Stream Hydrological Fragmentation Drives Bacterioplankton Community Composition

PLoS ONE

Volumn 8, Issue 5, 2013, Pages

  Fazi, Stefano ^a   Vázquez, Eusebi ^b   Casamayor, Emilio O ^c   Amalfitano, Stefano ^a   Butturini, Andrea ^b  

^a WATER RESEARCH INSTITUTE   (Italy)

^b UNIVERSITY OF BARCELONA   (Spain)

^c CENTRE D ESTUDIS AVANÇATS DE BLANES CEAB CSIC   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ORGANIC CARBON; RNA 16S;

16S RRNA GENE; ACTINOBACTERIA; ARTICLE; AUTUMN; BACTERIOPLANKTON; BETAPROTEOBACTERIA; DNA FINGERPRINTING; GENE SEQUENCE; HABITAT FRAGMENTATION; HYDROLOGICAL FRAGMENTATION; IN SITU HYBRIDIZATION; MICROBIAL COMMUNITY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POPULATION ABUNDANCE; SEASONAL VARIATION; SPAIN; STREAM (RIVER); SUMMER; UNINDEXED SEQUENCE; WATER FLOW;

ACTINOBACTERIA; BACTEROIDETES; COLONY COUNT, MICROBIAL; DNA, BACTERIAL; ECOSYSTEM; FRESH WATER; HYDROLOGY; MICROBIAL CONSORTIA; PHYLOGENY; PLANKTON; PROTEOBACTERIA; RNA, RIBOSOMAL, 16S; SEASONS; SEAWATER; SEQUENCE ANALYSIS, DNA; SPAIN;

ACTINOBACTERIA; BACTERIA (MICROORGANISMS); BETAPROTEOBACTERIA;

EID: 84878570819     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0064109     Document Type: Article

References (70)

