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J Bacteriol. Nov 2012; 194(22): 6302–6303.
PMCID: PMC3486343
Genome Sequences of Two Freshwater Betaproteobacterial Isolates, Limnohabitans Species Strains Rim28 and Rim47, Indicate Their Capabilities as Both Photoautotrophs and Ammonia Oxidizers
Yonghui Zeng,ab Vojtěch Kasalický,cd Karel Šimek,cd and Michal Koblížekcorresponding authorad
aInstitute of Microbiology CAS, Opatovický Mlýn, Třeboň, Czech Republic
bGuangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Guangdong Ocean University, Zhanjiang, China
cBiology Centre of the Academy of Sciences ČR, v.v.i., Institute of Hydrobiology, Na Sádkách 7, České Budějovice, Czech Republic
dFaculty of Science, University of South Bohemia, Branišovská 31, České Budějovice, Czech Republic
corresponding authorCorresponding author.
Address correspondence to Michal Koblížek, koblizek/at/alga.cz.
Received August 21, 2012; Accepted August 29, 2012.
Abstract
Betaproteobacterial genus Limnohabitans represents an important part of freshwater bacterioplankton. Here, we report genome sequences of two Limnohabitans isolates, Rim28 and Rim47. They contain a complete photosynthesis gene cluster, RuBisCO, CO dehydrogenase, ammonia monooxygenase, and sulfur-oxidizing genes, which indicates a great metabolic versatility of the Limnohabitans species.
Limnohabitans is a recently established betaproteobacterial genus (3, 6), encompassing species formerly described as the Rhodoferax sp. BAL47 cluster (13) or the R-BT065 cluster (10). These organisms represent one of the most important bacterial groups in many freshwater habitats (8). In spite of the accumulating ecological data (4, 7, 9, 10), little is known about its metabolism and genome composition. Here, we report the whole genome sequences of two Limnohabitans isolates, Rim28 and Rim74, which were isolated from the Římov reservoir (Czech Republic) (5) with the aim of elucidating the physiological potential of this ecologically important group.
The strains were grown under aerobic conditions. After DNA extraction and preparation of a 300-bp library, the genome sequencing was performed with Illumina HiSeq 2000. About 9.0 GB of raw data of 101-bp paired-end reads was generated from each sample. The sequence quality control and trimming were conducted on the Galaxy server (2). The reads were de novo assembled using SeqMan NGen 4.0 (Dnastar Inc., Madison, WI). Annotation was performed with the RAST server (1).
The draft genomes of Limnohabitans spp. Rim28 and Rim47 consisted of 73 and 230 contigs with N50 values of 236,333 bp and 183,460 bp and with a total size of 3.41 and 3.03 Mb, containing 3,342 and 2,877 open reading frames (ORFs) and 40 and 46 tRNAs, respectively. The G+C content of both genomes was 58.5%. Each genome contained single copies of 5S, 16S, and 23S rRNA genes, forming a complete rRNA operon. Sequence identities of the 16S and 23S rRNA genes of the two strains were 98.8% and 98.6%, respectively.
A complete photosynthesis gene cluster (PGC) was found in both genomes with an identical gene organization of crtEF-bchCXYZ-pufBALMC-crtADC-pucBAC-crtBI-puhE-acsF-puhCBA-lhaA-bchMLHBNF-aerR-ppsR-bchGPODI. The PGC size was 58.6 kb for Rim28 and 46.0 kb for Rim47. Nucleotide sequence identities of the same genes of the two PGCs were between 84% and 89%. The PGC gene organization of the two Limnohabitans strains differs from other purple phototrophic bacteria sequenced so far (12). However, it was similar to an incomplete PGC found in the environmental fosmid clone DelRiverFos 06H03 obtained from the Delaware River (11).
The genomes contain genes encoding ribulose-1,5-bisphosphate carboxylase (RuBisCO) and carbonic anhydrases, which indicates the metabolic potential for autotrophic carbon fixation. There are nitrogen cycling-related genes encoding ammonia transporter and ammonia monooxygenase, nitrate transporter, nitrate reductase, nitrite reductase, urea transporter, and urease. In addition, there are the soxBXAZYDCR gene cluster, which contains sulfur-oxidizing-related genes, and the coxMSLGDEF gene cluster, encoding carbon monoxide dehydrogenase and related accessory proteins. These findings suggest a great metabolic versatility in the Limnohabitans species (5, 6). A more detailed genome analysis and experimental verification of the identified metabolic pathways will provide further insights about the physiology of this ecologically important group.
Nucleotide sequence accession numbers.
The Limnohabitans species Rim28 and Rim47 genome sequences have been deposited at DDBJ/EMBL/GenBank under the accession numbers ALKN00000000 and ALKO00000000, respectively. The versions described here are the first versions, ALKN01000000 and ALKO01000000.
ACKNOWLEDGMENTS
We thank Yunxu Li and Yapeng Liu (Inner Mongolia Agriculture University, China) and Jian Chen (Jingju Biotech Co., Xiamen, China) for their help on the mailing of DNA samples and the genome raw data CDs. We are grateful to Bei Wang (Guangdong Ocean University, China) for helpful discussions on genome data submission.
This work was supported by funds from the Czech project Algatech (CZ.1.05/2.1.00/03.0110) to M. K., the Czech project GACR (206/08/0015) to K.Š., the project cofinanced by the European Social Fund and the state budget of the Czech Republic (CZ.1.07/2.3.00/30.0032) (Postdok_BIOGLOBE, postdoctoral position contracting V. K.), and the Chinese projects NSFC 30900045, the Guangdong NSF B09292, and the Xiamen University MEL Open Fund MELRS0923 to Y. Z.
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