dissertation defense.pptx
DESCRIPTION
Dissertation Defense Presentation of Malcolm Burbank, Ph.D.TRANSCRIPT
Using microbes to keep buildings from falling down
PRECIPITATION OF CALCITE BY INDIGENOUS MICROORGANISMS TO STRENGTHEN SOILS
Malcolm Burbank
Dissertation DefenseDepartment of Microbiology, Molecular Biology and Biochemistry
Major Professor: Dr. Ronald Crawford
1
The problem Soil Liquefaction
Liquefaction is a soil phenomenon that occurs during earthquakes in which saturated soils act like liquids and can no longer support structures and buildings.
Before the earthquake, water pressure in the soil is low and soil particles are in contact with each other. Water pressure increases due to shaking or rapid loading of forces and pushes the soil particles apart, allowing them to move relative to one another.
Soils transition from a solid to a liquid phase.
This reduces the stiffness and shear strength of the soil and can cause structures built on the soil to fail.
2
Examples of liquefaction-induced damage:
1964 Niigata, Japan M = 7.5 earthquake - 36 dead, 385 injured 3,534 houses destroyed, 11,000 houses damaged
1971 San Fernando, Calif. M = 6.6 earthquake -over $500 million in property damage and 65 deaths.
1989 Loma Prieta Calif. M = 6.9 earthquake 63 deaths 3,757 injuries $ 5.9 billion dollars in property damage
1999 Chi-Chi, Taiwan M = 7.6 earthquake. 2400 killed, 11,000 injuries. ~20 billion dollars in damage.
2010 Haiti M=7.0
http://fiveblocks.wordpress.com/2008/06/08/photos-that-work/
3
http://pubs.usgs.gov/of/2002/of02-296/of02-296_2liq-sg.pdf
Former Alameda Naval Complex
International Airport
Oakland Coliseum
5
Current Technologies to Mitigate Seismic-Induced Liquefaction of Developed Sites
Permeation: Grout is injected into the soil at low pressure and fills the voids
Compaction Grouting: A viscous grout is injected into a compactable soil. The grout acts as a radial, hydraulic jack and physically displaces the soil particles.
Jet Grouting: Breaks up the soil structure completely and performs deep soil mixing to create a homogeneous soil, which in turn solidifies.
http://www.geotechnical.com
6
Injection of Sporosarcina pasteurii
Inject model ureolytic microorganism, S. pasteurii, into soil followed by injections of a solution to promote the precipitation of calcite
Process is being investigated in several laboratories but there are some obstacles that must be overcome before this is a reasonably viable treatment solution
7
Chemistry
Urea is hydrolyzed by the enzyme urease
CO(NH2)2 + 2H2O 2NH4+ + CO32-
Ca2+ + CO32- CaCO3 (calcium carbonate)
8
9
Challenges of Transport of Bacteria into Soil
Cell surface properties
Ionic strength of the carrier solution
van der Waals forces
Pore space geometry
Straining
Flow rate
10
Once in the soil
Biotic stresses
Predation
Competition
Abiotic stresses
pH
Osmotic pressure
Temperature
The reality is that bacteria introduced into soil tend to rapidly decline in number and rarely grow after being introduced.
http://www.bam.gov/sub_diseases/images/ip_microbes.jpg
11
Our approach - Stimulate Indigenous Ureolytic Bacteria to Induce Calcite Precipitation
Advantages
Ureolytic bacteria are already there
Bacteria are evenly distributed = more evenly distributed calcite
No need to grow large volumes of bacteria in the lab
No need to autoclave equipment or media for field applications
Lower energy demand
Lower overall costs
Indigenous Ureolytic Microorganisms
Common in many types of soil. In one study, ureolytic bacteria comprised between 17-30% of the cultivable aerophilic, micro-aerophilic, and anaerobic microorganisms*
Urea plays a crucial role in microbial nitrogen metabolism for many microorganisms
Production of urease is stringently regulated in many microorganisms by the availability of nitrogen but constitutively expressed in others
* (Lloyd and Sheaffe 1973)
13
Urease Regulation
Constitutive expression: Urease is made regardless of nitrogen concentration
S. pasteurii
S. ureae
Inducible: Urease is expressed only in the presence of urea
Proteus mirabilis
For most of the characterized ureolytic soil bacteria, urease is negatively regulated by the presence of ammonia or other nitrogen compounds but de-repressed in nitrogen-poor conditions
