Nontuberculous mycobacteria (NTM) are widely distributed in the environment. On one hand, they are opportunistic pathogens for humans and animals, and on the other hand, they are effective in biodegradation of some persistent pollutants. Following the recently recorded large abundance of NTM in extreme geothermal environments, the aim of the study was to ascertain the occurrence of NTM in the extreme environment of the water zone of the Hranice Abyss (HA). The HA mineral water is acidic, with large concentrations of free CO2, and bacterial slimes creating characteristic mucilaginous formations. Both culture and molecular methods were used to compare the mycobacterial diversity across the linked but distinct ecosystems of HA and the adjacent Zbrašov Aragonite Caves (ZAC) with consideration of their pathogenic relevance. Six slowly growing NTM species (M. arupense, M. avium, M. florentinum, M. gordonae, M. intracellulare) and two rapidly growing NTM species (M. mucogenicum, M. sediminis) were identified in the water and in the dry zones at both sites. Proteobacteria were dominant in all the samples from both the HA and the ZAC. The bacterial microbiomes of the HA mineral water and HA slime were similar, but both differed from the microbiome in the ZAC mineral water. Actinobacteria, a phylum containing mycobacteria, was identified in all the samples at low proportional abundance. The majority of the detected NTM species belong among environmental opportunistic pathogens.

Faculty of AgriSciences Mendel University in Brno Zemedelska 1 613 00 Brno Czech Republic

Faculty of Pharmacy University of Veterinary and Pharmaceutical Sciences Brno Palackeho tr 1 612 42 Brno Czech Republic

Faculty of Regional Development and International Studies Mendel University in Brno tr Generala Piky 7 61300 Brno Czech Republic

Faculty of Science Masaryk University Kotlarska 2 611 37 Brno Czech Republic

Public Health Institute Ostrava Partyzanske nam 7 702 00 Ostrava Czech Republic

School of Science and the Environment Memorial University of Newfoundland 20 University Drive Corner Brook A2H 5G4 Canada

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Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410 DOI

Band JD, Ward JI, Fraser DW, Peterson NJ, Silcox VA, Good RC, Ostroy PR, Kennedy J (1982) Peritonitis due to a Mycobacterium chelonei-like organism associated with intermittent chronic peritoneal dialysis. J Infect Dis 145:9–17 DOI

Barton HA, Taylor NM, Kreate MP, Springer AC, Oehrle SA, Bertog JL (2007) The impact of host rock geochemistry on bacterial community structure in oligotrophic cave environments. Int J Speleol 36:93–104 DOI

Bernardet J-F (2015) Flavobacteriales ord. nov. In Bergey’s Manual of Systematics of Archaea and Bacteria, John Wiley & Sons, Inc., in association with Bergey’s Manual Trust. p 1–2. https://doi.org/10.1002/9781118960608.obm00033

Bland CS, Ireland JM, Lozano E, Alvarez ME, Primm TP (2005) Mycobacterial ecology of the Rio Grande. Appl Environ Microbiol 71:5719–5727 DOI

Bomberg M, Lamminmäki T, Itävaara M (2016) Microbial communities and their predicted metabolic characteristics in deep fracture groundwaters of the crystalline bedrock at Olkiluoto, Finland. Biogeosciences 13:6031–6047 DOI

Brooks RW, Parker BC, Gruft H, Falkinham JO III (1984) Epidemiology of infection by non-tuberculous mycobacteria. V. Numbers in eastern United States soils and correlation with soil characteristics. Am Rev Respir Dis 130:630–633

Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335–336 DOI

Caroli G, Levre’ E, Armani G, Biffi-Gentili S, Molinari G (1985) Search for acid-fast bacilli in bottled mineral waters. J Appl Bacteriol 58:461–464 DOI

Chan ED, Iseman MD (2009) Slender, older women appear to be more susceptible to nontuberculous mycobacterial lung disease. Gend Med 7:5–18 DOI

Cook GM, Berney M, Gebhard S, Heinemann M, Cox RA, Danilchanka O, Niederwis M (2009) Physiology of mycobacteria. Adv Microb Physiol 55:81–319 DOI

