Biochar impacts soil microbial community composition and nitrogen cycling in an acidic soil planted with rape

Environmental Science and Technology

Volumn 48, Issue 16, 2014, Pages 9391-9399

  Xu, Hui Juan ^a,c   Wang, Xiao Hui ^b,c   Li, Hu ^a,c   Yao, Huai Ying ^a   Su, Jian Qiang ^a   Zhu, Yong Guan ^a,b  

^a INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^b RESEARCH CENTER FOR ECO ENVIRONMENTAL SCIENCES   (China)

^c UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

[No Author keywords available]

Indexed keywords

CARBON; FORESTRY; GREENHOUSE GASES; MICROORGANISMS; NITROGEN; NITROGEN FERTILIZERS; PLANTS (BOTANY);

CATION EXCHANGE CAPACITIES; HIGH-THROUGHPUT SEQUENCING; MICROBIAL COMMUNITIES; NITRIFICATION AND DENITRIFICATION; REDUNDANCY ANALYSIS; SOIL CHEMICAL PROPERTY; SOIL MICROBIAL COMMUNITY; SOIL MICROBIAL COMMUNITY COMPOSITIONS;

SOILS;

CARBON; CHARCOAL; NITROGEN; NITROGEN OXIDE; BIOCHAR; FERTILIZER; NITROUS OXIDE; SOIL;

ACID SOIL; COMMUNITY COMPOSITION; DENITRIFICATION; EMISSION; GREENHOUSE GAS; MICROBIAL COMMUNITY; NITROGEN CYCLE; NITROUS OXIDE; RELATIVE ABUNDANCE; SOIL EMISSION; SOIL MICROORGANISM; SOIL NITROGEN; SOIL REMEDIATION;

ACIDOBACTERIACEAE; ARTICLE; BACILLACEAE; BACTERIAL GENE; BACTERIUM; BRADYRHIZOBIACEAE; CARBON CYCLING; CARBON FOOTPRINT; CATION EXCHANGE; CHITINOPHAGACEAE; CLOSTRIDIACEAE; CONTROLLED STUDY; DENITRIFICATION; FLAMMEOVIRGACEAE; GAIELLACEAE; GENETIC TRANSCRIPTION; HIGH THROUGHPUT SEQUENCING; HYPHOMICROBIACEAE; KORIBACTERACEAE; MICROBIAL DIVERSITY; NITRIFICATION; NITROGEN CYCLING; NONHUMAN; NOSZ GENE; PLANT GROWTH; POPULATION ABUNDANCE; REDUCTION; RHODOSPIRILLACEAE; SOIL ACIDITY; SOIL MICROFLORA; SOIL PROPERTY; SOLIBACTERACEAE; SPHINGOMONADACEAE; XANTHOMONADACEAE; BIOMASS; BRASSICA; CHEMISTRY; DRUG EFFECTS; GENETICS; GROWTH, DEVELOPMENT AND AGING; MICROBIOLOGY; MICROFLORA; NITROGEN CYCLE; PH; SOIL; STANDARDS;

BIOMASS; BRASSICA; CHARCOAL; DENITRIFICATION; FERTILIZERS; HYDROGEN-ION CONCENTRATION; MICROBIOTA; NITRIFICATION; NITROGEN CYCLE; NITROUS OXIDE; SOIL; SOIL MICROBIOLOGY;

EID: 84906261462     PISSN: 0013936X     EISSN: 15205851     Source Type: Journal    
DOI: 10.1021/es5021058     Document Type: Article

References (60)

