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    Removal behavior and chemical speciation distributions of heavy metals in sewage sludge during bioleaching and combined bioleaching/Fenton-like processes

    Bioleaching processVariation of pH and ORP during bioleaching processpH and ORP of the sludge are widely known to be the important parameters influencing heavy metal solubilization during bioleaching process, as well as the activity of iron-oxidizing microorganisms10,26,27. The variation of sludge pH and ORP during the single bioleaching process is presented in Fig. 1.Figure 1Variation of pH and ORP during bioleaching process.Full size imageAn appropriate pH could enhance the activities of microbes, affecting the release of metals and the stability of metal ions in the liquid phase5. As shown in Fig. 1, the pH value of sewage sludge quickly decreased from 6.44 to 3.07 in the first 6 days, due to the oxidation of Fe2+ and metal sulfides, the production of sulfuric acid, ferric hydroxide and jarosite from the hydrolysis of Fe3+18. Then the pH gradually decreased to 2.89 on the 10th day. The change of ORP followed an opposite trend. ORP value of the sludge rapidly increased from − 155.6 mV to 480.0 mV in the first 6 days, then to 505.0 mV in the following 4 days, due to the oxidation of Fe2+ to Fe3+ by leaching microorganisms.Heavy metals solubilization and chemical speciation distribution during bioleaching processThe removal of heavy metals during bioleaching process and the distribution of chemical fractions of heavy metals before and after bioleaching are presented in Figs. 2 and 3, respectively. The single bioleaching led to the removal of Zn, Cu, Cd, Cr, Mn, Ni, As and Pb of 67.28%, 50.78%, 64.86%, 6.32%, 56.15%, 49.83%, 20.78% and 10.52% in 10 days, respectively. The solubilization efficiency was highly related to the evolution of pH and ORP, the chemical fraction distributions and the nature of heavy metals.Figure 2Removal of heavy metals during bioleaching process.Full size imageFigure 3Chemical speciation distributions of heavy metals in raw sludge and bioleached sludge, total concentration of heavy metals in the raw sludge was set as 100% (RS raw sludge, BS bioleached sludge).Full size imageFigure 2 illustrated that Zn had the highest solubilization and removal efficiency. It was found that below the threshold pH of 6–6.5, Zn could be dissolved28. Thus, the dissolving out of Zn had started at the beginning of leaching experiment with a removal percentage of 10.15% on the 2nd day. Yet the quick solubilization of Zn was observed from the 4th day (pH 4.01). And until the 6th day (pH 3.00) when the solubilization percentage of Zn was 65.71%, the leaching rate of Zn was slowed down due to the stable pH. In the raw sludge, Zn mainly existed in mobile forms (exchangeable/acid soluble and reducible forms) as shown in Fig. 3. After bioleaching, the solubilization efficiencies of Zn in exchangeable/acid soluble form and reducible form was 58.66% and 87.93%, respectively. Meanwhile, 48.27% of Zn in oxidizable form was also dissolved out due to the oxidation of metal sulfide and loss of sludge organic matter. However, Zn in residual form remained almost unchanged in the bioleached sludge due to its high stability.It has been pointed out that Cu could be rapidly solubilized below pH of 3.7 or under a high ORP condition29. As shown in Fig. 2, in the first 4 days, the solubilization efficiency of Cu was relatively low (11.44%). The removal rate of Cu increased rapidly to 43.54% on the 6th day due to the increase of ORP (480 mV). The proportion of Cu in exchangeable/acid soluble form increased by 55.16% after bioleaching, probably because the solubilized Cu2+ was re-adsorbed on the EPS of sludge cells30,31. Most of Cu was present in reducible and oxidizable forms in the raw sludge as shown in Fig. 3, because the complexation of copper and organic materials was relatively stable30,32,33. The removal percentages of Cu in reducible and oxidizable forms were 71.11% and 61.83% after bioleaching, respectively, which was the main reason for Cu removal.Cd could be solubilized rapidly under acidic conditions as shown in Fig. 2, which is consistent with the previous study34. The solubilization of Cd could be finished in 6 days with the removal rate of 64.36%. Cd was mainly present in mobile forms (91.07%) as shown in Fig. 3, which agreed with the findings of Zeng et al.35 Thus, the acid dissolution was the main removal mechanism of Cd34. Due to the low pH of the bioleached sludge, the content of Cd in mobile forms decreased by 62.77% after