Pseudomonas lalkuanensis sp. nov., isolated from a bacterial consortia of contaminated soil enriched for the remediation of e-waste

Abstract

A novel e-waste-degrading strain, PE08T, was isolated from contaminated soil collected from a paper mill yard in Lalkuan, Uttarakhand, India. Strain PE08T was Gram-stain-negative, rod-shaped, aerobic, oxidase-positive and catalase-positive. Optimum growth was observed at 30 °C (range, 5–40 °C), with 1–2 % NaCl (range, 0–3 %) and at pH 7 (range 6–11). The phylogeny based on 16S rRNA gene sequences delineated strain PE08T to the genus Pseudomonas and showed highest sequence similarity to Pseudomonas furukawaii KF707T (98.70 %), followed by Pseudomonas aeruginosa DSM 50071T (98.62 %) and Pseudomonas resinovorans DSM 21078T (97.93 %). The genome of strain PE08T was sequenced and had one scaffold of 6056953 bp, 99.84 % completeness and 182× coverage were obtained. The G+C content in the genome was 64.24 mol%. The DNA–DNA hybridization and average nucleotide identity values between strain PE08T and its closely related type strain, P. resinovorans DSM 21078T were below 34.8 % and 87.96 %, respectively. The phylogenetic analysis based on whole-genome sequence and concatenated GyrB and RpoB proteins revealed that strain PE08T forms a district clade in the family Pseudomonadaceae . The predominant fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 :1 ω6c), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C12 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The phenotypic, chemotaxonomic and genetic analysis, including overall genome relatedness index values, indicated that strain PE08T represents a novel species of the genus Pseudomonas , for which the name Pseudomonas lalkuanensis sp. nov. is proposed. The type strain is PE08T (=MCC 3792=KCTC 72454=CCUG 73691).

Pseudomonas insulae sp. nov., isolated from island soil

“…The genome included an array of genes potentially related to plant growth promoting activity, including those for indole-3glycerol phosphate synthase and subunits of tryptophan synthase that are potentially related to IAA production, phosphonate *Data were taken from original studies [27][28][29]. All other data were obtained in this study.…”

“…*Data for P. carbonaria, P. lalkuanensis and P. thermotolerans, and those for isolation source, growth ranges and diagnostic polar lipids were taken from original studies[4,[27][28][29][30]. Data for DNA G+C contents were from GenBank Microbial Genomes database (www.ncbi.nlm.nih.gov/genome/ microbes/).…”

Pseudomonas boanensis sp. nov., a bacterium isolated from river water used for household purposes in Boane District, Mozambique

“…TYGS uses digital DNA–DNA hybridization (dDDH) to delineate species circumscriptions based on a 70 % threshold for species definition [10]. The whole genome-based maximum likelihood phylogeny showed that DB1 T was distant from other Pseudomonas species, with Pseudomonas resinovorans , Pseudomonas lalkuanensis [11] and Pseudomonas furukawaii [12] being close relatives. The dDDH and average nucleotide identity values towards the closest relatives were 39.5 and 81.93 % for P.…”

PCB-77 biodegradation potential of biosurfactant producing bacterial isolates recovered from contaminated soil

“…Bacteria play a significant role in the remediation of the PCB-contaminated environment ( Jing et al, 2018 ). Many PCB-degrading bacteria have been isolated including Gram-negative strains belonging to the genera Achromobacter ( Hong et al, 2009 ), Burkholderia ( Totevova et al, 2002 ; Goris et al, 2004 ), Pseudomonas ( Hatamian-Zarmi et al, 2009 ; Kimura et al, 2018 ; Hirose et al, 2019 ; Thorat et al, 2020 ), Ochrobactrum ( Murinova and Dercov, 2014 ) and Gram-positive strains belonging to the genera Rhodococcus ( Seto et al, 1995 ) and Bacillus ( Shimura et al, 1999 ). These bacteria carry out biodegradation (through the metabolic pathway) using enzymes that convert organic pollutants into simpler compounds ( Abramowicz, 1990 ).…”