Differential responses of soil bacterial taxa to long-term P, N, and organic manure application

Banerjee S, Palit R, Sengupta C, Standing D (2010) Stress induced phosphate solubilization by Arthrobacter sp. and Bacillus sp. isolated from tomato rhizosphere. Aust J Crop Sci 4:378–383 Beauregard MS, Hamel C, Atul-Nayyar S-AM (2010) Long-term phosphorus fertilization impacts soil fungal and bacterial diversity but not AM fungal community in alfalfa. Microb Ecol 59:379–389 Berg J, Brandt KK, Al-Soud WA, Holm PE, Hansen LH, Sorensen 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 Campbell BJ, Polson SW, Hanson TE, Mack MC, Schuur EA (2010) The effect of nutrient deposition on bacterial communities in Arctic tundra soil. Environ Microbiol 12:1842–1854 Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, Fierer N, Knight R (2011) Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci U S A 108:4516–4522 Cederlund H, Wessén E, Enwall K, Jones CM, Juhanson J, Pell M, Philippot L, Hallin S (2014) Soil carbon quality and nitrogen fertilization structure bacterial communities with predictable responses of major bacterial phyla. Appl Soil Ecol 84:62–68 Chan Y-K, McCormick WA, Ma BL (2013) Effects of inorganic fertilizer and manure on soil archaeal abundance at two experimental farms during three consecutive rotation-cropping seasons. Appl Soil Ecol 68:26–35 Chen Y, Yang X, Cao Y (2011) Study on isolation, identification and phosphate accumulating capacity of Arthrobacter sp. J Anhui Agr Sci 39:447–450 Chu H, Fujii T, Morimoto S, Lin X, Yagi K, Hu J, Zhang J (2007) Community structure of ammonia-oxidizing bacteria under long-term application of mineral fertilizer and organic manure in a sandy loam soil. Appl Environ Microbiol 73:485–491 Dong W-Y, Zhang X-Y, Dai X-Q, Fu X-L, Yang F-T, Liu X-Y, Sun X-M, Wen X-F, Schaeffer S (2014) Changes in soil microbial community composition in response to fertilization of paddy soils in subtropical China. Appl Soil Ecol 84:140–147 Edgar RC (2013) UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods 10:996–998 Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27:2194–2200 Eilers KG, Lauber CL, Knight R, Fierer N (2010) Shifts in bacterial community structure associated with inputs of low molecular weight carbon compounds to soil. Soil Biol Biochem 42:896–903 Enwall K, Nyberg K, Bertilsson S, Cederlund H, Stenström J, Hallin S (2007) Long-term impact of fertilization on activity and composition of bacterial communities and metabolic guilds in agricultural soil. Soil Biol Biochem 39:106–115 Fan J, Hao M (2003) Study on long-term experiment of crop rotation and fertilization in the Loess Plateau II. Relationship between soil enzyme activities and soil fertility. Plant Nutr Fert Sci 9:146–150 Fanin N, Hättenschwiler S, Schimann H, Fromin N, Bailey JK (2015) Interactive effects of C, N and P fertilization on soil microbial community structure and function in an Amazonian rain forest. Function Ecol 29:140–150 Fierer N, Jackson RB (2006) The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci U S A 103:626–631 Fierer N, Bradaford MA, Jackson RB (2007) Toward an ecological classification of soil bacteria. Ecol 88:1354–1364 Fierer N, Lauber CL, Ramirez KS, Zaneveld J, Bradford MA, Knight R (2012) Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. ISME J 6:1007–1017 Fulthorpe RR, Roesch LF, Riva A, Triplett EW (2008) Distantly sampled soils carry few species in common. ISME J 2:901–910 Ge Y, Zhang J, Zhang L, Yang M, He J (2008) Long-term fertilization regimes affect bacterial community structure and diversity of an agricultural soil in northern China. J Soils Sediments 8:43–50 Goldfarb KC, Karaoz U, Hanson CA, Santee CA, Bradford MA, Treseder KK, Wallenstein MD, Brodie EL (2011) Differential growth responses of soil bacterial taxa to carbon substrates of varying chemical