Table 4 Predicted heavy metals resistance genes detected in cadmium-amended SL5 metagenome and their taxonomic affiliations

Cadmium, cobalt, mercury, lead, zinc

Heavy metal-translocating P-type ATPase, Cd/Co/Hg/Pb/Zn-transporting; ApaG protein; protein disulphide isomerase I, dsbA gene product (Cd/Zn/Hg); DSBA oxidoreductase (Cd); RND divalent metal cation efflux transporter CzcA (Zn/Cd); membrane-bound cation-proton-antiporter CzrA gene (Zn/Cd); cobalt-zinc-cadmium resistance protein; cation diffusion facilitator family transporter; CzrB gene

Mycobacterium sp. Spyr1; Saccharomonospora viridis DSM 43017; Mycobacterium vanbaalenii PYR-1; Mycobacterium gilvum PYR-GCK; Shewanella sediminis HAW-EB3; Serratia symbiotica str. ‘Cinara cedri’; Candidatus Blochmannia pennsylvanicus str. BPEN; Paenibacillus mucilaginosus KNP414; Pseudomonas aeruginosa PA7; Pseudomonas aeruginosa 39016, Pseudomonas aeruginosa 138244; Pseudomonas putida; Pseudomonas sp. 2_1_26; Xanthomonas gardneri ATCC 19865; Pseudomonas aeruginosa

Copper, magnesium, silver

Copper-resistance protein A (copA); multicopper oxidase type 3 (cutO); copper resistance protein C (copC); putative copper binding protein; multicopper oxidase; multicopper oxidase type 2; molecular chaperone DnaK; copper-translocating P-type ATPase; magnesium-transporting ATPase; copper exporting ATPase; heavy metal-translocating P-type ATPase; blue copper oxidase cueO precursor; P-ATPase superfamily P-type ATPase copper transporter, ctpV; apolipoprotein N-acyltransferase; ApaG protein; cation-transporting ATPase; twin-arginine translocation pathway signal: copper resistance protein; cation efflux system protein CusB (Cu/Ag); heavy metal-translocating P-type ATPase, copB; lnt gene product (Cu); Cu(I)-responsive transcriptional regulator; MerE family transcriptional regulator (Cu); MerR family transcriptional regulator (Cu); lipoprotein involved with copper homeostasis and adhesion, cutF/nlpE; heavy metal transport/detoxification protein, copP; copper/silver efflux P-type ATPase

Acidobacterium capsulatum ATCC 51196; Acetobacter pomorum DM001; Achromobacter xylosoxidans A8; Anaeromyxobacter sp. Fw109-5; Halalkalicoccus jeotgali B3; Stenotrophomonas maltophila R5513; Frankia sp. CcI3; Halorubrum Iacusprofundi ATCC 49239; Corynebacterium ammoniagenes DSM 20306; Corynebacterium lipophiloflavum DSM 44291; Xanthobacter autotrophicus Py2; Haladaptatus paucihalophilus DX253; Rhodococcus jostii RHA1; Intrasporangium calvum DSM 43043; Streptomyces sp. S4; Streptomyces albus J1074; Halobacterium sp. DL1; Achromobacter xylosoxidans C54; Cupriavidus metallidurans CH34; Methanosaeta harundinacea 6Ac; Rhodoferax ferrireducens; Erwinia sp. Ejp617; Micrococcus luteus NCTC 2665; Kytococcus sedentarius DSM 20547; Mycobacterium parascrofulaceum ATCC BAA-614; Proteus mirabilis ATCC 29906; Shewanella sediminis HAW-EB3; Bacillus amyloliquefaciens TA208; Pseudomonas syringae pv. glycinea str. B076; Klebsiella pneumoniae 342; Gordonia polyisoprenivorans NBRC 16320; Methylobacterium chloromethanicum CM4; Shigella dysenteriae 1012; Acaryochloris sp. CCMEE 5410; Hyphomonas neptunium ATCC 15444; Caulobacter sp. K31; Pseudomonas syringae pv. aceris str. M302273PT; Pseudomonas entomophila L48; Pseudomonas putida S16; Rahnella sp. Y9602; Pseudonocardia sp. P1; Citromicrobium bathyomarinum JL354

Nickel

Peptide/nickel transport system, substrate-binding protein, nikA; transcriptional regulator NikR, CopG family (nikR); nickel transporter ATP-binding protein, nikD; nickel ABC transporter, periplasmic nickel-binding protein; nickel transporter ATP-binding protein, nikE

