Comparison of Bacterial Communities Associated with Microcrustaceans from the Floodwater of a Paddy Field Microcosm: Estimation Based on DGGE Pattern and Sequence Analyses

Soil Science and Plant Nutrition

Volumn 51, Issue 2, 2005, Pages 281-290

  Niswati, Ainin ^a,b   Murase, Jun ^a   Kimura, Makoto ^a  

^a NAGOYA UNIVERSITY   (Japan)

^b UNIVERSITY OF LAMPUNG   (Indonesia)

Author keywords

Bacteria; Cfb; Dgge; Floodwater; Microcrustacean

Indexed keywords

BACTERIA (MICROORGANISMS); BACTEROIDES; CYPRETTA; CYTOPHAGA; FLAVOBACTERIUM; HETEROCYPRIS SP.; INVERTEBRATA; MESOCYCLOPS; MOINA; NEGIBACTERIA; PODOCOPIDA;

EID: 18444409963     PISSN: 00380768     EISSN: 17470765     Source Type: Journal    
DOI: 10.1111/j.1747-0765.2005.tb00032.x     Document Type: Article

References (53)

1. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, and Lipman DJ 1997: Gapped BLAST and PSI- BLAST: A new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402
2. Aoki S 1996: http://aoki2.si.gunma-u.ac.jp/BlackBox/BlackBox. html
3. Braun ST, Proctor LM, Zani S, Mellon MT, and Zehr JP 1999: Molecular evidence for zooplankton-associated nitrogen-fixing anaerobes based on amplification of the nifH gene. FEMS Microbiol. Ecol., 28, 273-279
4. Carli A, Pane L, Casareto L, Bertone S, and Pruzzo C 1993: Occurrence of Vibrio alginolyticus in Ligurian Coast Rock Pools (Thyrrenian Sea, Italy) and its association with the copepod Tigriopus fulvus (Fisher 1860). Appl. Environ. Microbiol., 59, 1960-1962
5. Carman KR and Dobbs FC 1997: Epibiotic microorganisms on copepods and other marine crustaceans. Microsc. Res. Tech., 37, 116-135
6. Chang N and Jenkins DG 2000: Plastid endosymbionts in the freshwater crustacean Daphnia obtusa. J. Crustacean Biol., 20, 231-238
7. Chiavelli DA, Mills EL, and Threlkeld ST 1993: Host preference, seasonality, and community interactions of zooplank- ton epibionts. Limnol. Oceanogr., 38, 574-583
8. Cottrell MT and Kirchman DL 2000: Natural assemblages of marine proteobacteria and members of the Cytophaga-Fla- vobacter cluster consuming low- and high molecular weight dissolved organic matter. Appl. Environ. Microbiol., 66, 1692-1697
9. Dawson MP, Humphrey BA, and Marshall KC 1981: Adhesion, a tactic survival strategy of a marine vibrio during starvation. Curr. Microbiol., 6, 195-198
10. Dugas JE, Zurek L, Paster BJ, Keddie BA, and Leadbetter ER 2001: Isolation and characterization of a Chryseobacterium strain from the gut of the American cockroach, Periplaneta americana. Arch. Microbiol., 175, 259-262
11. Dumontet S, Krovacek K, Baloda SB, Grottoli R, Pasquale V, and Vanucci S 1996: Ecological relationship between Aero- monas and Vibrio spp. and planktonic copepods in the coastal marine environment in Southern Italy. Comp, lmmun. Microbiol. Infect. Dis., 19, 245-254
12. Eisen JA, Smith SW, and Cavanaugh CM 1992: Phylogenetic relationships of chemoautotrophic bacterial symbionts of Solemya velum Say (Mollusca: Bivalvia) determined by 16S rRNA gene sequence analysis. J. Bacteriol., 174, 3416— 3421
13. Evans MS, Sicko-Goad LM, and Omair M 1979: Seasonal occurrence of Tokophrya quadripartita (Suctoria) as epibionts on adult Limnocalanus macrurus (Copepoda: Cal- anoida) in Southeastern Lake Michigan. Trans. Am. Microsc. Soc., 98, 102-109
14. Hansen B and Bech G 1996: Bacteria associated with a marine planktonic copepod in culture. I. Bacterial genera in seawater, body surface, intestines and fecal pellets and succession during fecal pellet degradation. J. Plankton Res., 18, 257-273
