Open Access

Genome sequence of the Antarctic rhodopsins-containing flavobacterium Gillisia limnaea type strain (R-8282T)

  • Thomas Riedel
  • , Brittany Held,
  • , Matt Nolan
  • , Susan Lucas
  • , Alla Lapidus
  • , Hope Tice
  • , Tijana Glavina Del Rio
  • , Jan-Fang Cheng
  • , Cliff Han,
  • , Roxanne Tapia,
  • , Lynne A. Goodwin,
  • , Sam Pitluck
  • , Konstantinos Liolios
  • , Konstantinos Mavromatis
  • , Ioanna Pagani
  • , Natalia Ivanova
  • , Natalia Mikhailova
  • , Amrita Pati
  • , Amy Chen
  • , Krishna Palaniappan
  • , Miriam Land
  • , Manfred Rohde
  • , Brian J. Tindall
  • , John C. Detter,
  • , Markus Göker
  • , James Bristow
  • , Jonathan A. Eisen,
  • , Victor Markowitz
  • , Philip Hugenholtz,
  • , Nikos C. Kyrpides
  • , Hans-Peter Klenk
  • and Tanja Woyke
Corresponding author

DOI: 10.4056/sigs.3216895

Received: 10 October 2012

Published: 10 October 2012


Gillisia limnaea Van Trappen et al. 2004 is the type species of the genus Gillisia, which is a member of the well characterized family Flavobacteriaceae. The genome of G. limnea R-8282T is the first sequenced genome (permanent draft) from a type strain of the genus Gillisia. Here we describe the features of this organism, together with the permanent-draft genome sequence and annotation. The 3,966,857 bp long chromosome (two scaffolds) with its 3,569 protein-coding and 51 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.


aerobicmotilerod-shapedmoderately halotolerantpsychrophilicchemoheterotrophicproteorhodopsinmicrobial matyellow-pigmentedFlavobacteriaceaeGEBA


Strain R-8282T (= DSM 15749 = LMG 21470 = CIP 108418) is the type strain of the species Gillisia limnaea [1], which in turn is the type species of the Gillisia, a genus currently encompassing six known species [1]. The strain was isolated from a microbial mat in Lake Fryxell, Antarctica [1] during the MICROMAT project, which systematically collected novel strains from Antarctic lakes [2]. The genus was named after the Belgian bacteriologist Monique Gillis for her work on bacterial taxonomy [1]. The species epithet was derived from the Neo-Latin adjective ‘limnaeae’, living in the water, referring to the microbial mats in Lake Fryxell where the organism was first isolated [1]. PubMed records do not indicate any follow-up research with strain R-8282T after the initial description and valid publication of the new species name G. limnaea, and genus Gillisia [1]. Here we present a summary classification and a set of features for G. limnaea R-8282T, together with the description of the genomic sequencing and annotation.

Classification and features

A representative genomic 16S rRNA sequence of G. limnaea R-8282T was compared using NCBI BLAST [3,4] 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 of taxa and keywords (reduced to their stem [6]) were determined, weighted by BLAST scores. The most frequently occurring genera were Flavobacterium (80.2%), Gillisia (17.8%), Chryseobacterium (1.0%) and Cytophaga (1.0%) (94 hits in total). Regarding the single hit to sequences from members of the species, the average identity within HSPs was 99.1%, whereas the average coverage by HSPs was 98.2%. Regarding the five hits to sequences from other members of the genus, the average identity within HSPs was 95.6%, whereas the average coverage by HSPs was 94.3%. Among all other species, the one yielding the highest score was Gillisia hiemivivida (AY694006), which corresponded to an identity of 97.1% and an HSP coverage of 90.8%. (Note that the Greengenes database uses the INSDC (= EMBL/NCBI/DDBJ) annotation, which is not an authoritative source for nomenclature or classification.) The highest-scoring environmental sequence was EU735617 (Greengenes short name: 'archaeal structures and pristine soils China oil contaminated soil Jidong Oilfield clone SC78'), which showed an identity of 99.0% and an HSP coverage of 98.4%. The most frequently occurring keywords within the labels of all environmental samples which yielded hits were 'librari' (3.2%), 'dure' (3.0%), 'bioremedi, broader, chromat, groundwat, microarrai, polylact, sampl, stimul, subsurfac, typic, univers' (2.9%), 'spring' (2.5%) and 'soil' (2.4%) (156 hits in total). The most frequently occurring keywords within the labels of those environmental samples which yielded hits of a higher score than the highest scoring species were 'soil' (15.4%), 'archaeal, china, contamin, jidong, oil, oilfield, pristin, structur' (7.7%) and 'antarct, cover, lake' (7.7%) (2 hits in total). Whereas some of these keywords confirm the environment of G. limnaea, others are indicative of other habitats in which related taxa are found.

