Impact of sideways and bottom-up control factors on bacterial community succession over a tidal cycle

Proceedings of the National Academy of Sciences of the United States of America

Volumn 106, Issue 11, 2009, Pages 4301-4306

  Chauhan, Ashvini ^a   Cherrier, Jennifer ^a   Williams, Henry N ^a  

^a FLORIDA A AND M UNIVERSITY   (United States)

Author keywords

Bdellovibrio like organisms (blos); Dissolved organic matter predator prey interactions; Stable isotope probing; Tidal microbiota

Indexed keywords

ORGANIC CARBON; ORGANIC NITROGEN; RIBOSOME DNA;

ARTICLE; BACTERIAL COUNT; BDELLOVIBRIO; CHLAMYDIACEAE; COMMUNITY SUCCESSION; CONTROLLED STUDY; DELTAPROTEOBACTERIA; DISSOLUTION; ESTUARINE SPECIES; ESTUARY; FOOD CHAIN; GAMMAPROTEOBACTERIA; GRAM POSITIVE BACTERIUM; ISOTOPE LABELING; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; MICROCOSM; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; OSCILLATION; POLYMERASE CHAIN REACTION; PREDATION; PREY; PRIORITY JOURNAL; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; RIVER; SALINITY; SALT TOLERANCE; SEQUENCE ANALYSIS; TIDE; UNITED STATES;

BACTERIA; BDELLOVIBRIO; BIODIVERSITY; DNA, RIBOSOMAL; FOOD CHAIN; MOLECULAR SEQUENCE DATA; POLYMERASE CHAIN REACTION; RIVERS; SALINITY; TIDAL WAVES; WATER MICROBIOLOGY;

ACTINOBACTERIA (CLASS); ALPHAPROTEOBACTERIA; BACTERIA (MICROORGANISMS); BACTEROIDETES; BDELLOVIBRIO; BETAPROTEOBACTERIA; CHLAMYDIALES; DELTAPROTEOBACTERIA; GAMMAPROTEOBACTERIA; VERRUCOMICROBIA;

EID: 63149144977     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0809671106     Document Type: Article

References (43)

