Revealing the diversity and quantity of peritrich ciliates in environmental samples using specific primer-based PCR and quantitative PCR

Microbes and Environments

Volumn 27, Issue 4, 2012, Pages 497-503

  Liu, Xihan ^a,b   Gong, Jun ^a  

^a YANTAI INSTITUTE OF COASTAL ZONE RESEARCH   (China)

^b OCEAN UNIVERSITY OF CHINA   (China)

Author keywords

Ciliophora; Peritricha; qPCR; Specific primers; SSU rRNA gene copy number

Indexed keywords

BACTERIAL DNA; PRIMER DNA; RIBOSOME DNA; RNA 18S;

ARTICLE; BIODIVERSITY; CILIATE; CLASSIFICATION; COPY NUMBER VARIATION; DNA SEQUENCE; GENE LIBRARY; GENETIC VARIABILITY; GENETICS; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; OLIGOHYMENOPHOREA; PHYLOGENY; POLYMERASE CHAIN REACTION; RIVER; SALINITY;

BASE SEQUENCE; BIODIVERSITY; CILIOPHORA; DNA COPY NUMBER VARIATIONS; DNA PRIMERS; DNA, BACTERIAL; DNA, RIBOSOMAL; GENE LIBRARY; GENETIC VARIATION; MOLECULAR SEQUENCE DATA; OLIGOHYMENOPHOREA; PHYLOGENY; POLYMERASE CHAIN REACTION; RIVERS; RNA, RIBOSOMAL, 18S; SALINITY; SEQUENCE ANALYSIS, DNA; WATER MICROBIOLOGY;

CILIOPHORA; PERITRICHIA (CILIATES);

EID: 84871141498     PISSN: 13426311     EISSN: 13474405     Source Type: Journal    
DOI: 10.1264/jsme2.ME12056     Document Type: Article

References (46)

