BIODIVERSITY OF ARCHAEA IN MANZALA LAKE IN EGYPT BASED ON 16S rRNA GENE
Abstract
A first molecular genetic study was done on the diversity of archaeal communities in two sites, Bashtir and Genka, of the Manzala Lake, Egypt, based on culture-independent 16S rRNA gene analysis. Bulk microbial DNAs were extracted from surface water and sediment samples collected from both the two studied sites. The archaeal 16S rRNA gene was positively amplified from the DNAs of all samples by PCR. The amplicons were cloned and analyzed directly by sequencing followed by statistical and phylogenetic analyses. The results recorded 6, 10, 16 and 9 archaeal phylotypes in Bashtir water, Genka water, Bashtir sediment and Genka sediment, respectively. Based on Libshuff pairwise clone library comparisons, the 16S rRNA gene phylotypes from Bashtir sediment encompassed the phylotypes of Genka sediment, while the phylotypes of Genka sediment accounted only a minor portion of those of Bashtir sediment. The recovered phylotypes from water samples showed phylogenetic differentiation from those from sediment samples, an observation implicating the phylogenetic distinction between water and sediment archaeal communities. Several recovered phylotypes from water and sediment samples located in the phylogenetic branch of the phylum Euryarchaeota. On the other hand, the phylum Crenarchaeota characterized, mainly, the phylotypes recovered from sediment samples. In the term of affiliation to species, several phylotypes, mainly from water samples, closely related to known Euryarchaeotic methanogenic species Methanothrix soehngenii, Methanospirillum hungatei and Methanocorpusculum labreanum, implying uncommon occurrence of methanogens in surface waters. The Crenarchaeota- like phylotypes affiliated to the thermophilic species Thermofilum pendens and Staphylothermus achaiicus, implicating the global distribution of those species in even moderately temperate habitats like that of Manzala. Most of the recovered phylotypes belonged to unculturable archaeal species. Several recovered phylotypes from water and sediment samples grouped into unique phylogenetical clusters, suggesting new archaeal phyla and classes characterizing the sampling sites. The success of this study was identification of the total composition of archaeal communities in the studied sites and the discovery of novel archaeal species, that never recorded by traditional techniquesReferences
Abbassy, M. S., H. Z. Ibrahim and H. M. Abdel-Kader (2003). Persistent organochlorine pollutants in the aquatic ecosystem of Lake Manzala, Egypt. Bull. Environ. Contam. Toxicol., 70: 1158-1164.
Abdel-Karim, M. S., M. H. Ali and M. F. Sayed (2006). Spatial and temporal distribution of microphytobenthic algae in hypersaline Mediterranean lagoon (Bardawil Lagoon, Egypt), multivariate analysis approach. The Egyptian Journal of Aquatic Research, 32: 271-291.
Abdel-Monem, A. M. (2001). Biodiversity of phytoplankton structure in Qarun Lake (El-Fayoum, Egypt) and its use as indicator for environmental pollution. Egyptian J. Phycol., 2: 17-31.
Arab, H., H. Voelker and Thomm, M. (2000). Thermococcus aegaeicus sp. nov. and Staphylothermus hellenicus sp. nov., two novel hyperthermophilic archaea isolated from geothermally heated vents off Palaeochori Bay, Milos, Greece. Int. J. Syst. Evol. Microbiol., 50: 2101-2108.
Bapteste, E., C. Brochier and Y. Boucher (2005). Classification of the archaea: evolution of and methanogens. Archaea, 1: 353-363.
Barns, S. M., C. F. Delwiche, J. D. Palmer and N. R. Pace (1996). Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. Proc. Natl. Acad. Sci. (USA), 93: 9188-9193.
Chaban, B., S. Y. Ng and K. F. Jarrell (2006). Archaeal habitats: from the extreme to the ordinary. Can. J. Microbiol., 52: 73-116.
Chin, K. J., T. Lukow, S. Stubner and R. Conrad (1999). Structure and function of the methanogenic archaeal community in stable cellulosedegrading enrichment cultures at two different temperatures FEMS Microbiol. Ecol., 30: 313-326.
Cytryn, E., D. Minz, R. S. Oremland and Y. Cohen (2000). Distribution and diversity of archaea corresponding to the limnological cycle of a hypersaline stratified Lake (Solar Lake, Sinai, Egypt). Appl. Environ. Microbiol., 66: 3269- 3276.
DeLong, E. F. (1992). Archaea in coastal marine environments. Proc. Natl. Acad. Sci. (USA), 89: 5685-5689. DeLong, E. F. and N. R. Pace (2001). Environmental diversity of bacteria and archaea. Syst. Biol., 50: 470-478.
El-Naggar, M. E., S. A. Dessouki, M. I. Abdel-Hamid and E. M. Aly (1998). Studies on the phytoplankton populations and physicochemical conditions of treated sewage discharged into Lake Manzala in Egypt. New Microbiol., 21: 183-196.
Elsaied, H. E. (2007). Molecular genetic monitoring of bacterial communities in Manzala Lake, Egypt, based on 16S rRNA gene analysis. Egyptian J. Aqua. Res., 33. In press.
Elsaied, H. E. and T. Naganuma (2001). Phylogenetic diversity of ribulose- 1,5-bisphosphate carboxylase/ oxygenase large-subunit genes from deep-sea microorganisms. Appl. Environ. Microbiol., 67: 1751-1765.
Fuhrman J. A., K. McCallum and A. A. Davis (1992). Novel major archaebacterial group from marine plankton. Nature, 356: 148-149.
