Supplemental Material S2: Special functions of ECRs
pMaD1 (RepABC-9 type plasmid, 255-kb)
The largest ECR is a conjugative plasmid with a type IV secretion system. The most striking
feature of this replicon is the abundance of acyl- and acetyl-transferases that probably
participate in fatty acid metabolism. The presence of two branched-chain amino acid
transporters and multiple putative carnithine racemases, which are required for degradation
of valine, leucine or isoleucine, indicates the degradation of these amino acids. A citrate
synthetase on this replicon furthermore suggests that acetyl-CoA is directly funnelled into
the tricarboxylic acid (TCA) cycle. The presence of a phage transcriptional regulator AlpA
(MALG_03702) is conspicuous, since this replicon lacks other genes with a possible phagederived origin. It might thus either represent a solitary orphan gene, or it acts in trans on
chromosome-located prophages. A genetic chimera of phage and plasmid has recently been
reported for Phaeobacter gallaeciensis CIP105210 (Frank et al. 2014).
pMaD2 (RepABC-10 type chromid, 240-kb)
The largest chromid encodes a Na+ translocating NADH ubiquinone oxidoreductase complex
(Na+-NQR; MALG_03917-MALG_03922); an important component of the respiratory chain of
various marine and pathogenic bacteria (Bogachev et al. 2009). Export of sodium ions across
the inner bacterial membrane generates a redox-driven electrochemical Na+ potential
(sodium-motive force) and a knock-out of the Na+-NQR complex in Vibrio cholerae provoked
multiple defects of the central metabolism (Minato et al. 2014). The sodium-motive force is
considered as an ancestral equivalent of the common proton-motive force and the
preservation of both mechanisms is advantageous for life in habitats with fluctuating salinity
like estuaries (Mulkidjanian et al. 2008), matching the isolation sit of M. algicola DG898. The
absence of further chromosome encoded Na+-NQRs documents the pivotal role of this ECR.
Furthermore, a β-lactamase gene (MALG_03953), which is required for protein export from
the periplasm across the outer membrane, is located adjacent to a type II secretion system
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(Korotkov et al. 2012), indicating a secretion system that counters ß-lactam-antibiotics.
pMaD2 also encodes a sulfite exporter (MALG_03961) and a ß-galactosidase (MALG_04091).
pMaD3 (RepABC-5 type chromid, 190-kb)
This chromid encodes a sigma-70 factor (MALG_04127), which directs the core RNA
polymerase to specific promoter elements located 10 to 35 base-pairs upstream of
transcription-initiation (Paget and Helmann 2003). A homologous extrachromosomal sigma
factor of D. shibae DFL-12 assumingly regulates the expression of various chromosomal
genes (Petersen, unpublished). pMaD3 likely enables M. algicola DG898 to oxidize sulfite to
sulfate (MALG_04130) and to subsequently excrete the product (MALG_04154). It also
encodes for a [NiFe] hydrogenase complex (MALG_04134-MALG_04148), closely related to
the gammaproteobacterial equivalent of Thiocapsa roseopericina (Chromatiales), which is
probably used in concordance with sulfite oxidation during chemolithotrophic growth.
pMaD3 also contains a glycine cleavage system (MALG_04224-MALG_04228), which is
triggered in response to high concentrations of the amino acid (Kikuchi 1973).
pMaD4 (RepABC-6 type chromid, 188-kb)
This chromid encodes six tricarboxylic acid (TRAP) transporters (suppl. Tab. S1), an
oxoglutarate dehydrogenase (MALG_04326-MALG_04330) and a putative mucin desulfating
sulfatase (MALG_04385). It also comprises the minCDE genes (MALG_04405-MALG_04407),
which facilitate proper midpoint fission of cells, while restricting the formation of the Z-ring
during proliferation. These genes have also been detected on ECRs of Agrobacterium strains
(Slater et al. 2009).
pMaD5 (DnaA-like-I type flagellum chromid, 143-kb)
 See main manuscript.
