Reducing chemical fertilizer use mitigates obstacles in intensive monocropping of cucumber: a probable role of Pseudomonads in the process

References

• Acosta-Martínez V, Upchurch DR, Schubert AM, Porter D, Wheeler T. 2004. Early impacts of cotton and peanut cropping systems on selected soil chemical, physical, microbiological and biochemical properties. Biol Fert Soils. 40:44–54. doi: 10.1007/s00374-004-0745-3
   Web of Science ®Google Scholar
• Adesemoye AO, Torbert HA, Kloepper JW. 2008. Enhanced plant nutrient use efficiency with PGPR and AMF in an integrated nutrient management system. Can J Microbiol. 54:876–886. doi: 10.1139/W08-081
   PubMed Web of Science ®Google Scholar
• Adesemoye AO, Torbert HA, Kloepper JW. 2009. Plant growth-promoting rhizobacteria allow reduced application rates of chemical fertilizers. Microb Ecol. 58:921–929. doi: 10.1007/s00248-009-9531-y
   PubMed Web of Science ®Google Scholar
• Agaras BC, Scandiani M, Luque A, Fernández L, Farina F, Carmona M, Gally M, Romero A, Wall L, Valverde C. 2015. Quantification of the potential biocontrol and direct plant growth promotion abilities based on multiple biological traits distinguish different groups of Pseudomonas spp. isolates. Biol Control. 90:173–186. doi: 10.1016/j.biocontrol.2015.07.003
   Web of Science ®Google Scholar
• Al-Sa’di AM, Drenth A, Deadman ML, de Cock AWAM, Aitken EAB. 2007. Molecular characterization and pathogenicity of Pythium species associated with damping-off in greenhouse cucumber (Cucumis sativus) in Oman. Plant Pathol. 56:140–149. doi: 10.1111/j.1365-3059.2006.01501.x
   Web of Science ®Google Scholar
• Bongiovanni R, Lowenberg-Deboer J. 2004. Precision agriculture and sustainability. Precis Agric. 5:359–387. doi: 10.1023/B:PRAG.0000040806.39604.aa
   Google Scholar
• Bulluck III LR, Ristaino JB. 2002. Effect of synthetic and organic soil fertility amendments on southern blight, soil microbial communities, and yield of processing tomatoes. Phytopathology. 92:181–189. doi: 10.1094/PHYTO.2002.92.2.181
   PubMed Web of Science ®Google Scholar
• Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl MW, Shipley GL, et al. 2009. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem. 55:611–622. doi: 10.1373/clinchem.2008.112797
   PubMed Web of Science ®Google Scholar
• Chaparro JM, Sheflin AM, Manter DK, Vivanco JM. 2012. Manipulating the soil microbiome to increase soil health and plant fertility. Biol Fert Soils. 48:489–499. doi: 10.1007/s00374-012-0691-4
   Web of Science ®Google Scholar
• Ding C, Shen Q, Zhang R, Chen W. 2013. Evaluation of rhizosphere bacteria and derived bio-organic fertilizers as potential biocontrol agents against bacterial wilt (Ralstonia solanacearum) of potato. Plant Soil. 366:453–466. doi: 10.1007/s11104-012-1425-y
   Web of Science ®Google Scholar
• Dowling DN, O’Gara F. 1994. Metabolites of Pseudomonas involved in the biocontrol of plant disease. Trends Biotechnol. 12:133–141. doi: 10.1016/0167-7799(94)90091-4
   Web of Science ®Google Scholar
• Funnell-Harris DL, Pedersen JF, Sattler SE. 2010. Soil and root populations of fluorescent Pseudomonas spp. associated with seedlings and field-grown plants are affected by sorghum genotype. Plant Soil. 335:439–455. doi: 10.1007/s11104-010-0432-0
   Web of Science ®Google Scholar
