Physical constraints affecting bacterial habitats and activity in unsaturated porous media – a review

Aakra, 2000, Surface attachment of ammonia-oxidizing bacteria in soil, Microb Ecol, 39, 222

Adebayo, 1971, Fungal growth responses to osmotic as compared to matric water potential, Soil Sci Soc Am Proc, 35, 465, 10.2136/sssaj1971.03615995003500030038x

Alvarez, 2004, Physiological and morphological responses of the soil bacterium Rhodococcus opacus strain PD630 to water stress, Fems Microbiol Ecol, 50, 75, 10.1016/j.femsec.2004.06.002

Amellal, 1998, Colonization of wheat roots by an exopolysaccharide-producing Pantoea agglomerans strain and its effect on rhizosphere soil aggregation, Appl Environ Microbiol, 64, 3740, 10.1128/AEM.64.10.3740-3747.1998

Aon, 2001, Interaction between gas exchange rates, physical and microbiological properties in soils recently subjected to agriculture, Soil Till Res, 60, 163, 10.1016/S0167-1987(01)00191-X

Auerbach, 2000, Physical morphology and surface properties of unsaturated Pseudomonas putida biofilms, J Bacteriol, 182, 3809, 10.1128/JB.182.13.3809-3815.2000

Avnimelech, 1964, Biological clogging of sands, Soil Sci, 98, 222, 10.1097/00010694-196410000-00002

Axtell, 2002, Construction and characterization of a proU-gfp transcriptional fusion that measures water availability in a microbial habitat, Appl Environ Microbiol, 68, 4604, 10.1128/AEM.68.9.4604-4612.2002

Azam, 2003, Effect of sodium chloride on denitrification in glucose amended soil treated with ammonium and nitrate nitrogen, J Plant Nutr Soil Sci-Z Pflanzenernahr Bodenkd, 166, 594, 10.1002/jpln.200321163

Barton, 1995, Determination of effective transport coefficients for bacterial migration in sand columns, Appl Environ Microbiol, 61, 3329, 10.1128/AEM.61.9.3329-3335.1995

Baveye, 1998, Environmental impact and mechanisms of the biological clogging of saturated soils and aquifer materials, Crit Rev Environ Sci Technol, 28, 123, 10.1080/10643389891254197

Bees, 2002, Quantitative effects of medium hardness and nutrient availability on the swarming motility of Serratia liquefaciens, Bull Math Biol, 64, 565, 10.1006/bulm.2002.0287

Begonia, 1999, Chemotaxis of deleterious rhizobacteria to birdsfoot trefoil, Appl Soil Ecol, 11, 35, 10.1016/S0929-1393(98)00131-0

Bent, 2003, Spatial distribution of Rhodopseudomonas palustris ecotypes on a local scale, Appl Environ Microbiol, 69, 5192, 10.1128/AEM.69.9.5192-5197.2003

Bradford, 1996, Predicting two- and three-fluid capillary pressure saturation relationships of porous media with fractional wettability, Water Resour Res, 32, 251, 10.1029/95WR03239

Buckling, 2000, Disturbance and diversity in experimental microcosms, Nature, 408, 961, 10.1038/35050080

Bundt, 2001, Preferential flow paths: biological ‘hot spots’ in soils, Soil Biol Biochem, 33, 729, 10.1016/S0038-0717(00)00218-2

Cannavo, 2004, Fate of nitrogen and carbon in the vadose zone: in situ and laboratory measurements of seasonal variations in aerobic respiratory and denitrifying activities, Soil Biol Biochem, 36, 463, 10.1016/j.soilbio.2003.10.023

Chandra, 2002, Effect of potassium salts and distillery effluent on carbon mineralization in soil, Bioresour Technol, 83, 255, 10.1016/S0960-8524(01)00230-9

Chang, 2003, Reduced water availability influences the dynamics, development, and ultrastructural properties of Pseudomonas putida biofilms, J Bacteriol, 185, 6199, 10.1128/JB.185.20.6199-6204.2003

Chapatwala, 1996, Effect of temperature and yeast extract on microbial respiration of sediments from a shallow coastal subsurface and vadose zone, Appl Biochem Biotechnol, 57–58, 827, 10.1007/BF02941762

