Bacterial Indicator of Agricultural Management for Soil under No-Till Crop Production

PLoS ONE

Volumn 7, Issue 11, 2012, Pages

  Figuerola, Eva L M ^a   Guerrero, Leandro D ^a   Rosa, Silvina M ^a   Simonetti, Leandro ^a   Duval, Matías E ^b   Galantini, Juan A ^b   Bedano, José C ^c   Wall, Luis G ^d   Erijman, Leonardo ^a,e  

^a INSTITUTO DE INVESTIGACIONES EN INGENIERÍA GENÉTICA Y BIOLOGÍA MOLECULAR   (Argentina)

^b UNIVERSIDAD NACIONAL DEL SUR   (Argentina)

^c DEPARTAMENTO DE QUÍMICA   (Argentina)

^d UNIVERSIDAD NACIONAL DE QUILMES   (Argentina)

^e UNIVERSIDAD DE BUENOS AIRES   (Argentina)

Author keywords

[No Author keywords available]

Indexed keywords

CARBON; NITROGEN;

ACIDOBACTERIA; AGRICULTURAL PROCEDURES; ARTICLE; BACTERIUM; CLIMATE; COMMUNITY STRUCTURE; CONTROLLED STUDY; CROP ROTATION; FERTILIZATION; GEOGRAPHIC DISTRIBUTION; MICROBIAL COMMUNITY; NO TILL CROP PRODUCTION; NONHUMAN; PEST CONTROL; PH; PHYSICAL CHEMISTRY; PYROSEQUENCING; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; RUBELLIMICROBIUM; SEASONAL VARIATION; SEQUENCE ANALYSIS; SOIL ANALYSIS; SOIL MICROFLORA; SOIL MOISTURE; SOIL QUALITY; SOIL TEXTURE; VALIDATION PROCESS;

AGRICULTURE; ARGENTINA; BACTERIA; CROPS, AGRICULTURAL; GEOGRAPHY; PHYLOGENY; SOIL; SOIL MICROBIOLOGY;

ACIDOBACTERIA; ALPHAPROTEOBACTERIA; BACTERIA (MICROORGANISMS);

EID: 84870659166     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0051075     Document Type: Article

References (59)

