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Metagenomic Analysis from the Interior of a Speleothem in Tjuv-Ante's Cave, Northern Sweden.

https://arctichealth.org/en/permalink/ahliterature274797
Source
PLoS One. 2016;11(3):e0151577
Publication Type
Article
Date
2016
Author
Marie Lisandra Zepeda Mendoza
Johannes Lundberg
Magnus Ivarsson
Paula Campos
Johan A A Nylander
Therese Sallstedt
Love Dalen
Source
PLoS One. 2016;11(3):e0151577
Date
2016
Language
English
Publication Type
Article
Keywords
Actinobacteria - genetics
Biodiversity
Caves - microbiology
Metagenome
Metagenomics
Sweden
Abstract
Speleothems are secondary mineral deposits normally formed by water supersaturated with calcium carbonate percolating into underground caves, and are often associated with low-nutrient and mostly non-phototrophic conditions. Tjuv-Ante's cave is a shallow-depth cave formed by the action of waves, with granite and dolerite as major components, and opal-A and calcite as part of the speleothems, making it a rare kind of cave. We generated two DNA shotgun sequencing metagenomic datasets from the interior of a speleothem from Tjuv-Ante's cave representing areas of old and relatively recent speleothem formation. We used these datasets to perform i) an evaluation of the use of these speleothems as past biodiversity archives, ii) functional and taxonomic profiling of the speleothem's different formation periods, and iii) taxonomic comparison of the metagenomic results to previous microscopic analyses from a nearby speleothem of the same cave. Our analyses confirm the abundance of Actinobacteria and fungi as previously reported by microscopic analyses on this cave, however we also discovered a larger biodiversity. Interestingly, we identified photosynthetic genes, as well as genes related to iron and sulphur metabolism, suggesting the presence of chemoautotrophs. Furthermore, we identified taxa and functions related to biomineralization. However, we could not confidently establish the use of this type of speleothems as biological paleoarchives due to the potential leaching from the outside of the cave and the DNA damage that we propose has been caused by the fungal chemical etching.
Notes
Cites: Appl Environ Microbiol. 2006 Jul;72(7):5069-7216820507
Cites: Genome Biol. 2012;13(12):R12223259615
Cites: Protist. 2007 Jul;158(3):325-3617576099
Cites: Appl Environ Microbiol. 1989 Oct;55(10):2499-5042604392
Cites: Nucleic Acids Res. 1996 Apr 1;24(7):1304-78614634
Cites: J Antibiot (Tokyo). 1998 Aug;51(8):699-7079766461
Cites: Int J Syst Bacteriol. 1999 Jul;49 Pt 3:1053-7310425763
Cites: Nucleic Acids Res. 2005 Jan 1;33(Database issue):D294-615608200
Cites: Mol Microbiol. 2005 Jun;56(5):1386-9515882428
Cites: Int Microbiol. 2005 Sep;8(3):189-9416200497
Cites: FEMS Microbiol Rev. 2000 Oct;24(4):335-6610978542
Cites: Water Sci Technol. 2001;43(6):77-8611381975
Cites: Nucleic Acids Res. 2001 Dec 1;29(23):4793-911726688
Cites: Appl Environ Microbiol. 2003 Apr;69(4):2182-9312676699
Cites: Science. 2003 May 2;300(5620):791-512702808
Cites: Clin Chem. 2004 Jan;50(1):88-9214709639
Cites: Appl Environ Microbiol. 2004 Mar;70(3):1627-3215006787
Cites: Int J Syst Evol Microbiol. 2004 May;54(Pt 3):857-6415143036
Cites: Appl Environ Microbiol. 2004 Sep;70(9):5595-60215345448
Cites: J Bacteriol. 1970 Oct;104(1):462-725473903
Cites: J Bacteriol. 1979 Jan;137(1):524-30216663
Cites: Trends Biotechnol. 2006 Jun;24(6):255-6016647149
Cites: Science. 2007 Jul 6;317(5834):111-417615355
Cites: Anim Genet. 2007 Aug;38(4):378-8317596126
Cites: Appl Environ Microbiol. 2007 Oct;73(19):6172-8017693567
Cites: J Biotechnol. 2008 Mar 20;134(1-2):33-4518304669
Cites: Pak J Pharm Sci. 2010 Jan;23(1):1-620067859
Cites: Cold Spring Harb Protoc. 2010 Jan;2010(1):pdb.prot536820150127
Cites: BMC Bioinformatics. 2010;11:11920211023
Cites: Nat Methods. 2010 May;7(5):335-620383131
Cites: Cold Spring Harb Protoc. 2010 Jun;2010(6):pdb.prot544820516186
Cites: Photosynth Res. 2010 Jun;104(2-3):245-5520130996
Cites: Bioinformatics. 2010 Oct 1;26(19):2460-120709691
Cites: Nucleic Acids Res. 2010 Nov;38(20):e19120805240
Cites: Chemosphere. 2011 Jun;83(11):1560-721316734
Cites: Water Res. 2011 May;45(11):3512-2021536315
Cites: FEMS Microbiol Lett. 2012 Jan;326(1):47-5422092362
Cites: J Bacteriol. 2012 May;194(10):2752-322535935
Cites: PLoS One. 2012;7(10):e4765623082188
Cites: Proc Natl Acad Sci U S A. 2012 Dec 11;109(50):20532-623185018
Cites: Nucleic Acids Res. 2013 Jan;41(Database issue):D590-623193283
Cites: Microb Ecol. 2013 Feb;65(2):371-8323224253
Cites: Bioinformatics. 2013 Jul 1;29(13):1682-423613487
Cites: ISME J. 2013 Sep;7(9):1775-8923575369
Cites: Methods Enzymol. 2013;531:465-8524060133
Cites: ISME J. 2014 Feb;8(2):478-9124030597
Cites: Proc Natl Acad Sci U S A. 2014 Feb 11;111(6):2229-3424469802
Cites: Mol Biol Evol. 2007 Apr;24(4):998-100417255122
PubMed ID
26985997 View in PubMed
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