Complete genome sequence of Lutibacter profundi LP1T isolated from an Arctic deep-sea hydrothermal vent system
© The Author(s). 2017
Received: 25 August 2016
Accepted: 7 December 2016
Published: 7 January 2017
Lutibacter profundi LP1T within the family Flavobacteriaceae was isolated from a biofilm growing on the surface of a black smoker chimney at the Loki’s Castle vent field, located on the Arctic Mid-Ocean Ridge. The complete genome of L. profundi LP1T is the first genome to be published within the genus Lutibacter. L. profundi LP1T consists of a single 2,966,978 bp circular chromosome with a GC content of 29.8%. The genome comprises 2,537 protein-coding genes, 40 tRNA species and 2 rRNA operons. The microaerophilic, organotrophic isolate contains genes for all central carbohydrate metabolic pathways. However, genes for the oxidative branch of the pentose-phosphate-pathway, the glyoxylate shunt of the tricarboxylic acid cycle and the ATP citrate lyase for reverse TCA are not present. L. profundi LP1T utilizes starch, sucrose and diverse proteinous carbon sources. In accordance, the genome harbours 130 proteases and 104 carbohydrate-active enzymes, indicating a specialization in degrading organic matter. Among a small arsenal of 24 glycosyl hydrolases, which offer the possibility to hydrolyse diverse poly- and oligosaccharides, a starch utilization cluster was identified. Furthermore, a variety of enzymes may be secreted via T9SS and contribute to the hydrolytic variety of the microorganism. Genes for gliding motility are present, which may enable the bacteria to move within the biofilm. A substantial number of genes encoding for extracellular polysaccharide synthesis pathways, curli fibres and attachment to surfaces could mediate adhesion in the biofilm and may contribute to the biofilm formation. In addition to aerobic respiration, the complete denitrification pathway and genes for sulphide oxidation e.g. sulphide:quinone reductase are present in the genome. sulphide:quinone reductase and denitrification may serve as detoxification systems allowing L. profundi LP1T to thrive in a sulphide and nitrate enriched environment. The information gained from the genome gives a greater insight in the functional role of L. profundi LP1T in the biofilm and its adaption strategy in an extreme environment.
KeywordsLutibacter Flavobacteriaceae Loki’s castle Biofilm Deep-sea hydrothermal vent
The type strain Lutibacter profundi LP1T (=DSM 100437 T =JCM 30585 T) belongs to the family Flavobacteriaceae within the phylum Bacteroidetes . Members of this family are abundant in marine and freshwater habitats and have been isolated from seawater [2, 3], sea ice , fresh water , glaciers [6, 7], marine plants and animals [4, 8]. In addition, metagenomic studies have shown the presence of Bacteroidetes in marine sediments [9, 10]. Members of the Flavobacteriaceae are also found in the human microbiota [11, 12], soil , insects , food and dairy products . The family Flavobacteriaceae has been proposed to play an important role in the degradation of organic matter and nutrition turnover in the oceans . They have been identified either as free-living or attached to organic detritus particles and phytoplankton in marine surfaces [17, 18] and in deep-sea planktonic communities . Biopolymers, such as cellulose, chitin and proteins are part of the high molecular mass fraction of (dissolved) organic material in aquatic habitats. The ability to degrade such polymers has been shown for Flavobacteriaceae in both culture-dependent and independent studies [16, 20]. A multiplicity of strains has been isolated and several genomes sequenced [21–23]. Genomic analyses of marine isolates have revealed a large number of GHs, GTs, peptidases and adhesion proteins, as well as genes for gliding motility, supporting an organotrophic life style as HMW organic matter degraders [21–24].
