Stalactites Core Prospect as Environmental “Microbial Ark”: The Actinomycetota Diversity Paradigm, First Reported from a Greek Cave

Abagana AY, Sun P, Liu C, Cao T, Zheng W, Zhao S, Xiang W, Wang X. Actinomadura gamaensis sp. nov., a novel actinomycete isolated from soil in Gama, Chad. Antonie Van Leeuwenhoek. 2016 Jun;109(6):833–839. https://doi.org/10.1007/s10482-016-0683-8 Abagana AY Sun P Liu C Cao T Zheng W Zhao S Xiang W Wang X . Actinomadura gamaensis sp. nov., a novel actinomycete isolated from soil in Gama, Chad . Antonie Van Leeuwenhoek . 2016 Jun ; 109 ( 6 ): 833 – 839 . https://doi.org/10.1007/s10482-016-0683-8 Search in Google Scholar

Abdelkader MSA, Philippon T, Asenjo JA, Bull AT, Goodfellow M, Ebel R, Jaspars M, Rateb ME. Asenjonamides A–C, antibacterial metabolites isolated from Streptomyces asenjonii strain KNN 42.f from an extreme-hyper arid Atacama Desert soil. J Antibiot. 2018 Mar;71(4):425–431. https://doi.org/10.1038/s41429-017-0012-0 Abdelkader MSA Philippon T Asenjo JA Bull AT Goodfellow M Ebel R Jaspars M Rateb ME . Asenjonamides A–C, antibacterial metabolites isolated from Streptomyces asenjonii strain KNN 42.f from an extreme-hyper arid Atacama Desert soil . J Antibiot . 2018 Mar ; 71 ( 4 ): 425 – 431 . https://doi.org/10.1038/s41429-017-0012-0 Search in Google Scholar

Adachi K, Katsuta A, Matsuda S, Peng X, Misawa N, Shizuri Y, Kroppenstedt RM, Yokota A, Kasai H. Smaragdicoccus niigatensis gen. nov., sp. nov., a novel member of the suborder Corynebacterineae. Int J Syst Evol Microbiol. 2007 Feb;57(Pt 2):297–301. https://doi.org/10.1099/IJS.0.64254-0 Adachi K Katsuta A Matsuda S Peng X Misawa N Shizuri Y Kroppenstedt RM Yokota A Kasai H . Smaragdicoccus niigatensis gen. nov., sp. nov., a novel member of the suborder Corynebacterineae . Int J Syst Evol Microbiol . 2007 Feb ; 57 (Pt 2): 297 – 301 . https://doi.org/10.1099/IJS.0.64254-0 Search in Google Scholar

Affolter S, Häuselmann A, Fleitmann D, Edwards RL, Cheng H, Leuenberger M. Central Europe temperature constrained by speleothem fluid inclusion water isotopes over the past 14,000 years. Sci Adv. 2019 Jun;5(6):eaav3809. https://doi.org/10.1126/sciadv.aav3809 Affolter S Häuselmann A Fleitmann D Edwards RL Cheng H Leuenberger M . Central Europe temperature constrained by speleothem fluid inclusion water isotopes over the past 14,000 years . Sci Adv . 2019 Jun ; 5 ( 6 ): eaav3809 . https://doi.org/10.1126/sciadv.aav3809 Search in Google Scholar

Afgan E, Baker D, Batut B, van den Beek M, Bouvier D, Cech M, Chilton J, Clements D, Coraor N, Grüning BA, et al. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Res. 2018 Jul;46(W1): W537–W544. https://doi.org/10.1093/nar/gky379 Afgan E Baker D Batut B van den Beek M Bouvier D Cech M Chilton J Clements D Coraor N Grüning BA . The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update . Nucleic Acids Res . 2018 Jul ; 46 ( W1 ): W537 – W544 . https://doi.org/10.1093/nar/gky379 Search in Google Scholar

Albuquerque L, França L, Rainey FA, Schumann P, Nobre MF, da Costa MS. Gaiella occulta gen. nov., sp. nov., a novel representative of a deep branching phylogenetic lineage within the class Actinobacteria and proposal of Gaiellaceae fam. nov. and Gaiellales ord. nov. Syst Appl Microbiol. 2011 Dec;34(8):595–599. https://doi.org/10.1016/j.syapm.2011.07.001 Albuquerque L França L Rainey FA Schumann P Nobre MF da Costa MS . Gaiella occulta gen. nov., sp. nov., a novel representative of a deep branching phylogenetic lineage within the class Actinobacteria and proposal of Gaiellaceae fam. nov. and Gaiellales ord. nov . Syst Appl Microbiol . 2011 Dec ; 34 ( 8 ): 595 – 599 . https://doi.org/10.1016/j.syapm.2011.07.001 Search in Google Scholar

Appelt S, Armougom F, Le Bailly M, Robert C, Drancourt M. Polyphasic analysis of a middle ages coprolite microbiota, Belgium. PLoS One. 2014a Feb;9(2):e88376. https://doi.org/10.1371/journal.pone.0088376 Appelt S Armougom F Le Bailly M Robert C Drancourt M . Polyphasic analysis of a middle ages coprolite microbiota, Belgium . PLoS One . 2014a Feb ; 9 ( 2 ): e88376 . https://doi.org/10.1371/journal.pone.0088376 Search in Google Scholar

Appelt S, Fancello L, Le Bailly M, Raoult D, Drancourt M, Desnues C. Viruses in a 14th-century coprolite. Appl Environ Microbiol. 2014 May;80(9):2648–2655. https://doi.org/10.1128/AEM.03242-13 Appelt S Fancello L Le Bailly M Raoult D Drancourt M Desnues C . Viruses in a 14th-century coprolite . Appl Environ Microbiol . 2014 May ; 80 ( 9 ): 2648 – 2655 . https://doi.org/10.1128/AEM.03242-13 Search in Google Scholar

Araújo CL, Alves J, Lima A, Dias L, Silva P, Marques J, Azevedo V, Folador AS. The genus Corynebacterium in the genomic era. In: Enany S, editor. Basic biology and applications of Actinobacteria. London (UK): IntechOpen; 2018. https://doi.org/10.5772/intechopen.80445 Araújo CL Alves J Lima A Dias L Silva P Marques J Azevedo V Folador AS . The genus Corynebacterium in the genomic era . In: Enany S editor. Basic biology and applications of Actinobacteria . London (UK) : IntechOpen ; 2018 . https://doi.org/10.5772/intechopen.80445 Search in Google Scholar

Asem MD, Shi L, Jiao JY, Wang D, Han MX, Dong L, Liu F, Salam N, Li WJ. Desertimonas flava gen. nov., sp. nov. isolated from a desert soil, and proposal of Ilumatobacteraceae fam. nov. Int J Syst Evol Microbiol. 2018 Nov;68(11):3593–3599. https://doi.org/10.1099/ijsem.0.003038 Asem MD Shi L Jiao JY Wang D Han MX Dong L Liu F Salam N Li WJ . Desertimonas flava gen. nov., sp. nov. isolated from a desert soil, and proposal of Ilumatobacteraceae fam. nov . Int J Syst Evol Microbiol . 2018 Nov ; 68 ( 11 ): 3593 – 3599 . https://doi.org/10.1099/ijsem.0.003038 Search in Google Scholar