Figure 1 shows the phylogenetic neighborhood of G. limnaea in a 16S rRNA based tree. The sequences of the two 16S rRNA gene copies in the genome differ from each other by up to eleven nucleotides, and differ by up to eight nucleotides from the previously published 16S rRNA sequence (AJ440991), which contains seven ambiguous base calls.

Figure 1

Phylogenetic tree highlighting the position of G. limnaea relative to the type strains of the type species of the genera within the family Flavobacteriaceae. The tree was inferred from 1,366 aligned characters [7,8] of the 16S rRNA gene sequence under the maximum likelihood (ML) criterion [9]. Rooting was done initially using the midpoint method [10] and then checked for its agreement with the current classification (Table 1). The branches are scaled in terms of the expected number of substitutions per site. Numbers adjacent to the branches are support values from 1,000 ML bootstrap replicates [11] (left) and from 1,000 maximum-parsimony bootstrap replicates [12] (right) if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [13] are labeled with one asterisk, those also listed as 'Complete and Published' with two asterisks [14-16]; for Ornithobacterium rhinotracheale see CP003283)

Table 1

Classification and general features of G. limnaea G-8282T according to the MIGS recommendations [17] and NamesforLife [18].




     Evidence code

      Domain Bacteria

     TAS [19]

      Phylum Bacteroidetes

     TAs [20,21]

      Class Flavobacteria

     TAS [22-24]

     Current classification

      Order Flavobacteriales

     TAS [21,25]

      Family Flavobacteriaceae

     TAS [26-29]

      Genus Gillisia

     TAS [1]

      Species Gillisia limnaea

     TAS [1]

      Type strain R-8282

     TAS [1]

     Gram stain


     TAS [1]

     Cell shape


     TAS [1]


      gliding motility likely, but not proven




     TAS [1]

     Temperature range

      psychrophile, 5-30°C

     TAS [1]

     Optimum temperature


     TAS [1]


      0-5% NaCl (w/v)

     TAS [1]


     Oxygen requirement


     TAS [1]

     Carbon source

      yeast extract, peptone

     TAS [1]

     Energy metabolism

      chemoheterotrophic, phototrophic

     TAS [1]



      fresh water

     TAS [1]


     Biotic relationship

      free living

     TAS [1]





     Biosafety level


     TAS [30]



      microbial mats

     TAS [1]


     Geographic location

      Lake Fryxell, McMurdo Dry Valleys, Antarctica

     TAS [1]


     Sample collection time

      between November 1998 and February 2001

     TAS [1,2]











      not reported



      not reported

Evidence codes - TAS: Traceable Author Statement (i.e., a direct report exists in the literature); NAS: Non-traceable Author Statement (i.e., not directly observed for the living, isolated sample, but based on a generally accepted property for the species, or anecdotal evidence). Evidence codes are from the Gene Ontology project [31].

Cells of strain G. limnaea R-8282T are Gram-negative and rod-shaped [Figure 2] [1]. They are 0.7 µm in width and 3.0 µm in length [1], whereas scanning electron micrographs of strain R-8282T revealed a cell diameter that varies from 0.4 µm to 0.5 µm, and a length that varies from 1.6 µm to longer than 4.9 µm [Figure 2], which is more consistent with data previously reported for several Gillisia strains [32-34]. Motility, especially gliding motility, was not observed [1], despite the presence of numerous genes associated with gliding motility (see below), and the presence of pili-containing cells in scanning electron micrographs of strain R-8282T. It is unclear if these pili are involved in gliding motility or bacterial adhesion to surfaces. Cells are strictly aerobic, psychrophilic and chemoheterotrophic [1]. Growth occurs between 5°C and 30°C with an optimum at 20°C [1]; the strain is unable to grow at temperatures above 37°C [1]. Growth occurs within a salinity range of 0% to 5% NaCl, but not in 10% NaCl, indicating moderate halotolerance [1]. Peptone and yeast extract were required for growth [1]. When cultivated on marine agar, colonies are yellow in color, convex and translucent with diameters of 1-3 mm forming entire margins after 6 days of incubation [1]. When cultivated on Anacker & Ordal’s agar, colonies become flat and round with entire margins and 0.7 to 0.9 mm in diameter after 14 days incubation [1]. Additionally growth is both detectable on nutrient agar and R2A, but the strain does not grow on trypticase soy agar [1]. Further detailed physiological data such as carbon source utilization, carbon degradation, and enzyme activities have been reported previously [1].

