Dyadobacter pollutisoli sp. nov., isolated from plastic waste landfill soil

Abstract

A Gram-stain-negative, yellow-pigmented and facultatively aerobic bacterium, designated strain U1T, was isolated from plastic dumped soil sampled in the Republic of Korea. Cell of strain U1T were non-motile rods showing catalase-negative and oxidase-positive activities. Strain U1T was shown to grow at 10–37 °C (optimum, 25–30 °C) and pH 6.0–9.0 (optimum, pH 8.0), and in the presence of 0–0.5 % (w/v) NaCl (optimum, 0 %). Strain U1T contained iso-C15 : 0, C16 : 0, C16 : 1 ω5c and summed feature 3 (comprising C16 : 1 ω6c and/or C16 : 1 ω7c) as the major cellular fatty acids (>5 %) and menaquinone-7 as the sole respiratory quinone. Phosphatidylethanolamine, two unidentified aminolipids and three unidentified lipids were identified as the major polar lipids. The DNA G+C content of strain U1T calculated from the whole-genome sequence was 45.5 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain U1T formed a distinct phylogenetic lineage within the genus Dyadobacter . Strain U1T has the highest 16S rRNA sequence similarity to Dyadobacter bucti QTA69T (97.9 %). Average nucleotide identity and digital DNA–DNA hybridization values between strain U1T and D. bucti QTA69T were 74.6 % and 18.9 %, respectively. Based on phenotypic, chemotaxonomic and molecular features, strain U1T represents a novel species of the genus Dyadobacter , for which the name Dyadobacter pollutisoli sp. nov. is proposed. The type strain is U1T (= KACC 22210T=JCM 34491T).

Chitinophaga pollutisoli sp. nov., isolated from contaminated sediment

“…Strain GPA1 T was isolated from an enriched culture using PA and contaminated soil sediment in minimal salts basal (MSB) medium [12], following previously described methods [13,14]. To enrich PA-degrading bacteria, approximately 10 g sediment…”

“…Strain GPA1 T was isolated from an enriched culture using PA and contaminated soil sediment in minimal salts basal (MSB) medium [12], following previously described methods [13, 14]. To enrich PA-degrading bacteria, approximately 10 g sediment collected from a stream within an industrial complex in Incheon, Republic of Korea (37° 36′ 10.4″ N 126° 36′ 50.9″ E), was added to a cotton-plugged 500 ml Erlenmeyer flask containing 0.3 g PA as a sole carbon and energy source in 100 ml MSB medium.…”

“…Subsequently, the PCR products were double-digested with HaeIII and HhaI , followed by analysis using 2 % agarose gel electrophoresis. PCR products exhibiting distinct fragment patterns were partially sequenced with the universal primer 340F (5′-CCTACGGGAGGCAGCAG-3′) [14]. The obtained sequences were compared with those of all type strains of validly published species on the EzBioCloud server (www.ezbiocloud.net) [15].…”

“…The 16S rRNA amplicon of strain GPA1 T , amplified by the 27F and 1492R primers, was further sequenced using the universal primers 518R (5′-ATTACCGCGGCTGCTGG-3′) and 805F (5′-GATTAGATACCCTGGTAGTC-3′) [14]. The sequences obtained from the 340F, 518R, and 805F primers were assembled to generate a nearly complete 16S rRNA gene sequence (1461 nucleotides) of strain GPA1 T .…”

“…Colonies grown on R2A agar were subjected to PCR amplification of the 16S rRNA genes using universal primers 27F (5′-AGAGTTTGATCMTGGCTCAG-3′) and 1492R (5′-TACG GYTA CCTT GTTA CGACTT-3′) [14]. Subsequently, the PCR products were double-digested with HaeIII and HhaI, followed by analysis using 2 % agarose gel electrophoresis.…”