Barton AH, Taylor MR, Pace NR. Molecular phylogenetic analysis of a bacterial community in an oligotrophic cave environment. Geomicrobiol J. 2004 Aug;21(1):11–20. https://doi.org/10.1080/01490450490253428 Barton AH Taylor MR Pace NR . Molecular phylogenetic analysis of a bacterial community in an oligotrophic cave environment . Geomicrobiol J . 2004 Aug ; 21 ( 1 ): 11 – 20 . https://doi.org/10.1080/01490450490253428 Search in Google Scholar

Barton HA. Introduction to cave microbiology: A review for the non-specialist. J Cave Karst Stud. 2006 Aug;68(2):43–54. Barton HA . Introduction to cave microbiology: A review for the non-specialist . J Cave Karst Stud . 2006 Aug ; 68 ( 2 ): 43 – 54 . Search in Google Scholar

Bello MGD, Knight R, Gilbert JA, Blaser MJ. Preserving microbial diversity. Science. 2018 Oct;362(6410):33–34. https://doi.org/10.1126/science.aau8816 Bello MGD Knight R Gilbert JA Blaser MJ . Preserving microbial diversity . Science . 2018 Oct ; 362 ( 6410 ): 33 – 34 . https://doi.org/10.1126/science.aau8816 Search in Google Scholar

Borgonie G, Linage-Alvarez B, Ojo A, Shivambu S, Kuloyo O, Cason ED, Maphanga S, Vermeulen JG, Litthauer D, Ralston CD, et al. Deep subsurface mine stalactites trap endemic fissure fluid Archaea, Bacteria, and Nematoda possibly originating from ancient seas. Front Microbiol. 2015 Aug 11;6:833. https://doi.org/10.3389/fmicb.2015.00833 Borgonie G Linage-Alvarez B Ojo A Shivambu S Kuloyo O Cason ED Maphanga S Vermeulen JG Litthauer D Ralston CD . Deep subsurface mine stalactites trap endemic fissure fluid Archaea, Bacteria, and Nematoda possibly originating from ancient seas . Front Microbiol . 2015 Aug 11 ; 6 : 833 . https://doi.org/10.3389/fmicb.2015.00833 Search in Google Scholar

Boston PJ, Spilde MN, Northup DE, Melim LA, Soroka DS, Kleina LG, Lavoie KH, Hose LD, Mallory LM, Dahm CN, et al. Cave biosignature suites: microbes, minerals, and Mars. Astrobiology. 2001;1(1):25–55. https://doi.org/10.1089/153110701750137413 Boston PJ Spilde MN Northup DE Melim LA Soroka DS Kleina LG Lavoie KH Hose LD Mallory LM Dahm CN . Cave biosignature suites: microbes, minerals, and Mars . Astrobiology . 2001 ; 1 ( 1 ): 25 – 55 . https://doi.org/10.1089/153110701750137413 Search in Google Scholar

Brites D, Loiseau C, Menardo F, Borrell S, Boniotti MB, Warren R, Dippenaar A, Parsons SDC, Beisel C, Behr MA, et al. A new phylogenetic framework for the animal-adapted Mycobacterium tuberculosis complex. Front Microbiol. 2018 Nov;9:2820. https://doi.org/10.3389/fmicb.2018.02820 Brites D Loiseau C Menardo F Borrell S Boniotti MB Warren R Dippenaar A Parsons SDC Beisel C Behr MA . A new phylogenetic framework for the animal-adapted Mycobacterium tuberculosis complex . Front Microbiol . 2018 Nov ; 9 : 2820 . https://doi.org/10.3389/fmicb.2018.02820 Search in Google Scholar

Bull AT, Idris H, Sanderson R, Asenjo J, Andrews B, Goodfellow M. High altitude, hyper-arid soils of the Central-Andes harbor mega-diverse communities of actinobacteria. Extremophiles. 2018 Jan;22(1):47–57. https://doi.org/10.1007/s00792-017-0976-5 Bull AT Idris H Sanderson R Asenjo J Andrews B Goodfellow M . High altitude, hyper-arid soils of the Central-Andes harbor mega-diverse communities of actinobacteria . Extremophiles . 2018 Jan ; 22 ( 1 ): 47 – 57 . https://doi.org/10.1007/s00792-017-0976-5 Search in Google Scholar

Carrier BL, Beaty DW, Meyer MA, Blank JG, Chou L, DasSarma S, Des Marais DJ, Eigenbrode JL, Grefenstette N, Lanza NL, et al. Mars extant life: What’s next? Conference report. Astrobiology. 2020 Jun;20(6):785–814. https://doi.org/10.1089/ast.2020.2237 Carrier BL Beaty DW Meyer MA Blank JG Chou L DasSarma S Des Marais DJ Eigenbrode JL Grefenstette N Lanza NL . Mars extant life: What’s next? Conference report . Astrobiology . 2020 Jun ; 20 ( 6 ): 785 – 814 . https://doi.org/10.1089/ast.2020.2237 Search in Google Scholar

Cheeptham N, Sadoway T, Rule D, Watson K, Moote P, Soliman LC, Azad N, Donkor KK, Horne D. Cure from the cave: volcanic cave actinomycetes and their potential in drug discovery. Int. J. Speleol. 2013;42(1):35–47. https://doi.org/10.5038/1827-806X.42.1.5 Cheeptham N Sadoway T Rule D Watson K Moote P Soliman LC Azad N Donkor KK Horne D . Cure from the cave: volcanic cave actinomycetes and their potential in drug discovery . Int. J. Speleol . 2013 ; 42 ( 1 ): 35 – 47 . https://doi.org/10.5038/1827-806X.42.1.5 Search in Google Scholar

Chen RW, Li C, He YQ, Cui LQ, Long LJ, Tian XP. Rubrobacter tropicus sp. nov. and Rubrobacter marinus sp. nov., isolated from deep-sea sediment of the South China Sea. Int J Syst Evol Microbiol. 2020 Oct;70(10):5576–5585. https://doi.org/10.1099/ijsem.0.004449 Chen RW Li C He YQ Cui LQ Long LJ Tian XP . Rubrobacter tropicus sp. nov. and Rubrobacter marinus sp. nov., isolated from deep-sea sediment of the South China Sea . Int J Syst Evol Microbiol . 2020 Oct ; 70 ( 10 ): 5576 – 5585 . https://doi.org/10.1099/ijsem.0.004449 Search in Google Scholar

Chun SJ, Cui Y, Jin C, Cho AR, Wong SK, Lee HG, Oh HM, Ahn CY. Paraconexibacter algicola gen. nov., sp. nov., a novel actinobacterium isolated from a eutrophic lake during the end of cyanobacterial harmful algal blooms, and proposal of Paraconexibacteraceae fam. nov. in the order Solirubrobacterales. Int J Syst Evol Microbiol. 2020 Feb;70(2):915–922. https://doi.org/10.1099/ijsem.0.003846 Chun SJ Cui Y Jin C Cho AR Wong SK Lee HG Oh HM Ahn CY . Paraconexibacter algicola gen. nov., sp. nov., a novel actinobacterium isolated from a eutrophic lake during the end of cyanobacterial harmful algal blooms, and proposal of Paraconexibacteraceae fam. nov. in the order Solirubrobacterales . Int J Syst Evol Microbiol . 2020 Feb ; 70 ( 2 ): 915 – 922 . https://doi.org/10.1099/ijsem.0.003846 Search in Google Scholar

