Adams-Sapper, S., Nolen, S., Donzelli, G. F., Lal, M., Chen, K., Justo da Silva, L. H., et al. (2015). Rapid induction of high-level carbapenem resistance in heteroresistant KPC-producing Klebsiella pneumoniae. Antimicrob. Agents Chemother. 59, 3281-3289. doi: 10.1128/AAC.05100-14
Allen, H. K., Donato, J., Wang, H. H., Cloud-Hansen, K. A., Davies, J., and Handelsman, J. (2010). Call of the wild: antibiotic resistance genes in natural environments. Nat. Rev. Microbiol. 8, 251-259. doi: 10.1038/nrmicro2312
Axenov-Gribanov, D. V., Voytsekhovskaya, I. V., Tokovenko, B. T., Protasov, E. S., Gamaiunov, S. V., Rebets, Y. V., et al. (2016). Actinobacteria isolated from an underground lake and moonmilk speleothem from the biggest conglomeratic karstic cave in siberia as sources of novel biologically active compounds. PLoS ONE 11:e0149216. doi: 10.1371/journal.pone.0149216
Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M., Kulikov, A. S., et al. (2012). SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455-477. doi: 10.1089/cmb.2012.0021
Barton, H. A. (2015). "Starving artists: bacterial oligotrophic heterotrophy in caves, " in Life in Extreme Environments: Microbial Life of Cave Systems, ed. A. Engel (Berlin: DeGruyter).
Bascom-Slack, C. A., Ma, C., Moore, E., Babbs, B., Fenn, K., Greene, J. S., et al. (2009). Multiple, novel biologically active endophytic actinomycetes isolated from upper amazonian rainforests. Microb. Ecol. 58, 374-383. doi: 10.1007/s00248-009-9494-z
Berendonk, T. U., Manaia, C. M., Merlin, C., Fatta-Kassinos, D., Cytryn, E., Walsh, F., et al. (2015). Tackling antibiotic resistance: the environmental framework. Nat. Rev. Microbiol. 13, 310-317. doi: 10.1038/nrmicro3439
Bhullar, K., Waglechner, N., Pawlowski, A., Koteva, K., Banks, E. D., Johnston, M. D., et al. (2012). Antibiotic resistance is prevalent in an isolated cave microbiome. PLoS ONE 7:e34953. doi: 10.1371/journal.pone.0034953
Boquet, E., Boronat, A., and Ramos-Cormenzana, A. (1973). Production of calcite (Calcium Carbonate) crystals by soil bacteria is a general phenomenon. Nature 246, 527-529. doi: 10.1038/246527a0
Borsato, A., Frisia, S., Jones, B., and Borg, K. V. D. (2000). Calcite moonmilk: crystal morphology and environment of formation in caves in the italian Alps. J. Sediment. Res. 70, 1179-1190. doi: 10.1306/032300701171
Bull, A. T. (2010). "Actinobacteria of the extremobiosphere, " in Extremophiles Handbook, ed. K. Horikoshi (Berlin: Springer), 1203-1240.