15. Haygood MG, Schmidt EW, Davidson SK, and Faulkner DJ 1999: Microbial symbionts of marine invertebrates: Opportunities for microbial biotechnology. J. Mol. Microbiol. Bio- technol., 1, 33-43
16. Hiromi J, Kadota S, and Takano H 1985: Diatom infestation of marine copepods (review). Bull. Tokai Reg. Fish. Res. Lab., 117, 37-45
17. Ho JS and Perkins PS 1985: Symbionts of marine copepoda: An overview. Bull. Mar. Sci., 37, 586-598
18. Holland RS and Hergenrader GL 1981: Bacterial epibionts of diaptomid copepods. Trans. Am. Microsc. Soc., 98, 56-65
19. Horn M, Harzenetter MD, Linner T, Schmid EN, Muller KD, Michel R, and Wagner M 2001: Member of the Cytophaga- Flavobacterium-Bacteroides phylum as intracellular bacteria of acanthamoebae: Proposal of ‘Candidatus Amoebophilus asiaticus.’ Environ. Microbiol., 3, 440-449
20. Huq A, Small EB, West PA, Huq MI, Rahman R, and Colwell RR 1983: Ecological relationship between Vibrio cholerae and planktonic crustacean copepods. Appl. Environ. Microbiol., 45, 275-283
21. Huq A, West PA, Small EB, Huq MI, and Colwell RR 1984: Influence of water temperature, salinity, and pH on survival and growth of toxigenic Vibrio cholerae Serovar Ol associated with live Copepods in laboratory microcosms. Appl. Environ. Microbiol., 48, 420-424
22. Ikenaga M, Asakawa S, Muraoka Y, and Kimura M 2003: Bacterial communities associated with nodal roots of rice plants along with the growth stages: Estimation by PCR-DGGE and sequence analyses. Soil Sci. Plant Nutr., 49, 591-602
23. Jaspers E, Nauhaus K, Cypionka H, and Overmann J 2001: Multitude and temporal variability of ecological niches as indicated by the diversity of cultivated bacterioplankton. FEMS Microbiol. Ecol., 37, 161-173
24. Johnson PW, Sieburth JMcN, Sastry A, Arnold CR, and Doty MS 1971: Leucothrix mucor infestation of benthic crustacea, fish eggs, and tropical algae. Limnol. Oceanogr., 16, 962-969
25. Kaneko T and Colwell RR 1975: Adsorption of Vibrio para- haemolyticus onto chitin and copepods. Appl. Microbiol., 29, 269-274
26. Kimura M, Shibagaki T, Nakajima Y, Matsuya K, and Ikenaga M 2002: Community structure of the microbiota in the floodwater of a Japanese paddy field estimated from RFLP and DGGE pattern analyses. Biol. Fertil. Soils, 36, 306-312
27. Kirchman DL 2002: The ecology of Cytophaga-Flavobacteria in aquatic environments. FEMS Microbiol. Ecol., 39, 91-100
28. Kostanjsek R, Strus J, and Avgustin G 2002: Genetic diversity of bacteria associated with the hindgut of the terrestrial crustacean Porcellio scaber (Crustacea: Isopoda). FEMS Microbiol. Ecol., 40, 171-179
29. Lau WWY, Jumars PA, and Armbrust EV 2002: Genetic diversity of attached bacteria in the hindgut of the deposit-feeding shrimp Neotrypaea (formerly CaUianassa) califor- niensis (Decapoda: Thalassinidae). Microb. Ecol., 43, 455-466
30. McCoy E and Sarles WB 1969: Bacteria in lakes: Populations and functional relations. In Eutrophication: Causes, Consequences, Correctives, p. 331-339, National Academy of Science, Washington D.C.
31. Muyzer G, de Waal EC, and Uitterlinden AG 1993: Profiling ofcomplex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol., 59, 695-700
32. Nagasawa S 1986a: The bacterial adhesion to copepods in coastal waters in different parts of the world. La Mer, 24, 117-124
33. Nagasawa S 1986b: High incidence of copepod-bacteria associations in Tokyo Bay waters and Woods Hole waters. La Mer, 24, 177-185
34. Nagasawa S 1989: Bacterial epibionts of copepods. Sci. Prog., 73, 169-176
35. Nagasawa S, Simidu U, and Nemoto T 1985: Scanning electron microscopy investigation of bacterial colonization of marine copepod Acartia clausi. Mar. Biol., 87, 61-66