Azospirillum sp. B510; Streptococcus sanguinis SK1056; Methanococcus voltae A3; Metahnospirillum hungatei JF-1; Pseudomonas sp. TJI-51; Synergistetes bacterium SGP1; Rhodospirillum rubrum ATCC 11170

Zinc, tellurium

RND family efflux transporter MFP subunit; zinc resistance-associated protein, zraP; low-affinity inorganic phosphate transport

Protein; drug efflux pump transmembrane protein, mdtB; tellurite resistance gene, trgB; transcriptional regulatory protein, zraR (Zn); signal transduction histidine-protein kinase, baeS; lnt gene product (Zn); sensory histidine kinase in two-component regulatory system with BaeR; zinc-responsive transcriptional regulator; high-affinity zinc transporter, periplasmic component znuA; low-affinity inorganic phosphate transporter 1 (Zn/Te)

Pseudomonas putida KT2440; Citrobacter sp. 30_2; Citrobacter freundii 4_7_47CFAA; Citrobacter youngae ATCC 29220; Salmonella enterica subsp. enterica serovar Johannesburg str. S5-703; Salmonella enterica subsp. enterica serovar Typhi str. CT18; Sodalis glossinidius str. ‘morsitans’; Oxalobacter formigenes OXCC13; Roseobacter litoralis Och 149; Roseobacter denitrificans Och 114; Desulfovibrio magneticus RS-1; Escherichia coli 83972; Hyphomonas neptunium ATCC 15444; Ralstonia solanacearum CMR15; Photorhabdus luminescens subsp. laumondii TTO1; Haemophilus pittmaniae HK 85; Yersinia ruckeri ATCC 29473; Dickeya dadantii Ech703; Erwinia pyrifoliae DSM 12163; Erwinia amylovora CFBP1430

Arsenic

Arsenite oxidase, large subunit (aoxB); arsenite S-adenosylmethyltransferase; arsenite methyltransferase arsM; arsenical resistance protein, arsB; protein-tyrosine phosphatase, low molecular weight, arsC; arsenite oxidase, small subunit (aoxA); arsenical resistance protein ArsH; phosphate ABC superfamily ATP-binding cassette transporter, binding protein

Burkholderia oklahomensis C6786; Roseobacter litoralis och 149; Pseudovibrio sp. JE062; Desulfohalobium retbaense DSM 5692; Desulfovibrio alkaliphilus AHT2; Desulfovibrio salexigens DSM 2638; Magnetospirillum gryphiswaldense MSR-1; Rubrobacter xylanophilus DSM 9941; Mycobacterium parascrofulaceum ATCC BAA-614; Sphaerobacter thermophilus DSM 20745; Desulfobacca acetooxidans DSM 11109; Burkholderia multivorans ATCC 17616; Acidiphilium multivorum AIU301; Mannheimia haemolytica PHL213

Cadmium, cobalt, nickel, manganese, magnesium

Cadmium-translocating P-type ATPase; periplasmic solute-binding protein; czcD gene product; heavy metal-translocating P-type ATPase, Co/Ni; putative nrbE-like protein (Ni/Co); major facilitator transporter, nrsD/nreB (Ni/Co); magnesium and cobalt transport protein, corA (Mg/Co/Ni/Mn); probable NreB protein (Ni/Co); manganese transport protein (Mn/Fe/Cd/Co/Zn); magnesium-translocating P-type ATPase (Co/Mg); ApaG gene product (Co/Mg)

Streptomyces flavogriseus ATCC 33331; Thermobacillus composti KWC4; Alkanivorax borkumensis SK2; Actinosynnema mirum DSM 43827; Hoeflea phototrophica DFL-43; Roseiflexus sp. RS-1; Micromonospora sp. ATCC 39149; Paenibacillus vortex V453; Photobacterium leiognathi subsp. mandapamensis svers.1.1.; Photobacterium sp. SKA34; Vibrio angustum S14; Oceanospirillum sp. MED92; Pantoea stewartii subsp. stewartii; Serratia sp. AS12; Vibrio caribbenthicus ATCC BAA-2122; Saccharophagus degradans 2-40

Chromium, tellurium, selenium

ATP-dependent DNA helicase RecG; tellurite resistance protein TehB; chromate transporter; chromate ion transporter family protein; chromate transport protein ChrA; tellurite resistance gene, trgB; manganese/iron superoxide dismutase, chrC

