Abundance and diversity of Planctomycetes in a Tyrrhenian coastal system of central Italy

Aquatic Microbial Ecology

Volumn 65, Issue 2, 2011, Pages 129-141

  Pizzetti, Ilaria ^a,b   Gobet, Angélique ^c   Fuchs, Bernhard M ^a   Amann, Rudolf ^a   Fazi, Stefano ^b  

^a MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY   (Germany)

^b WATER RESEARCH INSTITUTE   (Italy)

^c STATION BIOLOGIQUE DE ROSCOFF   (France)

Author keywords

16S rRNA gene sequencing; Bacterial diversity; CARD FISH; Coastal lake ecology; FISH; Planctomycetes

Indexed keywords

EID: 83655211676     PISSN: 09483055     EISSN: None     Source Type: Journal    
DOI: 10.3354/ame01535     Document Type: Article

References (72)

1. Alonso C, Gómez-Pereira PR, Ramette A, Ortega L, Fuchs BM, Amann R (2010) Multilevel analysis of the bacterial diversity along the environmental gradient Río de la Plata- South Atlantic Ocean. Aquat Microb Ecol 61: 57-72
2. Amalfitano S, Fazi S, Zoppini A, Barra Caracciolo A, Grenni P, Puddu A (2008) Responses of benthic bacteria to experimental drying in sediments from Mediterranean temporary rivers. Microb Ecol 55:270-279 (Pubitemid 351171468)
3. Bauld J, Staley JT (1976) Planctomyces maris sp. nov.: a marine isolate of Planctomyces-Blastocaulis group of budding bacteria. J Gen Microbiol 97:45-55
4. Brümmer IHM, Felske ADM, Wagner-Döbler I (2004) Diversity and seasonal changes of uncultured Planctomyce tales in river biofilms. Appl Environ Microbiol 70: 5094-5101 (Pubitemid 39279577)
5. Chouari R, Le Paslier D, Daegelen P, Ginestet P, Weissenbach J, Sghir A (2003) Molecular evidence for novel planctomycete diversity in a municipal wastewater treatment plant. Appl Environ Microbiol 69:7354-7363 (Pubitemid 38585388)
6. Crump BC, Armbrust EV, Baross JA (1999) Phylogenetic analysis of particle-Attached and free-living bacterial communities in the Columbia River, its estuary, and the adjacent coastal ocean. Appl Environ Microbiol 65: 3192-3204 (Pubitemid 29315598)
7. DeLong EF, Franks DG, Alldredge AL (1993) Phylogenetic diversity of aggregate-Attached vs. free-living marine bacterial assemblages. Limnol Oceanogr 38:924-934 (Pubitemid 24408401)
8. Eiler A, Bertilsson S (2004) Composition of freshwater bacterial communities associated with cyanobacterial blooms in four Swedish lakes. Environ Microbiol 6:1228-1243 (Pubitemid 39606293)
9. Elshahed MS, Youssef NH, Luo QW, Najar FZ and others (2007) Phylogenetic and metabolic diversity of Planctomycetes from anaerobic, sulfide and sulfur-rich Zod - letone Spring, Oklahoma. Appl Environ Microbiol 73: 4707-4716 (Pubitemid 47237218)
10. Fieseler L, Horn M, Wagner M, Hentschel U (2004) Discovery of the novel candidate phylum 'Poribacteria' in marine sponges. Appl Environ Microbiol 70:3724-3732 (Pubitemid 38745923)
11. Franzmann PD, Skerman VBD (1984) Gemmata obscuri - globus, a new genus and species of the budding bacteria. Antonie van Leeuwenhoek 50:261-268 (Pubitemid 14031418)
12. Fuerst JA (1995) The planctomycetes: emerging models for microbial ecology, evolution and cell biology. Microbiology 141:1493-1506
13. Fuerst JA (2005) Intracellular compartmentation in Planctomycetes. Annu Rev Microbiol 59:299-328 (Pubitemid 41507434)
14. Fukunaga Y, Kurahashi M, Sakiyama Y, Ohuchi M, Yokota A, Harayama S (2009) Phycisphaera mikurensis gen. nov., sp. nov., isolated from a marine alga, and proposal of Phycisphaeraceae fam. nov., Phycisphaerales ord. nov. and Phycisphaerae classis nov. in the phylum Planctomycetes. J Gen Appl Microbiol 55:267-275
15. Giovannoni SJ, Schabtach E, Castenholz RW (1987) Iso - sphaera pallida, gen. and comb. nov., a gliding, budding eubacterium from hot-springs. Arch Microbiol 147: 276-284