De Mandal S, Panda AK, Lalnunmawii E, Bisht SS Kumar NS (2015a) Illumina-based analysis of bacterial community in Khuangcherapuk Cave of Mizoram, Northeast India. Genom Data 5:13–14. https://doi.org/10.1016/j.gdata.2015.04.023 DOI

De Mandal S, Sanga Z, Kumar NS (2015b) Metagenome sequencing reveals Rhodococcus dominance in Farpuk Cave, Mizoram, India, an Eastern Himalayan biodiversity hot spot region. Genome Announc 3:e00610-15. https://doi.org/10.1128/genomeA.00610-15 DOI

De Mandal S, Zothansanga PAK, Bisht SS, Kumar NS (2015c) First report of bacterial community from a bat guano using Illumina next-generation sequencing. Genom Data 4:99–101. https://doi.org/10.1016/j.gdata.2015.04.001 DOI

De Mandal S, Chatterjee R, Kumar NS (2017) Dominant bacterial phyla in caves and their predicted functional roles in C and N cycle. BMC Microbiol 17:90. https://doi.org/10.1186/s12866-017-1002-x DOI

Dimov I, Gonzalez E (1986) Sources of cattle infection with atypical mycobacteria and the frequency of their isolation from healthy slaughter animals in Cienfuegos Province, Cuba. Vet Med Nauki 23:47–52

Eberl L, Vandamme P (2016) Members of the genus Burkholderia: good and bad guys. F1000Res 5. https://doi.org/10.12688/f1000research.8221.1

Engbaek HC, Vergmann B, Weis Bentzon B (1967) The sodium lauryl sulphate method in culturing sputum for mycobacteria. Scand J Respir Dis 48:268–284

Estrada-De Los Santos P, Bustillos-Cristales R, Caballero-Mellado J (2001) Burkholderia, a genus rich in plant-associated nitrogen fixers with wide environmental and geographic distribution. Appl Environ Microbiol 67:2790–2798 DOI

Falkinham JO III (2009) Surrounded by mycobacteria: nontuberculous mycobacteria in the human environment. J Appl Microbiol 107:356–367 DOI

Falkinham JO III (2016) Current epidemiologic trends of the nontuberculous mycobacteria (NTM). Curr Environ Health Rep 3:161–167 DOI

Fleming EJ, Cetinic I, Chan CS, King DW, Emerson D (2014) Ecological succession among iron-oxidizing bacteria. ISME J 8:804–815 DOI

Gersl M (2009) Hranice Karst. In: Hromas J (ed) Caves CR, Protected natural area CR, vol 15. Czech Republic, Agentura Ochrany Prirody a Krajiny CR & EkoCentrum Brno, pp 365–367 (in Czech)

Gersl M (2016) Discrimination of the Hranice karst waters (Czech Republic) based on the archival data. Geoscience Research Reports 49:247–252. https://doi.org/10.3140/zpravy.geol.2016.25 DOI

Gersl M, Hladil J, Hypr D, Stepisnik U (2004) Variability of carbon dioxide concentrations in Zbrašov Aragonite Caves and its assessment on the base of nine-year monitoring research. In Gersl M (ed) proceedings of the 3rd National Speleological Congress, Czech speleological. Society:15–19

Gersl M, Kosina M, Sedlacek I, Novakova D, Travenec F (2007) Biodiversity of culturable prokaryotes from the Hranice Abyss and the role of microorganisms in carbonate speleothemes forming. Geol Výzk Mor Slez v r 2006. Brno 14:86–91

Ghaemi E, Ghazisaidi K, Koohsari H, Khodabakhshi B, Mansoorian A (2006) Environmental mycobacteria in areas of high and low tuberculosis prevalence in the Islamic Republic of Iran. East Mediterr Health J 12:280–285

Hammer Ø, Harper DAT, Ryan PD (2001) PAST: paleontological statistics software package for education and data analysis. Palaeontol Electron http://palaeo-electronica.org/2001_1/past/issue1_01.htm

Hennessee CT, Li QX (2016) Effects of polycyclic aromatic hydrocarbon mixtures on degradation, gene expression, and metabolite production in four Mycobacterium species. Appl Environ Microbiol 82:3357–3369 DOI

