Kelly LC, Cockell CS, Herrera-Belaroussi A, Piceno Y, Andersen G, DeSantis T, Brodie E, Thorsteinsson T, Marteinsson V, Poly F. Bacterial diversity of terrestrial crystalline volcanic rocks, Iceland. Microb Ecol. 2011;62(1):69–79.
Article
CAS
Google Scholar
Kelly LC, Cockell CS, Piceno YM, Andersen GL, Thorsteinsson T, Marteinsson V. Bacterial diversity of weathered terrestrial Icelandic volcanic glasses. Microb Ecol. 2010;60(4):740–52.
Article
Google Scholar
Olsson-Francis K, Pearson V, Boardman C, Schofield P, Oliver A, Summers S. A culture-independent and culture-dependent study of the bacteria community from the bedrock soil interface. Adv Microbiol. 2015;5(13):842–57.
Article
CAS
Google Scholar
Staudigel H, Hart SR. Alteration of basaltic glass: mechanisms and significance for the oceanic crust-seawater budget. Geochim Cosmochim Acta. 1983;47(3):337–50.
Article
CAS
Google Scholar
Gomez-Alvarez V, King GM, Nüsslein K. Comparative bacterial diversity in recent Hawaiian volcanic deposits of different ages. FEMS Microbiol Ecol. 2007;60(1):60–73.
Article
CAS
Google Scholar
Mason OU, Di Meo-Savoie CA, Van Nostrand JD, Zhou J, Fisk MR, Giovannoni SJ. Prokaryotic diversity, distribution, and insights into their role in biogeochemical cycling in marine basalts. ISME J. 2009;3(2):231–42.
Article
CAS
Google Scholar
Chen J, Blume H-P, Beyer L. Weathering of rocks induced by lichen colonization—a review. Catena. 2000;39(2):121–46.
Article
CAS
Google Scholar
King GM. Contributions of atmospheric CO and hydrogen uptake to microbial dynamics on recent Hawaiian volcanic deposits. Appl Environ Microbiol. 2003;69(7):4067–75.
Article
CAS
Google Scholar
Cockell CS, Olsson K, Knowles F, Kelly L, Herrera A, Thorsteinsson T, Marteinsson V. Bacteria in weathered basaltic glass, Iceland. Geomicrobiol J. 2009;26(7):491–507.
Article
CAS
Google Scholar
Fujimura R, Sato Y, Nishizawa T, Nanba K, Oshima K, Hattori M, Kamijo T, Ohta H. Analysis of early bacterial communities on volcanic deposits on the island of Miyake (Miyake-jima), Japan: a 6-year study at a fixed site. Microbes Environ. 2012;27(1):19–29.
Article
Google Scholar
Kelly LC, Cockell CS, Thorsteinsson T, Marteinsson V, Stevenson J. Pioneer microbial communities of the Fimmvorethuhals lava flow, Eyjafjallajokull, Iceland. Microb Ecol. 2014;68(3):504–18.
Article
Google Scholar
Nemergut DR, Anderson SP, Cleveland CC, Martin AP, Miller AE, Seimon A, Schmidt SK. Microbial community succession in an unvegetated, recently deglaciated soil. Microb Ecol. 2007;53(1):110–22.
Article
Google Scholar
Thordarson T, Larsen G. Volcanism in Iceland in historical time: volcano types, eruption styles and eruptive history. J Geodyn. 2007;43(1):118–52.
Article
Google Scholar
Summers S, Whiteley AS, Kelly LC, Cockell CS. Land coverage influences the bacterial community composition in the critical zone of a sub-Arctic basaltic environment. FEMS Microbiol Ecol. 2013;86(3):381–93.
Article
CAS
Google Scholar
Lukito HP, Kouno K, Ando T. Phosphorus requirements of microbial biomass in a regosol and an andosol. Soil Biol Biochem. 1998;30(7):865–72.
Article
CAS
Google Scholar
Santelli CM, Edgcomb VP, Bach W, Edwards KJ. The diversity and abundance of bacteria inhabiting seafloor lavas positively correlate with rock alteration. Environ Microbiol. 2009;11(1):86–98.