Chenu, 1993, Clay- or sand-polysaccharide associations as models for the interface between micro-organisms and soil: water related properties and microstructure, Geoderma, 56, 143, 10.1016/0016-7061(93)90106-U

Chenu, 1995, Extracellular polysaccharides: an interface between microorganisms and soil constituents, 217

Chenu, 1991, Mechanical strength of clay-minerals as influenced by an adsorbed polysaccharide, Soil Sci Soc Am J, 55, 1076, 10.2136/sssaj1991.03615995005500040030x

Chenu, 1996, Diffusion of glucose in microbial extracellular polysaccharide as affected by water potential, Soil Biol Biochem, 28, 877, 10.1016/0038-0717(96)00070-3

Chenu, 2002, Interactions between microorganisms and soil particles: an overview, 3

Cho, 2000, Biogeography and degree of endemicity of fluorescent Pseudomonas strains in soil, Appl Environ Microbiol, 66, 5448, 10.1128/AEM.66.12.5448-5456.2000

Chopp, 2002, A mathematical model of quorum sensing in a growing bacterial biofilm, J Ind Microbiol Biotechnol, 29, 339, 10.1038/sj.jim.7000316

Cockell, 2005, Effects of a simulated Martian UV flux on the cyanobacterium, Chroococcidiopsis sp 029, Astrobiology, 5, 127, 10.1089/ast.2005.5.127

Crawford, 2005, Towards an evolutionary ecology of life in soil, Trends Ecol Evol, 20, 81, 10.1016/j.tree.2004.11.014

Crowe, 1984, Preservation of membranes in anhydrobiotic organisms – the role of trehalose, Science, 223, 701, 10.1126/science.223.4637.701

Csahok, 1997, Hydrodynamics of bacterial motion, Physica A, 243, 304, 10.1016/S0378-4371(97)00283-5

Cunningham, 1991, Influence of biofilm accumulation on porous-media hydrodynamics, Environ Sci Technol, 25, 1305, 10.1021/es00019a013

Curtis, 2002, Estimating prokaryotic diversity and its limits, Proc Natl Acad Sci USA, 99, 10494, 10.1073/pnas.142680199

Davey, 2000, Microbial biofilms: from ecology to molecular genetics, Microb Mol Biol Rev, 64, 847, 10.1128/MMBR.64.4.847-867.2000

Dens, 2000, On the importance of taking space into account when modeling microbial competition in structured food products, Math Comput Simulat, 53, 443, 10.1016/S0378-4754(00)00239-1

Dens, 2001, On the need for another type of predictive model in structured foods, Int J Food Microbiol, 64, 247, 10.1016/S0168-1605(00)00472-4

Eberl, 1999, Surface motility of Serratia liquefaciens MG1, J Bacteriol, 181, 1703, 10.1128/JB.181.6.1703-1712.1999

Ehrlich, 1999, Microbes as geologic agents: their role in mineral formation, Geomicrobiol J, 16, 135, 10.1080/014904599270659

Eisenmann, 1998, Grazing of a Tetrahymena sp. on adhered bacteria in percolated columns monitored by in situ hybridization with fluorescent oligonucleotide probes, Appl Environ Microbiol, 64, 1264, 10.1128/AEM.64.4.1264-1269.1998

El-Kadi, 2001, Modeling hydrocarbon biodegradation in tidal aquifers with water-saturation and heat inhibition effects, J Contam Hydrol, 51, 97, 10.1016/S0169-7722(01)00119-X

Entry, 2000, The influence of vegetation in riparian filterstrips on coliform bacteria: I. Movement and survival in water, J Environ Qual, 29, 1206, 10.2134/jeq2000.00472425002900040026x

Fan, 1993, Biodegradation of trichloroethylene and toluene by indigenous microbial-populations in soil, Appl Environ Microbiol, 59, 1911, 10.1128/AEM.59.6.1911-1918.1993

Fenchel, 2002, Microbial behavior in a heterogeneous world, Science, 296, 1068, 10.1126/science.1070118

Ferris, 2003, Cyanobacterial ecotypes in different optical microenvironments of a 68°C hot spring mat community revealed by 16S–23S rRNA internal transcribed spacer region variation, Appl Environ Microbiol, 69, 2893, 10.1128/AEM.69.5.2893-2898.2003