1. Hobbs PR, Sayre K, Gupta R, (2008) The role of conservation agriculture in sustainable agriculture. Phil Trans Royal Soc B: Biol Sci 363: 543-555.
2. Bronick CJ, Lal R, (2005) Soil structure and management: a review. Geoderma 124: 3-22.
3. Abid M, Lal R, (2009) Tillage and drainage impact on soil quality: II. Tensile strength of aggregates, moisture retention and water infiltration. Soil Till Res 103: 364-372.
4. Derpsch R, Friedrich T, Kassam A, Li H, (2010) Current status of adoption of no-till farming in the world and some of its main benefits. Intl J Agric Biol Eng 3: 1-25.
5. Montgomery DR, (2007) Soil erosion and agricultural sustainability. Proc Natl Acad Sci USA 104: 13268-13272.
6. Viglizzo EF, Frank FC, Carreño LV, Jobbágy EG, Pereyra H, et al. (2011) Ecological and environmental footprint of 50 years of agricultural expansion in Argentina Global Change Biol. 17: 959-973.
7. Cook RJ, (2006) Toward cropping systems that enhance productivity and sustainability. Proc Natl Acad Sci USA 103: 18389-18394.
8. Bockstaller C, Guichard L, Makowski D, Aveline A, Girardin P, et al. (2008) Agri-environmental indicators to assess cropping and farming systems. A review. Agron Sustain Dev 28: 139-149.
9. Govaerts B, Sayre KD, Deckers J, (2006) A minimum data set for soil quality assessment of wheat and maize cropping in the highlands of Mexico. Soil Tillage Res 87: 163-174.
10. Imaz M, Virto IP, Bescansa P, Enrique A, Fernandez-Ugalde O, et al. (2010) Soil quality indicator response to tillage and residue management on semi-arid Mediterranean cropland. Soil Tillage Res 107: 17-25.
11. Rodrigues de Lima AC, Hoogmoed W, Brussaard L, (2008) Soil quality assessment in rice production systems: establishing a minimum data set. J Environ Qual 37: 623-630.
12. Shukla MK, Lal R, Ebinger M, (2006) Determining soil quality indicators by factor analysis. Soil Tillage Res 87: 194-204.
13. Yemefack M, Jetten VG, Rossiter DG, (2006) Developing a minimum data ser for characterizing soil dynamics in shifting cultivation Systems. Soil Tillage Res 86: 84-98.
14. Hartmann M, Fliessbach A, Oberholzer HR, Widmer F, (2006) Ranking the magnitude of crop and farming system effects on soil microbial biomass and genetic structure of bacterial communities. FEMS Microbiol Ecol 57: 378-388.
15. Grayston SJ, Wang S, Campbell CD, Edwards AC, (1998) Selective influence of plant species on microbial diversity in the rhizosphere. Soil Biol Biochem 30: 369-378.
16. Marschner P, Crowley D, Yang CH, (2004) Development of specific rhizosphere bacterial communities in relation to plant species, nutrition and soil type. Plant and Soil 261: 199-208.
17. Smalla K, Wieland G, Buchner A, Zock A, Parzy J, et al. (2001) Bulk and rhizosphere soil bacterial communities studied by denaturing gradient gel electrophoresis: plant-dependent enrichment and seasonal shifts revealed. Appl Environ Microbiol 67: 4742-4751.
18. Nacke H, Thürmer A, Wollherr A, Will C, Hodac L, et al. (2011) Pyrosequencing-based assessment of bacterial community structure along different management types in german forest and grassland soils. PloS One 6: 1387-1390.
19. Girvan MS, Bullimore J, Pretty JN, Osborn AM, Ball AS, (2003) Soil type is the primary determinant of the composition of the total and active bacterial communities in arable soils. Appl Environ Microbiol 69: 1800-1809.
20. Acosta-Martinez V, Dowd S, Sun Y, Allen V, (2008) Tag-encoded pyrosequencing analysis of bacterial diversity in a single soil type as affected by management and land use. Soil Biol Biochem 40: 2762-2770.
21. Lagomarsino A, Moscatelli MC, Di Tizio A, Mancinelli R, Grego S, et al. (2009) Soil biochemical indicators as a tool to assess the short-term impact of agricultural management on changes in organic C in a Mediterranean environment. Ecol Indic 9: 518-527.
22. Laudicina VA, Badalucco L, Palazzolo L, (2011) Effects of compost input and tillage intensity on soil microbial biomass and activity under Mediterranean conditions. Biol Fertil Soils 47: 63-70.
23. Lupwayi NZ, Rice WA, Clayton GW, (1998) Soil microbial diversity and community structure under wheat as influenced by tillage and crop rotation. Soil Biol Biochem 30: 1733-1741.
24. Yin C, Jones KL, Peterson DE, Garrett KA, Hulbert SH, et al. (2010) Members of soil bacterial communities sensitive to tillage and crop rotation. Soil Biol Biochem 42: 2111-2118.
25. Schloter M, Dilly O, Munch JC, (2003) Indicators for evaluating soil quality. Agric Ecosyst Environ 98: 255-262.
26. Wall LG (2011) The BIOSPAS Consortium: Soil Biology and Agricultural Production. In: Bruijn FJd, editor. Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches. Hoboken, NJ, USA: John Wiley & Sons, Inc. pp. ch. 34.
27. Parameswaran P, Jalili R, Tao L, Shokralla S, Gharizadeh B, et al. (2007) A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing. Nucl Acids Res 35: e130.
28. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, et al. (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537-7741.
29. Huse SM, Huber JA, Morrison HG, Sogin ML, Welch DM, (2007) Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol 8: R143.
30. Schloss PD, Gevers D, Westcott SL, (2011) Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS One 6: e27310.
31. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, et al. (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucl Acids Res 35: 7188-7196.