Figure 2

Scanning electron micrograph of G. limnaea R-8282T


The principal cellular fatty acids of strain R-8282T are iso-C15:0, anteiso-C15:0, iso-C15:1, iso-C16:0, C17:0 2-OH, iso-C17:0 3-OH, iso-C17:1 ω9c, anteiso-C17:1 ω9c and summed feature 3 (containing iso-C15:0 2-OH and/or C16:1 ω7c) [1]. The major polar lipids were not reported for strain R-8282T.

Genome sequencing and annotation

Genome project history

This organism was selected for sequencing on the basis of its phylogenetic position [35], and is part of the Genomic Encyclopedia of Bacteria and Archaea project [36]. The genome project is deposited in the Genomes On Line Database [13] and the complete genome sequence is deposited in GenBank. Sequencing, finishing and annotation were performed by the DOE Joint Genome Institute (JGI). A summary of the project information is shown in Table 2.

Table 2

Genome sequencing project information





     Finishing quality



     Libraries used

     Four genomic libraries: one 454 pyrosequence standard library,     two 454 PE libraries (4 kb and 10 kb insert size), one Illumina library


     Sequencing platforms

     Illumina GAii, 454 GS FLX Titanium


     Sequencing coverage

     309.5 × Illumina; 36.0 × pyrosequence



     Newbler version 2.3, Velvet 1.0.13, phrap version SPS - 4.24


     Gene calling method




     GenBank Date of Release

     January 24, 2012

     GOLD ID


     NCBI project ID


     Database: IMG-GEBA



     Source material identifier

     DSM 15749

     Project relevance

     Tree of Life, GEBA

Growth conditions and DNA isolation

G. limnaea strain R-8282T, DSM 15749, was grown in DSMZ medium 514 (BACTO Marine Broth) [37] at 20°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 as described by Wu et al. 2009 [36] for optimized cell lysis. DNA is available through the DNA Bank Network [38].

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 [39]. Pyrosequencing reads were assembled using the Newbler assembler (Roche). The initial Newbler assembly consisting of 93 contigs in one scaffold was converted into a phrap [40] assembly by making fake reads from the consensus, to collect the read pairs in the 454 paired end library. Illumina GAii sequencing data (1,096.5Mb) was assembled with Velvet [41] 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 178.7 Mb 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 [40] 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 [39], Dupfinisher [42], or sequencing cloned bridging PCR fragments with subcloning. Gaps between contigs were closed by editing in Consed, by PCR and by Bubble PCR primer walks (J.-F. Chang, unpublished). A total of 893 additional reactions and one shatter library were necessary to close gaps and to raise the quality of the final sequence. Illumina reads were also used to correct potential base errors and increase consensus quality using the software Polisher developed at JGI [43]. The error rate of the final genome sequence is less than 1 in 100,000. Together, the combination of the Illumina and 454 sequencing platforms provided 127.9 x coverage of the genome. The final assembly contained 597,282 pyrosequence and 33,599,185 Illumina reads.

Genome annotation

Genes were identified using Prodigal [44] as part of the Oak Ridge National Laboratory genome annotation pipeline, followed by a round of manual curation using the JGI GenePRIMP pipeline [45]. The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) non-redundant database, UniProt, TIGRFam, Pfam, PRIAM, KEGG, COG, and InterPro databases. These data sources were combined to assert a product description for each predicted protein. Additional gene prediction analysis and functional annotation was performed within the Integrated Microbial Genomes - Expert Review (IMG-ER) platform [46].

Genome properties

The genome consists of two scaffolds with 3,558,876 bp and 407,981 bp length, respectively, with a G+C content of 37.6% (Table 3 and Figure 3). Of the 3,620 genes predicted, 3,569 were protein-coding genes, and 51 RNAs; 135 pseudogenes were also identified. The majority of the protein-coding genes (66.0%) were assigned a putative function while the remaining ones were annotated as hypothetical proteins. The distribution of genes into COGs functional categories is presented in Table 4.

Table 3

Genome Statistics



     % of Total

Genome size (bp)



DNA coding region (bp)



DNA G+C content (bp)



Number of scaffolds


Total genes



RNA genes



rRNA operons


tRNA genes



Protein-coding genes



Pseudo genes



Genes with function prediction (proteins)



Genes in paralog clusters



Genes assigned to COGs



Genes assigned Pfam domains



Genes with signal peptides



Genes with transmembrane helices



CRISPR repeats


* one 23S rRNA gene, two 16S rRNA genes

Figure 3

Graphical map of the largest scaffold. From bottom to top: Genes on forward strand (colored by COG categories), Genes on reverse strand (colored by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content(black), GC skew (purple/olive).

