Reconstructing a Thauera genome from a hydrogenotrophic-denitrifying consortium using metagenomic sequence data.
Here, shotgun metagenomic sequencing was conducted to reveal the hydrogen-oxidizing autotrophic-denitrifying metabolism in an enriched Thauera-dominated consortium. A draft genome named Thauera R4 of over 90 % completeness (3.8 Mb) was retrieved mainly by a coverage-defined binning method from 3.5 Gb paired-end Illumina reads. We identified 1,263 genes (accounting for 33 % of total genes in the finished genome of Thauera aminoaromatica MZ1T) with average nucleotide identity of 87.6 % shared between Thauera R4 and T. aminoaromatica MZ1T. Although Thauera R4 and T. aminoaromatica shared quite similar nitrogen metabolism and a high nucleotide similarity (98.8 %) in their 16S ribosomal RNA genes, they showed different functional potentials in several important environmentally relevant processes. Unlike T. aminoaromatica MZ1T, Thauera R4 carries an operon of [NiFe]-hydrogenase (EC 1.12.99.6) catalyzing molecular hydrogen oxidation in nitrate-rich solution. Moreover, Thauera R4 is a mixtrophic bacterium possessing key enzymes for autotrophic CO2-fixation and heterotrophic acetate assimilation metabolism. This Thauera R4 bin provides another genetic reference to better understand the niches of Thauera and demonstrates a model pipeline to reveal functional profiles and reconstruct novel and dominant genomes from a simplified mixed culture in environmental studies.
Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Hong Kong, SAR, China.
Yanping
Y
Mao
Yu
Y
Xia
Zhiping
Z
Wang
Tong
T
Zhang
D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D019149:Bioreactors / Q000382:microbiology; D058440:Denitrification; D016680:Genome, Bacterial; D006859:Hydrogen / Q000378:metabolism*; D006864:Hydrogenase / Q000235:genetics / Q000378:metabolism; D056186:Metagenomics; D059013:Microbial Consortia; D008969:Molecular Sequence Data; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D020628:Thauera / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification / Q000378:metabolism
D001426:Bacterial Proteins; D006859:Hydrogen; C043296:nickel-iron hydrogenase; D006864:Hydrogenase