Welcome to International Network for Natural Sciences | INNSpub

Paper Details

Research Paper | June 1, 2015

VIEWS 1
| Download 2

Studies of sediments, dry mud and water samples from lake elmenteita reveal the presence of thaumarchaeota and euryarchaeota

Jacqueline O. Akanga, Hamadi I. Boga, Hans-Peter Klenk

Key Words:


J. Bio. Env. Sci.6(6), 341-355, June 2015

Certification:

JBES 2015 [Generate Certificate]

Abstract

So as to provide new insight into the diversity of Archaea in dry mud, sediment and water from Lake Elmenteita in Kenya, an investigation using a culture-independent approach was conducted after extraction of total genomic DNA from the environmental samples using suitable extraction methods. Small insert clone libraries were constructed by amplifying 16S rRNA genes using archaea-specific primers, followed by cloning from which 94 non-chimeric sequences were obtained and a total of 34 operational taxonomic units (OTUs) were identified. The OTUs were grouped into Thaumarchaeota (6%) and Euryarchaeota (94%). Approximately 90% of the clones were related with genes from uncultured Archaea, compared to the 10% that showed affiliation with genes from previously cultured Archaea. The similarity of the sequenced clones to type strains was consistently lower than the similarity to uncultured members of Archaea. Clones from water and sediment were dominated by sequences from Euryarchaea, while clones from the dry mud samples showed affiliations to both Euryarchaeota and Thaumarchaeota, with the predominant phylum being Euryarchaeota. This is the first study reporting the presence of representatives of Thaumarachaeota from Lake Elmenteita and adds sequences from Lake Elmenteita to the developing database of 16S rRNA clone libraries obtained from environmental sources.

VIEWS 1

Copyright © 2015
By Authors and International Network for
Natural Sciences (INNSPUB)
http://innspub.net
This article is published under the terms of the Creative
Commons Attribution Liscense 4.0

Studies of sediments, dry mud and water samples from lake elmenteita reveal the presence of thaumarchaeota and euryarchaeota

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. Journal of Molecular Biology 215, 403- 410.

Anderson I, Ulrich LE, Lupa B, Susanti D, Porat I, Hooper SD, Lykidis A, Sieprawska-Lupa M, Dharmarajan L, Goltsman E, Lapidus A, Saunders E, Han C, Land M, Lucas S, Mukhopadhyay B, Whitman WB, Woese C, Bristow J Kyrpides N. 2009. Genomic characterization of methanomicrobiales. PLoS One 4(6), e5797. http://dx.doi.org/10.1371/journal.pone.0005797

Antony  CP,  Murrell  JC,  Shouche  YS.  2012. Molecular diversity of methanogens and identification of Methanolobus sp. as active methylotrophic Archaea in Lonar Crater Lake sediments. FEMS Microbiology Ecology 81, 43– 51. http://dx.doi.org/10.1111/j.1574-6941.2011.01274.x

Ashelford KE, Chuzhanova NA, Fry JC, Jones AJ, Weightman AJ. 2006. New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras. Applied and Environmental Microbiology 72(9), 5734- 5741. http://dx.doi.org/10.1128/AEM.00556-06

Baumgarte S. 2003. Microbial Diversity of Soda Lake Habitats. Doktors der Naturwissenschaften, Universität Carolo-Wilhelmina zu Braunschweig. Page 1- 23

Beman JM, Francis CA. 2006. Diversity of ammonia-oxidizing Archaea and bacteria in the sediment of a hypernutrified subtropical estuary: Bahía del To´bari, Mexico. Applied and Environmental Microbiology 72, 7767– 7777. http://dx.doi.org/10.1128/AEM.00946-06

Bennun LA, Njoroge P. 1999. Important Bird Areas of Kenya. East Africa Natural History. Society. Nairobi, Kenya.

Bintrim SB, Donohue TJ, Handelsman J, Roberts GP, Goodman RM. 1997. Molecular phylogeny of Archaea from soil. Proceedings of the National Academy of Sciences, USA 94(1), 277– 282.

