Virioplankton community structure in Tunisian solar salterns

Applied and Environmental Microbiology

Volumn 78, Issue 20, 2012, Pages 7429-7437

  Boujelben, Ines ^a,b   Yarza, Pablo ^b   Almansa, Cristina ^b   Villamor, Judith ^b   Maalej, Sami ^a   Antón, Josefa ^b   Santos, Fernando ^b  

^a University of Sfax   (Tunisia)

^b UNIVERSITY OF ALICANTE   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVE PARTS; AQUATIC SYSTEM; COMMUNITY STRUCTURES; DINUCLEOTIDES; EAST COAST; FREQUENCY ANALYSIS; GENE CONTENT; HYPERSALINE; HYPERSALINE ENVIRONMENT; IN-SILICO; METAGENOMIC ANALYSIS; METAGENOMIC DNA; MICROBIAL COMMUNITIES; MICROBIAL GROUPS; PULSED FIELD GEL ELECTROPHORESIS; SALINITY GRADIENTS; SEARCH RESULTS; TRANSMISSION ELECTRON MICROSCOPY TEM; TUNISIA; VIRAL CONCENTRATION; VIRUS-LIKE PARTICLES;

CELL CULTURE; CLONING; ELECTROPHORESIS; FACTOR ANALYSIS; LAKES; NUCLEOTIDES; SALINITY MEASUREMENT; SOCIAL SCIENCES; TRANSMISSION ELECTRON MICROSCOPY;

VIRUSES;

SEA WATER; VIRUS DNA;

COMMUNITY STRUCTURE; HYPERSALINE ENVIRONMENT; MARINE ECOSYSTEM; MICROBIAL COMMUNITY; MOLECULAR ANALYSIS; PLANKTON; SEA SURFACE SALINITY; VIRUS;

ARTICLE; BIOTA; CHEMISTRY; DNA BASE COMPOSITION; DNA SEQUENCE; GENETICS; METAGENOME; MOLECULAR CLONING; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PULSED FIELD GEL ELECTROPHORESIS; TRANSMISSION ELECTRON MICROSCOPY; TUNISIA; VIROLOGY; VIRUS LOAD;

BASE COMPOSITION; BIOTA; CLONING, MOLECULAR; DNA, VIRAL; ELECTROPHORESIS, GEL, PULSED-FIELD; METAGENOME; MICROSCOPY, ELECTRON, TRANSMISSION; MOLECULAR SEQUENCE DATA; SEAWATER; SEQUENCE ANALYSIS, DNA; TUNISIA; VIRAL LOAD;

TUNISIA;

EID: 84868352655     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.01793-12     Document Type: Article

References (57)