In 2006 the first Lutibacter strain, L. litoralis CL-TF09T, was isolated and introduced as a new organotrophic genus of the Flavobacteriaceae family . Until now, all published strains have been isolated from Korean coastal waters or the Sea of Japan, and found either as free-living or in association with invertebrates [3, 25–31]. In contrast, L. profundi LP1T was isolated from a biofilm attached to the outer surface of a black smoker chimney from the LCVF located at the AMOR . In the biofilm, the Bacteroidetes population was attached as ectobionts on the outer surface of filamentous Epsilonproteobacteria . Here we present the complete genome of Lutibacter profundi LP1T, the first genome to be published from the genus Lutibacter . The genomic features of L. profundi are presented and its possible role in the biofilm community and its biotechnological potential is discussed.
Classification and features
L. profundi LP1T was isolated from a biofilm attached to the surface of a black smoker chimney wall at the LCVF, on the AMOR [32–34]. A steep temperature gradient between the up to 320°C hydrothermal fluids and the −0.7°C cold surrounding seawater places the biofilm in a mesophilic temperature range [33, 35]. Artificial seawater medium  supplemented with modified Wolfe’s mineral solution without NaCl or CaCl2 (0.001%), Wolfe’s vitamin solution (0.5%), 10mM Na2S and yeast extract (0.01%) under microaerobic conditions was used for primary enrichments and isolation of L. profundi LP1T .
Classification and general features of Lutibacter profundi LP1T according to MIGS standards 
Species Lutibacter profundi
Type strain: LP1 (DSMZ 100437T = T)
pH range; optimum
Marine, biofilm attached to black smoker chimney
Loki’s Castle, Arctic mid-Ocean ridge
In the current study, L. profundi LP1T tested negative for the utilization of the following additional carbohydrates; D-maltose, D-mannose, L-arabinose, D-trehalose, D-xylose, D-cellulose and chitin.
The composition of the major cellular fatty acids in L. profundi LP1T varies depending on the used media and growth condition . After growth on marine broth 2216 agar plates the major cellular fatty acids are iso-C15:0 (25.2%), iso-C15:0 3-OH (14.5%), iso-C17:0 3-OH (9.6%), iso-C15:1 (G) (9.0%), anteiso-C15:0 (8.2%), iso-C16:0 3-OH (5.4%) and summed feature I iso-C15:1 (H)/C13:0 3OH (7.4%) . The major cellular fatty acid composition varied between the different Lutibacter type strains . The major polar lipids of L. profundi LP1T are DPG, PE, one unidentified aminolipid and two unidentified lipids, where PE is the main polar lipid. In accordance with the genus, menaquinone-6 (MK-6) is the only respiratory quinone .
Genome sequencing information
Genome project history
L. profundi LP1T as the type strain is the first Lutibacter isolate from a deep-sea hydrothermal vent system. The bacterium was chosen for sequencing to study its genomic features in relation to the environmental system it originated from and its biotechnological potential.
Pacific Biosciences 10 kb library
Hierarchical Genome Assembly Process (HGAP) v2
Gene calling method
Genbank Date of Release
February 1., 2016
Source Material Identifier
DSMZ 100437T =JCM 30585T
Growth conditions and genomic DNA preparation
L. profundi LP1T was grown by gently shaking in M1 broth medium at microaerophilic conditions and 23 °C. The high molecular DNA of a 60 ml culture was isolated using a modified method of Marmur [40, 41].
Genome sequencing and assembly
A 10 kb library was prepared using Pacific Bioscience 10 kb library preparation protocol and BluePippin (Sage Science) for the final size selection. Two SMRT cells were used for sequencing the library on a Pacific Bioscience RS II instrument in combination with the P4-C2 chemistry. In total, 63,994 reads with an average length of 5671 bp were obtained generating a total number of 362.9 Mbp. The raw reads were filtered prior de novo assembly using HGAP v2 (Pacific Bioscience) , which resulted in one 2,978,418 bp contig with an average coverage of 76.29. Using the Gepard dotplot , verified a single highly accurate self-overlapping contig. Minimus2 from the AMOS software package  was used to perform the circularization and trimming of the chromosomal contig. Final polishing steps using the RS_Resequencing protocol implemented in the SMRT Analysis software (Pacific Biosciences), resulted in a 2,966,978 bp circular chromosome with a consensus concordance of 99.9%. The location of the dnaA gene was manually relocated and used as start of the chromosome.