Coolen MJ, van de Giessen J, Zhu EY, Wuchter C. Bioavailability of soil organic matter and microbial community dynamics upon permafrost thaw. Environ Microbiol. 2011 Aug;13(8):2299–2314. https://doi.org/10.1111/j.1462-2920.2011.02489x Coolen MJ van de Giessen J Zhu EY Wuchter C . Bioavailability of soil organic matter and microbial community dynamics upon permafrost thaw . Environ Microbiol . 2011 Aug ; 13 ( 8 ): 2299 – 2314 . https://doi.org/10.1111/j.1462-2920.2011.02489x Search in Google Scholar

Coolen MJ. 7000 years of Emiliania huxleyi viruses in the Black Sea. Science. 2011 Jul;333(6041):451–452. https://doi.org/10.1126/science.1200072 Coolen MJ . 7000 years of Emiliania huxleyi viruses in the Black Sea . Science . 2011 Jul ; 333 ( 6041 ): 451 – 452 . https://doi.org/10.1126/science.1200072 Search in Google Scholar

Dance A. The search for microbial dark matter. Nature. 2020 Jun; 582(7811):301–303. https://doi.org/10.1038/d41586-020-01684-z Dance A . The search for microbial dark matter . Nature . 2020 Jun ; 582 ( 7811 ): 301 – 303 . https://doi.org/10.1038/d41586-020-01684-z Search in Google Scholar

Dawson W, Hör J, Egert M, van Kleunen M, Pester M. A small number of low-abundance bacteria dominate plant species-specific responses during rhizosphere colonization. Front Microbiol. 2017 May;8:975. https://doi.org/10.3389/fmicb.2017.00975 Dawson W Hör J Egert M van Kleunen M Pester M . A small number of low-abundance bacteria dominate plant species-specific responses during rhizosphere colonization . Front Microbiol . 2017 May ; 8 : 975 . https://doi.org/10.3389/fmicb.2017.00975 Search in Google Scholar

De Mandal S, Chatterjee R, Kumar NS. Dominant bacterial phyla in caves and their predicted functional roles in C and N cycle. BMC Microbiol. 2017 Apr;17(1):90. https://doi.org/10.1186/s12866-017-1002-x De Mandal S Chatterjee R Kumar NS . Dominant bacterial phyla in caves and their predicted functional roles in C and N cycle . BMC Microbiol . 2017 Apr ; 17 ( 1 ): 90 . https://doi.org/10.1186/s12866-017-1002-x Search in Google Scholar

Dekio I, Asahina A, Shah HN. Unravelling the eco-specificity and pathophysiological properties of Cutibacterium species in the light of recent taxonomic changes. Anaerobe. 2021 Oct;71:102411. https://doi.org/10.1016/j.anaerobe.2021.102411 Dekio I Asahina A Shah HN . Unravelling the eco-specificity and pathophysiological properties of Cutibacterium species in the light of recent taxonomic changes . Anaerobe . 2021 Oct ; 71 : 102411 . https://doi.org/10.1016/j.anaerobe.2021.102411 Search in Google Scholar

Durazzi F, Sala C, Castellani G, Manfreda G, Remondini D, De Cesare A. Comparison between 16S rRNA and shotgun sequencing data for the taxonomic characterization of the gut microbiota. Sci Rep. 2021 Feb;11(1):3030. https://doi.org/10.1038/s41598-021-82726-y Durazzi F Sala C Castellani G Manfreda G Remondini D De Cesare A . Comparison between 16S rRNA and shotgun sequencing data for the taxonomic characterization of the gut microbiota . Sci Rep . 2021 Feb ; 11 ( 1 ): 3030 . https://doi.org/10.1038/s41598-021-82726-y Search in Google Scholar

Farda B, Djebaili R, Vaccarelli I, Del Gallo M, Pellegrini M. Actinomycetes from caves: An overview of their diversity, biotechnological properties, and insights for their use in soil environments. Microorganisms. 2022 Feb;10(2):453. https://doi.org/10.3390/microorganisms10020453 Farda B Djebaili R Vaccarelli I Del Gallo M Pellegrini M . Actinomycetes from caves: An overview of their diversity, biotechnological properties, and insights for their use in soil environments . Microorganisms . 2022 Feb ; 10 ( 2 ): 453 . https://doi.org/10.3390/microorganisms10020453 Search in Google Scholar

Fernández-Gómez B, Díez B, Polz MF, Arroyo JI, Alfaro FD, Marchandon G, Sanhueza C, Farías L, Trefault N, Marquet PA, et al. Bacterial community structure in a sympagic habitat expanding with global warming: brackish ice brine at 85–90°N. ISME J. 2019 Feb;13(2):316–333. https://doi.org/10.1038/s41396-018-0268-9 Fernández-Gómez B Díez B Polz MF Arroyo JI Alfaro FD Marchandon G Sanhueza C Farías L Trefault N Marquet PA . Bacterial community structure in a sympagic habitat expanding with global warming: brackish ice brine at 85–90°N . ISME J . 2019 Feb ; 13 ( 2 ): 316 – 333 . https://doi.org/10.1038/s41396-018-0268-9 Search in Google Scholar

García-Descalzo L, García-López E, Postigo M, Baquero F, Alcazar A, Cid C. Eukaryotic microorganisms in cold environments: examples from Pyrenean glaciers. Front Microbiol. 2013 Mar;4:55. https://doi.org/10.3389/fmicb.2013.00055 García-Descalzo L García-López E Postigo M Baquero F Alcazar A Cid C . Eukaryotic microorganisms in cold environments: examples from Pyrenean glaciers . Front Microbiol . 2013 Mar ; 4 : 55 . https://doi.org/10.3389/fmicb.2013.00055 Search in Google Scholar

Ghosh S, Kuisiene N, Cheeptham N. The cave microbiome as a source for drug discovery: Reality or pipe dream? Biochem Pharmacol. 2017 Jun;134:18–34. https://doi.org/10.1016/j.bcp.2016.11.018 Ghosh S Kuisiene N Cheeptham N . The cave microbiome as a source for drug discovery: Reality or pipe dream? Biochem Pharmacol . 2017 Jun ; 134 : 18 – 34 . https://doi.org/10.1016/j.bcp.2016.11.018 Search in Google Scholar

Goodfellow M, Nouioui I, Sanderson R, Xie F, Bull AT. Rare taxa and dark microbial matter: novel bioactive actinobacteria abound in Atacama Desert soils. Antonie Van Leeuwenhoek. 2018 Aug;111(8):1315–1332. https://doi.org/10.1007/s10482-018-1088-7 Goodfellow M Nouioui I Sanderson R Xie F Bull AT . Rare taxa and dark microbial matter: novel bioactive actinobacteria abound in Atacama Desert soils . Antonie Van Leeuwenhoek . 2018 Aug ; 111 ( 8 ): 1315 – 1332 . https://doi.org/10.1007/s10482-018-1088-7 Search in Google Scholar

Goodfellow M. Phylum XXVI. Actinobacteria phyl. nov. In: Goodfellow M, Kämpfer P, Busse H-J, Trujillo ME, Suzuki K, Ludwig W, Whitman WB, editors. Bergey’s manual of systematic bacteriology. Volume 5: The Actinobacteria. New York (USA): Springer New York; 2012. p. 33–34. https://doi.org/10.1007/978-0-387-68233-4_3 Goodfellow M . Phylum XXVI. Actinobacteria phyl. nov . In: Goodfellow M Kämpfer P Busse H-J Trujillo ME Suzuki K Ludwig W Whitman WB editors. Bergey’s manual of systematic bacteriology. Volume 5: The Actinobacteria . New York (USA) : Springer New York ; 2012 . p. 33 – 34 . https://doi.org/10.1007/978-0-387-68233-4_3 Search in Google Scholar

