Supplemental Information
Supplemental Fig. S1. Schematic diagram of the experimental set-up showing the continuous culture vessel and flow cell.
Supplemental Fig. S2. Luria-Bertani agar plates seeded with the reporter strain showing the positive control giving a purple halo (A); LB medium as negative control (B); and 5 (C), 10 (D), 50 (E), and 70 µl (F) of ‘Ferroplasma acidarmanus’ Fer1 medium extract.
Supplemental Table S1. Known proteins involved in biofilm formation & maintenance homologues searched for in the ‘Ferroplasma acidarmanus’ Fer1 genome.
Gene product / UniProt accession number1 / Description / MicroorganismAbrB / P08874 / transition state regulatory protein / Bacillus subtilis
AdrA / Q9L401 / GGDEF (diguanylate cyclase) required for cellulose production and biofilm formation in rich medium / Salmonella typhimurium
Ag43 / P39180 / glycoprotein, mediates cell agreggation / Escherichia coli
AgrA / Q309Y7 / response regulator for AgrC-AIP / Staphylococcus aureus
AgrB / P0C1P7 / processes autoinducer peptide encoded by agrD / Staphylococcus aureus
AgrC / Q2YUC9 / membrane bound sensor kinase, detects AIP / Staphylococcus aureus
AgrD / Q53643 / autoinducer pepetide / Staphylococcus aureus
AIDA / Q03155 / glycoprotein, mediates cell agreggation / Escherichia coli
Alg44 / Q9HY69 / alginate synthase, PilZ domain protein / Pseudomonas aeruginosa
AtlE / O33635 / major autolysin / Staphylococcus epidermidis
Aur / P81177 / metalloprotease aureolysin / Staphylococcus aureus
Bap / Q79LN3 / surface protein involved in intercellular adhesion / Staphylococcus aureus
Bap1 / Q9KQW0 / carbohydrate binding protein / Vibrio cholerae
BapA / A9LS56 / biofilm associated protein A / Salmonella typhimurium
BarA / P0AEC5 / member of the two-component regulatory system uvrY/barA / Escherichia coli
BcsA / O82859 / catalytic subunit of cellulose synthase / Acetobacter xylinus
BcsA / P37653 / catalytic subunit of cellulose synthase / Escherichia coli
BcsB / P37652 / cellulose synthase regulatory subunit / Escherichia coli
BcsC / P37650 / cellulose synthase operon protein C / Escherichia coli
BcsE / P37657 / uncharacterized protein yhjS / Escherichia coli
BcsF / B1LJ86 / cellulose biosynthesis protein / Escherichia coli
BcsG / B5MX25 / endoglucanase / Salmonella enterica
BcsZ / P37651 / endoglucanase / Escherichia coli
BifA / B0KFP0 / diguanylate cyclase/phosphodiesterase / Pseudomonas putida
CdgC / Q9KLF9 / phosphodiesterase, negative regulator of biofilm formation / Vibrio cholerae
CpxR / Q8ZKR6 / response reguator in two-component regulatory system with CpxA / Salmonella typhimurium
CqsS / Q9KM66 / membrane bound sensor kinase-response regulator hybrid / Vibrio cholerae
CsgA / P28307 / major curlin subunit / Escherichia coli
CsgB / P0ABK7 / minor curlin subunit / Escherichia coli
CsgC / P52107 / curli assembly protein csgC / Escherichia coli
CsgD / O54294 / transcriptional regulator / Salmonella typhimurium
CsrA / P69913 / RNA binding protein involved in posttranscriptional regulation / Escherichia coli
CupA / Q9I1Y7 / fimbrial subunit / Pseudomonas aeruginosa
