PMC · DOI:10.1128/mra.00569-25·September 23, 2025
A collection of metagenome-assembled genomes from platinum mine tailings in South Africa
Monono Mobanga, Ayomide Emmanuel Fadiji, Kalonji Abondance Tshisekedi, Tonderayi Dave Kawadza, Olubukola Oluranti Babalola
TL;DR
This study provides 84 assembled genomes from South African platinum mine tailings, offering insights into microbial diversity and environmental restoration.
Contribution
The novelty lies in assembling genomes from platinum mine tailings to explore microbial roles in pollution and restoration.
Findings
01
The genomes include diverse Proteobacteria species.
02
The findings suggest potential for pollutant degradation and resource recovery.
03
The study highlights ecological restoration strategies in mining-affected areas.
Abstract
This study presents 84 metagenome-assembled genomes from platinum mine tailings and non-mined soil. The analysis reveals diverse Proteobacteria. This work offers insights into pollutant degradation, resource recovery, and potential strategies for ecological restoration in mining-impacted environments.
Linked entities
Genes, proteins, chemicals, diseases, species, mutations and cell lines named across the full text — each resolved to its canonical identifier and authoritative record.
Chemicals1
Figures1
Click any figure to enlarge with its caption.
Fig 1Tables1
| MAG_Name | GTDB-Tk classification | Size (Mbp) | No. of contigs | N50 | GC content | No. of | Comp/ | NCBI SRA Accession no. | NCBI Genbank accession no. |
|---|---|---|---|---|---|---|---|---|---|
| NC_bin.4_Soil | Bacteria; Actinobacteriota; Actinomycetia; Propionibacteriales; Propionibacteriaceae; | 2.03 | 674 | 3,291.0 | 72.4 | 2,318 | 59.74/0.0 |
|
|
| NC_bin.3_Soil | Bacteria; Acidobacteriota; Blastocatellia; UBA7656; UBA7656; JADGNW01 | 3.59 | 134 | 62,162.0 | 72.7 | 5,500 | 93.88/5.55 |
|
|
| NC_bin.2_Soil | Bacteria; Acidobacteriota; Thermoanaerobaculia; UBA5704; UBA5704; UBA5704 | 3.44 | 2,086 | 3,489.0 | 68.8 | 5,333 | 67.67/2.84 |
|
|
| NC_bin.1_Soil | Bacteria; Acidobacteriota; Thermoanaerobaculia; Gp7-AA8; Gp7-AA8; QHVT01 | 1.79 | 1,155 | 2,557.0 | 68.1 | 3,181 | 56.52/1.79 |
|
|
| N_bin.9_Tailings | Bacteria; Actinobacteriota; UBA4738; AC-67; AC-67; | 2.04 | 135 | 27,483.0 | 64.0 | 2,062 | 97.09/0.85 |
|
|
| N_bin.8_Tailings | Bacteria; Proteobacteria; Gammaproteobacteria; Nevskiales; Nevskiaceae; Fontimonas | 3.5 | 976 | 3,983 | 68.8 | 3,840 | 72.57/2.58 |
|
|
| N_bin.7_Tailings | Bacteria; Actinobacteriota; Actinomycetia; Mycobacteriales; SCTD01; | 2.6 | 187 | 17,651.0 | 74.0 | 2,586 | 65.51/0.0 |
|
|
| N_bin.6_Tailings | Bacteria; Actinobacteriota; Acidimicrobiia; Acidimicrobiales; JACDCH01; | 3.24 | 75 | 109,669.0 | 72.8 | 3,160 | 94.01/4.7 |
|
|