recalcitrance. Front Microbiol 2:1–10 Guo S, Wu J, Coleman K, Zhu H, Li Y, Liu W (2011) Soil organic carbon dynamics in a dryland cereal cropping system of the Loess Plateau under long-term nitrogen fertilizer applications. Plant Soil 353:321–332 Hallin S, Jones CM, Schloter M, Philippot L (2009) Relationship between N-cycling communities and ecosystem functioning in a 50-year-old fertilization experiment. ISME J 3:597–605 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 9:3152–3152 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 culture-independent approaches. J Soils Sediments 8:349–358 Huanga M, Danga T, Gallichandb J, Goulet M (2003) Effect of increased fertilizer applications to wheat crop on soil-water depletion in the Loess Plateau. Chin Agr Water Manage 58:267–278 Jangid K, Williams MA, Franzluebbers AJ, Sanderlin JS, Reeves JH, Jenkins MB, Endale DM, Coleman DC, Whitman WB (2008) Relative impacts of land-use, management intensity and fertilization upon soil microbial community structure in agricultural systems. Soil Biol Biochem 40:2843–2853 Joergensen R, Brookes P (1990) Ninhydrin-reactive nitrogen measurements of microbial biomass in 0.5 M K2SO4 soil extracts. Soil Biol Biochem 22:1023–1027 Kielak A, Pijl AS, van Veen JA, Kowalchuk GA (2009) Phylogenetic diversity of Acidobacteria in a former agricultural soil. ISME J 3:378–382 Lai L, Hao M, Peng L, Zhang Z (2003) Variation of organic phosphorus in soil under long-term fertilization on Loess Plateau. Soils 35:413–418 Lai L, Mingde H, Wang Y (2004) Changes of long-term rotation and fertilization on soil microbial phosphorus under dryland in Loess Plateau. Plant Nutr Fert Sci 10:546–549 Li C, Yan K, Tang L, Jia Z, Li Y (2014) Change in deep soil microbial communities due to long-term fertilization. Soil Biol Biochem 75:264–272 Magoc T, Salzberg SL (2011) FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27:2957–2963 Meyer K, Georg R, Joergensen, Meyer B (1996) The effects of reduced tillage on microbial biomass C and P in sandy loess soils. Appl Soil Ecol 5:71–79 Ning Q, Gu Q, Shen J, Lv X, Yang J, Zhang X, He J, Huang J, Wang H, Xu Z, Han X (2015) Effects of nitrogen deposition rates and frequencies on the abundance of soil nitrogen-related functional genes in temperate grassland of northern China. J Soils Sediments 15:694–704 Nunes da Rocha U, Plugge CM, George I, van Elsas JD, van Overbeek LS (2013) The rhizosphere selects for particular groups of acidobacteria and verrucomicrobia. PLoS One 8:e82443 Pan Y, Cassman N, de Hollander M, Mendes LW, Korevaar H, Geerts RH, van Veen JA, Kuramae EE (2014) Impact of long-term N, P, K, and NPK fertilization on the composition and potential functions of the bacterial community in grassland soil. FEMS Microbiol Ecol 90:195–205 Peck JE (2010) Multivariate analysis for community ecologists: step-by-step using PC-ORD. MjM Software Design, Gleneden Beach Prosser JI (2012) Ecosystem processes and interactions in a morass of diversity. FEMS Microbiol Ecol 81:507–519 Ramirez KS, Craine JM, Fierer N (2012) Consistent effects of nitrogen amendments on soil microbial communities and processes across biomes. Global Change Biol 18:1918–1927 Searle PL (1984) The Berthelot or indophenol reaction and its use in the analytical chemistry of nitrogen. Analyst A Rev 109:549–568 Shi Y, Lalande R, Ziadi N, Sheng M, Hu Z (2012) An assessment of the soil microbial status after 17 years of tillage and mineral P fertilization management. Appl Soil Ecol 62:14–23 Su JQ, Din LJ, Xue K, Yao HY, Quensen J, Bai SJ, Wei WX, Wu JS, Zhou J, Tiedje JM, Zhu YG (2015) Long-term balanced fertilization increases the soil microbial functional diversity in a phosphorus-limited paddy soil. Mol Ecol 24:136–150 Tan H, Barret M, Mooij MJ, Rice O, Morrissey JP, Dobson A, Griffiths B, O’Gara F (2012) Long-term phosphorus fertilisation increased