Ichiyama S, Shimokata K, Tsukamura M (1988) The isolation of Mycobacterium avium complex from soil, water, and dust. Microbiol Immunol 32:733–739 DOI

Iino T (2014) The family Ignavibacteriaceae. In: Rosenberg E, EF DL, Lory S, Stackebrandt E, Thompson F (eds) The prokaryotes: Other major lineages of bacteria and the Archaea, 4th edn. Springer, Berlin, pp 701–703

Iivanainen EK, Martikainen PJ, Väänänen PK, Katila M-L (1993) Environmental factors affecting the occurrence of mycobacteria in brook waters. Appl Environ Microbiol 59:398–404

Iivanainen EK, Martikainen PJ, Räisänen ML, Katila M-L (1997) Mycobacteria in boreal coniferous forest soils. FEMS Microbiol Ecol 23:325–332 DOI

Iivanainen EK, Martikainen PJ, Väänänen PK, Katila M-L (1999) Environmental factors affecting the occurrence of mycobacteria in brook sediments. Appl Environ Microbiol 86:673–681 DOI

Ikner LA, Toomey RS, Nolan G, Neilson JW, Pryor BM, Maier RM (2007) Culturable microbial diversity and the impact of tourism in Kartchner Caverns, Arizona. Microb Ecol 53:30–42 DOI

Jetten MS, den Camp HJO, Gijs Kuenen J, Strous M (2015) “Candidatus Brocadiales” ord. nov, In Bergey’s Manual of Systematics of Archaea and Bacteria, John Wiley & Sons, Inc., in association with Bergey’s Manual Trust. p 1. https://doi.org/10.1002/9781118960608.obm00068

Jones RT (2015) A comprehensive survey of soil Rhizobiales diversity using high-throughput DNA sequencing. In: de Bruijn FJ (ed) Biological Nitrogen Fixation. John Wiley & Sons Inc, Hoboken, pp 769–776 DOI

Juni E, Bøvre K (2015) Moraxella. In Bergey’s Manual of Systematics of Archaea and Bacteria. John Wiley & Sons, Inc., in association with Bergey's Manual p 1–17. doi: https://doi.org/10.1002/9781118960608.gbm01204

Kato S, Krepski S, Chan C, Itoh T, Ohkuma M (2014) Ferriphaselus amnicola gen. nov., sp. nov., a neutrophilic, stalk-forming, iron-oxidizing bacterium isolated from an iron-rich groundwater seep. Int J Syst Evol Microbiol 64:921–925 DOI

Kazda J (2000) The ecology of mycobacteria. Kluwer Academic Publishers, Dordrecht DOI

Kazda J, Pavlik I, Falkinham JO, Hruska K (2009) The ecology of mycobacteria: impact on Animal’s and Human’s health. Springer, New York DOI

Kielak AM, Barreto CC, Kowalchuk GA, van Veen JA, Kuramae EE (2016) The ecology of Acidobacteria: moving beyond genes and genomes. Front Microbiol 7:744. https://doi.org/10.3389/fmicb.2016.00744 DOI

Kirschner RA Jr, Parker BC, Falkinham JO III (1992) Epidemiology of infection by nontuberculous mycobacteria Mycobacterium avium, Mycobacterium intracellulare, and Mycobacterium scrofulaceum in acid, brown-water swamps of the southeastern United States and their association with environmental variables. Am Rev Respir Dis 145:271–275 DOI

Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, Glöckner FO (2013) Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res 41:e1–e11. https://doi.org/10.1093/nar/gks808 DOI

Kušar D, Zajc U, Jenčič V, Ocepek M, Higgins J, Žolnir-Dovč M, Pate M (2017) Mycobacteria in aquarium fish: results of a 3-year survey indicate caution required in handling pet-shop fish. J Fish Dis 40:773–784 DOI

Leclerc MC, Thomas F, Guegan JF (2003) Evidence for phylogenetic inheritance in pathogenicity of Mycobacterium. Anton Leeuw Int J G 83:265–274 DOI

