Dynamics of bacterial communities in relation to soil aggregate formation during the decomposition of 13C-labelled rice straw

Applied Soil Ecology

Volumn 53, Issue 1, 2012, Pages 1-9

  Blaud, A ^a   Lerch, T Z ^b,c   Chevallier, T ^a   Nunan, N ^b   Chenu, C ^b   Brauman, A ^a  

^a UMR ECO SOLS   (France)

^b CNRS   (France)

^c AGROPARISTECH   (France)

Author keywords

13C labelling; FAME SIP; Microscale biogeography; Mineralisation; Soil aggregation; Soil bacterial communities structure

Indexed keywords

ACTINOBACTERIA; BACTERIA (MICROORGANISMS); NEGIBACTERIA; POSIBACTERIA;

EID: 82955207728     PISSN: 09291393     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.apsoil.2011.11.005     Document Type: Article

References (71)

1. Amellal N., Burtin G., Bartoli F., Heulin T. Colonization of wheat roots by an exopolysaccharide-producing Pantoea agglomerans strain and its effect on rhizosphere soil aggregation. Appl. Environ. Microbiol. 1998, 64:3740-3747.
2. Balesdent J., Chenu C., Balabane M. Relationship of soil organic matter dynamics to physical protection and tillage. Soil Till. Res. 2000, 53:215-230.
3. Bastian F., Bouziri L., Nicolardot B., Ranjard L. Impact of wheat straw decomposition on successional patterns of soil microbial community structure. Soil Biol. Biochem. 2009, 41:262-275.
4. Baumann K., Marschner P., Smernik R., Baldock J. Residue chemistry and microbial community structure during decomposition of eucalypt, wheat and vetch residues. Soil Biol. Biochem. 2009, 41:1966-1975.
5. 13C-labelled wheat residue as estimated by DNA- and RNA-SIP techniques. Environ. Microbiol. 2007, 9:752-764.
6. Bossuyt H., Denef K., Six J., Frey S., Merckx R., Paustian K. Influence of microbial populations and residue quality on aggregate stability. Appl. Soil Ecol. 2001, 16:195-208.
7. Bossuyt H., Six J., Hendrix P. Aggregate-protected carbon in no-tillage and conventional tillage agroecosystems using carbon-14 labeled plant residue. Soil Sci. Soc. Am. J. 2002, 66:1965-1973.
8. Buyanovsky G., Aslam M., Wagner G. Carbon turnover in toil physical fractions. Soil Sci. Soc. Am. J. 1994, 58:1167-1173.
9. Chevallier T., Blanchart E., Albrecht A., Feller C. The physical protection of soil organic carbon in aggregates: a mechanism of carbon storage in a Vertisol under pasture and market gardening (Martinique, West Indies). Agric. Ecosyst. Environ. 2004, 103:375-387.
10. Coplen T. Reporting of stable hydrogen, carbon, and oxygen isotopic abundances. Geothermics 1995, 24:707-712.
11. Dalias P., Anderson J., Bottner P., Couteaux M. Temperature responses of carbon mineralization in conifer forest soils from different regional climates incubated under standard laboratory conditions. Global Change Biol. 2001, 7:181-192.
12. Degens B. Macro-aggregation of soils by biological bonding and binding mechanisms and the factors affecting these: a review. Aust. J. Soil Res. 1997, 35:431-460.
13. Denef K., Six J., Bossuyt H., Frey S., Elliott E., Merckx R., Paustian K. Influence of dry-wet cycles on the interrelationship between aggregate, particulate organic matter, and microbial community dynamics. Soil Biol. Biochem. 2001, 33:1599-1611.
14. Denef K., Six J., Merckx R., Paustian K. Short-term effects of biological and physical forces on aggregate formation in soils with different clay mineralogy. Plant Soil 2002, 246:185-200.
15. Denef K., Six J., Merckx R., Paustian K. Carbon sequestration in microaggregates of no-tillage soils with different clay mineralogy. Soil Sci. Soc. Am. J. 2004, 68:1935-1944.
16. Dorioz J.M., Robert M., Chenu C. The role of roots, fungi and bacteria on clay particle organization. An experimental approach. Geoderma 1993, 56:179-194.
17. Drazkiewicz M. Relationship between dehydrogenase activity and properties of soil aggregates. Folia Microbiol. 1995, 40:315-319.
18. 13C labelling. Soil Biol. Biochem. 2008, 40:2530-2539.
19. Elliott E. Aggregate structure and carbon, nitrogen, and phosphorus in native and cultivated soils. Soil Sci. Soc. Am. J. 1986, 50:627-633.
20. Fall S., Nazaret S., Chotte J., Brauman A. Bacterial density and community structure associated with aggregate size fractions of soil-feeding termite mounds. Microb. Ecol. 2004, 482:191-199.
21. Feeney D., Crawford J., Daniell T., Hallett P., Nunan N., Ritz K., Rivers M., Young I.M. Three-dimensional microorganization of the soil-root-microbe system. Microb. Ecol. 2006, 52:151-158.