Enrichments
Favor ureolytic bacteria which constitutively or inducibly produce urease
Can thrive in high pH
Can thrive in high [CaCl2]
Can thrive on an inexpensive carbon source with very little added micronutrients
15
Indigenous Experiments (overview)
Determine the effects of carbon concentration on the number of ureolytic microorganisms and on the amount of calcite precipitated in column experiments
Determine the effects of two concentrations of CaCl2 on pH and on the amount of calcite precipitated in a column experiments
Test multiple soil types in column experiments
Do a large scale test and quantify the change in shear strength of treated soil using cone penetration testing
Identify some of the microorganisms involved and characterize how each regulate urease
Effects of Carbon Concentrations on ureC* gene copy number and Calcite %
Soil samples were enriched in columns with a solution containing either 1% molasses and 170 mM sodium acetate [H] or 0.1% molasses and 50 mM sodium acetate [L], urea and calcium chloride
Samples were then treated with a biomineralization solution containing either 170 mM sodium acetate [H] or 50 mM sodium acetate [L], urea and calcium chloride
* ureC codes for a functional unit of the urease enzyme and is highly conserved among most known ureolytic bacteria
17
Effects of [Carbon] on ureC gene copy number
Sample Depth (cm)Initial ureC#/gm soilureC#/gm treated soilUntreatedLow CarbonHigh Carbon304.49 x 1062.37 x 1093.81 x 109602.74 x 1071.01 x 1082.27 x 108901.53 x 1063.38 x 1095.64 x 1091504.99 x 1065 x 1096.11 x 1091 enrichment & 3 treatments
* All sequenced ureolytic strains have one copy of ureC per genome
18
H = 1 pretreatment (enrichment) with 1% molasses and 170 mM sodium acetate, urea and calcium chloride. 3 treatments with 170 mM sodium acetate
L = 1 pretreatment (enrichment) with 0.1% molasses and 50 mM sodium acetate, urea and calcium chloride. 3 treatments with 50 mM sodium acetate
* Pretreatments (enrichments) were followed by three treatments with a biominerlization solution.
19
Effects of [Ca2+] on pH
Treatment #Time (h)Average pH50 mM CaCl2250 mM CaCl2Enrichment369.57.42488.67.63488.98.54249.28.16249.27.97249.37.720
% wt/wt
L=50 mM [CaCl2] H=250 mM [CaCl2]
1 pretreatment, 7 biomineralization treatments
In addition to CaCl2, solutions contained urea and sodium acetate
21
Effects of [CaCl2] on calcite
46 cm H46 cm L90 cm H90 cm L150 cm H150 cm L3.4781944383812782.1241910379290633.6396324518394852.4121693365957374.520260130065033.875505449188906
Depth & concentration
% calcite
Soil from 150 cm
No urea control
Calcite undetectable
50 mM CaCl2
3.9% calcite
250 mM CaCl2
4.5 % calcite
22
Test of 6 other soil types
Soil Type# Treatments% Calcite (wt/wt)Mined silica32.5Mined alluvial32.3Tidal #133.7Tidal #234.5Palouse loess1019.1High organic *1011ureC copy number was below the threshold of detection by qPCR before enrichments.
1.6 x 109 copies of ureC/gm soil were detected following the 2nd treatment
23
Field Test Overview
Chemicals were mixed off-site in 55 gallon barrels
250 liters of water from the Snake River was pumped to the barrels then delivered by gravity into a ring infiltrometer
Originally, we modeled the experiment to treat saturated soil.
One enrichment treatment was followed by 10 biomineralization treatments. The experiment lasted ~5 weeks.
24
25
http://pubs.usgs.gov/fs/2003/fs028-03/
http://pubs.usgs.gov/
26
Comparison of CPT and Calcite Precipitation
27
0.008736966814997150.01025034593077460.01045653648690510.01043146826259190.01014984285986740.01809922098093780.01725576456310680.01745623419046230.01886394772894920.02446638594453310.023935725955290.02029635784517370.030.4799999999999961.091.591.591.5121.9121.9170.02185.27230.52245.7200000000001