bioleaching. Furthermore, Cd in immobile forms (oxidizable and residual forms) also reduced significantly.The previous study found that Cr was relatively stable with the dissolved pH threshold of 2.3–3.028. Although the percentage of Cr present in mobile forms was over 40%, the removal rate of Cr (6.32%) was the lowest among all the heavy metals investigated as shown in Fig. 2, because the lowest pH of the bioleached sludge was about 2.9, which was close to the dissolution threshold limit of Cr.As shown in Fig. 2, Mn and Ni were solubilized quickly in the first 4 days. The solubilization percentage of Mn and Ni were 56.14% and 49.83% after bioleaching, respectively. Mn and Ni mainly existed in the mobile forms (Mn 82.05%, Ni 76.08%). In the early stage of bioleaching, the removal rates of Mn and Ni were closely related to the variation of pH and displayed obvious acid dissolution mechanism. After bioleaching, the concentrations of Mn in exchangeable/acid soluble, reducible and oxidizable forms were reduced by 34.65%, 78.82% and 90.84%, respectively. As for Ni, the removal rates in such forms were 34.66%, 74.58% and 64.99%, respectively. Thus, the higher extraction efficiency of Mn and Ni arose from mixed bioleaching mechanisms, which contain acid dissolution, oxidation and reduction by Fe2+/Fe3+.Relatively low removal efficiency of As (20.78%) was observed in this study. One reason, as shown in Fig. 3, was that As was mainly distributed in residual form with high stability. The other reason was that the dissolved As3+ could be oxidized to As5+ (AsO43-) by Fe3+ generated from the metabolism of iron-oxidizing bacteria, and then insoluble FeAsO4 could be produced through the reaction of AsO43- and Fe3+, which resulted in the reprecipitation of As34.Pb in exchangeable/acid soluble form was not detected in the raw sludge, and mainly existed in reducible (59.20%) and oxidizable (23.19%) forms. The removal rates of Pb in reducible and oxidizable forms were 33.51% and 58.17% after bioleaching, respectively. However, the insoluble compounds such as PbSO4 (Ksp = 1.62 × 10–8) could be generated during the bioleaching process36, which resulted in a significant increase in the concentration of Pb in residual form (from 10.89 to 25.00 mg/kg), and thus led to the low removal ratio of Pb (10.52%).To summarize, the solubilization efficiencies of Zn, Cu, Cd, Mn and Ni, which mainly existed in mobile forms in the raw sludge, were relatively high due to the instability of these metals, while the removal rates of Cr, As and Pb, which mainly existed in immobile forms, were relatively low. However, the contents of most heavy metals in mobile forms decreased obviously after bioleaching and would lead to the corresponding reduction of the environmental risk of the sludge.Combined bioleaching/Fenton-like processEffect of H2O2 dosage on the removal of heavy metals under various pH conditionsPrevious studies have shown that the production ability of hydroxyl radical during the Fenton-like reaction process could be enhanced under pH range of 2.5–4.5, and meanwhile, the amount of H2O2 directly influences the production of hydroxyl radical10,18. Therefore, as shown in Fig. 4, the effects of H2O2 dosage on the solubilization efficiencies of heavy metals were investigated at different stages of the bioleaching process, when the pH values of the bioleached sludge were 4.5 (about 3.5th day), 4.0 (4th day) and 3.0 (6th day).Figure 4Effects of H2O2 dosage on the removal efficiency of heavy metals under various pH conditions.Full size imageWith the increasing concentrations of H2O2 (0.0–8.0 g/L), the solubilization efficiency of Zn increased significantly at pH of 4.5 (Fig. 4) due to the oxidation of metal sulfide and organics by hydroxyl radical10. However, the solubilization percentages of Zn barely changed with further increase of H2O2 dosage (from 8.0 to 15.0 g/L). The solubilization percentage of Zn at the H2O2 dosage of 8.0 g/L (pH of 4.5) was significantly higher than when only using single bioleaching (75.31% vs. 67.64%). The enhancement of solubilization efficiency of Zn at a pH of 4.0 and 3.0 was not very noticeable (Fig. 4), because most of the Zn in immobile forms was dissolved out by bioleaching. The highest solubilization percentages of Zn were 74.96% at a pH of 4.0 and 75.53% at a pH of 3.0, which were 7.32% and 7.89% higher than that of the single bioleaching process.Due to the lower dissolved pH threshold of Cu compared with Zn, the solubilization efficiency of Cu was significantly affected by the dosage of H2O2 at a pH of 4.5 and 4.0 as shown in Fig. 4, while when