Cultivable Microbiota Associated with Gold Ore from the Rozália Gold Mine, Hodruša-Hámre, Slovakia

References

• Akcil A, Mudder T. 2003. Microbial destruction of cyanide wastes in gold mining: process review. Biotechnol Lett 25(6):445–450.
   PubMed Web of Science ®Google Scholar
• Anderson CR, Cook GM. 2004. Isolation and characterization of arsenate-reducing bacteria from arsenic-contaminated sites in New Zealand. Curr Microbiol 48(5):341–347.
   PubMed Web of Science ®Google Scholar
• Baker BJ, Moser DP, MacGregor BJ, Fishbain B, Wagner M, Fry NK, Jackson B, Speolstra N, Loos S, Takai K, et al. 2003. Related assemblages of sulphate-reducing bacteria associated with ultradeep gold mines of South Africa and deep basalt aquifers of Washington State. Environ Microbiol 5(4):267–277.
   PubMed Web of Science ®Google Scholar
• Barba C, Folch A, Sanchez-Vila X, Martínez-Alonso M, Gaju N. 2019. Are dominant microbial sub-surface communities affected by water quality and soil characteristics? J Environ Manage 237:332–343.
   PubMed Web of Science ®Google Scholar
• Bartelme RP, Custer JM, Dupont CHL, Espinoza JL, Torralba M, Khalili B, Carini P. 2020. Influence of substrate concentration on the culturability of heterotrophic soil microbes isolated by high-throughput dilution-to-extinction cultivation. mSphere 5(1):e00024–20.
   PubMed Web of Science ®Google Scholar
• Cornejo M, Pretell K, Arévalo A, Sernaqué Y, Mialhe E. 2015. Culture/co-culture dependent and independent identification of bacterial communities along a chronosequence of spontaneous reclamation on gold mine spoils in Peru. AMR 1130:589–593.
   Google Scholar
• Das R, Kazy SK. 2014. Microbial diversity, community composition and metabolic potential in hydrocarbon contaminated oily sludge: prospects for in situ bioremediation. Environ Sci Pollut Res Int 21(12):7369–7389.
   PubMed Web of Science ®Google Scholar
• Djurić A, Gojgić-Cvijović G, Jakovljević D, Kekez B, Kojić JS, Mattinen M-L, Harju IE, Vrvić MM, Beškoski VP. 2017. Brachybacterium sp. CH-KOV3 isolated from an oil-polluted environment-a new producer of levan. Int J Biol Macromol 104(Pt A):311–321.
   PubMed Web of Science ®Google Scholar
• Drewniak L, Styczek A, Majder-Lopatka M, Sklodowska A. 2008. Bacteria, hypertolerant to arsenic in the rocks of an ancient gold mine, and their potential role in dissemination of arsenic pollution. Environ Pollut 156(3):1069–1074.
   PubMed Web of Science ®Google Scholar
• Ellis RJ, Morgan P, Weightman AJ, Fry JC. 2003. Cultivation-dependent and -independent approaches for determining bacterial diversity in heavy-metal-contaminated soil. Appl Environ Microbiol 69(6):3223–3230.
   PubMed Web of Science ®Google Scholar
• Fernandes CC, Kishi LT, Lopes EM, Omori WP, Souza JAM, Alves LMC, Lemos EGM. 2018. Bacterial communities in mining soils and surrounding areas under regeneration process in a former ore mine. Braz J Microbiol 49(3):489–502.
   PubMed Web of Science ®Google Scholar
• Georgiev GZ. 2020. Chi-square calculator [online]. Accessed October 30, 2020. Available at https://www.gigacalculator.com/calculators/chi-square-calculator.php.
   Google Scholar
• Gericke M, Pinches A. 2006. Microbial production of gold nanoparticles. Gold Bull 39(1):22–28.
   Web of Science ®Google Scholar
• Greenblatt C, Baum J, Klein BY, Nachshon S, Koltunov V, Cano RJ. 2004. Micrococcus luteus – survival in amber. Microb Ecol 48(1):120–127.