Brochier-Armanet C, Boussau B, Gribaldo S, Forterre P. 2008. Mesophilic crenarchaeota: proposal for a third Archaeal phylum, the Thaumarchaeota. Nature Reviews Microbiology 6, 245– 252. http://dx.doi.org/10.1038/nrmicro1852

Burggraf S, Huber H, Stetter KO. 1997. Reclassification of the Crenarchaeal orders and families in accordance with 16S rRNA sequence data. International Journal of Systematic Bacteriology 47(3), 657- 660. http://dx.doi.org/10.1099/00207713-47-3-657

Callieri C, Corno G, Caravati E, Rasconi S, Contesini M, Roberto B. 2009. Bacteria, Archaea, and Crenarchaeota in the Epilimnion and Hypolimnion of a Deep Holo-Oligomictic Lake. Applied  and  Environmental  Microbiology 75(22), 7298–7300. http://dx.doi.org/10.1128/AEM.01231-09

Chin KJ, Lukow T, Conrad R. 1999. Effect of temperature on structure and function of the methanogenic archaeal community in an anoxic rice field soil. Applied and Environmental Microbiology 65, 2341– 2349.

Clementino MM, de Filippis I, Nascimento CR, Branquinho R, Rocha CL, Martins OB. 2001. PCR analyses of tRNA intergenic transcribed spacer, and  randomly  amplified  polymorphic  DNA  reveal inter- and intraspecific relationships of Enterobacter cloacae strains. Journal of Clinical Microbiology 39, 3865– 3870. http://dx.doi.org/10.1128/JCM.39.11.38653870.2001

Cole JR, Chai B, Marsh TL, Farris RJ, Wang Q, Kulam SA, Chandra S, McGarrell DM, Schmidt TM, Garrity GM, Tiedje JM. 2003. The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Research 31, 442– 443. http://dx.doi.org/10.1093/nar/gkg039

Dawson S, DeLong EF, Pace NR. 2006. Phylogenetic and ecological perspectives on uncultured Crenarchaeota and Korarchaeota. In: Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E (editors). The prokaryotes, volume 3, 3rd edition. Springer, New York.

DeLong EF. 1992. Archaea in coastal marine environments. Proceedings of the National Academy of Sciences USA 89, 5685– 5689.

Dorador C, Vila I, Remonsellez F, Imhoff JF, Witzel K-P. 2010. Unique clusters of Archaea in Salar de Huasco, an athalassohaline evaporitic basin of the Chilean Altiplano. FEMS Microbiology Ecology 73, 291–302. http://dx.doi.org/10.1111/j.1574-6941.2010.00891.x

Duckworth AW, Grant WD, Jones BE, Steenbergen R. 1996. Phylogenetic diversity of soda lake alkaliphiles. FEMS Microbiology Ecology 19, 181- 191. http://dx.doi.org/10.1111/j.1574-6941.1996.tb00211.x

Etheridge DM, Steele LP, Francey RJ, Langenfelds RL. 1998. Atmospheric methane between 1000 A.D. and present: Evidence of anthropogenic emissions and climatic variability, Journal of Geophysical Research 103(D13), 15979–15993. http://dx.doi.org/10.1029/98JD00923.

Felsenstein J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39(4), 783– 791.

Francis CA, Roberts KJ, Beman JM, Santoro AE, Oakley BB. 2005. Ubiquity and diversity of ammonia-oxidizing Archaea in water columns and sediments of the ocean. Proceedings of the National Academy of Sciences USA 102(41), 14683– 14688. http://dx.doi.org/10.1073/pnas.0506625102

Fuhrman JA, McCallum K, Davis AA. 1993. Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific Oceans. Applied and Environmental Microbiology 59(5), 1294– 1302.

Fuhrman JA, McCallum K, Davis AA. 1992. Novel major archaebacterial group from marine plankton. Nature 356(6365), 148– 149.

Grant S, Grant WD, Jones BE, Kato C, Li L. 1999. Novel archaeal phylotypes from an East African alkaline saltern. Extremophiles 3, 139– 145.

Großkopf R, Janssen PH, Liesack W. 1998. Diversity and Structure of the Methanogenic Community in Anoxic Rice Paddy Soil Microcosms as Examined by Cultivation and Direct 16S rRNA Gene Sequence Retrieval. Applied and Environmental Microbiology 64(3), 960- 969.

Handelsman J. 2004. Metagenomics: Application of Genomics to Uncultured Microorganisms. Microbiology and Molecular Biology Reviews 68(4), 669- 685. http://dx.doi.org/10.1128/MMBR.68.4.669-685.

Hatzenpichler R. 2012. Diversity, Physiology, and Niche Differentiation of Ammonia-Oxidizing Archaea. Applied and Environmental Microbiology 78(21), 7501. http://dx.doi.org/10.1128/AEM.01960-12.