Groth I, Saiz-Jimenez C. Actinomycetes in hypogean environments. Geomicrobiol J. 1999;6(1):1–8. https://doi.org/10.1080/014904599270703 Groth I Saiz-Jimenez C . Actinomycetes in hypogean environments . Geomicrobiol J . 1999 ; 6 ( 1 ): 1 – 8 . https://doi.org/10.1080/014904599270703 Search in Google Scholar

Habib N, Khan IU, Xiao M, Li S, Saqib M, Xian WD, Butt S, Li WJ. Marmoricola caldifontis sp. nov., a novel actinobacterium isolated from a hot spring. Int J Syst Evol Microbiol. 2020 Mar; 70(3):2053–2058. https://doi.org/10.1099/ijsem.0.004016 Habib N Khan IU Xiao M Li S Saqib M Xian WD Butt S Li WJ . Marmoricola caldifontis sp. nov., a novel actinobacterium isolated from a hot spring . Int J Syst Evol Microbiol . 2020 Mar ; 70 ( 3 ): 2053 – 2058 . https://doi.org/10.1099/ijsem.0.004016 Search in Google Scholar

Han C, Zhang Y, Yu B, Shan Q, Zhao J, Shi H, Tian Y, Zhang Y, Zhu C, Xiang W. Cellulomonas triticagri sp. nov., isolated from the rhizosphere soil of wheat (Triticum aestivum L.). Arch Microbiol. 2022 Jul;204(7):449. https://doi.org/10.1007/s00203-022-03036-z Han C Zhang Y Yu B Shan Q Zhao J Shi H Tian Y Zhang Y Zhu C Xiang W . Cellulomonas triticagri sp. nov., isolated from the rhizosphere soil of wheat (Triticum aestivum L.) . Arch Microbiol . 2022 Jul ; 204 ( 7 ): 449 . https://doi.org/10.1007/s00203-022-03036-z Search in Google Scholar

He YQ, Chen RW, Li C, Shi SB, Cui LQ, Long LJ, Tian XP. Actinomarinicola tropica gen. nov. sp. nov., a new marine actinobacterium of the family Iamiaceae, isolated from South China Sea sediment environments. Int J Syst Evol Microbiol. 2020 Jun;70(6):3852–3858. https://doi.org/10.1099/ijsem.0.004251 He YQ Chen RW Li C Shi SB Cui LQ Long LJ Tian XP . Actinomarinicola tropica gen. nov. sp. nov., a new marine actinobacterium of the family Iamiaceae, isolated from South China Sea sediment environments . Int J Syst Evol Microbiol . 2020 Jun ; 70 ( 6 ): 3852 – 3858 . https://doi.org/10.1099/ijsem.0.004251 Search in Google Scholar

Idris H, Goodfellow M, Sanderson R, Asenjo JA, Bull AT. Actinobacterial rare biospheres and dark matter revealed in habitats of the Chilean Atacama Desert. Sci Rep. 2017 Aug;7(1):8373. https://doi.org/10.1038/s41598-017-08937-4 Idris H Goodfellow M Sanderson R Asenjo JA Bull AT . Actinobacterial rare biospheres and dark matter revealed in habitats of the Chilean Atacama Desert . Sci Rep . 2017 Aug ; 7 ( 1 ): 8373 . https://doi.org/10.1038/s41598-017-08937-4 Search in Google Scholar

Jiao JY, Liu L, Hua ZS, Fang BZ, Zhou EM, Salam N, Hedlund BP, Li WJ. Microbial dark matter coming to light: challenges and opportunities. Natl Sci Rev. 2021 Mar;8(3):nwaa280. https://doi.org/10.1093/nsr/nwaa280 Jiao JY Liu L Hua ZS Fang BZ Zhou EM Salam N Hedlund BP Li WJ . Microbial dark matter coming to light: challenges and opportunities . Natl Sci Rev . 2021 Mar ; 8 ( 3 ): nwaa280 . https://doi.org/10.1093/nsr/nwaa280 Search in Google Scholar

Jin D, Kong X, Li H, Luo L, Zhuang X, Zhuang G, Deng Y, Bai Z. Patulibacter brassicae sp. nov., isolated from rhizosphere soil of Chinese cabbage (Brassica campestris). Int J Syst Evol Microbiol. 2016 Dec;66(12):5056–5060. https://doi.org/10.1099/ijsem.0.001469 Jin D Kong X Li H Luo L Zhuang X Zhuang G Deng Y Bai Z . Patulibacter brassicae sp. nov., isolated from rhizosphere soil of Chinese cabbage (Brassica campestris) . Int J Syst Evol Microbiol . 2016 Dec ; 66 ( 12 ): 5056 – 5060 . https://doi.org/10.1099/ijsem.0.001469 Search in Google Scholar

Jones DS, Havlena ZE, Macalady JL. Microbial ecology, evolution, and biosignature potential in isolated chemosynthetic cave ecosystems. Paper presented at: The Mars Extant Life: What’s Next?; 2019 November 5–8; Carlsbad (USA). Houston (USA): Lunar and Planetary Institute; 2019. Available from http://wwwhou.usra.edu/meetings/lifeonmars2019/pdf/5030.pdf Jones DS Havlena ZE Macalady JL . Microbial ecology, evolution, and biosignature potential in isolated chemosynthetic cave ecosystems . Paper presented at: The Mars Extant Life: What’s Next?; 2019 November 5–8 ; Carlsbad (USA). Houston (USA) : Lunar and Planetary Institute ; 2019 . Available from http://wwwhou.usra.edu/meetings/lifeonmars2019/pdf/5030.pdf Search in Google Scholar

Kim DU, Kim SG, Lee H, Park AY, Ka JO. Oryzihumus soli sp. nov , isolated from soil and emended description of the genus Oryzihumus. Int J Syst Evol Microbiol. 2017 Oct;67(10):3960–3964. https://doi.org/10.1099/ijsem.0.002231 Kim DU Kim SG Lee H Park AY Ka JO . Oryzihumus soli sp. nov , isolated from soil and emended description of the genus Oryzihumus . Int J Syst Evol Microbiol . 2017 Oct ; 67 ( 10 ): 3960 – 3964 . https://doi.org/10.1099/ijsem.0.002231 Search in Google Scholar

Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, Glöckner FO. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 2013 Jan;41(1):e1. https://doi.org/10.1093/nar/gks808 Klindworth A Pruesse E Schweer T Peplies J Quast C Horn M Glöckner FO . Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies . Nucleic Acids Res . 2013 Jan ; 41 ( 1 ): e1 . https://doi.org/10.1093/nar/gks808 Search in Google Scholar