Table 4

Number of genes associated with the 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




    Nuclear structure




    Defense mechanisms




    Signal transduction mechanisms




    Cell wall/membrane biogenesis




    Cell motility








    Extracellular structures




    Intracellular trafficking and 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




    Function unknown




    Not in COGs

Insights into the genome sequence

Genome analysis of G. limnaea R-8282T revealed the presence of three rhodopsin genes related to proteorhodopsin (PR, GenBank Accession No. EHQ04368, Gilli_0216) and xanthorhodopsin (XR, EHQ02967, Gilli_2340) protein-encoding sequences, whereas a third rhodopsin protein sequence (EHQ02971, Gilli_2344) seems to be truncated. Another finding was a set of genes involved in β-carotene biosynthesis, together with a gene encoding a β-carotene 15,15'-monooxygenase (EHQ04367, Gilli_0215), an enzyme that oxidatively cleaves β-carotene into two molecules of retinal, which is necessary for rhodopsin function. PRs and XRs are photoactive transmembrane opsins that bind retinal and which belong to the microbial rhodopsin superfamily [47]. When exposed to light, a change in protein conformation causes a proton translocation with respect to its cofactor retinal from the inside to the outside of the cell [48]. This proton-pump activity generates a proton motive force across the cell membrane, which can be used in heterologously PR-expressing E. coli cells for ATP synthesis [49] as well as to power general cellular functions like transmembrane nutrient transport or flagella rotation [50]. In contrast to PRs, XRs are light-driven proton pumps containing a dual chromophore: one retinal molecule and one carotenoid antenna [51,52], that was first discovered in Salinibacter ruber M31T [53,54]. Its carotenoid antenna salinixanthin transfers as much as 40-45% of the absorbed photons to retinal [55], resulting in a potentially much more efficient light capturing system compared to PRs from Bacteria [56,57] or bacteriorhodopsins from Archaea [58].

NCBI BLAST analysis [3] revealed that the protein encoded by Gilli_0216 shares distinct identities with many PR protein sequences, found in other species within the Flavobacteriaceae (Figure 4). It shows typical features necessary for proton pump activity: K224 (K231) for retinal-binding, and D88 (D97) as well as E99 (E108) (EBAC31A08 numbering shown in brackets), which act as a proton acceptor and proton donor in the retinylidene Schiff’s base transfer during the PR photocycle [60,61]. Furthermore, the putative PR (Gilli_0216 protein) has a M96 (L105) (EBAC31A08 numbering in parentheses), which mainly indicates that it is a green light-absorbing proteorhodopsin [48,62].

Figure 4

Rhodopsin tree for Gillisia and relatives. Amino acid sequences were processed in the same way as the 16S rRNA sequences used in Figure 1 except for the explicit determination of an optimal maximum-likelihood model, which turned out to be Lateral Gene Transfer [59]. GenBank Accession Numbers are shown in parentheses.

The gene encoding the putative XR (Gilli_2340) of strain R-8282T shows identities to XR-related proteins, but provides evidence of a new cluster of rhodopsins found in very few flavobacterial isolates like Dokdonia donghaensis PRO95 (EHQ04368) [63] and Krokinobacter sp. 4H-3-7-5 (AEE18495) [64], which was reclassified into the genus Dokdonia [65,66] (Figure 4). This rhodopsin-encoding sequence also reveals typical features necessary for rhodopsin function: K316 (K231) for retinal binding and L181 (L105), which mainly indicates a green-light absorbing rhodopsin [48,62] (EBAC31A08 numbering shown in brackets). But amino acid residues functioning as proton acceptor and proton donor in proteorhodopsin differ from those commonly known. Instead of D97 and E108 (EBAC31A08 numbering), the related amino acids N173 and Q184 are found in the protein sequence encoded by Gilli_2340, which indicates a possible new kind of rhodopsins.

Interestingly, no rhodopsin-encoding sequence could be detected in the genome sequence of Gillisia sp. strain CBA3202 [67], which was isolated from the littoral zone on Jeju Island, Republic of Korea [67]. Digital DNA-DNA hybridization (DDH) [68] between strain R-8282T and CBA3202 revealed an estimate between 9.7% and 13.9% (depending on the formula used), indicating that Gillisia sp. strain CBA3202 does not belong to the species G. limnaea.