22. Fierer N., Bradford M., Jackson R. Toward an ecological classification of soil bacteria. Ecology 2007, 88:1354-1364.
23. Franzluebbers A., Arshad M. Soil microbial biomass and mineralizable carbon of water-stable aggregates. Soil Sci. Soc. Am. J. 1997, 61:1090-1097.
24. Frostegard A., Tunlid A., Baath E. Phospholipid fatty acid composition, biomass, and activity of microbial communities from two soil types experimentally exposed to different heavy metals. Appl. Environ. Microbiol. 1993, 59:3605-3617.
25. Gaillard V., Chenu C., Recous S., Richard G. Carbon, nitrogen and microbial gradients induced by plant residues decomposing in soil. Eur. J. Soil Sci. 1999, 50:567-578.
26. 13C-carrier DNA shortens the incubation time needed to detect benzoate-utilizing denitrifying bacteria by stable-isotope probing. Appl. Environ. Microbiol. 2005, 71:5192-5196.
27. 3 plants. Phytochem. Rev. 2003, 21:145-161.
28. Hattori T. Soil aggregates in microhabitats of microorganisms. Rep. Inst. Agric. Res. Tohoku Univ. 1988, 37:23-36.
29. Horn R., Smucker A. Structure formation and its consequences for gas and water transport in unsaturated arable and forest soils. Soil Till. Res. 2005, 82:5-14.
30. Jastrow J. Soil aggregate formation and the accrual of particulate and mineral-associated organic matter. Soil Biol. Biochem. 1996, 28:665-676.
31. King A., Freeman K., McCormick K., Lynch R., Lozupone C., Knight R., Schmidt S. Biogeography and habitat modelling of high-alpine bacteria. Nat. Commun. 2010, 1:53.
32. Legendre P., Legendre L. Numerical Ecology 1998, Elsevier Science, Oxford, UK. second ed.
33. Lensi R., Clays-Josser A., Jocteur Monrozier L. Denitrifiers and denitrifying activity in size fractions of a mollisol under permanent pasture and continuous cultivation. Soil Biol. Biochem. 1995, 27:61-69.
34. 13C-labelling technique and fatty acid profiling. J. Microbiol. Methods 2007, 71:162-174.
35. Lerch T., Nunan N., Dignac M., Chenu C., Mariotti A. Variations in microbial isotopic fractionation during soil organic matter decomposition. Biogeochemistry 2011, 106:5-21.
36. Martiny J., Bohannan B., Brown J., Colwell R., Fuhrman J., Green J., Horner-Devine M., Kane M., Krumins J.A., Kuske C.R., Morin P.J., Naeem S., Øvreås L., Reysenbach A.-L., Smith V.H., Staley J.T. Microbial biogeography: putting microorganisms on the map. Nat. Rev. Microbiol. 2006, 4:102-112.
37. McMahon S., Williams M., Bottomley P., Myrold D. Dynamics of microbial communities during decomposition of carbon-13 labeled ryegrass fractions in soil. Soil Sci. Soc. Am. J. 2005, 69:1238-1247.
38. Monreal C., Schulten H., Kodama H. Age, turnover and molecular diversity of soil organic matter in aggregates of a gleysol. Can. J. Soil Sci. 1997, 77:379-388.
39. Mummey D., Stahl P. Analysis of soil whole- and inner-microaggregate bacterial communities. Microb. Ecol. 2004, 48:41-50.
40. Mummey D., Holben W., Six J., Stahl P. Spatial stratification of soil bacterial populations in aggregates of diverse soils. Microb. Ecol. 2006, 51:404-411.
41. Nicolardot B., Recous S., Mary B. Simulation of C and N mineralization during crop residue decomposition: a simple dynamic model based on the C:N ratio of the residues. Plant Soil 2001, 228:83-103.
42. Oades J. Soil organic matter and structural stability: mechanisms and implications for management. Plant Soil 1984, 76:319-337.
43. Oades J., Waters A. Aggregate hierarchy in soils. Aust. J. Soil Res. 1991, 29:815-828.
44. Odum E.P. The strategy of ecosystem developement an understand of ecological succesion provides a basis for resolving man's conflict with nature. Nature 1969, 164:262-270.
45. O'leary W., Wilkinson S. Gram-positive bacteria. Microbial Lipids 1988, 117-202. Academic Press, London, UK. C. Ratledge, S. Wilkinson (Eds.).
46. O'Malley M., Dupré J. Size doesn't matter: towards a more inclusive philosophy of biology. Biol. Philos. 2007, 22:155-191.
47. Poll C., Ingwersen J., Stemmer M., Gerzabek M., Kandeler E. Mechanisms of solute transport affect small-scale abundance and function of soil microorganisms in the detritusphere. Eur. J. Soil Sci. 2006, 57:583-595.
48. Poly F., Ranjard L., Nazaret S., Gourbiere F., Jocteur Monrozier L. Comparison of nifH gene pools in soils and soil microenvironments with contrasting properties. Appl. Environ. Microbiol. 2001, 67:2255-2262.