In order to comply to NCBI standards, the annotation of the genome was performed using the automatic NCBI PGAAP . In addition, SignalP and TMHH-plugins in CLC Genomics Workbench (Qiagen, version 9) was used for the identification of genes with signal peptides and transmembrane helices, respectively.
Percent of total
Genome size (bp)
DNA coding (bp)
DNA G + C (bp)
Protein coding genes
Genes in internal clusters
Genes with function prediction
Genes assigned to COGs
Genes with Pfam domains
Genes with signal peptides
Genes with transmembrane helices
Number of genes associated with general COG functional categories
Translation, ribosomal structure and biogenesis
RNA processing and modification
Replication, recombination and repair
Chromatin structure and dynamics
Cell cycle control, cell division, chromosome partitioning
Signal transduction mechanisms
Cell wall/membrane/envelope biogenesis
Intracellular trafficking, secretion, and vesicular transport
Posttranslational modification, protein turnover, chaperones
Energy production and conversion
Carbohydrate transport and metabolism
Amino acid transport and metabolism
Nucleotide transport and metabolism
Coenzyme transport and metabolism
Lipid transport and metabolism
Inorganic ion transport and metabolism
Secondary metabolites biosynthesis, transport and catabolism
General function prediction only
Not in COGs
Insights from the genome sequence
In addition to the automatic genome annotation by PGAAP, KAAS  was used to analyse metabolic features of the strain LP1T. The L. profundi LP1T genome encodes for all central carbohydrate metabolic pathways (Additional file 1: Table S1); Embden-Meyerhof-Parnas pathway, gluconeogenesis and the TCA cycle. The genome contains genes for the non-oxidative branch of the pentose-phosphate-pathway, however misses the genes for the oxidative branch. Genes for the glyoxylate shunt of the TCA cycle are not present. The key enzyme ATP citrate lyase (EC 22.214.171.124) of the rTCA was not found. Besides the pyruvate dehydrogenase complex, a pyruvate:ferredoxin oxidoreductase (Lupro_00440) was identified, which may also catalyse the reverse reaction from acetyl-CoA to pyruvate. L. profundi LP1T harbours the gene for phosphoenolpyruvate carboxylase (Lupro_02180), which may convert phosphoenolpyruvate into oxaloacetate, fixing CO2 in an anaplerotic reaction [22, 23]. Genes for energy generation via oxidative phosphorylation were identified (Additional file 1: Table S1). The major components comprise the NADH-dehydrogenase complex I, the succinate dehydrogenase/fumarate reductase complex II, a variety of quinone, and cytochrome c terminal oxidoreductases. Energy generation in form of ATP could be provided by the encoded F0F1-type ATP synthase. In addition to a H(+)-translocating NADH-dehydrogenase complex, a Na(+)-translocating NADH-quinone reductase is encoded in the genome, a feature common in marine bacteria . Different aerobic terminal oxidoreductases could be identified, such as cytochrome c oxidases, cytochrome bo3 ubiquinol oxidase, cbb3-type cytochrome c oxidase and quinol oxidizing cytochrome bd-I terminal oxidase.
All genes for the complete denitrification pathway, from nitrate to nitrogen (NapAB, NirS, NorBC, NosZ), were identified in the strain LP1T (Additional file 1: Table S1). Nitrate reduction to nitrite was confirmed in growth experiments under aerobic and microaerophilic conditions, while anaerobic growth using nitrate as the sole electron acceptor was not observed . One ammonium transporter (Lupro_05500) was detected for ammonia assimilation. Ammonia can be fixed indirectly by glutamine synthetase and GOGAT, or directly by NADP-dependent glutamate dehydrogenase forming glutamate. Two different forms of GOGAT were identified, a NADPH dependent and a ferredoxin-dependent. The absence of genes encoding for urease is in concordance with the phenotypic characterization . Genes for oxidation of sulphide, SQR, polysulfide reductase and sulphate permease, were identified in the genome of L. profundi LP1T (Additional file 1: Table S1). However, growth of L. profundi LP1T was not stimulated in the presence of thiosulfate under microaerobic or anaerobic conditions . The presence of a SQR could also be an adaptation to the elevated concentration of sulphide emitted from the vent fluids at LCVF, rather than growth.