Tolumonas auensis DSM 9187; Yersinia pestis KIM10 + ; Methylobacterium sp. 4-46; Methylobacterium nodulans ORS 2060; Desulfovibrio sp. A2; Alpha-proteobacterium BAL199; Roseobacter litoralis Och 149; Roseobacter denitrificans Och 114; Beijerinckia indica subsp. indica ATCC 9039; Cupriavidus basilensis OR16; Enterobacter cloaceae subsp. cloaceae NCTC 9394; Alicycliphilus denitrificans; Cupriavidus metallidurans CH34 (plasmid); Zunongwangia profunda SM-AB7

Manganese, iron, cobalt, zinc, nickel, copper, cadmium, gallium

TonB-dependent siderophore receptor; ferripyoverdine receptor; ABC transporter-like protein; zinc/iron permease; iron-dependent regulatory protein, ideR; DNA protection protein, dpsA; fpvA2 gene product; aconitate hydratase 1; ABC transporter transmembrane region family protein (Fe); lipoprotein inner membrane ABC transporter, Irp6; permease and ATP-binding protein of yersiniabactin-iron ABC transporter YbtP; ABC transporter precursor of the inner membrane lipoprotein; iron(III)-transport ATP-binding protein, fbpC; ferroxidase; zinc/iron ZIP family permease (Zn/Fe/Co/Ni/Cu/Cd); czcD gene product (Fe/Zn/Co/Cd/Ni); zinc transporter zupT (Zn/Fe/Co/Ni/Cu/Cd); ferric uptake regulator, Fur family; ctpC gene product (Mn/Zn)

Stenotrophomonas maltophila R5513; Stenotrophomonas sp. SKA14; Verminephrobacter eiseniae EF01-2; Ethanoligenes herbinense YUAN-3; Pseudomonas fulva 12-X; Kocuria rhizophila DC2201; Synechococcus sp. CC9311; Prochlorococcus marinus str. MIT 9303; Azoarcus sp. BH72; Pseudomonas fluorescens PF-5; Streptomyces hygroscopicus ATCC 53653; Streptomyces violaceusniger Tu 4113; Escherichia coli DECBC; Yersinia enterocolitica; Escherichia coli 55989; Escherichia coli O104:H4 str. 01-09591; Escherichia coli NA114; Yersinia pseudotuberculosis IP 32953; Yersinia pestis KIM10 + ; Neisseria meningitidis ATCC 13091; Neisseria meningitidis MC58; Neisseria meningitidis M01-240355; Neisseria meningitidis alpha153; Rhodococcus equi 103S; Methanosaeta harundinacea 6Ac; Aeromonas salmonicida subsp. salmonicida A449; Erwinia billingiae Eb661; Serratia sp. AS12; Serratia odorifera 4Rx13; Serratia proteamaculans 568; Serratia odorifera DSM 4582; Prevotella dentalis DSM 3688; Mycobacterium ulcerans Agy99; Mycobacterium marinum M

Mercury

Mercuric (Hg(II)) reductase, merA; mercuric transport protein, merT; MerR family transcriptional regulator; Hg(II)-responsive transcriptional regulator; mercuric transporter, merH; merR gene product; mercuric reductase, merB1

Thiomonas sp. 3As; Endoriftia Persephone ‘Hot96_1 + Hot96_2′; Bacillus cellulosilyticus DSM 2522; Agrobacterium tumefaciens F2; Leptospirillum ferrodiazotrophum; Meiothermus silvanus DSM 9946; Thermus thermophilus HB27; Thermus thermophilus HB8; Oceanithermus profundus DSM 14977; Enterobacter cloaceae subsp. cloaceae ATCC 13047; Sphingopyxis alaskensis RB2256; Methyloversatilis universalis FAM5; Novosphingobium nitrogenifigens DSM 19370; Burkholderia glumae BGR1; Acidovorax sp. JS42; Mycobacterium sp.; Sphingobium sp. SYK-6; Xanthobacter autotrophicus Py2

Molybdenum, tungsten

Molydbenum ABC transporter ATP-binding; extracellular solute-binding protein, wtpA; signal transduction histidine-protein kinase, baeS; sensory histidine kinase in two-component regulatory system with BaeR; ABC transporter family protein; molybdate ABC transporter, permease protein modB

Methanosarcina acetivorans C2A; Methanohalobium evestigatum Z-7303; Escherichia coli 83972; Ralstonia solanacearum CMR15; Desulfovibrio sp. A2; Raphidiopsis brookii D9