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Marinobacter adhaerens sp. nov., prominent in aggregate formation<br />
with the diatom Thalassiosira weissflogii<br />
Eva C. Kaeppel 1 , Astrid Gärdes 1 , Shalin Seebah 1 , Hans-Peter Grossart 2 , Matthias S.<br />
Ullrich 1<br />
1 <strong>Jacobs</strong> <strong>University</strong> Bremen, Campus Ring 1, 28759 Bremen, Germany<br />
2 Leibniz Institute of Freshwater Ecology and Inland Fisheries - Neuglobsow, Alte Fischerhütte 2, 16775<br />
Stechlin, Germany<br />
Correspondence:<br />
Matthias S. Ullrich<br />
m.ullrich@jacobs-university.de<br />
______________________________________________________________________<br />
The Gram-negative, motile, and rod-shaped bacterial strain, HP15 T , was isolated from<br />
particles sampled in surface waters of the German Wadden Sea. It was identified<br />
among 82 other marine isolates due to its high potential to induce production of<br />
transparent exopolymeric particles and aggregate formation while interacting with the<br />
diatom, Thalassiosira weissflogii. HP15 T grew optimally at a range of 34-38 °C, a pH of<br />
7-8.5, and was able to tolerate salt concentrations between 0.5-20 % (w/v) NaCl. HP15 T<br />
was chemotaxonomically characterized by possessing ubiquinone-9 as the major<br />
respiratory lipoquinone as well as C 16:0 , C 18:1 !9c, C 16:1 !7c/iso, and C 15:0 2-OH as<br />
predominant fatty acids. The G+C content of its DNA was 56.9 mol%. The closest<br />
relative by means of 16S rRNA sequence analysis was Marinobacter flavimaris with a<br />
similarity level of 99 %. The whole-genome relatedness of HP15 T to M. flavimaris, M.<br />
salsuginis, M. lipolyticus, and M. algicola was determined to be lower than 70 % by<br />
DNA-DNA hybridization. On the basis of phenotypic and chemotaxonomic properties as<br />
well as phylogenetic analyses, strain HP15 T (=DSM 23420 T = CIP 110141 T ) is proposed<br />
to represent the novel species, Marinobacter adhaerens sp. nov.<br />
______________________________________________________________________<br />
The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain HP15 T is<br />
AY241552.<br />
A transmission electron micrograph of HP15 T and the comparison of cellular fatty acid composition between<br />
strain HP15 T and type strains of seven other Marinobacter species are available as supplementary<br />
material in IJSEM Online.<br />
!"#$%&'(#!%")<br />
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23349:$ ;$ +
Fig. 1. Transmission electron micrograph of<br />
strain HP15 T cultivated in marine broth for 24<br />
hours.<br />
*&/$!3+'#-&5&$/#7.?#/$=7
Table 1. Phenotypic and genotypic differentiation between HP15 T and the closest<br />
related Marinobacter type strains.<br />
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R6I3E ! g$J8$K:$-.0
Fig. 2. Maximum likelihood phylogenetic tree based on 16S rRNA sequences of<br />
HP15 T , all type strains of the genus Marinobacter and the type strains of Halospina<br />
denitrificans HGD 1-3 T (DQ072719) and Salicola marasensis 7Sm5 T (DQ019934) as<br />
out groups. The tree was inferred from 1,531 alignment positions using the RAxML<br />
algorithm (Stamatakis, 2006). Support values from 1,000 bootstrap replicates were<br />
displayed above branches if larger than 50 %. Bar, 0.01 nucleotide substitutions per<br />
site.<br />
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$5C525B357$<br />
Antunes, A., Franca, L., Rainey, F. A., Huber, R., Nobre, M. F., Edwards, K. J. & Da<br />
Costa, M. S. (2007). Marinobacter salsuginis sp. nov., isolated from the brine-seawater interface<br />
of the Shaban Deep, Red Sea. Int J Syst Evol Microbiol 57, 1035-1040.<br />
Gauthier, M. J., Lafay, B., Christen, R., Fernandez, L., Acquaviva, M., Bonin, P. &<br />
Bertrand, J. C. (1992). Marinobacter hydrocarbonoclasticus gen. nov., sp. nov., a new,<br />
extremely halotolerant, hydrocarbon-degrading marine bacterium. Int J Syst Evol Microbiol 42,<br />
568-576.<br />
Green, D. H., Bowman, J. P., Smith, E. A., Gutierrez, T. & Bolch, C. J. S. (2006).<br />
Marinobacter algicola sp. nov., isolated from laboratory cultures of paralytic shellfish toxinproducing<br />
dinoflagellates. Int J Syst Evol Microbiol 56, 523-527.<br />
Huu, N. B., Denner, E. B. M., Ha Dang, T. C., Wanner, G. & Stan-Lotter, H. (1999).<br />
Marinobacter aquaeolei sp. nov., a halophilic bacterium isolated from a Vietnamese oilproducing<br />
well. Int J Syst Evol Microbiol 49, 367-375.
