細菌在土壤中的移動主要受到土壤物理、土壤化學與生物因子的影響，但對於細菌細胞表面特性因子仍不清楚。本研究目的是設計一個土壤管柱系統快速模擬觀察細菌在土壤中移動，並測定不同特性之細菌在管柱內之移動速率，探討多種生物因子與移動之相關性。本研究設計一飽和水土壤管柱系統，將細菌接種至十公分高之土壤管柱後給予固定5 ± 0.1公分高之水壓，分析三小時期間所流出之濾液菌數，並於三小時後測定不同深度土壤之菌數。此外，本研究嘗試以即時定量聚合酶連鎖反應 (real-time PCR) 針對細菌之16S rRNA基因進行偵測。結果顯示乾熱滅菌法具有良好的滅菌效果，滅菌後的土壤土粒乾燥，較能填充均勻的土柱。水流流量會影響Serratia marcescens CC-YM2-1菌株通過土柱的速度，流量較多時，能帶動較多的菌通過土柱。隨著土壤黏粒含量的增加，S. marcescens CC-YM2-1通過土柱的速度變慢，且土壤黏粒含量對S. marcescens CC-YM2-1通過土柱的影響力大於土壤有機質。YEM培養基培養的Rhizobium sp. CC-SB136菌株通過砂質土柱的速度較以NB培養基培養的CC-SB136快，原因可能為生長在YEM培養基的CC-SB136產生較多分泌物質。比較三株Serratia marcescens菌株通過砂質土柱的速度發現，同菌屬菌種的不同菌株，通透土柱的速度會不同，經過鞭毛突變後不具有移動性的F1菌株比具運動性的野生株CH-1略有較多細胞通過土柱。本研究比較八株不同菌屬的細菌通過土柱的速度，結果發現革蘭氏陰性菌通過砂壤土柱的速度較革蘭氏陽性菌快。經比較發現細菌細胞壁組成對細菌通過土柱的影響力大於細菌的運動性。使用3F/4R引子對進行即時定量聚合酶連鎖反應，可以有效增殖DNA片段，並在一小時內即可被偵測到。本研究建議細菌細胞表面特性包括分泌物質與細胞壁組成是影響細菌通過土壤的重要因子，未來應用細菌到環境上進行生物復育及到農業上作為生物肥料的施用時，需要考慮細菌細胞表面特性來選擇合適的菌株。即時定量聚合酶連鎖反應靈敏且快速，未來可應用於偵測細菌在土壤移動的研究上。

Transport of microorganisms in the soil is affected by many factors such as physical, chemical and biological properties of soil. It is still being investigated for a clear understanding of the mechanisms of bacterial transport with an emphasis on the bacterial cell surface. The present study was undertaken to evaluate the transport behavior of bacteria in a specially designed flow-through saturated soil column. Based on the data obtained on transport velocity of bacteria the relationship between many biotic factors and bacterial transport was predicted. The influence of physiological characteristics of bacteria on transport in soil was examined in the soil column system with constant volumetric water flow. Experiment was carried out in a 10 cm long acrylic column packed with three different soil types with different texture. Total cells transported within different depth of column and in the eluants were calculated. Vertical translocation of the introduced bacteria was also visualized after 3 h. In addition, quantification of bacteria was performed by real-time PCR of bacterial 16S rDNA fragment amplified from pure culture. Homogeneous soil particles were packed into column after dry sterilization. Among the tested strains, strain Serratia marcescens (CC-YM2-1) showed better transport behavior in low clay content soil and high flow rate. It is hence, suggested that clay content of the soil plays a significant role in bacterial transport compared to organic matter content in soil. Introduced Rhizobium sp. (CC-SB136) was detected at higher number (10 fold) when YEM compared with NB was used as medium either in different depth of column or in the eluants probably due to the production of secondary metabolites. Significant difference was observed in the transport behavior of three Serratia marcescens strains indicating that even though they represent same species but, display wide physiological diversity. Gram-negative bacteria exhibited higher fractional recovery compared to Gram-positive strains of similar size. All the tested isolates were capable of producing specific pigments, favoring the tracking of bacterial transport behavior easily. The detection limit in real-time PCR amplification was 2 log CFU mL-1 reaction-1 showing higher sensitivity and usefulness of this technique in the detection of bacteria and its further applications in such kind of studies. Transport of Gram-positive strains resulted in a significantly lower number in comparison with Gram-negative strains at constant flow rate. These results hence indicate that cell wall characteristics and cellular secretions are the major biotic factors influencing the transport behavior of bacteria in soils. Hence, further studies are warranted to clearly derive the exact mechanisms of bacterial transport in the natural soil.