Koitsanou E, Sarantopoulou J, Komnenou A, Exadactylos A, Dendrino P, Papadopoulos E, Gkafas GA. First report of the parasitic nematode Pseudoterranova spp. found in Mediterranean monk seal (Monachus monachus) in Greece: Conservation implications. Conserv. 2022;2(1):122–133. https://doi.org/10.3390/conservation2010010 Koitsanou E Sarantopoulou J Komnenou A Exadactylos A Dendrino P Papadopoulos E Gkafas GA . First report of the parasitic nematode Pseudoterranova spp. found in Mediterranean monk seal (Monachus monachus) in Greece: Conservation implications . Conserv . 2022 ; 2 ( 1 ): 122 – 133 . https://doi.org/10.3390/conservation2010010 Search in Google Scholar

Komnenou AT, Gkafas GA, Kofidou E, Sarantopoulou J, Exadactylos A, Tounta E, Koemtzopoulos K, Dendrinos P, Karamanlidis AA, Gulland F, et al. First report of Uncinaria hamiltoni in orphan Eastern Mediterranean monk seal pups in Greece and its clinical significance. Pathogens. 2021 Dec 3;10(12):1581. https://doi.org/10.3390/pathogens10121581 Komnenou AT Gkafas GA Kofidou E Sarantopoulou J Exadactylos A Tounta E Koemtzopoulos K Dendrinos P Karamanlidis AA Gulland F . First report of Uncinaria hamiltoni in orphan Eastern Mediterranean monk seal pups in Greece and its clinical significance . Pathogens . 2021 Dec 3 ; 10 ( 12 ): 1581 . https://doi.org/10.3390/pathogens10121581 Search in Google Scholar

Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl Environ Microbiol. 2013 Sep; 79(17): 5112–5120. https://doi.org/10.1128/AEM.01043-13 Kozich JJ Westcott SL Baxter NT Highlander SK Schloss PD . Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform . Appl Environ Microbiol . 2013 Sep ; 79 ( 17 ): 5112 – 5120 . https://doi.org/10.1128/AEM.01043-13 Search in Google Scholar

Laiz L, Groth I, Gonzalez I, Saiz-Jimenez C. Microbiological study of the dripping waters in Altamira cave (Santillana del Mar, Spain). J Microbiol Methods. 1999 May;36(1–2):129–138. https://doi.org/10.1016/S0167-7012(99)00018-4 Laiz L Groth I Gonzalez I Saiz-Jimenez C . Microbiological study of the dripping waters in Altamira cave (Santillana del Mar, Spain) . J Microbiol Methods . 1999 May ; 36 ( 1–2 ): 129 – 138 . https://doi.org/10.1016/S0167-7012(99)00018-4 Search in Google Scholar

Lee D, Jang JH, Cha S, Seo T. Thalassiella azotovora gen. nov., sp. nov , a new member of the family Kineosporiaceae isolated from sea water in South Korea. Curr Microbiol. 2016 Nov;73(5):676–683. https://doi.org/10.1007/s00284-016-1112-y Lee D Jang JH Cha S Seo T . Thalassiella azotovora gen. nov., sp. nov , a new member of the family Kineosporiaceae isolated from sea water in South Korea . Curr Microbiol . 2016 Nov ; 73 ( 5 ): 676 – 683 . https://doi.org/10.1007/s00284-016-1112-y Search in Google Scholar

Lee DW, Lee SD. Allocatelliglobosispora scoriae gen. nov., sp. nov., isolated from volcanic ash. Int J Syst Evol Microbiol. 2011 Feb; 61(2): 264–270. https://doi.org/10.1099/ijs.0.020313-0 Lee DW Lee SD . Allocatelliglobosispora scoriae gen. nov., sp. nov., isolated from volcanic ash . Int J Syst Evol Microbiol . 2011 Feb ; 61 ( 2 ): 264 – 270 . https://doi.org/10.1099/ijs.0.020313-0 Search in Google Scholar

Lee SD. Conexibacter stalactiti sp. nov., isolated from stalactites in a lava cave and emended description of the genus Conexibacter. Int J Syst Evol Microbiol. 2017 Sep;67(9):3214–3218. https://doi.org/10.1099/ijsem.0.002083 Lee SD . Conexibacter stalactiti sp. nov., isolated from stalactites in a lava cave and emended description of the genus Conexibacter . Int J Syst Evol Microbiol . 2017 Sep ; 67 ( 9 ): 3214 – 3218 . https://doi.org/10.1099/ijsem.0.002083 Search in Google Scholar

Lemma E, Zimhony O, Greenblatt CL, Koltunov V, Zylber MI, Vernon K, Spigelman M. Attempts to revive Mycobacterium tuberculosis from 300-year-old human mummies. FEMS Microbiol Lett. 2008 Jun;283(1):54–61. https://doi.org/10.1111/j.1574-6968.2008.01150x Lemma E Zimhony O Greenblatt CL Koltunov V Zylber MI Vernon K Spigelman M . Attempts to revive Mycobacterium tuberculosis from 300-year-old human mummies . FEMS Microbiol Lett . 2008 Jun ; 283 ( 1 ): 54 – 61 . https://doi.org/10.1111/j.1574-6968.2008.01150x Search in Google Scholar

Li X, Wang Z, Lu F, Zhang H, Tian J, He L, Chu Y, Tian Y. Actinocorallia populi sp. nov., an endophytic actinomycete isolated from a root of Populus adenopoda (Maxim.). Int J Syst Evol Microbiol. 2018 Jul;68(7):2325–2330. https://doi.org/10.1099/ijsem.0.002840 Li X Wang Z Lu F Zhang H Tian J He L Chu Y Tian Y . Actinocorallia populi sp. nov., an endophytic actinomycete isolated from a root of Populus adenopoda (Maxim.) . Int J Syst Evol Microbiol . 2018 Jul ; 68 ( 7 ): 2325 – 2330 . https://doi.org/10.1099/ijsem.0.002840 Search in Google Scholar

Liang Y, Xiao X, Nuccio EE, Yuan M, Zhang N, Xue K, Cohan FM, Zhou J, Sun B. Differentiation strategies of soil rare and abundant microbial taxa in response to changing climatic regimes. Environ Microbiol. 2020 Apr;22(4):1327–1340. https://doi.org/10.1111/1462-2920.14945 Liang Y Xiao X Nuccio EE Yuan M Zhang N Xue K Cohan FM Zhou J Sun B . Differentiation strategies of soil rare and abundant microbial taxa in response to changing climatic regimes . Environ Microbiol . 2020 Apr ; 22 ( 4 ): 1327 – 1340 . https://doi.org/10.1111/1462-2920.14945 Search in Google Scholar

Liu C, Guo Y, Li L, Wang X, Lin J, Wang X, Li J, Chu Y. Catellatospora sichuanensis sp. nov., a novel actinobacterium isolated from soil. Int J Syst Evol Microbiol. 2020 May;70(5):3309–3315. https://doi.org/10.1099/ijsem.0.004175 Liu C Guo Y Li L Wang X Lin J Wang X Li J Chu Y . Catellatospora sichuanensis sp. nov., a novel actinobacterium isolated from soil . Int J Syst Evol Microbiol . 2020 May ; 70 ( 5 ): 3309 – 3315 . https://doi.org/10.1099/ijsem.0.004175 Search in Google Scholar

Long Y, Jiang J, Hu X, Zhou J, Hu J, Zhou S. Actinobacterial community in Shuanghe Cave using culture-dependent and -independent approaches. World J Microbiol Biotechnol. 2019 Oct; 35(10):153. https://doi.org/10.1007/s11274-019-2713-y Long Y Jiang J Hu X Zhou J Hu J Zhou S . Actinobacterial community in Shuanghe Cave using culture-dependent and -independent approaches . World J Microbiol Biotechnol . 2019 Oct ; 35 ( 10 ): 153 . https://doi.org/10.1007/s11274-019-2713-y Search in Google Scholar