Fierer, 2006, The diversity and biogeography of soil bacterial communities, Proc Natl Acad Sci USA, 103, 626, 10.1073/pnas.0507535103

Foster, 1988, Microenvironments of soil microorganisms, Biol Fert Soils, 6, 189, 10.1007/BF00260816

Friedman, 1999, Transport of bacteria through saturated and unsaturated soils (in Hebrew), Israel J Agric Res, 10, 99

Gaillard, 1999, Carbon, nitrogen and microbial gradients induced by plant residues decomposing in soil, Eur J Soil Sci, 50, 567, 10.1046/j.1365-2389.1999.00266.x

Gardner, 1993, A call for action, Soil Sci Soc Am J, 57, 1403, 10.2136/sssaj1993.03615995005700060001x

Glascoe, 1999, Modeling the influence of heat/moisture exchange during bioventing, J Environ Eng – ASCE, 125, 1093, 10.1061/(ASCE)0733-9372(1999)125:12(1093)

Griffin, 1968, Movement of bacteria in moist, particulate systems, Aust J Biol Sci, 21, 579, 10.1071/BI9680579

Grundmann, 2004, Spatial scales of soil bacterial diversity – the size of a clone, Fems Microbiol Ecol, 48, 119, 10.1016/j.femsec.2004.01.010

Grundmann, 2000, Microscale diversity of the genus Nitrobacter in soil on the basis of analysis of genes encoding rRNA, Appl Environ Microbiol, 66, 4543, 10.1128/AEM.66.10.4543-4546.2000

Hadas, 1994, Short-term variations of soil physical-properties as a function of the amount and C/N ratio of decomposing cotton residues.1. Soil aggregation and aggregate tensile-strength, Soil Till Res, 32, 183, 10.1016/0167-1987(94)90019-1

Hallett, 2004, Millimeter-scale spatial variability in soil water sorptivity: scale, surface elevation, and subcritical repellency effects, Soil Sci Soc Am J, 68, 352, 10.2136/sssaj2004.3520

Hallett, 1999, Changes to water repellence of soil aggregates caused by substrate-induced microbial activity, Eur J Soil Sci, 50, 35, 10.1046/j.1365-2389.1999.00214.x

Hallsworth, 2003, Chaotropic solutes cause water stress in Pseudomonas putida, Environ Microbiol, 5, 1270, 10.1111/j.1462-2920.2003.00478.x

Halverson, 2000, Differential effects of permeating and nonpermeating solutes on the fatty acid composition of Pseudomonas putida, Appl Environ Microbiol, 66, 2414, 10.1128/AEM.66.6.2414-2421.2000

Halverson, 2000, Release of intracellular solutes by four soil bacteria exposed to dilution stress, Soil Sci Soc Am J, 64, 1630, 10.2136/sssaj2000.6451630x

Harms, 1994, Influence of substrate diffusion on degradation of dibenzofuran and 3-chlorodibenzofuran by attached and suspended bacteria, Appl Environ Microbiol, 60, 2736, 10.1128/AEM.60.8.2736-2745.1994

Harris, 1994, Consequences of the spatial distribution of microbial communities in soil, 239

Harris, 1981, Effect of water potential on microbial growth and activity, 23

Harshey, 2003, Bacterial motility on a surface: many ways to a common goal, Annu Rev Microbiol, 57, 249, 10.1146/annurev.micro.57.030502.091014

Hendry, 1999, Quantification of transient CO2 production in a sandy unsaturated zone, Water Resour Res, 35, 2189, 10.1029/1999WR900060

Hengge-Aronis, 2002, Recent insights into the general stress response regulatory network in Escherichia coli, J Mol Microbiol Biotechnol, 4, 341

Hill, 2002, Effects of biofilm growth on flow and transport through a glass parallel plate fracture, J Contam Hydrol, 56, 227, 10.1016/S0169-7722(01)00210-8

Hiraishi, 2000, Seasonal microbial community dynamics in a flowerpot-using personal composting system for disposal of household biowaste, J Gen Appl Microbiol, 46, 133, 10.2323/jgam.46.133

Hissett, 1976, Microsites and time changes in soil microbe ecology, 23

Holden, 1997, Toluene diffusion and reaction in unsaturated Pseudomonas putida biofilms, Biotechnol Bioeng, 56, 656, 10.1002/(SICI)1097-0290(19971220)56:6<656::AID-BIT9>3.0.CO;2-M