CPT 1 - Untreated0.00.0352580.0321920.0797140.1057750.170160.154830.1900880.1502310.0919780.1992860.2958630.3127260.3157920.3188580.4859510.4399620.5043470.4307640.4936160.505880.4752210.5687320.5978580.6009240.6131880.6361820.6561110.6392480.7051660.7465560.800210.8017430.7649520.7450230.7802820.7542210.8216720.8507980.8032760.7419570.856930.8538640.9228480.8492650.9213150.8768590.8661280.928980.9443090.9351111.0332209999999991.0853421.1083371.1696561.2202441.1635241.1987821.2769641.2325081.1957161.3045571.2125791.3382821.2708321.3812061.3290851.4486561.4011339999999991.5345031.6479421.6540741.6832011.7015961.698531.615751.6709371.6050191.4777831.5728271.5620961.5820251.5237719999999991.4885131.5253049999999991.4808491.5406341.5345031.5345031.5360351.5866231.5973541.5605631.631081.6648051.7261241.7153931.7905081.7598491.7199921.7813111.796641.8165691.8656241.8242341.8671571.910081.8978161.9622011.9637342.0250529999999982.080242.1139652.0051240000000012.0020579999999991.9346082.0051240000000011.9468711.9008821.8855531.9085471.8395631.838031.8288331.8257671.7951071.7889751.8441621.8564261.8181021.8518269999999991.8671571.8181021.7981731.9192781.9637341.96681.9989922.008191.9959262.0756409999999972.147692.1384922.1584212.189082.2779930000000012.2366029999999972.1277622.2151412.2013442.219742.2228062.1952122.1645532.3101852.2810589999999992.302522.3239822.3730372.0679761.9897941.9499372.3791689999999962.3853012.5125372.5508612.5539272.5324659999999832.5202022.4634822.4190259999999972.3715039999999982.3485092.4711469999999982.4512179999999992.4558169999999972.5907182.5431960000000012.5968499999999822.5585259999999992.5462619999999992.5891862.5569932.5937840000000012.4604162.4435529999999992.4052292.4282242.3592399999999982.3009872.1752839999999992.1553552.1584212.0189212.0526459999999822.0388489999999822.0327179999999992.0633770000000012.1262292.0327179999999992.1798829999999982.2381362.2887230000000012.2412012.3101852.302522.3239822.3699709999999992.4803452.4726799999999962.3669049999999992.4067619999999992.3362459999999822.3684382.3715039999999982.302522.2519322.121632.1415582.1185642.1415582.1461569999999992.2105422.2059429999999992.2672622.4113612.3623059999999982.3147842.2212732.2243392.1599539999999992.0848391.9974591.8610249999999991.8548931.8610249999999991.8257671.8456949999999991.8763551.8272999999999991.8472281.8778881.8410961.8886181.8794211.9407391.8640911.8625580000000011.925411.8625580000000011.9376731.8732891.9116131.9361411.8778881.8824871.9284761.8732891.910081.8242341.8564261.8487611.796641.8012391.8181021.8165691.8610249999999991.7935741.7613821.7629151.7460521.7675141.8119699999999991.8824871.9346081.910081.9989921.9070141.9913271.9652671.6832011.6034861.486980.00.620051.24011.860151.937656252.5577062500000013.1777562500000013.7978062500000013.9140656249999974.5341156249999785.1541656249999785.7742156255.8904749999999826.5105249999999817.1305749999999817.7506249999999987.8281312499999668.448181259.068231259.688281259.80454062500000410.42459062511.04464062511.66469062511.74219687512.3622468750000112.9822968750000113.60234687513.7186062514.3386562514.9587062500000115.5787562515.656262516.2763124999999916.896362517.5164124999999917.63267187518.2527218749998218.8727718749999819.4928218749999819.5703281250000120.1903781250000120.8104281250000121.4304781250000121.5467374999999822.1667874999999922.7868374999999923.406887523.6006531250000124.22070312524.84075312525.4608031249999925.577062526.197112526.817162527.4372124999999927.5147187500000128.1347687500000128.7548187529.3748687500000129.49112812530.1111781250000130.7312281250000131.3512781250000131.4287843749998332.0488343750000132.66888437533.2889343750000133.4051937534.0252437534.6452937535.2653437500000135.38160312536.00165312536.6217031250000137.24175312537.31925937537.93930937538.55935937539.1794093750000139.2956687500000139.9157187500000140.5357687541.1558187541.2333250000000141.85337542.47342543.0934750000000143.1709812543.7910312500000144.4110812499999745.0311312545.14739062545.7674406250000146.38749062547.00754062547.123847.7438548.363948.9839549.0614562500000149.6815062500000150.3015562550.9216062551.03786562551.65791562552.27796562552.8980156250000253.01427553.6343250000000154.25437554.87442554.9519312555.5719812556.1920312500000256.8120812556.9283406250000157.5483906250000158.16844062558.78849062558.9047559.5248000000000160.1448560.7649000000000160.8424062561.4624562562.0825062562.7025562500000162.8188156250000163.4388656250000164.0589156249999864.67896562564.7564718749995865.3765218