Cañaveras, J. C., Cuezva, S., Sanchez-Moral, S., Lario, J., Laiz, L., Gonzalez, J. M., et al. (2006). On the origin of fiber calcite crystals in moonmilk deposits. Naturwissenschaften 93, 27-32. doi: 10.1007/s00114-005-0052-3
Cañaveras, J. C., Hoyos Gómez, M., Sánchez-Moral, S., Sanz Rubio, E., Bedoya, J., Hoyos, V., et al. (1999). Microbial communities associated with hydromagnesite and needle-fiber aragonite deposits in a karstic cave (Altamira, Northern Spain). Geomicrobiol. J. 16, 9-25. doi: 10.1080/014904599270712
Cheeptham, N., Sadoway, T., Rule, D., Watson, K., Moote, P., Soliman, L. C., et al. (2013). Cure from the cave: volcanic cave actinomycetes and their potential in drug discovery. Int. J. Speleol. 42, 35-47. doi: 10.5038/1827-806X.42.1.5
Claverías, F., Undabarrena, A., González, M., Seeger, M., and Cámara, B. (2015). Culturable diversity and antimicrobial activity of actinobacteria from marine sediments in Valparaíso bay, Chile. Front. Microbiol 6:737. doi: 10.3389/fmicb.2015.00737
Colson, S., van Wezel, G. P., Craig, M., Noens, E. E. E., Nothaft, H., Mommaas, A. M., et al. (2008). The chitobiose-binding protein, DasA, acts as a link between chitin utilization and morphogenesis in Streptomyces coelicolor. Microbiology 154, 373-382. doi: 10.1099/mic.0.2007/011940-0
Dantas, G., Sommer, M. O., Oluwasegun, R. D., and Church, G. M. (2008). Bacteria subsisting on antibiotics. Science 320, 100-103. doi: 10.1126/science.1155157
Davies, J., and Ryan, K. S. (2012). Introducing the parvome: Bioactive compounds in the microbial world. ACS Chem. Biol. 7, 252-259. doi: 10.1021/cb200337h
Eagle, H., and Musselman, A. D. (1948). The rate of bactericidal action of penicillin in vitro as a function of its concentrations, and its paradoxically reduced activity at high concentrations against certain organisms. J. Exp. Med. 88, 99-131. doi: 10.1084/jem.88.1.99
EUCAST (2015). EUCAST: Disk Diffusion Methodology v 5.0. Available at: http://www.eucast.org/antimicrobial_susceptibility_testing/disk_diffusion_methodology/
Frère, J.-M., and Rigali, S. (2016). The alarming increase in antibiotic-resistant bacteria. Drug Targets Rev. 3, 26-30.
Giraud, S., Favennec, L., Bougnoux, M.-E., and Bouchara, J.-P. (2013). Rasamsonia argillacea species complex: taxonomy, pathogenesis and clinical relevance. Future Microbiol. 8, 967-978. doi: 10.2217/fmb.13.63
Groth, I., Vettermann, R., Schuetze, B., Schumann, P., and Saiz-Jimenez, C. (1999). Actinomycetes in karstic caves of northern Spain (Altamira and Tito Bustillo). J. Microbiol. Methods 36, 115-122. doi: 10.1016/S0167-7012(99)00016-0
Guo, Y. P., Zheng, W., Rong, X. Y., and Huang, Y. (2008). A multilocus phylogeny of the Streptomyces griseus 16S rRNA gene clade: use of multilocus sequence analysis for streptomycete systematics. Int. J. Syst. Evol. Microbiol. 58, 149-159. doi: 10.1099/ijs.0.65224-0
Gurevich, A., Saveliev, V., Vyahhi, N., and Tesler, G. (2013). QUAST: quality assessment tool for genome assemblies. Bioinformatics 29, 1072-1075. doi: 10.1093/bioinformatics/btt086
Han, J. H., Cho, M. H., and Kim, S. B. (2012). Ribosomal and protein coding gene based multigene phylogeny on the family Streptomycetaceae. Syst. Appl. Microbiol. 35, 1-6. doi: 10.1016/j.syapm.2011.08.007
Hill, C. A., and Forti, P. (1997). Cave Minerals of the World, 2nd Edn. Huntsville, AL: National Speleological Society, 285-287.
Hodgson, D. A. (2000). Primary metabolism and its control in streptomycetes: a most unusual group of bacteria. Adv. Microb. Physiol. 42, 47-238. doi: 10.1016/S0065-2911(00)42003-5
Hopwood, D. A. (2007). Streptomyces in Nature and Medicine: The Antibiotic Makers. New York, NY: Oxford University Press.
