A phototrophy-driven microbial food web in a rice soil

Journal of Soils and Sediments

Volumn 11, Issue 2, 2011, Pages 301-311

  Feng, Youzhi ^a   Lin, Xiangui ^a   Zhu, Jianguo ^a   Jia, Zhongjun ^a  

^a INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

Author keywords

DNA based stable isotope probing; Formate; Microbial food web; Phototrophy

Indexed keywords

BACTERIUM; CYANOBACTERIUM; ELECTROKINESIS; FOOD WEB; MICROBIAL COMMUNITY; MITOCHONDRIAL DNA; MOLECULAR ANALYSIS; PADDY FIELD; PHOTOAUTOTROPHY; POLYMERASE CHAIN REACTION; PRIMARY PRODUCTION; PROTOZOAN; REAL TIME; SOIL MICROORGANISM; TROPHIC LEVEL;

ALGAE; BACTERIA (MICROORGANISMS); CYANOBACTERIA; EUKARYOTA; FUNGI; PHOTOBACTERIA; PROTOZOA;

EID: 85027940399     PISSN: 14390108     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11368-010-0303-6     Document Type: Article

References (50)

1. Achenbach LA, Carey J, Madigan MT (2001) Photosynthetic and phylogenetic primers for detection of anoxygenic phototrophs in natural environments. Appl Environ Microbiol 67: 2922-2926.
2. Al-Najjar MAA, de Beer D, Jorgensen BB, Kuhl M, Polerecky L (2010) Conversion and conservation of light energy in a photosynthetic microbial mat ecosystem. ISME J 4: 440-449.
3. Asari N, Ishihara R, Nakajima Y, Kimura M, Asakawa S (2008) Cyanobacterial communities of rice straw left on the soil surface of a paddy field. Biol Fertil Soils 44: 605-612.
4. Bass D, Chao EE-Y, Nikolaev S, Yabuki A, Ishida K-I, Berney C, Pakzad U, Wylezich C, Cavalier-Smith T (2009) Phylogeny of novel naked filose and reticulose Cercozoa: Granofilosea cl. n. and proteomyxidea revised. Protist 160: 75-109.
5. Baziramakenga R, Simard RR, Leroux GD (1995) Determination of organic acids in soil extracts by ion chromatography. Soil Biol Biochem 27: 349-356.
6. Beatriz D, Carlos P-A, Terence LM, Ramon M (2001) Application of denaturing gradient gel electrophoresis (DGGE) to study the diversity of marine picoeukaryotic assemblages and comparison of DGGE with other molecular techniques. Appl Environ Microbiol 67: 2942-2951.
7. Biddle JF, Fitz-Gibbon S, Schuster SC, Brenchley JE, House CH (2008) Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment. Proc Natl Acad Sci USA 105: 10583-10588.
8. Cahyani VR, Matsuya K, Asakawa S, Kimura M (2004) Succession and phylogenetic profile of eukaryotic communities in the composting process of rice straw estimated by PCR-DGGE analysis. Biol Fertil Soils 40: 334-344.
9. Callieri C, Karjalainen SM, Passoni S (2002) Grazing by ciliates and heterotrophic nanoflagellates on picocyanobacteria in Lago Maggiore, Italy. J Plankton Res 24: 785-796.
10. Chauhan A, Cherrier J, Williams HN (2009) Impact of sideways and bottom-up control factors on bacterial community succession over a tidal cycle. Proc Natl Acad Sci USA 106: 4301-4306.
11. Deines P, Bodelier PLE, Eller G (2007) Methane-derived carbon flows through methane-oxidizing bacteria to higher trophic levels in aquatic systems. Environ Microbiol 9: 1126-1134.
12. Dillon A, Parry JD (2009) Amoebic grazing of freshwater Synechococcus strains rich in phycocyanin. FEMS Microbiol Ecol 69: 106-112.
13. 2 emission in an intensively cultivated loam as affected by long-term application of organic manure and nitrogen fertilizer. Soil Biol Biochem 39: 669-679.
14. 2 enrichment (FACE) enhances the biodiversity of purple phototrophic bacteria in flooded paddy soil. Plant Soil 324: 317-328.
15. Ferry JG (1990) Formate dehydrogenase. FEMS Microbiol Rev 87: 377-382.
16. Field CB, Behrenfeld MJ, Randerson JT, Falkowski P (1998) Primary production of the biosphere: integrating terrestrial and oceanic components. Science 281: 237-240.
17. Fujita Y, Nakahara H (2006) Variations in the microalgal structure in paddy soil in Osaka, Japan: comparison between surface and subsurface soils. Limnol 7: 83-91.
18. Haddock JD, Ferry JG (1989) Purification and properties of phloroglucinol reductase from Eubacterium oxidoreducens. J Boil Chem 264: 4423-4427.
19. Hahn MW, Höfle MG (1998) Grazing pressure by a bacterivorous flagellate reverses the relative abundance of Comamonas acidovorans PX54 and Vibrio strain CB5 in chemostat cocultures. Appl Environ Microbiol 64: 1910-1918.
20. Haque MZ, Kobayashi M, Fujii K, Takahashi E (1969) Seasonal changes of photosynthetic bacteria and their products. Soil Sci Plant Nutr 15: 51-55.
21. Harada N, Otsuka S, Nishiyama M, Matsumoto S (2003) Characteristics of phototrophic purple bacteria isolated from a Japanese paddy soil. Soil Sci Plant Nutr 49: 521-526.