   PubMed Web of Science ®Google Scholar
• Grigor’eva NV, Kondrat’eva TF, Krasil’nikova EN, Karavaiko GI. 2006. Mechanism of cyanide and thiocyanate decomposition by an association of Pseudomonas putida and Pseudomonas stutzeri strains. Microbiology 75(3):266–273.
   Web of Science ®Google Scholar
• Hammer Ø, Harper DAT, Ryan PD. 2001. PAST: Paleontological statistics software package for education and data analysis. Palaeontol Electron 4(1).
   Google Scholar
• Hirayama H, Takai K, Inagaki F, Yamato Y, Suzuki M, Nealson KH, Horikoshi K. 2005. Bacterial community shift along a subsurface geothermal water stream in a Japanese gold mine. Extremophiles. 9(2):169–184.
   PubMed Web of Science ®Google Scholar
• Hlaing PPT, Junqueira ACM, Uchida A, Purbojati RW, Houghton JNI, Chénard C, Wong A, Clare ME, Kushwaha KK, Putra A, et al. 2019. Complete genome sequence of Brachybacterium sp. strain SGAir0954, isolated from Singapore Air. Microbiol Resour Announc 8(32):e00619–19.
   PubMed Web of Science ®Google Scholar
• Huang X, Madan A. 1999. CAP3: a DNA sequence assembly program. Genome Res. 9(9):868–877.
   PubMed Web of Science ®Google Scholar
• Inagaki F, Takai K, Hirayama H, Yamato Y, Nealson KH, Horikoshi K. 2003. Distribution and phylogenetic diversity of the subsurface microbial community in a Japanese epithermal gold mine. Extremophiles 7(4):307–317.
   PubMed Web of Science ®Google Scholar
• Jamal Q, Ahmed I, Rehman SU, Abbas S, Kim KY, Anees M. 2016. Isolation and characterization of bacteria from coal mines of Dara Adam Khel, Pakistan. Geomicrobiol J. 33(1):1–9.
   Web of Science ®Google Scholar
• Jiang Y, Li Q, Chen X, Jiang C. 2016. Actinobacteria – basics and biotechnological applications: isolation and cultivation methods of Actinobacteria. Croatia: InTech.
   Google Scholar
• Kaksonen A, Mudunuru BM, Hackl R. 2014. The role of microorganisms in gold processing and recovery—a review. Hydrometallurgy 142:70–83.
   Web of Science ®Google Scholar
• Karelova E, Harichova J, Stojnev T, Pangallo D, Ferianc P. 2011. The isolation of heavy-metal resistant culturable bacteria and resistance determinants from a heavy-metal-contaminated site. Biologia 66(1):18–26.
   Web of Science ®Google Scholar
• Khamar Z, Makhdoumi-Kakhki A, Mahmudy Gharaie MH. 2015. Remediation of cyanide from the gold mine tailing pond by a novel bacterial co-culture. Int Biodeterior Biodegradation 99:123–128.
   Web of Science ®Google Scholar
• Koděra P, Lexa J, Rankin AH, Fallick AE. 2005. Epithermal gold veins in a caldera setting: Banská Hodruša. Miner Deposita 39(8):921–943.
   Web of Science ®Google Scholar
• Kubač A, Chovan M, Koděra P, Kyle JR, Žitňan P, Lexa J, Vojtko R. 2018. Mineralogy of the epithermal precious and base metal deposit Banská Hodruša at the Rozália Mine (Slovakia). Miner Petrol 112(5):705–731.
   Web of Science ®Google Scholar
• Letnik I, Avrahami R, Port R, Greiner A, Zussman E, Rokem JS, Greenblatt C. 2017. Biosorption of copper from aqueous environments by Micrococcus luteus in cell suspension and when encapsulated. Int Biodeterior Biodegradation 116:64–72.
   Web of Science ®Google Scholar
• Li M, Haixia T, Wang L, Duan J. 2017. Bacterial diversity in Linglong gold mine, China. Geomicrobiol J 34(3):267–273.
   Web of Science ®Google Scholar
• Lin LH, Hall J, Onstott T, Gihring T, Lollar BS, Boice E, Pratt L, Lippmann-Pipke J, Bellamy RES. 2006. Planktonic microbial communities associated with fracture-derived groundwater in a deep gold mine of South Africa. Geomicrobiol J 23(6):475–497.