16. Glöckner FO, Amann R, Alfreider A, Pernthaler J, Psenner R, Trebesius K, Schleifer KH (1996) An in situ hybrid ization protocol for the detection and identification of planktonic bacteria. Syst Appl Microbiol 19: 403-406 (Pubitemid 26388335)
17. Glöckner FO, Kube M, Bauer M, Teeling H and others (2003) Complete genome sequence of the marine planctomycete Pirellula sp. strain 1. Proc Natl Acad Sci USA 100:8298-8303 (Pubitemid 36842539)
18. Good IJ (1953) The population frequencies of species and the estimation of population parameters. Biometrika 40: 237-264
19. Inagaki F, Nunoura T, Nakagawa S, Teske A and others (2006) Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments, on the Pacific Ocean margin. Proc Natl Acad Sci USA 103:2815-2820
20. Janse I, Zwart G, van der Maarel MJEC, Gottschal JC (2000) Composition of the bacterial community degrading Phaeocystis mucopolysaccharides in enrichment cultures. Aquat Microb Ecol 22:119-133 (Pubitemid 34235216)
21. Kalyuzhnaya MG, Lidstrom ME, Chistoserdova L (2004) Utility of environmental primers targeting ancient enzymes: methylotroph detection in Lake Washington. Microb Ecol 48:463-472 (Pubitemid 40564224)
22. Kalyuzhnaya MG, Nercessian O, Lidstrom ME, Chistoserdova L (2005) Development and application of polymerase chain reaction primers based on fhcD for environmental detection of methanopterin-linked C1-metabolism in bacteria. Environ Microbiol 7:1269-1274 (Pubitemid 41026527)
23. Kemp PF, Aller JY (2004) Bacterial diversity in aquatic and other environments: what 16S rDNA libraries can tell us. FEMS Microbiol Ecol 47:161-177 (Pubitemid 38177581)
24. Kulichevskaya IS, Ivanova AO, Belova SE, Baulina OI and others (2007) Schlesneria paludicola gen. nov., sp. nov., the first acidophilic member of the order Planctomyce - tales, from Sphagnum-dominated boreal wetlands. Int J Syst Evol Microbiol 57:2680-2687 (Pubitemid 350187440)
25. Kulichevskaya IS, Ivanova AO, Baulina OI, Bodelier PLE, Damste JSS, Dedysh SN (2008) Singulisphaera acidiphila gen. nov., sp. nov., a non-filamentous, Isosphaera-like planctomycete from acidic northern wetlands. Int J Syst Evol Microbiol 58:1186-1193
26. Kulichevskaya IS, Baulina OI, Bodelier PLE, Rijpstra WIC, Damste JSS, Dedysh SN (2009) Zavarzinella formosa gen. nov., sp. nov., a novel stalked, Gemmata-like planctomycete from a Siberian peat bog. Int J Syst Evol Microbiol 59:357-364
27. Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. John Wiley & Sons, New York, NY, p 115-175
28. Legendre P, Legendre L (1998) Numerical ecology, 2nd English edn. Elsevier, Amsterdam
29. Lindsay MR, Webb RI, Fuerst JA (1997) Pirellulosomes: a new type of membrane-bounded cell compartment in planctomycete bacteria of the genus Pirellula. Microbiology 143:739-748 (Pubitemid 27192751)
30. Lindsay MR, Webb RI, Strous M, Jetten MS, Butler MK, Forde RJ, Fuerst JA (2001) Cell compartmentalisation in planctomycetes: novel types of structural organisation for the bacterial cell. Arch Microbiol 175:413-429 (Pubitemid 32646349)
31. Llobet-Brossa E, Rossello-Mora R, Amann R (1998) Microbial community composition of Wadden Sea sediments as revealed by fluorescence in situ hybridization. Appl Environ Microbiol 64:2691-2696 (Pubitemid 28303320)
32. Lorenzen CJ (1967) Determination of chlorophyll and pheo - pigments: spectrophotometric equations. Limnol Oceanogr 12:343-346
33. LudwigW, Strunk O, Westram R, Richter L and others (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32:1363-1371 (Pubitemid 38854737)
34. Manganelli M (2005) Sviluppo di criteri di valutazione del rischio ambientale e sanitario associato a microrganismi patogeni in ambienti acquatici. Final Report ISPELS Project, Roma