Potential role of Lutibacter profundi LP1T as complex organic compound degrader in the deep-sea biofilm
The organotroph L. profundi LP1T was isolated from a microbial biofilm where a Bacteroidetes population was found attached to filamentous Epsilonproteobacteria producing a sugar biopolymer resembling chitin or cellulose . The dbCAN analysis detected 101 proteins exhibiting one or more functional activities within CAZy [51, 52]. GTs (45) are mainly represented, followed by GHs (24), CEs (24), PLs (1) and CBMs (7). Ten GH families (Additional file 2: Table S2) are found in the genome, whereof GH13 and GH74 represent half of the enzymes. Diverse GH13 hydrolases, partially located in a Sus, cluster enable the bacterium to utilize starch. Characterization of L. profundi LP1T has shown its ability to grow on starch and sucrose as the single C-source . The strain also has the ability to catabolise monosaccharides such as mannose-6P, fructose-6P and glucose, as well as the disaccharides maltose, sucrose and trehalose. A sugar kinase (Lupro_07775) could activate monosaccharides such as mannose and fructose by phosphorylation . The ability of the strain LP1T to degrade starch  was supported by the presence of a Sus (Lupro_12175-Lupro_12250). Additional, two other SusD proteins (Lupro_05305 and Lupro_02600) and three signal peptide containing proteins (Lupro_10330, Lurpo_05115 and Lurpo_05135), described as ‘Starch-binding associating with outer membrane’, were found in the genome adjacent to TonB-linked outer membrane transporter proteins. These proteins harbour a SusD-like_2 domain and facilitate extracellular starch-binding, while being associated to the outer membrane with an N-terminal lipid tail . For the polysaccharide degradation specialist Bacteroides thetaiotaomicron , SusC and SusD alone account for ~60% of the polysaccharide-degrading ability . Furthermore, a gene for a bacterial glycogen synthase (Lupro_08100) was found in the L. profundi LP1T genome that would allow energy conservation in form of glycogen.
Conserved domain  prediction revealed a possible neuraminidase/sialidase function for the GH74 hydrolases, alongside with a general function for β-1,4-linked glucan hydrolase activity for this family based on CAZypedia . Bacterial sialidases are involved in the removal of sialic acid from various glycoconjugates  and are so far classified in the GH families 33 and 58 . However, most GH74 hydrolases exhibit specificities towards xyloglucans and/or xyloglucan-oligosaccharides found in plant cell walls . Either way, these predicted enzymes might be involved in the degradation of oligosaccharides. GHs, belonging to GH3, GH20, GH23, GH73 and GH109, can be linked to modification/degradation of cell wall components such as peptidoglycan, glycoproteins and lipopolysaccharide. Two peptidoglycan-modifying enzymes, Lupro_08335 (GH23) and Lupro_11420 (GH73), are supplemented with a CBM family 50 mediating the binding to N-acetylglucosamine residues . Various outer membrane proteins containing SusC domains and TonB-dependent receptors enable oligosaccharide import into the periplasm and from there through sodium/glucose co-transporter and L-fucose-proton symporter to the cytosol. Compared to carbohydrate active enzymes, L. profundi LP1T harbours a larger number of proteases. Positive degradation of gelatine and casein on agar plates was observed for L. profundi LP1T . 131 gene-encoding sequences were assigned to 51 MEROPS peptidase families, mostly metallo- and serine proteases (Additional file 3: Table S3), whereof 27 contained a signal peptide. From marine sedimentary bacteria the majority of extracellular peptidases have been identified as serine- and metalloproteases [61, 62]. The peptidase families C26, M01, M14, M20, M23, S09, S12, S33, and S41 were found more frequently than others. The amount of M01 and S09 peptidases are similar to the deep-sea Bacteroidetes Zunongwangia profunda SM-A87, as well as the high number of peptidase genes from the families M01, M23, S09, and S41 . Secreted M01 aminopeptidase in Z. profunda SM-A87 has been proposed as a response to HMW dissolved organic nitrogen degradation, whereas the prolyl oligopeptidases of family S09 specifically hydrolyse oligopeptides shorter than 30 residues .