Martin, S., Marquez, M. C., Sanchez-Porro, C., Mellado, E., Arahal, D. R. & Ventosa, A.<br />
(2003). Marinobacter lipolyticus sp. nov., a novel moderate halophile with lipolytic activity. Int<br />
J Syst Evol Microbiol 53, 1383-1387.<br />
Montes, M. J., Bozal, N. & Mercade, E. (2008). Marinobacter guineae sp. nov., a novel<br />
moderately halophilic bacterium from an Antarctic environment. Int J Syst Evol Microbiol 58,<br />
1346.<br />
Romanenko, L. A., Schumann, P., Rohde, M., Zhukova, N. V., Mikhailov, V. V. &<br />
Stackebrandt, E. (2005). Marinobacter bryozoorum sp. nov. and Marinobacter sediminum sp.<br />
nov., novel bacteria from the marine environment. Int J Syst Evol Microbiol 55, 143-148.<br />
Yoon, J. H., Yeo, S. H., Kim, I. G. & Oh, T. K. (2004). Marinobacter flavimaris sp. nov. and<br />
Marinobacter daepoensis sp. nov., slightly halophilic organisms isolated from sea water of the<br />
Yellow Sea in Korea. Int J Syst Evol Microbiol 54, 1799-1803.<br />
$
Martin, S., Marquez, M. C., Sanchez-Porro, C., Mellado, E., Arahal, D. R. & Ventosa, A.<br />
(2003). Marinobacter lipolyticus sp. nov., a novel moderate halophile with lipolytic activity. Int<br />
J Syst Evol Microbiol 53, 1383-1387.<br />
Montes, M. J., Bozal, N. & Mercade, E. (2008). Marinobacter guineae sp. nov., a novel<br />
moderately halophilic bacterium from an Antarctic environment. Int J Syst Evol Microbiol 58,<br />
1346.<br />
Romanenko, L. A., Schumann, P., Rohde, M., Zhukova, N. V., Mikhailov, V. V. &<br />
Stackebrandt, E. (2005). Marinobacter bryozoorum sp. nov. and Marinobacter sediminum sp.<br />
nov., novel bacteria from the marine environment. Int J Syst Evol Microbiol 55, 143-148.<br />
Yoon, J. H., Yeo, S. H., Kim, I. G. & Oh, T. K. (2004). Marinobacter flavimaris sp. nov. and<br />
Marinobacter daepoensis sp. nov., slightly halophilic organisms isolated from sea water of the<br />
Yellow Sea in Korea. Int J Syst Evol Microbiol 54, 1799-1803.<br />
$
Complete genome sequence of Marinobacter adhaerens type strain<br />
(HP15), a diatom-interacting marine microorganism<br />
Astrid Gärdes 1 , Eva Kaeppel 1 , Aamir Shehzad 1 , Shalin Seebah 1 , Hanno Teeling 2 , Pablo<br />
Yarza 3 , Frank Oliver Glöckner 2 , Hans-Peter Grossart 4 and Matthias S. Ullrich 1 *<br />
1 <strong>Jacobs</strong> <strong>University</strong> Bremen, School of Engineering and Science, Bremen, Germany<br />
2 Max Planck Institute for Marine Microbiology, Microbial Genomics and Bioinformatics<br />
Group, Bremen, Germany<br />
3 Institut Mediterrani d'Estudis Avançats, Marine Microbiology Group, Esporles, Spain<br />
4 IGB-Neuglobsow, Dept. Limnology of Stratified Lakes, Stechlin, Germany<br />
* Corresponding author: Matthias S. Ullrich (m.ullrich@jacobs-university.de)<br />
Keywords: marine heterotrophic bacteria, diatoms, attachment, marine aggregate<br />
formation<br />
______________________________________________________________________<br />
Marinobacter adhaerens HP15 is the type strain of a newly identified marine species,<br />
which is phylogenetically related to M. flavimaris, M. algicola, and M. aquaeolei. It is of<br />
special interest for research on marine aggregate formation because it showed specific<br />
attachment to diatom cells. In vitro it led to exopolymer formation and aggregation of<br />
these algal cells to form marine snow particles. M. adhaerens HP15 is a free-living,<br />