32. Dufrene M, Legendre P, (1997) Species assemblages and indicator species: the need for a flexible asymmetrical approach. Ecol Monogr 67: 345-366.
33. Storey J, Tibshirani R, (2003) Statistical significance for genomewide studies. Proc Natl Acad Sci USA 100: 9440-9445.
34. Ashelford KE, Weightman AJ, Fry JC, (2002) PRIMROSE: a computer program for generating and estimating the phylogenetic range of 16S rRNA oligonucleotide probes and primers in conjunction with the RDP-II database. Nucleic Acids Res 30: 3481-3489.
35. Garbisu C, Alkorta I, Epelde L, (2011) Assessment of soil quality using microbial properties and attributes of ecological relevance. Appl Soil Ecol 49: 1-4.
36. Bending GD, Turner MK, Rayns F, Marx MC, Wood M, (2004) Microbial and biochemical soil quality indicators and their potential for differentiating areas under contrasting agricultural management regimes. Soil Biol Biochem 36: 1785-1792.
37. Romaniuk R, Giuffré L, Costantini A, Nannipieri P, (2011) Assessment of soil microbial diversity measurements as indicators of soil functioning in organic and conventional horticulture systems. Ecol Indic 11: 1345-1353.
38. Zelles L, (1999) Fatty acid patterns of phospholipids and lipopolysaccharides in the characterisation of microbial communities in soil: a review. Biol Fertil Soils 29: 111-129.
39. Wu T, Chellemi DO, Graham JH, Martin KJ, Rosskopf EN, (2008) Comparison of soil bacterial communities under diverse agricultural land management and crop production practices. Microb Ecol 55: 293-310.
40. Martiny JB, Bohannan BJ, Brown JH, Colwell RK, Fuhrman JA, et al. (2006) Microbial biogeography: putting microorganisms on the map. Nat Rev Microbiol 4: 102-112.
41. Kuramae E, Gamper H, van Veen J, Kowalchuk G, (2011) Soil and plant factors driving the community of soil-borne microorganisms across chronosequences of secondary succession of chalk grasslands with a neutral pH. FEMS Microbiol Ecol 77: 285-294.
42. Ge Y, He J, Zhu Y, Zhang J, Xu Z, et al. (2008) Differences in soil bacterial diversity: driven by contemporary disturbances or historical contingencies? ISME J 2: 254-264.
43. Philippot L, Andersson SG, Battin TJ, Prosser JI, Schimel JP, et al. (2010) The ecological coherence of high bacterial taxonomic ranks. Nat Rev Microbiol 8: 523-529.
44. Sait M, Davis KER, Janssen PH, (2006) Effect of pH on isolation and distribution of members of subdivision 1 of the phylum Acidobacteria occurring in soil. Appl Environ Microbiol 72: 1852-1857.
45. Lee SH, Ka JO, Cho JC, (2008) Members of the phylum Acidobacteria are dominant and metabolically active in rhizosphere soil. FEMS Microbiol Lett 285: 263-269.
46. Fierer N, Bradford MA, Jackson RB, (2007) Toward an ecological classification of soil bacteria. Ecology 88: 1354-1364.
47. Ganzert L, Lipski A, Hubberten HW, Wagner D, (2011) The impact of different soil parameters on the community structure of dominant bacteria from nine different soils located on Livingston Island, South Shetland Archipelago, Antarctica. FEMS Microbiol Ecol 76: 476-491.
48. Liles MR, Turkmen O, Manske BF, Zhang M, Rouillard JM, et al. (2010) A phylogenetic microarray targeting 16S rRNA genes from the bacterial division Acidobacteria reveals a lineage-specific distribution in a soil clay fraction. Soil Biol Biochem 42: 739-747.
49. Mummey D, Holben W, Six J, Stahl P, (2006) Spatial stratification of soil bacterial populations in aggregates of diverse soils. Microb Ecol 51: 404-411.
50. Chenu C, Hassink J, Bloem J, (2001) Short-term changes in the spatial distribution of microorganisms in soil aggregates as affected by glucose addition. Biol Fertil Soils 34: 349-356.
51. Davis KE, Sangwan P, Janssen PH, (2011) Acidobacteria, Rubrobacteridae and Chloroflexi are abundant among very slow-growing and mini-colony-forming soil bacteria. Environ Microbiol 13: 798-805.
52. Ward NL, Challacombe JF, Janssen PH, Henrissat B, Coutinho PM, et al. (2009) Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils. Appl Environ Microbiol 75: 2046-2056.
53. Denner EB, Kolari M, Hoornstra D, Tsitko I, Kampfer P, et al. (2006) Rubellimicrobium thermophilum gen. nov., sp. nov., a red-pigmented, moderately thermophilic bacterium isolated from coloured slime deposits in paper machines. Int J Syst Evol Microbiol 56: 1355-1362.
54. Dastager SG, Lee JC, Ju YJ, Park DJ, Kim CJ, (2008) Rubellimicrobium mesophilum sp. nov., a mesophilic, pigmented bacterium isolated from soil. Int J Syst Evol Microbiol 58: 1797-1800.
55. Cao YR, Jiang Y, Wang Q, Tang SK, He WX, et al. (2010) Rubellimicrobium roseum sp. nov., a Gram-negative bacterium isolated from the forest soil sample. Antonie Van Leeuwenhoek 98: 389-394.
56. Weon HY, Son JA, Yoo SH, Hong SB, Jeon YA, et al. (2009) Rubellimicrobium aerolatum sp. nov., isolated from an air sample in Korea. Int J Syst Evol Microbiol 59: 406-410.
57. Koberl M, Muller H, Ramadan EM, Berg G, (2011) Desert farming benefits from microbial potential in arid soils and promotes diversity and plant health. PLoS One 6: e24452.
58. Carignan V, Villard MA, (2002) Selecting indicator species to monitor ecological integrity: A review. Environ Monit Assess 78: 45-61.
59. Dale VH, Beyeler SC, (2001) Challenges in the development and use of ecological indicators. Ecol indic 1: 3-10.