- Open Access
Complete genome sequence of Cellulophaga algicola type strain (IC166T)
- Birte Abt1,
- Megan Lu2, 3,
- Monica Misra2, 3,
- Cliff Han2, 3,
- Matt Nolan2,
- Susan Lucas2,
- Nancy Hammon2,
- Shweta Deshpande2,
- Jan-Fang Cheng2,
- Roxane Tapia2, 3,
- Lynne Goodwin2, 3,
- Sam Pitluck2,
- Konstantinos Liolios2,
- Ioanna Pagani2,
- Natalia Ivanova2,
- Konstantinos Mavromatis2,
- Galina Ovchinikova2,
- Amrita Pati2,
- Amy Chen4,
- Krishna Palaniappan4,
- Miriam Land2, 5,
- Loren Hauser2, 5,
- Yun-Juan Chang2, 5,
- Cynthia D. Jeffries2, 5,
- John C. Detter2, 3,
- Evelyne Brambilla1,
- Manfred Rohde6,
- Brian J. Tindall1,
- Markus Göker1,
- Tanja Woyke2,
- James Bristow2,
- Jonathan A. Eisen2, 7,
- Victor Markowitz4,
- Philip Hugenholtz2, 8,
- Nikos C. Kyrpides2,
- Hans-Peter Klenk1 and
- Alla Lapidus2
- Published: 4 March 2011
Abstract
Cellulophaga algicola Bowman 2000 belongs to the family Flavobacteriaceae within the phylum ‘Bacteroidetes’ and was isolated from Melosira collected from the Eastern Antarctic coastal zone. The species is of interest because its members produce a wide range of extracellular enzymes capable of degrading proteins and polysaccharides with temperature optima of 20–30°C. This is the first completed genome sequence of a member of the genus Cellulophaga. The 4,888,353 bp long genome with its 4,285 protein-coding and 62 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
Keywords
- aerobic
- motile by gliding
- Gram-negative
- agarolytic
- chemoorganotrophic
- cold adapted enzymes
- Flavobacteriaceae
- GEBA
Introduction
Strain IC166T (= DSM 14237 = CIP 107446 = LMG 21425) is the type strain of C. algicola, which belongs to the family Flavobacteriaceae within the phylum ‘Bacteroidetes’. The strain was isolated from the surface of the chain-forming sea-ice diatom Melosira collected from the Eastern Antarctic coastal zone, and was described by Bowman in 2000 [1]. Currently, there are six species placed in the genus Cellulophaga, namely C. algicola [1], C. baltica, C. fucicola, C. lytica [2], C. pacifica [3] and C. tyrosinoxydans [4]. C. lytica is the type species of the genus Cellulophaga [2]. The generic name of the genus derives from the Neo Latin word ‘cellulosum’ meaning ‘cellulose’ and the Greek word ‘phagein’ meaning ‘to eat’, referring to an eater of cellulose. Here we present a summary classification and a set of features for C. algicola IC166T, together with the description of the complete genomic sequencing and annotation.
Classification and features
A representative genomic 16S rRNA sequence of C. algicola 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 [5] and the relative frequencies, weighted by BLAST scores, of taxa and keywords (reduced to their stem [6]) were determined. The five most frequent genera were Cellulophaga (39.5%), Maribacter (7.8%), Flavobacterium (5.6%), Cytophaga (5.4%) and Formosa (4.7%) (135 hits in total). Regarding the 21 hits to sequences from members of the species, the average identity within HSPs was 95.8%, whereas the average coverage by HSPs was 94.9%. Regarding the 16 hits to sequences from other members of the genus, the average identity within HSPs was 94.7%, whereas the average coverage by HSPs was 94.7%. Among all other species, the one yielding the highest score was C. baltica, which corresponded to an identity of 98.1% and a HSP coverage of 97.8%. The highest-scoring environmental sequence was GU452686 (‘sediments coast oil polluted Black Sea coastal sediment clone 70SZ2’), which showed an identity of 96.5% and a HSP coverage of 98.1%. The five most frequent keywords within the labels of environmental samples which yielded hits were ‘marin’ (4.7%), ‘water’ (4.3%), ‘sediment’ (4.3%), ‘sea’ (3.5%) and ‘coastal’ (2.6%) (115 hits in total). Environmental samples which yielded hits of a higher score than the highest scoring species were not found.
The environmental samples database (env_nt) contains the marine metagenome clone ctg_1101667042524 (AACY022635173) isolated from Sargasso Sea near Bermuda, sharing 92% identity with IC166T [7] (as of January 2011).
