Contrasting trends in distribution of four major planktonic betaproteobacterial groups along a pH gradient of epilimnia of 72 freshwater habitats

FEMS Microbiology Ecology

Volumn 81, Issue 2, 2012, Pages 467-479

  Jezbera, Jan ^a,b   Jezberová, Jitka ^a,b   Koll, Ulrike ^a   Horňák, Karel ^b   Šimek, Karel ^b   Hahn, Martin W ^a  

^a ERICH SCHMID INSTITUTE OF MATERIALS SCIENCE   (Austria)

^b INSTITUTE OF HYDROBIOLOGY   (Czech Republic)

Author keywords

Competition; Ecological diversification; Limnohabitans; Polynucleobacter

Indexed keywords

FRESH WATER;

ABUNDANCE; ADAPTATION; ALKALINITY; BACTERIOPLANKTON; COMPETITION (ECOLOGY); FLUORESCENCE; FRESHWATER ENVIRONMENT; GENETIC ANALYSIS; HABITAT TYPE; HYBRIDIZATION; PH; PHYLOGENETICS; POPULATION DISTRIBUTION; RESERVOIR; TAXONOMY;

ARTICLE; BETAPROTEOBACTERIA; CHEMISTRY; CLASSIFICATION; ECOSYSTEM; FLUORESCENCE IN SITU HYBRIDIZATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; MICROBIOLOGY; PHYLOGENY; PLANKTON; PROTON MOTIVE FORCE;

BETAPROTEOBACTERIA; ECOSYSTEM; FRESH WATER; IN SITU HYBRIDIZATION, FLUORESCENCE; PHYLOGENY; PLANKTON; PROTON-MOTIVE FORCE;

ALGAE; BETAPROTEOBACTERIA; METHYLOPHILUS; POLYNUCLEOBACTER; POLYNUCLEOBACTER NECESSARIUS;

EID: 84863776378     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1111/j.1574-6941.2012.01372.x     Document Type: Article

References (55)