Article
CAS
Google Scholar
Herrera A, Cockell CS. Exploring microbial diversity in volcanic environments: a review of methods in DNA extraction. J Microbiol Methods. 2007;70(1):1–12.
Article
CAS
Google Scholar
Cockell CS, Kelly LC, Marteinsson V. Actinobacteria—an ancient phylum active in volcanic rock weathering. Geomicrobiol J. 2013;30(8):706–20.
Article
CAS
Google Scholar
Lysnes K, Thorseth IH, Steinsbu BO, Øvreås L, Torsvik T, Pedersen RB. Microbial community diversity in seafloor basalt from the Arctic spreading ridges. FEMS Microbiol Ecol. 2004;50(3):213–30.
Article
CAS
Google Scholar
Lechevalier HA, Lechevalier MP. Biology of actinomycetes. Annu Rev Microbiol. 1967;21(1):71–100.
Article
CAS
Google Scholar
Bergen B, Herlemann DP, Labrenz M, Jürgens K. Distribution of the verrucomicrobial clade Spartobacteria along a salinity gradient in the Baltic Sea. Environ Microbiol Rep. 2014;6(6):625–30.
Article
CAS
Google Scholar
Paul D, Kumbhare SV, Mhatre SS, Chowdhury SP, Shetty SA, Marathe NP, Bhute S, Shouche YS. Exploration of microbial diversity and community structure of Lonar Lake: the only hypersaline meteorite crater Lake within basalt rock. Front Microbiol. 2016;6:1553. https://doi.org/10.3389/fmicb.2015.01553.
Henri PA, Rommevaux-Jestin C, Lesongeur F, Mumford A, Emerson D, Godfroy A, Ménez B. Structural Iron (II) of basaltic glass as an energy source for Zetaproteobacteria in an abyssal plain environment, off the mid Atlantic ridge. Front Microbiol. 1518;6:2016.
Google Scholar
Kim JS, Lee KC, Kim DS, Ko SH, Jung MY, Rhee SK, Lee JS. Pyrosequencing analysis of a bacterial community associated with lava-formed soil from the Gotjawal forest in Jeju, Korea. MicrobiologyOpen. 2015;4(2):301–12.
Article
CAS
Google Scholar
Einen J, Kruber C, Øvreås L, Thorseth I, Torsvik T. Microbial colonization and alteration of basaltic glass. Biogeosci Discuss. 2006;3(2):273–307.
Article
Google Scholar
Oh T-J, Han S-R, Kang S, Park H, Kim AY. Complete genome sequence of the xylan-degrading Mucilaginibacter sp. strain PAMC26640 isolated from an Arctic lichen. J Biotechnol. 2016;227:23–4.
Article
CAS
Google Scholar
Erlacher A, Cernava T, Cardinale M, Soh J, Sensen CW, Grube M, Berg G. Rhizobiales as functional and endosymbiontic members in the lichen symbiosis of Lobaria pulmonaria L. Front Microbiol. 2015;6:53.
Article
Google Scholar
Walsh J, Clarke E. The role of fractional crystallization in the formation of granitic and intermediate rocks of the Beinn Chaisgidle Centre, Mull, Scotland. Mineral Mag. 1982;45(337):247–55.
Article
CAS
Google Scholar
Herrera A, Cockell CS, Self S, Blaxter M, Reitner J, Arp G, Drose W, Thorsteinsson T, Tindle AG. Bacterial colonization and weathering of terrestrial obsidian in Iceland. Geomicrobiol J. 2008;25(1):25–37.
Article
CAS
Google Scholar
Tebo BM, Davis RE, Anitori RP, Connell LB, Schiffman P, Staudigel H. Microbial communities in dark oligotrophic volcanic ice cave ecosystems of Mt. Erebus, Antarctica. Front Microbiol. 2015;6:179. https://doi.org/10.3389/fmicb.2015.00179.
Carson JK, Campbell L, Rooney D, Clipson N, Gleeson DB. Minerals in soil select distinct bacterial communities in their microhabitats. FEMS Microbiol Ecol. 2009;67(3):381–8.
Article
CAS
Google Scholar
Teixeira LC, Peixoto RS, Cury JC, Sul WJ, Pellizari VH, Tiedje J, Rosado AS. Bacterial diversity in rhizosphere soil from Antarctic vascular plants of Admiralty Bay, maritime Antarctica. ISME J. 2010;4(8):989–1001.
