High-quality permanent draft genome sequence of the extremely osmotolerant diphenol degrading bacterium Halotalea alkalilenta AW-7T, and emended description of the genus Halotalea
Standards in Genomic Sciences volume 10, Article number: 52 (2015)
Members of the genus Halotalea (family Halomonadaceae) are of high significance since they can tolerate the greatest glucose and maltose concentrations ever reported for known bacteria and are involved in the degradation of industrial effluents. Here, the characteristics and the permanent-draft genome sequence and annotation of Halotalea alkalilenta AW-7T are described. The microorganism was sequenced as a part of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG) project at the DOE Joint Genome Institute, and it is the only strain within the genus Halotalea having its genome sequenced. The genome is 4,467,826 bp long and consists of 40 scaffolds with 64.62 % average GC content. A total of 4,104 genes were predicted, comprising of 4,028 protein-coding and 76 RNA genes. Most protein-coding genes (87.79 %) were assigned to a putative function. Halotalea alkalilenta AW-7T encodes the catechol and protocatechuate degradation to β-ketoadipate via the β-ketoadipate and protocatechuate ortho-cleavage degradation pathway, and it possesses the genetic ability to detoxify fluoroacetate, cyanate and acrylonitrile. An emended description of the genus Halotalea Ntougias et al. 2007 is also provided in order to describe the delayed fermentation ability of the type strain.
The genus Halotalea includes a single species, i.e., H. alkalilenta , which is a motile, rod-shaped, alkalitolerant and halotolerant Gram-negative staining heterotrophic bacterium . Strain AW-7T (=DSM 17697T =CECT 7134T =CIP 109710T ) is the type species of the genus Halotalea and of the type strain of the species H. alkalilenta . The strain was isolated from alkaline olive mill waste, which was generated by a two-phase centrifugal olive oil extraction system located in the Toplou Monastery area, Sitia, Crete . The Neo-Latin genus name derived from the Greek and the Latin nouns halos and talea, meaning salt-living and rod-shaped cells, respectively. The Neo-Latin species epithet halotalea composed of the Arabic term al qaliy and the Latin epithet lentus (a), meaning alkali and slow respectively which refer to slowly-growing cells under alkaline conditions (alkalitolerant) .
Halotalea alkalilenta belongs to the family Halomonadaceae [1–4], which has accommodated in chronological order the genera Halomonas , Chromohalobacter , Zymobacter , Carnimonas , Cobieta , Halotalea , Modicisalibacter , Salinicola , Kushneria , Aidingimonas  and Larsenimonas [13–15]. By employing multilocus sequence analysis, de la Haba et al.  found that all genera of the family Halomonadaceae , apart from Halomonas and Modicisalibacter , are phylogenetically distinct. Carnimonas nigrificans and Zymobacter palmae are the closest phylogenetic relatives of H. alkalilenta , and were isolated from cured meat and palm sap respectively [7, 8]. H. alkalilenta differs from C. nigrificans in its higher DNA G+C content and salt upper limit for growth, colony color, motility, its ability to grow at 5 °C and 37 °C, to utilize mannitol, in its inability to hydrolyze starch, to deaminize phenylalanine and to produce acids from D-mannitol and sucrose, in the proportion of the major membrane fatty acids and in the presence/absence of C10:0, C12:0, C12:02-OH, C14:0, C16:0 3-OH, cyclo-C17:0, C18:0 and C18:1t9 [1, 8]. H. alkalilenta can be distinguished from Z. palmae in its higher DNA G+C content, colony color, pH and emperature range for growth, optimum growth temperature, its higher D-glucose tolerance, its ability to utilize citrate, its inability to give positive methyl red and Voges-Proskauer reactions, in the proportion of the major membrane fatty acids and in the presence/absence of C10:0, C10:0 3-OH, C12:0 2-OH, C15:0, C17:0, cyclo-C17:0, C18:1 ω9 and C18: 1 ω7 [1, 7].
Here, a summarized classification and key characteristics are presented for H. alkalilenta AW-7T, together with the description of the high-quality permanent draft genome sequence and annotation.