the reaction pH was 3.0, the subsequent Fenton treatment had a relatively small impact on the removal of Cu. The highest removal rate of Cu (52.17%) was obtained at pH of 3.0 and H2O2 dosage of 13.0 g/L, which was slightly higher than that of the single bioleaching (50.78%). The change in solubilization efficiency of Cd was similar to that of Cu. When the pH values were 4.5 and 4.0, the solubilization percentages of Cd with H2O2 dosage of 15.0 g/L were 4.59% and 1.23% higher than that of the single bioleaching process, respectively. Meanwhile, the highest solubilization percentage of Cd (71.91%) could be reached at a pH of 3.0 and H2O2 dosage of 13.0 g/L, which was higher than that of the single bioleaching process (64.86%).The addition of H2O2 did not increase the removal rate of Cr significantly as shown in Fig. 4. At a reaction pH of 4.5, the solubilization percentage of Cr was 7.59% with H2O2 dosage of 15.0 g/L, which was a little higher than that of the single bioleaching process (6.32%), while the highest solubilization percentages of Cr could reach 11.63% and 9.18% at pH of 4.0 and 3.0, respectively, with H2O2 dosage of 15.0 g/L.The solubilization process of Mn and Ni displayed similar trend as shown in Fig. 4. The solubilization percentage of Mn was not significantly improved when the H2O2 dosage was increased from 5.0 to 11.0 g/L at pH of 4.5 and 4.0, but a much faster increase of the removal rate was observed with the H2O2 dosage over 13.0 g/L. It could be due to the enhanced oxidizing ability of Fenton-like reaction with abundant H2O2. However, the solubilization efficiency of Mn under a pH of 3.0 began to increase with H2O2 concentration of 11.0 g/L, which could be attributed to the high efficiency of Fenton action under lower pH15. The highest removal percentage of Mn was 66.29% at pH of 3.0 and H2O2 dosage of 15.0 g/L, while the removal percentage of Mn in the single bioleaching process was 56.14%. The removal behavior of Ni at various pH was consistent with Mn. The highest removal rate of Ni (65.81%) was found at a pH of 3.0 with H2O2 dosage of 15.0 g/L, which was significantly improved, compared with the single bioleaching process (49.83%).On the contrary, the removal efficiency of As and Pb in the combined process was not promoted compared with the single bioleaching process. Due to the strong oxidizing capacity of Fenton-like process, the yield of SO42− and insoluble FeAsO4 could be improved. Correspondingly, Pb2+ could be transformed into residual form, such as insoluble PbSO410. Therefore, the removal efficiencies of As and Pb decreased in the combined process. The highest removal rates of As and Pb after Fenton-like treatment were 12.46% and 10.20%, respectively.In the combined process, higher solubilization efficiencies of most heavy metals (Zn, Cu, Cd, Mn, Ni, Cr) could be achieved in 6 days. The removal efficiency of heavy metals (except Cr, As and Pb) of combined process (pH of 3.0, H2O2 dosage of 15 g/L) is higher than that of the single bioleaching process. The removal rate of Zn, Cu, Cd, Mn and Ni increased by 7.89%, 0.38%, 5.56%, 10.15% and 15.35%, respectively. Meanwhile, the total concentrations of heavy metals measured in this study after treatment could meet the control standards of pollutants in sludge for agricultural use of China (National Standard GB 4284-2018). The removal of As and Pb was not improved by the combined process, other methods such as chemical leaching, electrokinetic remediation and phytoremediation could be considered as alternatives. However, their transformation into insoluble forms may also reduce the bioavailability of heavy metals and increase the environmental safety of the treated sludge. For that reason, the chemical speciation distributions of heavy metals in the combined process were further analyzed in detail.Chemical fraction distributions of heavy metals in the combined processIt can be seen in Fig. 4 that the solubilization efficiency of most heavy metals did not change significantly with H2O2 dosage below 8.0 g/L. Therefore, the chemical speciation changes of heavy metals after Fenton treatment under H2O2 dosage of 11.0, 13.0 and 15.0 g/L, as shown in Fig. 5, were discussed.Figure 5Change of chemical speciation distributions of heavy metals under different H2O2 dosage at a pH of 4.5, 4.0 and 3.0, total concentration of heavy metal in the raw sludge was set as 100%.Full size imageUnder various pH conditions, the contents of Zn in all of the four forms showed a downward trend along with the increasing H2O2 dosage (Fig. 5). After bioleaching, Zn mainly existed in exchangeable/acid