目錄
摘要 I
Abstract III
目錄 V
表次 VIII
圖次 X
壹、前言 1
貳、文獻回顧 3
一、影響細菌在土壤中移動的因子 3
(一)土壤物理因子 3
(二)土壤化學因子 4
(三)生物因子 6
(四)土壤管柱因子 8
二、偵測細菌的方法 8
(一)平板測定法 (plate count) 8
(二)螢光染劑 9
(三)基因工程標定 9
(四)放射性物質標定 10
(五)以分子生物學技術進行核酸偵測 10
三、細菌細胞壁結構的區別 11
(一)革蘭氏陽性菌 11
(二)革蘭氏陰性菌 12
參、材料與方法 13
一、土壤管柱試驗系統之建立 13
(一)土壤基本理化性質測定 13
(二)壓克力管柱設計 14
(三)土壤滅菌方法 15
(四)培養基配方 17
(五)固定水壓飽和土柱試驗系統 17
二、試驗菌株之培養及基本特性 21
(一)運動性測試 21
(二)革蘭氏染色 22
(三)菌種16S rRNA基因鑑定 23
(四)測試菌株資訊 28
三、利用即時定量聚合酶連鎖反應 (Real-time quantitative PCR) 偵測細菌之存在 34
(一)即時定量聚合酶連鎖反應之引子選擇 34
(二)即時定量聚合酶連鎖反應之條件最適化 34
(三)即時定量聚合酶連鎖反應之標準曲線測定 36
肆、結果與討論 38
一、固定水壓飽和土柱試驗系統的建立 38
(一)比較溼熱滅菌與乾熱滅菌對土壤外觀、pH、菌數與萃取DNA之影響 38
(二)水流流量對細菌通透土柱之影響 40
(三)土壤質地對細菌通透土柱之影響 43
二、生物因子對細菌通透土柱之影響 49
(一)培養基對細菌通透土柱之影響 49
(二)運動性對細菌通透土柱之影響 55
(三)細胞壁組成對細菌通透土柱之影響 60
三、以即時定量聚合酶連鎖反應分析菌株之可行性評估 67
伍、結論 73
陸、參考文獻 75




表次
表 一、三種土壤之基本性質分析 20
表 二、16S rDNA PCR試劑及濃度 25
表 三、16S rRNA基因定序用引子 26
表 四、BigDye試劑與濃度 27
表 五、十株菌株在NA培養基上生長72小時之狀態 30
表 六、所測試菌屬之生理特性 31
表 七、本研究測試菌株之16S rDNA序列比對結果 32
表 八、Serratia marcescens各菌株基因型和運動性的比較 32
表 九、本研究所測試菌株之革蘭氏染色及運動性試驗結果 33
表 十、即時定量PCR反應之試劑 37
表 十一、即時定量PCR各引子所增殖片段長度與黏合作用的溫度 37
表 十二、不同質地土壤土柱接入YM2-1菌株後水流平均流量、總濾液量與濾液總菌數的比較 48
表 十三、兩種培養基加入砂壤土柱後與接種以兩種培養基培養的Rhizobium sp. SB136到砂壤土柱後水流平均流量的比較 53
表 十四、Serratia marcescens各菌株平均流量、平均接入總菌數與濾液總菌數的比較 57
表 十五、八株菌株平均流量、平均接入總菌數與濾液總菌數的比較 66
表 十六、菌株Kocuria sp. CC-LTT-1經即時定量PCR增殖16S rDNA片段結果 69
表 十七、Kocuria sp. CC-LTT-1 DNA連續稀釋後經過即時定量PCR增殖16S rDNA片段結果 70
表 十八、Rhizobium sp. CC-SB136 DNA連續稀釋後經過即時定量PCR增殖16S rDNA片段結果 71
表 十九、七株菌株以3F/4R引子對，經過即時定量PCR增殖16S rDNA片段結果 72













圖次
圖 一、本研究所設計之壓克力管柱 16
圖 二、固定水壓飽和土柱試驗系統 19
圖 三、16S rDNA PCR操作條件 25
圖 四、BigDye反應操作條件 27
圖 五、即時定量PCR反應之操作條件 37
圖 六、砂質壤土經兩種滅菌處理之DNA電泳圖譜 39
圖 七、接入Serratia marcescens CC-YM2-1至砂質壤土柱三小時後，在兩種水流流量下不同深度土壤之菌數比較 41
圖 八、接入Serratia marcescens CC-YM2-1至砂質壤土柱三小時期間在兩種水流流量下不同時間所收集濾液之菌數比較 42
圖 九、三種質地土壤填充的土柱接入Serratia marcescens CC-YM2-1菌株三小時後，不同深度土柱之菌數比較 46
圖 十、三種質地土壤所填充的土柱接入Serratia marcescens CC-YM2-1三小時期間，不同時間所收集濾液之菌數比較 47