Compared to free-living bacteria, representatives of the Bacteroidetes phylum were frequently found attached to aggregates [69] and during an algae-bloom collapse [70,71]. They were also known to move over surfaces by gliding motility [72,73]. In strain R-8282T several genes were detected that are thought to be involved in gliding motility (gldA (Gilli_1140), gldB (Gilli_2923), gldC (Gilli_2942), gldD (Gilli_1840), gldE (Gilli_1841), gldF (Gilli_3447), gldG (Gilli_3446), gldH (Gilli_2158), gldI (Gilli_0258), gldJ (Gilli_1638), gldK (Gilli_2747), gldL (Gilli_2748), gldM (Gilli_2749), gldN (Gilli_2750), espA (Gilli_3049), espB (Gilli_3050), remB (Gilli_2697), sprA (Gilli_2693) and sprE (Gilli_2130)). This observation indicates the possible gliding motility of strain R-8282T, but has never been reported in literature.



We would like to gratefully acknowledge the help of Helga Pomrenke for growing G. limnaea cultures and Evelyne-Marie Brambilla for DNA extraction and quality control (both at the DSMZ). 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 as well as TRR 51.

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


  1. Van Trappen S, Vandecandelaere I, Mergaert J and Swings J. Gillisia limnaea gen. nov., sp. nov., a new member of the family Flavobacteriaceae isolated from a microbial mat in Lake Fryxell, Antarctica. Int J Syst Evol Microbiol. 2004; 54:445-448 View ArticlePubMed
  2. Van Trappen S, Mergaert J, Van Eygen S, Dawyndt P, Cnockaert MC and Swings J. Diversity of 746 heterotrophic bacteria isolated from microbial mats from ten Antarctic lakes. Syst Appl Microbiol. 2002; 25:603-610 View ArticlePubMed
  3. Altschul SF, Gish W, Miller W, Myers EW and Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990; 215:403-410PubMed
  4. Korf I, Yandell M, Bedell J. BLAST, O'Reilly, Sebastopol, 2003.
  5. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P and Andersen GL. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol. 2006; 72:5069-5072 View ArticlePubMed
  6. Porter MF. An algorithm for suffix stripping. Program: electronic library and information systems 1980; 14:130-137.
  7. Lee C, Grasso C and Sharlow MF. Multiple sequence alignment using partial order graphs. Bioinformatics. 2002; 18:452-464 View ArticlePubMed
  8. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 2000; 17:540-552 View ArticlePubMed
  9. Stamatakis A, Hoover P and Rougemont J. A rapid bootstrap algorithm for the RAxML web servers. Syst Biol. 2008; 57:758-771 View ArticlePubMed
  10. Hess PN and De Moraes Russo CA. An empirical test of the midpoint rooting method. Biol J Linn Soc Lond. 2007; 92:669-674 View Article
  11. Pattengale ND, Alipour M, Bininda-Emonds ORP, Moret BME and Stamatakis A. How many bootstrap replicates are necessary? Lect Notes Comput Sci. 2009; 5541:184-200 View Article
  12. Swofford DL. PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods), Version 4.0 b10. Sinauer Associates, Sunderland, 2002.
  13. Pagani I, Liolios K, Jansson J, Chen IM, Smirnova T, Nosrat B, Markowitz VM and Kyrpides NC. The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res. 2012; 40:D571-D579 View ArticlePubMed
  14. Qin QL, Zhang XY, Wang XM, Liu GM, Chen XL, Xie BB, Dang HY, Zhou BC, Yu J and Zhang YZ. The complete genome of Zunongwangia profunda SM-A87 reveals its adaptation to the deep-sea environment and ecological role in sedimentary organic degradation. BMC Genomics. 2010; 11:247 View ArticlePubMed
  15. Pati A, Abt B, Teshima H, Nolan M, Lapidus A, Lucas S, Hammon N, Deshpande S, Cheng JF and Tapia R. Complete genome sequence of Cellulophage lytica type strain (LIM21T). Stand Genomic Sci. 2011; 4:221-232 View ArticlePubMed
  16. Mavrommatis K, Gronow S, Saunders E, Land M, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Lucas S and Chen F. Complete genome sequence of Capnocytophaga ochracea type strain (VPI 2845T). Stand Genomic Sci. 2009; 1:101-109 View ArticlePubMed