Horner-Devine, 2004, An ecological perspective on bacterial biodiversity, Proc R Soc London, Ser B – Biol Sci, 271, 113, 10.1098/rspb.2003.2549

Huang, 2004, Soil mineral–organic matter–microorganism interactions: fundamentals and impacts, 391, 10.1016/S0065-2113(03)82006-0

Iwamatsu, 1996, Capillary condensation and adhesion of two wetter surfaces, J Colloid Interface Sci, 182, 400, 10.1006/jcis.1996.0480

Jones, 1998, Factors affecting degradation of aldicarb and ethoprop, J Nematol, 30, 45

Joseph, 2003, Laboratory cultivation of widespread and previously uncultured soil bacteria, Appl Environ Microbiol, 69, 7210, 10.1128/AEM.69.12.7210-7215.2003

Kaiser, 2000, Bacterial motility: how do pili pull?, Curr Biol, 10, 777, 10.1016/S0960-9822(00)00764-8

Kets, 1996, Physiological response of Pseudomonas putida S12 subjected to reduced water activity, Fems Microbiol Lett, 139, 133, 10.1111/j.1574-6968.1996.tb08192.x

Kets, 1996, Mannitol, a novel bacterial compatible solute in Pseudomonas putida S12, J Bacteriol, 178, 6665, 10.1128/jb.178.23.6665-6670.1996

Kidron, 1999, Two causes for runoff initiation on microbiotic crusts: hydrophobicity and pore clogging, Soil Sci, 164, 18, 10.1097/00010694-199901000-00004

Kieft, 1998, Microbial transport, survival, and succession in a sequence of buried sediments, Microb Ecol, 36, 336, 10.1007/s002489900120

Kildsgaard, 2002, Tracer tests and image analysis of biological clogging in a two-dimensional sandbox experiment, Ground Water Monit Remediat, 22, 60, 10.1111/j.1745-6592.2002.tb00313.x

Kim, 2000, Biomass evolution in porous media and its effects on permeability under starvation conditions, Biotechnol Bioeng, 69, 47, 10.1002/(SICI)1097-0290(20000705)69:1<47::AID-BIT6>3.0.CO;2-N

Koch, 1990, Diffusion – the crucial process in many aspects of the biology of bacteria, Adv Microb Ecol, 11, 37, 10.1007/978-1-4684-7612-5_2

Konopka, 1999, Theoretical analysis of the starvation response under substrate pulses, Microb Ecol, 38, 321, 10.1007/s002489900178

Korona, 1994, Evidence for multiple adaptive peaks from populations of bacteria evolving in a structured habitat, Proc Natl Acad Sci USA, 91, 9037, 10.1073/pnas.91.19.9037

Linders, 1997, Effect of added carbohydrates on membrane phase behavior and survival of dried Lactobacillus plantarum, Cryobiology, 35, 31, 10.1006/cryo.1997.2021

Long, 2005, Aquatic habitats and diffusion constraints affecting microbial coexistence in unsaturated porous media, Water Resour Res, 41, 1, 10.1029/2004WR003796

Luna-Guido, 2003, Mineralization of C-14 labelled maize in alkaline saline soils, Plant Soil, 250, 29, 10.1023/A:1022865728953

Macur, 2004, Bacterial populations associated with the oxidation and reduction of arsenic in an unsaturated soil, Environ Sci Technol, 38, 104, 10.1021/es034455a

Massol-Deya, 1995, Channel structures in aerobic biofilms of fixed-film reactors treating contaminated groundwater, Appl Environ Microbiol, 61, 769, 10.1128/AEM.61.2.769-777.1995

Matsuyama, 1996, Bacterial wetting agents working in colonization of bacteria on surface environments, Colloids Surf, B – Biointerfaces, 7, 207, 10.1016/0927-7765(96)01300-8

McBride, 2001, Bacterial gliding motility: multiple mechanisms for cell movement over surfaces, Annu Rev Microbiol, 55, 49, 10.1146/annurev.micro.55.1.49

Mendelson, 2004, A new form of bacterial movement, dragging of multicellular aggregate structures over solid surfaces, is powered by macrofiber supercoiling, Res Microbiol, 155, 113, 10.1016/j.resmic.2003.11.004