Hatzenpichler R, Lebedeva EV, Spieck E, Stoecker K, Richter A, Daims H, Wagner M. 2008. A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring. Proceedings of the National Academy of Sciences USA 105(6), 2134–2139. http://dx.doi.org/10.1073/pnas.0708857105

Hu A, Jiao N, Zhang R, Yang Z. 2011. Niche Partitioning of Marine Group I Crenarchaeota in the Euphotic and Upper Mesopelagic Zones of the East China Sea. Applied and Environmental Microbiology 77(21), 7469– 7478. http://dx.doi.org/10.1128/AEM.00294-11

Huang X, Madan A. 1999. CAP3: A DNA sequence assembly program. Genome Research 9, 868- 877. http://dx.doi.org/10.1101/gr.9.9.868

Jones BE, Grant WD, Duckworth AW, Owenson GG. 1998. Microbial diversity of soda lakes. Extremophiles 2(3), 191– 200.

Jukes TH, Cantor CR. 1969. Evolution of protein molecules. (Munroled, H.N., Ed). Mammalian Protein Metabolism , III. New York: Academic Press 21- 132

Kim BS, Oh HM, Kang H, Chun J. 2005. Archaeal diversity in tidal flat sediment as revealed by 16S rDNA analysis. Journal of Microbiology 43(2), 144– 151.

Kim J, Jung M, Park S, Rijpstra WIC, Damste JSS, Madsen EL, Min D, Kim J, Kim G, Rhee S. 2012. Cultivation of a highly enriched ammonia-oxidizing archaeon of thaumarchaeotal group I.1b from an agricultural soil. Environmental Microbiology 14(6), 1528– 1543. http://dx.doi.org/10.1111/j.1462-2920.2012.02740.x

Kimura H, Nashimoto H, Shimizu M, Hattori S, Yamada K, Koba K, Yoshida N, Kato K. 2010. Microbial methane production in deep aquifer associated with the accretionary prism in Southwest Japan. The ISME Journal 4, 531– 541. http://dx.doi.org/10.1038/ismej.2009.132

Konneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB, Stahl DA. 2005. Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437(7058), 543- 546. http://dx.doi.org/10.1038/nature03911

Liu YQ ,Yao TD, Gleixner G, Claus P, Conrad R. 2013.  Methanogenic  Pathways,  C-13  Isotope Fractionation, And Archaeal Community Composition In Lake Sediments And Wetland Soils On The Tibetan Plateau[J]. Journal of Geophysical Research-biogeosciences 118(2), 650- 664.

Marusenko Y, Bates ST, Anderson I, Johnson SL, Soule T, Garcia-Pichel F. 2013. Ammonia-oxidizing archaea and bacteria are structured by geography in biological soil crusts across North American arid lands. Ecological Processes 2, 9. http://dx.doi.org/10.1186/2192-1709-2-9

Massana R, Murray AE, Preston CM, DeLong EF. 1997. Vertical distribution and phylogenetic characterization of marine planktonic Archaea in the Santa Barbara Channel. Applied and Environmental Microbiology 63(1), 50- 56.

Melack JM. 1988. Primary producer dynamics associated with evaporative concentration in a shallow, equatorial soda lake (Lake Elmenteita, Kenya). Hydrobiologia 158, 1- 14.

Muller F, Brissac T, Le Bris N, Felbeck H, Gros O. 2010. First description of giant Archaea (Thaumarchaeota) associated with putative bacterial ectosymbionts in a sulfidic marine habitat. Environmental Microbiology 12, 2371- 2383. http://dx.doi.org/10.1111/j.1462-2920.2010.02309.x

Mwaura F. 1999. A spatio-chemical survey of hydro geothermal springs in Lake Elementaita, Kenya. International Journal of Salt Lake Research 8, 127– 138.

Mwirichia R, Cousin S, Muigai AW, Boga HI, Stackenbrandt E. 2010. Archaeal Diversity in the Haloalkaline Lake Elmenteita in Kenya. Current Microbiology 60(1), 47– 52. http://dx.doi.org/10.1007/s00284-009-9500-1.

Neufeld JD, Yu Z, Lam W, Mohn WW. 2004. Serial analysis of ribosomal sequence tags (SARST): a high-throughput method for profiling complex microbial communities. Environmental Microbiology 6(2), 131– 144. http://dx.doi.org/10.1046/j.1462-2920.2003.00547.x

Nishizawa T, Komatsuzaki M, Kaneko N, Ohta H. 2008. Archaeal Diversity of Upland Rice Field Soils Assessed by the Terminal Restriction Fragment Length Polymorphism Method Combined with Real Time Quantitative-PCR and a Clone Library Analysis. Microbes and Environments 23(3), 237- 243. http://dx.doi.org/10.1264/jsme2.23.237