| N_bin.5_Tailings | Bacteria; Actinobacteriota; Actinomycetia; Propionibacteriales; Nocardioidaceae; Nocardioides_B | 2.0 | 210 | 30,316.0 | 71.6 | 2,072 | 54.31/0.0 |
|
|
| N_bin.4_Tailings | Bacteria; Actinobacteriota; UBA4738; CADDZG01; WHSQ01; | 1.93 | 427 | 5,789.0 | 63.9 | 2,253 | 78.04/2.73 |
|
|
| N_bin.32_Tailings | Bacteria; Actinobacteriota; Actinomycetia; Actinomycetales; Microbacteriaceae; Yonghaparkia | 1.91 | 210 | 23,569.0 | 71.8 | 1,996 | 80.89/2.81 |
|
|
| N_bin.31_Tailings | Bacteria; Actinobacteriota; Acidimicrobiia; UBA5794; ZC4RG35; | 2.75 | 313 | 14,481.0 | 65.8 | 2,977 | 92.54/1.28 |
|
|
| N_bin.30_Tailings | Bacteria; Actinobacteriota; Actinomycetia; Actinomycetales; Microbacteriaceae; Agrococcus Agrococcus sediminis | 1.36 | 178 | 8,318.0 | 73.4 | 1,438 | 59.28/0.25 |
|
|
| N_bin.3_Tailings | Bacteria; Actinobacteriota; Acidimicrobiia; Acidimicrobiales; AC-14; | 2.87 | 95 | 62,162.0 | 72.0 | 3,591 | 71.44/1.21 |
|
|
| N_bin.29_Tailings | Bacteria; Proteobacteria; Alphaproteobacteria; Caulobacterales; Caulobacteraceae; Brevundimonas Brevundimonas sp001794825 | 2.63 | 485 | 2,670.0 | 70.2 | 1,696 | 57.7/6.41 |
|
|
| N_bin.28_Tailings | Bacteria; Acidobacteriota; Vicinamibacteria; Vicinamibacterales; UBA2999; | 2.19 | 918 | 2,692.0 | 71.7 | 2,564 | 53.44/1.72 |
|
|
| N_bin.27_Tailings | Bacteria; Proteobacteria; Gammaproteobacteria; Acidiferrobacterales; Sulfurifustaceae; | 2.65 | 251 | 15,632.0 | 63.6 | 2,751 | 95.38/1.43 |
|
|
| N_bin.26_Tailings | Bacteria; Actinobacteriota; Acidimicrobiia; Acidimicrobiales; JACDCH01; | 2.8 | 229 | 14,640.0 | 73.8 | 2,844 | 78.63/1.7 |
|
|
| N_bin.25_Tailings | Bacteria; Proteobacteria; Gammaproteobacteria; Burkholderiales; Burkholderiaceae; Hydrogenophaga | 2.67 | 367 | 11,962.0 | 65.6 | 2,877 | 79.67/1.19 |
|
|
| N_bin.24_Tailings | Bacteria; Actinobacteriota; Thermoleophilia; Solirubrobacterales; Solirubrobacteraceae; CADCVQ01 | 4.21 | 122 | 50,696.0 | 72.6 | 4,194 | 98.29/4.72 |
|
|
| N_bin.23_Tailings | Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales; Pseudomonadaceae; Pseudomonas_A Pseudomonas_A sp003205815 | 4.1 | 932 | 7,399.0 | 64.5 | 4,565 | 65.51/6.89 |
|
|
| N_bin.22_Tailings | Bacteria; Actinobacteriota; Acidimicrobiia; Acidimicrobiales; CADCTF01; | 2.25 | 724 | 3,383.0 | 68.7 | 2,692 | 62.61/2.56 |
|
|
| N_bin.21_Tailings | Bacteria; Actinobacteriota; Actinomycetia; Actinomycetales; Micrococcaceae; Pseudarthrobacter Pseudarthrobacter phenanthrenivorans | 3.34 | 1392 | 2,916.0 | 66.4 | 4,010 | 54.88/0.0 |
|
|
| N_bin.20_Tailings | Bacteria; Proteobacteria; Gammaproteobacteria; Nevskiales; Nevskiaceae; | 2.1 | 140 | 25,891.0 | 68.1 | 2,068 | 84.48/0.0 |
|
|