Mills, 1996, Bacterial interactions with surfaces in soils, 25

Morbach, 2002, Body shaping under water stress: osmosensing and osmoregulation of solute transport in bacteria, Chembiochem, 3, 385, 10.1002/1439-7633(20020503)3:5<384::AID-CBIC384>3.0.CO;2-H

Nevo, 1967, Factors affecting biological clogging of sand associated with ground water recharge, Water Res, 1, 231, 10.1016/0043-1354(67)90013-9

Normander, 1998, Effect of bacterial distribution and activity on conjugal gene transfer on the phylloplane of the bush bean (Phaseolus vulgaris), Appl Environ Microbiol, 64, 1902, 10.1128/AEM.64.5.1902-1909.1998

Norris, 2002, Soil microbial community structure across a thermal gradient following a geothermal heating event, Appl Environ Microbiol, 68, 6300, 10.1128/AEM.68.12.6300-6309.2002

Nunan, 2002, In situ spatial patterns of soil bacterial populations, mapped at multiple scales, in an arable soil, Microbial Ecol, 44, 296, 10.1007/s00248-002-2021-0

Nunan, 2003, Spatial distribution of bacterial communities and their relationships with the micro-architecture of soil, Fems Microbiol Ecol, 44, 203, 10.1016/S0168-6496(03)00027-8

Oades, 1993, The role of biology in the formation, stabilization and degradation of soil structure, Geoderma, 56, 377, 10.1016/0016-7061(93)90123-3

Oda, 2003, Biogeography of the purple nonsulfur bacterium Rhodopseudomonas palustris, Appl Environ Microbiol, 69, 5186, 10.1128/AEM.69.9.5186-5191.2003

Okabe, 1999, In situ analysis of nitrifying biofilms as determined by in situ hybridization and the use of microelectrodes, Appl Environ Microbiol, 65, 3182, 10.1128/AEM.65.7.3182-3191.1999

Okubo, 1979, Effect of infiltration-rate on biological clogging and water-quality changes during artificial recharge, Water Resour Res, 15, 1536, 10.1029/WR015i006p01536

Ophir, 1994, A role for exopolysaccharides in the protection of microorganisms from desiccation, Appl Environ Microbiol, 60, 740, 10.1128/AEM.60.2.740-745.1994

Or, 1999, Liquid retention and interfacial area in variably saturated porous media: upscaling from single-pore to sample-scale model, Water Resour Res, 35, 3591, 10.1029/1999WR900262

Or, 2000, Flow in unsaturated fractured porous media: hydraulic conductivity of rough surfaces, Water Resour Res, 36, 1165, 10.1029/2000WR900020

Papendick, 1981, Theory and measurement of water potential, 1

Papke, 2004, The importance of physical isolation to microbial diversification, Fems Microbiol Ecol, 48, 293, 10.1016/j.femsec.2004.03.013

Parales, 2000, Toluene-degrading bacteria are chemotactic towards the environmental pollutants benzene, toluene, and trichloroethylene, Appl Environ Microbiol, 66, 4098, 10.1128/AEM.66.9.4098-4104.2000

Parkin, 1987, Soil microsites as a source of denitrification variability, Soil Sci Soc Am J, 51, 1194, 10.2136/sssaj1987.03615995005100050019x

Perrot, 1998, Gel immobilization improves survival of Escherichia coli under temperature stress in nutrient-poor natural water, Water Res, 32, 3521, 10.1016/S0043-1354(98)00155-9

Pivetz, 1995, Soil matrix and macropore biodegradation of 2,4-D, J Environ Qual, 24, 564, 10.2134/jeq1995.00472425002400040002x

Poolman, 2002, How do membrane proteins sense water stress?, Mol Microbiol, 44, 889, 10.1046/j.1365-2958.2002.02894.x

Potts, 1994, Desiccation tolerance of prokaryotes, Microbiol Rev, 58, 755, 10.1128/MMBR.58.4.755-805.1994

Potts, 1996, The anhydrobiotic cyanobacterial cell, Physiol Plant, 97, 788, 10.1111/j.1399-3054.1996.tb00545.x

Potts, 2001, Desiccation tolerance: a simple process?, Trends Microbiol, 9, 553, 10.1016/S0966-842X(01)02231-4