Katoh, K., and Standley, D. M. (2013). MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Mol. Biol. Evol. 30, 772-780. doi: 10.1093/molbev/mst010
Kieser, T., Bibb, M. J., Buttner, M. J., Chater, K. F., and Hopwood, D. A. (2000). Practical Streptomyces Genetics. Norwich: John Innes Centre Ltd, doi: 10.4016/28481.01
Labeda, D. P. (2011). Multilocus sequence analysis of phytopathogenic species of the genus Streptomyces. Int. J. Syst. Evol. Microbiol. 61, 2525-2531. doi: 10.1099/ijs.0.028514-0
Laiz, L., Groth, I., Gonzalez, I., and Saiz-Jimenez, C. (1999). Microbiological study of the dripping waters in Altamira cave (Santillana del Mar, Spain). J. Microbiol. Methods 36, 129-138. doi: 10.1016/S0167-7012(99)00018-4
Laxminarayan, R., Duse, A., Wattal, C., Zaidi, A. K. M., Wertheim, H. F. L., Sumpradit, N., et al. (2013). Antibiotic resistance-the need for global solutions. Lancet Infect. Dis. 13, 1057-1098. doi: 10.1016/S1473-3099(13)70318-9
Leach, B. E., Ford, J. H., and Whiffen, A. J. (1947). Actidione, an antibiotic from Streptomyces griseus. J. Am. Chem. Soc. 69:474. doi: 10.1021/ja01194a519
Legatzki, A., Ortiz, M., Neilson, J. W., Casavant, R. R., Palmer, M. W., Rasmussen, C., et al. (2012). Factors influencing observed variations in the structure of bacterial communities on calcite formations in Kartchner Caverns, AZ, USA. Geomicrobiol. J. 29, 422-434. doi: 10.1080/01490451.2011.581326
Liao, L., Chen, R., Jiang, M., Tian, X., Liu, H., Yu, Y., et al. (2016). Bioprospecting potential of halogenases from Arctic marine actinomycetes. BMC Microbiol 16:34. doi: 10.1186/s12866-016-0662-2
Linares, J. F., Gustafsson, I., Baquero, F., and Martinez, J. L. (2006). Antibiotics as intermicrobial signaling agents instead of weapons. Proc. Natl. Acad. Sci. U.S.A. 103, 19484-19489. doi: 10.1073/pnas.0608949103
Maciejewska, M., Pessi, I. S., Arguelles-Arias, A., Noirfalise, P., Luis, G., Ongena, M., et al. (2015). Streptomyces lunaelactis sp. nov., a novel ferroverdin A-producing Streptomyces species isolated from a moonmilk speleothem. Antonie van Leeuwenhoek 107, 519-531. doi: 10.1007/s10482-014-0348-4
Migliore, L., Rotini, A., and Thaller, M. C. (2013). Low doses of tetracycline trigger the E. coli growth: A case of hormetic response. Dose-Response 11, 550-557. doi: 10.2203/dose-response.13-002.Migliore
Mohammadipanah, F., and Wink, J. (2015). Actinobacteria from arid and desert habitats: diversity and biological activity. Front. Microbiol. 6:1541. doi: 10.3389/fmicb.2015.01541
Nimaichand, S., Devi, M. A., Tamreihao, K., Ningthoujam, D. S., and Li, W. J. (2015). Actinobacterial diversity in limestone deposit sites in Hundung, Manipur (India) and their antimicrobial activities. Front. Microbiol. 6:413. doi: 10.3389/fmicb.2015.00413
Philippe, H. (1993). MUST, a computer package of management utilities for sequences and trees. Nucleic Acids Res. 21, 5264-5272. doi: 10.1093/nar/21.22.5264
Porca, E., Jurado, V., Žgur-Bertok, D., Saiz-Jimenez, C., and Pašic, L. (2012). Comparative analysis of yellow microbial communities growing on the walls of geographically distinct caves indicates a common core of microorganisms involved in their formation. FEMS Microbiol. Ecol. 81, 255-266. doi: 10.1111/j.1574-6941.2012.01383.x
Portillo, M. C., and Gonzalez, J. M. (2011). Moonmilk deposits originate from specific bacterial communities in Altamira Cave (Spain). Microb. Ecol. 61, 182-189. doi: 10.1007/s00248-010-9731-5
Prieto-Davó, A., Villarreal-Gómez, L. J., Forschner-Dancause, S., Bull, A. T., Stach, J. E. M., Smith, D. C., et al. (2013). Targeted search for actinomycetes from nearshore and deep-sea marine sediments. FEMS Microbiol. Ecol. 84, 510-518. doi: 10.1111/1574-6941.12082
Quintana, E. T., Badillo, R. F., and Maldonado, L. A. (2013). Characterisation of the first actinobacterial group isolated from a Mexican extremophile environment. Antonie van Leeuwenhoek 104, 63-70. doi: 10.1007/s10482-013-9926-0
Reinbacher, W. (1994). Is it gnome, is it berg, is it mont, it it mond? An updated view of the origin and etymology of moonmilk. Natl. Speleol. Soc. 56, 1-13.