Classification and features
The 16S rRNA gene sequence of H. alkalilenta AW-7T was compared using NCBI BLAST under default settings (e.g., considering only the high-scoring segment pairs (HSPs) from the best 250 hits) with the most recent release of the Greengenes database  and the relative frequencies of taxa and keywords (reduced to their stem ) were determined and weighted by BLAST scores. The frequency of genera that belonged to the family Halomonadaceae was 95.2 %. The closest match of H. alkalilenta AW-7T in 16S rRNA gene, submitted in INSDC (=EMBL/NCBI/DDBJ) under the accession number DQ421388 (=NR_043806), were Zymobacter palmae ATCC 51623T (NR_041786)  and Carnimonas nigrifaciens CTCBS1T (NR_029342)  showing BLAST similarities of 96.2 % and 95.3 % respectively and HSP coverages of 99.7 % and 100 % respectively.
Figure 1 shows the phylogenetic allocation of H. alkalilenta AW-7T within the family Halomonadaceae in a 16S rRNA gene sequence-based tree. The sequence of the only 16S rRNA gene copy in the genome differs by 5 nucleotides from the previously published 16S rRNA sequence (DQ421388= NR_043806, coverage 95.0 %).
H. alkalilenta AW-7T is a Gram-negative motile rod-shaped bacterium  with a length of 1.4-2.1 μm and a width of 0.6-0.9 μm (Table 1 and Fig. 2). The temperature range for growth is 5–45 °C, with an optimum temperature for growth at 32–37 °C . H. alkalilenta AW-7T is halotolerant and alkalitolerant, growing at salinity and pH ranges of 0–150 g L−1 NaCl and 5–11, respectively . The optimum salt and pH for growth are 0–3 % w/v NaCl and 7, respectively .
H. alkalilenta AW-7T is a non-denitrifying chemoorganotroph; it utilizes mostly L-glutamine and L-proline, followed by D-galactose, D-glucose, glycerol, D-mannitol, protocatechuate, L-serine, succinate and sucrose, while it grows weakly on acetate, citrate, D-fructose, maltose, sorbitol and gallate . H. alkalilenta AW-7T also produces acid aerobically from D-fructose, D-galactose, D-glucose, maltose, D-mannose and melibiose, and hydrolyses Tween 20 . Despite the fact that urea hydrolysis is encoded in H. alkalilenta AW-7T genome, no positive reaction was detected by Ntougias et al.  and the present study (using the EnteroPluri-Test). H. alkalilenta AW-7T is susceptible to kanamycin, polymixin B, rifampicin, streptomycin and tetracycline (50 mg L−1 each) .
In the past, H. alkalilenta AW-7T and C. nigrificans CTCBS1T were reported as oxidase positive [1, 8]. However, genome comparisons showed that both H. alkalilenta AW-7T and C. nigrificans CTCBS1T possessed an identical oxidative phosphorylation pathway that lacks cytochrome c oxidase, which was distinct from that of Z. palmae T109T. In addition, no fermentation ability was previously detected for H. alkalilenta AW-7T using standard incubation periods , although the pyruvate fermentation to acetate II MetaCyc pathway is encoded in both H. alkalilenta AW-7T and Z. palmae T109T. For this reason, the fermentation ability of H. alkalilenta AW-7T was re-examined under prolonged incubation period using the EnteroPluri-Test (BD, USA). No fermentation reaction was observed for incubations up to 4–days, although, thereafter, a positive reaction was obtained for glucose(at the 5th day of incubation, without gas production) and dulcitol (at 9th day of incubation). H. alkalilenta AW-7T could not ferment adonitol, lactose, arabinose and sorbitol after a 9–days incubation period. In agreement to what was previously reported by Ntougias et al. , no growth of H. alkalilenta AW-7T was observed in the present study on yeast extract-peptone-glucose agar plates placed for an incubation period of 1 month in an anaerobic jar containing the Anaerocult A system (Merck). However, exposure of culture plates to oxygen led to fastidious growth. In this sense, it is concluded that H. alkalilenta AW-7T can tolerate anaerobic conditions through a slow fermentation mechanism.