Phylogenetic tree highlighting the position of C. algicola IC166T relative to the other type strains within the family Flavobacteriaceae. The tree was inferred from 1,458 aligned characters [8,9] of the 16S rRNA gene sequence under the maximum likelihood criterion [10] and rooted in accordance with the current taxonomy. The branches are scaled in terms of the expected number of substitutions per site. Numbers above branches are support values from 350 bootstrap replicates [11] if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [12] are shown in blue, published genomes in bold.
Scanning electron micrograph of C. algicola IC166T
Classification and general features of C. algicola IC166T according to the MIGS recommendations [13].
MIGS ID | Property | Term | Evidence code |
---|---|---|---|
Current classification | Domain Bacteria | TAS [14] | |
Phylum Bacteroidetes | |||
Class Flavobacteria | TAS [17] | ||
Order ‘Flavobacteriales’ | TAS [15] | ||
Family Flavobacteriaceae | |||
Genus Cellulophaga | TAS [2] | ||
Species Cellulophaga algicola | TAS [1] | ||
Type strain IC166 | TAS [1] | ||
Gram stain | negative | TAS [1] | |
Cell shape | rod-shaped | TAS [1] | |
Motility | motile by gliding | TAS [1] | |
Sporulation | none | TAS [1] | |
Temperature range | −2 °C–28°C | TAS [1] | |
Optimum temperature | 20°C | TAS [1] | |
Salinity | 0.5–10% NaCl | TAS [1] | |
MIGS-22 | Oxygen requirement | aerobic | TAS [1] |
Carbon source | carbohydrates | TAS [1] | |
Energy source | chemoheterotroph | TAS [1] | |
MIGS-6 | Habitat | sea ice diatoms, macrophyte surfaces | TAS [1] |
MIGS-15 | Biotic relationship | free-living | NAS |
MIGS-14 | Pathogenicity | none | NAS |
Biosafety level | 1 | TAS [22] | |
Isolation | surfaces of Antarctic algae | TAS [1] | |
MIGS-4 | Geographic location | eastern Antarctic coastal zone | TAS [1] |
MIGS-5 | Sample collection time | 1996 | NAS |
MIGS-4.1 | Latitude | not reported | NAS |
MIGS-4.2 | Longitude | not reported | NAS |
MIGS-4.3 | Depth | not reported | NAS |
MIGS-4.4 | Altitude | not reported | NAS |
The organism is strictly aerobic and chemoorganotrophic [1]. C. algicola can hydrolyze agar, starch, gelatine, carboxymethylcellulose (CMC), casein, Tween 80, tributyrin and L-tyrosine, but not urate, xanthine or dextran, when grown in presence of 1% L-tyrosine a reddish-brown diffusible pigment is formed [1]. Nitrate reduction is positive, whereas denitrification, H2S production and indole production are negative [1,18]. Acid is formed oxidatively from D-galactose, D-glucose, D-fructose, sucrose, cellobiose, lactose and mannitol. Strain IC166T is sensitive to ampicillin, streptomycin and carbenicillin and shows resistance to tetracycline [3].
Chemotaxonomy
The fatty acid profile of seven Antarctic strains, including strain IC166T, was analyzed by Bowman in 2000 [1]. The hypothetical median representative of the Antarctic isolates was published. The predominant cellular fatty acids of these seven strains were branched-chain saturated and unsaturated fatty acids and straight-chain saturated and mono-unsaturated fatty acids, namely iso-C15:0 (7.5%), iso-C15:1ω10c (7.5%), iso -C17:1ω7c (6.1%), C15:0 (14.3%), C16:1ω7c (19.2%), iso -C15:0 3-OH (8.6%), iso-C16:0 3-OH (6.5%) and iso -C17:0 3-OH (4.5%) [1]. The isoprenoid quinones of C. algicola were not determined, but for C. pacifica the presence of MK-6 as the major lipoquinone was described [3]. Polar lipids not have been studied.