Powelson, 1996, Bacterial enrichment at the gas–water interface of a laboratory apparatus, Appl Environ Microbiol, 62, 2593, 10.1128/AEM.62.7.2593-2597.1996

Prigent-Combaret, 1999, Abiotic surface sensing and biofilm-dependent regulation of gene expression in Escherichia coli, J Bacteriol, 181, 5993, 10.1128/JB.181.19.5993-6002.1999

Rainey, 1998, Adaptive radiation in a heterogeneous environment, Nature, 394, 69, 10.1038/27900

Rawitz, 1994, Short-term variations of soil physical-properties as a function of the amounts and C/N ratio of decomposing cotton residues. 2. Soil compressibility, water-retention and hydraulic conductivity, Soil Till Res, 32, 199, 10.1016/0167-1987(94)90020-5

Reynolds, 1989, Mechanisms of microbial movement in subsurface materials, Appl Environ Microbiol, 55, 2280, 10.1128/AEM.55.9.2280-2286.1989

Rietz, 2003, Effects of irrigation-induced salinity and sodicity on soil microbial activity, Soil Biol Biochem, 35, 845, 10.1016/S0038-0717(03)00125-1

Rittmann, 1993, The significance of biofilms in porous-media, Water Resour Res, 29, 2195, 10.1029/93WR00611

Ritz, 2004, Interactions between soil structure and fungi, Mycologist, 18, 52, 10.1017/S0269915X04002010

Rivkina, 2000, Metabolic activity of permafrost bacteria below the freezing point, Appl Environ Microbiol, 66, 3230, 10.1128/AEM.66.8.3230-3233.2000

Roberson, 1993, Microstructural changes in bacterial exopolysaccharides during desiccation, Soil Biol Biochem, 25, 1299, 10.1016/0038-0717(93)90230-9

Roberson, 1992, Relationship between desiccation and exopolysaccharide production in a soil Pseudomonas, Appl Environ Microbiol, 58, 1284, 10.1128/AEM.58.4.1284-1291.1992

Rockhold, 2002, Considerations for modeling bacterial-induced changes in hydraulic properties of variably saturated porous media, Adv Water Resour, 25, 477, 10.1016/S0309-1708(02)00023-4

Saari, 2004, Methane oxidation in boreal forest soils: kinetics and sensitivity to pH and ammonium, Soil Biol Biochem, 36, 1037, 10.1016/j.soilbio.2004.01.018

Savin, 2001, Biogeophysical factors influencing soil respiration and mineral nitrogen content in an old field soil, Soil Biol Biochem, 33, 429, 10.1016/S0038-0717(00)00182-6

Schafer, 1998, Transport of bacteria in unsaturated porous media, J Contam Hydrol, 33, 149, 10.1016/S0169-7722(98)00069-2

Schjonning, 1999, Turnover of organic matter in differently textured soils – I. Physical characteristics of structurally disturbed and intact soils, Geoderma, 89, 177, 10.1016/S0016-7061(98)00083-4

Schjonning, 2003, Linking soil microbial activity to water- and air-phase contents and diffusivities, Soil Sci Soc Am J, 67, 156, 10.2136/sssaj2003.0156

Schnider-Keel, 2001, The Sigma factor AlgU (AlgT) controls exopolysaccharide production and tolerance towards desiccation and osmotic stress in the biocontrol agent Pseudomonas fluorescens CHA0, Appl Environ Microbiol, 67, 5683, 10.1128/AEM.67.12.5683-5693.2001

Seki, 1998, Effects of microorganisms on hydraulic conductivity decrease in infiltration, Eur J Soil Sci, 49, 231, 10.1046/j.1365-2389.1998.00152.x

Seymour, 2004, Anomalous fluid transport in porous media induced by biofilm growth, Phys Rev Lett, 93, 198103, 10.1103/PhysRevLett.93.198103

Sharma, 1993, In situ growth and activity and modes of penetration of Escherichia coli in unconsolidated porous materials, Appl Environ Microbiol, 59, 3686, 10.1128/AEM.59.11.3686-3694.1993

Skopp, 1990, Steady-state aerobic microbial activity as a function of soil–water content, Soil Sci Soc Am J, 54, 1619, 10.2136/sssaj1990.03615995005400060018x