Lugli GA, Calvete-Torre I, Alessandri G, Milani C, Turroni F, Laiolo P, Ossiprandi MC, Margolles A, Ruiz L, Ventura M. Phylogenetic classification of ten novel species belonging to the genus Bifidobacterium comprising B. phasiani sp. nov., B. pongonis sp. nov., B. saguinibicoloris sp. nov., B. colobi sp. nov., B. simiiventris sp. nov., B. santillanense sp. nov., B. miconis sp. nov., B. amazonense sp. nov., B. pluvialisilvae sp. nov., and B. miconisargentati sp. nov. Syst Appl Microbiol. 2021 Nov;44(6):126273. https://doi.org/10.1016/j.syapm.2021.126273 Lugli GA Calvete-Torre I Alessandri G Milani C Turroni F Laiolo P Ossiprandi MC Margolles A Ruiz L Ventura M . Phylogenetic classification of ten novel species belonging to the genus Bifidobacterium comprising B. phasiani sp. nov., B. pongonis sp. nov., B. saguinibicoloris sp. nov., B. colobi sp. nov., B. simiiventris sp. nov., B. santillanense sp. nov., B. miconis sp. nov., B. amazonense sp. nov., B. pluvialisilvae sp. nov., and B. miconisargentati sp. nov . Syst Appl Microbiol . 2021 Nov ; 44 ( 6 ): 126273 . https://doi.org/10.1016/j.syapm.2021.126273 Search in Google Scholar

Mann J. Natural products as immunosuppressive agents. Nat Prod Rep. 2001 Aug;18(4):417–430. https://doi.org/10.1039/B001720P Mann J . Natural products as immunosuppressive agents . Nat Prod Rep . 2001 Aug ; 18 ( 4 ): 417 – 430 . https://doi.org/10.1039/B001720P Search in Google Scholar

Martiny JB, Bohannan BJ, Brown JH, Colwell RK, Fuhrman JA, Green JL, Horner-Devine MC, Kane M, Krumins JA, Kuske CR, et al. Microbial biogeography: putting microorganisms on the map. Nat Rev Microbiol. 2006 Feb;4(2):102–112. https://doi.org/10.1038/nrmicro1341 Martiny JB Bohannan BJ Brown JH Colwell RK Fuhrman JA Green JL Horner-Devine MC Kane M Krumins JA Kuske CR . Microbial biogeography: putting microorganisms on the map . Nat Rev Microbiol . 2006 Feb ; 4 ( 2 ): 102 – 112 . https://doi.org/10.1038/nrmicro1341 Search in Google Scholar

Melim LA, Northup DE, Boston PJ, Spilde MN. Preservation of fossil microbes and biofilm in cave pool carbonates and comparison to other microbial carbonate environments. Palaios. 2016 Apr; 31(4):177–189. https://doi.org/10.2110/palo.2015.033 Melim LA Northup DE Boston PJ Spilde MN . Preservation of fossil microbes and biofilm in cave pool carbonates and comparison to other microbial carbonate environments . Palaios . 2016 Apr ; 31 ( 4 ): 177 – 189 . https://doi.org/10.2110/palo.2015.033 Search in Google Scholar

Michail G, Karapetsi L, Madesis P, Reizopoulou A, Vagelas I. Metataxonomic analysis of bacteria entrapped in a stalactite’s core and their possible environmental origins. Microorganisms. 2021 Nov; 9(12):2411. https://doi.org/10.3390/microorganisms9122411 Michail G Karapetsi L Madesis P Reizopoulou A Vagelas I . Metataxonomic analysis of bacteria entrapped in a stalactite’s core and their possible environmental origins . Microorganisms . 2021 Nov ; 9 ( 12 ): 2411 . https://doi.org/10.3390/microorganisms9122411 Search in Google Scholar

Northup DE, Hathaway JJM, Spilde MN, Moser DP, Blank JG. Investigating the mineral: microbe continuum in lava caves to enhance selection of life detection targets. Paper presented at: The Mars Extant Life: What’s Next?; 2019 November 5–8; Carlsbad (USA). Houston (USA): Lunar and Planetary Institute; 2019. Available from https://wwwhou.usra.edu/meetings/lifeonmars2019/pdf/5037.pdf Northup DE Hathaway JJM Spilde MN Moser DP Blank JG . Investigating the mineral: microbe continuum in lava caves to enhance selection of life detection targets . Paper presented at: The Mars Extant Life: What’s Next?; 2019 November 5–8 ; Carlsbad (USA). Houston (USA) : Lunar and Planetary Institute ; 2019 . Available from https://wwwhou.usra.edu/meetings/lifeonmars2019/pdf/5037.pdf Search in Google Scholar

Northup DE, Melim LA, Spilde MN, Hathaway JJ, Garcia MG, Moya M, Stone FD, Boston PJ, Dapkevicius ML, Riquelme C. Lava cave microbial communities within mats and secondary mineral deposits: implications for life detection on other planets. Astrobiology. 2011 Sep;11(7):601–618. https://doi.org/10.1089/ast.2010.0562 Northup DE Melim LA Spilde MN Hathaway JJ Garcia MG Moya M Stone FD Boston PJ Dapkevicius ML Riquelme C . Lava cave microbial communities within mats and secondary mineral deposits: implications for life detection on other planets . Astrobiology . 2011 Sep ; 11 ( 7 ): 601 – 618 . https://doi.org/10.1089/ast.2010.0562 Search in Google Scholar

Oren A, Garrity GM. Notification that new names of prokaryotes, new combinations, and new taxonomic opinions have appeared in volume 71, part 10 of the IJSEM. Int J Syst Evol Microbiol. 2022 Feb; 72(1):005165. https://doi.org/10.1099/ijsem.0.005165 Oren A Garrity GM . Notification that new names of prokaryotes, new combinations, and new taxonomic opinions have appeared in volume 71, part 10 of the IJSEM . Int J Syst Evol Microbiol . 2022 Feb ; 72 ( 1 ): 005165 . https://doi.org/10.1099/ijsem.0.005165 Search in Google Scholar

Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol. 2020 Nov; 70(11):5607–5612 https://doi.org/10.1099/ijsem.0.004332 Parte AC Sardà Carbasse J Meier-Kolthoff JP Reimer LC Göker M . List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ . Int J Syst Evol Microbiol . 2020 Nov ; 70 ( 11 ): 5607 – 5612 https://doi.org/10.1099/ijsem.0.004332 Search in Google Scholar

Rangseekaew P, Pathom-Aree W. Cave Actinobacteria as producers of bioactive metabolites. Front Microbiol. 2019 Mar;10:387. https://doi.org/10.3389/fmicb.2019.00387 Rangseekaew P Pathom-Aree W . Cave Actinobacteria as producers of bioactive metabolites . Front Microbiol . 2019 Mar ; 10 : 387 . https://doi.org/10.3389/fmicb.2019.00387 Search in Google Scholar