• Funnell-Harris DL, Sattler SE, Pedersen JF. 2013. Characterization of fluorescent Pseudomonas spp. associated with roots and soil of two sorghum genotypes. Eur J Plant Pathol. 136:469–481. doi: 10.1007/s10658-013-0179-6
   Web of Science ®Google Scholar
• García-Orenes F, Morugán-Coronado A, Zornoza R, Scow K. 2013. Changes in soil microbial community structure influenced by agricultural management practices in a mediterranean agro-ecosystem. PLoS ONE. 8:e80522. doi: 10.1371/journal.pone.0080522
   PubMed Web of Science ®Google Scholar
• Guo R, Li X, Christie P, Chen Q, Jiang R, Zhang F. 2008. Influence of root zone nitrogen management and a summer catch crop on cucumber yield and soil mineral nitrogen dynamics in intensive production systems. Plant Soil. 313:55–70. doi: 10.1007/s11104-008-9679-0
   Web of Science ®Google Scholar
• Kumar S, Pandey P, Maheshwari DK. 2009. Reduction in dose of chemical fertilizers and growth enhancement of sesame (Sesamum indicum L.) with application of rhizospheric competent Pseudomonas aeruginosa LES4. Eur J Soil Biol. 45:334–340. doi: 10.1016/j.ejsobi.2009.04.002
   Web of Science ®Google Scholar
• Li Y, Zhang W, Ma L, Huang G, Oenema O, Zhang F, Dou Z. 2013. An analysis of China's fertilizer policies: impacts on the industry food security, and the environment. J Environ Qual. 42:972–981. doi: 10.2134/jeq2012.0465
   PubMed Web of Science ®Google Scholar
• Liang X, Gao Y, Zhang X, Tian Y, Zhang Z, Gao L. 2014. Effect of optimal daily fertigation on migration of water and salt in soil, root growth and fruit yield of cucumber (Cucumis sativus L.) in solar-greenhouse. PLoS ONE. 9:e86975. doi: 10.1371/journal.pone.0086975
   PubMed Web of Science ®Google Scholar
• Lievens B, Claes L, Vakalounakis DJ, Vanachter ACRC, Thomma BPHJ. 2007. A robust identification and detection assay to discriminate the cucumber pathogens Fusarium oxysporum f. sp. cucumerinum and f. sp. radicis-cucumerinum. Envion Microbiol. 9:2145–2161. doi: 10.1111/j.1462-2920.2007.01329.x
   PubMed Web of Science ®Google Scholar
• Lithourgidis AS, Vlachostergios DN, Dordas CA, Damalas CA. 2011. Dry matter yield, nitrogen content, and competition in pea - cereal intercropping systems. Eur J Agron. 34:287–294. doi: 10.1016/j.eja.2011.02.007
   Web of Science ®Google Scholar
• Liu M, Hu F, Chen X, Huang Q, Jiao J, Zhang B, Li H. 2009. Organic amendments with reduced chemical fertilizer promote soil microbial development and nutrient availability in a subtropical paddy field: the influence of quantity, type and application time of organic amendments. Appl Soil Ecol. 42:166–175. doi: 10.1016/j.apsoil.2009.03.006
   Web of Science ®Google Scholar
• Ma B, Wang H, Dsouza M, Lou J, He Y, Dai Z, Brookes PC, Xu J, Gilbert JA. 2016. Geographic patterns of co-occurrence network topological features for soil microbiota at continental scale in eastern China. ISME J. doi:10.1038/ismej.2015.261.
   Web of Science ®Google Scholar
• Matson PA, Parton WJ, Power AG, Swift MJ. 1997. Agricultural intensification and ecosystem properties. Science. 277:504–509. doi: 10.1126/science.277.5325.504
   PubMed Web of Science ®Google Scholar
• Mazurier S, Corberand T, Lemanceau P, Raaijmakers JM. 2009. Phenazine antibiotics produced by fluorescent pseudomonads contribute to natural soil suppressiveness to Fusarium wilt. ISME J. 3:977–991. doi: 10.1038/ismej.2009.33
   PubMed Web of Science ®Google Scholar
• Muyzer G, de Waal EC, Uitterlinden AG. 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.