圖 十一、兩種培養基培養的Rhizobium sp. SB136菌株接種至砂壤土柱三小時後，不同深度土柱之菌數比較 51
圖 十二、兩種培養基培養的Rhizobium sp. SB136菌株接種至砂壤土柱後，三小時期間，不同時間所收集濾液之菌數比較 52
圖 十三、Rhizobium sp. CC-SB136生長於YEMA培養基24小時 54
圖 十四、Rhizobium sp. CC-SB136生長於NA培養基24小時 54
圖 十五、有無運動性的Serratia marcescens菌株接種至砂壤土柱三小時後，不同深度土柱的菌數比較 58
圖 十六、有無運動性的Serratia marcescens菌株CC-YM2-1、CH-1與F1接種至砂壤土柱於不同時期所收集濾液中菌數之比較 59
圖 十七、本研究測試菌株之親緣分類樹狀圖 (依據16S rDNA序列) 63
圖 十八、八株不同菌屬菌株接入砂壤土柱三小時後，不同深度土柱的菌數比較 64
圖 十九、八株不同菌屬菌株接入砂壤土柱後，三小時期間，收集不同時間濾液的菌數比較 65

李銘亮。2002。微生物生理學。藝軒圖書出版社。
Abu-Ashour, J., D.M. Joy, H. Lee, H.R. Whiteley, and S. Zelin. 1994. Transport of microorganisms through soil. Water Air and Soil Pollut. 75:141-158.
Ajithkumar B., V.P. Ajithkumar, R. Iriye, Y. Doi, and T. Sakai. 2003. Spore-forming Serratia marcescens subsp. sakuensis subsp. nov., isolated from a domestic wastewater treatment tank. In. J. Syst. Evol. Microbiol. 53:253-258.
Albinger, O., B.K. Biesemeyer, R.G. Arnold, and B.E. Logan. 1994. Effect of bacterial heterogeneity on adhesion to uniform collectors by monoclonal populations. FEMS Microbiol. Lett. 124:321.
Ammons, D., J. Rampersad, and G.E. Fox. 1998. A genomically modified marker strain of Escherichia coli. Curr Microbiol. 37:341-346.
Arya, M., I.S. Shergill, M. Williamson, L. Gommersall, N. Arya, and H.R. Patel. 2005. Basic principles of real-time quantitative PCR. Expert Rev. Mol. Diagn. 2:209-219.
Banks, M.K., W. Yu and R.S. Govindaraju. 2003. Bacterial adsorption and transport in saturated soil columns. J. Environ. Sci. Health. A Tox Hazard Subst. Environ. Eng. 38:2749-2758.
Barton, J.W., and R.M. Ford. 1995. Determination of effective transport coefficients for bacterial migration in sand columns. Appl. Environ. Microbiol. 61:3329-3335.
Becker, M.W., D.W. Metge, S.A. Collins, A.M. Shapiro and R.W. Harvey. 2003. Bacterial transport experiments in fractured crystalline bedrock. Ground Water. 41:682-689.