The main membrane fatty acids of H. alkalilenta AW-7T are in the descending order of concentration: C18:1 ω7c, C16:0, C19:0 cyclo ω8c, C12:0 3-OH and C16:1 ω7c/iso-C15:0 2-OH . The only respiratory quinone found in H. alkalilenta AW-7T is ubiquinone-9 .
Genome sequencing and annotation
Genome project history
H. alkalilenta AW-7T was selected for sequencing on the basis of its phylogenetic position [19–21], and is part of Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes project  which aims not only to increase the sequencing coverage of key reference microbial genomes . The genome project is accessible in the Genomes On Line Database  and the entire genome sequence is deposited in GenBank. Sequencing, finishing and annotation were accomplished by the DOE Joint Genome Institute  using state of the art genome sequencing technology . The project information is summarized in Table 2.
Growth conditions and genomic DNA preparation
H. alkalilenta AW-7T was cultivated aerobically in trypticase soy yeast extract medium at 28 °C. Genomic DNA was obtained using the Invitrogen PureLink® Genomic DNA Mini Kit (Life Technologies Inc.) following the standard protocol. In addition, DNA prepared by the DSMZ is available via the DNA Bank Network .
Genome sequencing and assembly
The draft genome of was generated at the DOE Joint Genome Institute using the Illumina technology . An Illumina std shotgun library was constructed and sequenced using the Illumina HiSeq 2000 platform which generated 13,537,536 reads totaling 2,030.6 Mb. All general aspects of library construction and sequencing performed can be found at JGI website . All raw Illumina sequence data was passed through DUK, a filtering program developed at JGI, which removes known Illumina sequencing and library preparation artifacts (Mingkun L, et al., unpublished). Following steps were then performed for assembly: (1) filtered Illumina reads were assembled using Velvet (version 1.2.07) , (2) 1–3 kb simulated paired end reads were created from Velvet contigs using wgsim , (3) Illumina reads were assembled with simulated read pairs using Allpaths–LG (version r46652) . Parameters for assembly steps were: 1) Velvet (velveth: 63 –shortPaired and velvetg: −very clean yes –exportFiltered yes –min contig lgth 500 –scaffolding no –cov cutoff 10) 2) wgsim (−e 0 –1 100 –2 100 –r 0 –R 0 –X 0) 3) Allpaths–LG (PrepareAllpathsInputs:PHRED 64 = 1 PLOIDY = 1 FRAG COVERAGE = 125 JUMP COVERAGE = 25 LONG JUMP COV = 50, RunAllpathsLG: THREADS = 8 RUN = std shredpairs TARGETS = standard VAPI WARN ONLY = True OVERWRITE = True). The final draft assembly contained 56 contigs in 40 scaffolds, totaling 4.5 Kb in size. The final assembly was based on 1,500.0 Mb of Illumina data. Based on a presumed genome size of 5.0 Mb, the average input read coverage used for the assembly was 300.0 ×.
Genes were detected using the Prodigal software  at the DOE-JGI Genome Annotation pipeline [34, 35]. The CDSs predicted were translated and searched against the National Center for Biotechnology Information non-redundant database, UniProt, TIGRFam, Pfam, PRIAM, KEGG, COG, and InterPro databases. Additional gene prediction and functional annotation analysis was carried out in the Integrated Microbial Genomes – Expert Review platform . The genome sequence and the annotations described in this paper are available from the Integrated Microbial Genome system .
The genome is 4,467,826 bp long and comprised of 40 scaffolds with 64.62 % average GC content (Table 3). A total of 4,104 genes were predicted, consisting of 4,028 protein-coding and 76 RNA genes. The majority of protein-coding genes (87.79 %) were assigned to a putative function, whereas the remaining ones were annotated as hypothetical proteins. Distribution of genes into COGs functional categories is displayed in Table 4.