Rigali, S., Titgemeyer, F., Barends, S., Mulder, S., Thomae, A. W., Hopwood, D. A., et al. (2008). Feast or famine: the global regulator DasR links nutrient stress to antibiotic production by Streptomyces. EMBO Rep. 9, 670-675. doi: 10.1038/embor.2008.83
Riquelme, C., Hathaway, J. J. M., Dapkevicius, M., de, L. N. E., Miller, A. Z., Kooser, A., et al. (2015). Actinobacterial diversity in volcanic caves and associated geomicrobiological interactions. Front. Microbiol. 6:1342. doi: 10.3389/fmicb.2015.01342
Rong, X., and Huang, Y. (2012). Taxonomic evaluation of the Streptomyces hygroscopicus clade using multilocus sequence analysis and DNA-DNA hybridization, validating the MLSA scheme for systematics of the whole genus. Syst. Appl. Microbiol. 35, 7-18. doi: 10.1016/j.syapm.2011.10.004
Rooney, D. C., Hutchens, E., Clipson, N., Baldini, J., and McDermott, F. (2010). Microbial community diversity of moonmilk deposits at Ballynamintra Cave, co. waterford, Ireland. Microb. Ecol. 60, 753-761. doi: 10.1007/s00248-010-9693-7
Roure, B., Rodriguez-Ezpeleta, N., and Philippe, H. (2007). SCaFoS: a tool for selection, concatenation and fusion of sequences for phylogenomics. BMC Evol. Biol. 7(Suppl. 1):S2. doi: 10.1186/1471-2148-7-S1-S2
Rule, D., and Cheeptham, N. (2013). The effects of UV light on the antimicrobial activities of cave actinomycetes. Int. J. Speleol. 42, 147-153. doi: 10.5038/1827-806X.42.2.7
Saito, A., Shinya, T., Miyamoto, K., Yokoyama, T., Kaku, H., Minami, E., et al. (2007). The dasABC gene cluster, adjacent to dasR, encodes a novel ABC transporter for the uptake of N, N 9-diacetylchitobiose in Streptomyces coelicolor A3(2). Appl. Env. Microbiol. 73, 3000-3008. doi: 10.1128/AEM.02612-06
Saiz-Jimenez, C., and Hermosin, B. (1999). Thermally assisted hydrolysis and methylation of dissolved organic matter in dripping waters from the Altamira Cave. J. Anal. Appl. Pyrolysis 49, 337-347. doi: 10.1016/S0165-2370(98)00112-0
Saiz-Jimenez, I. G. C. (1999). Actinomycetes in hypogean environments. Geomicrobiol. J. 16, 1-8. doi: 10.1080/014904599270703
Sengupta, S., Chattopadhyay, M. K., and Grossart, H. P. (2013). The multifaceted roles of antibiotics and antibiotic resistance in nature. Front. Microbiol. 4:47. doi: 10.3389/fmicb.2013.00047
Shirling, E. B., and Gottlieb, D. (1966). Methods for characterization of Streptomyces species. Int. J. Syst. Bacteriol. 16, 313-340. doi: 10.1099/00207713-16-3-313
Shivlata, L., and Satyanarayana, T. (2015). Thermophilic and alkaliphilic Actinobacteria: biology and potential applications. Front. Microbiol. 6:1014. doi: 10.3389/fmicb.2015.01014
Simon, K. S., Pipan, T., and Culver, D. C. (2007). A conceptual model of the flow and distribution of organic carbon in caves. J. Cave Karst Stud. 69, 279-284.