1. Martiny JBH, Bohannan BJM, Brown JH, Colwell RK, Fuhrman JA, et al. (2006) Microbial biogeography: putting microorganisms on the map. Nature Reviews Microbiology 4: 102-112.
2. Chaffron S, Rehrauer H, Pernthaler J, von Mering C, (2010) A global network of coexisting microbes from environmental and whole-genome sequence data. Genome Research 20: 947-959.
3. Barberan A, Casamayor EO, (2010) Global phylogenetic community structure and beta-diversity patterns in surface bacterioplankton metacommunities. Aquatic Microbial Ecology 59: 1-10.
4. Logue JB, Mouquet N, Peter H, Hillebrand H, Metacommunity Working G, (2011) Empirical approaches to metacommunities: a review and comparison with theory. Trends in Ecology & Evolution 26: 482-491.
5. Portillo MC, Anderson SP, Fierer N, (2012) Temporal variability in the diversity and composition of stream bacterioplankton communities. Environmental Microbiology 14: 2417-2428.
6. Besemer K, Hodl I, Singer G, Battin TJ, (2009) Architectural differentiation reflects bacterial community structure in stream biofilms. Isme Journal 3: 1318-1324.
7. Östman O, Drakare S, Kritzberg ES, Langenheder S, Logue JB, et al. (2010) Regional invariance among microbial communities. Ecology Letters 13: 118-127.
8. Barberan A, Casamayor EO, (2011) Euxinic Freshwater Hypolimnia Promote Bacterial Endemicity in Continental Areas. Microbial Ecology 61: 465-472.
9. Schimel J, Balser TC, Wallenstein M, (2007) Microbial stress-response physiology and its implications for ecosystem function. Ecology 88: 1386-1394.
10. Curtis TP, Sloan WT, (2005) Exploring microbial diversity- A vast below. Science 309: 1331-1333.
11. Fierer N, Morse JL, Berthrong ST, Bernhardt ES, Jackson RB, (2007) Environmental controls on the landscape-scale biogeography of stream bacterial communities. Ecology 88: 2162-2173.
12. Jackson RB, Fierer N, Schimel JP, (2007) New directions in microbial ecology. Ecology 88: 1343-1344.
13. Hervas A, Camarero L, Reche I, Casamayor EO, (2009) Viability and potential for immigration of airborne bacteria from Africa that reach high mountain lakes in Europe. Environmental Microbiology 11: 1612-1623.
14. Comte J, del Giorgio PA, (2009) Links between resources, C metabolism and the major components of bacterioplankton community structure across a range of freshwater ecosystems. Environmental Microbiology 11: 1704-1716.
15. Sommaruga R, Casamayor EO, (2009) Bacterial 'cosmopolitanism' and importance of local environmental factors for community composition in remote high-altitude lakes. Freshwater Biology 54: 994-1005.
16. Logue JB, Lindström ES, (2008) Biogeography of bacterioplankton in inland waters. Freshwater Reviews 1: 99-114.
17. Van der Gucht K, Cottenie K, Muylaert K, Vloemans N, Cousin S, et al. (2007) The power of species sorting: Local factors drive bacterial community composition over a wide range of spatial scales. Proceedings of the National Academy of Sciences of the United States of America 104: 20404-20409.
18. Logue JB, Robinson CT, Meier C, Van der Meer JR, (2004) Relationship between sediment organic matter, bacteria composition, and the ecosystem metabolism of alpine streams. Limnology and Oceanography 49: 2001-2010.
19. Reche I, Pulido-Villena E, Morales-Baquero R, Casamayor EO, (2005) Does ecosystem size determine aquatic bacterial richness? Ecology 86: 1715-1722.
20. Lindstrom ES, Forslund M, Algesten G, Bergstrom AK, (2006) External control of bacterial community structure in lakes. Limnology and Oceanography 51: 339-342.
21. Larned ST, Datry T, Arscott DB, Tockner K, (2010) Emerging concepts in temporary-river ecology. Freshwater Biology 55: 717-738.
22. Romaní AM, Amalfitano S, Artigas J, Fazi S, Sabater S, et al. (2012) Microbial biofilm structure and organic matter use in mediterranean streams. Hydrobiologia pp. 1-16.
23. Romaní AM, Vazquez E, Butturini A, (2006) Microbial availability and size fractionation of dissolved organic carbon after drought in an intermittent stream: biogeochemical link across the stream-riparian interface. Microb Ecol 52: 501-512.
24. Casamayor EO, Schafer H, Baneras L, Pedros-Alio C, Muyzer G, (2000) Identification of and spatio-temporal differences between microbial assemblages from two neighboring sulfurous lakes: Comparison by microscopy and denaturing gradient gel electrophoresis. Applied and Environmental Microbiology 66: 499-508.
25. Gasith A, Resh VH, (1999) Streams in Mediterranean climate regions: Abiotic influences and biotic responses to predictable seasonal events. Annual Review of Ecology and Systematics 30: 51-81.