35. Mevik BH, Wehrens R (2007) The pls package: principal component and partial least squares regression in R. J Stat Softw 18:1-24
36. Miskin IP, Farrimond P, Head IM (1999) Identification of novel bacterial lineages as active members of microbial populations in a freshwater sediment using a rapid RNA extraction procedure and RT-PCR. Microbiology 145: 1977-1987 (Pubitemid 29396928)
37. Morris RM, Longnecker K, Giovannoni SJ (2006) Pirellula and OM43 are among the dominant lineages identified in an Oregon coast diatom bloom. Environ Microbiol 8:1361-1370 (Pubitemid 44025330)
38. Musat N, Werner U, Knittel K, Kolb S and others (2006) Microbial community structure of sandy intertidal sediments in the North Sea, Sylt-Rømø Basin, Wadden Sea. Syst Appl Microbiol 29:333-348
39. Neef A, Amann R, Schlesner H, Schleifer KH (1998) Monitoring a widespread bacterial group: in situ detection of planctomycetes with 16S rRNA-targeted probes. Microbiology 144:3257-3266 (Pubitemid 29011955)
40. Parsons TR, Maita Y, Lalli CM (1984) A manual of chemical and biological methods for seawater analysis. Pergamon Press, Oxford
41. Peplies J, Kottmann R, Ludwig W, Glöckner FO (2008) A standard operating procedure for phylogenetic inference (SOPPI) using (rRNA) marker genes. Syst Appl Microbiol 31:251-257
42. Pernthaler A, Pernthaler J, Amann R (2002) Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria. Appl Environ Microbiol 68:3094-3101 (Pubitemid 34602035)
43. Pernthaler A, Pernthaler J, Amann R (2004) Sensitive multi-color fluorescence in situ hybridization for the identification of environmental microorganisms. In: Kowalchuk G, de Bruijn FJ, Head IM, Akkermans ADL, van Elsas JD (eds) Molecular microbial ecology manual, 2nd edn. Kluwer Academic Publishers, Dordrecht, p 711-726
44. Pettine M, Patrolecco L, Manganelli M, Capri S, Farrace MG (1999) Seasonal variations of dissolved organic matter in the northern Adriatic Sea. Mar Chem 64:153-169 (Pubitemid 29103174)
45. Pizzetti I, Fuchs BM, Gerdts G, Wichels A, Wiltshire KH, Amann R(2011)Temporal variability of coastal Planctomycetes clades at Kabeltonne station, North Sea. Appl Environ Microbiol 77:5009-5017
46. Polz MF, Cavanaugh CM (1998) Bias in template-to-product ratios in multitemplate PCR. Appl Environ Microbiol 64: 3724-3730 (Pubitemid 28462964)
47. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, Glöckner FO (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35:7188-7196
48. R Development Core Team (2009) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna. www.r-project.org
49. Rath J, Wu KY, Herndl GJ, DeLong EF (1998) High phylo - genetic diversity in a marine-snow-Associated bacterial assemblage. Aquat Microb Ecol 14:261-269 (Pubitemid 128487636)
50. Rosselló-Mora R, Amann R (2001) The species concept for prokaryotes. FEMS Microbiol Rev 25:39-67 (Pubitemid 32057196)
51. Rusch A, Huettel M, Reimers CE, Taghon GL, Fuller CM (2003) Activity and distribution of bacterial populations in Middle Atlantic Bight shelf sands. FEMS Microbiol Ecol 44:89-100 (Pubitemid 37034603)
52. Schlesner H (1994) The development of media suitable for the microorganisms morphologically resembling Planctomyces spp., Pirellula spp., and other Planctomycetales from various aquatic habitats using dilute media. Syst Appl Microbiol 17:135-145 (Pubitemid 24193432)
53. Schloss PD, Handelsman J (2005) Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71:1501-1506 (Pubitemid 40396689)
54. Shu QL, Jiao NZ (2008a) Different Planctomycetes diversity patterns in latitudinal surface seawater of the open sea and in sediment. J Microbiol 46:154-159