1. Guo, J. H.; Liu, X. J.; Zhang, Y.; Shen, J. L.; Han, W. X.; Zhang, W. F.; Christie, P.; Goulding, K. W. T.; Vitousek, P. M.; Zhang, F. S. Significant acidification in major Chinese croplands Science 2010, 327 (5968) 1008-1010
2. Zhou, J.; Xia, F.; Liu, X.; He, Y.; Xu, J.; Brookes, P. C. Effects of nitrogen fertilizer on the acidification of two typical acid soils in South China J. Soils Sediments 2014, 14 (2) 415-422
3. 2O emissions, soil quality and crop production in a sandy loam soil Soil Biol. Biochem. 2005, 37 (11) 2037-2045
4. Pietri, J. C. A.; Brookes, P. C. Relationships between soil pH and microbial properties in a UK arable soil Soil Biol. Biochem. 2008, 40 (7) 1856-1861
5. 2O) product ratios of denitrification Soil Biol. Biochem. 2012, 55, 104-112
6. 2) product ratio of denitrification, primarily due to acidification of the soils Glob. Change Biol. 2014, 20 (5) 1685-98
7. Yuan, J. H.; Xu, R. K. The amelioration effects of low temperature biochar generated from nine crop residues on an acidic Ultisol Soil Use Manage. 2011, 27 (1) 110-115
8. Novak, J. M.; Cantrell, K. B.; Watts, D. W.; Busscher, W. J.; Johnson, M. G. Designing relevant biochars as soil amendments using lignocellulosic-based and manure-based feedstocks J. Soils Sediments 2014, 14 (2) 330-343
9. Khan, S.; Chao, C.; Waqas, M.; Arp, H. P. H.; Zhu, Y. G. Sewage sludge biochar influence upon rice (Oryza sativa L) yield, metal bioaccumulation and greenhouse gas emissions from acidic paddy soil Environ. Sci. Technol. 2013, 47 (15) 8624-8632
10. Rees, F.; Simonnot, M. O.; Morel, J. L. Short-term effects of biochar on soil heavy metal mobility are controlled by intra-particle diffusion and soil pH increase Eur. J. Soil Sci. 2014, 65 (1) 149-161
11. 2O emissions? Sci. Rep. 2013, 3, 1732
12. 2O and NO emissions Soil Biol. Biochem. 2014, 70, 244-255
13. 2O production in a cultivated Black Chernozem Biol. Fertil. Soils 2012, 48 (8) 941-946
14. Clough, T. J.; Bertram, J. E.; Ray, J. L.; Condron, L. M.; O'Callaghan, M.; Sherlock, R. R.; Wells, N. S. Unweathered wood biochar impact on nitrous oxide emissions from a bovine-urine-amended pasture soil Soil Sci. Soc. Am. J. 2010, 74 (3) 852-860
15. 2O- producing microbial communities in soils- what matters for their functioning? Adv. Appl. Microbiol. 2011, 75, 33-70
16. 2O emission in paddy soils Soil Biol. Biochem. 2013, 67, 174-182
17. 2O emissions from soil resulting from rewetting air-dried soil in short-term laboratory experiments Soil Sci. Plant Nutr. 2007, 53 (2) 181-188
18. 2 from Ferrosol Aust. J. Soil Res. 2010, 48 (6-7) 555-568
19. 2O to biochars and other organic and inorganic materials under anhydrous conditions Environ. Sci. Technol. 2013, 47 (14) 7704-7712
20. Spokas, K. A.; Baker, J. M.; Reicosky, D. C. Ethylene: Potential key for biochar amendment impacts Plant Soil 2010, 333 (1-2) 443-452
21. Thies, J. E.; Rillig, M. C. Characteristics of Biochar: Biological Properties. In Biochar for Environmental Management: Science and Technology; Lehmann; Joseph, Eds.; Earthscan: London, 2009; pp 85-105.
22. Smith, J. L.; Collins, H. P.; Bailey, V. L. The effect of young biochar on soil respiration Soil Biol. Biochem. 2010, 42 (12) 2345-2347
23. Zimmerman, A. R. Abiotic and microbial oxidation of laboratory-produced black carbon (biochar) Environ. Sci. Technol. 2010, 44 (4) 1295-1301
24. Anderson, C. R.; Condron, L. M.; Clough, T. J.; Fiers, M.; Stewart, A.; Hill, R. A.; Sherlock, R. R. Biochar induced soil microbial community change: Implications for biogeochemical cycling of carbon, nitrogen and phosphorus Pedobiologia 2011, 54 (5-6) 309-320