Becker, M.W., S.A. Collins, D.W. Metge, R.W. Harvry and A.M. Shapiro. 2004. Effect of cell physicochemical characteristics and motility on bacterial transport in groundwater. J. Contam. Hydrol. 69:195-213.
Bengtsson, G., and R. Lindqvist. 1995. Transport of soil bacteria controlled by density-dependent sorption kinetics. Water Resour. Res. 31:1247-1256.
Bitton, G., N. Lahav, and Y. Henis. 1974. Movement and retention of Klebsiella aerogenes in soil columns. Plant and Soil. 40:373-380.
Bosshard, P.P., R. Zbinden, and M. Altwegg. 2002. Paenibacillus turicensis sp. nov., a novel bacterium harbouring heterogeneities between 16S rRNA genes. Int. J. Syst. Bacteriol. 52:2241-2249
Bramer, C.O., P. Vandamme, L.F. da Silva, J.G.C. Gomez, and A. Steinbuchel. 2001. Burkholderia sacchari sp. nov., a polyhydroxyalkanoate-accumulating bacterium isolated from soil of a sugar-cane plantation in Brazil. In. J. Syst. Evol. Microbiol. 51:1709-1713.
Breitenbeck, G.A., H. Yang, and E.P. Dumigan. 1988. Water-facilitated by inoculant Bradyrhizobium in soils. Biol. Fert. Soils. 7:58-62.
Bremner, J.M. 1960. Determination of nitrogen in soil by the Kjeldahl method. J. Agric. Sci. 55:11-33.
Buonaurio R., V.M. Stravato, Y. Kosako, N. Fujiwara, T. Naka, K. Kobayashi, C. Cappelli, and E. Yabuuchi. 2002. Sphingomonas melonis sp. nov., a novel pathogen that causes brown spots on yellow Spanish melon fruits. Int. J. Syst. Evol. Microbiol. 52:2081-2087.
Burlage, R.S., Z.K. Yang, and T. Mehlhorn. 1996. A transposon for gerrn fluorescent protein transcriptional fusion: application for bacterial transport experiments. Gene 173:53-58.
Camesano, T.A., B.E. Logan. 1998. Influence of fluid velocity and cell concentration on the transport of motile and nonmotile bacteria in porous media. Environ. Sci. Technol. 32:1699-1708.
Camper, A.K., J.T. Hayes, P.J. Sturman, W.L. Jones, and A.B. Cunningham. 1993. Effects of motility and adsorption rate coefficient on transport of bacteria through saturated porous media. Appl. Environ. Microbiol. 59:3455-3462.
Chen, J., and B. Koopman. 1997. Effect of fluorochromes on bacterial surface properties and interaction with granular media. Appl. Environ. Microbiol. 63:3941-3945.
Corapcioglu, M.Y., and S.H. Kim. 1995. Modeling facilitated contaminant transport by mobile bacteria. Water Resour. Res. 31:2639-2647.
Cowan, S. T. (1974). Cowan and Steel’s Manual for the Identification of Medical Bacteria, 2nd edn. Cambridge: Cambridge University Press.
Crane, S.R., and J.A. Moore. 1984. Bacteria pollution of groundwater: a review. Water Air and Soil Pollution. 22: 67-83.
Davies, B.E. 1974. Loss-on-ignition as an estimate of soil organic matter, Soil Sci. Soc. Am. Proc. 38:150-151.
DeFlaun, M.F., M.E. Fuller, P. Zhang, W.P. Johnson, B.J. Mailloux, W.E. Holben, W.P. Kovacik, D.L. Balkwill, and T.C. Onstott. 2001. Comparison of methods for monitoring bacterial transport in the subsurface. J. Microbiol. Methods. 47:219-231.
Dickson, J.S., and M. Koohmaraie. 1989. Cell surface charge characteristics and their relationship to bacterial attachment to meat surfaces. Appl. Environ. Microbiol. 55:832-836.
Edwards, U., T. Rogall, H. Blocker, M. Emde, and E.C. Bottger. 1989. Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA. Nucleic Acids Res. 17:7843-7853.
Eleaume, H., and S. Jabbouri. 2005. Comparison of two standardisation methods in real-time quantitative RT-PCR to follow Staphylococcus aureus genes expression during in vitro growth. J. Microbiol. Methods. 2004 59:363-70.