749996765.99657187566.6166218749999866.7328812499999867.3529312499997367.9729812499999868.5930312499999868.7480437569.3680937569.9881437570.6081937570.6856999999999871.3057499999999571.9257999999999872.5458572.66210937573.2821593749999873.90220937574.52225937574.6385187499999575.2585687499999875.8786187499997576.4986687576.5761749999999877.1962250000000277.81627578.43632578.5525843749996879.1726343749995379.7926843749999879.9089437580.5289937581.1490437581.7690937581.8853531249996782.50540312583.1254531249995983.74550312583.861762584.481812585.1018624999999885.721912585.8381718749995386.4582218749999887.0782718749994987.6983218749995687.7758281249995688.3958781249994689.01592812589.6359781249994189.7522374999999890.3722874999997490.9923374999999891.6123874999997391.7286468749996892.34869687592.9687468749996493.588796874999593.7050562594.3251062499999894.9451562595.5652062595.60395937596.2240093749999896.8440593750000297.46410937597.5803687499999898.2004187499999898.8204687499999599.4405187599.5567781249994100.176828125100.7968781249999101.416928125101.5331875102.1532375102.7732875103.3933375103.509596875104.1296468749999104.749696875105.369746875105.4472531250001106.067303125106.687353125107.307403125107.4236625108.0437125108.6637625109.2838125109.36131875109.98136875110.60141875111.22146875111.37648125111.99653125112.61658125113.23663125113.352890625113.972940625114.592990625115.213040625115.3293115.94935116.5694117.18945117.3057093749999117.925759375118.545809375119.165859375119.28211875119.90216875120.52221875121.14226875121.219775121.839825122.459875123.079925123.196184375123.816234375124.436284375125.0563343749999125.17259375125.79264375126.41269375127.03274375127.149003125127.769053125128.389103125129.0091531249999129.1254125129.7454624999999130.3655125130.9855625131.101821875131.721871875132.3419218750001132.961971875133.07823125133.69828125134.3183312500001134.93838125135.0158875135.6359375136.2559875136.8760375000001136.9922968750001137.6123468750001138.2323968750001138.8524468750001CPT 4 - Treated0.0240820.0026040.019480.0118090.0041380.0026040.008740.008740.0286850.0286850.0302190.0731760.0915870.09925800000000010.1145990.1069280.1007920.1575570.1744330.23580.301770.3646720.3754110.433710.4689970.5272960.5349670.5441720.6208810.6807150.6699750.6945220.7512870.7942440.803450.8433380.9169790.982950.9553341.0351121.038181.0826721.0918771.0903431.1026161.1409711.1501761.1501761.1194919999999991.0857399999999991.0581251.0750011.0136331.0274411.0228380.9844840.9200480.8832270.8786250.8755560.8847620.9031720.8924320.9522660.9998261.0519881.0703981.1056851.1348341.2069411.1869961.236091.2759791.3066631.2989919999999991.3081971.3220051.2882531.2759791.2851841.2452959999999991.2115431.1900651.1409711.1225611.1056851.0995481.1133551.1302321.1962021.1977361.2744451.3434841.4232609999999991.4309321.5214491.6012271.6840731.6840731.7285651.737771.7362361.7239621.6886761.6595261.6150351.6181031.576681.5613381.5475311.5521331.5413939999999991.5628721.5782141.5720781.6150351.6625951.6656631.6810051.6764021.7101541.6994151.7147571.7162911.7300991.7699881.7699881.785331.8083421.7991371.7976031.7791931.7592481.774591.774591.785331.8390261.8835181.9080651.983242.0967699999999982.1857532.181152.2977482.3284322.4204829999999992.4404282.5340129999999992.6414059999999982.7058419999999992.7303892.7825522.7181162.6275990000000012.6245300000000012.5340129999999992.4542352.4066759999999962.4281542.4128119999999972.4051412.4281542.4557699999999982.4956579999999972.5754359999999982.6674872.6460089999999982.69052.7487990000000012.8285772.7978932.7288552.8377822.8316459999999822.8746029999999962.8930129999999982.9681882.9850639999999993.0602393.1047310000000013.1139363.0832523.1139363.1047310000000013.1400173.1783723.1492223.2765599999999993.4468549999999983.3870213.6248213.7536923.9255213.9163159999999974.0099024.0835434.3842434.2170169999999814.3857784.2829869999999814.437944.3612314.3919139999999944.3566284.3520249999999814.3689009999999784.4394740000000014.4885684.4256664.5069784.5284569999999844.8690475.2710040000000015.3139609999999955.5747735.6161959999999825.731260000000015.7665459999999955.7910930000000015.7711490000000025