Soil microbial communities changed with a continuously monocropped processing tomato system

References

• Acosta-Martínez V, Burow G, Zobeck TM, Allen VG. 2010. Soil microbial communities and function in alternative systems to continuous cotton. Soil Sci Soc Am J. 74:1181–1192. doi: 10.2136/sssaj2008.0065
   Web of Science ®Google Scholar
• Allison SD. 2012. A trait-based approach for modelling microbial litter decomposition. Ecol Lett. 15:1058–1070. doi: 10.1111/j.1461-0248.2012.01807.x
   PubMed Web of Science ®Google Scholar
• Anderson JPE, Domsch KH. 1978. A physiological method for the quantitative measurement of microbial biomass in soils. Soil Biol Biochem. 10:215–221. doi: 10.1016/0038-0717(78)90099-8
   Web of Science ®Google Scholar
• Berendsen RL, Pieterse CM, Bakker PA. 2012. The rhizosphere microbiome and plant health. Trends Plant Sci. 17:478–486. doi: 10.1016/j.tplants.2012.04.001
   PubMed Web of Science ®Google Scholar
• Bever JD, Platt TG, Morton ER. 2012. Microbial population and community dynamics on plant roots and their feedbacks on plant communities. Annu Rev Microbiol. 66:265–283. doi: 10.1146/annurev-micro-092611-150107
   PubMed Web of Science ®Google Scholar
• Bossio D, Girvan MS, Verchot L, Bullimore J, Borelli T, Albrecht A, Scow K, Ball AS, Pretty J, Osborn AM. 2005. Soil microbial community response to land use change in an agricultural landscape of western Kenya. Microbial Eco. 49:50–62. doi: 10.1007/s00248-003-0209-6
   PubMed Web of Science ®Google Scholar
• Brookes PC, Powlson DS, Jenkinson DS. 1982. Measurement of microbial biomass phosphorus in soil. Soil Bio Biochem. 14:319–329. doi: 10.1016/0038-0717(82)90001-3
   Web of Science ®Google Scholar
• Ding XF, Wu CD, Huang J, Zhou RQ. 2015. Interphase microbial community characteristics in the fermentation cellar of Chinese Luzhou-flavor liquor determined by PLFA and DGGE profiles. Food Res Int. 72:16–24. doi: 10.1016/j.foodres.2015.03.018
   Web of Science ®Google Scholar
• Fang SZ, Liu D, Tian Y, Deng SP, Shang XL. 2013. Tree species composition influences enzyme activities and microbial biomass in the rhizosphere: a rhizobox approach. PloS One. 8(4):e61461. doi: 10.1371/journal.pone.0061461
   PubMed Web of Science ®Google Scholar
• Feng Y, Motta A, Reeves D, Burmester C, Van Santen E, Osborne J. 2003. Soil microbial communities under conventional-till and no-till continuous cotton systems. Soil Bio Biochem. 35:1693–1703. doi: 10.1016/j.soilbio.2003.08.016
   Web of Science ®Google Scholar
• Ferris MJ, Ward DM. 1997. Seasonal distributions of dominant 16S rRNA-defined populations in a hot spring microbial mat examined by denaturing gradient gel electrophoresis. Appl Environ Microb. 63:1375–1381.
   PubMed Web of Science ®Google Scholar
• Francisco R, Stone D, Creamer RE, Sousa JP, Morais PV. 2016. European scale analysis of phospholipid fatty acid composition of soils to establish operating ranges. Appl Soil Ecol. 97:49–60. doi: 10.1016/j.apsoil.2015.09.001
   Web of Science ®Google Scholar
• Frostegård Å, Bååth E. 1996. The use of phospholipid fatty acid analysis to estimate bacterial and fungal biomass in soil. Biol Fert Soils. 22:59–65. doi: 10.1007/BF00384433
   Web of Science ®Google Scholar
• Frostegård Å, Tunlid A, Bååth E. 1993. Phospholipid fatty acid composition, biomass, and activity of microbial communities from two soil types experimentally exposed to different heavy metals. Appl Environ Microb. 59:3605–3617.