25. Ducey, T. F.; Ippolito, J. A.; Cantrell, K. B.; Novak, J. M.; Lentz, R. D. Addition of activated switchgrass biochar to an aridic subsoil increases microbial nitrogen cycling gene abundances Appl. Soil Ecol. 2013, 65, 65-72
26. 2O emissions from biochar-amended soil to the structure and function of the N-cycling microbial community ISME J. 2014, 8 (3) 660-674
27. 2O flux from soil following biochar application Agri., Ecosyst. Environ. 2014, 191 (0) 53-62
28. Zhou, H. W.; Li, D. F.; Tam, N. F. Y.; Jiang, X. T.; Zhang, H.; Sheng, H. F.; Qin, J.; Liu, X.; Zou, F. BIPES, a cost-effective high-throughput method for assessing microbial diversity ISME J. 2011, 5 (4) 741-749
29. Braker, G.; Zhou, J. Z.; Wu, L. Y.; Devol, A. H.; Tiedje, J. M. Nitrite reductase genes (nirK and nirS) as functional markers to investigate diversity of denitrifying bacteria in Pacific northwest marine sediment communities Appl. Environ. Microbiol. 2000, 66 (5) 2096-2104
30. Kloos, K.; Mergel, A.; Rosch, C.; Bothe, H. Denitrification within the genus Azospirillum and other associative bacteria Aust. J. Plant Physiol. 2001, 28 (9) 991-998
31. Francis, C. A.; Roberts, K. J.; Beman, J. M.; Santoro, A. E.; Oakley, B. B. Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean Proc. Natl. Acad. Sci. U.S.A. 2005, 102 (41) 14683-14688
32. 2) in denitrifying cultures J. Microbiol. Methods 2007, 71 (3) 202-211
33. He, J. Z.; Shen, J. P.; Zhang, L. M.; Zhu, Y. G.; Zheng, Y. M.; Xu, M. G.; Di, H. Quantitative analyses of the abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea of a Chinese upland red soil under long-term fertilization practices Environ. Microbiol. 2007, 9 (9) 2364-2374
34. Guo, G. X.; Deng, H.; Qiao, M.; Mu, Y. J.; Zhu, Y. G. Effect of pyrene on denitrification activity and abundance and composition of denitrifying community in an agricultural soil Environ. Pollut. 2011, 159 (7) 1886-1895
35. Huse, S. M.; Dethlefsen, L.; Huber, J. A.; Welch, D. M.; Relman, D. A.; Sogin, M. L. Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing PloS Genet. 2008, 4, e1000255
36. Hamady, M.; Walker, J. J.; Harris, J. K.; Gold, N. J.; Knight, R. Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex Nat. Methods 2008, 5 (3) 235-237
37. Ahn, S. J.; Costa, J.; Emanuel, J. R. PicoGreen quantitation of DNA: effective evaluation of samples pre- or post-PCR Nucleic Acids Res. 1996, 24 (13) 2623-2625
38. Griffiths, R. I.; Whiteley, A. S.; O'Donnell, A. G.; Bailey, M. J. Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA- and rRNA-based microbial community composition Appl. Environ. Microbiol. 2000, 66 (12) 5488-5491
39. Caporaso, J. G.; Kuczynski, J.; Stombaugh, J.; Bittinger, K.; Bushman, F. D.; Costello, E. K.; Fierer, N.; Pena, A. G.; Goodrich, J. K.; Gordon, J. I.; Huttley, G. A.; Kelley, S. T.; Knights, D.; Koenig, J. E.; Ley, R. E.; Lozupone, C. A.; McDonald, D.; Muegge, B. D.; Pirrung, M.; Reeder, J.; Sevinsky, J. R.; Tumbaugh, P. J.; Walters, W. A.; Widmann, J.; Yatsunenko, T.; Zaneveld, J.; Knight, R. QIIME allows analysis of high-throughput community sequencing data Nat. Methods 2010, 7 (5) 335-336
40. Lozupone, C.; Hamady, M.; Knight, R. UniFrac-An online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics 2006, 7.
41. Oksanen, J. Multivariate analysis of ecological communities in R: vegan tutorial. [WWW document]. URL http://cc.oulu.fi/∼jarioksa/opetus/metodi/ vegantutor.pdf. 2-8- 2013. Ref Type: Internet Communication.
42. Bolan, N. S.; Hedley, M. J.; White, R. E. Processes of soil acidification during nitrogen cycling with emphasis on legume based pastures Plant Soil 1991, 134 (1) 53-63