22. Hatamoto M, Tanahashi T, Murase J, Matsuya K, Hayashi M, Kimura M, Asakawa S (2008) Eukaryotic communities associated with the decomposition of rice straw compost in a Japanese rice paddy field estimated by DGGE analysis. Biol Fertil Soils 44: 527-532.
23. Imhoff JF (1988) Anoxygenic phototrophic bacteria. Wiley, New York.
24. Jia ZJ, Conrad R (2009) Bacteria rather than Archaea dominate microbial ammonia oxidation in an agricultural soil. Environ Microbiol 11: 1658-1671.
25. Jiao NZ, Zhang Y, Zeng YH, Hong N, Liu RL, Chen F, Wang PX (2007) Distinct distribution pattern of abundance and diversity of aerobic anoxygenic phototrophic bacteria in the global ocean. Environ Microbiol 9: 3091-3099.
26. Jürgens K, Matz C (2002) Predation as a shaping force for the phenotypic and genotypic composition of planktonic bacteria. Anton Leeuw Int J G 81: 413-434.
27. Kalyuzhnaya MG, Lapidus A, Ivanova N, Copeland AC, McHardy AC, Szeto E, Salamov A, Grigoriev IV, Suciu D, Levine SR, Markowitz VM, Rigoutsos I, Tringe SG, Bruce DC, Richardson PM, Lidstrom ME, Chistoserdova L (2008) High-resolution metagenomics targets specific functional types in complex microbial communities. Nat Biotechnol 26: 1029-1034.
28. Kimura M (2000) Anaerobic microbiology in waterlogged rice fields. Marcel Dekker, New York.
29. Kudryavtsev A, Wylezich C, Schlegel M, Walochnik J, Michel R (2009) Ultrastructure, SSU rRNA gene sequences and phylogenetic relationships of Flamella Schaeffer, 1926 (Amoebozoa), with description of three new species. Protist 160: 21-40.
30. Lakshmi KVNS, Sasikala C, Ramana CV (2009) Rhodoplanes pokkaliisoli sp nov., a phototrophic alphaproteobacterium isolated from a waterlogged brackish paddy soil. Int J Syst Evol Microbiol 59: 2153-2157.
31. Liesack W, Schnell S, Revsbech NP (2000) Microbiology of flooded rice paddies. FEMS Microbiol Rev 24: 625-645.
32. 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.
33. 2 as the energy source. J Bacteriol 137: 524-530.
34. 2 fixation in paddy fields through rice straw application. Australian Academy of Science, Canberra.
35. Moran MA, Miller WL (2007) Resourceful heterotrophs make the most of light in the coastal ocean. Nat Rev Microbiol 5: 792-800.
36. Murase J, Frenzel P (2007) A methane-driven microbial food web in a wetland rice soil. Environ Microbiol 9: 3025-3034.
37. Murase J, Noll M, Frenzel P (2006) Impact of protists on the activity and structure of the bacterial community in a rice field soil. Appl Environ Microbiol 72: 5436-5444.
38. Muyzer G, Brinkhoff T, Nübel U, Santegoeds C, Schäfer H, Wawer C (1998) Denaturing gradient gel electrophoresis (DGGE) in microbial ecology. Kluwer Academic, Dordrecht.
39. Nagashima KVP, Hiraishi A, Shimada K, Matsuura K (1997) Horizontal transfer of genes coding for the photosynthetic reaction centers of purple bacteria. J Mol Evol 45: 131-136.
40. Neufeld JD, Dumont MG, Vorha J, Murrell JC (2007) Methodological considerations for the use of stable isotope probing in microbial ecology. Microb Ecol 53: 435-442.
41. Overmann J, Garcia-Pichel F (2006) The phototrophic way of life. Prokaryotes 2: 32-85.
42. Penning H, Conrad R (2006) Carbon isotope effects associated with mixed-acid fermentation of saccharides by Clostridium papyrosolvens. Geochim Cosmochim Acta 70: 2283-2297.
43. Pfennig N (1978) In: Clayton RK, Sistrom W (eds) General physiology and ecology of photosynthetic bacteria. Plenum, New York.
44. Pickup ZL, Pickup R, Parry JD (2007) Growth of Acanthamoeba castellanii and Hartmannella vermiformis on live, heat-killed and DTAF-stained bacterial prey. FEMS Microbiol Ecol 61: 264-272.
45. Radajewski S, McDonald IR, Murrell JC (2003) Stable-isotope probing of nucleic acids: a window to the function of uncultured microorganisms. Curr Opin Biotechnol 14: 296-302.
46. Roeselers G, van Loosdrecht MCM, Muyzer G (2007) Heterotrophic pioneers facilitate phototrophic biofilm development. Microb Ecol 54: 578-585.
47. Rønn R, McCaig AE, Griffiths BS, Prosser JI (2002) Impact of protozoan grazing on bacterial community structure in soil microcosms. Appl Environ Microbiol 68: 6094-6105.
48. Sugano A, Tsuchimoto H, Tun CC, Asakawa S, Kimura M (2007) Succession and phylogenetic profile of eukaryotic communities in rice straw incorporated into a rice field: estimation by PCR-DGGE and sequence analyses. Soil Sci Plant Nutr 53: 585-594.
49. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4. 0. Mol Biol Evol 24: 1596-1599.
50. Tittel J, Bissinger V, Zippel B, Gaedke U, Bell E, Lorke A, Kamjunke N (2003) Mixotrophs combine resource use to outcompete specialists: implications for aquatic food webs. Proc Natl Acad Sci USA 100: 12776-12781.