   PubMed Web of Science ®Google Scholar
• Garland JL, Mills AL. 1991. Classification and characterization of heterotrophic microbial communities on the basis of patterns of community-level sole-carbon-source utilization. Appl Environ Microb. 57:2351–2359.
   PubMed Web of Science ®Google Scholar
• Ge T, Li B, Zhu Z, Hu Y, Yuan H, Dorodnikov M, Jones DL, Wu J, Kuzyakov Y. 2017. Rice rhizodeposition and its utilization by microbial groups depends on N fertilization. Biol Fert Soils. 53:37–48. doi: 10.1007/s00374-016-1155-z
   Web of Science ®Google Scholar
• Gentry LF, Ruffo ML, Below FE. 2013. Identifying factors controlling the continuous corn yield penalty. Agron J. 105:295–303. doi: 10.2134/agronj2012.0246
   Web of Science ®Google Scholar
• Grayston S, Campbell C, Bardgett R, Mawdsley J, Clegg C, Ritz K, Griffiths B, Rodwell J, Edwards S, Davies W. 2004. Assessing shifts in microbial community structure across a range of grasslands of differing management intensity using CLPP, PLFA and community DNA techniques. Appl Soil Ecol. 25:63–84. doi: 10.1016/S0929-1393(03)00098-2
   Web of Science ®Google Scholar
• Guan SY. 1986. Soil enzyme and its research methods. Agricultural, Beijing (in Chinese).
   Google Scholar
• Guo ZY, Kong CH, Wang JG, Wang YF. 2011. Rhizosphere isoflavones (daidzein and genistein) levels and their relation to the microbial community structure of mono-cropped soybean soil in field and controlled conditions. Soil Bio Biochem. 43:2257–2264. doi: 10.1016/j.soilbio.2011.07.022
   Web of Science ®Google Scholar
• Hao X, Liu S, Wu J, Hu R, Tong C, Su Y. 2008. Effect of long-term application of inorganic fertilizer and organic amendments on soil organic matter and microbial biomass in three subtropical paddy soils. Nutr Cycl Agroecosys. 81:17–24. doi: 10.1007/s10705-007-9145-z
   Web of Science ®Google Scholar
• Herrmann R, Shann J. 1997. Microbial community changes during the composting of municipal solid waste. Microbial Ecol. 33:78–85. doi: 10.1007/s002489900010
   PubMed Web of Science ®Google Scholar
• Huang LF, Song LX, Xia XJ, Mao WH, Shi K, Zhou Y-H, Yu JQ. 2013. Plant-soil feedbacks and soil sickness: from mechanisms to application in agriculture. J Chem Ecol. 39:232–242. doi: 10.1007/s10886-013-0244-9
   PubMed Web of Science ®Google Scholar
• Jenkinson DS. 1988. Determination of microbial biomass carbon and nitrogen in soil.
   Google Scholar
• Jiang GY, Liu JG, Li YB. 2015. Allelochemicals from cotton (Gossypium hirsutum) rhizosphere soil: inhibitory effects on cotton seedlings. Allelopathy J. 35:153–162.
   Web of Science ®Google Scholar
• Joergensen RG, Potthoff M. 2005. Microbial reaction in activity, biomass, and community structure after long-term continuous mixing of a grassland soil. Soil Bio Biochem. 37:1249–1258. doi: 10.1016/j.soilbio.2004.11.021
   Web of Science ®Google Scholar
• Keiblinger KM, Hall EK, Wanek W, Szukics U, Hämmerle I, Ellersdorfer G, Böck S, Strauss J, Sterflinger K, Richter A. 2010. The effect of resource quantity and resource stoichiometry on microbial carbon-use-efficiency. FEMS Microbiol Ecol. 73:430–440.