soluble form under the final pH of 4.5 (64.89%), pH of 4.0 (73.33%) and pH of 3.0 (80.82%). The removal of Zn in exchangeable/acid soluble form showed good correlation to the dosage of H2O2, which might be attributed to the destruction of EPS, and the released heavy metals were transferred to the liquid phase. Meanwhile, the improvement of sludge dewaterability could also promote the removal of heavy metals. After Fenton-like reaction at a pH of 4.5, the percentages of Zn in exchangeable/acid soluble forms were reduced by 30.35%, 31.41% and 40.09% at H2O2 dosage of 11.0, 13.0 and 15.0 g/L, respectively, compared with the percentage of Zn in the sludge at the end of the single bioleaching process. However, the percentage of Zn in other forms did not change significantly after Fenton-like treatment. Therefore, the further removal of Zn in exchangeable/acid soluble form and the dewaterability improvement of sludge may be the main reasons for the higher removal efficiency of Zn in the combined process.Cu was still mainly associated with the oxidizable form after bioleaching ended at pH of 4.5, 4.0 and 3.0 (Fig. 5), which might be attributed to the preference of Cu for organic materials22. The addition of H2O2 at pH 4.5 significantly boosted the solubilization efficiency of Cu in exchangeable/acid soluble form. The percentages of Cu in exchangeable/acid soluble form in the sludge after Fenton treatment at pH 4.5 were 24.69% (11.0 g/L), 29.50% (13.0 g/L) and 38.15% (15.0 g/L), which were lower than that at the end of the single bioleaching process. Meanwhile, the content of Cu in reducible form was reduced by nearly 50% with H2O2 dosage of 13.0 and 15.0 g/L, compared with its content after bioleaching ended at pH 4.5. However, the highest removal rate of Cu in oxidizable form was only 33.20% with H2O2 dosage of 15.0 g/L. The removal efficiency of Cu in exchangeable/acid soluble and reducible forms increased with the increasing H2O2 dosage at pH 4.0 and 3.0, similar to the observation at pH 4.5. Under a reaction pH of 4.0, 47.2% of Cu in oxidizable form was removed after Fenton treatment with H2O2 dosage of 13.0 g/L, while only 28.6% was removed at H2O2 dosage of 15.0 g/L. In addition, the removal rates of Cu in oxidizable form were only 4.9–17.7% at various H2O2 dosage at a Fenton reaction pH of 3.0. The removal efficiency of Cu was reduced in despite of the increasing oxidation capacity of Fenton-like reaction. The macro-molecular organic matters could be degraded into small organic molecules during Fenton treatment process, releasing partial Cu. However, the generated small molecule organic matters had more undissociated carboxyl that would combine with released Cu31, which formed Cu in oxidizable form. Thus, it could explain the low removal efficiency of Cu in oxidizable form under stronger oxidizing condition. However, the highest removal rate of Cu (52.17%) was observed at pH 3.0 and H2O2 dosage of 15.0 g/L, due to the high reduction ratio of Cu in mobile forms at that condition.Cd mainly existed in mobile forms in the sludge after bioleaching and Fenton treatment, as shown in Fig. 5. The contents of Cd in mobile and oxidizable forms decreased with the increasing H2O2 dosage at pH 4.5. The content of Cd in exchangeable/acid soluble form after Fenton treatment at pH 4.5 and H2O2 dosage of 15.0 g/L was 29.10% lower than that at the end of the single bioleaching process. Meanwhile, the content of Cd in mobile form was decreased by 27.54% (11.0 g/L), 26.56% (13.0 g/L) and 36.72% (15.0 g/L) after Fenton treatment at pH 4.0. The removal of Cd in exchangeable/acid soluble form after Fenton treatment could be largely due to the improvement of sludge dewaterability. However, the reduction of Cd was not obvious after Fenton treatment at pH 3.0, because the solubilization threshold of most of Cd in various forms were reached after the bioleaching process ended at pH 3.0.The removal efficiency of Cr was not improved obviously by Fenton treatment in this study, as shown in Fig. 5. It was also reported that Cr was difficult to be removed by bioleaching or combined process due to its relatively high stability10. However, the content of Cr in oxidizable form after Fenton treatment at pH 4.5 was 4.76% (11.0 g/L), 9.20% (13.0 g/L) and 9.84% (15.0 g/L) lower than that at the end of the single bioleaching process, due to the strong oxidizing capacity of hydroxyl radical. And the lowest content of Cr in oxidizable form was observed after Fenton treatment at pH 4.0 and H2O2 dosages of 13.0 g/L, which was 39.4% lower than that in the bioleached sludge. Meanwhile, the