Table 3 Predicted heavy metals resistance genes detected in SL4 metagenome and their taxonomic affiliations

Copper

Copper resistance protein CopC; multicopper oxidase type 3; copper exporting ATPase; putative multicopper oxidase (laccase-like); copper resistance protein B precursor; copper homeostasis protein, cutC; copper resistance protein A, copA; twin-arginine translocation pathway signal; putative copper binding protein; copper-translocating P-type ATPase, copB; multicopper oxidase type 2; apolipoprotein N-acyltransferase; two-component heavy metal transcriptional regulator; apolipoprotein N-acyltransferase/copper homeostasis protein, cutE; heavy-metal transporting P-type ATPase; P-ATPase superfamily P-type ATPase copper transporter; penicillinase repressor/transcription regulator, copY/tcrY; two-component sensor, copS; lipoprotein involved with copper homeostasis and adhesion, cutF; blue copper oxidase CueO; copper tolerance protein; heavy metal transport/detoxification protein, copP; putative laccase

Frankia sp. CcI3; Shigella dysenteriae 1012; Haloalkalicoccus jeotgali B3; Intrasporangium calvum DSM 43,043; Methanosaeta harundinacea 6Ac; Rhodococcus pyridinivorans AK37; Halorubrum lacusprofundi ATCC 49239; Azospirillum brasilense Sp245; Geobacillus thermodenitrificans NG80-2; Pseudomonas aeruginosa 2192; Citrobacter rodentium ICC168; Citrobacter koseri ATCC BAA-895; Acetobacter pomorum DM001; Kytococcus sedentarius DSM 20547; Azorhizobium caulinodans ORS 571; Nitrosomonas eutropha C91; Corynebacterium ammoniagenes DSM 20306; Salmonella enterica subsp. enterica serovar Weltevreden str. HI_N05-537; Oceanicola sp. S124; Polymorphum gilvum SL-003B-26A1; Xanthobacter autotrophicus Py2; Bradyrhizobium sp. ORS 375; Delftia acidovorans SPH-1; Achromobacter sp. AO22; Vibrio sp. RC586; Oxalobacter formigenes OXCC13; Mycobacterium parascrofulaceum ATCC BAA-614; Lactobacillus pentosus MP-10; Lactobacillus pentosus IG1; Lactobacillus plantarum JDM1; Pseudomonas aeruginosa PA01; Pseudomonas aeruginosa M18; Pectobacterium carotovorum subsp. brasiliensis PBR1692; Rahnella sp. Y9602; Providencia rustigianii DSM 4541; Rhodobacterales bacterium Y4I; Thermomonospora curvata DSM 43183; Verrucomicrobiaceae bacterium CNC16

Chromium, nickel, cobalt

NADPH-dependent FMN reductase, transcriptional regulator NikR, CopG family (Ni); integral membrane sensor signal transduction histidine kinase nrsS; nickel ABC transporter, nickel/metallophore periplasmic binding protein; chromate resistance protein, chrB; binding-protein-dependent transport system inner membrane; nickel ABC transporter, periplasmic nickel-binding protein, nikA; iron-dicitrate transporter subunit, membrane component of ABC superfamily (Ni/Co); chromate transporter, chrA; major facilitator superfamily protein (Ni/Co); ArsR family transcriptional regulator (Co/Ni); peptide/nickel transport system substrate -binding protein; regulatory protein, chrB1; cation diffusion facilitator family transporter (Ni/Co); permeases of the major facilitator superfamily (Ni/Co); binding-protein-dependent transport system inner membrane protein, nikB; cadmium-translocating P-type ATPase (Co/Ni)