Insights into the genome sequence
The genome size of H. alkalilenta AW-7T (4.47 Mbp) is 50 % and 60 % greater than those of Z. palmae T109T and C. nigrificans CTCBS1T (2.73 and 2.98 Mbp) respectively. In H. alkalilenta AW-7T, protein coding genes involved in the major functional categories (i.e., amino acid, carbohydrate and lipid metabolism, membrane transport, energy metabolism) are 50 % and 30 % greater in number than those detected in Z. palmae T109T and C. nigrificans CTCBS1T, respectively. Moreover, genes encoding xenobiotic metabolic proteins are 69 % and 57 % more in H. alkalilenta AW-7T than those identified in Z. palmae T109T and C. nigrificans CTCBS1T respectively.
Genome data uncovered the genetic ability of H. alkalilenta AW-7T to degrade several recalcitrant substrates. H. alkalilenta AW-7T encodes the bioconversion of catechol and protocatechuate to β-ketoadipate via the β-ketoadipate and protocatechuate degradation II (ortho-cleavage) pathway respectively, as verified by the ability of strain AW-7T to catabolize certain phenolic compounds. Aerobic benzoate degradation I is also encoded, permitting its catabolism via the catechol degrading pathway. Genes encoding fluoroacetate dehalogenase were identified in the genome of H. alkalilenta AW-7T, indicating its ability for fluoroacetate degradation. The detection of genes involved in cyanate and acrylonitrile degradation was also verified. Lastly, H. alkalilenta AW-7T is genetically able to produce ectoine and glycine betaine, which appear to serve as the main osmolytes for the adaptation of this species under high osmotic conditions.
Based on genome metabolic features, H. alkalilenta AW-7T is prototrophic for L-arginine, L-histidine, L-isoleucine, L-leucine, L-lysine, L-phenylalanine, L-tryptophan, L-tyrosine and L-valine auxotroph, and L-aspartate, L-glutamate, L-glutamine and glycine. Strain AW-7T can synthesize selenocysteine but not biotin.
Genome sequence and biochemical data of the highly osmotolerant species Halotalea alkalilenta AW-7T revealed the presence of an oxidative phosphorylation pathway that lacks cytochrome c oxidase, and the encoding of the pyruvate fermentation to acetate II (MetaCyc pathway). H. alkalilenta AW-7T could ferment glucose and ducitol after a prolonged incubation period, which is indicative of the induction of a slow fermentation mechanism, and results in the emendation of the genus Halotalea Ntougias et al. 2007. Comparisons to its closest phylogenetic relatives Zymobacter palmae T109T and Carnimonas nigrificans CTCBS1T, confirm the distinct taxonomic position of H. alkalilenta AW-7 on the basis of its larger genome size and number of protein coding genes involved in the major functional categories and in xenobiotics metabolism. Furthermore, H. alkalilenta AW-7T encodes the biotransformation of catechol and protocatechuate to β-ketoadipate via the β-ketoadipate and protocatechuate degradation II (ortho-cleavage) pathway respectively, verifying at the genome level the ability of strain AW-7T to degrade phenolic compounds.
Emended description of the genus Halotalea Ntougias et al. 2007
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This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, A.L. was supported in part by Russian Ministry of Science Mega-grant no.11.G34.31.0068 (PI. Dr Stephen J O'Brien).
The authors declare that they have no competing interests.
SN and GIZ performed the fermentation tests, conducted the phylogenetic analyses and drafted the paper, CF prepared the electron micrographs, and all other authors were involved in either sequencing/annotation of the genome and/or editing the paper. All authors read and approved the final manuscript.
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Ntougias, S., Lapidus, A., Copeland, A. et al. High-quality permanent draft genome sequence of the extremely osmotolerant diphenol degrading bacterium Halotalea alkalilenta AW-7T, and emended description of the genus Halotalea . Stand in Genomic Sci 10, 52 (2015). https://doi.org/10.1186/s40793-015-0052-7
- Alkaline two-phase olive mill waste
- Protocatechuate ortho-cleavage
- Catechol to β-ketoadipate degradation pathway
- Cyanate and acrylonitrile detoxification