| N_bin.2_Tailings | Bacteria; Proteobacteria; Gammaproteobacteria; SURF-13; SURF-13; SURF-13 SURF-13 sp003599485 | 1.12 | 449 | 2,841.0 | 62.6 | 1,418 | 69.93/2.22 |
|
|
| N_bin.19_Tailings | Bacteria; Chloroflexota; Limnocylindria; Limnocylindrales; CSP1-4; SPCO01 | 2.13 | 121 | 33,539.0 | 72.9 | 2,785 | 87.64/0.0 |
|
|
| N_bin.18_Tailings | Bacteria; Actinobacteriota; UBA4738; CADDZG01; WHSQ01; MB1-2 | 2.5 | 99 | 62,812.0 | 65.4 | 2,614 | 95.72/0.15 |
|
|
| N_bin.17_Tailings | Bacteria; Gemmatimonadota; Gemmatimonadetes; Gemmatimonadales; Gemmatimonadaceae; SCN-70-22 | 3.13 | 1064 | 3,496.0 | 69.7 | 3,392 | 67.48/0.83 |
|
|
| N_bin.16_Tailings | Bacteria; Proteobacteria; Gammaproteobacteria; Xanthomonadales; Xanthomonadaceae; Vulcaniibacterium_B | 2.0 | 243 | 10,585.0 | 72.8 | 1,898 | 83.4/1.51 |
|
|
| N_bin.15_Tailings | Bacteria; Actinobacteriota; Actinomycetia; Actinomycetales; Micrococcaceae; Arthrobacter_D Arthrobacter_D subterraneus | 2.93 | 342 | 17,640.0 | 65.5 | 2,956 | 90.51/3.26 |
|
|
| N_bin.14_Tailings | Bacteria; Actinobacteriota; Actinomycetia; Mycobacteriales; Geodermatophilaceae; Blastococcus | 2.79 | 1541 | 9,834.0 | 67.1 | 4,226 | 66.72/1.72 |
|
|
| N_bin.13_Tailings | Bacteria; Actinobacteriota; Actinomycetia; Nitriliruptorales; ; | 3.11 | 37 | 113,821.0 | 74.5 | 2,863 | 84.61/0.85 |
|
|
| N_bin.12_Tailings | Bacteria; Actinobacteriota; Actinomycetia; Actinomycetales; Quadrisphaeraceae; | 3.31 | 187 | 22,874.0 | 74.1 | 3,229 | 88.26/1.42 |
|
|
| N_bin.11_Tailings | Bacteria; Actinobacteriota; Actinomycetia; Actinomycetales; Demequinaceae; Demequina | 2.24 | 241 | 12,269.0 | 70.6 | 2,245 | 88.39/1.73 |
|
|
| N_bin.10_Tailings | Bacteria; Actinobacteriota; Acidimicrobiia; Acidimicrobiales; GCA-2861595; | 2.83 | 573 | 6,312.0 | 76.0 | 2,999 | 75.06/4.34 |
|
|
| N_bin.1_Tailings | Bacteria; Proteobacteria; Alphaproteobacteria; Sphingomonadales; Sphingomonadaceae; Sphingomicrobium | 3.68 | 195 | 75,733.0 | 71.8 | 2,251 | 93.58/2.56 |
|
|
| BC_bin_7_Soil | Bacteria; Proteobacteria; Gammaproteobacteria; Burkholderiales; Burkholderiaceae; SCN-69-89 | 2.32 | 1405 | 1,755.0 | 67.7 | 3,081 | 57.37/3.98 |
|
|
| BC_bin_6_Soil | Bacteria; Actinobacteriota; Actinomycetia; Actinomycetales; Micrococcaceae; Pseudarthrobacter | 2.5 | 1242 | 2,168.0 | 66.6 | 3,025 | 71.03/3.21 |
|
|
| BC_bin_5_Soil | Bacteria; Proteobacteria; Gammaproteobacteria; Burkholderiales; Burkholderiaceae; Massilia | 4.81 | 885 | 8295.0 | 65.9 | 4,743 | 83.32/2.57 |
|
|
| BC_bin_3_Soil | Bacteria; Actinobacteriota; Actinomycetia; Actinomycetales; Quadrisphaeraceae; | 7.35 | 309 | 95,072.0 | 60.1 | 2,857 | 98.29/5.98 |
|
|
| BC_bin_2_Soil | Bacteria; Actinobacteriota; Actinomycetia; Propionibacteriales; Propionibacteriaceae; Brevilactibacter | 4.73 | 197 | 16039.0 | 69.5 | 2,303 | 52.26/6.35 |
|
|