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pMaD6 (RepABC-1 type plasmid, 126-kb)
Besides pMaD1, pMaD6 is the second plasmid with a type IV secretion system. In addition to
heavy metal resistance genes against arsenite and mercury, it encodes lipoproteins and
apolipoproteins, which are involved in colonization of eukaryotic hosts and the evasion of
their defense mechanisms (Kovacs-Simon et al. 2011). The probably most astonishing finding
on pMaD6 is an operon containing the nitrate/nitrite antiporter NarK (MALG_04637), all four
subunits of the respiratory nitrate reductase (NarGHJI, MALG_04638-MALG_04641) and the
molybdopterin molybdotransferase MoeA (EC 2.10.1.1, MALG_04645), whereas the nitrate
transporter (NrtABCD) and two subunits of the nitrite reductase (NirB, NirD) which are
crucial for the assimilatory reduction of nitrate to ammonia are encoded on the
chromosome. Two additional genes that are involved in NO signaling are also located on the
126-kb plasmid (MALG_04632, MALG_04634).
pMaD7 (RepB-II type chromid, 115-kb)
This chromid comprises a gene for cellulose biosynthesis (celD; MALG_04734) and a cluster
with two genes for the degradation of N-acetyl-glucosamine 6-phosphate (nagA, nagB;
MALG_04827-MALG_04836) required for the decomposition of cell walls. Putative Nacetylglucosamine transporters are located on pMaD3. pMaD7 also carries a fructose-1,6bisphosphatase (FBP; MALG_04737) which represents, together with the chromosomeencoded 6-phosphofructokinase (PFK; MALG_00578), a relay of two unidirectional key
enzymes, whose regulation allows a switch between gluconeogenesis and glycolysis,
respectively. Moreover, the biosynthesis pathway of thiamine (vitamin B1, Vander Horn et al.
1993) is a prime example of metabolic interplay of chromosome-, chromid- and plasmidencoded enzymes in M. algicola DG898. pMaD7 contains an operon with six genes
(thiCOSGEF, MALG_04801-MALG_04796) representing the gross of enzymes for thiamine
biosynthesis. Additional thiC and thiE genes on pMaD1 do not just reflect a horizontal
recruitment of redundant copies, because this ECR also contains thiD (MALG_03665), which
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is required for two central metabolic reactions of thiamine biosynthesis (see KEGG map: EC
2.7.1.49, EC 2.7.4.7). A homologous thiD gene on pMaD2 (MALG_03962) indicates that the
two respective enzymatic conversions are catalyzed by two different enzymes. The sole
chromosome-encoded enzyme for the biosynthesis of vitamin B1 is the thiamine
pyrophosphokinase ThiN (MALG_02199, EC 2.7.6.2). The extrachromosomal localization of
three thiC genes in D. shibae DSM 16493T has been explained by frequent genomic
rearrangements (Wagner-Döbler et al. 2010). The distribution of eleven genes for thiamine
metabolism in M. algicola DG898 does in contrast reflect a more complex evolutionary
pattern driven by horizontal recruit- and replacement of xenologous thi genes. The crucial
function of chromid pMaD7 is supported by a toxin/antitoxin module that prevents replicon
loss (MALG_04735, MALG_04736; Zielenkiewicz and Cegłowski 2001).
pMaD8 (DnaA-like-II type chromid, 111-kb)
pMaD8 has a well-structured gene composition with putative operons containing up to 35
genes and is also stabilized by a toxin/antitoxin module (MALG_04899, MALG_04900). It
encodes e.g., an aldolase of the Entner-Doudoroff pathway (MALG_04927), a fructose-1,6bisphosphatase and a glucose-6-phosphate isomerase of the archaeal type (MALG_04886;
MALG_04928), which are uncommon in the Roseobacter group.
pMaD9 (RepB-I type chromid, 99-kb)
M. algicola DG898 contains, like many other roseobacters (Newton et al. 2010), two genes
for the conversion of the osmolyte dimethylsulfoniopropionate (DMSP), which is released by
phytoplankton and represents a major source of carbon and sulfur for marine bacteria
(Curson et al. 2011). The DMSP lyase DddP is chromosome-encoded (MALG_02013; EC
4.4.1.3), but the DMSP demethylase gene dmdA (MALG_05026; EC 2.1.1.26) is located in a
gene cluster on pMaD9. This chromid also harbors many genes for biosynthesis and export of
lipopolysaccharides putatively involved in cell wall biogenesis, hence indicating an
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involvement of pMaD9 in surface attachment, as experimentally already shown for the RepAI type biofilm chromid pMaD10.
pMaD10 (RepA-I type biofilm chromid, 52-kb)
pMaD10 encodes a variety of typical pathogen genes such as a sialic acid synthetase
(MALG_05073; Severi et al. 2007), an RTX-toxin (MALG_05091) and a tetratricopeptide
(MALG_05077; Cerveny et al. 2013).
 Biofilm related characteristics are described in the main manuscript.
pMaD11 (RepA-II type cryptic plasmid, 6-kb)
This cryptic plasmid contains a solitary RepA-II type replicase, some short pseudogenes and
the N-terminal domain of a resolvase that mediates site-specific recombination (Garnier et
al. 1987).
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