Long-term nickel exposure altered the bacterial community composition but not diversity in two contrasting agricultural soils

Environmental Science and Pollution Research

Volumn 22, Issue 14, 2015, Pages 10496-10505

  Li, Jing ^a,b   Hu, Hang Wei ^d   Ma, Yi Bing ^c   Wang, Jun Tao ^a,b   Liu, Yu Rong ^a   He, Ji Zheng ^a,d  

^a RESEARCH CENTER FOR ECO ENVIRONMENTAL SCIENCES   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c INSTITUTE OF PLANT PROTECTION   (China)

^d UNIVERSITY OF MELBOURNE   (Australia)

Author keywords

Abundance; Community composition; Diversity; Field experiment; Nickel pollution; Soil bacterial community; Soil microbial biomass carbon

Indexed keywords

ABUNDANCE; AGRICULTURAL SOIL; BACTERIUM; BIOMASS; FIELD METHOD; MICROBIAL ACTIVITY; MICROBIAL COMMUNITY; NICKEL; POLLUTION EXPOSURE; SOIL CARBON; SOIL ECOSYSTEM; SOIL MICROORGANISM; SPECIES DIVERSITY;

ACIDOBACTERIA; ACTINOBACTERIA; BACTERIA (MICROORGANISMS); PLANCTOMYCETES;

BACTERIAL DNA; NICKEL; RNA 16S; SOIL; SOIL POLLUTANT;

AGRICULTURE; BACTERIUM; BIODIVERSITY; BIOMASS; DRUG EFFECTS; GENETICS; MICROBIOLOGY; PHYLOGENY; SOIL; SOIL POLLUTANT; TOXICITY;

AGRICULTURE; BACTERIA; BIODIVERSITY; BIOMASS; DNA, BACTERIAL; NICKEL; PHYLOGENY; RNA, RIBOSOMAL, 16S; SOIL; SOIL MICROBIOLOGY; SOIL POLLUTANTS;

EID: 84957412119     PISSN: 09441344     EISSN: 16147499     Source Type: Journal    
DOI: 10.1007/s11356-015-4232-1     Document Type: Article

References (51)