  17. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ and Angiuoli SV. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol. 2008; 26:541-547 View ArticlePubMed
  18. Garrity G. NamesforLife. BrowserTool takes expertise out of the database and puts it right in the browser. Microbiol Today. 2010; 37:9
  19. Woese CR, Kandler O and Wheelis ML. Towards a natural system of organisms. Proposal for the domains Archaea and Bacteria. Proc Natl Acad Sci USA. 1990; 87:4576-4579 View ArticlePubMed
  20. Krieg NR, Ludwig W, Euzéby J, Whitman WB. Phylum XIV. Bacteroidetes phyl. nov. In: Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ, Ward NL, Ludwig W, Whitman WB (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 4, Springer, New York, 2011, p. 25.
  21. Editor L. Validation List No. 143. [PubMed]. Int J Syst Evol Microbiol. 2012; 62:1-4
  22. Bernardet JF. Class II. Flavobacteriia class. nov. In: Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ, Ward NL, Ludwig W, Whitman WB (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 4, Springer, New York, 2011, p. 105.
  23. Ludwig W, Euzeby J, Whitman WG. Draft taxonomic outline of the Bacteroidetes, Planctomycetes, Chlamydiae, Spirochaetes, Fibrobacteres, Fusobacteria, Acidobacteria, Verrucomicrobia, Dictyoglomi, and Gemmatimonadetes
  24. . The nomenclatural types of the orders Acholeplasmatales, Halanaerobiales, Halobacteriales, Methanobacteriales, Methanococcales, Methanomicrobiales, Planctomycetales, Prochlorales, Sulfolobales, Thermococcales, Thermoproteales and Verrucomicrobiales are the genera Acholeplasma, Halanaerobium, Halobacterium, Methanobacterium, Methanococcus, Methanomicrobium, Planctomyces, Prochloron, Sulfolobus, Thermococcus, Thermoproteus and Verrucomicrobium, respectively. Opinion 79. Int J Syst Evol Microbiol. 2005; 55:517-518 View ArticlePubMed
  25. Bernardet JF. Order I. Flavobacteriales ord. nov. In: Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ, Ward NL, Ludwig W, Whitman WB (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 4, Springer, New York, 2011, p. 105.
  26. Reichenbach H. Order 1. Cytophagales Leadbetter 1974, 99AL. In: Holt JG (ed), Bergey's Manual of Systematic Bacteriology, First Edition, Volume 3, The Williams and Wilkins Co., Baltimore, 1989, p. 2011-2013.
  27. Bernardet JF, Segers P, Vancanneyt M, Berthe F, Kersters K and Vandamme P. Cutting a Gordian knot: emended classification and description of the genus Flavobacterium, emended description of the family Flavobacteriaceae, and proposal of Flavobacterium hydatis nom. nov. (Basonym, Cytophaga aquatilis Strohl and Tait 1978). Int J Syst Bacteriol. 1996; 46:128-148 View Article
  28. Bernardet JF, Nakagawa Y and Holmes B. Proposed minimal standards for describing new taxa of the family Flavobacteriaceae, and emended description of the family. [PubMed]. Int J Syst Evol Microbiol. 2002; 52:1049-1070 View ArticlePubMed
  29. Validation of the publication of new names and new combinations previously effectively published outside the IJSB. List No. 41. Int J Syst Bacteriol. 1992; 42:327-328 View Article
  30. BAuA. 2010, Classification of Bacteria and Archaea in risk groups. TRBA 466, p. 93.Web Site
  31. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS and Eppig JT. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000; 25:25-29 View ArticlePubMed
  32. Lee OO, Lau SC, Tsoi MM, Li X, Plakhotnikova I, Dobretsov S, Wu MC, Wong PK and Qian PY. Gillisia myxillae sp. nov., a novel member of the family Flavobacteriaceae, isolated from the marine sponge Myxilla incrustans. Int J Syst Evol Microbiol. 2006; 56:1795-1799 View ArticlePubMed