Genome sequencing and annotation
Genome project history
Genome sequencing project information
MIGS ID | Property | Term |
---|---|---|
MIGS-31 | Finishing quality | Finished |
MIGS-28 | Libraries used | Three genomic libraries: one 454 pyrosequence standard library, one 454 PE library (12 kb insert size), one Illumina library |
MIGS-29 | Sequencing platforms | Illumina GAii, 454 GS FLX Titanium |
MIGS-31.2 | Sequencing coverage | 146.0 × Illumina; 53.5 × pyrosequence |
MIGS-30 | Assemblers | Newbler version 2.0.00.20-PostRelease-10-28-2008-g-3.4.6, Velvet version 0.7.63, phrap version SPS D 4.24 |
MIGS-32 | Gene calling method | Prodigal 1.4, GenePRIMP |
INSDC ID | CP002453 | |
Genbank Date of Release | January 18, 2011 | |
GOLD ID | Gc01592 | |
NCBI project ID | 41529 | |
Database: IMG-GEBA | 2503904003 | |
MIGS-13 | Source material identifier | DSM 14237 |
Project relevance | Tree of Life, GEBA |
Growth conditions and DNA isolation
C. algicola IC166T, DSM 14237, was grown in DSMZ medium 514 (BACTO marine broth) [26] at 15°C. DNA was isolated from 0.5–1 g of cell paste using MasterPure Gram-positive DNA purification kit (Epicentre MGP04100) following the standard protocol as recommended by the manufacturer with modification st/DL for cell lysis as described in Wu et al. [25]. DNA is available through the DNA Bank Network [27].
Genome sequencing and assembly
The genome was sequenced using a combination of Illumina and 454 sequencing platforms. All general aspects of library construction and sequencing can be found at the JGI website [28]. Pyrosequencing reads were assembled using the Newbler assembler version 2.3-PreRelease-09-14-2009-bin (Roche). The initial Newbler assembly consisting of 128 contigs in two scaffolds was converted into a phrap assembly by [29] making fake reads from the consensus, to collect the read pairs in the 454 paired end library. Illumina GAii sequencing data (710 Mb) was assembled with Velvet [30] and the consensus sequences were shredded into 1.5 kb overlapped fake reads and assembled together with the 454 data. The 454 draft assembly was based on 263.4Mb 454 draft data and all of the 454 paired end data. Newbler parameters are -consed -a 50 -l 350 -g -m -ml 20. The Phred/Phrap/Consed software package [29] was used for sequence assembly and quality assessment in the subsequent finishing process. After the shotgun stage, reads were assembled with parallel phrap (High Performance Software, LLC). Possible mis-assemblies were corrected with gapResolution [28], Dupfinisher [31], or sequencing cloned bridging PCR fragments with subcloning or transposon bombing (Epicentre Biotechnologies, Madison, WI). Gaps between contigs were closed by editing in Consed, by PCR and by Bubble PCR primer walks (J.-F.Chang, unpublished). A total of 1,054 additional reactions and three shatter libraries were necessary to close gaps and to raise the quality of the finished sequence. Illumina reads were also used to correct potential base errors and increase consensus quality using a software Polisher developed at JGI [32]. The error rate of the completed genome sequence is less than 1 in 100,000. Together, the combination of the Illumina and 454 sequencing platforms provided 199.5 × coverage of the genome. The final assembly contained 697,305 pyrosequence and 20,331,123 Illumina reads
Genome annotation
Genes were identified using Prodigal [33] as part of the Oak Ridge National Laboratory genome annotation pipeline, followed by a round of manual curation using the JGI GenePRIMP pipeline [34]. The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) nonredundant database, UniProt, TIGR-Fam, Pfam, PRIAM, KEGG, COG, and InterPro databases. Additional gene prediction analysis and functional annotation was performed within the Integrated Microbial Genomes - Expert Review (IMG-ER) platform [35].
Genome properties
Graphical circular map of the chromosome. From outside to the center: Genes on forward strand (color by COG categories), Genes on reverse strand (color by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew.
