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Genome sequencing reveals mechanisms for heavy metal resistance and polycyclic aromatic hydrocarbon degradation in Delftia lacustris strain LZ-C

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Abstract

Strain LZ-C, isolated from a petrochemical wastewater discharge site, was found to be resistant to heavy metals and to degrade various aromatic compounds, including naphenol, naphthalene, 2-methylnaphthalene and toluene. Data obtained from 16S rRNA gene sequencing showed that this strain was closely related to Delftia lacustris. The 5,889,360 bp genome of strain LZ-C was assembled into 239 contigs and 197 scaffolds containing 5855 predicted open reading frames (ORFs). Among these predicted ORFs, 464 were different from the type strain of Delftia. The minimal inhibitory concentrations were 4 mM, 30 µM, 2 mM and 1 mM for Cr(VI), Hg(II), Cd(II) and Pb(II), respectively. Both genome sequencing and quantitative real-time PCR data revealed that genes related to Chr, Czc and Mer family genes play important roles in heavy metal resistance in strain LZ-C. In addition, the Na+/H+ antiporter NhaA is important for adaptation to high salinity resistance (2.5 M NaCl). The complete pathways of benzene and benzoate degradation were identified through KEGG analysis. Interestingly, strain LZ-C also degrades naphthalene but lacks the key naphthalene degradation gene NahA. Thus, we propose that strain LZ-C exhibits a novel protein with a function similar to NahA. This study is the first to reveal the mechanisms of heavy metal resistance and salinity tolerance in D. lacustris and to identify a potential 2-methylnaphthalene degradation protein in this strain. Through whole-genome sequencing analysis, strain LZ-C might be a good candidate for the bioremediation of heavy metals and polycyclic aromatic hydrocarbons.

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Acknowledgments

This research was supported by a National Natural Science Foundation Grants 31470224, 31200085, MOST international cooperation Grant 2014DFA91340 and Gansu Provincial International Cooperation Grant 134WCGA176.

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    1. MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, People’s Republic of China

      Wenyang Wu, Haiying Huang, Zhenmin Ling, Zhengsheng Yu, Yiming Jiang, Pu Liu & Xiangkai Li

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    Wenyang Wu and Haiying Huang have contributed equally to this work.

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    Cell growth over a range of temperatures (A) and pH values (B) (TIFF 957 kb)

    10646_2015_1583_MOESM2_ESM.tif

    COG functional classification. The total number of classification is based on the 5204 COG assignments across the 5179 protein-coding genes with at least one COG assignment. Within the COG category, not comprises hypothetical protein-coding and RNA genes (TIFF 41213 kb)

    10646_2015_1583_MOESM3_ESM.tif

    Global gene conservation in Delftia. Each circle represents the total number of gene types in each genome. Overlapping regions depict the number of genes types shared between the respective genomes. The numbers outside the circles indicate the total number of genes identified in each genome, including paralogs and gene duplications. Abbreviations: CCUG 15835, Delftia acidovorans CCUG 15835; CCUG 274B, Delftia acidovorans CCUG 274B; Cs1-4, Delftia sp. Cs1-4; SPH-1, Delftia acidovorans SPH-1 (TIFF 23312 kb)

    10646_2015_1583_MOESM4_ESM.tif

    The LZ-C genome was compared with other Delftia genomes. Dot plots were constructed using MUMmer 3.22 software, and nucleotide-based alignments were performed with MUMmer. The dot plots were generated using the MUMmerplot script and the gnuplot program (www.gnuplot.info/docs_4.0/gnuplot.html). The aligned segments are represented as dots or lines. Forward matches are shown in red, and reverse complement matches are shown in blue. Abbreviations: CCUG 15835, Delftia acidovorans CCUG 15835; CCUG 274B, Delftia acidovorans CCUG 274B; Cs1-4, Delftia sp. Cs1-4; SPH-1, Delftia acidovorans SPH-1 (TIFF 26060 kb)

    The unique genes in LZ-C compared to other Delftia strains (XLSX 25 kb)

    High salt tolerance genes identified in strain LZ-C (XLSX 9 kb)

    Heavy metal resistance genes identified in strain LZ-C (XLSX 13 kb)

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    Wu, W., Huang, H., Ling, Z. et al. Genome sequencing reveals mechanisms for heavy metal resistance and polycyclic aromatic hydrocarbon degradation in Delftia lacustris strain LZ-C. Ecotoxicology 25, 234–247 (2016). https://doi.org/10.1007/s10646-015-1583-9

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