For the accessibility of nutrition deriving from HMW organic matter, hydrolytic enzymes need to be exported across the cell envelope into the extracellular environment. In total, 71 genes encoding for proteins of the double-membrane-spanning secretion systems type I (T1SS), and efflux pumps are incorporated in the L. profundi LP1T genome (Additional file 4: Table S4). Both systems are often associated with nutrition acquisition and antimicrobial resistance mechanisms . The T1SS use ABC transporters for substrate translocation across the cytoplasma membrane, whereas efflux pumps use Na+/H+ drug antiports or the proton-motive force . 32 proteins were associated with ABC transport across the inner membrane. Whereas 6 RND transporters, 13 major facility transporters and 7 multidrug and toxic compound extrusion family proteins was identified as efflux pumps. In total, 10 outer membrane channel proteins TolC were identified, transporting substrate from the periplasm across the outer membrane in both systems .
Six genes related to the curli biogenesis system (Lupro_11990-Lupro_12015) were found. Curli fibers produced by the curli biogenesis system have shown to be involved in adhesion to surfaces, cell aggregation and biofilm formation . Cell morphology changes were observed in L. profundi LP1T into filamentous rods and cell aggregation under sub-optimal cultivation condition, such as the presence of ampicillin, non-optimal temperatures, unfavourable carbon source or extended growth periods above one week (Fig. 2b) . The abilities to aggregate or produce biofilms are also beneficial, and perhaps vital for L. profundi LP1T to survive the fluctuating chemical and physical conditions of the deep-sea hydrothermal vent system. A variety of protein domains involved in adhesion was identified using NCBI Batch web CD-Search Tool . In total 60 ORFs were revealed from the genome, containing adhesion domains such as FN3, TSP_3, vWA, CBM’s, LamG, PKD, among others (Additional file 5: Table S5). Many bacterial species also produce extracellular polysaccharides that are able to promote adhesion . In the genome of L. profundi LP1T three genes encoding for poly-β-1,6-N-acetyl-D-glucosamine synthase/GT family 2 (Lupro_00610, Lupro_00765, Lupro_09885) and a potential polysaccharide deacetylase gene (Lupro_10410) were found, which may enable the bacteria to produce poly-β-1,6-N-acetyl-D-glucosamine (PGA). The homopolymer PGA mediates cell-to-cell and cell-to-surface adhesion in biofilms in E. coli and has effects on diverse host-microbe interactions . The O-antigen of lipopolysaccharides can mediate attachment to host surfaces and biofilm formation [68, 69]. The strain LP1T comprises extracellular polysaccharide gene clusters containing several glycosyl transferases, besides genes encoding for lipid A synthesis, which may also attribute towards cell adhesion and biofilm formation.