Genome Statistics
Attribute | Value | % of Total |
---|---|---|
Genome size (bp) | 4,888,353 | 100.00% |
DNA coding region (bp) | 4,301,528 | 88.00% |
DNA G+C content (bp) | 1,650,610 | 33.77% |
Number of replicons | 1 | |
Extrachromosomal elements | 0 | |
Total genes | 4,347 | 100.00% |
RNA genes | 62 | 1.43% |
rRNA operons | 5 | |
Protein-coding genes | 4,285 | 98.57% |
Pseudo genes | 122 | 2.81% |
Genes with function prediction | 2,587 | 59.51% |
Genes in paralog clusters | 698 | 16.06% |
Genes assigned to COGs | 2,539 | 58.41% |
Genes assigned Pfam domains | 2,822 | 64.92% |
Genes with signal peptides | 1,220 | 28.07% |
Genes with transmembrane helices | 1,010 | 23.23% |
CRISPR repeats | 0 |
Number of genes associated with the general COG functional categories
Code | value | %age | Description |
---|---|---|---|
J | 160 | 5.8 | Translation, ribosomal structure and biogenesis |
A | 0 | 0.0 | RNA processing and modification |
K | 174 | 6.3 | Transcription |
L | 147 | 5.4 | Replication, recombination and repair |
B | 1 | 0.0 | Chromatin structure and dynamics |
D | 20 | 0.7 | Cell cycle control, cell division, chromosome partitioning |
Y | 0 | 0.0 | Nuclear structure |
V | 63 | 2.3 | Defense mechanisms |
T | 167 | 6.1 | Signal transduction mechanisms |
M | 239 | 8.7 | Cell wall/membrane/envelope biogenesis |
N | 7 | 0.3 | Cell motility |
Z | 0 | 0.0 | Cytoskeleton |
W | 0 | 0.0 | Extracellular structures |
U | 41 | 1.5 | Intracellular trafficking, secretion, and vesicular transport |
O | 99 | 3.6 | Posttranslational modification, protein turnover, chaperones |
C | 135 | 4.9 | Energy production and conversion |
G | 172 | 6.3 | Carbohydrate transport and metabolism |
E | 208 | 7.6 | Amino acid transport and metabolism |
F | 70 | 2.6 | Nucleotide transport and metabolism |
H | 131 | 4.8 | Coenzyme transport and metabolism |
I | 97 | 3.5 | Lipid transport and metabolism |
P | 174 | 6.3 | Inorganic ion transport and metabolism |
Q | 52 | 1.9 | Secondary metabolites biosynthesis, transport and catabolism |
R | 345 | 12.6 | General function prediction only |
S | 247 | 9.0 | Function unknown |
- | 1,808 | 41.6 | Not in COGs |
Insights from genome sequence
A closer look on the genome sequence of strain IC166T revealed a set of genes which might be responsible for the yellow-orange color of C. algicola cells by encoding enzymes that are involved in the synthesis of carotenoids. Carotenoids are produced by the action of geranylgeranyl pyrophosphate synthase (Celal_1770), phytoene synthase (Celal_2446), phytoene desaturase (Celal_2447), lycopene cyclase (Celal_1771) and carotene hydroxylase (Celal_2445). Geranylgeranyl pyrophosphate synthases start the biosynthesis of carotenoids by combining farnesyl pyrophosphate with C5 isoprenoid units to C20-molecules, geranylgeranyl pyrophosphate. The phytoene synthase catalyzes the condensation of two geranylgeranyl pyrophosphate molecules followed by the removal of diphosphate and a proton shift leading to the formation of phytoene. Sequential desaturation steps are conducted by the phytoene desaturase followed by cyclisation of the ends of the molecules catalyzed by the lycopene cyclase [36].
Strain IC166T produces a wide range of extracellular enzymes degrading proteins and polysaccharides. These enzymes are cold adapted, they have temperature optima between 15–30°C and can tolerate temperatures below 0°C [37]. For that reason they are of special interest for industrial and biotechnical applications. C. algicola like the other members of the genus Cellulophaga, cannot hydrolyze filter paper or cellulose in its crystalline form, though they can hydrolyze the soluble cellulose derivative carboxymethylcellulose (CMC). The genome sequence of strain IC166T revealed the presence of three cellulases (Celal_0025, Celal_2753, Celal_3912), probably responsible for the hydrolysis of CMC. In addition two β-glucosidases (Celal_0470, Celal_1802) were identified in the genome, catalyzing the break down of the glycosidic β-1,4 bond between two glucose molecules in cellobiose.
The IC166T genome contains 22 genes coding for sulfatases, which are located in close proximity to glycoside hydrolase genes suggesting that sulfated polysaccharides may be used as substrates. α-L-fucoidan could be a substrate, as five α-L-fucosidases (Celal_2459, Celal_2466, Celal_2469, Celal_2470, Celal_2473) are located in close proximity to three sulfatases (Celal_2464, Celal_2468, Celal_2472). Sakai and colleagues report the existence of intracellular α-L-fucosidases and sulfatases, which enable ‘Fucophilus fucoidanolyticus’ to degrade fucoidan [38]. This fucoidan degrading ability could be also shared by Coraliomargarita akajimensis, as the annotation of the genome sequence revealed the existence of 49 sulfatases and twelve α-L-fucosidases [39]. In addition, three β-agarases (Celal_2463, Celal_2494, Celal_3979) were identified, with two of them located in the above mentioned region, which is rich in genes encoding glycoside hydrolases and sulfatases.
Declarations
Acknowledgements
We would like to gratefully acknowledge the help of Regine Fähnrich (DSMZ) for growing C. algicola cultures. 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, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, UT-Battelle and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-2.
Authors’ Affiliations
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