   PubMed Web of Science ®Google Scholar
• Klose S, Acostamartinez V, Ajwa HA. 2006. Microbial community composition and enzyme activities in a sandy loam soil after fumigation with methyl bromide or alternative biocides. Soil Bio Biochem. 38:1243–1254. doi: 10.1016/j.soilbio.2005.09.025
   Web of Science ®Google Scholar
• Li CG, Li XM, Kong WD, Ying W, Wang JG. 2010. Effect of monoculture soybean on soil microbial community in the Northeast China. Plant Soil. 330:423–433. doi: 10.1007/s11104-009-0216-6
   Web of Science ®Google Scholar
• Li JG, Ren GD, Jia ZJ, Dong YH. 2014. Composition and activity of rhizosphere microbial communities associated with healthy and diseased greenhouse tomatoes. Plant Soil. 380:337–347. doi: 10.1007/s11104-014-2097-6
   Web of Science ®Google Scholar
• Liang C, Jesus EDC, Duncan DS, Jackson RD, Tiedje JM, Balser TC. 2012. Soil microbial communities under model biofuel cropping systems in southern Wisconsin, USA: impact of crop species and soil properties. Appl Soil Ecol. 54:24–31. doi: 10.1016/j.apsoil.2011.11.015
   Web of Science ®Google Scholar
• Luo P, Han X, Wang Y, Han M, Shi H, Liu N. 2015. Influence of long-term fertilization on soil microbial biomass, dehydrogenase activity, and bacterial and fungal community structure in a brown soil of northeast China. Ann Microbiol. 65:533–542. doi: 10.1007/s13213-014-0889-9
   PubMed Web of Science ®Google Scholar
• Lupwayi NZ, Lafond GP, May WE, Holzapfel CB, Lemke RL. 2012. Intensification of field pea production: impact on soil microbiology. Agron J. 104:1189–1196. doi: 10.2134/agronj2012.0046
   Web of Science ®Google Scholar
• Mahmoudi N, Robeson MS, Castro HF, Fortney JL, Techtmann SM, Joyner DC, Paradis CJ, Pfiffner SM, Hazen TC. 2015. Microbial community composition and diversity in Caspian Sea sediments. FEMS Microbiol Ecol. 91:1–11. doi: 10.1093/femsec/fiu013
   PubMed Web of Science ®Google Scholar
• Mccarthy CM, Murray L. 1996. Viability and metabolic features of bacteria indigenous to a contaminated deep aquifer. Microbial Ecol. 32:305–321. doi: 10.1007/BF00183065
   PubMed Web of Science ®Google Scholar
• Myers RM, Fischer SG, Lerman LS, Maniatis T. 1985. Nearly all single base substitutions in DNA fragments joined to a GC-clamp can be detected by denaturing gradient gel electrophoresis. Nucleic Acids Res. 13:3131–3145. doi: 10.1093/nar/13.9.3131
   PubMed Web of Science ®Google Scholar
• Nayyar A, Hamel C, Lafond G, Gossen BD, Hanson K, Germida J. 2009. Soil microbial quality associated with yield reduction in continuous-pea. Appl Soil Ecol. 43:115–121. doi: 10.1016/j.apsoil.2009.06.008
   Web of Science ®Google Scholar
• Paul EA, Clark FE. 1989. Soil microbiology and biochemistry. Sandiego, CA: Academic Press.
   Google Scholar
• Rutigliano FA, Romano M, Marzaioli R, Baglivo I, Baronti S, Miglietta F, Castaldi S. 2014. Effect of biochar addition on soil microbial community in a wheat crop. Eur J Soil Biol. 60:9–15. doi: 10.1016/j.ejsobi.2013.10.007
   Web of Science ®Google Scholar
• Sparling GP. 1997. Soil microbial biomass, activity and nutrient cycling as indicators of soil health. In: Pankhurst CE, Doube BM, Gupta VVSR, editors. Biological indicators of soil health. Wallingford: CAB International; p. 97–119.