.6821659999999845.6668239999999965.6913715.5747735.6867690000000015.6606869999999785.6269349999999695.4673799999999995.1544059999999745.0915044.8168839999999954.4977734.3489569999999824.3136714.3136714.3842434.5453334.6067014.6389189999999814.7232994.7417090000000014.9012650000000034.9672349999999844.947294.833764.8276239999999974.6435209999999854.2891244.0605299999999964.1188289999999954.0252433.7813083.6309573.6156149999999993.4330469999999973.1829753.3455983.3195169999999983.2197953.0893893.1062649999999992.9252312.9160259999999962.6705559999999992.0016499999999971.8804491.1348340.9660730.9660730.6686200000000011.3572631.4973939999999992.0899470000000022.5904153.1068973.1869720000000013.6594130000000014.1198429999999994.5962880000000014.6123030000000015.1167750000000015.6012270000000026.1497396.1857730000000016.7983450000000017.4549589999999858.1476068.227688.9603650000000019.62898900000000110.27359110.37768910.9462211.48272111.995212.01521812.4556300000000112.90805213.34846413.36047513.79688314.09315914.57360814.66969815.22221415.9348816.63553416.76765717.26412117.9647759999999918.62539318.7294899999999819.2699950000000119.7864769999999820.238920.2789369999999820.93955421.54411922.28080722.36888923.16963723.9263439999999824.7591219999999924.8872419999999925.7040050000000126.4366889999999927.08929927.16136627.8099720000000128.4185399999999829.0671459999999929.21928829.9399610000000130.4244139999999831.1170610000000131.16510631.78968932.2941600000000132.8186532.8907180000000133.4672560000000134.15990334.80450534.92061435.68132436.4580537.1907340000000137.2788170000000138.30777839.12454140.08143440.2255690000000141.18646742.2714843.3444819999999943.49262144.45351845.2822920000000145.9148829999999946.04700746.80771747.4683340000000148.16498548.25707148.84962549.5262570000000150.1508450.1988850000000150.8675090000000151.4960970000000152.0966580000000152.2007550000000152.93744353.6741310000000154.50690954.57497255.2756270000000155.81613256.48475656.5328010000000157.0973290000000157.58578558.0462150000000158.1142780000000158.67880659.18327759.7998530000000159.84389460.34436260.8688510000000161.4734160000000161.5614980000000162.1500480000000162.76662463.30312563.41122664.08385564.70443465.26495865.3290179999999565.9015520000000266.61421867.25481667.3549099999999867.99550868.6641329999999869.28070969.3327569999997569.8812770.4738230000000270.97429171.1104180000000171.6709409999997472.1393789999995472.7239250000000272.8280219999999873.3925574.0451590000000274.6337090000000174.6857579999995975.358385999999776.0069919999999876.75969576.8557849999997377.5924730000000178.5613779999999579.414174000000179.5623129999999580.3870829999999581.0236779999999581.74435181.9045000000000282.66521183.461955000000184.24668884.2987369999999585.0154060000000185.55190786.2045170000000286.2805879999999886.4287259999999887.033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Tip Resistance, Mpa
Depth, cm
Soil Microcosm Experiment
A 240-liter microcosm measuring 76 cm x 102 cm x 31 cm (h x l x w) was constructed from aluminum (30 x 40 x 12)
Box was filled with 56 cm of compacted sand
For each treatment, 99 liters of solution was gravity fed through the soil from the bottom of the microcosm. Approx 17 cm of solution was allowed to pool on the top of the soil
6.5 volumes of treatment solution was delivered before the soil clogged
At 46 cm there is a 12.5 fold increase after 5 treatments and 34.1 fold increase after 6.5 treatments (7.14 Mpa = 149,122 psf or 1035 psi)
Untreated0.00.00.006137000000000060.004601999999999990.00.00.00.00.00.0138080.01073900000000010.00.004601999999999990.009205000000000020.0122730.0153420.006137000000000060.00.006137000000000060.0122730.01073900000000010.006137000000000060.0214780.0306840.0138080.007670999999999980.0245470.02761500000000010.0153420.0168760.02301300000000010.0306840.0414230.02761500000000010.0291490.036820.02761500000000010.02761500000000010.0306840.03988900000000010.047560.0383550.0322180.036820.0414230.0414230.0337520.0460250.0414230.05676499999999990.0429570.0414230.036820.03988900000000010.047560.0414230.0506280.0414230.0444910.0490940.0383550.0460250.0490940.0582990.0552310.0644360.0598330