motile, rod-shaped, Gram-negative Gammaproteobacterium, which was originally<br />
isolated from marine particles sampled in the German Wadden Sea. M. adhaerens<br />
HP15 grows heterotrophically on various media, is easy to access genetically, and<br />
serves as a model organism to investigate the cellular and molecular interactions with<br />
the diatom Thalassiosira weissflogii. Here we describe the complete and annotated<br />
genome sequence of M. adhaerens HP15 as well as some details on flagellaassociated<br />
genes. M. adhaerens HP15 possesses three replicons; the chromosome<br />
comprises 4,422,725 bp and codes for 4,180 protein-coding genes, 51 tRNAs and three<br />
rRNA operons, while the two circular plasmids are ~187 kb and ~42 kb in size and<br />
contain 178 and 52 protein-coding genes, respectively.<br />
______________________________________________________________________<br />
Introduction<br />
Strain HP15 (DSM 23420) is the type<br />
strain of the newly established species<br />
Marinobacter adhaerens sp. nov. and<br />
represents one of 27 species currently<br />
assigned to the genus Marinobacter [1].<br />
Strain HP15 was first described by<br />
Grossart et al. in 2004 [2] as a marine<br />
particle-associated, Gram-negative,<br />
gammaproteobacterium isolated from the<br />
German Wadden Sea. The organism is<br />
of interest because of its capability to<br />
specifically attach in vitro to the surface<br />
of the diatom Thalassiosira weissflogiiinducing<br />
exopolymer and aggregate<br />
formation and thus generating marine<br />
snow particles [3]. Marine snow<br />
formation is an important process of the<br />
biological pump, by which atmospheric<br />
carbon dioxide is taken up, recycled, and<br />
partly exported to the sediments. This<br />
sink of organic carbon plays a major role
for marine biogeochemical cycles [4].<br />
Several studies reported on the<br />
formation and properties of marine<br />
aggregates [5–8]. Although it was shown<br />
that heterotrophic bacteria control the<br />
development and aggregation of marine<br />
phytoplankton [3], specific functions of<br />
individual bacterial species on diatom<br />
aggregation have not been explored thus<br />
far.<br />
A better understanding of the molecular<br />
basis of bacteria-diatom interactions that<br />
lead to marine snow formation is<br />
currently gained by establishing a<br />
bilateral model system, for which M.<br />
adhaerens sp. nov. HP15 serves as the<br />
bacterial partner of the easy-to-culture<br />
diatom, T. weissflogii [3]. Herein, we<br />
present a set of features for M.<br />
adhaerens sp. nov. HP15 (Table 1)<br />
together with its annotated complete<br />
genomic sequence, and a detailed<br />
analysis of its flagella-associated genes.<br />
Classification and features<br />
M. adhaerens sp. nov. strain HP15 is a<br />
motile, Gram-negative, non-sporeforming<br />
rod (Figure 1). Based on its<br />
16S rRNA sequence, strain HP15 was<br />
affiliated to the Marinobacter genus of<br />
Gammaproteobacteria. Two other<br />
Marinobacter species were identified<br />
based on their interactions with<br />
eukaryotes - M. algicola isolated from<br />
dinoflagellate cultures [9] and M.<br />
bryozoorum derived from Bryozoa [10].<br />
Strain HP15’s 16S rRNA gene is most<br />
closely related to those of the type<br />
strains of M. flavimaris (99%), M.<br />
salsuginis (98%) and M. algicola (96%).<br />