Fontes, D.E., A.L. Mills, G..M. Hornbeger, and J.S. Herman. 1991. Physical and chemical factors influencing transport of microorganisms through porous media. Appl. Environ. Microbiol. 57:2473-2481.
Gee, G.W., and J.W. Bauder. 1986. Particle-size analysis. In A. Klute (ed.), Methods of Soil Analysis, Part 1. 2nd ed. Agronomy. 9:383-411.
Graham, D.W., D.G. Korich, R.P. Leblanc, N.A. Sinclair, and R.G. Arnold. 1992. Applications of a colorimetric plate assay for soluble methane monooxygenase activity. Appl. Environ. Microbiol. 58:2231-2236.
Gué, M., V. Dupont, A. Dufour, and O. Sire. 2001. Bacterial swarming: a biochemical time-resolved FTIR-ATR study of proteus mirabilis swarm-cell differentiation. Biochemistry. 40:11938-11945.
Guimares, V.F., I.V. Cruz, A. N. Hagler, L.C. Mendonca-Hagler, and J.D. van Elsas. 1997. Transport of a genetically modified Pseudomonas fluorescens and its parent strain through undisturbed tropical soil cores. Appl. Soil Ecol. 7:41-50
Hall, J.A., B.J. Mailloux, T.C. Onstott, T.D. Scheibe, M.E. Fuller, H. Dong, and M.F. DeFlaun. 2005. Physical vesus chemical effects on bacterial and bromide transport as determined from on site sediment column pulse experiments. J. Contam. Hydrol. 76:295-314.
Harvey, R.W., Kinner, N.E., MacDonald, D., Metge, D.W. and Bunn, A. 1993. Role of physical heterogeneity in the interpretation of small-scale laboratory and field observations of microorganism, microsphere, and bromide transport through aquifer sediments. Water Resour. Res. 29:2713-2721.
Harvey, R.W., L. George, R. Smith, and D. LeBlanc. 1989. Transport of microspheres and indigenous bacteria through a sandy aquifer: results of natural- and forced-gradient tracer experiments. Environ. Sci. Technol. 23:51-56.
Hekman, W.E., C.E. Heijnen, S. Burgers, J.A. Vanveen, and J.D. Vanelsas. 1995. Transport of bacterial inoculants through intact cores of 2 different soils as affected by water percolation and the presence of wheat plants. FEMS Microbiol. Ecol. 16:143-157.
Hietala, S.K., P.J. Hullinger, B.M. Crossley, H. Kinde, and A.A. Ardans. 2005. Environmental air sampling to detect exotic Newcastle disease virus in two California commercial poultry flocks. J Vet Diagn Invest. 17:198-200.
Holben, W.E. and P.H. Ostrom. Monitoring bacterial transport by stable isotope enrichment of cells. 2000. Appl. Environ. Microbiol. 66:4935-4939.
Hutchins, S., M. Tomson, J. Wilson, and C. Ward. 1984. Microbial removal of wastewater organic compounds as a function of input concerntration in soil columns. Appl. Environ. Microbiol. 48:1039-1045.
Huysman, F., and W. Verstraete. 1993. Water-facilitated transport of bacteria in unsaturated soil columns-influence of cell-surface hydrophobicity and soil properties. Soil Biol. Biochem.25:83-90.
Jaspers, M.C.M., S. Totevova, K. Demnerova, H. Harms, and J.R. van der Meer. 1999. The use of whole cell living biosensors to determine the bioavailability of pollutants to microorganisms, p.153-158. In P. Baveye, et al. Bioavailability of Organic Xenobiotics in the Environment. Kluwer Academic Publishers, London, United Kingdom.
Jenneman, G.E., M.J. McInerney, M.E. Crocker, and R.M. Knapp. 1986. Effect of sterilization by dry heat or autoclaving on bacterial penetration through Berea sandstone. Appl. Environ. Microbiol. 51:383-391.
Jenneman, G.E., M.J. McInerney, and R.M. Knapp. 1985. Microbial penetration through nutrient-saturated Berea sandstone. Appl. Environ. Microbiol. 50:383-391.