CytR / C3NUT6 / repressor of biofilm formation / Vibrio cholerae
Esp / Q6VXQ3 / Bap-like, promotes biofilm formation / Enterococcus faecium
GacA / Q51373 / response regulator / Pseudomonas aeruginosa
GacS / P48027 / membrane-bound sensor histidine kinase / Pseudomonas syringae
GbpA / Q8DRV2 / glucan binding protein / Streptococcus mutans
GbpB / Q938V3 / glucan binding protein / Streptococcus mutans
GbpC / Q8DTF1 / glucan binding protein / Streptococcus mutans
GbpD / Q8DUW9 / glucan binding protein / Streptococcus mutans
GcpA / Q8ZNT5 / GGDEF required for biofilm formation in poor medium / Salmonella typhimurium
GcpC / Q8ZNQ6 / upstream of CsgD signaling cascade / Salmonella typhimurium
GcpF / Q8ZP53 / upstream of CsgD signaling cascade / Salmonella typhimurium
GelE / Q9S385 / extracellular protease, promotes autolysis / Enterococcus faecalis
HapA / C3LWC9 / hemagglutinin/protease / Vibrio cholerae
HapR / Q1WDD2 / transcriptional regulator / Vibrio cholerae
HmsF / A6BR56 / putative polysaccharide N-deacetylase/carbohydrate esterase / Yersinia pestisCA88-4125
HmsH / A6BR57 / putative outer membrane poly-beta-1,6-N-acetyl-D-glucosamine (PGA) translocation/docking protein / Yersinia pestisCA88-4125
HmsR / A6BR55 / putative polysaccharide polymerase / Yersinia pestisCA88-4125
HmsS / A6BR54 / haemin storage system / Yersinia pestisCA88-4125
IcaA / Q5HKQ0 / biofilm PIA synthesis N-acetylglucosaminyltransferase / Staphylococcus epidermidis
IcaB / Q5HKP8 / biofilm PIA synthesis deacetylase / Staphylococcus epidermidis
IcaC / Q5HKP7 / biofilm PIA synthesis protein / Staphylococcus epidermidis
IcaD / Q5HKP9 / biofilm PIA synthesis protein / Staphylococcus epidermidis
LadS / Q9HX42 / hybrid histidine kinase / Pseudomonas aeruginosa
LapA / Q3KK29 / Bap-like, promotes biofilm formation / Pseudomonas fluorescens
LasI / P33883 / acyl-homoserine-lactone synthase / Pseudomonas aeruginosa
LasR / P25084 / Transcriptional activator / Pseudomonas aeruginosa
LecA / Q05097 / PA-I galactophilic lectin / Pseudomonas aeruginosa
LecB / Q9HYN5 / fucose-binding lectin PA-IIL / Pseudomonas aeruginosa
LeuO / Q9KP88 / regulator of biofilm formation / Vibrio cholerae
LuxI / P12747 / acyl-homoserine-lactone synthase / Vibrio fischeri
LuxO / P0C5S5 / luminescence regulatory protein / Vibrio harveyi
LuxP / P54300 / autoinducer 2-binding periplasmic protein / Vibrio harveyi
LuxQ / P54302 / autoinducer 2 sensor kinase/phosphatase / Vibrio harveyi
LuxS / P45578 / S-ribosylhomocysteine lyase / Escherichia coli
LuxU / P0C5S4 / phosphorelay protein / Vibrio harveyi
MbaA / Q9KU26 / biofilm architecture maintenance protein / Vibrio cholerae
NhaR / P0A9G2 / transcriptional activator / Escherichia coli
NspS / Q9KU25 / norspermidine sensor / Vibrio cholerae
OmpR / P0AA19 / transcriptional regulatory protein / Salmonella typhimurium
PelA / Q9HZE4 / involved in matrix exopolysaccharide synthesis / Pseudomonas aeruginosa
PelB / Q9HZE5 / PEL exopolysaccharide synthesis / Pseudomonas aeruginosa
PelC / Q9HZE6 / PEL exopolysaccharide synthesis / Pseudomonas aeruginosa
PelD / Q9HZE7 / pellicile production and PEL exopolysaccharide synthesis / Pseudomonas aeruginosa