Rivera-Perez JI, Santiago-Rodriguez TM, Toranzos GA. Paleomicrobiology: a snapshot of ancient microbes and approaches to forensic microbiology. Microbiol Spectr. 2016 Aug;4(4):4.4.31. https://doi.org/10.1128/microbiolspec.EMF-0006-2015 Rivera-Perez JI Santiago-Rodriguez TM Toranzos GA . Paleomicrobiology: a snapshot of ancient microbes and approaches to forensic microbiology . Microbiol Spectr . 2016 Aug ; 4 ( 4 ): 4.4.31 . https://doi.org/10.1128/microbiolspec.EMF-0006-2015 Search in Google Scholar

Roh SG, Lee C, Kim MK, Kang HJ, Kim YS, Kim MJ, Malik A, Kim SB. Nocardioides euryhalodurans sp. nov., Nocardioides seonyuensis sp. nov. and Nocardioides eburneiflavus sp. nov., isolated from soil. Int J Syst Evol Microbiol. 2020 Apr;70(4):2682–2689. https://doi.org/10.1099/ijsem.0.004095 Roh SG Lee C Kim MK Kang HJ Kim YS Kim MJ Malik A Kim SB . Nocardioides euryhalodurans sp. nov., Nocardioides seonyuensis sp. nov. and Nocardioides eburneiflavus sp. nov., isolated from soil . Int J Syst Evol Microbiol . 2020 Apr ; 70 ( 4 ): 2682 – 2689 . https://doi.org/10.1099/ijsem.0.004095 Search in Google Scholar

Sakdapetsiri C, Kuntaveesuk A, Ngaemthao W, Suriyachadkun C, Muangchinda C, Chavanich S, Viyakarn V, Chen B, Pinyakong O. Paeniglutamicibacter terrestris sp. nov., isolated from phenanthrene-degrading consortium enriched from Antarctic soil. Int J Syst Evol Microbiol. 2019 Jun;71(3). https://doi.org/10.1099/ijsem.0.004689 Sakdapetsiri C Kuntaveesuk A Ngaemthao W Suriyachadkun C Muangchinda C Chavanich S Viyakarn V Chen B Pinyakong O . Paeniglutamicibacter terrestris sp. nov., isolated from phenanthrene-degrading consortium enriched from Antarctic soil . Int J Syst Evol Microbiol . 2019 Jun ; 71 ( 3 ). https://doi.org/10.1099/ijsem.0.004689 Search in Google Scholar

Sanmartín, I. Historical biogeography: Evolution in time and space. Evo Edu Outreach. 2012;5:555–568. https://doi.org/10.1007/s12052-012-0421-2 Sanmartín, I . Historical biogeography: Evolution in time and space . Evo Edu Outreach . 2012 ; 5 : 555 – 568 . https://doi.org/10.1007/s12052-012-0421-2 Search in Google Scholar

Savini V, Catavitello C, Masciarelli G, Astolfi D, Balbinot A, Bianco A, Febbo F, D’Amario C, D’Antonio D. Drug sensitivity and clinical impact of members of the genus Kocuria. J Med Microbiol. 2010 Dec;59(12):1395–1402. https://doi.org/10.1099/jmm.0.021709-0 Savini V Catavitello C Masciarelli G Astolfi D Balbinot A Bianco A Febbo F D’Amario C D’Antonio D . Drug sensitivity and clinical impact of members of the genus Kocuria . J Med Microbiol . 2010 Dec ; 59 ( 12 ): 1395 – 1402 . https://doi.org/10.1099/jmm.0.021709-0 Search in Google Scholar

Saygin H, Ay H, Guven K, Sahin N. Genome-based classification of three novel actinobacteria from the Karakum Desert: Jiangella asiatica sp. nov., Jiangella aurantiaca sp. nov. and Jiangella ureilytica sp. nov. Int J Syst Evol Microbiol. 2020 Mar;70(3):1993–2002. https://doi.org/10.1099/ijsem.0.004011 Saygin H Ay H Guven K Sahin N . Genome-based classification of three novel actinobacteria from the Karakum Desert: Jiangella asiatica sp. nov., Jiangella aurantiaca sp. nov. and Jiangella ureilytica sp. nov . Int J Syst Evol Microbiol . 2020 Mar ; 70 ( 3 ): 1993 – 2002 . https://doi.org/10.1099/ijsem.0.004011 Search in Google Scholar

Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009 Dec;75(23): 7537–7541. https://doi.org/10.1128/AEM.01541-09 Schloss PD Westcott SL Ryabin T Hall JR Hartmann M Hollister EB Lesniewski RA Oakley BB Parks DH Robinson CJ . Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities . Appl Environ Microbiol . 2009 Dec ; 75 ( 23 ): 7537 – 7541 . https://doi.org/10.1128/AEM.01541-09 Search in Google Scholar

Sen A, Daubin V, Abrouk D, Gifford I, Berry AM, Normand P. Phylogeny of the class Actinobacteria revisited in the light of complete genomes. The orders ‘Frankiales’ and Micrococcales should be split into coherent entities: proposal of Frankiales ord. nov., Geodermatophilales ord. nov., Acidothermales ord. nov. and Nakamurellales ord. nov. Int J Syst Evol Microbiol. 2014 Nov;64(11):3821–3832. https://doi.org/10.1099/ijs.0.063966-0 Sen A Daubin V Abrouk D Gifford I Berry AM Normand P . Phylogeny of the class Actinobacteria revisited in the light of complete genomes. The orders ‘Frankiales’ and Micrococcales should be split into coherent entities: proposal of Frankiales ord. nov., Geodermatophilales ord. nov., Acidothermales ord. nov. and Nakamurellales ord. nov . Int J Syst Evol Microbiol . 2014 Nov ; 64 ( 11 ): 3821 – 3832 . https://doi.org/10.1099/ijs.0.063966-0 Search in Google Scholar

Shin Y, Lee BH, Lee KE, Park W. Pseudarthrobacter psychrotolerans sp. nov., a cold-adapted bacterium isolated from Antarctic soil. Int J Syst Evol Microbiol. 2020 Dec;70(12):6106–6114. https://doi.org/10.1099/ijsem.0.004505 Shin Y Lee BH Lee KE Park W . Pseudarthrobacter psychrotolerans sp. nov., a cold-adapted bacterium isolated from Antarctic soil . Int J Syst Evol Microbiol . 2020 Dec ; 70 ( 12 ): 6106 – 6114 . https://doi.org/10.1099/ijsem.0.004505 Search in Google Scholar

Siddiqi MZ, Lee SY, Choi KD, Im WT. Aeromicrobium panacisoli sp. nov. isolated from soil of ginseng cultivating field. Curr Microbiol. 2018 May;75(5):624–629. https://doi.org/10.1007/s00284-017-1426-4 Siddiqi MZ Lee SY Choi KD Im WT . Aeromicrobium panacisoli sp. nov. isolated from soil of ginseng cultivating field . Curr Microbiol . 2018 May ; 75 ( 5 ): 624 – 629 . https://doi.org/10.1007/s00284-017-1426-4 Search in Google Scholar

Stackebrandt E. The family Dermabacteraceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F, editors. The Prokaryotes. Berlin, Heidelberg (Germany): Springer; 2014. https://doi.org/10.1007/978-3-642-30138-4_170 Stackebrandt E . The family Dermabacteraceae . In: Rosenberg E DeLong EF Lory S Stackebrandt E Thompson F editors. The Prokaryotes . Berlin, Heidelberg (Germany) : Springer ; 2014 . https://doi.org/10.1007/978-3-642-30138-4_170 Search in Google Scholar