   PubMed Web of Science ®Google Scholar
• Nathani NM, Patel AK, Dhamannapatil PS, Kothari RK, Singh KM, Joshi CG. 2013. Comparative evaluation of rumen metagenome community using qPCR and MG-RAST. AMB Express. 3:55(1-8). doi: 10.1186/2191-0855-3-55
   Web of Science ®Google Scholar
• O’Sullivan DJ, O’Gara F. 1992. Traits of fluorescent Pseudomonas spp. involved in suppression of plant root pathogens. Microbiol Mol Biol Rev. 56:662–676.
   Google Scholar
• Qiu M, Zhang R, Xue C, Zhang S, Li S, Zhang N, Shen Q. 2012. Application of bio-organic fertilizer can control Fusarium wilt of cucumber plants by regulating microbial community of rhizosphere soil. Biol Fert Soils. 48:807–816. doi: 10.1007/s00374-012-0675-4
   Web of Science ®Google Scholar
• Ryszkowski L, Szajdak L, Karg J. 1998. Effects of continuous cropping of rye on soil biota and biochemistry. Crit Rev Plant Sci. 17:225–244. doi: 10.1080/07352689891304221
   Web of Science ®Google Scholar
• Scarlett K, Tesoriero L, Daniel R, Guest D. 2013. Detection and quantification of Fusarium oxysporum f. sp. cucumerinum in environmental samples using a specific quantitative PCR assay. Eur J Plant Pathol. 137:315–324. doi: 10.1007/s10658-013-0244-1
   Web of Science ®Google Scholar
• Schippers B, Bakker AW, Bakker PAHM. 1987. Interactions of deleterious and beneficial rhizosphere microorganisms and the effect of cropping practices. Ann Rev Phytopathol. 25:339–358. doi: 10.1146/annurev.py.25.090187.002011
   Web of Science ®Google Scholar
• Schneemann I, Wiese J, Kunz AL, Imhoff JF. 2011. Genetic approach for the fast discovery of phenazine producing bacteria. Mar Drugs. 9:772–789. doi: 10.3390/md9050772
   PubMed Web of Science ®Google Scholar
• Shen W, Lin X, Gao N, Zhang H, Yin R, Shi W, Duan Z. 2008. Land use intensification affects soil microbial populations, functional diversity and related suppressiveness of cucumber Fusarium wilt in China’s Yangtze River Delta. Plant Soil. 306:117–127. doi: 10.1007/s11104-007-9472-5
   Web of Science ®Google Scholar
• Six J, Frey SD, Thiet RK, Batten KM. 2006. Bacterial and fungal contributions to carbon sequestration in agroecosystems. Soil Sci Soc Am J. 70:555–569. doi: 10.2136/sssaj2004.0347
   Web of Science ®Google Scholar
• Smith LED, Siciliano G. 2015. A comprehensive review of constraints to improved management of fertilizers in China and mitigation of diffuse water pollution from agriculture. Agr Ecosyst Environ. 209:15–25. doi: 10.1016/j.agee.2015.02.016
   Web of Science ®Google Scholar
• Spadaro D, Gullino ML. 2005. Improving the efficacy of biocontrol agents against soilborne pathogens. Crop Prot. 24:601–613. doi: 10.1016/j.cropro.2004.11.003
   Web of Science ®Google Scholar
• Sun B, Peng Y, Yang H, Li Z, Gao Y, Wang C, Yan Y, Liu Y. 2014. Alfalfa (Medicago sativa L.)/maize (Zea mays L.) intercropping provides a feasible way to improve yield and economic incomes in farming and pastoral areas of northeast China. PLoS ONE. 9:e110556. doi: 10.1371/journal.pone.0110556
   Google Scholar
• Svercel M, Duffy B, Défago G. 2007. PCR amplification of hydrogen cyanide biosynthetic locus hcnAB in Pseudomonas spp. J Microbiol Meth. 70:209–213. doi: 10.1016/j.mimet.2007.03.018
   PubMed Web of Science ®Google Scholar
• Tester CF. 1990. Organic amendment effects on physical and chemical properties of a sandy soil. Soil Sci Soc Am J. 54:827–831. doi: 10.2136/sssaj1990.03615995005400030035x
   Web of Science ®Google Scholar
• Tian Y, Gao L. 2014. Bacterial diversity in the rhizosphere of cucumbers grown in soils covering a wide range of cucumber cropping histories and environmental conditions. Microb Ecol. 68:794–806. doi: 10.1007/s00248-014-0461-y
   PubMed Web of Science ®Google Scholar
• Wallenstein MD, McNulty S, Fernandez IJ, Boggs J, Schlesinger WH. 2006. Nitrogen fertilization decreases forest soil fungal and bacterial biomass in three long-term experiments. Forest Ecol Manag. 222:459–468. doi: 10.1016/j.foreco.2005.11.002
   Web of Science ®Google Scholar
• White TJ, Bruns T, Lee S, Taylor J. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: PCR: protocols and applications—a laboratory manual. New York: Academic Press; p. 315–322.