1. Amann RI, et al. 1990. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol. 56: 1919-1925.
2. Antón J, Llobet-Brossa E, Rodríguez-Valera F, Amann R. 1999. Fluorescence in situ hybridization analysis of the prokaryotic community inhabiting crystallizer ponds. Environ. Microbiol. 1: 517-523.
3. Antón J, et al. 2008. Distribution, abundance and diversity of the extremely halophilic bacterium Salinibacter ruber. Saline Systems 4: 15-25.
4. Antón J, Rosselló-Mora R, Rodríguez-Valera F, Amann R. 2000. Extremely halophilic Bacteria in crystallizer ponds from solar salterns. Appl. Environ. Microbiol. 66: 3052-3057.
5. Atanasova NS, Roine E, Oren A, Bamford DH, Oksanen HM. 2011. Global network of specific virus-host interactions in hypersaline environments. Environ. Microbiol. 14: 426-440.
6. Aziz RK, et al. 2008. The RAST server rapid annotations using subsystems technology. BMC Genomics 9: 75.
7. Baati H, Amdouni R, Gharsallah N, Sghir A, Ammar E. 2010. Isolation and characterization of moderately halophilic bacteria from Tunisian solar saltern. Curr. Microbiol. 60: 157-161.
8. Baati H, et al. 2008. Prokaryotic diversity of a Tunisian multipond solar saltern. Extremophiles 12: 505-518.
9. Baati H, Guermazi S, Gharsallah N, Sghir A, Ammar E. 2010. Microbial community of salt crystals processed from Mediterranean seawater based on 16S rRNA analysis. Can. J. Microbiol. 56: 44-51.
10. Baati H, Guermazi S, Gharsallah N, Sghir A, Ammar E. 2010. Novel prokaryotic diversity in sediments of Tunisian multipond solar saltern. Res. Microbiol. 161: 573-582.
11. Baati H, Jarboui R, Gharsallah N, Sghir A, Ammar E. 2011. Molecular community analysis of magnesium-rich bittern brine recovered from a Tunisian solar saltern. Can. J. Microbiol. 57: 975-981.
12. Bamford DH, Mindich L. 1984. Characterization of the DNA-protein complex at the termini of the bacteriophage PRD1 genome. J. Virol. 50: 309-315.
13. Bath C, Cukalac T, Porter K, Dyall-Smith ML. 2006. His1 and His2 are distantly related, spindle-shaped haloviruses belonging to the novel group, Salterprovirus. Virology 350: 228-239.
14. Bath C, Dyall-Smith ML. 1998. His1, an archaeal virus of the Fuselloviridae family that infects Haloarcula hispanica. J. Virol. 72: 9392-9395.
15. Baxter BK, et al. 2011. Haloviruses of Great Salt Lake: a model for understanding viral diversity, p 173-190. In Ventosa A, Oren A, Ma Y (ed), Halophiles and hypersaline environments. Springer, Berlin, Germany.
16. Benlloch S, et al. 2002. Prokaryotic genetic diversity throughout the salinity gradient of a coastal solar saltern. Environ. Microbiol. 4: 349-360.
17. Bettarel Y, et al. 2011. Ecological traits of planktonic viruses and prokaryotes along a full-salinity gradient. FEMS Microbiol. Ecol. 76: 360-372.
18. Bodaker I, et al. 2010. Comparative community genomics in the Dead Sea: an increasingly extreme environment. ISME J. 4: 399-407.
19. Bolhuis H, et al. 2006. The genome of the square archaeon Haloquadratum walsbyi: life at the limits of water activity. BMC Genomics 4: 169.
20. Bolhuis H, Poele EM, Rodríguez-Valera F. 2004. Isolation and cultivation of Walsby's square archaeon. Environ. Microbiol. 6: 349-360.
21. Boujelben I, et al. 2012. Spatial and seasonal prokaryotic community dynamics in ponds of increasing salinity of Sfax solar saltern in Tunisia. Antonie Van Leeuwenhoek 101: 845-857.
22. Brum JF, Steward GF. 2010. Morphological characterization of viruses in the stratified water column of alkaline, hypersaline Mono Lake. Microb. Ecol. 3: 636-643.
23. Burns DG, Camakaris HM, Janssen PH, Dyall-Smith ML. 2004. Cultivation of Walsby's square haloarchaeaon. FEMS Microbiol. Lett. 238: 469-473.
24. Cuadros-Orellana S, et al. 2007. Genomic plasticity in prokaryotes: the case of the square haloarchaeon. ISME J. 1: 235-245.
25. Díez B, Antón J, Guixa-Boixareu N, Pedrós-Alió C, Rodríguez-Valera F. 2000. Pulsed-field gel electrophoresis analysis of virus assemblages present in a hypersaline environment. Int. Microbiol. 3: 159-164.
26. Dinsdale EA, et al. 2008. Functional metagenomic profiling of nine biomes. Nature 452: 629-632.
27. Dyall-Smith M, Tang SL, Bath C. 2003. Haloarchaeal viruses: how diverse are they? Res. Microbiol. 154: 309-313.
28. García-Heredia I, et al. 2012. Reconstructing viral genomes from the environment using fosmid clones: the case of haloviruses. PLoS One 7: e33802. doi: 10.1371/journal.pone.0038802.
29. Ghai R, et al. 2011. New abundant microbial groups in aquatic hypersaline environments. Sci. Rep. 1: 135. doi: 10.1038/srep00135.