26. von Schiller D, Acuna V, Graeber D, Marti E, Ribot M, et al. (2011) Contraction, fragmentation and expansion dynamics determine nutrient availability in a Mediterranean forest stream. Aquatic Sciences 73: 485-497.
27. Butturini A, Bernal S, Nin E, Hellin C, Rivero L, et al. (2003) Influences of the stream groundwater hydrology on nitrate concentration in unsaturated riparian area bounded by an intermittent Mediterranean stream. Water Resources Research 39: 1-13.
28. McClain ME, Boyer EW, Dent CL, Gergel SE, Grimm NB, et al. (2003) Biogeochemical hot spots and hot moments at the interface of terrestrial and aquatic ecosystems. Ecosystems 6: 301-312.
29. Benstead JP, Leigh DS, (2012) An expanded role for river networks. Nature Geosci 5: 678-679.
30. Vazquez E, Amalfitano S, Fazi S, Butturini A, (2011) Dissolved organic matter composition in a fragmented Mediterranean fluvial system under severe drought conditions. Biogeochemistry 102: 59-72.
31. Judd KE, Crump BC, Kling GW, (2006) Variation in dissolved organic matter controls bacterial production and community composition. Ecology 87: 2068-2079.
32. Zwart G, Crump BC, Agterveld M, Hagen F, Han SK, (2002) Typical freshwater bacteria: an analysis of available 16S rRNA gene sequences from plankton of lakes and rivers. Aquatic Microbial Ecology 28: 141-155.
33. Amalfitano S, Fazi S, Zoppini A, Caracciolo AB, Grenni P, et al. (2008) Responses of benthic bacteria to experimental drying in sediments from Mediterranean temporary rivers. Microbial Ecology 55: 270-279.
34. Zoppini A, Amalfitano S, Fazi S, Puddu A, (2010) Dynamics of a benthic microbial community in a riverine environment subject to hydrological fluctuations (Mulargia River, Italy). Hydrobiologia 657: 37-51.
35. Allgaier M, Grossart HP, (2006) Diversity and seasonal dynamics of Actinobacteria populations in four lakes in northeastern Germany. Applied and Environmental Microbiology 72: 3489-3497.
36. Fazi S, Amalfitano S, Piccini C, Zoppini A, Puddu A, et al. (2008) Colonization of overlaying water by bacteria from dry river sediments. Environmental Microbiology 10: 2760-2772.
37. Gao XQ, Olapade OA, Leff LG, (2005) Comparison of benthic bacterial community composition in nine streams. Aquatic Microbial Ecology 40: 51-60.
38. Webster JR, (2007) Spiraling down the river continuum: stream ecology and the U-shaped curve. Journal of the North American Benthological Society 26: 375-389.
39. Muylaert K, Van der Gucht K, Vloemans N, De Meester L, Gillis M, et al. (2002) Relationship between bacterial community composition and bottom-up versus top-down variables in four eutrophic shallow lakes. Applied and Environmental Microbiology 68: 4740-4750.
40. Yannarell AC, Triplett EW, (2005) Geographic and environmental sources of variation in lake bacterial community composition. Applied and Environmental Microbiology 71: 227-239.
41. Findlay SEG, Sinsabaugh RL, Sobczak WV, Hoostal M, (2003) Metabolic and structural response of hyporheic microbial communities to variations in supply of dissolved organic matter. Limnology and Oceanography 48: 1608-1617.
42. Kirchman DL, Dittel AI, Findlay SEG, Fischer D, (2004) Changes in bacterial activity and community structure in response to dissolved organic matter in the Hudson River, New York. Aquatic Microbial Ecology 35: 243-257.
43. Anders HJ, Kaetzke A, Kampfer P, Ludwig W, Fuchs G, (1995) Taxonomic position of aromatic-degrading denitrifying Pseudomonad strains K-172 and KB-740 and their description as new members of the genera Thauera, as Thauera-aromatica sp-nov, and Azoarcus, as Azoarcus-evansii sp-nov, respectively, members of the beta-subclass of the proteobacteria. International Journal of Systematic Bacteriology 45: 327-333.
44. Song B, Haggblom MM, Zhou JZ, Tiedje JM, Palleroni NJ, (1999) Taxonomic characterization of denitrifying bacteria that degrade aromatic compounds and description of Azoarcus toluvorans sp nov and Azoarcus toluclasticus sp nov. International Journal of Systematic Bacteriology 49: 1129-1140.
45. Jezberova J, Jezbera J, Brandt U, Lindstrom ES, Langenheder S, et al. (2010) Ubiquity of Polynucleobacter necessarius ssp asymbioticus in lentic freshwater habitats of a heterogenous 2000 km2 area. Environmental Microbiology 12: 658-669.
46. Hahn MW, (2006) The microbial diversity of inland waters. Current Opinion in Biotechnology 17: 256-261.
47. Wu QLL, Hahn MW, (2006) High predictability of the seasonal dynamics of a species-like Polynucleobacter population in a freshwater lake. Environmental Microbiology 8: 1660-1666.