.0582990.065970.0629020.07824300000000010.065970.0721070.0690380.07364099999999990.0767090.07364099999999990.0828460.07824300000000010.0797780.0889830.07824300000000010.084380.1089270.0981880.0981880.1196660.1165980.1288720.113530.1304060.1242690.1258030.1380770.1365430.1472820.1626240.1580210.1810340.1779660.168760.1733630.1825680.1779660.1764310.1871710.1841020.1948420.2193890.2132520.2178540.2025130.2040470.2071150.1994440.2209230.2224570.2209230.216320.2147860.227060.2132520.216320.2285940.2055810.2239910.2193890.216320.216320.2331960.2285940.2301280.2424010.2439360.2700170.2730850.2700170.2761540.2669480.2700170.2776880.2853590.3099060.3175770.3283160.3221790.3513290.3712730.395820.3881490.4525850.4924740.5431020.5507730.6320850.7180.8161880.8253930.9956881.1583111.3746321.4022471.5050381.6032261.7873281.8011361.9652941.9422811.8456271.7474390.1047949999999980.2249070000000040.5812400000000030.8695090000000021.2098269999999991.2818951.7303130000000042.2187700000000012.7192370000000012.7792930000000043.1596490000000033.5400039999999983.9323700000000014.0164490000000034.5329314.9172900000000035.4337730000000035.5298620000000036.0783750000000036.6068687.1914149999999917.3235379999999917.8920690000000018.3204698.9810869.1532470000000029.55362100000000110.03807410.61861610.77876511.23919511.63956912.36024312.50838113.40121514.0698414.85857614.97868815.66733216.09973616.60420716.76435617.2608217.79732118.36184918.38987519.04248419.4228419.76716119.79919120.1194920.47181921.2325321.31660921.72098622.10934922.61782422.71391423.89902124.85991824.99604525.06010525.18021725.34837525.71671925.7287326.02500726.32128326.59353826.63757926.93385627.20210627.44633427.39828927.50238727.80667128.0829289999999928.17501528.73954229.2400129.44019729.5723230.3930869999999930.87353531.27390931.34197331.83443332.50305833.04356233.09160733.6721534.34878234.76917434.8412419999999935.36573235.8461836.25456236.35865936.9071710000000137.63184838.56071638.67282139.23334439.721840.12617840.15820840.5425670000000141.05104241.55951741.64359642.18810442.79667343.42926443.47730844.14192944.57032945.08681245.16688745.67936546.13579246.83644646.9765770000000147.52508947.83738148.08561348.0936248.48999149.03049649.3868279999999949.3988449.6510750000000149.91532250.26765150.27165550.50787650.82417151.44475151.53283352.32957753.07827653.73889453.7989554.04317854.27939854.53163454.53964254.7198154.91599355.00407555.04811655.25230755.36441255.46450555.48452455.5846180000000155.64467455.72074555.72875255.74076355.79281255.7687955.74476755.77279355.76478655.83685355.80482355.82083855.84886455.91692855.884897999999995 Treat0.00.004601999999999990.00.003068000000000070.007670000000000060.007670000000000060.00.0138070.004601999999999990.02761500000000010.0153410.0138070.0260810.0214780.0398880.02761500000000010.0337520.0398880.0429570.05369600000000010.05369600000000010.0644350.0629010.0721060.0951190.0905170.07824300000000010.08744800000000010.102790.09972200000000010.1073930.1150640.1258030.1304050.1334740.1396110.1426790.1534180.1488160.1626230.1672260.1794990.1702940.1856360.1948410.2132520.2071150.234730.2270590.2285930.234730.234730.253140.2362640.2439350.2562090.2592770.2715510.2838240.282290.2991660.3145080.3160420.3252470.3252470.3237130.3191110.3267810.3329180.348260.3559310.366670.3636020.395820.4034910.4203670.4541190.490940.4848030.5415680.4970760.5415680.5446360.5737860.6382220.6366870.6581660.6827130.707260.6673710.6750420.7394780.7563540.7594220.7793670.8269270.8499390.8760210.8821570.9465930.981881.0294391.0417131.0739311.1168881.1659821.161381.1767211.2074051.2564991.2396231.2687731.3086621.3270721.3255381.3424141.3715631.3915081.4007131.4221911.443671.4850931.4866271.5403241.6154991.6830031.6922081.7459051.7949991.9146661.9208021.963761.9944432.0082512.018992.0757552.1892852.1816142.1908192.2690632.2736662.1555332.1601362.2905422.3580459999999922.407142.4286182.6280632.6004472.568232.5436832.491522.4700419999999982.5498192.5436832.5989132.6909652.7017042.7109092.6280632.6219262.6572122.6495412.6541442.6326649999999972.6295972.6572122.6694862.8152343.0208153.0683753.4028279999999993.5547123.7296093.7863744.0548569999999894.4890324.