| BC_bin_1_Soil | Bacteria; Actinobacteriota; Thermoleophilia; Solirubrobacterales; 70-9; | 2.72 | 747 | 2,375.0 | 65.6 | 2,270 | 50.64/1.7 |
|
|
| B_bin_9_Tailings | Bacteria; Proteobacteria; Gammaproteobacteria; Burkholderiales; Burkholderiaceae; SCN-69-89 SCN-69-89 sp001724315 | 2.03 | 287 | 8,573.0 | 70.6 | 2,082 | 70.06/2.16 |
|
|
| B_bin_8_Tailings | Bacteria; Proteobacteria; Gammaproteobacteria; Burkholderiales; Thiobacillaceae; Thiobacillus | 1.81 | 318 | 11,559.0 | 67.1 | 2,011 | 65.39/7.63 |
|
|
| B_bin_7_Tailings | Bacteria; Bdellovibrionota; Bacteriovoracia; Bacteriovoracales; Bacteriovoracaceae; UBA4096 | 3.1 | 174 | 44,707.0 | 42.7 | 3,256 | 83.18/0.89 |
|
|
| B_bin_6_Tailings | Bacteria; Proteobacteria; Gammaproteobacteria; Burkholderiales; Thiobacillaceae; Thiobacillus | 1.75 | 188 | 33,998.0 | 65.7 | 1,827 | 64.26/1.79 |
|
|
| B_bin_5_Tailings | Bacteria; Proteobacteria; Gammaproteobacteria; Burkholderiales; Burkholderiaceae; Acidovorax Acidovorax sp001411535 | 4.15 | 2196 | 2,000.0 | 64.3 | 5,283 | 72.71/3.87 |
|
|
| B_bin_48_Tailings | Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales; Pseudomonadaceae; Pseudomonas_E Pseudomonas_E sp014268815 | 5.49 | 468 | 21,4476.0 | 61.9 | 5,382 | 84.78/1.43 |
|
|
| B_bin_47_Tailings | Bacteria; Proteobacteria; Alphaproteobacteria; Sphingomonadales; Sphingomonadaceae; Novosphingobium | 2.21 | 61 | 61,685.0 | 62.9 | 2,170 | 97.8/0.33 |
|
|
| B_bin_45_Tailings | Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales; JADFDG01; JADFDG01 | 2.06 | 210 | 11,887.0 | 65.6 | 2,008 | 66.37/0.0 |
|
|
| B_bin_44_Tailings | Bacteria; Proteobacteria; Gammaproteobacteria; Burkholderiales; Burkholderiaceae; Calidifontimicrobium | 3.7 | 323 | 16,194.0 | 72.8 | 3,649 | 94.81/2.57 |
|
|
| B_bin_41_Tailings | Bacteria; Proteobacteria; Gammaproteobacteria; Burkholderiales; Thiobacillaceae; Thiobacillus | 1.54 | 224 | 10,494.0 | 67.9 | 1,733 | 64.38/1.63 |
|
|
| B_bin_40_Tailings | Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales; Porticoccaceae; JAGPUQ01 | 1.89 | 199 | 17,365.0 | 63.6 | 1,901 | 78.45/0.92 |
|
|
| B_bin_4_Tailings | Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales; Pseudomonadaceae; Pseudomonas_E Pseudomonas_E peli | 4.61 | 158 | 56,147.0 | 59.9 | 4,449 | 96.35/0.36 |
|
|
| B_bin_39_Tailings | Bacteria; Proteobacteria; Gammaproteobacteria; Burkholderiales; Thiobacillaceae; Thiobacillus | 2.3 | 173 | 36,904.0 | 63.1 | 2,344 | 65.86/3.44 |
|
|
| B_bin_37_Tailings | Bacteria; Proteobacteria; Gammaproteobacteria; Burkholderiales; Thiobacillaceae; Thiobacillus | 1.61 | 134 | 32,181.0 | 64.6 | 1,693 | 56.51/3.81 |
|
|
| B_bin_36_Tailings | Bacteria; Proteobacteria; Alphaproteobacteria; Sphingomonadales; Sphingomonadaceae; Sphingobium Sphingobium sp001713415 | 3.91 | 1533 | 2,980.0 | 63.0 | 4,754 | 82.57/3.68 |