   Google Scholar
• Widmer F, Seidler RJ, Gillevet PM, Watrud LS, Di Giovanni GD. 1998. A highly selective PCR protocol for detecting 16S rRNA genes of the genus Pseudomonas (Sensu Stricto) in environmental samples. Appl Environ Microbiol. 64:2545–2553.
   PubMed Web of Science ®Google Scholar
• Wu K, Yuan S, Wang L, Shi J, Zhao J, Shen B, Shen Q. 2014. Effects of bio-organic fertilizer plus soil amendment on the control of tobacco bacterial wilt and composition of soil bacterial communities. Biol Fert soils. 50:961–971. doi: 10.1007/s00374-014-0916-9
   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
• Xue QY, Ding GC, Li SM, Yang Y, Lan CZ, Guo JH, Smalla K. 2013. Rhizocompetence and antagonistic activity towards genetically diverse Ralstonia solanacearum strains–an improved strategy for selecting biocontrol agents. Appl Microbiol Biotechnol. 97:1361–1371. doi: 10.1007/s00253-012-4021-4
   PubMed Web of Science ®Google Scholar
• Yao H, Jiao X, Wu F. 2006. Effects of continuous cucumber cropping and alternative rotations under protected cultivation on soil microbial community diversity. Plant Soil. 284:195–203. doi: 10.1007/s11104-006-0023-2
   Web of Science ®Google Scholar
• Yu JQ, Shou SY, Qian YR, Zhu ZJ, Hu WH. 2000. Autotoxic potential of cucurbit crops. Plant Soil. 223:149–153. doi: 10.1023/A:1004829512147
   Web of Science ®Google Scholar
• Yu JQ, Ye SF, Zhang MF, Hu WH. 2003. Effects of root exudates and aqueous root extracts of cucumber (Cucumis sativus) and allelochemicals, on photosynthesis and antioxidant enzymes in cucumber. Biochem Syst Ecol. 31:129–139. doi: 10.1016/S0305-1978(02)00150-3
   Web of Science ®Google Scholar
• Yu Z, Yang J, Amalfitano S, Yu X, Liu L. 2014. Effects of water stratification and mixing on microbial community structure in a subtropical deep reservoir. Sci Rep. 4:5821.
   PubMed Web of Science ®Google Scholar
• Zhao S, Liu D, Ling N, Chen F, Fang W, Shen Q. 2014. Bio-organic fertilizer application significantly reduces the Fusarium oxysporum population and alters the composition of fungi communities of watermelon Fusarium wilt rhizosphere soil. Biol Fert Soils. 50:765–774. doi: 10.1007/s00374-014-0898-7
   Web of Science ®Google Scholar
• Zhou X, Wu F. 2012. Dynamics of the diversity of fungal and Fusarium communities during continuous cropping of cucumber in the greenhouse. FEMS Microbiol Ecol. 80:469–478. doi: 10.1111/j.1574-6941.2012.01312.x
   PubMed Web of Science ®Google Scholar
• Zhou X, Yu G, Wu F. 2011. Effects of intercropping cucumber with onion or garlic on soil enzyme activities, microbial communities and cucumber yield. Eur J Soil Biol. 47:279–287. doi: 10.1016/j.ejsobi.2011.07.001
   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 Sci. 63:332–340. doi: 10.1111/j.1365-2389.2012.01442.x
   Web of Science ®Google Scholar