Taxonomic profiling and metagenome analysis of a microbial community from a habitat contaminated with industrial discharges
Microbial Ecology
Varun Shah, Martha Zakrzewski, Daniel Wibberg, Felix Eikmeyer, Andreas Schlüter and Datta Madamwar*
*Corresponding author:- E-mail:
Tel: +91-02692-229380; Fax: +91-02692-231042/236475
Affiliation: BRD School of Biosciences, Sardar Patel Maidan, Vadtal Road, Satellite Campus, Post Box No. 39,
Sardar Patel University, Vallabh Vidyanagar - 388 120, Anand, Gujarat, India.
Legends to supplementary
Figure S1 The rarefaction curves at rank phylum (a) and rank genus (b) for all the three microbial classification (RDP, CARMA and LCA)
Table S2 Selected gene ontology (GO) terms relevant to xenobiotic biodegradation are described
Table S3 Selected cluster of orthologous groups of proteins (COGs) playing a role in xenobiotic biodegradation are described
Table S4 Selected protein family members (Pfam) relevant in xenobiotic biodegradation are described
Table S5 Enzymes identified in metagenome sequences and also characterized in UM-BBD (University of Minnesota - Biocatalysis/Biodegradation Database) for xenobiotic biodegradation along with their possible reactions and pathways are described
a
b
Fig. S1
Table S2: Selected gene ontology (GO) terms relevant to xenobiotic biodegradation are described.
GO terms / Description0005975 / Carbohydrate metabolic process
0006096 / Glycolysis
0016787 / Hydrolase activity
0016740 / Transferase
0005215 / Transporter
0016829 / Lyase
0006099 / TCA cycle
0009055 / Electron carrier activity
0033014 / Tetrapyrrole biosynthetic process
0006807 / N compound metabolic process
0016866 / Intramolecular transferase
0008901 / Ferredoxin hydrogenase activity
0006725 / Cellular aromatic compound metabolic process
0008137 / NADH dehrogenase (ubiquinone)
0008113 / Peptide methionine-(S)-oxide reductase
0008410 / CoA transferase activity
0006979 / Response to oxidative stress
0015109 / Chromate transmembrane transporter
0015703 / Chromate transport
0015948 / Methanogenesis
0016836 / Hydro lyase
0004109 / Coproporphyrinogen oxidase
0004096 / Catalase
0004089 / Carbonate dehydratase
0000103 / Sulfate assimilation
0019438 / Aromatic compounds biosynthetic process
0009325 / Nitrate reductase complex
0008940 / Nitrate reductase activity
0004455 / Ketol-acid reductoisomerase activity
0004129 / Cytochrome c-oxidase
0006790 / Sulfur metabolic process
0006097 / Glyoxylate cycles
0016833 / Oxo-acid lyase
0004781 / Sulfate adenyl transferase activity (ATP)
0004497 / Monooxygenase activity
0004602 / Glutathione peroxidase
0015105 / Arsenite transmembrane transporter
0016846 / Carbon-sulfur lyase
0009375 / Ferredoxin hydrogenase
0004174 / Electron transferring flavoprotein dehydrogenase
0016840 / C-N lyase
0008146 / Sulfotransferase
0046685 / Response to arsenic
0004601 / Peroxidase
0006801 / Superoxide metabolic
0004597 / Peptide-aspartate β-dioxygenase activity
0018492 / Carbon monoxide dehydrogenase
0019645 / Anaerobic electron transport chain
0018759 / Methenyltetrahydromethanopterin cyclohydrolase activity
0008827 / Cytochrome O ubiquinol oxidase
0018822 / Nitrile hydratase
0004301 / Epoxide hydrolase
0004784 / Superoxide dismutase
0019439 / Aromatic compound catabolic process
0045482 / Trichodiene synthase
0008937 / Ferredoxin reductase
0046413 / Organomercury catabolic process
0018836 / Alkyl mercury lyase
0003937 / IMP cyclohydrolase activity
0016811 / Hydrolase activity
0016705, 0016616, 0016651, 0016712, 0016625, 0016620, 0016655, 0016669, 0016614 and 0016730 / Oxidoreductase activity
0018576 / Catechol I
0016813 / Hydrolase activity
Table S3: Selected cluster of orthologous groups of proteins (COGs) playing a role in xenobiotic biodegradation are described.