Tamura T, Hayakawa M, Hatano K. Sporichthya brevicatena sp. nov. Int J Syst Bacteriol. 1999 Oct;49(4):1779–1784. https://doi.org/10.1099/00207713-49-4-1779 Tamura T Hayakawa M Hatano K . Sporichthya brevicatena sp. nov . Int J Syst Bacteriol . 1999 Oct ; 49 ( 4 ): 1779 – 1784 . https://doi.org/10.1099/00207713-49-4-1779 Search in Google Scholar

Tierney JE, Poulsen CJ, Montañez IP, Bhattacharya T, Feng R, Ford HL, Hönisch B, Inglis GN, Petersen SV, Sagoo N, et al. Past climates inform our future. Science. 2020 Nov;370(6517):eaay3701. https://doi.org/10.1126/science.aay3701 Tierney JE Poulsen CJ Montañez IP Bhattacharya T Feng R Ford HL Hönisch B Inglis GN Petersen SV Sagoo N . Past climates inform our future . Science . 2020 Nov ; 370 ( 6517 ): eaay3701 . https://doi.org/10.1126/science.aay3701 Search in Google Scholar

Tomczyk-Zak K, Zielenkiewicz U. Microbial diversity in caves. Geomicrobiol J. 2016;33(1):20–38. https://doi.org/10.1080/01490451.2014.1003341 Tomczyk-Zak K Zielenkiewicz U . Microbial diversity in caves . Geomicrobiol J . 2016 ; 33 ( 1 ): 20 – 38 . https://doi.org/10.1080/01490451.2014.1003341 Search in Google Scholar

Troussellier M, Escalas A, Bouvier T, Mouillot D. Sustaining rare marine microorganisms: Macroorganisms as repositories and dispersal agents of microbial diversity. Front Microbiol. 2017 May;8:947. https://doi.org/10.3389/fmicb.2017.00947 Troussellier M Escalas A Bouvier T Mouillot D . Sustaining rare marine microorganisms: Macroorganisms as repositories and dispersal agents of microbial diversity . Front Microbiol . 2017 May ; 8 : 947 . https://doi.org/10.3389/fmicb.2017.00947 Search in Google Scholar

Uckert K, Chanover NJ, Getty S, Voelz DG, Brinckerhoff WB, McMillan N, Xiao X, Boston PJ, Li X, McAdam A, et al. The characterization of biosignatures in caves using an instrument suite. Astrobiology. 2017 Dec;17(12):1203–1218. https://doi.org/10.1089/ast.2016.1568 Uckert K Chanover NJ Getty S Voelz DG Brinckerhoff WB McMillan N Xiao X Boston PJ Li X McAdam A . The characterization of biosignatures in caves using an instrument suite . Astrobiology . 2017 Dec ; 17 ( 12 ): 1203 – 1218 . https://doi.org/10.1089/ast.2016.1568 Search in Google Scholar

Undabarrena A, Salvà-Serra F, Jaén-Luchoro D, Castro-Nallar E, Mendez KN, Valencia R, Ugalde JA, Moore ERB, Seeger M, Cámara B. Complete genome sequence of the marine Rhodococcus sp. H-CA8f isolated from Comau fjord in Northern Patagonia, Chile. Mar Genomics. 2018 Jul;40:13–17. https://doi.org/10.1016/J.MARGEN.2018.01.004 Undabarrena A Salvà-Serra F Jaén-Luchoro D Castro-Nallar E Mendez KN Valencia R Ugalde JA Moore ERB Seeger M Cámara B . Complete genome sequence of the marine Rhodococcus sp. H-CA8f isolated from Comau fjord in Northern Patagonia, Chile . Mar Genomics . 2018 Jul ; 40 : 13 – 17 . https://doi.org/10.1016/J.MARGEN.2018.01.004 Search in Google Scholar

Xie YG, Fang BZ, Han MX, Liu L, Jiao JY, Zhang XT, Xiao M, Li WJ. Microlunatus speluncae sp. nov., a novel actinobacterium isolated from a Karstic subterranean environment sample. Antonie Van Leeuwenhoek. 2020 Jan;113(1):117–125. https://doi.org/10.1007/s10482-019-01321-4 Xie YG Fang BZ Han MX Liu L Jiao JY Zhang XT Xiao M Li WJ . Microlunatus speluncae sp. nov., a novel actinobacterium isolated from a Karstic subterranean environment sample . Antonie Van Leeuwenhoek . 2020 Jan ; 113 ( 1 ): 117 – 125 . https://doi.org/10.1007/s10482-019-01321-4 Search in Google Scholar

Yang ZW, Asem MD, Li X, Li LY, Salam N, Alkhalifah DHM, Hozzein WN, Nie GX, Li WJ. Blastococcus deserti sp. nov., isolated from a desert sample. Arch Microbiol. 2019 Mar;201(2):193–198. https://doi.org/10.1007/s00203-018-1604-1 Yang ZW Asem MD Li X Li LY Salam N Alkhalifah DHM Hozzein WN Nie GX Li WJ . Blastococcus deserti sp. nov., isolated from a desert sample . Arch Microbiol . 2019 Mar ; 201 ( 2 ): 193 – 198 . https://doi.org/10.1007/s00203-018-1604-1 Search in Google Scholar

Zhang YG, Liu Q, Wang HF, Zhang DF, Zhang YM, Park DJ, Kim CJ, Li WJ. Haloactinopolyspora alkaliphila sp. nov., and emended description of the genus Haloactinopolyspora. Int J Syst Evol Microbiol. 2014 Jun;64(6):1945–1951. https://doi.org/10.1099/ijs.0.062646-0 Zhang YG Liu Q Wang HF Zhang DF Zhang YM Park DJ Kim CJ Li WJ . Haloactinopolyspora alkaliphila sp. nov., and emended description of the genus Haloactinopolyspora . Int J Syst Evol Microbiol . 2014 Jun ; 64 ( 6 ): 1945 – 1951 . https://doi.org/10.1099/ijs.0.062646-0 Search in Google Scholar

Zhi XY, Li WJ, Stackebrandt E. An update of the structure and 16S rRNA gene sequence-based definition of higher ranks of the class Actinobacteria, with the proposal of two new suborders and four new families and emended descriptions of the existing higher taxa. Int J Syst Evol Microbiol. 2009 Mar;59(3):589–608. https://doi.org/10.1099/ijs.0.65780-0 Zhi XY Li WJ Stackebrandt E . An update of the structure and 16S rRNA gene sequence-based definition of higher ranks of the class Actinobacteria, with the proposal of two new suborders and four new families and emended descriptions of the existing higher taxa . Int J Syst Evol Microbiol . 2009 Mar ; 59 ( 3 ): 589 – 608 . https://doi.org/10.1099/ijs.0.65780-0 Search in Google Scholar

Zhu HZ, Zhang ZF, Zhou N, Jiang CY, Wang BJ, Cai L, Liu SJ. Diversity, distribution and co-occurrence patterns of bacterial communities in a karst cave system. Front Microbiol. 2019 Aug;10:1726. https://doi.org/10.3389/fmicb.2019.01726 Zhu HZ Zhang ZF Zhou N Jiang CY Wang BJ Cai L Liu SJ . Diversity, distribution and co-occurrence patterns of bacterial communities in a karst cave system . Front Microbiol . 2019 Aug ; 10 : 1726 . https://doi.org/10.3389/fmicb.2019.01726 Search in Google Scholar