49. Puget P., Chenu C., Balesdent J. Total and young organic matter distributions in aggregates of silty cultivated soils. Eur. J. Soil Sci. 1995, 46:449-459.
50. Puget P., Chenu C., Balesdent J. Dynamics of soil organic matter associated with particle-size fractions of water-stable aggregates. Eur. J. Soil Sci. 2000, 51:595-605.
51. Ranjard L., Poly F., Combrisson J., Richaume A., Gourbière F., Thioulouse J., Nazaret S. Heterogeneous cell density and genetic structure of bacterial pools associated with various soil microenvironments as determined by enumeration and DNA fingerprinting approach (RISA). Microb. Ecol. 2000, 39:263-272.
52. Ranjard L., Richaume A. Quantitative and qualitative microscale distribution of bacteria in soil. Res. Microbiol. 2001, 152:707-716.
53. Ritchie N.J., Schutter M.E., Dick R.P., Myrold D.D. Use of length heterogeneity PCR and fatty acid methyl ester profiles to characterize microbial communities in soil. Appl. Environ. Microbiol. 2000, 66:1668-1675.
54. Ruamps L., Nunan N., Chenu C. Microbial biogeography at the soil pore scale. Soil Biol. Biochem. 2011, 43:280-286.
55. Salomé C., Nunan N., Pouteau V., Lerch T.Z., Chenu C. Carbon dynamics in topsoil and in subsoil may be controlled by different regulatory mechanisms. Global Change Biol. 2010, 16:416-426.
56. Schutter M.E., Dick R.P. Comparison of fatty acid methyl ester (FAME) methods for characterizing microbial communities. Soil Sci. Soc. Am. J. 2000, 64:1659-1668.
57. Schutter M.E., Dick R.P. Shifts in substrate utilization potential and structure of soil microbial communities in response to carbon substrates. Soil Biol. Biochem. 2001, 33:1481-1491.
58. Schutter M.E., Dick R.P. Microbial community profiles and activities among aggregates of winter fallow and cover-cropped soil. Soil Sci. Soc. Am. J. 2002, 66:142-153.
59. Sexstone A., Revsbech N., Bailey T., Tiedje J. Direct measurement of oxygen profiles and denitrification rates in soil aggregates. Soil Sci. Soc. Am. J. 1985, 493:645-651.
60. Sey B., Manceur A., Whalen J., Gregorich E., Rochette P. Small-scale heterogeneity in carbon dioxide, nitrous oxide and methane production from aggregates of a cultivated sandy-loam soil. Soil Biol. Biochem. 2008, 40:2468-2473.
61. Six J., Elliott E., Paustian K. Soil macroaggregate turnover and microaggregate formation: a mechanism for C sequestration under no-tillage agriculture. Soil Biol. Biochem. 2000, 3214:2099-2103.
62. Six J., Bossuyt H., Degryze S., Denef K. A history of research on the link between (micro)aggregates, soil biota, and soil organic matter dynamics. Soil Till. Res. 2004, 79:7-31.
63. Strong D., Wever H., Merckx R., Recous S. Spatial location of carbon decomposition in the soil pore system. Eur. J. Soil Sci. 2004, 55:739-750.
64. Tisdall J., Oades J. Organic matter and water-stable aggregates in soils. Eur. J. Soil Sci. 1982, 33:141-163.
65. Van Gestel M., Ladd J., Amato M. Carbon and nitrogen mineralization from two soils of contrasting texture and microaggregate stability: influence of sequential fumigation, drying and storage. Soil Biol. Biochem. 1991, 23:313-322.
66. Yoder R.E. A direct method of aggregate analysis of soils a study of the physical nature of erosion losses. J. Am. Soc. Agron. 1936, 28:337-351.
67. Young I., Ritz K. Can there be a contemporary ecological dimension to soil biology without a habitat?. Soil Biol. Biochem. 1998, 30:1229-1232.
68. Young I., Crawford J. Interactions and self-organization in the soil-microbe complex. Science 2004, 304:1634-1637.
69. Young J., Crossman L., Johnston A., Thomson N., Ghazoui Z., Hull K., Wexler M., Curson A.R.J., Todd J.D., Poole P.S., Mauchline T.H., East A.K., Quail M.A., Churcher C., Arrowsmith C., Cheverach I., Chillingworth T., Clarke K., Cronin A., Davis P., Fraser A., Hance Z., Hauser H., Jagels K., Moule S., Mungall K., Norbertczak H., Rabbinowitsch E., Sanders M., Simmonds M., Whitehead S., Parkhill J. The genome of Rhizobium leguminosarum has recognizable core and accessory components. Genome Biol. 2006, 7:R34.
70. Zelles L., Bai Q., Ma R., Rackwitz R., Winter K., Beese F. Microbial biomass, metabolic activity and nutritional status determined from fatty acid patterns and poly-hydroxybutyrate in agriculturally-managed soils. Soil Biol. Biochem. 1994, 26:439-446.
71. Zelles L. Fatty acid patterns of phospholipids and lipopolysaccharides in the characterisation of microbial communities in soil: a review. Biol. Fertil. Soils 1999, 29:111-129.