   Web of Science ®Google Scholar
• Lors C, Ryngaert A, Périé F, Diels L, Damidot D. 2010. Evolution of bacterial community during bioremediation of PAHs in a coal tar contaminated soil. Chemosphere 81(10):1263–1271.
   PubMed Web of Science ®Google Scholar
• Maldonado J, Diestra E, Huang L, Domenech AM, Villagrasa E, Puyen ZM, Duran R, Esteve I, Sole A. 2010. Isolation and identification of a bacterium with high tolerance to lead and copper from a marine microbial mat in Spain. Ann Microbiol 60(1):113–120.
   Web of Science ®Google Scholar
• Maltman C, Piercey-Normore MD, Yurkov V. 2015. Tellurite-, tellurate-, and selenite-based anaerobic respiration by strain CM-3 isolated from gold mine tailings. Extremophiles. 19(5):1013–1019.
   PubMed Web of Science ®Google Scholar
• McGivney E, Gao X, Liu Y, Lowry GV, Casman E, Gregory KB, VanBriesen JM, Avellan A. 2019. Biogenic cyanide production promotes dissolution of gold nanoparticles in soil. Environ Sci Technol. 53(3):1287–1295.
   PubMed Web of Science ®Google Scholar
• Metsalu T, Vilo J. 2015. ClustVis: a web tool for visualizing clustering of multivariate data using principal component analysis and heatmap. Nucleic Acids Res 43(W1):W566–W570.
   PubMed Web of Science ®Google Scholar
• Missiakas DM, Schneewind O. 2018. Growth and laboratory maintenance of Staphylococcus aureus. Curr Protoc Microbiol 9:Unit 9C.1-9C.1.9.
   Google Scholar
• Nema P, Paul D, Karmalkar NR, Shouche YS. 2019. Bacterial diversity in the metal-rich terrestrial deep subsurface sediments of Krishna Godavari Basin, India. Geomicrobiol J 36(10):917–932.
   Web of Science ®Google Scholar
• Niewerth H, Schuldes J, Parschat K, Kiefer P, Vorholt JA, Daniel R, Fetzner S. 2012. Complete genome sequence and metabolic potential of the quinaldine-degrading bacterium Arthrobacter sp. Rue61a. BMC Genomics 13(1):534.
   PubMed Web of Science ®Google Scholar
• Ohadi M, Forootanfar H, Dehghannoudeh G, Eslaminejad T, Ameri A, Shakibaie M, Najafi A. 2020. Biosynthesis of gold nanoparticles assisted by lipopeptide biosurfactant derived from Acinetobacter junii B6 and evaluation of its antibacterial and cytotoxic activities. BioNanoSci 10(4):899–908.
   Web of Science ®Google Scholar
• Parmar TK, Rawtani D, Agrawal YK. 2016. Bioindicators: the natural indicator of environmental pollution. Front Life Sci 9(2):110–118.
   Web of Science ®Google Scholar
• Pires C, Franco AR, Pereira SIA, Henriques I, Correia A, Magan N, Castro PML. 2017. Metal(loid)-contaminated soils as a source of culturable heterotrophic aerobic bacteria for remediation applications. Geomicrobiol J 34(9):760–768.
   Web of Science ®Google Scholar
• Popovic NT, Kazazic SP, Strunjak-Perovic I, Coz-Rakovac R. 2017. Differentiation of environmental aquatic bacterial isolates by MALDI-TOF MS. Environ Res 152:7–16.
   PubMed Web of Science ®Google Scholar
• Rana S, Mishra P, Wahid Z, Thakur S, Pant D, Singh L. 2020. Microbe-mediated sustainable bio-recovery of gold from low-grade precious solid waste: a microbiological overview. J Environ Sci 89:47–64.
   Web of Science ®Google Scholar
• Rastogi G, Muppidi GL, Gurram RN, Adhikari A, Bischoff KM, Hughes SR, Apel WA, Bang SS, Dixon DJ, Sani RK. 2009b. Isolation and characterization of cellulose-degrading bacteria from the deep subsurface of the Homestake gold mine, Lead, South Dakota, USA. J Ind Microbiol Biotechnol 36(4):585–589.