1. Adamo P, Dudka S, Wilson MJ, McHardy WJ (1996) Chemical and mineralogical forms of Cu and Ni in contaminated soils from the Sudburymining and smelting region Canada. Environ Pollut 91:11-19
2. Ager D, Evans S, Li H, Lilley AK, van der Gast CJ (2010) Anthropogenic disturbance affects the structure of bacterial communities. Environ Microbiol 12:670-678
3. Awasthi A, Singh M, Soni SK, Singh R, Kalra A (2014) Biodiversity acts as insurance of productivity of bacterial communities under abiotic perturbations. ISME J 8:2445-2452
4. Bååth E, Frostegård Å, Pennanen T, Fritze H (1995) Microbial community structure and pH response in relation to soil organic matter quality in wood-ash fertilized, clear-cut or burned coniferous forest soils. Soil Biol Biochem 27:229-240
5. Bardgett RD, Lovell RD, Hobbs PJ, Jarvis SC (1999) Seasonal changes in soil microbial communities along a fertility gradient of temperate grasslands. Soil Biol Biochem 31:1021-1030
6. Bates ST, Berg-Lyons D, Caporaso JG, Walters WA, Knight R, Fierer N (2011) Examining the global distribution of dominant archaeal populations in soil. ISME J 5:908-917
7. Berg J, Brandt KK, Al-Soud WA, Holm PE, Hansen LH, Sørensen SJ, Nybroe O (2012) Selection for Cu-tolerant bacterial communities with altered composition, but unaltered richness, via long-term Cu exposure. Appl Environ Microbiol 78:7438-7446
8. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK et al (2010a) QIIME allows analysis of highthroughput community sequencing data. Nat Methods 7:335-336
9. Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL, Knight R (2010b) PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 26:266-267
10. Cempel M, Nikel G (2006) Nickel: a review of its sources and environmental toxicology. Polish J of Environ Stud 15:375-382
11. Chen X, Zhang LM, Shen JP, Xu ZH, He JZ (2010) Soil type determines the abundance and community structure of ammonia-oxidizing bacteria and archaea in flooded paddy soils. J Soil Sediment 10:1510-1516
12. Edgar RC (2013) UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods 10:996-998
13. Falkowski PG, Fenchel T, Delong EF (2008) The microbial engines that drive Earth’s biogeochemical cycles. Science 320:1034-1039
14. Field D, Tiwari B, Booth T, Houten S, Swan D, Bertrand N, Thurston M (2006) Open software for biologists: from famine to feast. Nat Biotechnol 24:801-804
15. Fierer N, Jackson RB (2006) The diversity and biogeography of soil bacterial communities. PNAS 103:626-631
16. Fierer N, Schimel JP, Holden PA (2003) Influence of drying-rewetting frequency on soil bacterial community structure. Microb Ecol 45: 63-71
17. Fierer N, Ladau J, Clemente JC, Leff JW, Owens SM, Pollard KS, Knight R, Gilbert JA, McCulley RL (2013) Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the united states. Science 342:621-624
18. Fuerst JA, Sagulenko E (2011) Beyond the bacterium: Planctomycetes challenge our concepts of microbial structure and function. Nat Rev 9:403-413
19. Giller KE, Witter E, McGrath SP (1998) Toxicity of heavy metals to microorganisms and microbial processes in agricultural soils: a review. Soil Biol Biochem 30:1389-1414
20. Griffiths BS, Philippot L (2012) Insights into the resistance and resilience of the soil microbial community. FEMS Microbiol Rev 37:112-129
21. Guo XY, Zuo YB, Wang BR, Li JM, Ma YB (2010) Toxicity and accumulation of copper and nickel in maize plants cropped on calcareous and acidic field soils. Plant Soil 333:365-373
22. Haferburg G, Kothe E (2007) Microbes and metals: interactions in the environment. J Basic Microbiol 47:453-467
23. He JZ, Shen JP, Zhang LM, Zhu YG, Zheng YM, Xu MG, Di HJ (2007) 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 9:2364-2374
24. He JZ, Zheng Y, Chen CR, He YQ, Zhang LM (2008) Microbial composition and diversity of an upland red soil under long-term fertilization treatments as revealed by culture-dependent and cultureindependent approaches. J Soil Sediment 8:349-358
25. He JZ, Ge Y, Xu ZH, Chen CR (2009) Linking soil bacterial diversity to ecosystem multifunctionality using backward-elimination boosted tree analysis. J Soil Sediment 9:547-554
26. He JZ, Hu HW, Zhang LM (2012) Current insights into the autotrophic thaumarchaeal ammonia oxidation in acidic soils. Soil Biol Biochem 55:146-154