Lewis AH, Falkinham JO III (2015) Microaerobic growth and anaerobic survival of Mycobacterium avium, Mycobacterium intracellulare and Mycobacterium scrofulaceum. Int J Mycobacteriol 4:25–30 DOI

Liu T, Liu S, Zheng M, Chen Q, Ni J (2016) Performance assessment of full-scale wastewater treatment plants based on seasonal variability of microbial communities via high-throughput sequencing. PLoS One 11:e0152998. https://doi.org/10.1371/journal.pone.0152998 DOI

Lukins HB, Foster JW (1963) Utilization of hydrocarbons and hydrogen by mycobacteria. Z Allg Mikrobiol 3:251–264 DOI

McInerney MJ, Stams AJM, Boone DR (2015) Syntrophobacter. In Bergey’s Manual of Systematics of Archaea and Bacteria, John Wiley & Sons, Inc., in association with Bergey's Manual Trust. p 1–10. https://doi.org/10.1002/9781118960608.gbm01068

Meyberg M, Rinne B (1995) Messung des 3He/4He-Isotopenverhältnisses im Hranicka Propast (Tschechische Republik). Die Höhle Zeitschrift für Karst und Höhlenkunde 46:5–8

Modra H, Bartos M, Hribova P, Ulmann V, Hubelova D, Konecny O, Gersl M, Kudelka J, Voros D, Pavlik I (2017) Detection of mycobacteria in the environment of the Moravian Karst (Bull Rock Cave and the relevant water catchment area): the impact of water sediment, earthworm castings and bat guano. Vet Med-Czech 62:153–168 DOI

Muangchinda C, Yamazoe A, Polrit D, Thoetkiattikul H, Mhuantong W, Champreda V, Pinyakong O (2017) Biodegradation of high concentrations of mixed polycyclic aromatic hydrocarbons by indigenous bacteria from a river sediment: a microcosm study and bacterial community analysis. Environ Sci Pollut Res 24:4591–4602 DOI

Mukai T, Miyamoto Y, Yamazaki T, Makino M (2006) Identification of Mycobacterium species by comparative analysis of the dnaA gene. FEMS Microbiol Lett 254:232–239 DOI

Musil J (2017) The Hranice Abyss became the deepest underwater abyss in the world! In: Bosak P, Gersl M, Novotna J (eds) Speleoforum vol. 36. Proceedings from Meeting of cavers in the Moravian Karst. Czech Speleological Society, Sloup, pp 10–15

National Center for Biotechnology Information (NCBI) BLAST Analysis. http://blast.ncbi.nlm.nih.gov/Blast.cgi . Accessed July 27, 2016

Nelson MB, Berlemont R, Martiny AC, Martiny JBH (2015) Nitrogen cycling potential of a grassland litter microbial community. Appl Environ Microbiol 81:7012–7022 DOI

Neumann M, Schulze-Robbecke R, Hagenau C, Behringer K (1997) Comparison of methods for isolation of Mycobacteria from water. Appl Environ Microbiol 63:547–552

Palleroni NJ (2015) Burkholderia. In: Bergey's manual of systematics of archaea and Bacteria. Wiley, pp 1–50. https://doi.org/10.1002/9781118960608.gbm00935

Park SS, DeCicco BT (1976) Hydrogenase and ribulose diphosphate carboxylase during autotrophic, heterotrophic, and mixotrophic growth of scotochromogenic mycobacteria. J Bacteriol 127:731–738

Paul S, Cortez Y, Vera N, Villen GK, Gutiérrez-Correa M (2016) Metagenomic analysis of microbial communities in the soil-mousse surrounding of an Amazonian geothermal spring in Peru. Br Biotechnol J 15:27519. https://doi.org/10.9734/BBJ/2016/27519 DOI

Pontiroli A, Kheira TT, Oakley BB, Mason S, Dowd SE, Travis ER, Erenso G, Aseffa A, Courtenay O, Wellington EMH (2013) Prospecting environmental mycobacteria: combined molecular approaches reveal unprecedented diversity. PLoS One 8:e68648. https://doi.org/10.1371/journal.pone.0068648 DOI