COG category/ COG no. / DescriptionC Energy production and conversion
COG1032 / Fe-S oxidoreductases family 2
COG0247 / Fe-S oxidoreductases
COG0437 / Fe-S-cluster-containing hydrogenase components 1
COG1905 / NADH:ubiquinone oxidoreductase 24 kD subunit
COG0526 / Thiol-disulfide isomerase and thioredoxins
COG0778 / Nitroreductase
COG0543 / 2-polyprenylphenol hydroxylase and related flavodoxin oxidoreductases
COG1145 / Ferredoxin 2
COG1007 / NADH:ubiquinone oxidoreductase subunit 2 (chain N)
COG0348 / Polyferredoxin
COG1251 / NAD(P)H-nitrite reductase
COG0852 / NADH:ubiquinone oxidoreductase 27 kD subunit
COG0649 / NADH:ubiquinone oxidoreductase 49 kD subunit 7
COG1008 / NADH:ubiquinone oxidoreductase subunit 4 (chain M)
COG0731 / Fe-S oxidoreductases
COG1005 / NADH:ubiquinone oxidoreductase subunit 1 (chain H)
COG0377 / NADH:ubiquinone oxidoreductase 20 kD subunit and related Fe-S oxidoreductases
COG1034 / NADH dehydrogenase/NADH:ubiquinone oxidoreductase 75 kD subunit (chain G)
COG0713 / NADH:ubiquinone oxidoreductase subunit 11 or 4L (chain K)
COG2181 / Nitrate reductase gamma subunit
COG0674 / Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, alpha subunit
COG1013 / Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, beta subunit
COG1144 / Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, delta subunit
COG1014 / Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, gamma subunit
COG2710 / Nitrogenase molybdenum-iron protein, alpha and beta chains
COG1347 / Na+-transporting NADH:ubiquinone oxidoreductase subunit 4
COG3259 / Coenzyme F420-reducing hydrogenase, alpha subunit
COG2080 / Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs
COG2878 / Predicted alternative beta subunit of Na+-transporting NADH:ubiquinone oxidoreductase
COG1148 / Heterodisulfide reductase, subunit A and related polyferredoxins
COG0243 / Anaerobic dehydrogenases, typically selenocysteine-containing
COG1902 / NADH:flavin oxidoreductases, Old Yellow Enzyme family
P Inorganic ion transport and metabolism
COG2059 / Chromate transport protein ChrA
COG0659 / Sulfate permease and related transporters (MFS superfamily)
COG3256 / Nitric oxide reductase large subunit
COG2897 / Rhodanese-related sulfurtransferases
COG0607 / Rhodanese-related sulfurtransferases
COG3420 / Nitrous oxidase accessory protein
COG3142 / Uncharacterized protein involved in copper resistance
COG2920 / Sulfite reductase, gamma subunit
COG0715 / ABC-type nitrate/sulfonate/taurine/bicarbonate transport systems, periplasmic components
COG0600 / ABC-type nitrate/sulfonate/taurine/bicarbonate transport systems, permease components
H Coenzyme metabolism
COG0043 / 3-polyprenyl-4-hydroxybenzoate decarboxylase and related decarboxylases
COG0163 / 3-polyprenyl-4-hydroxybenzoate decarboxylase
COG0382 / 4-hydroxybenzoate polyprenyltransferase and related prenyltransferases
COG2227 / 2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase
COG0147 / Anthranilate/para-aminobenzoate synthases component I
COG0512 / Anthranilate/para-aminobenzoate synthases component II (E/H)
Q Secondary metabolites biosynthesis, transport and catabolism
COG1228 / Imidazolonepropionase and related amidohydrolases
COG1225 / Peroxiredoxin
T Signal transduction mechanisms
COG0589 / Universal stress protein UspA and related nucleotide-binding proteins
R General function predictions only
COG2070 / Dioxygenases related to 2-nitropropane dioxygenase
O Post translational modification, protein turnover, chaperones
COG3634 / Alkyl hydroperoxide reductase, large subunit
Table S4: Selected protein family members (Pfam) relevant in xenobiotic biodegradation are described.