43. Prommer, J.; Wanek, W.; Hofhansl, F.; Trojan, D.; Offre, P.; Urich, T.; Schleper, C.; Sassmann, S.; Kitzler, B.; Soja, G.; Hood-Nowotny, R. C. Biochar decelerates soil organic nitrogen cycling but stimulates soil nitrification in a temperate arable field trial PloS One 2014, 9, e86388
44. Ulyett, J.; Sakrabani, R.; Kibblewhite, M.; Hann, M. Impact of biochar addition on water retention, nitrification and carbon dioxide evolution from two sandy loam soils Eur. J. Soil Sci. 2014, 65 (1) 96-104
45. Yeomans, J. C.; Beauchamp, E. G. Limited inhibition of nitrous-oxide reduction in soil in presence of acetylene Soil Biol. Biochem. 1978, 10 (6) 517-519
46. Peterjohn, W. T. Denitrification-enzyme content and activity in desert soils Soil Biol. Biochem. 1991, 23 (9) 845-855
47. Simek, M.; Cooper, J. E. The influence of soil pH on denitrification: Progress towards the understanding of this interaction over the last 50 years Eur. J. Soil Sci. 2002, 53 (3) 345-354
48. Shen, C.; Xiong, J.; Zhang, H.; Feng, Y.; Lin, X.; Li, X.; Liang, W.; Chu, H. Soil pH drives the spatial distribution of bacterial communities along elevation on Changbai Mountain Soil Biol. Biochem. 2013, 57 (2) 204-211
49. Fierer, N.; Jackson, R. B. The diversity and biogeography of soil bacterial communities Proc. Natl. Acad. Sci. U.S.A. 2006, 103 (3) 626-631
50. Högberg, M. N.; Högberg, P.; Myrold, D. D. Is microbial community composition in boreal forest soils determined by pH, C-to-N ratio, the trees, or all three? Oecologia 2007, 150 (4) 590-601
51. Yoon, J.; Ishikawa, S.; Kasai, H.; Yokota, A. Perexilibacter aurantiacus gen. nov., sp nov., a novel member of the family 'Flammeovirgaceae' isolated from sediment Int. J. Syst. Evol. Microbiol. 2007, 57, 964-968
52. White, D. C.; Sutton, S. D.; Ringelberg, D. B. The genus Sphingomonas: Physiology and ecology Curr. Opin. Biotechnol. 1996, 7 (3) 301-306
53. Liu, Z. P.; Wang, B. J.; Liu, Y. H.; Liu, S. J. Novosphingobium taihuense sp. nov., a novel aromatic-compound-degrading bacterium isolated from Taihu Lake, China Int. J. Syst. Evol. Microbiol. 2005, 55, 1229-1232
54. Rivas, R.; Velazquez, E.; Willems, A.; Vizcaino, N.; Subba-Rao, N. S.; Mateos, P. F.; Gillis, M.; Dazzo, F. B.; Martinez-Molina, E. A new species of Devosia that forms a unique nitrogen-fixing root-nodule symbiosis with the aquatic legume Neptunia natans (L.f.) Druce Appl. Environ. Microbiol. 2002, 68 (11) 5217-5222
55. Liessens, J.; Germonpre, R.; Kersters, I.; Beernaert, S.; Verstraete, W. Removing nitrate with a methylotrophic fluidized bed: Microbiological water quality Am. Water Works Assn. J. 1993, 85 (4) 155-161
56. Novak, J. M.; Busscher, W. J.; Laird, D. L.; Ahmedna, M.; Watts, D. W.; Niandou, M. A. S. Impact of biochar amendment on fertility of a southeastern coastal plain soil Soil Sci. 2009, 174 (2) 105-112
57. Verhamme, D. T.; Prosser, J. I.; Nicol, G. W. Ammonia concentration determines differential growth of ammonia-oxidising archaea and bacteria in soil microcosms ISME J. 2011, 5 (6) 1067-1071
58. Levicnik-Hoefferle, S.; Nicol, G. W.; Ausec, L.; Mandic-Mulec, I.; Prosser, J. I. Stimulation of thaumarchaeal ammonia oxidation by ammonia derived from organic nitrogen but not added inorganic nitrogen FEMS Microbiol. Ecol. 2012, 80 (1) 114-123
59. Shoun, H.; Kim, D. H.; Uchiyama, H.; Sugiyama, J. Denitrification by fungi FEMS Microbiol. Lett. 1992, 94 (3) 277-281
60. Philippot, L. Denitrifying genes in bacterial and Archaeal genomes Biochim. Biophys.Acta. 2002, 1577 (3) 355-376