   PubMed Web of Science ®Google Scholar
• Rastogi G, Osman S, Kukkadapu R, Engelhard M, Vaishampayan PA, Andersen GL, Sani RK. 2010. Microbial and mineralogical characterizations of soils collected from the deep biosphere of the former Homestake gold mine, South Dakota. Microb Ecol 60(3):539–550.
   PubMed Web of Science ®Google Scholar
• Rastogi G, Stetler LD, Peyton BM, Sani RK. 2009a. Molecular analysis of prokaryotic diversity in the deep subsurface of the former Homestake gold mine, South Dakota, USA. J Microbiol 47(4):371–384.
   PubMed Web of Science ®Google Scholar
• Rawlings DE. 2002. Heavy metal mining using microbes. Annu Rev Microbiol 56(1):65–91.
   PubMed Web of Science ®Google Scholar
• Rea MA, Zammit CM, Reith F. 2016. Bacterial biofilms on gold grains – implication for geomicrobial transformations of gold. Fems Microbiol Ecol 92(6):fiw082.
   PubMed Web of Science ®Google Scholar
• Reith F, Falconer DM, Van Nostrand J, Craw D, Shuster J, Wakelin S. 2020. Functional capabilities of bacterial biofilms on gold particles. FEMS Microbiol Ecol 96(1):fiz196.
   PubMed Web of Science ®Google Scholar
• Reith F, Lengke M, Falconer D, Craw D, Southam G. 2007. The geomicrobiology of gold. ISME J 1(7):567–584.
   PubMed Web of Science ®Google Scholar
• Reith F, Rea MAD, Sawley P, Zammit CM, Nolze G, Reith T, Rantanen K, Bissett A. 2018. Biogeochemical cycling of gold: Transforming gold particles from arctic Finland. Chem Geol 483:511–529.
   Web of Science ®Google Scholar
• Sait M, Hugenholtz P, Janssen PH. 2002. Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys. Environ Microbiol 4(11):654–666.
   PubMed Web of Science ®Google Scholar
• Sar P, Dutta A, Bose H, Mandal S, Kazy SK. 2019. Deep biosphere: microbiome of the deep terrestrial subsurface. Microbial diversity in ecosystem sustainability and biotechnological applications. Singapore: Springer.
   Google Scholar
• Schoenborn L, Yates PS, Grinton BE, Hugenholtz P, Janssen PH. 2004. Liquid serial dilution is inferior to solid media for isolation of cultures representative of the phylum-level diversity of soil bacteria. Appl Environ Microbiol 70(7):4363–4366.
   PubMed Web of Science ®Google Scholar
• Sejkora J, Stevko M, Ozdin D, Prsek J, Jelen S. 2015. Unusual morphological forms of hodrušite from the Rozália vein, Hodruša – Hámre, near Banská Štiavnica (Slovac Republic). J Geosci 60:11–12.
   Web of Science ®Google Scholar
• Seuylemezian A, Aronson HS, Tan J, Lin M, Schubert W, Vaishampayan P. 2018. Development of a custom MALDI-TOF MS database for species-level identification of bacterial isolates collected from spacecraft and associated surfaces. Front Microbiol 9:780.
   PubMed Web of Science ®Google Scholar
• Shannon CE. 1948. A mathematical theory of communication (Reprinted with correction). Bell Syst Tech J 27(3):379–423.
   Google Scholar
• Sibanda T, Selvarajan R, Tekere M. 2017. Synthetic extreme environments: overlooked sources of potential biotechnologically relevant microorganisms. Microb Biotechnol 10(3):570–585.
   PubMed Web of Science ®Google Scholar
• Spitaels F, Wieme A, Vandamme P. 2016. MALDI-TOF MS as a novel tool for dereplication and characterization of microbiota in bacterial diversity studies. In: Demirev, P, Sandrin, T, editor. Applications of Mass Spectrometry in Microbiology. Cham, Germany: Springer.
   Google Scholar
• Stevko M, Sejkora J, Macek I. 2015. Unusual morphological type of gold from the Rozália mine, Hodruša-Hámre (Slovac Republic). Bull Miner Petrolog 23:26–29.