Article
Google Scholar
Barker W, Welch S, Chu S, Banfield J. Experimental observations of the effects of bacteria on aluminosilicate weathering. Am Mineral. 1998;83(11):1551–63.
Article
CAS
Google Scholar
Bennett P, Rogers J, Choi W, Hiebert F. Silicates, silicate weathering, and microbial ecology. Geomicrobiol J. 2001;18(1):3–19.
Article
CAS
Google Scholar
Hall K, Lindgren BS, Jackson P. Rock albedo and monitoring of thermal conditions in respect of weathering: some expected and some unexpected results. Earth Surf Process Landf. 2005;30(7):801–12.
Article
Google Scholar
Wolff-Boenisch D, Gislason SR, Oelkers EH, Putnis CV. The dissolution rates of natural glasses as a function of their composition at pH 4 and 10.6, and temperatures from 25 to 74 C. Geochim Cosmochim Acta. 2004;68(23):4843–58.
Article
CAS
Google Scholar
Edwards KJ, Bach W, McCollom TM, Rogers DR. Neutrophilic iron-oxidizing bacteria in the ocean: their habitats, diversity, and roles in mineral deposition, rock alteration, and biomass production in the deep-sea. Geomicrobiol J. 2004;21(6):393–404.
Article
CAS
Google Scholar
Berney M, Hammes F, Bosshard F, Weilenmann HU, Egli T. Assessment and interpretation of bacterial viability by using the LIVE/DEAD BacLight kit in combination with flow cytometry. Appl Environ Microbiol. 2007;73(10):3283–90.
Article
CAS
Google Scholar
Buysschaert B, Byloos B, Leys N, Van Houdt R, Boon N. Reevaluating multicolor flow cytometry to assess microbial viability. Appl Microbiol Biotechnol. 2016;100(21):9037–51.
Article
CAS
Google Scholar
Van Nevel S, Koetzsch S, Weilenmann HU, Boon N, Hammes F. Routine bacterial analysis with automated flow cytometry. J Microbiol Methods. 2013;94(2):73–6.
Article
Google Scholar
Griffiths RI, Whiteley AS, O'Donnell AG, Bailey MJ. Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA- and rRNA-based microbial community composition. Appl Environ Microbiol. 2000;66(12):5488–91.
Article
CAS
Google Scholar
Vilchez-Vargas R, Geffers R, Suárez-Diez M, Conte I, Waliczek A, Kaser VS, Kralova M, Junca H, Pieper DH. Analysis of the microbial gene landscape and transcriptome for aromatic pollutants and alkane degradation using a novel internally calibrated microarray system. Environ Microbiol. 2013;15(4):1016–39.
Article
CAS
Google Scholar
Mysara M, Njima M, Leys N, Raes J, Monsieurs P. From reads to operational taxonomic units: an ensemble processing pipeline for MiSeq amplicon sequencing data. Gigascience. 2017;6(2):1–10.
Article
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;79(17):5112–20.
Article
CAS
Google Scholar
Mysara M, Leys N, Raes J, Monsieurs P. IPED: a highly efficient denoising tool for Illumina MiSeq paired-end 16S rRNA gene amplicon sequencing data. BMC Bioinformatics. 2016;17(1):192.
Article
Google Scholar
Mysara M, Saeys Y, Leys N, Raes J, Monsieurs P. CATCh, an ensemble classifier for chimera detection in 16S rRNA sequencing studies. Appl Environ Microbiol. 2015;81(5):1573–84.
Article
Google Scholar
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41(D1):D590–6.
Article
CAS
Google Scholar
Edgar RC. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods. 2013;10(10):996–8.
Article
CAS
Google Scholar
Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, Glöckner FO. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 2007;35(21):7188–96.
Article
CAS
Google Scholar
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;75(23):7537–41.
Article
CAS
Google Scholar
Jost L. Entropy and diversity. Oikos. 2006;113(2):363–75.
Article
Google Scholar
Schloss PD, Handelsman J. Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol. 2005;71(3):1501–6.
Article
CAS
Google Scholar