55. Shu QL, Jiao NZ (2008b) New primers for amplification of the Planctomycetes 16S rRNA gene from environmental samples. J Rapid Meth Automat Microbiol 16:330-336
56. Shu QL, Jiao NZ (2008c) Profiling Planctomycetales diversity with reference to anammox-related bacteria in a South China Sea, deep-sea sediment. Mar Ecol 29: 413-420
57. Simonato F, Gómez-Pereira PR, Fuchs BM, Amann R (2010) Bacterioplankton diversity and community composition in the Southern Lagoon of Venice. Syst Appl Microbiol 33:128-138
58. Strous M, Fuerst JA, Kramer EHM, Logemann S and others (1999) Missing lithotroph identified as new planctomycete. Nature 400:446-449 (Pubitemid 29361796)
59. Suzuki MT, Giovannoni SJ (1996) Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microbiol 62:625-630 (Pubitemid 26047427)
60. Tadonléké RD (2007) Strong coupling between natural Planctomycetes and changes in the quality of dissolved organic matter in freshwater samples. FEMS Microbiol Ecol 59:543-555 (Pubitemid 46376227)
61. Valderrama JC (1981) The simultaneous analysis of total nitrogen and total phosphorus in natural waters. Mar Chem 10:109-122 (Pubitemid 11111734)
62. Vergin KL, Urbach E, Stein JL, DeLong EF, Lanoil BD, Giovannoni SJ (1998) Screening of a fosmid library of marine environmental genomic DNA fragments reveals four clones related to members of the order Planctomycetales. Appl Environ Microbiol 64:3075-3078 (Pubitemid 28363188)
63. Wagner M, Horn M (2006) The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance. Curr Opin Biotechnol 17:241-249 (Pubitemid 43850263)
64. Wallner G, Amann R, Beisker W (1993) Optimizing fluorescent in situ hybridization with rRNA-targeted oligonucleotide probes for flow cytometric identification of microorganisms. Cytometry 14:136-143 (Pubitemid 23042736)
65. Wang J, Jenkins C, Webb RI, Fuerst JA (2002) Isolation of Gemmata-like and Isosphaera-like planctomycete bacteria from soil and freshwater. Appl Environ Microbiol 68: 417-422 (Pubitemid 34031207)
66. Ward N, Staley JT, Fuerst JA, Giovannoni S, Schlesner H, Stackebrandt E (2006) The order Planctomycetales, in - cluding the genera Planctomyces, Pirellula, Gemmata and Isophaera and the Candidatus genera Brocadia, Kuenenia and Scalindua. In: Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E (eds) The Prokaryotes, a handbook on the biology of bacteria, 3rd edn. Vol 7: Proteobacteria: Delta and Epsilon subclasses. Springer, New York, NY, p 757-793
67. Winkelmann N, Harder J (2009) An improved isolation method for attached-living Planctomycetes of the genus Rhodopirellula. J Microbiol Methods 77:276-284
68. Woebken D, Fuchs BM, Kuypers MMM, Amann R (2007a) Potential interactions of particle-Associated anammox bacteria with bacterial and archaeal partners in the Namibian upwelling system. Appl Environ Microbiol 73:4648-4657 (Pubitemid 47122610)
69. Woebken D, Teeling H, Wecker P, Dumitriu A and others (2007b) Fosmids of novel marine Planctomycetes from the Namibian and Oregon coast upwelling systems and their cross-comparison with planctomycete genomes. ISME J 1:419-435 (Pubitemid 47373248)
70. Wold S, Sjöström M, Eriksson L (2001) PLS-regression: a basic tool of chemometrics. Chemom Intell Lab Syst 58: 109-130 (Pubitemid 33033283)
71. Xu KD, Stewart PS, Xia F, Huang CT, McFeters GA (1998) Spatial physiological heterogeneity in Pseudomonas aeru - ginosa biofilm is determined by oxygen availability. Appl Environ Microbiol 64:4035-4039 (Pubitemid 28463010)
72. Zhou J, Bruns MA, Tiedje JM (1996) DNA recovery from soils of diverse composition. Appl Environ Microbiol 62: 316-322 (Pubitemid 26047397)