1. Alonso C, Zeder M, Piccini C, Conde D & Pernthaler J (2009) Ecophysiological differences of betaproteobacterial populations in two hydrochemically distinct compartments of a subtropical lagoon. Environ Microbiol 11: 867-876.
2. Barberan A & Casamayor EO (2010) Global phylogenetic community structure and beta-diversity patterns in surface bacterioplankton metacommunities. Aquat Microb Ecol 1: 1-10.
3. Boenigk J, Stadler P, Wiedlroither A & Hahn MW (2004) Strain-specific differences in the grazing sensitivities of closely related ultramicrobacteria affiliated with the Polynucleobacter cluster. Appl Environ Microbiol 70: 5787-5793.
4. Buck U, Grossart HP, Amann R & Pernthaler J (2009) Substrate incorporation patterns of bacterioplankton populations in stratified and mixed waters of a humic lake. Environ Microbiol 11: 1854-1865.
5. Crump BC, Kling GW, Bahr M & Hobbie JE (2003) Bacterioplankton community shifts in an Arctic lake correlate with seasonal changes in organic matter source. Appl Environ Microbiol 69: 2253-2268.
6. Eiler A, Heinrich F & Bertilsson S (2011) Coherent dynamics and association networks among lake bacterioplankton taxa. ISME J 1: 1-13.
7. Friedrich U, Van Langenhove H, Altendorf K & Lipski A (2003) Microbial community and physicochemical analysis of an industrial waste gas biofilter and design of 16S rRNA-targeting oligonucleotide probes. Environ Microbiol 3: 183-201.
8. Ginige MP, Hugenholtz P, Daims H, Wagner M, Keller J & Blackall LL (2004) Use of stable-isotope probing, full-cycle rRNA analysis, and fluorescence in situ hybridization-microautoradiography to study a methanol-fed denitrifying microbial community. Appl Environ Microbiol 1: 588-596.
9. Giroldo D, Ortolano PIC & Vieira AAH (2007) Bacteria-algae association in batch cultures of phytoplankton from a tropical reservoir: the significance of algal carbohydrates. Freshw Biol 7: 1281-1289.
10. Glöckner FO, Zaichikov E, Belkova N, Denissova L, Pernthaler J, Pernthaler A & Amann R (2000) Comparative 16S rRNA analysis of lake bacterioplankton reveals globally distributed phylogenetic clusters including an abundant group of Actinobacteria. Appl Environ Microbiol 66: 5053-5065.
11. Hahn MW (2003) Isolation of strains belonging to the cosmopolitan Polynucleobacter necessarius cluster from freshwater habitats located in three climatic zones. Appl Environ Microbiol 69: 5248-5254.
12. Hahn MW, Pöckl M & Wu QL (2005) Low intraspecific diversity in a Polynucleobacter subcluster population numerically dominating bacterioplankton of a freshwater pond. Appl Environ Microbiol 71: 4539-4547.
13. Hahn MW, Lang E, Brandt U, Wu QL & Scheuerl T (2009) Emended description of the genus Polynucleobacter and the species P. necessarius and proposal of two subspecies, P. necessarius subspecies necessarius subsp. nov. and P. necessarius subsp. asymbioticus subsp. nov. Int J Syst Evol Microbiol 59: 2002-2009.
14. Hahn MW, Kasalický V, Jezbera J, Brandt U, Jezberová J & Šimek K (2010a) Limnohabitans curvus gen. nov., sp. nov., a planktonic bacterium isolated from a freshwater lake. Int J Syst Evol Microbiol 6: 1358-1365.
15. Hahn MW, Kasalický V, Jezbera J, Brandt U & Šimek K (2010b) Limnohabitans australis sp. nov., isolated from a freshwater pond, and emended description of the genus Limnohabitans. Int J Syst Evol Microbiol 60: 2946-2950.
16. Hahn MW, Lang E, Brandt U, Lünsdorf H, Wu QL & Stackebrandt E (2010c) Polynucleobacter cosmopolitanus sp. nov., free-living planktonic bacteria inhabiting freshwater lakes and rivers. Int J Syst Evol Mirobiol 1: 166-173.
17. Hahn MW, Lang E, Brandt U & Sproer C (2011a) Polynucleobacter acidiphobus sp. nov., a representative of an abundant group of planktonic freshwater bacteria. Int J Syst Evol Microbiol 61: 788-794.
18. Hahn MW, Lang E, Tarao M & Brandt U (2011b) Polynucleobacter rarus sp. nov., a free-living planktonic bacterium isolated from an acidic lake. Int J Syst Evol Microbiol 61: 781-787.
19. Hahn MW, Minasyan A, Lang E, Koll U & Sproer C (2012a) Polynucleobacter difficilis sp. nov., a planktonic freshwater bacterium affiliated with subcluster B1 of the genus Polynucleobacter. Int J Syst Evol Microbiol 62: 376-383.
20. Hahn MW, Scheuerl T, Jezberová J, Koll U, Jezbera J, Šimek K, Vannini C, Petroni G & Wu QL (2012b) The passive yet successful way of planktonic life: genomic and experimental analysis of the ecology of a free-living Polynucleobacter population. PLoS ONE 3: e32772.
21. Heckmann K & Schmidt HJ (1987) Polynucleobacter necessarius gen. nov., sp. nov., an obligately endosymbiotic bacterium living in the cytoplasm of Euplotes. Int J Syst Bacteriol 37: 456-457.
22. Hiorns WD, Methé EA, Nierzwickibauer SA & Zehr JP (1997) Bacterial diversity in Adirondack mountain lakes as revealed by 16S rRNA gene sequences. Appl Environ Microbiol 63: 2957-2960.
23. Horňák K, Jezbera J, Nedoma J, Gasol JM & Šimek K (2006) Bacterial leucine incorporation under different levels of resource availability and bacterivory in a freshwater reservoir. Aquat Microb Ecol 45: 277-289.
24. Hutalle-Schmelzer KML, Zwirnmann E, Krueger A & Grossart HP (2010) Enrichment and cultivation of pelagic bacteria from a humic lake using phenol and humic matter additions. FEMS Microbiol Ecol 1: 58-73.
25. Jezbera J, Horňák K & Šimek K (2005) Food selection by bacterivorous protists: insight from the analysis of the food vacuole content by means of fluorescence in situ hybridization. FEMS Microbiol Ecol 52: 351-363.
26. Jezbera J, Jezberová J, Brandt U & Hahn MW (2011) Ubiquity of Polynucleobacter necessarius subspecies asymbioticus results from ecological diversification. Environ Microbiol 13: 922-931.
27. 2 area. Environ Microbiol 12: 658-669.
