Abstract
Microbial communities in the termite hindgut are essential for degrading plant material. We present the high-quality draft genome sequence of the Opitutaceae bacterium strain TAV1, the first member of the phylum Verrucomicrobia to be isolated from wood-feeding termites. The genomic analysis reveals genes coding for lignocellulosic degradation and nitrogen fixation.
GENOME ANNOUNCEMENT
The Opitutaceae bacterium strain TAV1 was isolated from the hindgut of the wood-feeding termite Reticulitermes flavipes (10). This termite-associated Verrucomicrobia (TAV) isolate is a Gram-negative, coccoid-shaped, microaerophilic bacterium. Owing to the importance of microbial symbionts in the termite hindgut for the degradation of cellulose and hemicellulose into acetate, hydrogen, and methane (2, 3), we investigated the genetic potential of strain TAV1 for the degradation of lignocellulosic material and overall functional attributes associated with its ecological role.
The genomic DNA of strain TAV1 was isolated using a cetyltrimethylammonium bromide method (http://my.jgi.doe.gov/general/). Genome sequence was generated with a combination of Illumina and 454 pyrosequencing platforms. The individual reads were assembled with the Newbler assembler (Roche) and generated 82 contigs with the largest being 590 kb and the smallest contig being 530 bp. All contigs span up to the length of 7.1 Mbp, and the average GC content of the genome is approximately 63.2%. Genes were identified using Prodigal (5) as part of the Oak Ridge National Laboratory genome annotation pipeline, followed by a round of manual curation using the JGI GenePRIMP pipeline (9). The predicted protein-coding genes (coding sequences [CDS]) were translated and used to search the National Center for Biotechnology Information (NCBI) nonredundant database and the UniProt, TIGRFam, Pfam, PRIAM, KEGG, COG, and InterPro databases. These data sources were combined to produce a product description for each predicted protein. Noncoding genes and miscellaneous features were predicted using tRNAscan-SE (8), RNAMMer (7), Rfam (4), TMHMM (6), and signalP (1).
The draft genome contains 6,051 genes with 5,987 CDS. A total of 64 structural RNAs were identified in the genome, with the presence of one rRNA operon. Protein coding genes were classified according to the cluster of orthologous groups (COG categories). The top five functional groups were as follows: (i) general function prediction only (526 genes), (ii) transcription (476 genes), (iii) carbohydrate metabolism (406 genes), (iv) amino acid metabolism (403 genes), and (v) energy production and conversion (310 genes). Further inspection using the carbohydrate-active enzyme database (http://www.cazy.org) revealed that the TAV1 genome contains a large number of genes encoding glycoside hydrolases (GH), which are involved in the breakage of bonds between two or more carbohydrate moieties. These GH enzymes contained both catalytic and carbohydrate-binding modules, such as glycoside hydrolase family 5, cellulase, endo-1,4-beta-xylanase, N-acetylglucosamine-6-phosphate deacetylase, peptidoglycan glycosyltransferase, and 1,4-alpha-glucan branching enzyme. Moreover, 13 genes associated with nitrogen fixation were identified, such as nitrogen iron reductase protein (nifH), nitrogenase molybdenum-iron (nifD), FeS assembly protein (nifU), and nitrogenase MoFe cofactor biosynthesis protein (nifE) genes, among others. In addition, the TAV1 genome contains the cbb3-type cytochrome oxidase, which has high affinity for oxygen. Effective removal of O2 is essential for the homoacetogenic and methanogenic process to occur. The presence of genes associated with lignocellulose degradation, nitrogen fixation, and oxygen consumption implies an important ecological role for strain TAV1 in the functioning of the hindgut ecosystem.
Nucleotide sequence accession number.
The high-quality draft genome sequence of the Opitutaceae bacterium was deposited in GenBank under the accession number AHKS00000000.
ACKNOWLEDGMENT
The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under contract no. DE-AC02-05CH11231.
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