Effects of microorganisms on hydraulic conductivity decrease in infiltration

European Journal of Soil Science, June 1998,49, 231–236

Effects of microorganisms on hydraulic conductivitydecrease in infiltration

K . S E K I , T . M I YA Z A K I & M . N A K A N ODepartment of Biological and Environmental Engineering, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113, Japan

Summary

Microorganisms can clog pores in soils and decrease hydraulic conductivity and infiltration. We didthree column experiments to clarify the effects. In all three columns, glucose solution of 50µg cm23

was percolated for 120 days, and both the saturated hydraulic conductivity,Ks, and the volumeratio of the gas phase,a, were measured continuously. TheKs decreased rapidly for the initial10 days, and it slowly decreased for the following 110 days. By adding chloramphenicol to thesecond column as bactericide and cycloheximide to the third column as fungicide, we observedclogging by bacteria and fungi, respectively, bacterial clogging proceeding more rapidly than thefungal clogging. The volume of the gas phase increased and reached the maximum value of 30.6%after 103 days from the beginning of percolation. This large amount of gas was retained in thesoil pores as bubbles and occluded the pathways of water, resulting in the decrease inKs. Whenthe percolating solution was changed to sodium azide (a strong biocide), after 120 days the volumeof the gas phase decreased rapidly, andKs increased simultaneously.

Introduction

When soil is continuously submerged with nutrient solutionits saturated hydraulic conductivity,Ks, decreases with time.Allison (1947) explained that one of the causes of thisdecrease is biological clogging of soil pores with microbialcells and their synthesized products, slimes, or poly-saccharides.

Biological clogging can occur when wastewater is recycledby sprinkler irrigation (de Vries, 1972), in septic tank filters(Kristiansen, 1981; Joneset al., 1993), and in bioremediationpractices (Leeet al., 1988; Jenningset al., 1995). It is thena nuisance. In other circumstances it can be advantageous.Preul (1968) reported that infiltration rate of domesticwastewater stabilization ponds decreased in 3 years ofoperation and prevented excess infiltration. Changet al.(1974) showed that the growth of microorganisms thatproduce polysaccharides sealed animal wastewater ponds.Biological clogging can also control seepage in irrigationchannels (Ragusaet al., 1994) and small dams (Rengasamyet al., 1996) at little cost.

The microbial cells responsible for biological clogginginclude bacteria (Gupta & Swartzendruber, 1962; Franken-berger & Troeh, 1982), fungi (Sekiet al., 1996), and algae(Ragusaet al., 1994). Cunninghamet al. (1991) showedthat theKs of glass spheres and quartz sand decreases with

Correspondence: K. Seki. E-mail: [email protected] 3 December 1996; revised version accepted 15 October 1997

© 1998 Blackwell Science Ltd 231

the development of biofilms ofPseudomonas aeruginosa.Biofilms form when a solution rich in nutrients is percolatedin coarse-textured porous media (Rittman, 1993; Vandevivereet al., 1995), whereas in natural soils microcoloniespredominate (Harveyet al., 1984). Microbially synthesizedpolysaccharides (Fehrmann & Weaver, 1978; Whitfield, 1988)and polyuronide (Thomaset al., 1966) also cause decreases inKs (Avnimelech & Nevo, 1964; Vandevivere & Baveye, 1992).

Bacterially synthesized gas such as methane can alsocauseKs to decrease by occluding pore necks as bubblesin sand (Sanchez de Lozadaet al., 1994), peat (Reynoldset al., 1992), and Andisols (Sekiet al., 1996). Faybishenko(1995) showed that entrapped air exists in soil pores aseither mobile air or immobile air, and it reduces thehydraulic conductivity of soil.