1. Altschul, S.F., T.L. Madden, A.A. Schäffer, J. Zhang, Z. Zhang, W. Miller, and D.J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
2. Ashelford, K.E., N.A. Chuzhanova, J.C. Fry, A.J. Jones, and A.J. Weightman. 2006. New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras. Appl. Environ. Microbiol. 72:5734-5741.
3. Balazi, P., and D. Matis. 2002. Composition, seasonal dynamics and feeding groups of ciliated protozoa in the pelagial of the Morava river. Biologia 57:153-160.
4. Calvo, P., M.C. Fernandez-Aliseda, J. Garrido, and A. Torres. 2003. Ultrastructure, eneystment and cyst wall composition of the resting cyst of the peritrich ciliate Opisthonecta henneguyi. J. Eukaryot. Microbiol. 50:49-56.
5. Clamp, J.C., and D.W. Coats. 2000. Planeticovorticella finleyi n.g., n.sp. (Peritrichia, Vorticellidae), a planktonic ciliate with a polymorphic life cycle. Invertebr. Biol. 119:1-16.
6. Countway, P.D., R.J. Gast, P. Savai, and D.A. Caron. 2005. Protistan diversity estimates based on 18S rDNA from seawater incubations in the western North Atlantic. J. Eukaryot. Microbiol. 52:95-106.
7. Doherty, M., B.A. Costas, G.B. McManus, and L.A. Katz. 2007. Culture-independent assessment of planktonic ciliate diversity in coastal northwest Atlantic waters. Aquat. Microb. Ecol. 48:141-157.
8. Dopheide, A., G. Lear, R. Stott, and G. Lewis. 2008. Molecular characterization of ciliate diversity in stream biofilms. Appl. Environ. Microbiol. 74:1740-1747.
9. Dubber, D., and N.F. Gray. 2011. The effect of anoxia and anaerobia on ciliate community in biological nutrient removal systems using laboratory-scale sequencing batch reactors (SBRs). Water Res. 45:2213-2226.
10. Edgar, R.C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792-1797.
11. Felsenstein, J. 2005. PHYLIP (Phylogeny Inference Package) version 3.69. Department of Genome Sciences, University of Washington, Seattle, USA.
12. Fernandez-Leborans, G., and M.L. Tato-Porto. 2000. A review of the species of protozoan epibionts on crustaceans. I. Peritrich ciliates. Crustaceana 73:643-683.
13. Foissner, W., S. Agatha, and H. Berger. 2002. Soil ciliates (Protozoa, Ciliophora) from Namibia (Southwest Africa), with emphasis on two contrasting environments, the Etosha region and the Namib Desert. Denisia 5:1-1459.
14. Foissner, W., H. Berger, and F. Kohmann. 1992. Taxonomische und ökologische Revision der Ciliaten des Saprobiensystems, Band II: Peritrichia, Heterotrichia, Odontostomatida. Informationsberichte des Bayerischen Landesamt für Wasserwirtschaft, 5/92:1-502.
15. Foissner, W., H. Berger, and J. Schaumburg. 1999. Identification and ecology of limnetic plankton ciliates. Informationsberichte des Bayerischen Landesamtes für Wasserwirtschaft, 3/99:1-793.
16. Foissner, W., N. Blake, K. Wolf, H.W. Breiner, and T. Stoeck. 2009. Morphological and molecular characterization of some peritrichs (Ciliophora: Peritrichida) from tank bromeliads, including two new genera: Orborhabdostyla and Vorticellides. Acta Protozool. 48:291-319.
17. Fried, J., G. Mayr, H. Berger, W. Transpurger, R. Psenner, and H. Lemmer. 2000. Monitoring protozoa and metazoa biofilm communities for assessing wastewater quality impact and reactor up-scaling effects. Water Sci. Technol. 41:309-316.
18. Gentekaki, E., and D.H. Lynn. 2010. Evidence for cryptic speciation in Carchesium polypinum Linnaeus, 1758 (Ciliophora: Peritrichia) inferred from mitochondrial, nuclear, and morphological markers. J. Eukaryot. Microbiol. 57:508-519.
19. Godhe, A., M.E. Asplund, K. Harnstrom, V. Saravanan, A. Tyagi, and I. Karunasagar. 2008. Quantification of diatom and dinoflagellate biomasses in coastal marine seawater samples by real-time PCR. Appl. Environ. Microbiol. 74:7174-7182.
20. Gong, J., W. Song, and A. Warren. 2005. Periphytic ciliate colonization: annual cycle and responses to environmental conditions. Aquat. Microb. Ecol. 39:159-170.
21. Hou, Y., H. Zhang, L. Miranda, and S. Lin. 2010. Serious overestimation in quantitative PCR by circular (supercoiled) plasmid standard: microalgal pcna as the model gene. PLoS ONE 5:e9545.
22. Hu, X., and W. Song. 2001. Description of Zoothamnium chlamydis sp. n. (Protozoa: Ciliophora: Peritrichida), an ectocommensal peritrichous ciliate from cultured scallop in North China. Acta Protozool. 40:215-220.
23. Huber, T., G. Faulkner, and P. Hugenholtz. 2004. Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20:2317-2319.
24. Ji, D., W. Song, K.A.S. Al-Rasheid, and L. Li. 2005. Taxonomic characterization of two marine peritrichous ciliates, Pseudovorticella clampi n. sp. and Zoothamnium pararbuscula n. sp. (Ciliophora: Peritrichia), from North China. J. Eukaryot. Microbiol. 52:159-169.
