Complete Genome Sequences of Arcobacter butzleri ED-1 and Arcobacter sp. Strain L, Both Isolated from a Microbial Fuel Cell

GENOME ANNOUNCEMENT

Arcobacter butzleri strain ED-1 is a microaerobic exoelectrogenic epsilonproteobacterium isolated from the electrode of an acetate-fed microbial fuel cell (MFC) (1). It was the first epsilonproteobacterium demonstrated to act as an exoelectrogen and can readily transfer electrons to an external solid electron acceptor as a pure culture when supplied with acetate as the sole carbon source. The liquid phase of the same laboratory MFC was dominated by a different Arcobacter sp., strain L (1); together, these two Arcobacter spp. made up >90% of the fuel cell community. The 16S rRNA gene sequence of A. butzleri ED-1 is identical to that in the sequenced genome of A. butzleri strain RM4018 (4), while that of Arcobacter sp. strain L is more closely related to those of other Arcobacter spp. such as Arcobacter nitrofigilis (1). Neither the interspecies interactions between the Arcobacter spp. nor the mechanism by which A. butzleri ED-1 transfers electrons from acetate to the electrode has been characterized. We therefore carried out whole-genome sequencing of these two Arcobacter species as a tool for investigating these questions.

The complete genome sequences of A. butzleri ED-1 and Arcobacter sp. strain L were determined using a combination of the Sanger method (ABI 3730xl sequencers) and 454 pyrosequencing (GS-FLX sequencers). We generated 13,300 (3730xl) and 493,869 (GS-FLX) sequences from the ED-1 genome and 18,223 (3730xl) and 244,537 (GS-FLX) sequences from the Arcobacter sp. strain L genome. The 454 pyrosequencing reads were first assembled using the Newbler assembler software according to the supplier's protocol, and then 366 (strain ED-1) and 214 (strain L) of the GS-FLX contigs were imported into the Sanger data as “pseudoreads” using the Phred/Phrap/Consed system (2). The hybrid assembly of the Sanger and 454 data eventually generated 26 (strain ED-1) and 20 (strain L) contigs. Gap closing and resequencing of low-quality regions in the assembled data were performed by PCR, primer walking, and direct sequencing of appropriate plasmid clones. The overall accuracy of the finished sequence was estimated to have an error rate of <1 per 10,000 bases (Phrap score of ≥40). Prediction and annotation of protein-coding genes were performed as described previously (3, 5).

The ED-1 genome consists of a circular 2,256,675-bp chromosome with a G+C content of 27.1% and contains 2,158 predicted protein-coding genes. We could assign known functions to 1,454 (67%) of them, 639 (30%) as conserved hypothetical genes and 65 (3%) as novel hypothetical genes. ED-1 and RM4018 share 1,950 orthologous genes. The Arcobacter sp. strain L genome consists of a circular 2,945,673-bp chromosome (G+C content, 26.6%) containing 2,845 predicted protein-coding genes and a small plasmid (1,989 bp; G+C content, 46.6%) containing three protein-coding genes. We could assign known functions to 1,812 (64%) of them, 748 (26%) as conserved hypothetical genes and 288 (10%) as novel hypothetical genes. The Arcobacter sp. strain L genome also contains the region (2,051 bp) known as clustered regularly interspersed short palindromic repeats (CRISPR). Arcobacter ED-1 and Arcobacter sp. strain L encode five rRNA gene operons (5S, 16S, and 23S rRNAs), and there were 53 tRNA genes in the ED-1 genome and 56 in that of Arcobacter sp. strain L. Arcobacter ED-1 and Arcobacter sp. strain L share 1,744 orthologous genes.