Abstract
Background, Aims, and Scope
Knowledge about shifts of microbial community structure and diversity following different agricultural management practices could improve our understanding of soil processes and thus help us to develop sound management strategies. A long-term fertilization experiment was established in 1989 at Fengqiu (35°00′N, 114°24′E) in northern China. The soil (sandy loam) is classified as aquic inceptisols and has received continuous fertilization treatments since then. The fertilization treatments included control (CK, no fertilizer), chemical fertilizers nitrogen (N) and potassium (K) (NK), phosphorous (P) and K (PK), NP, NPK, organic manure (OM), and half chemical fertilizers NPK plus half organic manure (1/2NPKOM). The objective of this study was to examine if the microbial community structure and diversity were affected by the long-term fertilization regimes.
Materials and Methods
Soil samples were collected from the long-term experimental plots with seven treatments and four replications in April 2006. Microbial DNAs were extracted from the soil samples and the 16S rRNA genes were PCR amplified. The PCR products were analyzed by DGGE, cloning and sequencing. The bacterial community structures and diversity were assessed using the DGGE profiles and the clone libraries constructed from the excised DGGE bands.
Results
The bacterial community structure of the OM and PK treatments were significantly different from those of all other treatments. The bacterial community structures of the four Ncontaining treatments (NK, NP, NPK and 1/2NPKOM), as well as CK, were more similar to each other. The changes in bacterial community structures of the OM and PK treatments showed higher richness and diversity. Phylogenetic analyses indicated that Proteobacteria (30.5%) was the dominant taxonomic group of the soil, followed by Acidobacteria (15.3%), Gemmatimonadetes (12.7%), etc.
Discussion
Irrespective of the two fertilization treatments of OM and PK, the cluster analysis showed that bacterial communities of the remaining five treatments of CK, NK, NP, NPK and 1/2NPKOM seemed to be more similar to each other, which indicated the relatively weak effects of the four N-containing treatments on soil bacterial communities. N fertilizer may be considered as a key factor to counteract the effects of other fertilizers on microbial communities.
Conclusions
Our results show that long-term fertilization regimes can affect bacterial community structure and diversity of the agricultural soil. The OM and PK treatments showed a trend towards distinct community structures, higher richness and diversity when compared to the other treatments. Contrasting to the positive effects of OM and PK treatments on the bacterial communities, N fertilizer could be considered as a key factor in the soil to counteract the effects of other fertilizers on soil microbial communities.
Recommendations and Perspectives
Because of the extremely high abundance and diversity of microorganisms in soil and the high heterogeneity of the soil, it is necessary to further examine the effects of fertilization regimes on microbial community and diversity in different type soils for comprehensively understanding their effects through the appropriate combination of molecular approaches.
Similar content being viewed by others
References
Bell T, Newman JA, Silverman BW, Turner SL, Lilley AK (2005): The contribution of species richness and composition to bacterial services. Nature 436, 1157–1160
Cardinale BJ, Srivastava DS, Duffy JE, Wright JP, Downing AL, Sankaran M, Jouseau C (2006): Effects of biodiversity on the functioning of trophic groups and ecosystems. Nature 443, 989–992
Costa AL, Paixão SM, Caçador I, Carolino M (2007): CLPP and EEA profiles of microbial communities in salt marsh sediments. J Soils Sediments 7(6) 418–425
Crecchio C, Gelsomino A, Ambrosoli R, Minati JL, Ruggiero P (2004): Functional and molecular responses of soil microbial communities under differing soil management practices. Soil Biol Biochem 36, 1873–1883
Daniel R (2005): The metagenomics of soil. Nat Rev Micro 3, 470–478
Dolfing J, Vos A, Bloem J, Ehlert PAI, Naumova NB, Kuikman PJ (2004): Microbial diversity in archived soils. Science 306, 813
Enwall K, Philippot L, Hallin S (2005): Activity and composition of the denitrifying bacterial community respond differently to long-term fertilization. Appl Environ Microbiol 71, 8335–8343
Felsenstein J (1989): PHYLIP — phylogeny inference package (version 3.2). Cladistics 5, 164–166