the diversity of the total bacterial community and the phoD phosphorus mineraliser group in pasture soils. Biol Fert Soils 49:661–672 Turlapati SA, Minocha R, Bhiravarasa PS, Tisa LS, Thomas WK, Minocha SC (2013) Chronic N-amended soils exhibit an altered bacterial community structure in Harvard Forest, MA, USA. FEMS Microbiol Ecol 83:478–493 van der Heijden MG, Bardgett RD, van Straalen NM (2008) The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems. Ecol Lett 11:296–310 Wakelin S, Mander C, Gerard E, Jansa J, Erb A, Young S, Condron L, O’Callaghan M (2012) Response of soil microbial communities to contrasted histories of phosphorus fertilisation in pastures. Appl Soil Ecol 61:40–48 Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naïve bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73:5261–5267 Wang Y, Zhu G, Song L, Wang S, Yin C (2014) Manure fertilization alters the population of ammonia-oxidizing bacteria rather than ammonia-oxidizing archaea in a paddy soil. J Basic Microbiol 54:190–197 Wei F, Hao M (2011) Effects of long-term fertilization on soil water and nutrient with Triticum aestivum L. succession in dryland of Loess Plateau. Sci Soil Water Conserv 9:104–109 Wessén E, Hallin S, Philippot L (2010) Differential responses of bacterial and archaeal groups at high taxonomical ranks to soil management. Soil Biol Biochem 42:1759–1765 Whitman WB, Coleman DC, Wiebe WJ (1998) Prokaryotes: the unseen majority. Proc Natl Acad Sci U S A 95:6578–6583 Wu M, Qin H, Chen Z, Wu J, Wei W (2011) Effect of long-term fertilization on bacterial composition in rice paddy soil. Biol Fert Soils 47:397–405 Yao M, Rui J, Dai Y, Bai Y, Heděnec P, Wang J, Zhang S, Pei K, Liu C, Wang Y, He Z, Frouz J, Li X (2014) Rate-specific responses of prokaryotic diversity and structure to nitrogen deposition in the Leymus chinensis steppe. Soil Biol Biochem 79:81–90 Youssef NH, Farag IF, Rinke C, Hallam SJ, Woyke T, Elshahed MS (2015) In silico analysis of the metabolic potential and niche specialization of Candidate Phylum “Latescibacteria” (WS3). PLoS One 10:e0127499 Zhalnina K, de Quadros PD, Gano KA, Davis-Richardson A, Fagen JR, Brown CT, Giongo A, Drew JC, Sayavedra-Soto LA, Arp DJ, Camargo FA, Daroub SH, Clark IM, McGrath SP, Hirsch PR, Triplett EW (2013) Ca. Nitrososphaera and Bradyrhizobium are inversely correlated and related to agricultural practices in long-term field experiments. Front Microbiol 4:104 Zhalnina KV, Dais R, Leonard MT, Dorr de Quadros P, Camargo FA, Drew JC, Farmerie WG, Daroub SH, Triplett EW (2014) Genome sequence of Candidatus Nitrososphaera evergladensis from group I.1b enriched from everglades soil reveals novel genomic features of the ammonia-oxidizing archaea. PLoS One 9:e101648 Zhang QC, Shamsi IH, Xu DT, Wang GH, Lin XY, Jilani G, Hussain N, Chaudhry AN (2012) Chemical fertilizer and organic manure inputs in soil exhibit a vice versa pattern of microbial community structure. Appl Soil Ecol 57:1–8 Zhao B, Chen J, Zhang J, Xin X, Hao X (2013) How different long-term fertilization strategies influence crop yield and soil properties in a maize field in the North China Plain. J Plant Nutr Soil Sci 176:99–109 Zhengchao Z, Zhuoting G, Zhouping S, Fuping Z (2013) Effects of long-term repeated mineral and organic fertilizer applications on soil organic carbon and total nitrogen in a semi-arid cropland European. J Agron 45:20–26 Zhong WH, Cai ZC (2007) Long-term effects of inorganic fertilizers on microbial biomass and community functional diversity in a paddy soil derived from quaternary red clay. Appl Soil Ecol 36:84–91 Zhu XM, Li YS, Peng XL, Zhang SG (1983) Soils of the loess region in China. Geoderma 29:237–255 Zimmerman N, Izard J, Klatt C, Zhou J, Aronson E (2014) The unseen world: environmental microbial sequencing and identification methods for ecologists. Front Ecol Environ 12:224–231