Slieman, 2000, Artificial and solar UV radiation induces strand breaks and cyclobutane pyrimidine dimers in Bacillus subtilis spore DNA, Appl Environ Microbiol, 66, 199, 10.1128/AEM.66.1.199-205.2000

Soby, 1983, Motility and chemotaxis of Rhizobium meliloti in soil, Appl Environ Microbiol, 46, 995, 10.1128/AEM.46.5.995-998.1983

Starink, 1994, Rates of benthic protozoan grazing on free and attached sediment bacteria measured with fluorescently stained sediment, Appl Environ Microbiol, 60, 2259, 10.1128/AEM.60.7.2259-2264.1994

Stark, 1995, Mechanisms for soil-moisture effects on activity of nitrifying bacteria, Appl Environ Microbiol, 61, 218, 10.1128/AEM.61.1.218-221.1995

Steil, 2003, Genome-wide transcriptional profiling analysis of adaptation of Bacillus subtilis to high salinity, J Bacteriol, 185, 6358, 10.1128/JB.185.21.6358-6370.2003

Steinle, 2000, Effect of environmental factors on the degradation of 2,6-dichlorophenol in soil, Environ Sci Technol, 34, 771, 10.1021/es990587l

Stevenson, 2004, New strategies for cultivation and detection of previously uncultured microbes, Appl Environ Microbiol, 70, 4748, 10.1128/AEM.70.8.4748-4755.2004

Tam, 2002, Preliminary study on biodegradation of phenanthrene by bacteria isolated from mangrove sediments in Hong Kong, Mar Pollut Bull, 45, 316, 10.1016/S0025-326X(02)00108-X

Taylor, 1990, Biofilm growth and the related changes in the physical properties of a porous medium. 1. Experimental investigation, Water Resour Res, 26, 2153

Taylor, 1990, Biofilm growth and the related changes in the physical properties of a porous medium. 3. Dispersivity and model verification, Water Resour Res, 26, 2171, 10.1029/WR026i009p02171

Thomas, 1997, Spatial interactions between subsurface bacterial colonies in a model system: a territory model describing the inhibition of Listeria monocytogenes by a nisin producing lactic acid bacterium, Microbiol – Sgm, 143, 2575, 10.1099/00221287-143-8-2575

Thompson, 1999, Bacteriophage inactivation at the air–water–solid interface in dynamic batch systems, Appl Environ Microbiol, 65, 1186, 10.1128/AEM.65.3.1186-1190.1999

Thullner, 2002, Interaction between water flow and spatial distribution of microbial growth in a two-dimensional flow field in saturated porous media, J Contam Hydrol, 58, 169, 10.1016/S0169-7722(02)00033-5

Thwaites, 1991, Mechanical behavior of bacterial cell walls, Adv Microb Physiol, 32, 173, 10.1016/S0065-2911(08)60008-9

Tokunaga, 1997, Water film flow along fracture surfaces of porous rock, Water Resour Res, 33, 1287, 10.1029/97WR00473

Torsvik, 2002, Microbial diversity and function in soil: from genes to ecosystems, Curr Opin Microbiol, 5, 240, 10.1016/S1369-5274(02)00324-7

Torsvik, 2002, Prokaryotic diversity – magnitude, dynamics, and controlling factors, Science, 296, 1064, 10.1126/science.1071698

Treves, 2003, A two-species test of the hypothesis that spatial isolation influences microbial diversity in soil, Microb Ecol, 45, 20, 10.1007/s00248-002-1044-x

Tuller, 1999, Adsorption and capillary condensation in porous media: liquid retention and interfacial configurations in angular pores, Water Resour Res, 35, 1949, 10.1029/1999WR900098

Ustohal, 1998, Measurement and modeling of hydraulic characteristics of unsaturated porous media with mixed wettability, J Contam Hydrol, 33, 5, 10.1016/S0169-7722(98)00063-1

van de Mortel, 2004, Cell envelope components contributing to biofilm growth and survival of Pseudomonas putida in low-water-content habitats, Mol Microbiol, 52, 735, 10.1111/j.1365-2958.2004.04008.x

van Loosdrecht, 1990, Influence of interfaces on microbial activity, Microbiol Rev, 54, 75, 10.1128/MMBR.54.1.75-87.1990