Pfam no. / DescriptionPF01558 / Pyruvate ferredoxin/flavodoxin oxidoreductase (POR)
PF10695 / Cell-wall-associated hydrolase (Cw-hydrolase)
PF01512 / Respiratory-chain NADH dehydrogenase 51 Kd subunit (Complex1_51K)
PF00909 / Ammonium transporter family (Ammonium_transp)
PF01257 / Respiratory-chain NADH dehydrogenase 24 Kd subunit (Complex1_24kDa)
PF01475 / Ferric uptake regulator family (FUR)
PF03060 / 2-nitropropane dioxygenase (NPD)
PF03807 / NADP oxidoreductase coenzyme F420-dependent (F420_oxidored)
PF02417 / Chromate transporter (Chromate_transp)
PF01625 / Peptide methionine sulfoxide reductase (PMSR)
PF00148 / Nitrogenase component 1 type Oxidoreductase (Oxidored_nitro)
PF00174 / Oxidoreductase molybdopterin binding domain (Oxidored_molyb)
PF01654 / Bacterial Cytochrome Ubiquinol Oxidase (Bac_Ubq_Cox)
PF01544 / CorA-like Mg2+ transporter protein (CorA)
PF04909 / Amidohydrolase (Amidohydro_2)
PF10589 / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region (NADH_4Fe-4S)
PF02578 / Multi-copper polyphenol oxidoreductase laccase (Cu-oxidase_4)
PF02028 / BCCT family transporter (BCCT)
PF02219 / Methylenetetrahydrofolate reductase (MTHFR)
PF01970 / Tripartite tricarboxylate transporter TctA family (TctA)
PF04324 / BFD-like [2Fe-2S] binding domain (Fer2_BFD)
PF01977 / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase (UbiD)
PF00199 / Catalase (Catalase)
PF03150 / Di-haem cytochrome c peroxidase (CCP_MauG)
PF01676 / Metalloenzyme superfamily (Metalloenzyme)
PF05690 / Thiazole biosynthesis protein ThiG (ThiG)
PF02421 / Ferrous iron transport protein B (FeoB_N)
PF02322 / Cytochrome oxidase subunit II (Cyto_ox_2)
PF02665 / Nitrate reductase gamma subunit (Nitrate_red_gam)
PF10588 / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region (NADH-G_4Fe-4S_3)
PF02657 / Fe-S metabolism associated domain (SufE)
PF06983 / 3-demethylubiquinone-9 3-methyltransferase (3-dmu-9_3-mt)
PF01070 / FMN-dependent dehydrogenase (FMN_dh)
PF04453 / Organic solvent tolerance protein (OstA_C)
PF05896 / Na(+)-translocating NADH-quinone reductase subunit A (NQRA) (NQRA)
PF07833 / Copper amine oxidase N-terminal domain (Cu_amine_oxidN1)
PF01794 / Ferric reductase like transmembrane component (Ferric_reduct)
PF02040 / Arsenical pump membrane protein (ArsB)
PF02335 / Cytochrome c552 (Cytochrom_C552)
PF00775 / Dioxygenase (Dioxygenase_C)
PF03594 / Benzoate membrane transport protein (BenE)
PF01880 / Desulfoferrodoxin (Desulfoferrodox)
PF07664 / Ferrous iron transport protein B C terminus (FeoB_C)
PF05425 / Copper resistance protein D (CopD)
PF08770 / Sulphur oxidation protein SoxZ (SoxZ)
PF00743 / Flavin-binding monooxygenase-like (FMO-like)
PF07879 / PHB/PHA accumulation regulator DNA-binding domain (PHB_acc_N)
PF05816 / Toxic anion resistance protein (TelA) (TelA)
PF08376 / Nitrate and nitrite sensing (NIT)
PF02342 / Bacterial stress protein (TerD)
PF02613 / Nitrate reductase delta subunit (Nitrate_red_del)
PF04386 / Stringent starvation protein B (SspB)
PF08803 / Putative mono-oxygenase ydhR (ydhR)