These four type strains form a discrete<br />
cluster in the phylogenetic tree<br />
(Figure 2). In contrast, DNA-DNA<br />
hybridization experiments revealed that<br />
the genome of M. adhaerens sp. nov.<br />
HP15 showed about 64% binding to that<br />
of M. flavimaris [1], which is below the<br />
generally accepted species<br />
differentiation limit of 70% [11].<br />
Figure 1. Transmission electron micrograph of<br />
M. adhaerens sp. nov. strain HP15.<br />
Chemotaxonomy<br />
Strain HP15 can grow in artificial sea<br />
water with a nitrogen-to-phosphorus ratio<br />
of 15:1 supplemented with glucose as<br />
the sole carbon source. In presence of<br />
diatom cells but without glucose, HP15<br />
utilized diatom-produced carbohydrates<br />
as sole source of carbon. Furthermore,<br />
M. adhaerens sp. nov. HP15 differed<br />
from M. flavimaris and other<br />
Marinobacter species in a number of<br />
chemotaxonomic properties, such as<br />
utilization of glycerol, fructose, lactic<br />
acid, gluconate, alanine, and glutamate<br />
[1]. Additionally, strain HP15 showed a<br />
unique fatty acid composition pattern.<br />
Genome sequencing and annotation<br />
Genome project history<br />
M. adhaerens HP15 was selected for<br />
sequencing because of its phylogenetic
position, its particular feature as a<br />
diatom-interacting marine organism [3],<br />
and its feasible genetic accessibility to<br />
act as a model organism. The respective<br />
genome project is deposited in the<br />
Genome OnLine Database [17] and the<br />
complete genome sequence in<br />
GenBank. The main project information<br />
is summarized in Table 2.<br />
Growth conditions and DNA isolation<br />
M. adhaerens sp. nov. HP15 was grown<br />
in 100 ml Marine Broth medium [18] at<br />
28°C. A total of 23 !g DNA was isolated<br />
from the cell paste using a Qiagen<br />
DNeasy Blood and Tissue Kit (Qiagen,<br />
Hilden, Germany) according to the<br />
manufacturer’s instructions.<br />
Genome sequencing and assembly<br />
The Marinobacter adhaerens sp. nov.<br />
HP15 genome was sequenced at<br />
AGOWA (AGOWA GmbH, Berlin,<br />
Germany) using the 454 FLX Ti platform<br />
of 454 Life Sciences (Branford, CT,<br />
USA). The sequencing library was<br />
prepared according to 454’s instructions<br />
from genomic M. adhaerens sp. nov.<br />
HP15 DNA with a final concentration of<br />
153 ng/!l. Sequencing was carried out<br />
on a quarter of a 454 picotiterplate,<br />
yielding 258.645 reads with an average<br />
length of 405 bp, totaling to almost<br />
105 Mb. These reads were assembled<br />
using the Newbler assembler version<br />
2.0.00.22 (Roche), resulting in 253.285<br />
fully and 4.763 partially assembled<br />
reads, leaving 932 singletons, 226<br />
Figure 2. Maximum likelihood phylogenetic tree based on 16S rRNA sequences of M. adhaerens type<br />
strain (HP15) plus all type strains of the genus Marinobacter and the type species of the neighbor order<br />
Pseudomonadales. Sequence selection and alignment improvements were carried out using the Living<br />
Tree Project database [12] and the ARB software package [13]. The tree was inferred from 1,531<br />
alignment positions using RAxML [14] with GTRGAMMA model. Support values from 1,000 bootstrap<br />
replicates are displayed above branches if larger than 50%. The scale bar indicates substitutions per<br />
site.