1. Cottrell MT, Kirchman DL (2003) Contribution of major bacterial groups to bacterial biomass production (thymidine and leucine incorporation) in the Delaware estuary. Limnol Oceanogr 48:168-178.
2. Mou X, Sun S, Edwards RA, Hodson RE, Moran MA (2008) Bacterial carbon processing by generalist species in the coastal ocean. Nature 451(7179):708-711.
3. Rappe MS, Vergin K, Giovannoni SJ (2000) Phylogenetic comparisons of a coastal bacterioplankton community with its counterparts in open ocean and freshwater systems. FEMS Microbiol Ecol 33:219-232.
4. Cherrier J, Bauer JE (2004) Bacterial utilization of transient plankton-derived dissolved organic carbon and nitrogen inputs in surface ocean waters. Aquat Microb Ecol 35:229-241.
5. Azam F (1998) Microbial control of oceanic carbon flux: The plot thickens. Science 280:694-696.
6. Cottrell MT, Kirchman DL (2000) Natural assemblages of marine proteobacteria and members of the Cytophaga-Flavobacter cluster consuming low-and high-molecular-weight dissolved organic matter. Appl Environ Microbiol 66:1692-1697.
7. Piccini C, Conde D, Alonso C, Sommaruga R, Pernthaler J (2006) Blooms of single bacterial species in a coastal lagoon of the southwestern Atlantic Ocean. Appl Environ Microbiol 72:6560-6568.
8. Bouvier TC, del Giorgio PA (2002) Compositional changes in free-living bacterial communities along a salinity gradient in two temperate estuaries. Limnol Oceanogr 47:453-470.
9. Kirchman DL, Dittel AI, Findlay SEG, Fisher D (2004) Changes in bacterial activity and community structure in response to dissolved organic matter in the Hudson River, New York. Aquat Microb Ecol 35:243-257.
10. Jürgens K, Matz C (2002) Predation as a shaping force for the phenotypic and genotypic composition of planktonic bacteria. Antonie Van Leeuwenhoek 81:413-434.
11. Bouvier T, del Giorgio PA (2007) Key role of selective viral-induced mortality in determining marine bacterial community composition. Environ Microbiol 9:287-297.
12. Pernthaler J (2005) Predation on prokaryotes in the water column and its ecological implications. Nat Rev Microbiol 3:537-546.
13. Zhang R, Weinbauer MG, Qian PY (2007) Viruses and flagellates sustain apparent richness and reduce biomass accumulation of bacterioplankton in coastal marine waters. Environ Microbiol 9:3008-3018.
14. Strom SL (2008) Microbial ecology of ocean biogeochemistry: A community perspective. Science 320:1043-1045.
15. Fuhrman JA, Hagstrom A (2008) Bacterial and archaeal community structure and its pattern. Microbial Ecology of the Oceans, ed Kirchman DL (Wiley, NewYork), 2nd Ed.
16. Williams HN, Piñeiro S (2006) Ecology of the predatory Bdellovibrio and like organisms. Predatory Prokaryotes, ed Jurkevitch E (Springer, New York), pp 214-244.
17. Jurkevitch E (2000) The genus Bdellovibrio. The Prokaryotes: An Evolving Electronic Resource for the Microbiological Community, ed Dworkin M, et al. (Springer, New York), 3rd Ed, release 3.7, November 2, 2001.
18. Pineiro SA, et al. (2007) Global survey of diversity among environmental saltwater Bacteriovoracaceae. Environ Microbiol 9:2441-2450.
19. Chauhan A, Williams HN (2006) Response of Bdellovibrio and like organisms (BALOs) to the migration of naturally occurring bacteria to chemo attractants. Curr Microbiol 53:516-522.
20. Kisand V, Andersson N, Wikner J (2005) Bacterial freshwater species successfully immigrate to the brackish water environment in the northern Baltic. Limnol Oceanogr 50:945-956.
21. Fandino LB, Riemann L, Steward GF, Long RA, Azam F (2001) Variations in bacterial community structure during a dinoflagellate bloom analyzed by DGGE and 16S rDNA sequencing. Aquatic Microbial Ecology 23:119-130.
22. Stoica E, Herndl GJ (2007) Bacterioplankton community composition in nearshore waters of the NW Black Sea during consecutive diatom and coccolithophorid blooms. Aquat Sci 69:413-418.
23. Bauer M, et al. (2006) Whole genome analysis of the marine Bacteroidetes 'Gramella forsetii' reveals adaptations to degradation of polymeric organic matter. Environ Microbiol 8:2201-2213.
24. Purdy KJ, Embley TM, Nedwell DB (2002) The distribution and activity of sulphate reducing bacteria in estuarine and coastal marine sediments. Antonie Van Leeuwen-hoek 81:181-187.
25. Alonso C, Pernthaler J (2006) Roseobacter and SAR11 dominate microbial glucose uptake in coastal North Sea waters. Environ Microbiol 8:2022-2030.
26. Moran MA, et al. (2007) Ecological genomics of marine roseobacters. Appl Environ Microbiol 73:4559-4569.
27. Eiler A, Langenheder S, Bertilsson S, Tranvik LJ (2003) Heterotrophic bacterial growth efficiency and community structure at different natural organic carbon concentrations. Appl Environ Microbiol 69:3701-3709.
28. Benner R (2003) Molecular indicators of the bioavailability of dissolved organic matter. Aquatic Ecosystems: Interactivity of Dissolved Organic Matter, eds Findlay SEG, Sinsabaugh RL (Academic, New York), pp 121-137.
29. Almeida MA, Cunha MA, Alcantara F (2001) Loss of estuarine bacteria by viral infection and predation in microcosm conditions. Microb Ecol 42:562-571.
30. Davidov Y, Friedjung A, Jurkevitch E (2006) Structure analysis of a soil community of predatory bacteria using culture-dependent and culture-independent methods reveals a hitherto undetected diversity of Bdellovibrio-and-like organisms. Environ Microbiol 8:1667-1673.
31. Zheng G, Wang C, Williams HN, Pineiro SA (2008) Development and evaluation of a quantitative real-time PCR assay for the detection of saltwater Bacteriovorax. Environ Microbiol 10:2515-2526.
32. Pineiro SA, Williams HN, Stine OC (2008) Phylogenetic relationships amongst the 435 saltwater members of the genus Bacteriovorax using rpoB sequences and reclassification of 436 Bacteriovorax stolpii as Bacteriolyticum stolpii gen. nov., comb.nov. Int J Syst Evol Microbiol 58:1203-1209.
33. Shemesh Y, Jurkevitch E (2004) Plastic phenotypic resistance to predation byBdellovibrio and like organisms in bacterial prey. Environ Microbiol 6:12-18.
34. Lueders T, Kindler R, Miltner A, Friedrich MW, Kaestner M (2006) Identification of bacterial micropredators distinctively active in a soil microbial food web. Appl Environ Microbiol 72:5342-5348.
35. Chauhan A, Ogram A (2006) Phylogeny of acetate-utilizing microorganisms in soils along a nutrientgradient in the Florida Everglades. Appl Environ Microbiol 72:6837-6840.
36. Suzuki Y, TanoueE, Ito H (1992) Ahigh-temperature catalytic oxidation method for the determination of dissolved organic carbon in seawater: Analysis and improvement. Deep Sea Res 39:185-198.
37. Braman RS, Hendrix SA (1989) Nanogram nitrite and nitrate determination in environmental and biological materials by vanadium (iii) reduction with chemilumines-cence detection. Anal Chem 61:2715-2718.
38. Solorzano L (1969) Determination of ammonia in natural waters by the phenolhypo-chlorite method. Limnol Oceanogr 14:799-801.
39. Lane DJ (1991) 16S/23S rRNA sequencing. Nucleic Acid Techniques in Bacterial Systematics, eds Stackebrandt E, Goodfellow M (Wiley, New York), pp 115-175.
40. Cole JR, et al. (2003) The Ribosomal Database Project (RDP-II): Previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res 31:442-443.
41. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basiclocal alignment search tool. J Mol Biol 215:403-410.
42. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The ClustalX windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24:4876-4882.
43. Lozupone C, Knight R (2005) UniFrac: A new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71:8228-8235.