PelE / Q9HZE8 / PEL exopolysaccharide synthesis / Pseudomonas aeruginosa
PelF / Q9HZE9 / PEL exopolysaccharide synthesis / Pseudomonas aeruginosa
PelG / Q9HZF0 / matrix exopolysaccharide synthesis / Pseudomonas aeruginosa
Pfs / P0AF12 / 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase / Escherichia coli
PgaA / P69434 / biofilm PGA synthesis protein / Escherichia coli
PgaB / P75906 / biofilm PGA synthesis lipoprotein / Escherichia coli
PgaC / P75905 / biofilm PGA synthesis N-glycosyltransferase / Escherichia coli
PgaD / P69432 / biofilm PGA synthesis protein / Escherichia coli
PilZ / Q51538 / type 4 fimbrial biogenesis protein / Pseudomonas aeruginosa
PleD / Q9A5I5 / response regulator (contains DGC, diguanylate cyclase domain) / Caulobacter crescentus
PlzC / VC2344 / contains PilZ domains, binds c-di-GMP / Vibrio cholerae
PlzD / Q9KNC3 / contains PilZ domains, , binds c-di-GMP / Vibrio cholerae
PotD / P0AFK9 / spermidine/putrescine-binding periplasmic protein / Escherichia coli
PslA / Q9I1N8 / capsular polysaccharide synthesis / Pseudomonas aeruginosa
RbmA / C3NSJ9 / autotransporter / Vibrio cholerae
RbmC / C3NSJ7 / hemolysin-related protein / Vibrio cholerae
RetS / Q9HUV7 / sensor protein / Pseudomonas aeruginosa
RhlI / P54291 / acyl-homoserine-lactone synthase / Pseudomonas aeruginosa
RhlR / P54292 / regulatory protein / Pseudomonas aeruginosa
SinI / P23308 / antagonizes SinR / Bacillus subtilis
SinR / P06533 / HTH-type transcriptional regulator / Bacillus subtilis
SipW / P54506 / signal peptidase I W / Bacillus subtilis
Spl / Q2FXC3 / serine protease / Staphylococcus aureus
Spo0A / P06534 / two component response regulator / Bacillus subtilis
SprE / Q833V8 / extracellular serine proteinase / Enterococcus faecalis
SpsB / P0A070 / signal peptidase IB / Staphylococcus aureus
SsoPox / Q97VT7 / lactonase / Sulfolobus solfataricus
TasA / P54507 / major protein component of the biofilm extracellular matrix / Bacillus subtilis
TibA / Q9XD84 / adhesin/invasin autotransporter / Escherichia coli
TM0504 / Q9WYX4 / triggers exopolysaccharide production / Thermotoga maritima
UvrY / P0AED5 / response regulator / Escherichia coli
VieA / O68318 / response regulator / Vibrio cholerae
VieB / Q9KRI9 / response regulator / Vibrio cholerae
VieS / O68317 / sensor protein / Vibrio cholerae
VpsR / Q9AQ41 / two component response regulator / Vibrio cholerae
VpsT / C3NZ07 / transcriptional regulator / Vibrio cholerae
WspA / Q9HXT3 / probable chemotaxis transducer / Pseudomonas aeruginosa
WspB / Q9HXT4 / cheW homolog / Pseudomonas aeruginosa
WspC / Q9HXT5 / cheR methyltransferase / Pseudomonas aeruginosa
WspD / Q9HXT6 / cheW homolog / Pseudomonas aeruginosa
WspE / Q9HXT7 / probable chemotaxis sensor/effector fusion protein / Pseudomonas aeruginosa
WspR / Q9HXT9 / hybrid two-component response regulator / Pseudomonas aeruginosa
YqxM / Q65HF1 / secreted biofilm formation protein / Bacillus licheniformis
1http://www.uniprot.org/
Supplemental Table S2. Genes present on the ‘Ferroplasma acidarmanus’ Fer 1 genome putatively involved in biofilm formation.