highest Cr removal rate was also obtained at this condition after Fenton-like treatment. Thus, the improvement of Cr removal in combined process was mainly due to the release of Cr in oxidizable form. Furthermore, the released metals could be absorbed on the surface of oxides31, thus inevitably caused the increase of Cr in reducible form as shown in Fig. 5. The chemical speciation change of Cr after Fenton treatment at pH 3.0 was similar to that at pH 4.0.The removal efficiency and chemical speciation distribution of Mn varied obviously after Fenton treatment with different dosages of H2O2. The removal rate of Mn was improved with the increasing dosage of H2O2 at various pH values. Because most of the Mn in reducible form (over 80%) was removed by bioleaching process, the reduction of Mn in exchangeable/acid soluble form should account for the removal of a substantial part of Mn after Fenton treatment. The highest removal rate of Mn in exchangeable/acid soluble form under different pH conditions was 26.27% (pH 4.5), 25.06% (pH 4.0) and 42.18% (pH 3.0), all with H2O2 dosage of 15.0 g/L. Although nearly 30% of Mn in reducible and oxidizable forms was also removed after Fenton treatment with H2O2 dosage of 15.0 g/L at various pH values, it contributed little to the removal of Mn considering the low concentration of Mn in reducible and oxidizable forms in the raw sludge. Furthermore, the changes of Mn in residual form were not obvious under different pH.The chemical speciation change of Ni was similar to that of Mn after Fenton treatment. The contents of Ni in mobile and oxidizable forms decreased along with the increasing dosage of H2O2, as shown in Fig. 5. Meanwhile, the reduction of Ni in exchangeable/acid soluble form after the addition of H2O2 was the prime reason for the higher removal efficiency of Ni after the combined process than that after the single bioleaching process. The highest removal rate of Ni in exchangeable/acid soluble form was found with H2O2 dosage of 15.0 g/L at pH 4.0, which was 34.47% lower than that in the sludge after the signal bioleaching process. However, the highest removal efficiency of Ni (65.19%) was reached when the reaction pH was 3.0 with H2O2 dosages of 15.0 g/L due to the simultaneous reduction of Ni in reducible and oxidizable forms. The contents of Ni in reducible and oxidizable forms were reduced by 50.30% and 52.83% under this reaction condition, respectively, compared with that at the end of the single bioleaching process.As and Pb were mainly present in residual form before Fenton treatment as shown in Fig. 5. The content of As in exchangeable/acid soluble form decreased significantly due to the degradation of EPS at various pH values with the addition of H2O2. However, the content of As in residual form gradually rose with the increasing dosage of H2O2, probably because As3+ could be oxidized to As5+ by hydroxyl radical and/or Fe3+ with the formation of insoluble FeAsO434. The content of Pb in reducible form showed a trend of increase after Fenton treatment. SO42− was generated due to the oxidation of sulfur elements and/or sulfide in sludge by hydroxyl radicals with the production of insoluble PbSO410, and thus the content of Pb in residual form also increased after further Fenton treatment. Although the Fenton treatment had a negative impact on the removal of As and Pb as shown in Fig. 5, because of the formation of insoluble compounds under strong oxidizing condition, the environmental risk of these two heavy metals decreased to some extent under an appropriate condition, due to the increased proportion of immobile fractions, especially residual form. compared with the bioleached sludge.The content and proportion of most heavy metals (Zn, Cu, Cd, Mn, Ni, As) in mobile forms were lower in the treated sludge after the combined bioleaching and Fenton-like process, compared with the single bioleaching process, which was also the main reason for the high removal efficiency of these metals. Their bioavailability and toxicity were also reduced. However, Fenton treatment was found to have a negative impact on the removal of As, but the increased proportion of As in residual form also lowered its bioavailability and mobility in the environment. The increase in the content of Pb in both mobile forms (mainly in reducible form) and immobile forms (mainly in residual form) was observed under different conditions, so special attention should be paid to the chemical speciation distributions of Pb during sludge treatment process.The effect of H2O2 dosage on sludge dewaterability at different pH