  33. Bowman JP and Nichols DS. Novel members of the family Flavobacteriaceae from Antarctic maritime habitats including Subsaximicrobium wynnwilliamsii gen. nov., sp. nov., Subsaximicrobium saxinquilinus sp. nov., Subsaxibacter broadyi gen. nov., sp. nov., Lacinutrix copepodicola gen. nov., sp. nov., and novel species of the genera Bizionia, Gelidibacter and Gillisia. Int J Syst Evol Microbiol. 2005; 55:1471-1486 View ArticlePubMed
  34. Nedashkovskaya OI, Kim SB, Lee KH, Mikhailov VV and Bae KS. Gillisia mitskevichiae sp. nov., a novel bacterium of the family Flavobacteriaceae, isolated from sea water. Int J Syst Evol Microbiol. 2005; 55:321-323 View ArticlePubMed
  35. Klenk HP and Göker M. En route to a genome-based classification of Archaea and Bacteria? Syst Appl Microbiol. 2010; 33:175-182 View ArticlePubMed
  36. Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M and Tindall BJ. A phylogeny-driven Genomic Encyclopaedia of Bacteria and Archaea. Nature. 2009; 462:1056-1060 View ArticlePubMed
  37. List of growth media used at DSMZ: Web Site
  38. Gemeinholzer B, Dröge G, Zetzsche H, Haszprunar G, Klenk HP, Güntsch A, Berendsohn WG and Wägele JW. The DNA Bank Network: the start from a German initiative. Biopreserv Biobank. 2011; 9:51-55 View Article
  39. . Web Site
  40. Phrap and Phred for Windows. MacOS, Linux, and Unix. Web Site
  41. Zerbino DR and Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008; 18:821-829 View ArticlePubMed
  42. Han C, Chain P. Finishing repeat regions automatically with Dupfinisher. In: Proceedings of the 2006 international conference on bioinformatics & computational biology. Arabnia HR, Valafar H (eds), CSREA Press. June 26-29, 2006: 141-146.
  43. Lapidus A, LaButti K, Foster B, Lowry S, Trong S, Goltsman E. POLISHER: An effective tool for using ultra short reads in microbial genome assembly and finishing. AGBT, Marco Island, FL, 2008.
  44. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW and Hauser LJ. Prodigal Prokaryotic Dynamic Programming Genefinding Algorithm. BMC Bioinformatics. 2010; 11:119 View ArticlePubMed
  45. Pati A, Ivanova N, Mikhailova N, Ovchinikova G, Hooper SD, Lykidis A and Kyrpides NC. GenePRIMP: A Gene Prediction Improvement Pipeline for microbial genomes. Nat Methods. 2010; 7:455-457 View ArticlePubMed
  46. Markowitz VM, Ivanova NN, Chen IMA, Chu K and Kyrpides NC. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics. 2009; 25:2271-2278 View ArticlePubMed
  47. Spudich JL, Yang CS, Jung KH and Spudich EN. Retinylidene proteins: structures and functions from archaea to humans. Annu Rev Cell Dev Biol. 2000; 16:365-392 View ArticlePubMed
  48. Fuhrman JA, Schwalbach MS and Stingl U. Proteorhodopsins: an array of physiological roles? Nat Rev Microbiol. 2008; 6:488-494PubMed
  49. Martinez A, Bradley AS, Waldbauer JR, Summons RE and DeLong EF. Proteorhodopsin photosystem gene expression enables photophosphorylation in a heterologous host. Proc Natl Acad Sci USA. 2007; 104:5590-5595 View ArticlePubMed
  50. Walter JM, Greenfield D and Bustamante C. Liphardt. Light-powering Escherichia coli with proteorhodopsin. Proc Natl Acad Sci USA. 2007; 104:2408-2412 View ArticlePubMed
  51. Balashov SP, Imasheva ES, Boichenko VA, Anton J, Wang JM and Lanyi JK. Xanthorhodopsin. A proton pump with a light-harvesting carotenoid antenna. Science. 2005; 309:2061-2064 View ArticlePubMed
  52. Balashov SP and Lanyi JK. Xanthorhodopsin: Proton pump with a carotenoid antenna. Cell Mol Life Sci. 2007; 64:2323-2328 View ArticlePubMed
  53. Antón J, Oren A, Benlloch S, Rodriguez-Valera F, Amann R and Rossello-Mora R. Salinibacter ruber gen. nov., sp. nov., a novel, extremely halophilic member of the Bacteria from saltern crystallizer ponds. Int J Syst Evol Microbiol. 2002; 52:485-491PubMed
  54. Mongodin EF, Nelson KE, Daugherty S, Deboy RT, Wister J, Khouri H, Weidman J, Walsh DA, Papke RT and Sanchez PG. The genome of Salinibacter ruber: convergence and gene exchange among hyperhalophilic bacteria and archaea. Proc Natl Acad Sci USA. 2005; 102:18147-18152 View ArticlePubMed