Ochsenreiter T, Pfeifer F, Schleper C. 2002. Diversity of Archaea in hypersaline environments characterized by molecular phylogenetic and cultivation studies. Extremophiles 6, 267– 274. http://dx.doi.org/10.1007/s00792-001-0253-4

Pester M, Schleper C, Wagner M. 2011. The Thaumarchaeota: an emerging view of their phylogeny and ecophysiology. Current Opinion in Microbiology 14(3), 300- 306. http://dx.doi.org/10.1016/j.mib.2011.04.007

Pouliot J, Galand P, Lovejoy C, Vincent WF. 2009. Vertical structures of Archaeal communities and the distribution of ammonia monooxygenase A gene variants in two meromictic High Arctic lakes. Environmental Microbiology 11(3), 687– 699. http://dx.doi.org/10.1111/j.1462-2920.2008.01846.x

Preston CM, Wu KY, Molinski TF, DeLong EF. 1996. A psychrophilic crenarchaeon inhabits a marine sponge: Cenarchaeum symbiosum gen. nov., sp. nov. Proceedings of the National Academy of Sciences of the United States of America 93(13), 6241- 6246.

Quaiser A, Ochsenreiter T, Klenk H-P, Kletzin A, Treusch AH, Meurer G, Eck J, Sensen CW, Schleper C. 2002. First insight into the genome of an uncultivated crenarchaeote from soil. Environmental Microbiology 4, 603– 611. http://dx.doi.org/10.1046/j.14622920.2002.00345.x

Rees HC, Grant WD, Jones BE, Heaphy S. 2004. Diversity of Kenyan soda lake alkaliphiles assessed by molecular methods. Extremophiles 8(1), 63– 71. http://dx.doi.org/10.1007/s00792-003-0361-4

Sambrook J, Russel DW. 2001. Molecular cloning: a laboratory manual, 3rd edition. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.

Sørensen KB, Lauer A, Teske A. 2004. Archaeal phylotypes in a metal-rich and low-activity deep subsurface sediment of the Peru Basin, ODP Leg 201, Site 1231. Geobiology 2(3), 151– 161. http://dx.doi.org/10.1111/j.1472-4677.2004.00028.x

Sorokin DY, Kuenen JG, Muyzer G. 2011. The microbial sulfur cycle at extremely haloalkaline conditions of soda lakes. FEMS Microbiological Letters 319(1), 88- 95. http://dx.doi.org/10.1111/j.1574-6968.2011.02272.x

Spang A, Poehlei, A, Offre P, Zumbrägel S, Haider S, Rychlik N, Nowka B, Schmeisser C, Lebedeva EV, Rattei T, Böhm C, Schmid M, Galushko A, Hatzenpichler R, Weinmaier T, Daniel R, Schleper C, Spieck E, Streit W, Wagner M. 2012. The genome of the ammonia-oxidizing Candidatus Nitrososphaera gargensis: insights into metabolic versatility and environmental adaptations. Environmental Microbiology 14(12), 3122– 3145. http://dx.doi.org/10.1111/j.1462-2920.2012.02893.x

Takai K, Horikoshi K. 1999. Genetic diversity of Archaea in deep-sea hydrothermal vent environments. Genetics 152(4), 1285– 1297.

Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Molecular Biology and Evolution 30(12), 2725- 2729. http://dx.doi.org/10.1093/molbev/mst197

Teske A, Hinrichs KU, Edgcomb V, Vera Gomez A, Kysela D, Sylva SP, Sogin ML, Jannasch HW. 2002. Microbial diversity of hydrothermal sediments in the Guaymas basin: evidence for anaerobic methanotrophic communities. Applied and Environmental Microbiology 68(4), 1994– 2007. http://dx.doi.org/10.1128/AEM.68.4.19942007.2002

Tindall BJ, Ross HNM, Grant WD. 1984. Natronobacterium gen. nov. and Natronococcus gen. nov., two new genera of haloalkaliphilic archaebacteria. Systematic and Applied Microbiology 5(1), 41- 57.

de la Torre JR, Walker CB, Ingalls AE, Könneke M, Stahl DA. 2008. Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol. Environmental Microbiology 10(3), 810– 818. http://dx.doi.org/10.1111/j.1462-2920.2007.01506.x

Vetriani C, Reysenbach AL, Dore J. 1998. Recovery and phylogenetic analysis of archaeal rRNA sequences from continental shelf sediments. FEMS Microbiology Letters 161(1), 83– 88. http://dx.doi.org/10.1111/j.1574-6968.1998.tb12932.x

SUBMIT MANUSCRIPT

Style Switcher

Select Layout
Chose Color
Chose Pattren
Chose Background