ZP_05570724 / COG 1157 Flagellar biosynthesis/type III secretory pathway ATPase / A1A0 ATP synthase, subunit A / flagellum structure and biogenesis
ZP_05570723 / COG1157 Flagellar biosynthesis/type III secretory pathway ATPase / V-type ATP synthase subunit B / flagellum structure and biogenesis
ZP_05571180 / COG1419 Flagellar GTP-binding protein / signal recognition particle receptor FtsY / flagellum structure and biogenesis
ZP_05569938 / COG1419 Flagellar GTP-binding protein / signal recognition particle protein Srp54 / flagellum structure and biogenesis
ZP_05571180 / COG2874 Predicted ATPase involved in biogenesis of flagella / signal recognition particle receptor FtsY / flagellum structure and biogenesis
ZP_05569891 / COG3063 Tfp pilus assembly protein PilF / TPR repeat-containing protein / flagellum structure and biogenesis
ZP_05571076 / COG3063 Tfp pilus assembly protein PilF / TPR repeat-containing protein / flagellum structure and biogenesis
ZP_05571596 / COG3063 Tfp pilus assembly protein PilF / TPR repeat-containing protein / flagellum structure and biogenesis
ZP_05571291 / COG2805 Tfp pilus assembly protein pilus retraction ATPase PilT / ATPase / flagellum structure and biogenesis
ZP_05571230 / COG2804 Type II secretory pathway ATPase PulE/Tfp pilus assembly pathway ATPase PilB / hypothetical protein Faci_07396 / flagellum structure and biogenesis
ZP_05571291 / COG2804 Type II secretory pathway ATPase PulE/Tfp pilus assembly pathway ATPase PilB / ATPase / flagellum structure and biogenesis
ZP_05571208 / COG0630 Type IV secretory pathway VirB11 protein involved in flagella biosynthesis / multidrug resistance ABC transporter ATP-binding and permease protein / flagellum structure and biogenesis
ZP_05570382 / COG2804 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB / hypothetical protein Faci_03101 / flagellum structure and biogenesis
ZP_05569933 / COG1215 Glycosyltransferases, probably involved in cell wall biogenesis / cell wall biosynthesis glycosyltransferase-like protein / cell wall biogenesis
ZP_05571748 / COG0463 Glycosyltransferases involved in cell wall biogenesis / cell wall biosynthesis glycosyltransferase / cell wall biogenesis
ZP_05570395 / COG0463 Glycosyltransferases involved in cell wall biogenesis / cell wall biosynthesis glycosyltransferase / cell wall biogenesis
ZP_05569919 / COG0463 Glycosyltransferases involved in cell wall biogenesis / cell wall biosynthesis glycosyltransferase / cell wall biogenesis
ZP_05571701 / COG0399 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis / perosamine synthetase / cell wall biogenesis
ZP_05571576 / COG0463 Glycosyltransferases involved in cell wall biogenesis / glycosyl transferase family 2 / cell wall biogenesis
ZP_05571710 / COG0463 Glycosyltransferases involved in cell wall biogenesis / glycosyltransferase / cell wall biogenesis
ZP_05571660 / COG1215 Glycosyltransferases, probably involved in cell wall biogenesis / cellulose synthase (UDP-forming) / cell wall biogenesis
ZP_05571616 / COG0517 FOG: CBS domain / CBS domain-containing protein / cell wall biogenesis
ZP_05571423 / COG1215 Glycosyltransferases, probably involved in cell wall biogenesis / glycosyltransferase / cell wall biogenesis
ZP_05571307 / COG0463 Glycosyltransferases involved in cell wall biogenesis / hypothetical protein Faci_07781 / cell wall biogenesis
ZP_05569950 / COG1215 Glycosyltransferases, probably involved in cell wall biogenesis / glycosyltransferase / cell wall biogenesis