Godon, J., E. Zumstein, P. Dabert, F. Habouzit and R. Molletta (1997). Molecular microbial diversity of an anaerobic digestor as determined by small-subunit rDNA sequence analysis. Appl. Environ. Microbiol., 63: 2802-2813.
Gribaldo, S. and C. Armanet (2006). The origin and evolution of Archaea: a state of the art. Phil. Trans. R. Soc. B, 361: 1007-1022.
Huber, H., M. J. Hohn, R. Rachel, T. Fuchs, V. C. Wimmer and K. O. Stetter (2002). A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. Nature, 417: 27-28.
Kjems, J., H. Leffers, T. Olesen, H. Ingelore and R. A. Garrett (1990). Sequence, organization and transcription of the ribosomal RNA operon and the downstream tRNA and protein genes in the archaebacterium Thermofilum pendens. Syst. Appl. Microbiol., 13: 117- 127.
Lai, M. C. and S. C. Chen (2001). Methanofollis aquaemaris sp. nov., a methanogen isolated from an aquaculture fish pond. Int. J. Syst. Evol. Microbiol., 51: 1873-1880.
Lai, M. C., C. M. Shu, M. S. Chiou, T. Y. Hong, M. J. Chuang and J. J. Hua (1999). Characterization of Methanosarcina mazei N2M9705 isolated from an aquaculture fishpond. Curr. Microbiol., 39: 79-84.
Leibo, A. I., A. I. Netrusov and R. Conrad (2006). Effect of hydrogen concentration on the hydrogenotrophic methanogenic community structure studied by T-RELP analysis of 16S rRNA gene amplicons. Mikrobiologiia, 75: 786-791.
Ma, K., X. Liu and X. Dong (2006). Methanosaeta harundinacea sp. nov., a novel acetate-scavenging methanogen isolated from a UASB reactor. Int. J. Syst. Evol. Microbiol., 56: 127-131.
Madigan, M. and J. Martinko (2005). Brock Biology of Microorganisms, 11th ed., Prentice Hall. p. 561-567.
Madsen, E. L. (2000). Nucleic-acid characterization of the identity and activity of subsurface microorganisms.
Hydrogeol. J., 8: 112-125. Martone, C. B., P. Borla and J. J. Sánchez (2005). Fishery by-product as a nutrient source for bacteria and archaea growth media. Bioresour. Technol., 96: 383-387.
Mesbah, N. M., S. H. Abou-El-Ela and J. Wiegel (2007). Novel and unexpected prokaryotic diversity in water and sediments of the alkaline, hypersaline lakes of the Wadi An Natrun, Egypt. Microbial Ecology, 54: 598-617.
Olsen, G. J., D. J. Lane, S. J. Giovannoni, N. R. Pace and D. A. Stahl (1986). Microbial ecology and evolution: a ribosomal RNA approach. Annu. Rev. Microbiol., 40: 337-365.
Pace, N. R. (1997). A molecular view of microbial diversity and the biosphere. Science, 276: 734-740.
Porteuous, L. A., J. L. Armstrong, R. J. Sadler and L. S. Watrud (1994). DNA extraction from sediment and cell suspensions. Curr. Microbiol., 29: 301-307.
Rothschild, L. J. and R. L. Mancinelli (2001). Life in extreme environments. Nature, 409: 1092-1101.
Sabae, S. Z. (2006). Spatial and temporal variations of saprophytic bacteria, fecal indicators and the nutrient cycle bacteria in Lake Bardawil, Sinai, Egypt. Int. J. Agri. Biol., 82: 178-185.
Schneider, S., D. Roesseli and L. Excoffier (2000). Arlequin version 2.000, a software for population genetics data analysis. Genetics and Biometry Laboratory, Univ. of Geneva, Geneva, Austria.
Singleton, D., M. Furlong, S. Rathbun and W. Whitman (2001). Quantitative comparisons of 16S rRNA gene sequence libraries from environmental samples Appl. Environ. Microbiol., 67: 4374-4376.
Skirnisdottir, S., G. O. Hreggvidsson, S. Rleifsdottir, V. T. Marteinsson, S. K. Petursdottir, O. Holst and J. K. Kristjansson (2000). Influence of sulfide and temperature on species composition and community structure of hot spring microbial mats. Appl. Environ. Microbiol., 66: 2835-2841.
Somerville, C. C., I. T. Knight, W. L. Straube and R. R. Colwell (1989). Simple, rapid method for direct isolation of nucleic acids from aquatic environments. Appl. Environ. Microbiol., 55: 548-554.
Spring, S., R. Schulze, J. Overmann and K. Schleifer (2000). Identification and characterization of ecologically significant prokaryotes in the sediment of freshwater lakes: molecular and cultivation studies. FEMS Microbiol. Rev., 24: 573- 590.
Suzuki, M. and S. Giovannoni (1996). Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl. Environ. Microbiol., 62: 625-630. Tailliez, O., C. Brochier, P. Forterre and H. Philippe (2002). Archaeal phylogeny based on ribosomal proteins. Mol. Biol. Evol., 19: 631- 639.
Takai, K. and K. Horikoshi (1999). Genetic diversity of archaea in deep-sea hydrothermal vent environments. Genetics, 152: 1285-1297.
Whitby, C., J. Earl, C. Lanyon, S. Gray, J. Robinson and C. Edwards (2004). The molecular diversity of the methanogenic community in a hypereutrophic freshwater lake determined by PCR-RFLP. J. Appl. Microbiol., 97: 973-84.
Woese, C. and G. Fox (1977). Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc. Natl. Acad. Sci. (USA), 74: 5088-5090.
Yannarell, A. C. and E. W. Triplett (2005). Geographic and environmental sources of variation in lake bacterial community composition. Appl. Environ. Microbiol., 71: 227-239.
