title: Surprising prokaryotic and eukaryotic diversity, community structure and biogeography of Ethiopian soda lakes.
abstract: Soda lakes are intriguing ecosystems harboring extremely productive microbial communities in spite of their extreme environmental conditions. This makes them valuable model systems for studying the connection between community structure and abiotic parameters such as pH and salinity. For the first time, we apply high-throughput sequencing to accurately estimate phylogenetic richness and composition in five soda lakes, located in the Ethiopian Rift Valley. The lakes were selected for their contrasting pH, salinities and stratification and several depths or spatial positions were covered in each lake. DNA was extracted and analyzed from all lakes at various depths and RNA extracted from two of the lakes, analyzed using both amplicon- and shotgun sequencing. We reveal a surprisingly high biodiversity in all of the studied lakes, similar to that of freshwater lakes. Interestingly, diversity appeared uncorrelated or positively correlated to pH and salinity, with the most "extreme" lakes showing the highest richness. Together, pH, dissolved oxygen, sodium- and potassium concentration explained approximately 30% of the compositional variation between samples. A diversity of prokaryotic and eukaryotic taxa could be identified, including several putatively involved in carbon-, sulfur- or nitrogen cycling. Key processes like methane oxidation, ammonia oxidation and 'nitrifier denitrification' were also confirmed by mRNA transcript analyses.
authors.affiliation: Department of Biology and Centre for Geobiology, University of Bergen, Bergen, Norway ; Computational Biology Unit, Uni Computing, Uni Research AS, Bergen, Norway.
authors.forename: Anders
authors.initials: A
authors.lastname: Lanzén
authors.forename: Addis
authors.initials: A
authors.lastname: Simachew
authors.forename: Amare
authors.initials: A
authors.lastname: Gessesse
authors.forename: Dominika
authors.initials: D
authors.lastname: Chmolowska
authors.forename: Inge
authors.initials: I
authors.lastname: Jonassen
authors.forename: Lise
authors.initials: L
authors.lastname: Øvreås
mesh_terms: D001419:Bacteria / Q000235:genetics / Q000302:isolation & purification; D001483:Base Sequence; D044822:Biodiversity; D030541:Databases, Genetic; D005002:Ethiopia; D056890:Eukaryota / Q000254:growth & development*; D005786:Gene Expression Regulation; D060106:Lakes / Q000382:microbiology*; D058974:Phylogeography; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D012335:RNA, Ribosomal / Q000235:genetics
chemical_list: D012333:RNA, Messenger; D012335:RNA, Ribosomal
references.citation: Mol Syst Biol. 2008;4:198
references.pmid: 18523433
references.citation: Appl Environ Microbiol. 2009 Aug;75(16):5227-36
references.pmid: 19561178
references.citation: Int J Syst Bacteriol. 1998 Jul;48 Pt 3:821-8
references.pmid: 9734036
references.citation: Int J Syst Evol Microbiol. 2012 Jul;62(Pt 7):1613-1618
references.pmid: 21890731
references.citation: Protist. 2011 Nov;162(5):738-61
references.pmid: 21715228
references.citation: J Microbiol. 2009 Aug;47(4):371-84
references.pmid: 19763410
references.citation: PLoS One. 2008 Jun 25;3(6):e2527
references.pmid: 18575584
references.citation: Proc Natl Acad Sci U S A. 2010 Mar 30;107(13):5881-6
references.pmid: 20231463
references.citation: Microb Ecol. 2012 Nov;64(4):955-63
references.pmid: 22644483
references.citation: ISME J. 2012 Jun;6(6):1127-36
references.pmid: 22170419
references.citation: ISME J. 2012 Sep;6(9):1640-52
references.pmid: 22418623
references.citation: Environ Microbiol. 2012 Sep;14(9):2457-66
references.pmid: 22676420
references.citation: Environ Microbiol. 2011 Nov;13(11):3000-9
references.pmid: 21910812
references.citation: PLoS One. 2012;7(9):e44224
references.pmid: 22970184
references.citation: Microbiol Mol Biol Rev. 1999 Jun;63(2):334-48
references.pmid: 10357854
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D141-5
references.pmid: 21062808
references.citation: Arch Microbiol. 2000 Jul-Aug;174(1-2):18-27
references.pmid: 10985738
references.citation: Bioinformatics. 2007 May 15;23(10):1282-8