epeats and 371 outliers. The assembly<br />
comprised 112 contigs, with 40<br />
exceeding 500 bp. The latter comprised<br />
more than 4.6 Mb, with an average<br />
contig size of almost 116 kb and a<br />
longest contig of more than 1.2 Mb.<br />
Gaps between contigs were closed in a<br />
conventional PCR-based gap closure<br />
approach, resulting in a fully closed<br />
circular chromosome of 4.421.911 bp,<br />
and two plasmids of 187.465 bp and<br />
42.349 bp, respectively. Together all<br />
sequences provided 22.5x coverage of<br />
the genome. The error rate of the<br />
completed genome sequence is about 3<br />
in 1,000 (99.7%).<br />
Genome annotation<br />
Potential protein-coding genes were<br />
identified using GLIMMER v3.02 [19],<br />
transfer RNA genes were identified using<br />
tRNAScan-SE [20] and ribosomal RNA<br />
genes were identified via BLAST<br />
searches [21] against public nucleotide<br />
databases. The annotation of the<br />
genome sequence was performed with<br />
the GenDB v2.2.1 system [22]. For each<br />
predicted gene, similarity searches were<br />
performed against public sequence<br />
databases (nr, SwissProt, KEGG) and<br />
protein family databases (Pfam, InterPro,<br />
COG). Signal peptides were predicted<br />
with SignalP v3.0 [23, 24] and<br />
transmembrane helices with TMHMM<br />
v2.0 [25]. Based on these observations,<br />
annotations were derived in an<br />
automated fashion using a fuzzy logicbased<br />
approach [26]. Finally, the<br />
predictions were manually checked with<br />
respect to missing genes in intergenic<br />
regions and putative sequencing errors,<br />
and the annotations were manually<br />
curated using the Artemis 11.3.2<br />
program and refined for each putative<br />
gene [27].<br />
Genome properties<br />
The genome of strain HP15 comprises<br />
three circular replicons: the 4,422,725 bp<br />
chromosome and two plasmids of<br />
~187 kb and ~42 kb, respectively (Table<br />
3A and Figure 3). The genome<br />
possesses a 56.9% GC content<br />
(Table 3B). Of the 4,482 predicted<br />
genes, 4,422 were protein coding genes,<br />
and 60 RNAs; 391 pseudogenes were<br />
also identified. The majority of the<br />
protein-coding genes (67.5%) were<br />
assigned with a putative function, while<br />
those remaining were annotated as<br />
hypothetical proteins. The distribution of<br />
genes into COGs functional categories is<br />
presented in Table 4.<br />
Table 1b. Classification and general features of M. adhaerens sp. nov. HP15 in<br />
accordance to the MIGS recommendations [15]<br />
MIGS ID Property Term Evidence<br />
code<br />
Domain Bacteria<br />
Phylum Proteobacteria<br />
Class Gammaproteobacteria TAS [16]<br />
Current classification Order Alteromonadales TAS [16]<br />
Family Alteromonadaceae TAS [16]<br />
Genus Marinobacter TAS [1]<br />
Species Marinobacter adhaerens TAS [1]<br />
Type strain HP15 TAS [1]<br />
Gram stain negative IDA
Table 1b. Classification and general features of M. adhaerens sp. nov. HP15 in<br />
accordance to the MIGS recommendations [15]<br />
MIGS ID Property Term Evidence<br />
code<br />
Cell shape rod-shaped IDA<br />
Motility motile, single polar flagellum IDA<br />
Sporulation non-sporulating NAS<br />
Temperature range mesophilic IDA<br />
Optimum temperature 34-38°C IDA<br />
Salinity<br />
0.4-10 g NaCl/l (optimum/growth IDA<br />
within 1 day)<br />
MIGS-22 Oxygen requirement strictly aerobic IDA<br />
Carbon source<br />
dextrin, Tween 40 and 80, pyruvic IDA<br />
acid methyl ester, succinic acid<br />
mono-methyl-ester, cis-aconitic<br />
acid, "-hydroxybutyric acid, #-<br />
hydroxybutyric acid, $-keto glutaric<br />
acid, $-keto valeric acid, D,L-lactic<br />
acid, bromosuccinic acid, L-<br />
alaninamide, D-alanine, L-alanine,<br />
L-glutamic acid, L-leucine and L-<br />
proline<br />
Energy source chemoorganoheterotrophic IDA<br />
MIGS-6 Habitat sea water IDA<br />
MIGS-15 Biotic relationship free-living and particle-associated TAS [2]<br />
MIGS-13 Culture deposition no. DSM 23420 IDA<br />
MIGS-14 Pathogenicity none NAS<br />
Biosafety level 1 NAS<br />
Isolation marine aggregates (0.1-1 mm) TAS [2]<br />
MIGS-4 Geographic location German Wadden Sea TAS [2]<br />
MIGS-4.1 Latitude 53°43’20’’N TAS [2]<br />
MIGS-4.2 Longitude 07°43’20’’E TAS [2]<br />
MIGS-4.3 Depth surface waters TAS [2]<br />
MIGS-4.4 Altitude sea level TAS [2]<br />
MIGS-5 Sample collection time 15 June 2000 TAS [2]<br />
Evidence codes – IDA: inferred from Direct Assay (first time in publication); TAS: Traceable Author<br />
Statement (i.e., a direct report exists in the literature); NAS: Non-traceable Author Statement (i.e.,<br />
not directly observed for the living, isolated sample, but based on a generally accepted property of<br />
the species, or anecdotal evidence). These evidence codes are from the Gene Ontology project<br />
[17]. If evidence code is IDA, then the property was directly observed for a live isolate by one of the<br />
authors or an expert mentioned in the acknowledgements.