6439849999999874.6654639999999964.7805280.07587400000000070.5723380.6243860000000031.2649850000000011.9015792.3780240000000022.4741140000000023.0146190000000013.6392020000000034.2197450000000014.3318494.9524295.5810165.8492670000000025.7852070000000016.173576.2376300000000016.6099770000000016.6940559999999877.0343740000000017.5308380000000017.9792568.0713420000000038.5397800000000028.8680879.2524469.3645500000000029.7008649999999989.98913410.32144410.35347410.62572810.91399811.3664211.41446511.81083512.23923612.65962812.71568113.10804713.51642913.87676513.88076914.2250910000000114.64147914.94576415.0578680000000115.37416415.79455716.17090816.23897216.6313380000000117.01169317.54018717.64028118.10871818.56514418.98954119.05360119.48200119.88237520.45090620.52697720.93535821.66403922.2966322.3927222.72102622.97726623.4216810000000123.4737290000000123.7539910000000124.00222324.32652624.37857524.76293425.0351880000000125.17131525.20734925.49962225.6477600000000125.75586125.78789125.95204426.29236226.55260526.5886389999999827.00502827.42942427.56555227.56555227.8458130000000128.31024728.68659928.7226319999999829.1270100000000129.5754290000000129.81565329.85969430.15997530.42422230.68846930.71649530.9607229999999231.28102231.47720531.5492730000000131.75346331.96165832.2419232.2819570000000132.56221932.9305630000000133.2508620000000133.2868960000000133.57516533.86743834.147734.20775634.52405134.84835435.08857935.08857935.28075835.47694135.7211735.77321836.0734990000000136.32173136.67005636.78216137.41475237.84715538.29557438.35963438.69194539.13235639.4486510000000139.52472239.85703340.0852460000000140.18133640.16932540.26941840.48962440.63776240.64176641.21029741.8709140000000142.7877742.84782643.70062344.4333070000000145.06189545.16198845.6784746.16692746.93164147.1038020000000148.19682349.2177760000000150.19468950.38686951.0915270000000151.6040050000000152.12449252.22858953.08538953.8781354.44265754.49470654.93111355.14331155.26742755.2914555.47962655.66780155.7518855.8039280000000155.886.5 Treat0.00.004603000000000020.0138080.009205000000000020.018410.0629020.0813120.07364100000000010.113530.17950.2285940.227060.2700170.2868930.3682050.3682050.3958210.4633250.4755980.5062820.6827140.6014020.6504960.7502180.9189791.0831371.3086621.3454831.5572011.7274951.9898412.0205252.3258292.7523333.125143.1466189999999983.2402039999999993.5194263.8784263.9137134.1653189999999914.3079994.42924.5350594.3770374.6562589999999985.0167945.0551484.8388279999999994.7114899999999994.7912684.9937815.0413415.3957385.5875109999999895.6473455.4371615.759345.6412085.664220999999995.8099696.3407976.5095586.7580966.7519599999999996.6322936.6629769999999856.9038446.9882256.9836227.0388537.298137.3610320.01.5974919999999993.3150963.5873509999999985.717347.3828960000000019.1365349.44081811.80702913.50461416.03497816.35928117.9127319999999820.66330121.56814621.7002722.58509623.61405725.05540425.479827.39358828.4225489999999828.49461628.57068730.45244531.4533832.19407232.25412833.25105933.99575534.95264835.00870135.8014409999999936.30591236.69827936.80237636.934537.09865337.53906437.61913937.9994940000000138.34381638.62007438.69214138.92035439.11253439.43283339.54894239.69307639.77315139.79717439.84521840.03739840.30564840.63795940.69401140.75006440.88619141.0783741.07036341.46272941.9591930000000141.99522742.45565742.94411343.42055843.42856643.97707844.51357945.3583680000000145.47447746.08704946.5434755 Treat (Calcite Precip)3.43.43.43.13.13.13.33.33.33.73.73.73.73.73.73.758.2555.051.7548.2545.041.7538.2535.031.7528.2525.2522.2519.2516.2513.2510.256.5 Treat (Calcite Precip)0.370.370.371.031.031.030.960.960.960.550.550.550.630.630.631.171.171.170.740.740.740.450.450.453.833.833.834.474.474.475.845.845.8410.7510.7510.7557.552.547.542.537.532.527.522.517.512.58.254.0
Tip Resistance, MPa
Depth, cm
Calcite Precipitation, %
Excavation
Urease activity
Ureolytic bacteria from enrichments were isolated into pure culture
Each bacteria was cultured in nutrient broth(NB) alone*, and in NB supplemented with 100 mM (NH4)2SO4 or with 100 mM urea.
16s analysis for identification
Cells were lysed by sonication and a crude extract was isolated by centrifugation.