28. Jones SE, Newton RJ & McMahon KD (2009) Evidence for structuring of bacterial community composition by organic carbon source in temperate lakes. Environ Microbiol 11: 2463-2472.
29. Kasalický V, Jezbera J, Šimek K & Hahn MW (2010) Limnohabitans planktonicus sp. nov. and Limnohabitans parvus sp. nov., planktonic Betaproteobacteria isolated from a freshwater reservoir, and emended description of the genus Limnohabitans. Int J Syst Evol Microbiol 60: 2710-2714.
30. Lindström ES & Bergström AK (2004) Influence of inlet bacteria on bacterioplankton assemblage composition in lakes of different hydraulic retention time. Limnol Oceanogr 49: 125-136.
31. Lindström ES, Kamst-Van Agterveld MP & Zwart G (2005) Distribution of typical freshwater bacterial groups is associated with pH, temperature, and lake water retention time. Appl Environ Microbiol 71: 8201-8206.
32. Manz W, Amann R, Ludwig W, Wagner M & Schleifer KH (1992) Phylogenetic oligodeoxynucleotide probes for the major subclasses of proteobacteria: problems and solutions. Syst Appl Microbiol 15: 593-600.
33. Moran MA & Zepp RG (1997) Role of photoreactions in the formation of biologically labile compounds from dissolved organic matter. Limnol Oceanogr 42: 1307-1316.
34. Newton RJ, Jones SE, Helmus MR & McMahon KD (2007) Phylogenetic ecology of the freshwater Actinobacteria acI lineage. Appl Environ Microbiol 73: 7169-7176.
35. Newton RJ, Jones SE, Eiler A, McMahon KD & Bertilsson S (2011) A guide to the natural history of freshwater lake bacteria. Microbiol Mol Biol Rev 75: 14-49.
36. Pernthaler A, Pernthaler J & Amann R (2002) Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria. Appl Environ Microbiol 6: 3094-3101.
37. Salcher MM, Pernthaler J, Zeder M, Psenner R & Posch T (2008) Spatio-temporal niche separation of planktonic Betaproteobacteria in an oligo-mesotrophic lake. Environ Microbiol 10: 2074-2086.
38. Salcher MM, Pernthaler J & Posch T (2010) Spatiotemporal distribution and activity patterns of bacteria from three phylogenetic groups in an oligomesotrophic lake. Limnol Oceanogr 2: 846-856.
39. Schauer M, Kamenik C & Hahn MW (2005) Ecological differentiation within a cosmopolitan group of planktonic freshwater bacteria (SOL cluster, Saprospiraceae, Bacteroidetes). Appl Environ Microbiol 71: 5900-5907.
40. Sekar R, Pernthaler A, Pernthaler J, Warnecke F, Posch T & Amann R (2003) An improved protocol for quantification of freshwater Actinobacteria by fluorescence in situ hybridization. Appl Environ Microbiol 5: 2928-2935.
41. Šimek K, Pernthaler J, Weinbauer MG, Horňák K, Dolan JR, Nedoma J, Mašín M & Amann R (2001) Changes in bacterial community composition and dynamics and viral mortality rates associated with enhanced flagellate grazing in a mesoeutrophic reservoir. Appl Environ Microbiol 6: 2723-2733.
42. Šimek K, Weinbauer MG, Horňák K, Jezbera J, Nedoma J & Dolan JR (2007) Grazer and virus-induced mortality of bacterioplankton accelerates development of Flectobacillus populations in a freshwater community. Environ Microbiol 3: 789-800.
43. Šimek K, Horňák K, Jezbera J, Nedoma J, Znachor P, Hejzlar J & Seďa J (2008) Spatio-temporal patterns of bacterioplankton production and community composition related to phytoplankton composition and protistan bacterivory in a dam reservoir. Aquat Microb Ecol 3: 249-262.
44. Šimek K, Kasalický V, Jezbera J, Jezberová J, Hejzlar J & Hahn MW (2010a) Broad habitat range of the phylogenetically narrow R-BT065 cluster representing a core group of the betaproteobacterial genus Limnohabitans. Appl Environ Microbiol 76: 631-639.
45. Šimek K, Kasalický V, Horňák K, Hahn MW & Weinbauer MG (2010b) Assessing niche separation among coexisting Limnohabitans strains through interactions with a competitor, viruses, and a bacterivore. Appl Environ Microbiol 5: 1406-1416.
46. Šimek K, Kasalický V, Zapomělová E & Horňák K (2011) Algal-derived substrates select for distinct betaproteobacterial lineages and contribute to niche separation in Limnohabitans strains. Appl Environ Microbiol 77: 7307-7315.
47. TerBraak CJF & Šmilauer P (1998) CANOCO for Windows Version 4.02. Centre for Biometry Wageningen, CPRO-DLO, Wageningen, the Netherlands.
48. Vannini C, Pöckl M, Petroni G, Wu QL, Lang E, Stackebrandt E, Schrallhammer M, Richardson PM & Hahn MW (2007) Endosymbiosis in statu nascendi: close phylogenetic relationship between obligately endosymbiotic and obligately free-living Polynucleobacter strains (Betaproteobacteria). Environ Microbiol 9: 347-359.
49. Watanabe K, Komatsu N, Ishii Y & Negishi M (2009) Effective isolation of bacterioplankton genus Polynucleobacter from freshwater environments grown on photochemically degraded dissolved organic matter. FEMS Microbiol Ecol 67: 57-68.
50. Whitaker RJ, Grogan DW & Taylor JW (2003) Geographic barriers isolate endemic populations of hyperthermophilic archaea. Science 301: 976-978.
51. Wu QL & Hahn MW (2006a) Differences in structure and dynamics of Polynucleobacter communities in a temperate and a subtropical lake revealed at three phylogenetic levels. FEMS Microbiol Ecol 57: 67-79.
52. Wu QL & Hahn MW (2006b) High predictability of the seasonal dynamics of a species-like Polynucleobacter population in a freshwater lake. Environ Microbiol 8: 1660-1666.
53. Wu QL, Schauer M, Kamst-van Agterveld MP, Zwart G & Hahn MW (2006) Bacterioplankton community composition along a salinity gradient of sixteen high mountain lakes located on the Tibetan Plateau, China. Appl Environ Microbiol 72: 5478-5485.
54. Yannarell AC & Triplett EW (2005) Geographic and environmental sources of variation in lake bacterial community composition. Appl Environ Microbiol 1: 227-239.
55. Zwart G, Crump BC, Kamst-van Agterveld MP, Hagen F & Han SK (2002) Typical freshwater bacteria: an analysis of available 16S rRNA gene sequences from plankton of lakes and rivers. Aquat Microb Ecol 28: 141-155.