Table 2: Genome sequencing project information for M. adhaerens sp.<br />
nov. HP15<br />
MIGS ID Property Term<br />
MIGS-31 Finishing quality Finished<br />
MIGS-28 Library used 454 pyrosequencing standard library<br />
MIGS-29 Sequencing platforms 454 FLX Ti<br />
MIGS-31.2 Sequencing coverage 22.5x pyrosequencing<br />
MIGS-30 Assemblers Newbler version 2.0.00.22<br />
MIGS-32 Gene calling method GLIMMER v3.02, tRNAScan-SE<br />
Genbank ID<br />
CP001978 (chromosome)<br />
CP001979 (pHP-42)<br />
CP001980 (pHP-187)<br />
Genbank Date of Release September 18, 2010<br />
GOLD ID<br />
Gi06214<br />
NCBI project ID 46089<br />
Database: IMG<br />
Project relevance<br />
pending<br />
Marine diatom-bacteria interactions<br />
Table 3A. Genome composition for M. adhaerens HP15<br />
Label<br />
Size Topology RefSeq ID<br />
(Mb)<br />
Chromosome § 4.423 circular CP001978<br />
Plasmid pHP-187 0.187 circular CP001980<br />
Plasmid pHP-42* 0.042 circular CP001979<br />
§ Number of protein-coding genes: 4,180; Number of protein-coding<br />
genes: 178;<br />
* Number of protein-coding genes: 52
Table 3B. Genome statistics for M. adhaerens HP15<br />
Attribute<br />
Genome (total)<br />
Value % of total a<br />
Genome size (bp) 4,651,725<br />
DNA Coding region (bp) 4,178,502 89.8<br />
DNA G+C content (bp) 2,644,970 56.9<br />
Number of replicons 3<br />
Extrachromosomal elements 2<br />
Total genes b 4,410<br />
tRNA genes 51 1.16<br />
5S rRNA genes 3 0.07<br />
16S rRNA genes 3 0.07<br />
23S rRNA genes 3 0.07<br />
Protein-coding genes 4,355 98.66<br />
Genes assigned to COGs 3,027 67.54<br />
Genes with Pfam domains 2,918 65.1<br />
1 Pfam domain 2,041 45.54<br />
2 Pfam domains 598 13.34<br />
3 Pfam domains 194 4.33<br />
4 or more Pfam domains 85 1.9<br />
Genes with signal peptides 765 17.07<br />
Genes with transmembrane helices 1,043 23.27<br />
1 transmembrane helix 341 7.61<br />
2 transmembrane helices 154 3.44<br />
3 transmembrane helices 72 1.61<br />
4 or more transmembrane helices 476 10.62<br />
Genes in paralogous clusters 570 12.72<br />
Genes with 1 paralog 364 8.12<br />
Genes with 2 paralogs 63 1.41<br />
Genes with 3 paralogs 26 0.58<br />
Genes with 4 or more paralogs 117 2.61<br />
Pseudo/hypothetical genes 391 8.72<br />
Conserved hypothetical genes 668 14.90<br />
Genes for function prediction 3,363 75.03<br />
a) The total is based on either the size of the genome in base pairs or the total number of<br />
protein coding genes in the annotated genome.<br />
b) Also includes 54 pseudogenes and 5 other genes.