  55. Balashov SP, Imasheva ES, Wang JM and Lanyi JK. Excitation energy-transfer and the relative orientation of retinal and carotenoid in xanthorhodopsin. Biophys J. 2008; 95:2402-2414 View ArticlePubMed
  56. Béjà O, Aravind L, Koonin EV, Suzuki MT, Hadd A, Nguyen LP, Jovanovich SB, Gates CM, Feldman RA and Spudich JL. Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science. 2000; 289:1902-1906 View ArticlePubMed
  57. Béjà O, Spudich EN, Spudich JL, Leclerc M and DeLong EF. Proteorhodopsin phototrophy in the ocean. Nature. 2001; 411:786-789 View ArticlePubMed
  58. Oesterhelt D and Stoeckenius W. Rhodopsin-like protein from the purple membrane of Halobacterium halobium. Nat New Biol. 1971; 233:149-152PubMed
  59. Le SQ and Gascuel O. An improved general amino acid replacement matrix. Mol Biol Evol. 2008; 25:1307-1320 View ArticlePubMed
  60. Dioumaev AK, Brown LS, Shih J, Spudich EN, Spudich JL and Lanyi JK. Proton transfers in the photochemical reaction cycle of proteorhodopsin. Biochemistry. 2002; 41:5348-5358 View ArticlePubMed
  61. Wang WW, Sineshchekov A, Spudich EN and Spudich JL. Spectroscopic and photochemical characterization of a deep ocean proteorhodopsin. J Biol Chem. 2003; 278:33985-33991 View ArticlePubMed
  62. Man D, Wang W, Sabehi G, Aravind L, Post AF, Massana R, Spudich EN, Spudich JL and Beja O. Diversification and spectral tuning in marine proteorhodopsins. EMBO J. 2003; 22:1725-1731 View ArticlePubMed
  63. Riedel T, Tomasch J, Buchholz I, Jacobs J, Kollenberg M, Gerdts G, Wichels A, Brinkhoff T, Cypionka H and Wagner-Döbler I. Constitutive expression of the proteorhodopsin gene by a flavobacterium strain representative of the proteorhodopsin-producing microbial community in the North Sea. Appl Environ Microbiol. 2010; 76:3187-3197 View ArticlePubMed
  64. Klippel B, Lochner A, Bruce DC, Walston DK, Detter C, Goodwin LA, Han J, Han S, Hauser L and Land ML. Complete Genome Sequences of Krokinobacter sp. Strain 4H-3-7-5 and Lacinutrix sp. Strain 5H-3-7-4, Polysaccharide-Degrading Members of the Family Flavobacteriaceae. J Bacteriol. 2011; 193:4545-4546 View ArticlePubMed
  65. Yoon JH, Kang SJ, Lee CH and Oh TK. Dokdonia donghaensis gen. nov., sp. nov., isolated from sea water. Int J Syst Evol Microbiol. 2005; 55:2323-2328 View ArticlePubMed
  66. Yoon JH, Kang SJ, Park S, Oh TK. Reclassification of the three Krokinobacter species into the genus Dokdonia as Dokdonia genika comb. nov., Dokdonia diaphora comb. nov. and Dokdonia eikasta comb. nov. and emended description of the genus Dokdonia Yoon et al. 2005. Int J Syst Evol Microbiol 2011; [Epup ahead of print].
  67. Nam YD, Lee HW, Lee M, Yim KJ, Kim KN, Roh SW and Kim D. Draft Genome Sequence of Gillisia sp strain CBA3202, a novel member of the genus Gillisia, which belongs to the family Flavobacteriaceae. J Bacteriol. 2012; 194:3739 View ArticlePubMed
  68. Auch AF and Klenk HP. Göker, M. Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs. Stand Genomic Sci. 2010; 2:142-148 View ArticlePubMed
  69. DeLong EF, Franks DG and Alldredge AL. Phylogenetic diversity of aggregate-attached versus free-living marine bacterial assemblages. Limnol Oceanogr. 1993; 38:924-934 View Article
  70. Pinhassi J, Sala MM, Havskum H, Peters F, Guadayol O, Malits A and Marrasé C. Changes in bacterioplancton composition under different phytoplankton regimes. Appl Environ Microbiol. 2004; 70:6753-6766 View ArticlePubMed
  71. Riemann L, Steward GF and Azam F. Dynamics of bacterial community composition and activity during a mesocosm diatom bloom. Appl Environ Microbiol. 2000; 66:578-587 View ArticlePubMed
  72. McBride MJ. Bacterial gliding motility: multiple mechanisms for cell movement over surfaces. Annu Rev Microbiol. 2001; 55:49-75 View ArticlePubMed
  73. McBride MJ. Cytophaga-Flavobacterium gliding motility. J Mol Microbiol Biotechnol. 2004; 7:63-71 View ArticlePubMed