Genome Sequence of a Typical Ultramicrobacterium, Curvibacter sp. Strain PAE-UM, Capable of Phthalate Ester Degradation.

Curvibacter sp. strain PAE-UM, isolated from river sediment, is a typical ultramicrobacterium capable of phthalate ester degradation. The genome of Curvibacter sp. PAE-UM consists of 3,284,473 bp, and its information will provide insights into the molecular mechanisms underlying its degradation ability.

GENOME ANNOUNCEMENT

Phthalate esters (PAEs) are widely used in the manufacture of household products, pharmaceuticals, etc. as plasticizers. However, PAEs constitute one of the most frequently detected persistent organic pollutants in the environment (1). Known as endocrine-disrupting chemicals, PAEs and their degradation intermediates are reported to pose potential risks to human health (2). Microbial degradation of PAEs has attracted considerable attention, and a number of bacteria capable of degrading PAEs have been reported (1, 3, 4). However, the degradation of PAEs under oligotrophic conditions (i.e., low-nutrient concentration) has largely been neglected. Curvibacter sp. strain PAE-UM is the first described ultramicrobacterium capable of utilizing various types of PAEs as its sole carbon and energy source under oligotrophic conditions.

Ultramicrobacteria are defined as bacteria with a cell volume of <0.1 µm3, and they retain this volume irrespective of growth conditions (5). The significance of such small bacteria in the biological cycling of nutrients has been recognized by microbial ecologists (6, 7). Curvibacter sp. PAE-UM is a typical ultramicrobacterium possessing a distinctive small biovolume (<0.05 µm³). It was isolated from sediment in the Songhua River using the extinction dilution method in combination with flow cytometric analysis (8). It was cultured under oligotrophic conditions with sterilized mineral water as the medium (7) and PAEs as the sole carbon and energy source. Strain PAE-UM can mineralize different PAEs, including dimethyl phthalate, diethyl phthalate, di-n-butyl phthalate, di(2-ethylhexyl) phthalate, and butyl benzyl phthalate.

The complete genome of Curvibacter sp. strain PAE-UM was sequenced using the Illumina HiSeq 2000 sequencing platform. Genomic libraries were constructed containing 500-bp paired-end (PE) and 6-kbp mate-pair (MP) inserts to generate hybrid 906 Mb of data, assembled into 3,632,663 bp and providing 249.4-fold coverage of the genome. The reads, assembled into 36 contigs utilizing de novo assembly, were used to construct 4 scaffolds. The genome was submitted to the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) for annotation. The functions of predicted protein-coding genes were annotated through comparisons with the NCBI nonredundant (NR) and Swiss-Prot databases from the European Bioinformatics Institute.

The genome has a total length of 3,632,663 bp, with a G+C content of 65.5%. Further analysis showed that the genome contains 3,409 genes, which make up 90.4% of the whole genome. According to tRNAscan-SE (9) and RNAmmer 1.2 (10), there are 3 rRNA operons and 48 tRNA genes in the genome. Strain PAE-UM belongs to the genus Curvibacter on the basis of 16S rRNA gene sequencing and genetic comparison with the strain Curvibacter sp. R-36930 (accession no. NC_ FR691424). Functional annotation showed that strain PAE-UM possesses a number of PAE-degrading genes, including genes encoding for esterase, 4,5-dihydroxyphthalate decarboxylase, protocatechuate 3,4-dioxygenase, 2-pyrone-4,6-dicarboxylate-degrading genes, 4-oxalomesaconate hydratase, 4-carboxy-4-hydroxy-2-oxoadipate aldolase, and others.

In summary, we have sequenced the complete genome of a typical ultramicrobacterium, Curvibacter sp. strain PAE-UM, capable of degrading PAEs under oligotrophic conditions. The complete genome sequence of strain PAE-UM will contribute toward a greater understanding of the molecular mechanisms underlying PAE degradation and provide new perspectives on the ecological functions of ultramicrobacteria.

Nucleotide sequence accession number.

The complete genome sequence of Curvibacter sp. strain PAE-UM has been deposited in GenBank under the accession number LKCX00000000.