   Google Scholar
• Sui Y, Jiao X, Liu X, Zhang X, Ding G. 2013. Response of soil microbial biomass and enzyme activity to soil fertilization in an eroded farmland of Chinese mollisols. Commun Soil Sci Plan. 44:2809–2819. doi: 10.1080/00103624.2013.811525
   Web of Science ®Google Scholar
• Tischer A, Potthast K, Hamer U. 2014. Land-use and soil depth affect resource and microbial stoichiometry in a tropical mountain rainforest region of southern Ecuador. Oecologia. 175:375–393. doi: 10.1007/s00442-014-2894-x
   PubMed Web of Science ®Google Scholar
• White DC, Davis WM, Nickels JS, King JD, Bobbie RJ. 1978. Determination of the sedimentary microbial biomass by extractible lipid phosphate. Oecologia. 40:51–62. doi: 10.1007/BF00388810
   Web of Science ®Google Scholar
• Xiao X, Cheng Z, Meng H, Liu L, Li H, Dong Y. 2013. Intercropping of green garlic (Allium sativum L.) induces nutrient concentration changes in the soil and plants in continuously cropped cucumber (Cucumis sativus L.) in a plastic tunnel. Plos One. 8: e62173. doi: 10.1371/journal.pone.0062173
   PubMed Web of Science ®Google Scholar
• Xiong W, Li Z, Liu H, Xue C, Zhang R, Wu H, Li R, Shen Q. 2015. The effect of long-term continuous cropping of black pepper on soil bacterial communities as determined by 454 pyrosequencing. Plos One. 10: e0136946. doi: 10.1371/journal.pone.0136946
   PubMed Web of Science ®Google Scholar
• Zelles L. 1999. Fatty acid patterns of phospholipids and lipopolysaccharides in the characterisation of microbial communities in soil: a review. Biol Fert Soils. 29:111–129. doi: 10.1007/s003740050533
   Web of Science ®Google Scholar
• Zelles L, Bai QY, Rackwitz R, Chadwick D, Beese F. 1995. Determination of phospholipid- and lipopolysaccharide-derived fatty acids as an estimate of microbial biomass and community structures in soils. Biol Fert Soils. 19:115–123. doi: 10.1007/BF00336146
   Web of Science ®Google Scholar
• Zhang Q, Zhou W, Liang G, Sun J, Wang X, He P. 2015. Distribution of soil nutrients, extracellular enzyme activities and microbial communities across particle-size fractions in a long-term fertilizer experiment. Appl Soil Ecol. 94:59–71. doi: 10.1016/j.apsoil.2015.05.005
   Web of Science ®Google Scholar
• Zhang W, Long X, Huo X, Chen Y, Lou K. 2013. 16S rRNA-based PCR-DGGE analysis of actinomycete communities in fields with continuous cotton cropping in Xinjiang, China. Microbial Ecol. 66:385–393. doi: 10.1007/s00248-012-0160-5
   PubMed Web of Science ®Google Scholar
• Zhao J, Zeng Z, He X, Chen H, Wang K. 2015. Effects of monoculture and mixed culture of grass and legume forage species on soil microbial community structure under different levels of nitrogen fertilization. Eur J Soil Biol. 68:61–68. doi: 10.1016/j.ejsobi.2015.03.008
   Web of Science ®Google Scholar
• Zhou X, Gao D, Liu J, Qiao P, Zhou X, Lu H, Wu X, Liu D, Jin X, Wu F. 2014. Changes in rhizosphere soil microbial communities in a continuously monocropped cucumber (Cucumis sativus L.) system. Eur J Soil Biol. 60:1–8. doi: 10.1016/j.ejsobi.2013.10.005
   Web of Science ®Google Scholar
• Zhou X, Wu F. 2013. Artificially applied vanillic acid changed soil microbial communities in the rhizosphere of cucumber (Cucumis sativus L.). Can J Soil Sci. 93:13–21. doi: 10.4141/cjss2012-039
   Web of Science ®Google Scholar
• Zhou X, Yu G, Wu F. 2012. Soil phenolics in a continuously mono-cropped cucumber (Cucumis sativus L.) system and their effects on cucumber seedling growth and soil microbial communities. Eur J Soil Biol. 63:332–340. doi: 10.1111/j.1365-2389.2012.01442.x
   Web of Science ®Google Scholar
• Zogg GP, Zak DR, Ringelberg DB, White DC, MacDonald NW, Pregitzer KS. 1997. Compositional and functional shifts in microbial communities due to soil warming. Soil Sci Soc Am J. 61:475–481. doi: 10.2136/sssaj1997.03615995006100020015x
   Web of Science ®Google Scholar