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| B_bin_34_Tailings | Bacteria; Proteobacteria; Alphaproteobacteria; Caulobacterales; Caulobacteraceae; Phenylobacterium Phenylobacterium sp002441055 | 2.99 | 119 | 52,743.0 | 67.4 | 3,026 | 96.32/1.29 |
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| B_bin_33_Tailings | Bacteria; Bacteroidota; Bacteroidia; Flavobacteriales; Flavobacteriaceae; Flavobacterium | 4.3 | 24 | 415,372.0 | 43.2 | 3,729 | 99.29/0.35 |
|
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| B_bin_32_Tailings | Bacteria; Proteobacteria; Gammaproteobacteria; Burkholderiales; Rhodocyclaceae; Thauera | 2.89 | 176 | 27,186.0 | 68.8 | 2,774 | 86.99/5.25 |
|
|
| B_bin_31_Tailings | Bacteria; Proteobacteria; Alphaproteobacteria; Rhodobacterales; Rhodobacteraceae; Tabrizicola | 3.5 | 201 | 34,443.0 | 67.2 | 3,653 | 93.86/1.0 |
|
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| B_bin_30_Tailings | Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales; Moraxellaceae; UBA2031 | 2.17 | 185 | 21,864.0 | 62.2 | 2,157 | 64.13/0.0 |
|
|
| B_bin_3_Tailings | Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales; JADFDG01; JADFDG01 | 2.22 | 182 | 17,739.0 | 67.6 | 2,157 | 62.06/0.0 |
|
|
| B_bin_29_Tailings | Bacteria; Actinobacteriota; Acidimicrobiia; Acidimicrobiales; Ilumatobacteraceae; | 1.34 | 1007 | 2,869.0 | 71.2 | 3,175 | 52.99/1.99 |
|
|
| B_bin_28_Tailings | Bacteria; Bdellovibrionota; Bacteriovoracia; Bacteriovoracales; Bacteriovoracaceae; UBA6144 | 2.64 | 421 | 10,321.0 | 56.1 | 2,880 | 81.74/1.78 |
|
|
| B_bin_27_Tailings | Bacteria; Bacteroidota; Bacteroidia; Sphingobacteriales; Sphingobacteriaceae; Pedobacter | 3.65 | 940 | 5,050.0 | 39.2 | 3,875 | 87.22/1.15 |
|
|
| B_bin_26_Tailings | Bacteria; Proteobacteria; Gammaproteobacteria; Burkholderiales; Burkholderiaceae; Hydrogenophaga | 2.17 | 260 | 9,728.0 | 65.0 | 2,246 | 67.46/3.97 |
|
|
| B_bin_25_Tailings | Bacteria; Proteobacteria; Alphaproteobacteria; Sphingomonadales; Sphingomonadaceae; Rhizorhabdus Rhizorhabdus sp018006725 | 3.02 | 737 | 5,123.0 | 65.8 | 3,274 | 81.71/4.07 |
|
|
| B_bin_24_Tailings | Bacteria; Bacteroidota; Bacteroidia; Flavobacteriales; | 2.03 | 180 | 21,039.0 | 35.7 | 2,056 | 80.65/1.43 |
|
|
| B_bin_22_Tailings | Bacteria; Proteobacteria; Alphaproteobacteria; | 1.43 | 773 | 1,970.0 | 57.6 | 1,871 | 57.66/1.08 |
|
|
| B_bin_21_Tailings | Bacteria; Proteobacteria; Alphaproteobacteria; Rhodobacterales; Rhodobacteraceae; EhC02 | 3.94 | 253 | 37,958.0 | 64.1 | 4,015 | 97.8/1.61 |
|
|
| B_bin_20_Tailings | Bacteria; Proteobacteria; Gammaproteobacteria; Burkholderiales; Burkholderiaceae; Quisquiliibacterium | 3.24 | 388 | 16,534.0 | 70.9 | 3,272 | 87.79/2.11 |