ZP_05569849 / COG1215 Glycosyltransferases, probably involved in cell wall biogenesis / cellulose synthase (UDP-forming) / cell wall biogenesis
ZP_05569793 / COG0463 Glycosyltransferases involved in cell wall biogenesis / hypothetical protein Faci_00140 / cell wall biogenesis
ZP_05571057 / COG1619 Uncharacterized proteins, homologs of microcin C7 resistance protein MccF / muramoyltetrapeptide carboxypeptidase / biosynthesis/degradation of murein sacculus and peptidoglycan
ZP_05570679 / COG1019 Predicted nucleotidyltransferase / phosphopantetheine adenylyltransferase/unknown domain fusion protein / biosynthesis/degradation of murein sacculus and peptidoglycan
ZP_05570216 / COG0615 Cytidylyltransferase / glycerol-3-phosphate cytidylyltransferase / biosynthesis/degradation of murein sacculus and peptidoglycan
ZP_05569884 / COG0067 Glutamate synthase domain 1 / glutamine amidotransferase class-II / biosynthesis/degradation of murein sacculus and peptidoglycan
ZP_05570472 / COG0463 Glycosyltransferases involved in cell wall biogenesis / glycosyltransferase / biosynthesis/degradation of surface polysaccharides and lipopolysaccharides
ZP_05571703 / COG0438 Glycosyltransferase / lipopolysaccharide N-acetylglucosaminyltransferase / biosynthesis/degradation of surface polysaccharides and lipopolysaccharides
ZP_05571704 / COG0438 Glycosyltransferase / lipopolysaccharide N-acetylglucosaminyltransferase / biosynthesis/degradation of surface polysaccharides and lipopolysaccharides
ZP_05571740 / COG1091 dTDP-4-dehydrorhamnose reductase / dTDP-4-dehydrorhamnose reductase / biosynthesis/degradation of surface polysaccharides and lipopolysaccharides
ZP_05571741 / COG1088 dTDP-D-glucose 4,6-dehydratase / dTDP-glucose 4,6-dehydratase / biosynthesis/degradation of surface polysaccharides and lipopolysaccharides
ZP_05571742 / COG1898 dTDP-4-dehydrorhamnose 3,5-epimerase and related enzymes / dTDP-4-dehydrorhamnose 3,5-epimerase / biosynthesis/degradation of surface polysaccharides and lipopolysaccharides
ZP_05570089 / COG0451 Nucleoside-diphosphate-sugar epimerases / nucleotide sugar epimerase related protein / biosynthesis/degradation of surface polysaccharides and lipopolysaccharides
ZP_05570512 / COG1736 Diphthamide synthase subunit DPH2 / diphthamide synthase subunit DPH2 / biosynthesis/degradation of surface polysaccharides and lipopolysaccharides
ZP_05570065 / COG0279 Phosphoheptose isomerase / phosphoheptose isomerase / biosynthesis/degradation of surface polysaccharides and lipopolysaccharides
ZP_05571079 / COG0661 Predicted unusual protein kinase / ubiquione biosynthesis protein / biosynthesis/degradation of surface polysaccharides and lipopolysaccharides
ZP_05570360 / COG2017 Galactose mutarotase and related enzymes / hypothetical protein Faci_02991 / biosynthesis/degradation of surface polysaccharides and lipopolysaccharides
ZP_05571000 / COG1287 Uncharacterized membrane protein, required for N-linked glycosylation / hypothetical protein Faci_06220 / biosynthesis/degradation of surface polysaccharides and lipopolysaccharides
ZP_05571293 / COG2244 Membrane protein involved in the export of O-antigen and teichoic acid / hypothetical protein Faci_07711 / biosynthesis/degradation of surface polysaccharides and lipopolysaccharides
ZP_05571422 / COG1109 Phosphomannomutase / phosphoglucomutase/phosphomannomutase / biosynthesis/degradation of surface polysaccharides and lipopolysaccharides