Jeong, Y.J., H.W. Choi, H.S. Shin, X.S. Cui, N.H. Kim, G.L. Gerton, and J.H. Jun. 2005. Optimization of real time RT-PCR methods for the analysis of gene expression in mouse eggs and preimplantation embryos. Mol Reprod Dev. (Epub ahead of print)
Johnson, W.p., and B.E. Logan. 1996. Enhanced transport of bacteria in porous media by sediment-phase and aqueous-phase natural organic matter. Water Res. 30:923-931.
Johnson, W.P., K.A. Blue, B.E. Logan, and R.G. Arnold. 1995. Modeling bacterial detachment during transport through porous media as a residence-time-dependent process. Water Resour. Res. 31:2649-2658.
Jung, R, K. Soondrum, and M. Neumaier. 2000. Quantitative PCR. Clin. Chem. Lab. Med. 38:833-836.
Kannenberg, E.L. and R.W. Carlson. 2001. Lipid A and O-chain modifications cause Rhizobium lipopolysaccharides to become hydrophobic during bacteroid development. Molecular Microbiol. 39:379-391.
Kittrick, J.A., and E.W. Hope. 1970. Preventing water resorption in weight loss determinations. Soil Sci. Soc. Am. Proc. 34:536-537.
Klánová, K. 1994. Effect of chemical fertilizers on the transport of Escherichia coli, Pseudomonas aeruginosa and Salmonella infantis through sand columns. Folia Microbiol. 39:283-286.
Köhler, T., L.K. Curty, F. Barja, C. van Delden, and J.C. Pechere. 2000. Swarming of Pseudomonas aeruginosa is dependent on cell-to-cell signaling and requires flagella and pili. J. bacterial. 182:5990-5996.
Krumme, M.L., R.L. Smith, J. Egestorff, S.M. Thiem, J.M. Tiedje, K.N. Timmis, and D.F. Dwyer. 1994. Behavior of pollutant-derading microorganisms in aquifers-predictions for genetically-engineered organisms. Environ. Sci. Technol. 28:1134-1138.
Kucukcolak, E., B. Koopman, G. Bitton, and S. Farrah. 1998. Validity of fluorochrome-stained bacteria as tracers of short-term microbial transport through porous media. J. Contam. Hydrol. 31:349-357.
Kummer, C., P. Schumann, and E. Stackebrandt. 1999. Gordonia alkanivorans sp. nov., isolated from tar-contaminated soil. Int. J. Syst. Bacteriol. 49:1513-1522.
Lahlou, M., H. Harms, D. Springael, and J.J. Ortegacalvo. 2000. Influence of soil components on the transport of polycyclic aromatic hydrocarbon-degrading bacteria through saturated porous media. Environ. Sci. Technol. 34:3649-3656.
Lambert, A.J., R.S. Nasci, B.C. Cropp, D.A. Martin, B.C. Rose, B.J. Russell, and R.S. Lanciotti. 2005. Nucleic Acid amplification assays for detection of lacrosse virus RNA. J Clin Microbiol. 43:1885-9.
Lindqvist, R., and C.G. Enfield. 1992. Biosorption of dichlorodiphenyl-
trichloroethane and hexachlorobenzene in groundwater and its implications for facilitated transport. Appl. Environ. Microbiol. 58:2211-2218.
Lindqvist, R., J.S. Cho, and C.G. Enfield. 1994. A kinetic model for cell-density dependent bacterial transport in porous media. Water Resour. Res. 30:3291-3299.
Lindqvist, R., and G. Bengtsson. 1995. Diffusion limited and chemical- interaction-dependent sorption of soil bacteria and microspheres. Soil Biology and Biochemistry. 27:941-948.
Liu, J.H., M.J. Lai, S. Ang, J.C. Shu, P.C. Soo, Y.T. Horng, W.C. Yi, H.C. Lai, K.T. Luh, S.W. Ho, and S. Swift. 2000. Role of flhDC in the expression of the nuclease gene nucA, cell division and flagellar synthesis in serratia marcescens. J. Biomed. Sci. 7:475-483.
Macler, B.A., and J.C. Merkle. 2000. Current knowledge on groundwater microbial pathogens and their control. Hydrogeol. J. 8:29-40.
McCaulou, D.R., R.C. Bales, and R.G. Arnold. 1995. Effect of temperature-controlled motility on transport of bacteria and microspheres through saturated sediment. Water Resou. Res. 31:271-280.