|
|
| B_bin_2_Tailings | Bacteria; Cyanobacteria; Sericytochromatia | 2.39 | 1083 | 16,039.000000000002 | 70.2 | 3,752 | 80.22/1.33 |
|
|
| B_bin_19_Tailings | Bacteria; Actinobacteriota; Thermoleophilia; Miltoncostaeales; Miltoncostaeaceae; | 2.89 | 427 | 6,178.0 | 72.7 | 2,402 | 91.82/1.08 |
|
|
| B_bin_18_Tailings | Bacteria; Proteobacteria; Gammaproteobacteria; Burkholderiales; Burkholderiaceae; Limnobacter Limnobacter sp001601825 | 1.85 | 1016 | 1,927.0 | 53.2 | 2,430 | 61.98/2.96 |
|
|
| B_bin_17_Tailings | Bacteria; Proteobacteria; Gammaproteobacteria; Burkholderiales; Burkholderiaceae; Giesbergeria Giesbergeria sp001770955 | 2.62 | 393 | 11,437.0 | 66.0 | 2,676 | 65.51/0.0 |
|
|
| B_bin_16_Tailings | Bacteria; Proteobacteria; Gammaproteobacteria; Burkholderiales; Burkholderiaceae; Pseudacidovorax Pseudacidovorax sp903864295 | 6.04 | 837 | 9,544.0 | 69.3 | 6,139 | 93.79/2.7 |
|
|
| B_bin_15_Tailings | Bacteria; Bdellovibrionota; Bdellovibrionia; Bdellovibrionales; Bdellovibrionaceae | 2.57 | 141 | 33,321.0 | 41.5 | 2,540 | 95.55/0.9 |
|
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| B_bin_14_Tailings | Bacteria; Proteobacteria; Gammaproteobacteria; JAHJQQ01; JAHJQQ01 | 3.36 | 427 | 2,465.0 | 73.6 | 2,982 | 64.57/8.15 |
|
|
| B_bin_13_Tailings | Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales; Pseudomonadaceae; Pseudomonas_E Pseudomonas_E sp002874965 | 6.98 | 218 | 5,6275.0 | 61.0 | 6,394 | 97.03/1.61 |
|
|
| B_bin_12_Tailings | Bacteria; Proteobacteria; Alphaproteobacteria; Azospirillales; Azospirillaceae; Azospirillum | 7.19 | 501 | 19,224.0 | 67.6 | 6,914 | 93.49/4.09 |
|
|
| B_bin_11_Tailings | Bacteria; Bdellovibrionota; Bacteriovoracia; Bacteriovoracales; Bacteriovoracaceae; UBA6144 | 3.01 | 131 | 41,998.0 | 44.6 | 3,142 | 82.06/0.94 |
|
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| B_bin_10_Tailings | Bacteria; Proteobacteria; Gammaproteobacteria; Immundisolibacterales; Immundisolibacteraceae; Immundisolibacter | 2.64 | 436 | 11,746.0 | 68.2 | 2,800 | 72.75/0.0 |
|
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| B_bin_1_Tailings | Bacteria; Actinobacteriota; Acidimicrobiia; Acidimicrobiales; JACDCH01 | 2.06 | 219 | 76,480.0 | 65.8 | 3,795 | 90.93/1.67 |
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Keywords
platinum mine tailingsheavy metalsbioremediationmetagenomics
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Taxonomy
TopicsGenomics and Phylogenetic Studies · Microbial Community Ecology and Physiology · Metal Extraction and Bioleaching
Full text
ANNOUNCEMENT