36. Niswati A, Murase J, Asakawa S, and Kimura M 2004: Analysis of communities of ammonia oxidizers, methanotrophs, and methanogens associated with microcrustaceans in the flood- water of a rice field microcosm. Soil Sci. Plant Nutr., 50, 447-455
37. Niswati A, Murase J, and Kimura M 2003: Effect of application of rice straw and compost on the community structure of bacteria associated with microcrustaceans in the floodwater of a paddy field microcosm. Soil Sci. Plant Nutr., 49, 191-200
38. Niswati A, Yamazaki M, Ikenaga M, and Kimura M 2002: Bacterial communities associated with aquatic organisms in the floodwater of a Japanese paddy field estimated by RFLP pattern analysis. Soil Sci. Plant Nutr., 48, 185-193
39. Polz MF, Distel DL, Zarda B, Amann R, Felbeck H, Ott JA, and Cavanaugh CM 1994: A highly specific association between ectosymbiotic, sulfur-oxidizing bacteria and a marine nematode and its phylogenetic relationship to endosymbionts and free-living bacteria. Appl. Environ. Microbiol., 60, 4461-4467
40. Proctor LM 1997: Nitrogen-fixing, photosynthetic, anaerobic bacteria associated with pelagic copepods. Aquat. Microb. Ecol., 12, 105-113
41. Reichard W, Gunn B, and Colwell RR 1983: Ecology and taxonomy of chitinoclastic cytophaga and related chitin-degrading bacteria isolated from an estuary. Microb. Ecol., 9, 273-294
42. Riemann L, Steward GF, and Azam F 2000: Dynamics of bacterial community composition and activity during a mesocosm diatom bloom. Appl. Environ. Microbiol., 66, 578-587
43. Riemann L, Steward GF, Fandino LB, Campbell L, Landry MR, and Azam F 1999: Bacterial community composition during two consecutive NE Monsoon periods in the Arabian Sea studied by denaturing gradient gel electrophoresis (DGGE) of rRNA genes. Deep-Sea Res. (II Top. Stud. Oceanogr.), 46, 1791-1811
44. Simidu U, Ashino K, and Kaneko E 1971: Bacterial flora of phyto- and zooplankton in the inshore water of Japan. Can. J. Microbiol., 17, 1157-1160
45. Singleton FL, Attwell R, Jangi S, and Colwell RR 1982: Effect of temperature and salinity on Vibrio cholerae growth. Appl. Environ. Microbiol., 44, 1047-1058
46. Sochard MR, Wilson DF, Austin B, and Colwell RR 1979: Bacteria associated with the surface and gut of marine copepods. Appl. Environ. Microbiol., 37, 750-759
47. Taniguchi M, Toyota K, and Kimura M 1997a: Epibiotic bacteria associated with microcrustaceans in the overlying water of paddy fields. Soil Sci. Plant Nutr., 43, 633-641
48. Taniguchi M, Toyota K, and Kimura M 1997b: Seasonal variation of microcrustaceans and microbial flora on their surface in the overlying water of a Japanese paddy field. Soil Sci. Plant Nutr., 43, 651-664
49. Taniguchi M, Toyota K, and Kimura M 1999: Epibiotic microorganisms associated with microcrustaceans in overlying water of Philippine paddy fields. Soil Sci. Plant Nutr., 45, 757-766
50. Threlkeld ST, Chiavelli DA, and Willey RL 1993: The organization of zooplankton epibiont communities. TREE, 8, 317— 321
51. Zchori-Fein E, Gottlieb Y, Kelly SE, Brown JK, Wilson JM, Karr TL, and Hunter M 2001: A newly discovered bacterium associated with parthenogenesis and a change in host selection behavior in parasitoid wasps. Proc. Natl. Acad. Sci. U.S.A., 98, 12555-12560
52. Zehr JP, Mellon MT, and Zani S 1998: New nitrogen-fixing microorganisms detected in oligotrophic oceans by amplification of nitrogenase (nifH) genes. Appl. Environ. Microbiol., 64, 3444-3450
53. Zhou J, Bruns MA, and Tiedje JM 1996: DNA recovery from soils of diverse composition. Appl. Environ. Microbiol., 62, 316-322