PF05275 / Copper resistance protein B precursor (CopB) (CopB)
PF05187 / Electron transfer flavoprotein-ubiquinone oxidoreductase (ETF_QO)
PF02411 / MerT mercuric transport protein (MerT)
PF01322 / Cytochrome C (Cytochrom_C_2)
PF02167 / Cytochrome C1 family (Cytochrom_C1)
PF00685 / Sulfotransferase domain (Sulfotransfer_1)
PF09678 / Cytochrome c oxidase caa3 assembly factor (Caa3_CtaG) (Caa3_CtaG)
PF00848 / Ring hydroxylating alpha subunit (catalytic domain) (Ring_hydroxyl_A)
PF03091 / CutA1 divalent ion tolerance protein (CutA1)
PF10399 / Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal (UCR_Fe-S_N)
PF05138 / Phenylacetic acid catabolic protein (PaaA_PaaC)
PF03892 / Nitrate reductase cytochrome c-type subunit (NapB) (NapB)
PF06778 / Chlorite dismutase (Chlor_dismutase)
PF03597 / Cytochrome oxidase maturation protein cbb3-type (CcoS)
PF00866 / Ring hydroxylating beta subunit (Ring_hydroxyl_B)
PF04234 / Copper resistance protein CopC (CopC)
PF06240 / Carbon monoxide dehydrogenase subunit G (CoxG) (COXG)
PF06953 / Arsenical resistance operon trans-acting repressor ArsD (ArsD)
PF04261 / Dyp-type peroxidase family (Dyp_perox)
PF03598 / CO dehydrogenase/acetyl-CoA synthase complex beta subunit (CdhC)
PF05233 / PHB accumulation regulatory domain (PHB_acc)
PF10670 / Nickel uptake substrate-specific transmembrane region (NikM)
PF00080 / Copper/zinc superoxide dismutase (SODC) (Sod_Cu)
PF05597 / Poly(hydroxyalcanoate) granule associated protein (phasin) (Phasin)
PF07357 / Dinitrogenase reductase ADP-ribosyltransferase (DRAT) (DRAT)
PF10138 / Tellurium resistance protein (Tellurium_res)
PF09828 / Chromate resistance exported protein (Chrome_Resist)
PF08802 / Cytochrome B6-F complex Fe-S subunit (CytB6-F_Fe-S)
PF03626 / Prokaryotic Cytochrome C oxidase subunit IV (COX4_pro)
PF08635 / Putative oxidoreductase C terminal (ox_reductase_C)
PF04444 / Catechol dioxygenase N terminus (Dioxygenase_N)
PF02289 / Cyclohydrolase (MCH) (MCH)
PF05099 / Tellurite resistance protein TerB (TerB)
PF06441 / Epoxide hydrolase N terminus (EHN)
PF06099 / Phenol hydroxylase subunit (Phenol_hyd_sub)
PF09055 / Nickel-containing superoxide dismutase (Sod_Ni)
PF02943 / Ferredoxin thioredoxin reductase catalytic beta chain (FeThRed_B)
PF03596 / Cadmium resistance transporter (Cad)
PF03284 / Phenazine biosynthesis protein A/B (PHZA_PHZB)
PF07746 / Aromatic-ring-opening dioxygenase LigAB
PF02979 / Nitrile hydratase
PF01179 / Copper amine oxidase
PF05494 / Toluene tolerance
PF07976 / Phenol hydroxylase
PF04896 / Ammonia monooxygenase/methane monooxygenase
PF09821 / ABC nitrate/sulfonate/bicarbonate family transporter
PF01058 / NADH ubiquinone oxidoreductase
PF02727 / Copper amine oxidase
PF07858 / Limonene-1
PF03712 / Copper type II ascorbate-dependent monooxygenase
PF09242 / Flavocytochrome c sulphide dehydrogenase
Table S5: Enzymes identified in metagenome sequences and also characterized in UM-BBD (University of Minnesota - Biocatalysis/Biodegradation Database) for xenobiotic biodegradation along with their possible reactions and pathways are described.