Stamatakis, A. (2014). RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312-1313. doi: 10.1093/bioinformatics/btu033
Stomeo, F., Portillo, M. C., Gonzalez, J. M., Laiz, L., and Saiz-Jimenez, C. (2008). Pseudonocardia in white colonizations in two caves with Paleolithic paintings. Int. Biodeterior. Biodegrad. 62, 483-486. doi: 10.1016/j.ibiod.2007.12.011
Subramani, R., and Aalbersberg, W. (2013). Culturable rare Actinomycetes: diversity, isolation and marine natural product discovery. Appl. Microbiol. Biotechnol. 97, 9291-9321. doi: 10.1007/s00253-013-5229-7
Swiatek, M., Urem, M., Tenconi, E., Rigali, S., and van Wezel, G. (2012). Engineering of N-acetylglucosamine metabolism for improved antibiotic production in Streptomyces coelicolor A3(2) and an unsuspected role of NagA in glucosamine metabolism. Bioengineered 3, 280-285. doi: 10.4161/bioe.21371
Verma, V. C., Gond, S. K., Kumar, A., Mishra, A., Kharwar, R. N., and Gange, A. C. (2009). Endophytic actinomycetes from azadirachta indica a. juss: isolation, diversity, and anti-microbial activity. Microb. Ecol. 57, 749-756. doi: 10.1007/s00248-008-9450-3
Waksman, S., and Lechevalier, H. (1961). The Actinomycetales, Classification, Identification and Description of Genera and Species, Vol. 2. Baltimore, MD: Williams and Wilkins.
Wang, H., Fewer, D. P., Holm, L., Rouhiainen, L., and Sivonen, K. (2014). Atlas of nonribosomal peptide and polyketide biosynthetic pathways reveals common occurrence of nonmodular enzymes. Proc. Natl. Acad. Sci. U.S.A. 111, 9259-9264. doi: 10.1073/pnas.1401734111
Weber, T., Blin, K., Duddela, S., Krug, D., Kim, H. U., Bruccoleri, R., et al. (2015). antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res. 43, W237-W243. doi: 10.1093/nar/gkv437
Whiffen, A. J., Bohonos, N., and Emerson, R. L. (1946). The production of an antifungal antibiotic by Streptomyces griseus. J. Bacteriol 52, 610-611.
Yücel, S., and Yamaç, M. (2010). Selection of Streptomyces isolates from Turkish karstic caves against antibiotic resistant microorganisms. Pak. J. Pharm. Sci. 23, 1-6.
Yun, Y., Xiang, X., Wang, H., Man, B., Gong, L., Liu, Q., et al. (2015). Five-year monitoring of bacterial communities in dripping water From the Heshang Cave in Central China: implication for paleoclimate reconstruction and ecological functions. Geomicrobiol. J. 33, 1-11. doi: 10.1080/01490451.2015.1062062
Zhanel, G. G., Hoban, D. J., and Harding, G. K. (1992). Subinhibitory antimicrobial concentrations: a review of in vitro and in vivo data. Can. J. Infect. Dis. 3, 193-201. doi: 10.1155/1992/793607
Zhang, G., Cao, T., Ying, J., Yang, Y., and Ma, L. (2014). Diversity and novelty of actinobacteria in arctic marine sediments. Antonie van Leeuwenhoek 105, 743-754. doi: 10.1007/s10482-014-0130-7
Zhao, K., Penttinen, P., Guan, T., Xiao, J., Chen, Q., Xu, J., et al. (2011). The diversity and anti-microbial activity of endophytic actinomycetes isolated from medicinal plants in Panxi Plateau. China. Curr. Microbiol. 62, 182-190. doi: 10.1007/s00284-010-9685-3
Zhong, H., Zhang, S., Pan, H., and Cai, T. (2013). Influence of induced ciprofloxacin resistance on efflux pump activity of Klebsiella pneumoniae. J. Zhejiang Univ. Sci. B 14, 837-843. doi: 10.1631/jzus.B1200221
Zhu, H., Swierstra, J., Wu, C., Girard, G., Choi, Y. H., van Wamel, W., et al. (2014). Eliciting antibiotics active against the ESKAPE pathogens in a collection of actinomycetes isolated from mountain soils. Microbiology 160, 1714-1726. doi: 10.1099/mic.0.078295-0