Miyazaki (1993) showed that biological clogging is severein the hardpan layer of paddy soils, whereas in upland andforest Andisols it is not. One possible reason for thedifference is that there are fewer microbes in paddy soilthan in upland and forest soil, but when nutrient solutionis supplied the microbes proliferate. Marshall (1988) showedthat in oligotrophic habitats, starved bacteria survive onsolid surfaces, and that when the substrate is continuallyreplenished biofilm develops rapidly.

It is difficult to distinguish the contributions of each ofthe above factors to the decrease inKs. Here we give theresults of a series of column experiments and discuss theeffects of microbial activities on decreases inKs.

232 K. Sekiet al.

Table 1 Soil sample and experimental set-up

Value

Soil characteristic% clay 15% silt 35% sand 50Particle density /g cm–3 2.64Total C /g kg–1 31.2Total N /g kg–1 2.51Number of bacteria /ga 2.0 3 107

Number of fungi /ga 2.4 3 104

Experimental conditionsBulk density /g cm–3 0.65% porosity 75.4

a Dilute plate counting method (Sekiet al., 1996).

Figure 1 Scheme of the flow system (not to scale).

Materials and methods

Soil

We used the hardpan layer (25–30 cm depth) from a paddyfield on Andisols in Tokyo for the column experiments.Characteristics of this soil are shown in Table 1. The soil wassieved to pass 2 mm and dried to a water content of 800 g kg–1.

Flow system and procedures

We packed the sample in an acrylic plastic column 5 cm indiameter and 1 cm high (Figure 1) and saturated the sampleovernight from the bottom. The column height was set at 1 cmbecause in most previous work biological clogging occurred

© 1998 Blackwell Science Ltd,European Journal of Soil Science, 49, 231–236

Table 2 Solutions applied to the flow system

Run Solution Bacteria Fungi

GCO Glucose 50µg cm–3 (Control) 1 1

GCH Glucose 50µg cm–3 1 chl. 2 mg cm–3 – 1

GCY Glucose 50µg cm–3 1 cyc. 1 mg cm–3 1 –SAZa Sodium azide 50µg cm–3 – –

chl., chloramphenicol; cyc., cycloheximide.1, expected growth; –,expected decline.a Seki et al. (1996).

within 1 cm from the inlet of nutrient solution (Thomaset al.,1966; Rice, 1974; Sekiet al., 1996).

After packing, glucose solution was applied to the soilsurface from a Mariotte bottle. The average hydraulic gradientin the column was set at 1 by keeping the height of theMariotte bottle and the drip tube constant. Glass filters 4 mmthick were used to support the sample at the top and bottomends of the column.

Experimental conditions

We conducted three column experiments (Table 2). In the firstcolumn glucose solution of 50µg cm–3 (GCO) was used assubstrate for microbial growth. In the second column glucosesolution with chloramphenicol (GCH) was used to kill bacteria.In the third column glucose solution with cycloheximide (GCY)was used to kill fungi. Bacterial clogging and fungal cloggingcan thus be identified separately. Sekiet al. (1996) also did anexperiment with sodium azide solution (SAZ), and we shallrefer to this in the discussion.

In all three experiments we changed the flowing solutionfrom glucose to sodium azide (50µg cm–3) to kill all microbesafter percolating glucose solution for a given period. Wecovered three columns with black sheets to prevent photosyn-thesis. In this way algal growth was prevented, and there wasno algal clogging (Ragusaet al., 1994). All the experimentswere done at 30°C to enhance microbial activity. This is onlya little warmer than the air temperature in August in Tokyowhere the average temperature over the last 30 years hasbeen 27.1°C.

