The reduction-annealing method is a common approach for preparing metal oxides with oxygen vacancies. In a reducing atmosphere (hydrogen, carbon monoxide, hydrogen sulfide, etc.), iron minerals are subjected to heat treatment to partially reduce lattice oxygen, thereby introducing oxygen vacancies. Defects were introduced into hematite using high temperature hydrogenation [36] in this research. Nanohematite (Hem, 500 nm) was treated in a tubular furnace with H₂ atmosphere heated to 400°C at a rate of 3°C/min and burned at 400°C for 3 h. Then the defective hematite (DHem) was obtained after annealing at room temperature.

The crystal structure alterations of Hem and DHem samples were obtained via X-ray diffraction (XRD) analysis, utilizing Cu Kα radiation within 2θ angles of 20°–70°. The composition and content of mineral surface were examined by X-ray photoelectron spectroscopy (XPS). Additionally, Raman spectroscopy was employed to characterize the minerals samples, employing a 632.8 nm HeNe laser source.

The experimental soil was obtained from the farmland of Jiangyin, Wuxi City, Jiangsu Province. The soil was dried, ground, and sieved for backup. Phenanthrene was completely dissolved in methanol and then mixed into the processed soil, continuously stirred for 30 minutes every 12 h for six times to allow complete uniform mixing into the soil and to ensure complete evaporation of methanol. The concentration of phenanthrene in the soil was 5 mg/kg based on the concentration level of PAHs in soil environment [37].

Hem and DHem were individually introduced into both the original soil and the phenanthrene-doped soil. They were then stirred continuously for 30 minutes every 12 hours, repeated four times to ensure thorough mixing. The soil contained a mass fraction of 3% iron oxide nanoparticles.

The single-chamber air-cathode Soil-MFCs was used in this experiment, comprising a cylindrical glass chamber (40 mm diameter × 150 mm height). The device was divided into four parts from top to bottom. The lower level of the buffer soil layer was composed of unpolluted original soil (10 g). The anode, constructed of carbon felt wrapped around a stainless steel mesh (35 mm diameter), was positioned above this layer. About 180 g of experimental soil was filled in the soil layer above the anode. The air cathode was then placed above the soil. Both the anode and cathode were positioned in parallel. Titanium wire (0.8 mm diameter) connected the anode and cathode, completing the circuit. The anode and cathode were both made of a stainless steel mesh (35 mm diameter). The anode was wrapped with carbon felt on both sides. The anode carbon felt (40 mm diameter × 5 mm thickness), pretreated with acid and alkali washes for 12 h, and dried for backup [38–39]. The prepared carbon felt was inoculated with acclimated sludge from a wastewater treatment plant in Nanjing for 48 h.

To maintain microbial activity, 5 ml of nutrient solution (NaAc, 1 mol/L) was added weekly, and deionized water (1–2 mL) was added daily to keep the soil water saturated. A covering cloth was used to maintain light avoidance conditions. The experimental setup diagram is shown in Fig. S1(a), (c).

In this experiment, two groups were established using soil with only phenanthrene added: one operated under open-circuit conditions labeled as O-0, and the other under closed-circuit conditions labeled as C-0. Additional groups were formed, both under open and closed circuits, containing both the pollutant and two types of iron minerals to investigate the impact of introducing defects on the performance of hematite-reinforced Soil-MFCs. These groups were labeled as O-Hem, C-Hem, O-DHem, and C-DHem. The experimental grouping is shown in Fig. S2. At the beginning, the devices remained open circuit state. Successful construction was indicated by daily measurements of the device’s anode potential, and stability in potential was considered the start point. After successful construction, the system operated with a resistance of 1000 Ω based on the power output, microbial activity, and previous research [40–41]. The experiment ran for 42 days, divided into weekly cycles, with three replicates per group. Weekly destructive sampling involved removing, mixing, and freezing the soil from the device for subsequent analysis.

Statistics of electrochemical performance, pollutant degradation and iron mineral dissolution during the experiment were plotted with origin 2018. XRD data was analyzed by Jade 6.0, PDF standard cards were exported, and relevant tables were calculated by origin 2018. XPS data was analyzed by Avantage. Potential correction was conducted with C elements, peak splitting fitting of Fe and O elements was carried, and element was analyzed in the full-scale XPS spectra.