McIntyre, D.S. 1974. Soil sampling techniques for physical measure- ments, chapter 3; Bulk density, chapter 5; and Appendix 1. In J. Loveday (ed.) Methods of analysis of irrigated soils. Technical Communication no. 54, Comw. Bur. Soils, Comw. Aggric Bureaux. Farnham Royal, Bucks, England.
McLean, E.O. 1982. Soil pH and lime requirement. In A. L. Page (ed.) Methods of Soil Analysis, Part 2. 2nd ed. Agronomy. 9:199-224.
Mehmannavaz, R., S.O. Prasher, and D. Ahmad. 2001. Effect of bioaugmentation on microbial transport, water infiltration, moisture loss and surface hardness in pristine and contaminated soils. J. Environ. Sci. Health 36:123-139.
Mireles, Ⅱ, J.R., A. Toguchi, and R.M. Harshey. 2001. Salmonella enterica serovar typhimurium swarming mutants with altered biofilm-forming abilities: surfactin inhibits biofilm formation. J. Bacteriol. 182:5848-5854.
Nakamura, L.K., M.S. Roberts, and F.M. Cohan. 1999. Relationship of Bacillus subtilis clades associated with strains 168 and W23: a proposal for Bacillus subtilis subsp. subtilis subsp. nov. and Bacillus subtilis subsp. spizizenii subsp. nov. Int. J. Syst. Bacteriol. 49:1211-1215.
Novakova, J. 1977. Effect of clays on the microbe adsorption. Zentralbl Bakteriol Parasitenkd Infektionskr Hyg. 132:418-422.
Parent, M.C., and D. Velegol. 2004. E. coli adhesion to silica in the presence of humic acid. Colloids. Surf. B:39:45-51.
Parolin, C., A. Montecucco, G. Ciarrocchi, G. Pedralinoy, S. Valisena, M. Palumbo, and G. Palu. 1990. The effect of the minor groove binding-agent dapi (2-amidino-diphenyl-indole) on DNA-directed enzymes: an attmpt to explain inhibition of plasmid expression in Escherichia coli. FEMS Microbiol. Lett. 68:341-346.
Powelson, D.K., and A.L. Mills. 1998. Water saturation and surfactant effects on bacterial transport in sand columns. Soil Sci. 163:694-704.
Powelson, D.K., and A.L. Mills. 2001. Transport of Escherichia coli in sand columns with constant and changing water contents. J. Environ. Qual. 30:238-245.
Raiders, R.A., M.J. McInerney, D.E. Revus, H.M. Torbati, R.M. Knapp, and G.E. Jenneman. 1986. Selectivity and depth of microbial plugging in Berea sandstone cores. J. Ind. Microbiol. 1:195-203.
Rashid, M.H., and A. Kornberg. 2000. Inorganic polyphosphate is needed for swimming, swarming, and twitching motilities of Pseudomonas aeruginosa. Proc. Natl. Acad. Sci. 97:4885-4890.
Reddy, G.S.N., J.S.S. Prakash, V. Prabahar, G.I. Matsumoto, E. Stackebrandt, and S. Shivaji. 2003. Kocuria polaris sp. nov., an orange-pigmented psychrophilic bacterium isolated from an Antarctic cyanobacterial mat sample. Int. J. Syst. Evol. Microbiol. 53:183-187.
Reynolds, P. J., P. Sharma, G.E. Jenneman, and M.J. McInerney. 1989. Mechanisms of microbial movement in subsurface materials. Appl. Environ. Microbiol. 55:2280-2286.
Rhoades, J.D. 1982. Cation exchange capacity. In A. L. Page (ed.) Methods of Soil Analysis, Part 2. 2nd ed. Agronomy. 9:149-157.
Schaub, S.A., and C.A. Sorber. 1977. Virus and bacteria removal from wastewater by rapid infiltration through soil. Appl. Environ. Microbiol. 33:609-619.
Scholl, M.A., A.L. Mills, J.S. Herman, and G.M. Hornberger. 1990. The influence of minertalogy and solution chemistry on the attachment of bacteria to representative aquifer materials. J. Contam. Hydrol. 6:321-336.