25. Jousson, O., C. Pretti, D. Di Bello, and A.M. Cognetti-Varriale. 2005. Non-invasive detection and quantification of the parasitic ciliate Ichthyophthirius multifiliis by real-time PCR. Dis Aquat Organ 65:251-255.
26. Lara, E., C. Berney, H. Harms, and A. Chatzinotas. 2007. Cultivationindependent analysis reveals a shift in ciliate 18S rRNA gene diversity in a polycyclic aromatic hydrocarbon-polluted soil. FEMS Microbiol. Ecol. 62:365-373.
27. Loy, A., R. Arnold, P. Tischler, T. Rattei, M. Wagner, and M. Horn. 2008. probeCheck-a central resource for evaluating oligonucleotide probe coverage and specificity. Environ. Microbiol. 10:2894-2898.
28. Lynn, D.H. 2008. The Ciliated Protozoa: Characterization, Classification and Guide to the Literature, 3rd ed. Springer, Dordrecht.
29. Martín-Cereceda, M., S. Serrano, and A. Guinea. 2001. Biofilm communities and operational monitoring of a rotating biological contactor system. Water Air Soil Pollut. 126:193-206.
30. Medlin, L., H.J. Elwood, S. Stickel, and M.L. Sogin. 1988. The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions. Gene 71:491-499.
31. Monchy, S., G. Sanciu, M. Jobard, et al. 2011. Exploring and quantifying fungal diversity in freshwater lake ecosystems using rDNA cloning/sequencing and SSU tag pyrosequencing. Environ. Microbiol. 13:1433-1453.
32. Nilsson, R.H., E. Kristiansson, M. Ryberg, N. Hallenberg, and K.H. Larsson. 2008. Intraspecific ITS variability in the kingdom fungi as expressed in the international sequence databases and its implications for molecular species identification. Evol. Bioinform. 4:193-201.
33. Puitika, T., Y. Kasahara, N. Miyoshi, Y. Sato, and S. Shimano. 2007. A taxon-specific oligonucleotide primer set for PCR-based detection of soil ciliate. Microbes Environ. 22:78-81.
34. Rodríguez-Martínez, R., M. Labrenz, J. del Campo, I. Forn, K. Jürgens, and R. Massana. 2009. Distribution of the uncultured protest MAST-4 in the Indian Ocean, Drake Passage and Mediterranean Sea assessed by real-time quantitative PCR. Environ. Microbiol. 11:397-408.
35. Schloss, P.D., and J. Handelsman. 2005. Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl. Environ. Microbiol. 71:1501-1506.
36. Sun, P., J. Clamp, D. Xu, Y. Kusuoka, and W. Miao. 2012. Vorticella Linnaeus, 1767 (Ciliophora, Oligohymenophora, Peritrichia) is a grade not a clade: redefinition of Vorticella and the families Vorticellidae and Astylozoidae using molecular characters derived from the gene coding for small subunit ribosomal RNA. Protist 163:129-142.
37. Sun, P., J.C. Clamp, and D. Xu. 2010. Analysis of the secondary structure of ITS transcripts in peritrich ciliates (Ciliophora, Oligohymenophorea): implications for structural evolution and phylogenetic reconstruction. Mol. Phylogenet. Evol. 56:242-251.
38. Tamura, K., J. Dudley, M. Nei, and S. Kumar. 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0. Mol. Biol. Evol. 24:1596-1599.
39. Tamura, M., L.A. Katz, and G.B. McManus. 2011. Distribution and diversity of oligotrich and choreotrich ciliates across an environmental gradient in a large temperate estuary. Aquat. Microb. Ecol. 64:51-67.
40. Taniguchi, A., H. Onishi, and M. Eguchi. 2011. Quantitative PCR assay for the detection of the parasitic ciliate Cryptocaryon irritans. Fisher. Sci. 77:607-613.
41. Utz, L.R.P., and D.W. Coats. 2005. Spatial and temporal patterns in the occurrence of peritrich ciliates as epibionts on calanoid copepods in the Chesapeake Bay, USA. J. Eukaryot. Microbiol. 52:236-244.
42. Utz, L.R.P., and D.W. Coats. 2008. Telotroch formation, survival, and attachment in the epibiotic peritrich Zoothamnium intermedium (Ciliophora, Oligohymenophorea). Invertebr. Biol. 127:237-248.
43. Utz, L.R.P., T.L.L. Simão, L.S.L. Safi, and E. Eizirik. 2010. Expanded phylogenetic representation of genera Opercularia and Epistylis sheds light on the evolution and higher-level taxonomy of peritrich ciliates (Ciliophora: Peritrichia). J. Eukaryot. Microbiol. 57:415-420.
44. Zhan, Z., K. Xu, A. Warren, and Y. Gong. 2009. Reconsideration of phylogenetic relationships of the subclass Peritrichia (Ciliophora, Oligohymenophorea) based on small subunit ribosomal RNA gene sequences, with the establishment of a new subclass Mobilia Kahl, 1933. J. Eukaryot. Microbiol. 56:552-558.
45. Zhu, F., R. Massana, F. Not, D. Marie, and D. Vaulot. 2005. Mapping of picoeucaryotes in marine ecosystems with quantitative PCR of the 18S rRNA gene. FEMS Microbiol. Ecol. 52:79-92.
46. Zinger, L., B. Shahnavaz, F. Baptist, R.A. Geremia, and P. Choler. 2009. Microbial diversity in alpine tundra soils correlates with snow cover dynamics. ISME J. 3:850-859.