27. Héry M, Nazaret S, Jaffré T, Normand P, Navarro E (2003) Adaptation to nickel spiking of bacterial communities in neocaledonian soils. Environ Microbiol 5:3-12
28. Hu HW, Zhang LM, Dai Y, Di HJ, He JZ (2013) pH-dependent distribution of soil ammonia oxidizers across a large geographical scale as revealed by high-throughput pyrosequencing. J Soil Sediment 13: 1439-1449
29. Hu HW, Xu ZH, He JZ (2014) Ammonia-oxidizing archaea play a predominant role in acid soil nitrification. Adv Agron 125:261-302
30. Jones RT, Robeson MS, Lauber CL, Hamady M, Knight R, Fierer N (2009) A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses. ISME J 3:442-453
31. Khan S, Hesham AE, Qiao M, Rehman S, He JZ (2010) Effects of Cd and Pb on soil microbial community structure and activities. Environ Sci Pollut Res 17:288-296
32. Lauber CL, Hamady M, Knight R, Fierer N (2009) Pyrosequencingbased assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol 75: 5111-5120
33. Lejon DPH, Pascault N, Ranjard L (2010) Differential copper impact on density, diversity and resistance of adapted culturable bacterial populations according to soil organic status. Eur J Soil Biol 46:168-174
34. Li J, Zheng YM, Liu YR, Ma YB, Hu HW, He JZ (2014) Initial copper stress strengthens the resistance of soil microorganisms to a subsequent copper stress. Microb Ecol 67:931-941
35. Liu YR, Zheng YM, Shen JP, Zhang LM, He JZ (2010) Effects of mercury on the activity and community composition of soil ammonia oxidizers. Environ Sci Pollut Res 17:1237-1244
36. Ma YB, Lombi E, Oliver IW, Nolan AL, Mclaughlin MJ (2006) Longterm aging of copper added to soils. Environ Sci Technol 40:6310-6317
37. Macdonald CA, Singh BK, Peck JA, van Schaik AP, Hunter LC, Horswell J, Campbell CD, Speir TW (2007) Long-term exposure to Zn-spiked sewage sludge alters soil community structure. Soil Biol Biochem 39:2576-2586
38. Macdonald CA, Clark IM, Zhao FJ, Hirsch PR, Singh BK, McGrath SP (2011) Long-term impacts of zinc and copper enriched sewage sludge additions on bacterial, archaeal and fungal communities in arable and grassland soils. Soil Biol Biochem 43:932-941
39. Magoè T, Salzberg SL (2011) FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27:2957-2963
40. Marcina C, Marcin G, Justynac M, Katarzynac K, Mariac N (2013) Diversity of microorganisms from forest soils differently polluted with heavy metals. Appl Soil Ecol 64:7-14
41. McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, Andersen GL, Knight R, Hugenholtz P (2011) An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J 6:610-618
42. Mirete S, de Figueras CG, González-Pastor JE (2007) Novel nickel resistance genes from the rhizosphere metagenome of plants adapted to acid mine drainage. Appl Environ Microbiol 73:6001-6011
43. Shen JP, Xu ZH, He JZ (2014) Frontiers in the microbial processes of ammonia oxidation in soils and sediments. J Soil Sediment 14: 1023-1029
44. Singh BK, Quince C, Macdonald CA, Khachane A, Thomas N, Al-Soud WA, Sørensen SJ, He ZL, White D, Sinclair A, Crooks B, Zhou JZ, Campbell CD (2014) Loss of microbial diversity in soils is coincident with reductions in some specialized functions. Environ Microbiol 16:2408-2420
45. Suzuki MT, Taylor LT, DeLong EF (2000) Quantitative analysis of smallsubunit rRNA genes in mixed microbial populations via 5’-nuclease assays. Appl Environ Microbiol 66:4605-4614
46. Trivedi P, Anderson IC, Singh BK (2013) Microbial modulators of soil carbon storage: integrating genomic and metabolic knowledge for global prediction. Trends Microbiol 21:614-651
47. Wakelin SA, Chu GX, Lardner R, Liang YC, McLaughlin MJ (2010) A single application of Cu to field soil has long term effects on bacterial community structure, diversity, and soil processes. Pedobiologia 53:149-158
48. Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73:5261-5267
49. Wittebolle L, Marzorati M, Clement L, Balloi A, Daffonchio D, Heylen K, Vos PD, Verstraete W, Boon N (2009) Initial community evenness favours functionality under selective stress. Nature 458:623-626
50. Wu JS, Joergensen RG, Pommerening B (1990) Measurement of soil microbial biomass C by fumigation-extraction-an automated procedure. Soil Biol Biochem 22:1167-1169
51. Yang GY, Luo W, Zhang TB, Wan HF, Gao YX (2007) The distribution of Ni contents in agricultural soils in the Pearl River Delta, China. Ecol Environ 16:818-821 (in Chinese)