Scholl, M.A., and R.W. Harvey. 1992. Laboratory investigations on the role of sediment surface and groundwater chemistry in transport of bacteria through a contaminated sandy aquifer. Environ. Sci. Technol. 26:1410-1417.
Sharma, P.K., and M.J. McInerney. 1994. Effect of grain size on bacterial penetration, reproduction, and metabolic activity in porous-glass bead chambers. Appl. Environ. Microbial. 60:1481-1486.
Sharma, P.K., M.J. McInerney, and R.M. Knapp. 1993. In situ growth and activity and modes of penetration of Escherichia coli in unconsolidated porous materials. Appl. Environ. Microbiol. 59:3686-3694.
Singh, T., A.K. Srivastava and D.K. Arora. 2002. Horizontal and vertical movement of Pseudomonas fluorescens toward exudates of Macrophomina phaseolina in soil: influence of motility and soil properties. Microbiol. Res. 157:139-148.
Smith, M.S., G.W. Thomas, R.E. White, and D. Ritonga. 1985. Transport of Escherichia coli through intact and disturbed soil columns. J. Environ. Qual. 14:87-91.
Stahlberg, A., N. Zoric, P. Aman, and M. Kubista. 2005. Quantitative real-time PCR for cancer detection: the lymphoma case. Expert. Rev. Mol. Diagn. 5:221-230.
Stenström, T.A. 1989. Bacterial hydrophobicity, an overall parameter for the measurement of adhesion potential to soil particles. Appl. Environ. Microbiol. 55:142-147.
Tiedje, J.M., R.K. Colwell, Y.L. Grossman, R.E. Hodson, R.E. Lenski, R.N. Mack, and R.J. Regal. 1989. The planned introduction of genetically engineered organsisms: ecological considerations and recommendations. Ecology.70:298-315.
Trevors, J.T., J.D. van Elsas, L.S. van Overbeek, and M.E. Starodub. 1990. Transport of a genetically engineered Pseudomonas fluorescens strain through a soil microcosm. Appl. Environ. Microbial. 56:401-408.
Van Loosdrecht, M.C.M., J. Lyklema, W. Norde, G. Schraa, and A.J.B. Zehnder. 1987. Electrophoretic mobility and hydrophobicity as a measure to predict the initial steps of bacterial adhesion. Appl. Environ. Microbiol. 53:1989-1901.
Vandevivere, P., and P. Baveye. 1992. Saturated hydraulic conductivity reduction caused by aerobic bacteria in sand columns. Soil Sci. Soc. Am. J. 56:1-13.
Vanelsas, J.D., J.T. Trevors, and L.S. Vanoverbeek. 1991. Influence of soil properties on the vertical movement of genetically-marked Pseudomonas fluorescens through large soil microcosms. Biol. Fertil. Soils 10:249-255.
Vanhaecke, E., J.P. Remon, M. Moors, F. Raes, D. De Rudder, and A. Van Peteghem. 1990. Kinetics of Pseudomonas aeruginosa adhesion too 304 and 316-L stainless steel: role of cell surface hydrophobicity. Appl. Environ. Microbiol. 56:788-795.
Vincent, J.M. 1970. A manual for the pratical study of root-nodule bacteria. IBP Handbook No. 15, Black well Sci., Ox ford, Great Britian.
Watts, D. and J.R. MacBeath. 2001. Automated fluorescent DNA sequencing on the ABI PRISM 310 Genetic Analyzer. Methods Mol. Biol. 167:153-170.
Wei G.H., E.T. Wang, Z.Y. Tan, M.E. Zhu, and W.X. Chen. 2002. Rhizobium indigoferae sp. nov. and Sinorhizobium kummerowiae sp. nov., respectively isolated from Indigofera spp. and Kummerowia stipulacea.Int. J. Syst. Evol. Microbiol. 52:2231-2239.
Yanaihara, A., Y. Otsuka, S. Iwasaki, T. Aida, T. Tachikawa, T. Irie, and T. Okai. 2005. Differences in gene expression in the proliferative human endometrium. Fertil. Steril. 83:1206-1215.
Yang, X., B.E. Scheffler, and L.A. Weston. 2004. Sor1, a gene associated with bioherbicide production in sorghum root hairs. J. Exp. Bot. 55:2251-2259.