Many members of the Bacteroidetes are able to glide along surfaces in search for nutrition or as response to environmental stimuli [21, 70]. Blast analysis of the L. profundi LP1T genome revealed 17 protein-encoding genes involved in gliding motility (Additional file 6: Table S6). However, no gliding motility has been observed for L. profundi LP1T . Bacteroidetes strains, such as the non-motile oral pathogen Porphyromonas gingivalis or F. johnsoniae use the gliding motility apparatus in addition for secretion of extracellular enzymes participating in accessing nutrition or serve as virulence factors [71, 72]. The gliding motility apparatus has been suggested to refer to PorSS as the type IX secretion system (T9SSs) . In the genome of strain LP1T, 17 proteins were found containing a Por_Secre_tail domain, which is responsible for translocation of proteins across the outer membrane via PorSS . Amongst these proteins are adhesins, proteases, an endonuclease, an α-amylase and a putative sialidase. Therefore the PorSS may not only add to the transportation system of L. profundi LP1T, but also enhances its hydrolytic capacity.
The genome of Lutibacter profundi LP1T comprises a single chromosome of 2,966 Mbp, smaller compared to other marine Bacteroidetes [21, 62, 74]. A reduced genome, a range of transporter systems and metabolic features indicate a highly specialized organism toward a life in a deep-sea hydrothermal vent biofilm.
L. profundi LP1T originated from a biofilm attached to the outer surface of a deep-sea hydrothermal chimney. The mat consisted of long recalcitrant sugar polymers produced by the Epsilonproteobacteria Sulfurovum with Bacteroidetes attached along the filament surface . As organotrophs, Flavobacteriaceae have been linked to HMW organic matter degradation such as polysaccharides and proteins. L. profundi LP1T features a small selected arsenal of 24 GHs, which is rather a minor amount compared to other members of the family [21, 74], nevertheless it offers the possibility to hydrolyse α-glucosidic poly- and oligosaccharides, peptidoglycans and β-glycans. The utilisation of starch and sucrose was confirmed by the presence of a Sus cluster. Together with the large number of proteases strain LP1T seems predestined to utilize complex organic matter efficiently, derived from a microbial biofilm. Diverse TonB-dependent receptors located close to glycoside hydrolases and proteases, as well as sodium/glucose cotransporter, amino acid permeases and transporter confirm the organotrophic life style. L. profundi LP1T contains a set of genes for gliding motility, which is common in Bacteroidetes , and may allow the strain to move in the biofilm. Furthermore, the gliding motility apparatus seems to add to the transportation system of L. profundi LP1T, by exporting Por secretion signal containing proteins such as protease, endonuclease, amylase, putative sialidase or proteins with adhesive properties, which contributes to accessibility of nutrition’s for the bacteria. L. profundi LP1T can mediate attachment to surfaces via a multitude of adhesins and extracellular polysaccharides and thereby may contribute to the biofilm generation. The presence of various cytochrome c oxidases with different oxygen affinities enables the bacteria to thrive in microaerophilic to aereophilic conditions, like they are present in biofilms or hydrothermal environments influenced by fluctuation of hydrothermal fluids mixed with sea water. The microaerobic life style is further indicated by diverse ferredoxin utilizing enzymes. The complete pathway for denitrification is present in L. profundi LP1T in addition to oxygen respiration and the activity of nitrate reduction to nitrite has been confirmed under microaerobic conditions, although it did not enhance the growth . Furthermore, SQR involved in the sulphur metabolisms may play an important role in sulphide detoxification in an environment with high sulphide concentration.
Arctic mid-Ocean ridge
Carbohydrate active enzyme families
Carbohydrate binding modules
KEGG automatic annotation server
Loki’s castle vent field
Norwegian sequencing centre
Prokaryotic Genome annotation pipeline
Resistance, Nodulation and cell Division
Starch utilization cluster
This work was funded by the Norwegian Research Council via the following projects; Mining of a Norwegian Biogoldmine through metagenomics, project nr. 208491, NorZymeD project nr. 221568 and Centre for Geobiology project nr. 179560.
Conceived and designed the experiments: IHS and RS. Performed bioinformatics analysis and assembly refinement: RS. Analysed the data: JW, SLMB, IHS and RS. Wrote the paper: JW, SLMB, IHS and RS. All authors read and approved the final manuscript.
The authors declare that they have no competing interests.
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