The mining industry in South Africa draws upon vast platinum, gold, coal, and diamond reserves (1). However, mining introduces toxic metals, suppresses soil regeneration, and challenges microbial survival (2–4). Many soil microbes remain uncultured, so metagenomics is crucial for revealing their diversity and functions, informing strategies for remediation, metal recovery, and sustainable mining (5–9).
We collected tailings dam samples from two platinum mines on the western limb of the Bushveld Igneous Complex, one 30 km northwest of Rustenburg in the North West Province (B) and the other 30 km south of Thabazimbi in Limpopo Province (N). Samples of the tailings were collected from the surface (10–15 cm deep) of each tailings dam using aseptic techniques, and soil samples (BC, NC) were also collected from non-mining areas. Genomic DNA was extracted from 0.25 g of each sample using the DNeasy PowerSoil kit (MO BIO Laboratories, USA). Sample integrity was verified with the Agilent 5400 fragment analyzer. Genomic DNA was sheared, end-repaired, A-tailed, adapter-ligated, PCR-amplified, size-selected, and purified. Libraries were prepared using the NEBNext Ultra II library preparation kit as per manufacturer’s instructions and were quantified (Qubit, qPCR, bioanalyzer), pooled, and sequenced on an Illumina MiSeq PE 250 bp platform by Novogene (Singapore).
Metagenome sequencing yielded a total of 181,695,000 paired-end reads across all samples (range: 18,914,000–27,873,000 reads per sample). Low-quality reads and adapters were removed with Trimmomatic v0.39 (5). Cleaned reads were taxonomically classified using Kraken2 v2.1.1 and Bracken v2.6.2 (10). Identified taxa were dominated by Bacteria, with minor proportions of Archaea, Eukarya, and Viruses. Quality-filtered reads were assembled via metaSPAdes v3.15.3 (11). Contigs ≥1,000 bp were binned using MaxBin v2.0 (12), metaBAT2 v2.8 (13), and CONCOCT v1.0.07 (14), then refined with MetaWRAP v1.3.2 (15). CheckM v1.2.218 was used to evaluate the completeness of the metagenome-assembled genomes (MAGs) and all demonstrated ≥50% completeness and ≤10% contamination (16), 42 of the 84 MAGs had high completeness levels (≤80%). The retained bins underwent phylogenomic analysis and taxonomic assignment via GTDB-tk v1.749 (17) and were functionally annotated with DRAM v0.1.2 (18) (Fig. 1). Default parameters were used for all software, unless otherwise stated. The recovered MAGs spanned 15 bacterial classes and 48 genera, whereas the read-base analysis spanned 13 bacterial classes and 67 genera (Table 1). From both analyses, Pseudomonas had higher abundance levels reflecting its pollutant-degrading capacity (19).
DRAM annotations of the MAGs recovered from platinum mine tailings in South Africa.
Bibliography19
The reference list from the paper itself. Each links out to its DOI / PubMed record.
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