Sr. No. / Enzyme / Possible pathways / Catalyzed reaction(s)1 / Azoreductase / Dye degradation pathway / From diazene to RNH2 + R’NH2
2 / 3-hydroxyacyl CoA dehydrogenase / Cyclohexane degradation pathway / From (3S)-3-Hydroxyadipyl-CoA to 3-Oxoadipyl-CoA
3 / Acetoacetyl CoA reductase / Benzoate degradation pathway (anaerobic) / From (3S)-3-Hydroxybutyryl-CoA to Acetoacetyl-CoA
4 / s-hydroxymethyl glutathione dehydrogenase / C1 Metabolic cycle pathway / From S-Hydroxymethylglutathione to S-Formylglutathione
5 / Quinoprotein alcohol dehydrogenase / 1,2 Dichloroethane degradation pathway / From 2-Chloroethanol to Chloroacetaldehyde
C1 Metabolic cycle pathway / From Methanol to Formaldehyde
6 / Formate dehydrogenase / Hexahydro-1,3,5-trinitro-1,3,5-triazine degradation pathway / From Formate to Carbon Dioxide
7 / Aldehyde dehydrogenase / 1,3-Dichloropropene family degradation pathway / Fromcis-3-Chloroallyl aldehyde tocis-3-Chloroacrylic acid
Fromtrans-3-Chloroallyl aldehyde totrans-3-Chloroacrylic acid
8 / Aldehyde dehydrogenase (NAD+) / 1,2 Dichloroethane degradation pathway / From Chloroacetaldehyde to Chloroacetate
Dodecyl sulphate degradation pathway / From Dodecanal to Lauric acid
n-octane degradation pathway / From 1-Octanal to Octanoate
9 / Aldehyde oxidase / Furfural degradation pathway / From Furfural to 2-Furoate
10 / Carbon monoxide dehydrogenase / Thiocyanate degradation pathway / From Carbon Monoxide to Carbon Dioxide
2,4,6 trinitrotoluene degradation pathway (anaerobic) / From 2,4-Diamino-6-nitrotoluene to 2,4-Diamino-6-hydroxylaminotoluene
11 / 2,5-Dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase / gamma-Hexachlorocyclohexane degradation pathway / From 2,5-Dichloro-2,5-cyclohexadiene-1,4-diol to 2,5-Dichlorohydroquinone
12 / Benzyl alcohol dehydrogenase / Toluene degradation pathway / From Benzyl alcohol to Benzaldehyde
m-cresol degradation pathway / From 3-Hydroxybenzyl alcohol to 3-Hydroxybenzaldehyde
o-xylene degradation pathway / From 2-Methylbenzyl alcohol to 2-Methylbenzaldehyde
m-xylene degradation pathway / From 3-Methylbenzyl alcohol to 3-Methylbenzaldehyde
p-xylene degradation pathway / From p-Methylbenzyl alcohol to p-Tolualdehyde
13 / Enoyl CoA reductase / Cyclohexane degradation pathway / From Adipyl-CoA to 5-Carboxy-2-pentenoyl-CoA
14 / Benzoyl CoA reductase / Benzoate degradation pathway (anaerobic) / From Benzoyl-CoA to Cyclohex-1,5-diene-1-carboxyl-CoA
15 / 4-hydroxy benzoyl CoA reductase / Phenol degradation pathway (anaerobic) / From 4-Hydroxybenzoyl-CoA to Benzoyl-CoA
16 / Trimethylamine dehydrogenase / N,N-Diethyl-m-toluamide degradation pathway / From Diethylamine to Acetaldehyde and Ethyl amine