Vandevivere, 1992, Saturated hydraulic conductivity reduction caused by aerobic-bacteria in sand columns, Soil Sci Soc Am J, 56, 1, 10.2136/sssaj1992.03615995005600010001x

Vandevivere, 1995, Microbial clogging of saturated soils and aquifer materials – evaluation of mathematical-models, Water Resour Res, 31, 2173, 10.1029/95WR01568

Vandevivere, 1993, Attachment stimulates exopolysaccharide synthesis by a bacterium, Appl Environ Microbiol, 59, 3280, 10.1128/AEM.59.10.3280-3286.1993

Vayenas, 2002, Visualization experiments of biodegradation in porous media and calculation of the biodegradation rate, Adv Water Resour, 25, 203, 10.1016/S0309-1708(01)00023-9

Veeh, 1996, Soil depth and temperature effects on microbial degradation of 2,4-D, J Environ Qual, 25, 5, 10.2134/jeq1996.00472425002500010002x

Vinther, 1999, Microbial biomass and numbers of denitrifiers related to macropore channels in agricultural and forest soils, Soil Biol Biochem, 31, 603, 10.1016/S0038-0717(98)00165-5

Vogel, 2003, Relationship between spatial and genetic distance in Agrobacterium spp. in 1 cubic centimeter of soil, Appl Environ Microbiol, 69, 1482, 10.1128/AEM.69.3.1482-1487.2003

Wachinger, 2000, Variability of soil methane production on the micro-scale: spatial association with hot spots of organic material and Archaeal populations, Soil Biol Biochem, 32, 1121, 10.1016/S0038-0717(00)00024-9

Walker, 2003, Root exudation and rhizosphere biology, Plant Physiol, 132, 44, 10.1104/pp.102.019661

Wan, 1994, Visualization of the role of the gas–water interface on the fate and transport of colloids in porous media, Water Resour Res, 30, 11, 10.1029/93WR02403

Wan, 1994, Influence of the gas–water interface on transport of microorganisms through unsaturated porous media, Appl Environ Microbiol, 60, 509, 10.1128/AEM.60.2.509-516.1994

Watnick, 2000, Biofilm, city of microbes, J Bacteriol, 182, 2675, 10.1128/JB.182.10.2675-2679.2000

Welsh, 2000, Ecological significance of compatible solute accumulation by micro-organisms: from single cells to global climate, Fems Microbiol Rev, 24, 263, 10.1111/j.1574-6976.2000.tb00542.x

Welsh, 1999, Osmotically induced intracellular trehalose, but not glycine betaine accumulation promotes desiccation tolerance in Escherichia coli, Fems Microbiol Lett, 174, 57, 10.1111/j.1574-6968.1999.tb13549.x

Whitman, 1998, Prokaryotes: the unseen majority, Proc Natl Acad Sci USA, 95, 6578, 10.1073/pnas.95.12.6578

Willems, 1996, Mineralization of 2,4-D and atrazine in the unsaturated zone of a sandy loam soil, Soil Biol Biochem, 28, 989, 10.1016/0038-0717(96)00123-X

Williams, 2005, Geophysical imaging of stimulated microbial biomineralization, Environ Sci Technol, 39, 7592, 10.1021/es0504035

Wong, 1998, Effect of sewage sludge amendment on soil microbial activity and nutrient mineralization, Environ Int, 24, 935, 10.1016/S0160-4120(98)00075-0

Wood, 1993, In situ measurement of microbial activity and controls on microbial CO2 production in the unsaturated zone, Water Resour Res, 29, 647, 10.1029/92WR02315

Wright, 1995, Role of pore-size location in determining bacterial-activity during predation by protozoa in soil, Appl Environ Microbiol, 61, 3537, 10.1128/AEM.61.10.3537-3543.1995

Yarwood RR. Interactions between microbial dynamics, water flow, and solute transport in unsaturated porous media. PhD thesis, Oregon State University; 2001.

Young, 2004, Interactions and self-organization in the soil-microbe complex, Science, 304, 1634, 10.1126/science.1097394

Zhou, 2002, Spatial and resource factors influencing high microbial diversity in soil, Appl Environ Microbiol, 68, 326, 10.1128/AEM.68.1.326-334.2002