Bacillus coagulans 2-6; Methanococcus voltae A3; Acaryochloris sp. CCMEE 5410; Peptoniphilus sp. oral taxon 375 str. F0436; Burkholderia multivorans CGD1; Burkholderia multivorans CGD2M; Candidatus Desulforudis audaxviator MP104C; Synergistetes bacterium SGP1; Escherichia coli S88; Leptothrix cholodnii SP-6; Cellulomonas fimi ATCC 484; Jonesia denitrificans DSM 20603; Azospirillum sp. B510; Cupriavidus metallidurans CH34 (plasmid); Methylobacterium nodulans ORS 2060; Methylobacterium extorquens DM4; Sinorhizobium meliloti CCNWSX0020; Candidatus Desulforudis audaxviator MP104C; Streptomyces griseoflavus Tu4000

Mercury, silver, cadmium, lead

Copper-transporting ATPase RAN1, merP; mercuric ion reductase, merA; mercuric reductase merB1; right origin-binding protein robA (Ag/Hg/Cd); mercuric transport protein periplasmic protein, merP; Pb-efflux ATPase pbrA (Pb); organomercurial lyase, merB; MerR family transcriptional regulator; disulfide bond formation protein B (Cd/Hg); Pb/Cd/Zn/Hg transporting ATPase; sensor protein ZraS (Pb, Zn); mercuric transporter, merH

Verticillium dahliae VdLs. 17; Verticillium albo-atrum VaMs. 102; Pseudomonas fluorescens; Xanthobacter autotrophicus Py2; Yersinia ruckeri ATCC 29473; Delftia acidovorans SPH-1; Ralstonia metallidurans CH34 (plasmid); Janthinobacterium sp. Marseille (plasmid); Pseudomonas stutzeri (plasmid); Haliangium ochraceum DSM 14365; Vibrio caribbenthicus ATCC BAA-2122; Tolumonas auensis DSM 9187; Mesorhizobium amorphae CCNWGS0123; Citrobacter youngae ATCC 29220; Mycobacterium sp.

Zinc, manganese, cadmium

Zinc resistance protein, zraP; Fis family transcriptional regulator; periplasmic solute-binding protein (Mn/Cd); RND family efflux transporter, MFP subunit (Zn); DSBA Oxidoreductase (Cd); membrane fusion protein (MFP-RND) heavy metal cation tricomponent efflux HmxB (Zn); cation transporting ATPase, P-type; high-affinity zinc transporter periplasmic protein; DSBA gene product (Cd/Zn/Hg); cadmium-translocating P-type ATPase (Zn); dithiol-disulfide isomerase (Cd); heavy metal-translocating P-type ATPase (Zn); zinc/manganese/iron ABC transporter, periplasmic zinc/manganese/iron-binding protein

Escherichia sp. TW09308; Citrobacter freundi 4_7_47CFAA; Citrobacter youngae ATCC 29220; Salmonella enterica subsp. enterica serovar Hadar str. RI_05P066; Desulfovibrio vulgaris str. ‘Miyazaki F’; Thermobacillus composti KWC4; Pseudomonas putida S16; Paenibacillus mucilaginosus KNP414; Cupriavidus metallidurans CH34 (plasmid); Pyrococcus abyssi GE5; Dickeya dadantii Ech703; Candidatus Blochmannia pennsylvanicus str. BPEN; Thermaerobacter subterraneus DSM 13965; Rhodococcus equi 1035; Bacillus cytotoxicus NVH 391-98; Rhodobacterales bacterium HTCC2083

Iron, cobalt, nickel, gallium, cadmium, magnesium, manganese, zinc

Fe(III)-pyochelin outer membrane receptor precursor; peptide/nickel transport system substrate-binding protein; ferrichrome ABC transporter permease (Ni/Co); mgtB gene product (Mg/Co); magnesium-translocating P-type ATPase (Mg/Co); iron-dependent repressor, ideR; heavy metal-translocating P-type ATPase (Co/Ni); aconitase A (Fe); ABC transporter, ATP-binding protein YbbL (Fe); TonB-dependent siderophore receptor; zinc/iron ZIP family permease (Zn/Fe/Co/Ni/Cu/Cd); nickel–cobalt–cadmium resistance protein nccC (plasmid); aconitate hydratase (Fe); ferritin (Fe/Cu/Mn); fpvA2 gene product; predicted divalent heavy-metal cations transporter (Zn/Fe/Co/Ni/Cu/Cd); ferric uptake regulator family protein, furA (Fe); DNA-binding transcriptional regulator BasR (Fe); iron-dicitrate transporter ATP-binding subunit; NRAMP family Mn²⁺/Fe²⁺ transporter (Mn/Fe/Cd/Co/Zn); sensor protein BasS/PmrB (Fe); ferripyoverdine receptor 2