valuesThe changes of CST of treated sludge under various conditions are presented in Fig. 6. The CST of the raw sludge (98.7 s) was dramatically reduced by bioleaching and Fenton oxidation treatments. After bioleaching ended on the 10th day (pH 2.89), the 6th day (pH 3.0), the 4th day (4.0) and the 3.5th day (pH 4.5), CST values of 20.3 s, 24.2 s, 30.7 s and 35.0 s were observed. The decreased pH after bioleaching process could destroy the EPS and neutralize the negative charge of the sludge flocs, resulting in the release of bound water37. Moreover, sludge dewatering could also be improved by the coagulation effect of Fe2+ 10. Furthermore, hydroxyl radicals were essential to improve sludge dewatering performance by destroying EPS and porous structure during the Fenton treatment process35. Therefore, the CST value of treated sludge was reduced to 20.6 s after Fenton treatment with H2O2 dosage of 15 g/L at pH 4.5, which was comparable to the CST value at the end of the single bioleaching process. The CST values were further reduced along with the decreasing reaction pH (4.0 and 3.0) and the increasing H2O2 dosage. The lowest CST value of 12.4 s was observed at Fenton reaction pH 3.0 and H2O2 dosage of 15.0 g/L, which meant a reduction from the initial CST of 87.44%. Therefore, the combined process could lead to an obvious improvement of the sludge dewaterability and significantly reduced the treatment period.Figure 6Changes of CST under different H2O2 dosage and pH.Full size image More

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    Above- and belowground biodiversity jointly tighten the P cycle in agricultural grasslands

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    Effects of nitrogen fertilization on protein and carbohydrate fractions of Marandu palisadegrass

    In our studies with Marandu palisadegrass, a grazing management strategy with continuous stocking where 95% of the light is intercepted by the canopy resulted in forage at a height of 25 cm, a high green leaf proportion, and low amounts of dead material during the growing season23,24. The use of N fertilization4, different stocking rates, and supplementation25,26,27 are crucial for obtaining forage with a high nutritional value, resulting in a high weight gain per animal and area, and a reduction in slaughter age and greenhouse gas emissions. In the present study we did not find any interection N doses with years. Therefore, only the significative effects of N fertilization or variation within year are presented and discussed.Total and non-fibrous carbohydrates and total digestible nutrientsTotal carbohydrate concentrations decreased linearly with increasing N levels (P  More

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    Social familiarity improves fast-start escape performance in schooling fish

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    Microfluidic chips provide visual access to in situ soil ecology

    Chip designWe used our micro-engineered silicone chip termed the “Obstacle chip”26, representing a proxy of a soil pore space system containing different sets of microstructures. The chip consists of an artificial pore system open on one side for inoculum, and it is designed to investigate the growth and dispersal behaviour of soil microbes (Supplementary Fig. 1a, b). The chip’s pore-space dimensions are optimized to match the dimensions of fungal hyphae, with structure widths ranging between 4 and 100 µm, and a uniform height of ~7 µm to aid microscopy, since cells are located in the same focal plane and rarely overlay. It contains five different geometric sections accessible by soil microbes via a common entry area (Supplementary Fig. 1a). The entry area consists of an open area with round pillars of 100 µm diameter at a separation of 100 µm, holding up the chip’s ceiling. It was cut open longitudinally with a scalpel prior to bonding (see below, section ‘Chip fabrication’), ensuring direct contact of the soil with the chip’s interior. The inner section comprises a combination of differently shaped channels and obstacles constituting five experimental sections, of which two were systematically examined in this study: (1) Section C: A set of channels with sharp corners of three different types (n = 12, randomly distributed): zigzag channels (90° turns with all channel sections at ±45° angle from the main growth direction), meandering square channels (90° turns with each section oriented in either the main growth direction or perpendicular to it), ‘z’-shaped channels (sharp corners diverting 135° from the previous growth direction, with