Saturated hydraulic conductivity

We calculated the flux of solution from the measured value ofthe discharge rate. The hydraulic heads at the inlet and outletof the column were measured by piezometers. Then wecalculated the saturated hydraulic conductivity,Ks, fromDarcy’s equation:

∆HQ 5 –Ks , (1)

∆Z

Microbial effects on hydraulic conductivity233

whereQ is the flux of percolation,∆H is the head differencebetween the inlet and outlet of the column, and∆Z is thedifference in height between the inlet and outlet of the column.In this way,Ks of the column including the upper and lowerfilter was obtained. We assume that clogging at both the glassfilters and soil proceeds at the same rate, because Sekiet al.(1996) show that the clogging of glass filters proceeds at muchthe same rate as in the clogged region of the soil sample.Using this assumption, the observedKs equals theKs of thesoil sample. Actually we use the term ‘saturated hydraulicconductivity’, Ks, even though the soil was not completelywater-filled and the volume of gas phase increased to themaximum value of 30.6%. The term ‘saturated’ means thatthe water was not retained in the soil by capillary action(Sanchez de Lozadaet al., 1994).

Volume ratio of gas phase

During percolation we stopped the flow, removed the soilcolumns from the flow system, measured the mass of thecolumn, and after that, put the column back in the system andstarted percolation again. The volume ratio of the gas phase,a, was calculated by the following equation:

ρd ρt – ρda 5 1 – – , (2)

ρp ρw

whereρd is the dry bulk density,ρp is the particle density,ρt

is the wet soil density, andρw is the density of water. Wet soildensity was calculated from the mass and the volume of thecolumn, and the other variables used in this calculation aregiven in Table 1.

Results and discussion

Saturated hydraulic conductivity

Figure 2 shows the changes in saturated hydraulic conductivities(above) and in the volume ratio of gas phase (below). In theGCO run,Ks increased from the initial value of 23 1023 cm s21

to 4 3 10–3 cm s–1 at 0.65 days, and decreased rapidly until4 3 10–5 cm s–1 at 10 days, followed by a gradual decreaseuntil 3 3 10–6 cm s–1 at 120 days. After we altered thepercolation solution from glucose to sodium azide at 120 days,Ks increased rapidly to 53 10–4 cm s–1 at 128 days, and thendecreased to 23 10–5 cm s–1 at 137 days when it stabilized.

In the GCH run the change inKs was similar to that inGCO until 120 days, after which the change inKs was unlikethat in GCO. In the GCY run, the initial decrease ofKs wasmore rapid than in the GCO run, and after 120 daysKs didnot change as it did in the GCO run.

In the SAZ run saturated hydraulic conductivity in the top1-cm layer of the 12-cm high column did not change muchfor 39 days.


Figure 2 Change in saturated hydraulic conductivity,Ks (above), andvolume ratio of gas phase,a (below), of soil sample. The percolatingsolutions are GCO (d), GCH (s), and GCY (n). All solutions werechanged from glucose to sodium azide at 120 days. The closedtriangles (m) at the top of the figure are reference data (Sekiet al., 1996).

Volume ratio of gas phase

Initial values of the volume ratio of gas phase,a, were14.0%, 15.0% and 18.4% for the GCO, GCH and GCY runs,respectively. They decreased rapidly with percolation. In theGCO runa decreased initially and increased remarkably from3.6% at 40 days to 30.6% at 103 days. In the GCH runadecreased gradually until 120 days. In the GCY runa fluctuatedaround 10% until 120 days. When sodium azide was percolatedafter 120 days,a decreased rapidly in the GCO run and slightlyin the GCY run. The value ofa was not measured in theSAZ run.

Ks increase with air removal

The change ina as a function of cumulative discharge isshown in Figure 3. Linear regressions are also shown in thefigure. Absolute values of the slope of the linear regressions

234 K. Sekiet al.

Figure 3 Volume ratio of the gas phase as a function of cumulativedischarge. Percolating solutions are GCO (d), GCH (s), and GCY(n).

are the rate of air removal by dissolution. We can calculatethe amount of air dissolved in the unit volume of the percolatingsolution. These values are 0.74µg m–3 for GCO, 1.11µg m23

for GCH, and 0.72µg m–3 for GCY. For all the three columns,Ks increased with entrapped air dissolution. As an example,change inKs as a function ofa of the GCO run is shown inFigure 4. As entrapped air is removed from the start of thepercolation to 0.65 days,Ks increased from 23 10–3 cm s–1

to 4 3 10–3 cm s–1.In this experiment increase inKs due to the dissolution of

entrapped air started at the beginning of percolation andended in 1 day, whereas in most of the previous percolationexperiments it was followed by initial decrease inKs andstarted from 10 to 20 days (Allison, 1947; Sekiet al., 1996).This difference arose because the height of the column inour experiments was much less than that used in previouspercolation experiments. The volume of percolating solutionrequired for a certain decrease ina is inversely proportionalto the height of the column.

