Long-term fertilization regimes affect bacterial community structure and diversity of an agricultural soil in northern China

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