N-Methylmorpholine-N-oxide degradation pathway and Morpholine degradation pathway / From N-Methylmorpholine to Formaldehyde and Morpholine
Hexadecyltrimethylammonium chloride degradation pathway / From Trimethylamine to Formaldehyde and Dimethylamine
17 / Methylamine dehydrogenase / N,N-Diethyl-m-toluamide degradation pathway / From Ethyl amine to Acetaldehyde
2-Chloro-N-isopropylacetanilide degradation pathway / From Isopropylamine to Acetaldehyde and Methane
Glyphosate degradation pathway / From Methylamine to Formaldehyde
18 / Trimethylamine-N-oxide reductase / N-Methylmorpholine-N-oxide degradation pathway / From N-Methylmorpholine-N-oxide to N-Methylmorpholine
19 / Xenobiotic reductase / Nitroglycerin degradation pathway / From 1,2-Dinitroglycerol to 1-Mononitroglycerol or 2-Mononitroglycerol
From 1,3-Dinitroglycerol to 1-Mononitroglycerol
From 1-Mononitroglycerol to Glycerol
From 2-Mononitroglycerol to Glycerol
From Nitroglycerin (NG) to 1,2-Dinitroglycerol or 1,3-Dinitroglycerol
Pentaerythritol tetranitrate degradation pathway / From Pentaerythritol tetranitrate to Pentaerythritol trinitrate
From Pentaerythritol trinitrate to Pentaerythritol dinitrate
20 / NAD(P)H nitroreductase / 2,4,6-Trinitrotoluene degradation pathway (anaerobic/aerobic) / From 4-Amino-2,6-dinitrotoluene to 4-Amino-2-hydroxylamino-6-nitrotoluene or 2,4-Diamino-6-nitrotoluene
From 2-Amino-4,6-dinitrotoluene to 2,6-Diamino-4-nitrotoluene or 2,4-Diamino-6-nitrotoluene
From 2,4-Dihydroxylamino-6-nitrotoluene to 4-Amino-2-hydroxylamino-6-nitrotoluene
From 4-Hydroxylamino-2,6-dinitrotoluene to 4-Amino-2,6-dinitrotoluene
From 2-Hydroxylamino-4,6-dinitrotoluene to 2-Amino-4,6-dinitrotoluene
From 2,4,6-Trinitrotoluene to 4-Amino-2,6-dinitrotoluene or 2-Amino-4,6-dinitrotoluene or 2-Hydroxylamino-4,6-dinitrotoluene
2,4 dinitrotoluene degradation pathway / From 4-Amino-2-nitrotoluene to 2,4-Diaminotoluene
From 2-Amino-4-nitrotoluene to 2,4-Diaminotoluene
From 2,4-Dinitrotoluene to 4-Amino-2-nitrotoluene or 2-Amino-4-nitrotoluene
Parathion degradation pathway (anaerobic/aerobic) / From Parathion to Aminoparathion
21 / 2-Oxopropyl-CoM reductase / Propylene degradation pathway / From 2-Oxopropyl-CoM to Acetoacetate
22 / Dimethyl sulfoxide reductase / Dimethyl sulfoxide and
Organosulfide cycle pathway / From Dimethyl Sulfoxide to Dimethyl Sulfide
23 / Dissimilatory sulfite reductase / 2,4,6-Trinitrotoluene degradation pathway (anaerobic) / From 2,4-Diamino-6-hydroxylaminotoluene to 2,4,6-Triaminotoluene
24 / Lignin peroxidase / Anthracene degradation pathway / From Anthracene to 9,10-Anthraquinone