30. Guixa-Boixareu N, Calderón-Paz JI, Heldal M, Bratbak G, Pedrós-Alió C. 1996. Viral lysis and bacterivory as prokaryotic loss factors along a salinity gradient. Aquat. Microb. Ecol. 11: 215-227.
31. Jiang S, Steward G, Jellison R, Chu W, Choi S. 2004. Abundance, distribution and diversity of viruses in alkaline, hypersaline Mono Lake, California. Microb. Ecol. 47: 9-17.
32. Legault BA, et al. 2006. Environmental genomics of Haloquadratum walsbyi in a saltern crystallizer indicates a large pool of accessory genes in an otherwise coherent species. BMC Genomics 4: 171.
33. Maturrano L, Santos F, Rosselló-Mora R, Antón J. 2006. Microbial diversity in Maras salterns, a hypersaline environment in the Peruvian Andes. Appl. Environ. Microbiol. 72: 3887-3895.
34. Mongodin EF, et al. 2005. The genome of Salinibacter ruber: convergence and gene exchange among hyperhalophilic bacteria and archaea. Proc. Natl. Acad. Sci. U. S. A. 102: 18147-18152.
35. Mutlu MB, et al. 2008. Prokaryotic diversity in Tuz Lake, a hypersaline environment in inland Turkey. FEMS Microbiol. Ecol. 65: 474-483.
36. Narasingarao P, et al. 2012. De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities. ISME J. 6: 81-93.
37. Nogales B, et al. 2001. Combined use of 16S ribosomal DNA and 16S rRNA to study the bacterial community of polychlorinated biphenylpolluted soil. Appl. Environ. Microbiol. 67: 1874-1884.
38. Oren A, Bratbak G, Heldal M. 1997. Occurrence of virus-like particles in the Dead Sea. Extremophiles 1: 143-149.
39. Papke RT, Koening JE, Rodríguez-Valera F, Doolittle WF. 2004. Frequent recombination in saltern population of Halorubrum. Science 306: 1928-1029.
40. Pasić L, et al. 2009. Metagenomic islands of hyperhalophiles: the case of Salinibacter ruber. BMC Genomics 10: 570.
41. Paul JH, Sullivan MB, Segal AM, Rohwer F. 2002. Marine phage genomics. Comp. Biochem. Phys. 133: 463-476.
42. Peña A, et al. 2010. Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains. ISME J. 4: 882-895.
43. Ramette A. 2007. Multivariate analysis in microbial ecology. FEMS Microbiol. Ecol. 62: 142-160.
44. Rocha EP, Danchin A. 2002. Base competition bias might result from competition for metabolic resources. Trends Genet. 16: 276-277.
45. Rodríguez-Brito B, et al. 2010. Viral and microbial community dynamics in four aquatic environments. ISME J. 4: 739-751.
46. Roine E, Oksanen HM. 2011. Viruses from the hypersaline environment, p 153-172. In Ventosa A, Oren A, Ma Y (ed), Halophiles and hypersaline environments. Springer, Berlin, Germany.
47. Sabet S, Chu W, Jiang SC. 2006. Isolation and genetic analysis of haloalkaliphilic bacteriophages in a North American soda lake. Microb. Ecol. 51: 543-554.
48. Sandaa RA, Skjoldal EF, Bratbak G. 2003. Virioplankton community structure along a salinity gradient in a solar saltern. Extremophiles 7: 347-351.
49. Santos F, Antón J. 2011. Viral metagenomics and the regulation of prokaryotic communities, p 33-44. In Marco D (ed), Metagenomics: current innovations and future trends. Caister Academic Press, Norfolk, VA.
50. Santos F, et al. 2007. Metagenomic approach to the study of halophages: the environmental halophage 1. Environ. Microbiol. 9: 1711-1723.
51. Santos F, Yarza P, Briones C, Parro V, Antón J. 2010. The metavirome of a hypersaline environment. Environ. Microbiol. 12: 2965-2976.
52. Santos F, et al. 2012. Culture-independent approaches for studying viruses from hypersaline environments. Appl. Environ. Microbiol. 78: 1635-1643.
53. Sime-Ngando T, et al. 2011. Diversity of virus-host systems in hypersaline Lake Retba, Senegal. Environ. Microbiol. 13: 1956-1972.
54. Soler N, Marguet E, Verbavatz JM, Forterre P. 2008. Virus-like vesicles and extracellular DNA produced by hyperthermophilic archaea of the order Thermococcales. Res. Microbiol. 159: 390-399.
55. Trigui H, et al. 2011. Characterization of heterotrophic prokaryote subgroups in the Sfax coastal solar salterns by combining flow cytometry cell sorting and phylogenetic analysis. Extremophiles 15: 347-358.
56. Trigui H, Masmoudi S, Brochier-Armanet C, Maalej S, Dukan S. 2 Jun 2011. Characterization of Halorubrum sfaxense sp. nov., a new halophilic archaeon isolated from the solar saltern of Sfax in Tunisia. Int. J. Microbiol. doi: 10.1155/2011/240191.
57. Willner D, Vega Thurber R, Rohwer F. 2009. Metagenomic signatures of 86 microbial and viral metagenomes. Environ. Microbiol. 11: 1752-1766.