Clogging by bacteria and fungi

For the GCH and GCY runs smaller increases of the volumeratio of gas phase were observed than in the GCO run (Figure2). Therefore, we observed the single effect of biologicalclogging with microbial cells and their synthesized productsonKs. In the GCH run chloramphenicol worked as a bactericide,and fungi clogged the pores. In the GCY run cycloheximideworked as a fungicide, and the pores were clogged by bacteria.


Figure 4 Saturated hydraulic conductivity,Ks, as a function of volumeratio of the gas phase,a, for the GCO run.

Figure 2 shows that bacterial clogging proceeded more rapidlythan fungal clogging. It may be because bacteria grow fasterthan fungi on the soil surface. The rate of fungal clogging (therate of decrease inKs of the GCH run) is almost the same asthe rate of clogging in the GCO run. It suggests that fungalclogging was predominant in the GCO run, as Sekiet al.(1996) showed by the dilute plate counting method.

Possibility of dry bulk density increase

We calculated the volume ratio of the gas phase by assumingthat the dry bulk density is constant during percolation.However, dry bulk density may change, because part of theincrease in microbial cells and their synthesized productsaccumulates in soil pores. We obtained the dry bulk densityvalue of 0.65 g cm–3 gravimetrically after the end of thepercolation, and therefore microbial cells and their synthesizedproducts that accumulated in soil pores may have beendestroyed during drying at 105°C. Dry bulk density measuredin this way does not include the mass of microbial cells andtheir synthesized products destroyed by drying. In this sectionwe include the mass of microbial cells and their synthesizedproducts in the dry bulk density, in other words density of theentire solid phase.

Figure 2 shows that the volume of gas decreased graduallyfrom 15 to 108 days in the GCH run. The volume wascalculated from the increase of the measured value of wet soildensity during this period, but we cannot say whether thisincrease is the result of the decrease in volume of gas or the

Microbial effects on hydraulic conductivity235

Figure 5 Change in dry bulk density for the GCH run, calculatedassuming that volume ratio of the gas phase is constant after 15 days.

increase in dry bulk density or a combined effect of these twophenomena. Since the calculation based on the first assumptionwas done in Figure 2, we now take the second assumption;we assume that the volume of gas is constant from 15 daysto 120 days and calculate the change in dry bulk density(Figure 5). Dry bulk density increased from 0.65 g cm–3 to0.73 g cm–3 from 15 to 108 days. This is the largest estimateof the increase in dry bulk density, because we assumed thatgas was not removed between 15 and 120 days. From massbalance estimates, the bulk density cannot increase this muchif the applied glucose was the only source of mass increase.Part of the increase may have been due to the accumulationof chloramphenicol.

Occlusion of pore necks by bubbles

In the GCO run the decrease inKs was caused not only bybiological clogging but also by occlusion of pore necks bybubbles of gas which occupied the volume of 30.6% atmaximum. The bubbles were mainly of methane produced bybacteria (Sekiet al., 1996).

After percolation, the solution was changed to sodium azideat 120 days in the GCO run; the volume ratio of gas decreased,and hydraulic conductivity increased simultaneously (Figure4). It seems that the gas occlusion was one of the causes ofdecrease inKs. By linear regression between cumulativedischarge and the volume ratio of gas as in Figure 3, theamount of gas dissolved in the unit volume of solution was4.2 µg m–3. We could see bubbles of gas in the effluentdischarging from the soil column. It indicates that part of thegas dissolved in the solution became bubbles.