references.pmid: 17379688
references.citation: Proc Natl Acad Sci U S A. 2012 Oct 16;109(42):E2846-55
references.pmid: 23027979
references.citation: Microb Ecol. 2009 Oct;58(3):569-81
references.pmid: 19444496
references.citation: Environ Microbiol. 2005 Dec;7(12):1967-84
references.pmid: 16309394
references.citation: ISME J. 2012 Dec;6(12):2188-98
references.pmid: 22763650
references.citation: Stud Hist Philos Biol Biomed Sci. 2008 Sep;39(3):314-25
references.pmid: 18761283
references.citation: Appl Environ Microbiol. 2006 Aug;72(8):5478-85
references.pmid: 16885301
references.citation: FEMS Microbiol Ecol. 2010 Aug;73(2):278-90
references.pmid: 20500526
references.citation: Microb Ecol. 2007 Nov;54(4):598-617
references.pmid: 17450395
references.citation: Res Microbiol. 2006 Dec;157(10):928-37
references.pmid: 17070674
references.citation: FEMS Microbiol Ecol. 2012 Jul;81(1):43-51
references.pmid: 22150151
references.citation: Appl Environ Microbiol. 2008 Aug;74(15):4877-88
references.pmid: 18552187
references.citation: ISME J. 2011 Oct;5(10):1571-9
references.pmid: 21472016
references.citation: Appl Environ Microbiol. 2009 Jun;75(12):4211-5
references.pmid: 19395565
references.citation: BMC Microbiol. 2012 Jul 26;12:150
references.pmid: 22834535
references.citation: Wei Sheng Wu Xue Bao. 2010 Mar;50(3):334-41
references.pmid: 20499638
references.citation: Environ Microbiol. 2008 Sep;10(9):2200-10
references.pmid: 18637951
references.citation: PLoS One. 2011;6(11):e27597
references.pmid: 22125616
references.citation: Nature. 2010 Mar 25;464(7288):592-6
references.pmid: 20228792
references.citation: Environ Microbiol. 2004 Oct;6(10):1049-60
references.pmid: 15344930
references.citation: FEMS Microbiol Ecol. 2011 May;76(2):393-400
references.pmid: 21265869
references.citation: Geobiology. 2012 May;10(3):223-35
references.pmid: 22329601
references.citation: Microb Ecol. 2011 Feb;61(2):465-72
references.pmid: 21107832
references.citation: Microb Biotechnol. 2012 Jan;5(1):135-41
references.pmid: 21989224
references.citation: Appl Environ Microbiol. 2003 Feb;69(2):1030-42
references.pmid: 12571026
references.citation: Front Microbiol. 2011 Mar 21;2:44
references.pmid: 21747784
references.citation: FEMS Microbiol Ecol. 2012 May;80(2):402-16
references.pmid: 22251018
references.citation: Environ Microbiol. 2012 May;14(5):1308-24
references.pmid: 22364353
references.citation: Curr Opin Microbiol. 2011 Jun;14(3):300-6
references.pmid: 21546306
references.citation: BMC Bioinformatics. 2011 Jan 28;12:38
references.pmid: 21276213
references.citation: PLoS Comput Biol. 2012;8(10):e1002743
references.pmid: 23133348
references.citation: Extremophiles. 2004 Feb;8(1):63-71
references.pmid: 15064991
references.citation: Environ Microbiol. 2010 Apr;12(4):1075-88
references.pmid: 20132279
references.citation: Environ Microbiol. 2011 Aug;13(8):2146-57
references.pmid: 21410624
references.citation: J Basic Microbiol. 2010 Oct;50(5):465-74
references.pmid: 20586073
references.citation: FEMS Microbiol Ecol. 2011 Sep;77(3):577-89
references.pmid: 21627670
references.citation: J Gen Appl Microbiol. 2009 Aug;55(4):267-75
references.pmid: 19700920
references.citation: PLoS One. 2012;7(11):e49334
references.pmid: 23145153
references.citation: Nat Commun. 2010 Aug 10;1:53
references.pmid: 20975720
references.citation: Int J Syst Evol Microbiol. 2012 Jul;62(Pt 7):1666-1673
references.pmid: 21908678
references.citation: Science. 2011 Sep 2;333(6047):1282-5
references.pmid: 21798895
references.citation: Bioinformatics. 2009 May 15;25(10):1335-7
references.pmid: 19307242
references.citation: Int J Syst Evol Microbiol. 2009 Feb;59(Pt 2):248-53
references.pmid: 19196761
references.citation: Proc Natl Acad Sci U S A. 2005 Oct 11;102(41):14683-8
references.pmid: 16186488
references.citation: ISME J. 2007 Aug;1(4):283-90
references.pmid: 18043639
references.citation: Appl Environ Microbiol. 1996 Feb;62(2):625-30
references.pmid: 8593063
references.citation: ISME J. 2008 Oct;2(10):997-1006
references.pmid: 18650928
references.citation: Bioinformatics. 2011 Aug 15;27(16):2194-200
references.pmid: 21700674