ZP_05571420 / COG1215 Glycosyltransferases, probably involved in cell wall biogenesis / N-acetylglucosaminyltransferase / biosynthesis/degradation of surface polysaccharides and lipopolysaccharides
ZP_05571144 / COG0438 Glycosyltransferase / glycosyltransferase / biosynthesis/degradation of surface polysaccharides and lipopolysaccharides
ZP_05570194 / COG2246 Predicted membrane protein / glycosyltransferase involved in cell wall biogenesis / biosynthesis/degradation of surface polysaccharides and lipopolysaccharides
ZP_05570305 / COG0107 Imidazoleglycerol-phosphate synthase / imidazoleglycerol phosphate synthase, cyclase subunit / biosynthesis/degradation of surface polysaccharides and lipopolysaccharides
ZP_05571393 / COG0020 Undecaprenyl pyrophosphate synthase / undecaprenyl pyrophosphate synthetase / biosynthesis/degradation of surface polysaccharides and lipopolysaccharides
ZP_05571245 / COG1499 NMD protein affecting ribosome stability and mRNA decay / NMD protein affecting ribosome stability and mRNA decay / biosynthesis/degradation of surface polysaccharides and lipopolysaccharides
ZP_05570169 / COG2266 GTP:adenosylcobinamide-phosphate guanylyltransferase / hypothetical protein Faci_02024 / biosynthesis/degradation of surface polysaccharides and lipopolysaccharides
ZP_05571328 / COG0189 Glutathione synthase/Ribosomal protein S6 modification enzyme (glutaminyl transferase) / RimK-like protein / biosynthesis/degradation of surface polysaccharides and lipopolysaccharides
ZP_05570080 / COG0463 Glycosyltransferases involved in cell wall biogenesis / dolichol-phosphate mannosyltransferase / biosynthesis/degradation of surface polysaccharides and lipopolysaccharides
ZP_05570245 / COG0189 Glutathione synthase/Ribosomal protein S6 modification enzyme (glutaminyl transferase) / Rim K like protein / biosynthesis/degradation of surface polysaccharides and lipopolysaccharides
ZP_05571745 / COG0463 Glycosyltransferases involved in cell wall biogenesis / dolichol-phosphate-mannosyltransferase related protein / biosynthesis/degradation of surface polysaccharides and lipopolysaccharides
ZP_05570323 / COG2329 Uncharacterized enzyme involved in biosynthesis of extracellular polysaccharides / hypothetical protein Faci_02806 / biosynthesis/degradation of surface polysaccharides and lipopolysaccharides
ZP_05571054 / COG4934 Predicted protease / membrane associated serine protease / motility/biofilm dispersal
ZP_05571385 / COG0750 Predicted membrane-associated Zn-dependent proteases 1. / membrane metalloprotease / may be involved in signalling
ZP_05571751 / COG0750 Predicted membrane-associated Zn-dependent proteases 1. / zinc metalloprotease / may be involved in signalling
ZP_05571427 / COG1994 Zn-dependent proteases / membrane metalloprotease / may be involved in signalling
ZP_05570518 / COG0750 Predicted membrane-associated Zn-dependent proteases 1. / zinc metalloprotease / may be involved in signalling
ZP_05570462 / COG0750 Predicted membrane-associated Zn-dependent proteases 1. / zinc metalloprotease / may be involved in signalling
ZP_05570892 / COG0421 Spermidine synthase / spermidine synthase / polyamine synthesis
ZP_05570991 / COG0010 Arginase/agmatinase/formimionoglutamate hydrolase, arginase family / putative arginase / polyamine synthesis
ZP_05571091 / COG1945 Uncharacterized conserved protein / pyruvoyl-dependent arginine decarboxylase / polyamine synthesis
ZP_05571415 / COG1586 S-adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase proenzyme / polyamine synthesis
Supplemental Table S3. Details of ‘F. acidarmanus’ Fer1 protein identification.