy metals mercury and copper. As the study presented here shows, a variety of pseudomonads have inhabited the urban coastal waters of Lake Michigan.

SUBMITTER: Batrich M

PROVIDER: S-EPMC6384249 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Publications

<i>Pseudomonas</i> Diversity Within Urban Freshwaters.

Batrich Mary M Maskeri Laura L Schubert Ryan R Ho Brian B Kohout Melanie M Abdeljaber Malik M Abuhasna Ahmed A Kholoki Mutah M Psihogios Penelope P Razzaq Tahir T Sawhney Samrita S Siddiqui Salah S Xoubi Eyad E Cooper Alexandria A Hatzopoulos Thomas T Putonti Catherine C

Frontiers in microbiology 20190215

Freshwater lakes are home to bacterial communities with 1000s of interdependent species. Numerous high-throughput 16S rRNA gene sequence surveys have provided insight into the microbial taxa found within these waters. Prior surveys of Lake Michigan waters have identified bacterial species common to freshwater lakes as well as species likely introduced from the urban environment. We cultured bacterial isolates from samples taken from the Chicago nearshore waters of Lake Michigan in an effort to l ...[more]

PMID: 30828321

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Project description:The Pseudomonas fluorescens complex includes Pseudomonas strains that have been taxonomically assigned to more than fifty different species, many of which have been described as plant growth-promoting rhizobacteria (PGPR) with potential applications in biocontrol and biofertilization. So far the phylogeny of this complex has been analyzed according to phenotypic traits, 16S rDNA, MLSA and inferred by whole-genome analysis. However, since most of the type strains have not been fully sequenced and new species are frequently described, correlation between taxonomy and phylogenomic analysis is missing. In recent years, the genomes of a large number of strains have been sequenced, showing important genomic heterogeneity and providing information suitable for genomic studies that are important to understand the genomic and genetic diversity shown by strains of this complex. Based on MLSA and several whole-genome sequence-based analyses of 93 sequenced strains, we have divided the P. fluorescens complex into eight phylogenomic groups that agree with previous works based on type strains. Digital DDH (dDDH) identified 69 species and 75 subspecies within the 93 genomes. The eight groups corresponded to clustering with a threshold of 31.8% dDDH, in full agreement with our MLSA. The Average Nucleotide Identity (ANI) approach showed inconsistencies regarding the assignment to species and to the eight groups. The small core genome of 1,334 CDSs and the large pan-genome of 30,848 CDSs, show the large diversity and genetic heterogeneity of the P. fluorescens complex. However, a low number of strains were enough to explain most of the CDSs diversity at core and strain-specific genomic fractions. Finally, the identification and analysis of group-specific genome and the screening for distinctive characters revealed a phylogenomic distribution of traits among the groups that provided insights into biocontrol and bioremediation applications as well as their role as PGPR.

Dataset Information

Pseudomonas Diversity Within Urban Freshwaters.

Publications

<i>Pseudomonas</i> Diversity Within Urban Freshwaters.

Similar Datasets

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