Pseudomonas aeruginosa C3719; Pseudomonas aeruginosa M18; Pseudomonas aeruginosa PA01; Azospirillum sp. B510; Vibrio parahaemolyticus RIMD 2210633; Pectobacterium atrosepticum SCRI1043; Klebsiella pneumoniae 342; Klebsiella variicola At-22; Pseudomonas aeruginosa 138244; Kineococcus radiotolerans SRS30216; Actinosynnema mirum DSM 43827; Bifidobacterium bifidum NCIMB 41171; Bifidobacterium bifidum S17; Escherichia fergusonii ATCC 35469; Pseudomonas fulva 12-X; Comamonas testosteroni S44; Variovorax paradoxus EPS; Methanosaeta

Harundinacea 6Ac; Corynebacterium glucuronolyticum ATCC 51867; Streptomyces violaceusniger Tu 4113; Proteus mirabilis HI4320; Azoarcus sp. BH72; Solibacillus silvestris StLB046; Segniliparus rigosus ATCC BAA-974; Sodalis glossinidius str. ‘morsitans’; Citrobacter koseri ATCC BAA-895; Thermobaculum terrenum ATCC BAA-798; Enterobacter cloacae subsp. cloacae ATCC 13047; Achromobacter xylosoxidans A8

Molybdenum, tungsten; tellurium

modE gene product; tellurite resistance protein TrgB; KlaB protein (Te); molybdate ABC superfamily ATP-binding cassette transporter, ABC protein, modC; molybdate ABC transporter periplasmic molybdate-binding protein modA; tungstate ABC transporter binding protein WtpA; molybdenum ABC transporter permease protein modB; tellurite resistance protein TehA

Xenorhabdus bovienii SS-2004; Roseobacter sp. GAI101; uncultured bacterium (plasmid); Serratia odorifera DSM 4582; Sinorhizobium meliloti 1021; Desulfurobacterium thermolithotrophum DSM 11699; Gemmatimonas aurantiaca T-27; Neisseria mucosa ATCC 25996

Arsenic, antimony

ABC transporter; multidrug resistance protein, p-glycoprotein; arsenite oxidase, large subunit, AoxB; phosphate ABC transporter permease (As); phosphate ABC transporter substrate-binding protein; protein-tyrosine phosphatase, low molecular weight, arsC; arsenate reductase; arsenate reductase, glutathione/glutaredoxin type; arsenic resistance protein arsB; arsenite oxidase small subunit, AoxA; ABC thiol transporter; methyltransferase, arsM; methyltransferase type II; arsenite S-adenosylmethyltransferase; arsenate reductase (azurin); arsenical resistance protein ArsH; arsenical resistance protein arsB

Leishmania major strain Friedlin; Roseobacter litoralis och 149; Nitrosomonas sp. Is79A3; Acidovorax avenae subsp. avenae ATCC 19860; Sphaerobacter thermophilus DSM 20745; Staphylococcus saprophyticus subsp. saprophyticus; Staphylococcus aureus; Bacillus subtilis subsp. subtilis RO-NN-1; Microcoleus chthonoplastes PCC 7420; Thauera sp. MZIT; Rhodomicrobium vanielii ATCC 17100; Burkholderia multivorans ATCC 17616; Leishmania infantum JPCMS; Microlunatus phosphovorus NM-1; Leptonema illini DSM 21528; Desulfohalobium retbaense DSM 5692; Rhodoferax ferrireducens T118; Gluconacetobacter sp. SKCC-1; Peptoniphilus harei ACS-146-V-Sch2b; Acetivibrio cellulolyticus CD2