48. Crump BC, Kling GW, Bahr M, Hobbie JE, (2003) Bacterioplankton community shifts in an arctic lake correlate with seasonal changes in organic matter source. Applied and Environmental Microbiology 69: 2253-2268.
49. Ninyerola M, Pons X, Roure JM, (2000) A methodological approach of climatological modelling of air temperature and precipitation through GIS techniques. International Journal of Climatology 20: 1823-1841.
50. Butturini A, Alvarez M, Bernal S, Vazquez E, Sabater F, (2008) Diversity and temporal sequences of forms of DOC and NO3-discharge responses in an intermittent stream: Predictable or random succession? Journal of Geophysical Research-Biogeosciences 113.
51. Medici C, Butturini A, Bernal S, Vazquez E, Sabater F, et al. (2008) Modelling the non-linear hydrological behaviour of a small Mediterranean forested catchment. Hydrological Processes 22: 3814-3828.
52. Keeney DR, Nelson DW (1982) Nitrogen-inorganic forms. In: Methods of Soil Analysis, Part 2. 2nd Edn., Page, A. L., D. R Keeney, D. E Baker, R. H Miller, Jr. R Ellis and J. D Rhoades (Eds.). Madison, W. I. Agron. Monogr. 9. ASA and SSSA., ISBN: 0891180729.
53. Hach Company (1992) Hach water analysis handbook, 2nd edition. Hach Company, Loveland, Colorado.
54. Bleich ME, Silveira RML, Nogueira FMB, (2009) Limnological Patterns in Northern Pantanal Lagoons. Brazilian Archives of Biology and Technology 52: 755-764.
55. Stanhope JW, Anderson IC, Reay WG, (2009) Base Flow Nutrient Discharges from Lower Delmarva Peninsula Watersheds of Virginia, USA. Journal of Environmental Quality 38: 2070-2083.
56. Servais P, Anzil A, Ventresque C, (1989) Simple method for determination of biodegradable dissolved organic carbon in water. Applied and Environmental Microbiology 55: 2732-2734.
57. Weishaar JL, Aiken GR, Bergamaschi BA, Fram MS, Fujii R, et al. (2003) Evaluation of specific ultraviolet absorbance as an indicator of the chemical composition and reactivity of dissolved organic carbon. Environmental Science & Technology 37: 4702-4708.
58. Hood E, Williams MW, McKnight DM, (2005) Sources of dissolved organic matter (DOM) in a Rocky Mountain stream using chemical fractionation and stable isotopes. Biogeochemistry 74: 231-255.
59. McKnight DM, Boyer EW, Westerhoff PK, Doran PT, Kulbe T, et al. (2001) Spectrofluorometric characterization of dissolved organic matter for indication of precursor organic material and aromaticity. Limnology and Oceanography 46: 38-48.
60. Coble PG, (1996) Characterization of marine and terrestrial DOM in seawater using excitation emission matrix spectroscopy. Marine Chemistry 51: 325-346.
61. Stedmon CA, Markager S, (2005) Tracing the production and degradation of autochthonous fractions of dissolved organic matter by fluorescence analysis. Limnology and Oceanography 50: 1415-1426.
62. Fazi S, Amalfitano S, Pernthaler J, Puddu A, (2005) Bacterial communities associated with benthic organic matter in headwater stream microhabitats. Environmental Microbiology 7: 1633-1640.
63. Fazi S, Amalfitano S, Pizzetti H, Pernthaler J, (2007) Efficiency of fluorescence in situ hybridization for bacterial cell identification in temporary river sediments with contrasting water content. Systematic and Applied Microbiology 30: 463-470.
64. Loy A, Maixner F, Wagner M, Horn M, (2007) probeBase- an online resource for rRNA-targeted oligonucleotide probes: new features 2007. Nucleic Acids Research 35: D800-D804.
65. Demergasso C, Escudero L, Casamayor EO, Chong G, Balagué V, Pedros-Alio C, (2008) Novelty and spatio-temporal heterogeneity in the bacterial diversity of hypersaline Lake Tebenquiche (Salar de Atacama). Extremophiles 12: 491-504.
66. Ferrera I, Massana R, Casamayor EO, Balague V, Sanchez O, et al. (2004) High-diversity biofilm for the oxidation of sulfide-containing effluents. Applied Microbiology and Biotechnology 64: 726-734.
67. Casamayor EO, Pedros-Alio C, Muyzer G, Amann R, (2002) Microheterogeneity in 16S ribosomal DNA-defined bacterial populations from a stratified planktonic environment is related to temporal changes and to ecological adaptations. Applied and Environmental Microbiology 68: 1706-1714.
68. Casamayor EO, Muyzer G, Pedros-Alio C, (2001) Composition and temporal dynamics of planktonic archaeal assemblages from anaerobic sulfurous environments studied by 16S rDNA denaturing gradient gel electrophoresis and sequencing. Aquatic Microbial Ecology 25: 237-246.
69. Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 25: 3389-3402.
70. Clarke KR, Warwick RM (2001) Changes in marine communities: an approach to statistical analysis and interpretation, 2nd edition. PRIMER-E, Plymouth. 172 pp.