Fierer N, Jackson RB (2006): The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci USA 103, 626–631
Freitag TE, Chang L, Clegg CD, Prosser JI (2005): Influence of inorganic nitrogen management regime on the diversity of nitrite-oxidizing bacteria in agricultural grassland soils. Appl Environ Microbiol 71, 8323–8334
Gans J, Wolinsky M, Dunbar J (2005): Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 309, 1387–1390
Gelsomino A, Cacco G (2006): Compositional shifts of bacterial groups in a solarized and amended soil as determined by denaturing gradient gel electrophoresis. Soil Biol Biochem 38, 91–102
He JZ, Xu ZH, Hughes J (2005): Analyses of soil fungal communities in adjacent natural forest and hoop pine plantation ecosystems of subtropical Australia using molecular approaches based on 18S rRNA genes. FEMS Microbiol Lett 247, 91–100
He JZ, Xu ZH, Hughes J (2006): Molecular bacterial diversity of a forest soil under residue management regimes in subtropical Australia. FEMS Microbiol Ecol 55, 38–47
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
Hughes JB, Hellmann JJ, Ricketts TH, Bohannan BJM (2001): Counting the uncountable: statistical approaches to estimating microbial diversity. Appl Environ Microbiol 67, 4399–4406
Janssen PH (2006): Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl Environ Microbiol 72, 1719–1728
Knief C, Vanitchung S, Harvey NW, Conrad R, Dunfield PF, Chidthaisong A (2005): Diversity of methanotrophic bacteria in tropical upland soils under different land uses. Appl Environ Microbiol 71, 3826–3831
Kumar S, Tamura K, Nei M (2004): MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5, 150–163
Lagomarsino A, Knapp BA, Moscatelli MC, De Angelis P, Grego S, Insam H (2007): Structural and functional diversity of soil microbes is affected by elevated [CO2] and N addition in a poplar plantation. J Soils Sediments 7(6) 399–405
Mäeder P, Fließach A, Dubois D, Gunst L, Fried P, Niggli U (2002): Soil fertility and biodiversity in organic farming. Science 296, 1694–1697
Muyzer G, de Waal E, Uitterlinden A (1993): Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59, 695–700
Naeem S, Li S (1997): Biodiversity enhances ecosystem reliability. Nature 390, 507–509
Peacock AD, Mullen MD, Ringelberg DB, Tyler DD, Hedrick DB, Gale PM, White DC (2001): Soil microbial community responses to dairy manure or ammonium nitrate applications. Soil Biol Biochem 33, 1011–1019
Sarathchandra SU, Ghani A, Yeates GW, Burch G, Cox NR (2001): Effect of nitrogen and phosphate fertilisers on microbial and nematode diversity in pasture soils. Soil Biol Biochem 33, 953–964
Schloss PD, Handelsman J (2005): Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71, 1501–1506
Sessitsch A, Weilharter A, Gerzabek MH, Kirchmann H, Kandeler E (2001): Microbial population structures in soil particle size fractions of a long-term fertilizer field experiment. Appl Environ Microbiol 67, 4215–4224
Sun HY, Deng SP, Raun WR (2004): Bacterial community structure and diversity in a century-old manure-treated agroecosystem. Appl Environ Microbiol 70, 5868–5874
Tolli J, King GM (2005): Diversity and structure of bacterial chemolithotrophic communities in pine forest and agroecosystem soils. Appl Environ Microbiol 71, 8411–8418
Torsvik V, Salte K, Sørheim R, Goksøyr J (1990): Comparison of phenotypic diversity and DNA heterogeneity in a population of soil bacteria. Appl Environ Microbiol 56, 776–781
Torsvik V, Daae FL, Sandaa R-A, Øvreås L (1998): Novel techniques for analysing microbial diversity in natural and perturbed environments. J Biotechnol 64, 53–62
Yu Z, Morrison M (2004): Comparisons of different hypervariable regions of rrs genes for use in fingerprinting of microbial communities by PCR-denaturing gradient gel electrophoresis. Appl Environ Microbiol 70, 4800–4806
Zhou J, Xia B, Treves DS, Wu LY, Marsh TL, O’Neill RV, Palumbo AV, Tiedje JM (2002): Spatial and resource factors influencing high microbial diversity in soil. Appl Environ Microbiol 68, 326–334
Author information
Authors and Affiliations
Corresponding author
Additional information
ESS-Submission Editor: Chengrong Chen, PhD (c.chen@griffith.edu.au)
Rights and permissions
About this article
Cite this article
Ge, Y., Zhang, Jb., Zhang, Lm. et al. Long-term fertilization regimes affect bacterial community structure and diversity of an agricultural soil in northern China. J Soils Sediments 8, 43–50 (2008). https://doi.org/10.1065/jss2008.01.270
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1065/jss2008.01.270