channel sections in the main growth direction and at angles of 45° and 135° from it); (2) Section D: So-called ‘diamond channels,’ with a repeated combination of 10 µm wide and 400 µm long straight channels alternating with 140 µm wide diamond-shaped widenings. This channel type is replicated in 36 channels, each containing 33 diamond widenings. The widenings were used as quantification units to count bacteria and protist cell numbers, and for determination of liquid ingression, for the experiments on dispersal via fungal hyphae. Section A of the chip contains systems of hexagonal pillars of different diameters, Section B consists of straight channels with different widths, and Section E contains two types of obstacle courses comprised of complex structures. Those and the entrance system provided space for general observations. The design was constructed in AutoCad 2015 (Autodesk), in which patterns within experimental Sections A and C were randomized using a custom script from UrbanLISP (http://www.urbanlisp.com).Chip fabricationThe microfluidic chips were moulded in PDMS on a photoresist master defined by UV lithography and bonded to glass slides, according to Aleklett et al.26. The master was made by spin coating a thick negative photoresist (SU-8 5, MicroChem Corp, USA) on a glass plate for 60 s at 1250 rpm. This generated a photoresist layer of ~7 µm. The photoresist was soft baked for 5 min at 90 °C on a hot plate, patterned by UV exposure (Karl-Suss MA4 mask aligner) and post-exposure baked. It was then developed for 3 min in mr-Dev 600 (MicroChem) and finally rinsed with isopropanol (VWR International). The PDMS slabs were produced by thoroughly mixing a PDMS base and a curing agent (both Sylgard 184, Dow Corning, USA) in a 10:1 ratio, followed by pouring the mix onto the master in a 4-mm-thick layer, and degassing it in a vacuum chamber at −25 kPa for 45 min. Then the PDMS was cured in an oven for 2.5 h at 60 °C. Once cooled, the PDMS was cut slightly larger than the designed pattern, covering an area of about 40 × 65 mm, and cut though the entry system, creating a lateral opening to the chip along the pillar system.The PDMS slabs were bonded to glass slides. Glass slides, 55 × 75 mm and 1 mm thick (Thermo Scientific), were first cleaned with acetone, 75% ethanol and deionized water, and then dried under an air-blower. The pieces of PDMS and the glass slides were treated separately in an oxygen plasma chamber (Diener Electronic Zepto). For each chip, a glass slide was exposed to oxygen plasma under UV light for 1 min, followed by exposure of the PDMS piece for 10 s. Once both samples were plasma-treated, they were immediately brought in contact with their activated surfaces facing each other, and gently pressed to each other in the centre parts of the chip. To avoid collapse of the ceiling of the entrance, none of the chip edges were pressed. The chips were heated on a heating plate for ~15 s at 100 °C to ensure a proper bonding. After another 15 s, the chips with liquid treatments were filled with the different media using a micropipette, taking advantage of the PDMS’s temporary hydrophilia following plasma treatment so that liquids were readily drawn into its structures. The chips were filled with one of the following three treatments: (1) deionized water, (2) liquid malt medium, a complex medium to provide a nutrient-rich environment including reduced sugars such as disaccharide maltose and in lower proportion nitrogenous components such as peptides, amino acids purines and vitamins (malt extract for microbiology, Merck KGaA), or (3) chips were left empty, i.e., air-filled. The eight chips filled with liquid were then placed in a vacuum chamber for 30 min at −25 kPa to remove any bubbles. Finally, the chips were kept in sterile Petri dishes, sealed with Parafilm and stored overnight in a cold room before being dug down into or inoculated with soil.Expt. 1: in situ incubation of chipsTo evaluate the effect of different nutritional conditions on colonization of the soil chips by microbes, we evaluated three pore space filling treatments: (1) deionized water, (2) malt extract medium, or (3) air; n = 3 chips per treatment. The experimental site was a small grove of deciduous trees in the city of Lund, Sweden (55° 42′ 49.5′′ N, 13° 12′ 32.5′′ E; Supplementary Fig. 1c). The season chosen for burial of the chips was early autumn (October 2017) to guarantee a moist soil during the experiment. Groups of replicates of all three chip treatments were buried randomly within the inner parts of the grove (n = 3 chips per filling