Figure 3. Graphical circular maps of the genome and the two plasmids of HP15. From outside<br />
to the center: Genes on forward strand (color by COG categories), Genes on reverse strand<br />
(color by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC<br />
content, GC skew.
Table 4. Number of genes associated with the 21 general COG functional<br />
categories<br />
Code Value % of total a Description<br />
J 162 3.7 Translation<br />
A 0 0 RNA processing and modification<br />
K 161 3.6 Transcription<br />
L 132 3 Replication, recombination and repair<br />
B 0 0 Chromatin structure and dynamics<br />
D 32 0.7 Cell cycle control, mitosis and meiosis<br />
Y 0 0 Nuclear structure<br />
V 0 0 Defense mechanisms<br />
T 199 4.5 Signal transduction mechanisms<br />
M 151 3.4 Cell wall/membrane biogenesis<br />
N 166 3.8 Cell motility<br />
Z 0 0 Cytoskeleton<br />
W 0 0 Extracellular structures<br />
U 0 0 Intracellular trafficking and secretion<br />
O<br />
127 2.9 Posttranslational modification, protein<br />
turnover, chaperones<br />
C 192 4.3 Energy production and conversion<br />
G 82 1.9 Carbohydrate transport and metabolism<br />
E 254 5.7 Amino acid transport and metabolism<br />
F 51 1.1 Nucleotide transport and metabolism<br />
H 97 2.2 Coenzyme transport and metabolism<br />
I 141 3.2 Lipid transport and metabolism<br />
P 138 3.1 Inorganic ion transport and metabolism<br />
Q<br />
76 1.7 Secondary metabolites biosynthesis,<br />
transport and catabolism<br />
R 330 7.5 General function prediction only<br />
S 251 5.7 Function unknown<br />
multiple 285 6.4<br />
COGs<br />
3,027 68.6 Total<br />
- 1,383 31.4 Not in COGs<br />
a) The total is based on the total number of protein coding genes in the annotated genome<br />
b) Also includes 54 pseudogenes and 5 other genes.
Flagella-associated gene clusters of<br />
M. adhaerens HP15<br />
Because M. adhaerens HP15 was<br />
experimentally shown to adhere to<br />
diatom cells, gene clusters coding for<br />
secretion, assembly, and mechanistic<br />
function of the polar flagellum were<br />
analyzed in detail (Figure 4). Besides<br />
several other chemotactic mechanisms<br />
and various cell surface interactions,<br />
bacterial flagella and other cell<br />
appendages had previously been shown<br />
to be instrumental for chemotactic<br />
movement towards and adhesion to<br />
biotic surfaces [28, 29]. The amino acid<br />
sequences of proteins encoded by the<br />
three identified gene clusters showed<br />
significant similarities to orthologous and<br />
experimentally well-described gene<br />
products of P. aeruginosa PAO1 and<br />
various other bacterial species as<br />
determined by BLASTP algorithm<br />
comparison using the Blosum 62<br />
substitution matrix [21]. Not surprisingly,<br />
hook and motor switch complex<br />
components were most conserved.<br />
However, gene products involved in<br />
flagellar filament formation encoded by<br />
Cluster II also showed 53 to 78%<br />
similarity to the respective PAO1<br />
proteins. Mutagenesis of flagella-<br />
Figure 4. Schematic presentation of the three flagella-associated gene clusters of M.<br />
adhaerens HP15 coding for the basal body, the filament, and the hook and motor<br />
switch complex. Identities to the respective orthologs in the genome of P. aeruginosa<br />
PAO1 are indicated by gray-scale code. Numbers of CDS are shown below gene<br />
names.
associated genes of M. adhaerens HP15<br />
will be carried out in the near future to<br />
study the role of flagella in bacteriadiatom<br />
interactions and to further our<br />
understanding of the cell-to-cell<br />
communication between those<br />
organisms.<br />
Acknowledgements<br />
We thank Yannic Ramaye for help with<br />
TEM operation and Christian Quast for<br />
computer support. The work was<br />
financially supported by the Max Planck<br />
Society, the Helmholtz Foundation, and<br />
<strong>Jacobs</strong> <strong>University</strong> Bremen.<br />
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