   Google Scholar
• Stevovic S, Miloradovic M, Stevovic I. 2014. Management of environmental quality and Kostolac mine areas natural resources usage. Manag Environ Qual Int J. 25(3):285–300.
   Google Scholar
• Stewart EJ. 2012. Growing unculturable bacteria. J Bacteriol 194(16):4151–4160.
   PubMed Web of Science ®Google Scholar
• Swaroop BS, Victoria SN, Manivannan R. 2016. Azadirachta indica leaves extract as inhibitor for microbial corrosion of copper by Arthrobacter sulfureus in neutral pH conditions – a remedy to blue green water problem. J Taiwan Inst Chem Engrs 64:269–278.
   Web of Science ®Google Scholar
• Takai K, Moser DP, Onstott TC, Spoelstra N, Pfiffner SM, Dohnalkova A, Fredrickson JK. 2001. Alkaliphilus transvaalensis gen. nov., sp. nov., an extremely alkaliphilic bacterium isolated from a deep South African gold mine. Int J Syst Evol Microbiol 51(Pt 4):1245–1256.
   PubMed Web of Science ®Google Scholar
• Timperio AM, Gorrasi S, Zolla L, Fenice M. 2017. Evaluation of MALDI-TOF mass spectrometry and MALDI BioTyper in comparison to 16S rDNA sequencing for the identification of bacteria isolated from Arctic sea water. PLOS One 12(7):e0181860.
   PubMed Web of Science ®Google Scholar
• Tiwari S, Nanda M. 2019. Bacteremia caused by Comamonas testosteroni an unusual pathogen. J Lab Phys 11(1):87–90.
   Google Scholar
• Tomczyk - Zak K, Kaczanowski S, Drewniak L, Dmoch L, Sklodowska A, Zielenkiewicz U. 2013. Bacterial diversity and arsenic mobilization in rock biofilm from an ancient gold and arsenic mine. Sci Total Environ 461–462(1):330–340.
   PubMed Web of Science ®Google Scholar
• Uniyal S, Rawat M, Rai JPN. 2013. Cadmium biosorption by Stenotrophomonas humi and Micrococcus luteus: kinetics, equilibrium and thermodynamic studies. Desal Water Treat 51(40–42):7721–7731.
   Web of Science ®Google Scholar
• Wang Q, Garrity GM, Tiedje TM, Cole JR. 2007. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73(16):5261–5267.
   PubMed Web of Science ®Google Scholar
• Weisburg W, Barns SM, Pelletier DA, Lane DJ. 1991. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173(2):697–703.
   PubMed Web of Science ®Google Scholar
• White LO. 1972. The taxonomy of crown-gall organism Agrobacterium tumefaciens and its relationship to Rhizobia and other Agrobacteria. J Gen Microbiol 72(3):565–574.
   Google Scholar
• Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J. 2017. Introducing EzBioCloud: A taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 67(5):1613–1617.
   PubMed Web of Science ®Google Scholar
• Young J, Kuykendall LD, Martinez-Romero E, Kerr A, Sawada H. 2001. A revision of Rhizobium Frank 1889, with an emended description of the genus, and the inclusion of all species of Agrobacterium Conn 1942 and Allorhizobium undicola de Lajudie et al. 1998 as new combinations: Rhizobium radiobacter, R. rhizogenes, R. rubi, R. undicola and R. vitis. Int J Syst Evol Microbiol 51(Pt 1):89–103.
   PubMed Web of Science ®Google Scholar
• Zagury G, Oudjehani K, Deschenes L. 2004. Characterization and availability of cyanide in solid mine tailings from gold extraction plants. Sci Total Environ 320(2–3):211–224.
   PubMed Web of Science ®Google Scholar
• Zhao B, Liao L, Yu Y, Chen B. 2017. Complete genome of Brachybacterium sp. P6-10-X1 isolated from deep-sea sediments of the Southern Ocean. Mar Genomics 35:27–29.
   Web of Science ®Google Scholar
• Zhou W, Niu D, Zhang Z, Liu Y, Ning M, Cao X, Zhang CH, Shen H. 2016. Complete genome sequence of Aerococcus urinaeequi Strain AV208. Genome Announce 4(5):e01218-16.
   PubMedGoogle Scholar