treatment). The litter layer was removed, and 20 × 20 cm holes were carefully dug into the ground with a spade. The chips were placed horizontally in the soil at a depth of 10 cm in which the PDMS chip was facing up and the glass slide down. Horizontal placement was chosen to probe a single stratum of the soil, serving as a comparable inoculum to the whole of the entry system, and to aid nondestructive recovery. The soil was carefully placed back in its original orientation, and the litter layer was placed back. A string attached to each chip was placed with its opposite end above the soil surface and attached to a pin, to guide future retrieval. There was a minimum distance of one meter between each chip replicate.Preliminary experiments had shown that a 2-month incubation period would grant the colonization of different types of soil microorganisms and minerals, and a stabilization of the inner environmental conditions between the soil chip and the surrounding soil. Thus, after 64 days (December 2017), the chips were collected by carefully removing soil around the string leading to each chip. We carefully kept the adjacent soil atop the glass slide along the opening of the chip, to keep our artificial pore system connected to the real soil pore system, and to avoid such disturbances as hyphal tearing or evaporation of the liquid inside the chips (Supplementary Fig. 1d). We cleaned the chip windows by softly wiping them with a clean wipe and deionized water. Samples were carefully transported to the microscopy facilities, located adjacent to the burial site. The chips were harvested one at a time and analysed under the microscope immediately after collection and cleaning.We recorded the presence or absence of the main soil microbial groups in the entry systems and in the different channels, including their furthest extent into the chips, with help of the internal rulers.To analyse the effect of fungal hyphae on bacterial abundance, we recorded real-time videos slowly scanning along the whole length of the diamond-shaped opening channels (each 33 diamonds, Section D in Supplementary Fig. 1a; Fig. 3). The rather sparse hyphal colonization allowed us to select pairs of channels where in the first channel a hypha had proliferated far into the channel, combined with a directly adjacent channel without hyphae, n = 4. In each diamond-shaped widening we counted the number of bacterial cells, the presence or absence of fungal hyphae, and the presence or absence of liquid. After completion of all measurements, the chips were left uncovered at room temperature for 60 min to initiate air drying in the adjacent soil, in order to observe the real-time effects of drying on organisms and particles in the pore space system of the chips. The adjacent soil was re-wetted by adding 400 µl of water. The water inside the chips corresponded to the adjacent soil pore water, regressed upon evaporation, and refilled the chip structures upon rewetting of the adjacent soil.Expt. 2–3: laboratory incubation of soil on chipsIn a complementary approach, we collected soil from a lawn in Lund, Sweden, at 10 cm depth, and placed 5 g of this soil in front of the entry system of the chip. Chips received the three nutrient condition treatments as described above, air, water or malt medium (n = 2, Expt. 2). An additional set of air-filled chips was studied to quantify fungal highways (n = 3, Expt. 3). Chips were monitored under the microscope after inoculation, observation was documented with images and videos. Chips were kept in sealed Petri dishes with wet cotton cloths to maintain high humidity and were taken out for analysis only. The soil inoculum on the chips and the interior of the chips were kept moist with 500 µl of water added to the soil once a week. The artificial waterlogging event in the chips of Expt. 3 (‘fungal highways’) was achieved by adding a total of 2 ml of water to the inoculum soil over the course of a week, and the drying event was achieved by discontinuing the watering.During Expt. 2, we recorded the abundance and the furthest extent of bacteria, protists (including the morpho-groups ciliates, flagellated, and amoeboids), and the extent of hyphal colonization into the diamond section over time. After 2 months of incubation, we measured the furthest extent of colonization into the angled channels for the organism groups bacteria, fungi, and protists. During Expt. 3, we recorded the presence and the furthest extent of hyphae, liquid, bacteria, and protists in the diamond channels over time. We also recorded the number of protists, bacteria (in categories 0, More