In the GCH run methane-producing bacteria were killed,


and no gas was produced. In the GCY run the volume ratioof the gas phase increased gradually from 6.8% at 17 days to13.3% at 64 days, but it did not increase any more. The gasproduction was slower than that in the GCO run because theKs decreased more rapidly. The smaller value ofKs resultedin less solution percolating in any one period, which meansthat there was less substrate for methane production. This iswhy the volume of gas phase did not increase in the GCY runas much as in the GCO run.

Combined effect

The fact that in all columnsKs did not return to the initialvalue after the change of percolate to sodium azide shows thatnot all the dead microbial cells and their synthesized productswere removed (Ripley & Saleem, 1973; Sekiet al., 1996). Inthe GCO runKs increased from 120 to 128 days with gasremoval and decreased from 128 to 137 days. Reduction ofKs

in the GCO run was caused by the combined effect of bothbiological clogging and gas occlusion. Therefore, when gaswas removed from 120 to 128 days one of the causes ofKs

reduction, that is gas occlusion, was eliminated, andKs

approached the initial value.The reduction ofKs after 128 days is difficult to explain.

The microbes were killed during the 120–128-day period, sothe amount of living microbes did not change after 128 days.The volume ratio of the gas phase did not change after128 days, either. This means that the reduction ofKs duringthis period was not due to microbial clogging or gas occlusion,and may be due to some kind of change in soil structure.

One explanation is as follows. As the volume of the gas phaseincreased from 15 to 120 days, the microbially synthesized gaspushed apart soil particles. This gas was removed by dissolutionor discharge during 120–128 days. At 128 days the porespreviously occupied by the gas remained large, acting as thepath for water, with the result thatKs increased. From 128 to137 days, the pores previously occupied by the gas shrankand approached the initial size, and theKs decreased again.However, this explanation is not persuasive, because the gaspressure might not be strong enough to push apart soil particlesas postulated here.

The stabilized value ofKs at 150 days was approximatelythe same as in the GCH and GCY runs. Biological cloggingcan decreaseKs to the order of 10–6 cm s–1 by reducing thecross-sectional area of the pathway of percolating solution.Gas occlusion can also decreaseKs by blocking the pathwaysof water and also by changing the arrangement of the soilparticles. The combined effect of these two phenomena didnot decreaseKs to much less than 10–6 cm s–1.

Conclusions

When glucose solution of 50 mg kg–1 was percolated througha soil column,Ks diminished as a result of biological clogging

236 K. Sekiet al.

and gas occlusion. Fungal clogging was more important thanbacterial clogging in our experiment. When fungi were killedby cycloheximide, pores were clogged by bacteria. Bacterialclogging was more rapid than fungal clogging, which suggeststhat bacteria grow on the soil surface more rapidly than fungi.

The volume of the gas phase increased with time and reacheda maximum value of 30.6% after 103 days from the beginningof percolation. This large amount of gas was retained in the soilpores as bubbles and occluded the pathways of water, resultingin the decrease inKs. Decrease inKswas caused by the combinedeffect of biological clogging and gas occlusion. We concludethat gas occlusion was one of the causes of the decrease inKs

because when percolating solution was altered to sodium azide,a strong biocide, the volume of gas decreased rapidly andKs

increased simultaneously. We also suggested that occlusion ofgas in soil pores altered the arrangement of soil particles.

In the past biological clogging and gas occlusion have beenstudied separately. However, they proceed simultaneously innatural conditions and affectKs in a complex manner.

Acknowledgements

We thank Mr Hiromi Imoto of the University of Tokyo forhis support with our experiments and Dr Naoki Sakai of theUniversity of Tsukuba for providing us with the soil samplingsite.

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Effects of microorganisms on hydraulic conductivity decrease in infiltration

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