* Three isolates did not grow in NB alone
Isolation of ureolytic bacteria
IdentificationSoil sourceSoil typeSporosarcina WB1Willipa Bay, WATidal Sporosarcina WB5Willipa Bay, WATidal Sporosarcina WB6Willipa Bay, WATidal Bacillus WB7Willipa Bay, WATidal Sporosarcina R-31323Snake River, IDSandProvidencia vermicolaSpokane, WAHigh organicArthrobacter Tibet-ITa1Spokane, WAHigh organicLysininbacillus sphaericusLane Mountain, WAMined quartz silicaLysininbacillus sphaericusSnake River, IDMined alluvialBrevibacterium stationisMoscow, IDLoessUrease activity
NBE. coliWB1WB5WB6WB7LM4S1L8G1G8I1S. past.7.0506.710382513661299.6721311407.0218181999999445.8024691199.9347639484978116.1717682020802227.71NH3+E. coliWB1WB5WB6WB7LM4S1L8G1G8I1S. past.9.0506.8823529411756661.5453195123.144827586207744.4754.2154255236.194444484.6764091858037563.30684253915911206.31501.7257525083612973.0UreaE. coliWB1WB5WB6WB7LM4S1L8G1G8I1S. past.8.0389.5914994096802461.9264706430.07383627608352443.682077922078783.0197487871.994240550.560683760683741071.65991902834679.651016.1846153846151273.11004784689
Isolate
Specific activity (m/min/mg protein)
Summary
Calcite can be precipitated by indigenous bacteria in quantities sufficient to significantly strengthen soil
The process works in a range of soil types
Precipitation experiments were successful both on a laboratory scale and in in situ field experiments and simulations
The use of indigenous ureolytic bacteria results in less clogging and more even distribution of calcite
Soil bacteria capable of constitutive regulation of urease are more prevalent and more widely distributed than previously thought
The cost are comparable to existing methods and likely less expensive than the use of exogenous bacteria
Publications and Patent
Publications
Precipitation of calcite by indigenous microorganisms to strengthen liquefiable soils. Accepted by Geomicrobiology Journal.
Cone penetration tests on soil in which calcite was precipitated by indigenous bacteria in a soil microcosm. Pending submission to the Journal of Geotechnical and Geoenviromental Engineering.
Urease regulation of ureolytic bacteria isolated from six soils in which calcite was precipitated by indigenous bacteria. Pending submission to Geomicrobiology Journal.
Bio-induced Calcite, Iron, and Manganese Precipitation for Geotechnical Engineering Applications (Second Author). Geofrontiers conference paper accepted.
Patent
In situ precipitation of CaCO3 by indigenous microorganisms to improve mechanical properties of a geomaterial. Patent filed in July 2010
Acknowledgements
Committee Members
Dr. Ronald Crawford
Dr. Lee Fortunato
Dr. Thomas Weaver
Dr. Barbara Williams
Environmental Biotechnology Institute
Members
Tonia Green
Dr. Martina Ederer
Stephanie Smith
Dr. Lee Deobald
Department of Civil Engineering
Ryan Lewis
Aaron Lewis
Office of Technology Transfer
Dr. Gene Merrill
Dr. Karen Stevenson
Funding
NSF Grant 0700918
36
Urease specific activity and fold change
Approximate costs
* 3 treatments
Unimproved sites
Improved sites
*
Bio-Induced cementation can be used under existing structures and in situations where other methods may not suitable, such as sites with buried utilities
38
0
0.5
1
1.5
2
2.5
3
3.5
30 L 30 H 60 L 60 H 90 L 90 H 150 L 150 H
% Calcite (w
t/wt)
Depth (cm)
Effects of [C] on Calcite %
0
0.5
1
1.5
2
2.5
3
3.5
30L30H60L60H90L90H150L150H
%
C
a
l
c
i
t
e
(
w
t
/
w
t
)
Depth(cm)
Effectsof[C]onCalcite%
E. coli WB1 WB5 WB6 WB7 LM4 S1 L8 G1 G8 I1 S. pasteuriiMedia
NB 7 507 300 NG NG 407 446 200 116 228 NG NGNH4 9 507 662 123 744 754 236 85 63 206 502 871Urea 8 390 462 430 2444 783 872 51 1072 680 1016 1273
E. coliWB1WB5WB6WB7LM4S1L8G1G8I1S. pasteurii
Media
NB7507300NGNG407446200116228NGNG
NH495076621237447542368563206502871
Urea8390462430244478387251107268010161273
Isolate WB1 WB5 WB6 WB7 LM4 S1 L8 G1 G8 I1
Fold change from
NB to NH4 0.0 1.2 0.9 -0.5 -0.6 -0.5 -0.1
NB to urea -0.2 0.5 0.9 1.0 -0.7 8.2 2.0
NH4 to urea -0.2 -0.3 2.5 2.3 0.0 2.7 -0.4 15.9 2.3 1.0
Isolate WB1 WB5 WB6 WB7 LM4 S1 L8 G1 G8 I1
Fold change from
NB to NH
4
0.0 1.2 0.9 -0.5 -0.6 -0.5 -0.1
NB to urea -0.2 0.5 0.9 1.0 -0.7 8.2 2.0
NH
4
to urea -0.2 -0.3 2.5 2.3 0.0 2.7 -0.4 15.9 2.3 1.0
$-
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Deep Dynamic Compac6on
Vibrocompac6on
Vibroreplacement (stone colum
ns)
Deep Soil M
ixing
Jet Grou6ng
Compac6on Grou6ng
Bio Induced Cementa6on
Cost of Treatmen
t per m
3
Method of Soil Treatment