Revetta RP, Gomez-Alvarez V, Gerke TL, Santo Domingo JW, Ashbolt NJ (2016) Changes in bacterial composition of biofilm in a metropolitan drinking water distribution system. J Appl Microbiol 121:294–305 DOI

Shabarova T, Pernthaler J (2010) Karst pools in subsurface environments: collectors of microbial diversity or temporary residence between habitat types. Environ Microbiol 12:1061–1074 DOI

Shabarova T, Villiger F, Pernthale RJ (2013) Mass effects meet species sorting: transformations of microbial assemblages in epiphreatic subsurface karst water pools. Environ Microbiol 15:2476–2488 DOI

Shabarova T, Villiger J, Morenkov O, Niggemann J, Dittmar T, Pernthaler J (2014) Bacterial community structure and dissolved organic matter in repeatedly flooded subsurface karst water pools. FEMS Microbiol Ecol 89:111–126 DOI

Simeckova B (2013) Experience from floods in 2010. In: Simeckova B, Gersl M (eds) Zbrašov Aragonite Caves, Acta Speleologica, vol 4, pp 141–145 (in Czech)

Slany M, Svobodova J, Ettlova A, Slana I, Mrlik V, Pavlik I (2010) Mycobacterium arupense among the isolates of non-tuberculous mycobacteria from human, animal and environmental samples. Vet Med-Czech 55:369–376 DOI

Springer B, Böttger EC, Kirschner P, Wallace RJ Jr (1995) Phylogeny of the Mycobacterium chelonae-like organism based on partial sequencing of the 16S rRNA gene and proposal of Mycobacterium mucogenicum sp. nov. Int J Syst Evol Microbiol 45:262–267

Stout JE, Koh W-J, Yew WW (2016) Update on pulmonary disease due to non-tuberculous mycobacteria. Int J Infect Dis 45:123–134

Telenti A, Marchesi F, Balz M, Bally F, Böttger EC, Bodmer T (1993) Rapid identification of mycobacteria to the species level by polymerase chain reaction and restriction enzyme analysis. J Clin Microbiol 31:175–178

Totani T, Nishiuchi Y, Tateishi Y, Yoshida Y, Kitanaka H, Niki M, Kaneko Y, Matsumoto S (2017) Effects of nutritional and ambient oxygen condition on biofilm formation in Mycobacterium avium subsp. hominissuis via altered glycolipid expression. Sci Rep 7:41775. https://doi.org/10.1038/srep41775 DOI

Vigneron A, Bishop A, Alsop EB, Hull K, Rhodes I, Hendricks R, Head IM, Tsesmetzis N (2017) Microbial and isotopic evidence for methane cycling in hydrocarbon-containing groundwater from the Pennsylvania region. Front Microbiol 8:593. https://doi.org/10.3389/fmicb.2017.00593 DOI

Vysoka H (2017) Hydrogeological research of the Hranice Abbys within the project of Neuron Expedition—preliminary results. In: Bosak P, Gersl M, Novotna J (eds) Speleoforum, vol. 36. Proceedings from Meeting of cavers in the Moravian Karst. Czech Speleological Society, Sloup, pp 16–21

Walker JJ, Spear JR, Pace NR (2005) Geobiology of a microbial endolithic community in the Yellowstone geothermal environment. Nature 434:1011–1014 DOI

Willems A (2014) The family Comamonadaceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds) The prokaryotes: Alphaproteobacteria and Betaproteobacteria, 4th edn. Springer, Berlin, pp 777–851 DOI

Wolinsky E (1975) Nontuberculous mycobacteria and associated diseases. Am Rev Respir Dis 119:107–159

Zhang DF, Chen X, Zhang XM, Zhi XY, Yao JC, Jiang Y, Xiong Z, Li WJ (2013) Mycobacterium sediminis sp. nov. and Mycobacterium arabiense sp. nov., two rapidly growing members of the genus Mycobacterium. Int J Syst Evol Microbiol 63:4081–4086 DOI

River Sediments Downstream of Villages in a Karstic Watershed Exhibited Increased Numbers and Higher Diversity of Nontuberculous Mycobacteria

Socio-Economic and Environmental Factors Related to Spatial Differences in Human Non-Tuberculous Mycobacterial Diseases in the Czech Republic