The XRD patterns of the two minerals are shown in Fig. 1(a). It can be observed that the XRD diffraction peaks of the original hematite sample were found at 33.2°, 35.6°, 40.9°, 49.5°, 54.01°, 57.6°, 62.4°, and 63.4°, corresponding respectively to the (104), (110), (113), (024), (116), (018), (214), and (300) crystal planes of hematite (α-Fe₂O₃, PDF#33-0664) [42]. Similarly, the XRD diffraction peaks of DHem were observed at 30.2°, 35.6°, 43.3°, 53.7°, 57.3°, and 62.9°, corresponding respectively to the (220), (311), (400), (422), (440), and (511) crystal planes of maghemite (γ-Fe₂O₃, PDF#39-1346) [43]. The change in mineral phase before and after modification indicates the alteration in the crystal structure of DHem. Raman spectra was obtained to further analyze the crystal structure (Fig. 1(b)). Six major characteristic peaks were observed for Hem, corresponding to two types of Raman-active optical modes (4E_g + 2A_g) of Fe₂O₃ [44–45]. Four of the peaks were attributed to E_g-symmetric vibrations, located at 238.62, 285.79, 400.76, and 600.69 cm⁻¹, respectively. The remaining two peaks, located at 218.73 and 498.00, primarily originated from the A_g mode of Fe₂O₃. In the case of DHem, the six peak positions were slightly shifted, situated at 214.37, 252.21, 276.54, 394.53, 496.01, and 590.00 cm⁻¹. The A2 peak intensity was significantly weakened, suggesting the pristine Fe₂O₃ lattice symmetry was damaged owing to the defects generated by the hydrogenation process.

To further characterize whether the surface defects of the minerals occur after hydrogenation, XPS was used to examine the chemical bonding and valence band positions of Hem and DHem. As shown in Fig. 1(c), the characteristic peaks of C, O, and Fe were shown, indicating that the samples were not doped with other elements and owned high purity. As illustrated in Fig. 1(d), three peaks of O 1s spectra were presented, namely Lattice oxygen (mainly Fe-O bond, O_lat), Vacancy oxygen (O_vac), and Hydroxyl oxygen (O-H bond, O_hyd) [46]. Vacancy oxygen characterizes the presence of oxygen vacancies, indicating that the defects generated on the surface of hematite after high temperature annealing in hydrogen contain oxygen vacancies. After the modification, the O_vac area and the relative content of O_vac on the surface of DHem was significantly increased compared with Hem (Table S2). Two major peaks attributed to Fe 2p_1/2 and Fe 2p_3/2 states were shown in Fig. 1(e). After modification, the two primary bands were migrated to higher banding energies. Two other Fe²⁺ peaks appeared in DHem, and the ratio of the area of Fe²⁺ / Fe³⁺ was significantly higher than that in the Hem sample, further indicating the formation of defects.

The crystal structures of the two minerals were analyzed by XRD (Fig. S3). It can be seen that Hem was hematite phase, and the cell was hexagonal. Changes in the unit cell of DHem occurred after hydrogenation treatment, primarily consisting of hexagonal, tetrahedral, and octahedral cells. Based on the aforementioned characterization results, it can be inferred that the introduction of hydrogen induces the presence of oxygen vacancies, resulting in alterations to the spatial arrangement of lattice iron and oxygen ions due to the loss of oxygen atoms.

The concentrations of dissolved Fe(II) in the soil were measured (Fig. 2(a)). The concentration of dissolved Fe(II) in the C-DHem group surpassed that of the C-Hem group during the experiment. The concentration of dissolved Fe(II) in the C-DHem group at the end of the experiment was 1.87 times higher than C-Hem (p < 0.05), showing that the introduction of defects can promote the dissolution of Fe(II) [35]. Defects can allow the mineral surface to present a complex steric coordination structure, increasing the active site on its surface, and may better facilitate the dissolution of Fe²⁺. During the first week of the reaction, microorganisms acclimated to the internal environment of MFCs by electrical stimulation [47]. Therefore, the microbial dissolution process of iron was not strong, and the concentration of dissolved Fe(II) in soil was low. In the second week, the concentration of dissolved Fe in the two groups was the highest, indicating that the microorganisms in the system achieved a greater survival advantage through the proliferation period and promoted the dissolution of iron. After the third week, the system tended to be stable [39]. The dissolved iron in the soil maintained a relatively stable content. Researches suggested that the redox cycling of dissolved Fe(II) and Fe(III) can enhance extracellular electron transfer, transferring more electrons to the anode for electricity generation, and to refractory organic matter for the reduction degradation of pollutants [48]. More dissolved Fe(II) may mean stronger EET capability in the system. Therefore, the construction of defects on hematite in soil-MFCs may reinforce the electroproduction and removal of organic pollutants. Thus, further exploration of the electricity production and pollutant removal of the system is warranted.

In the first 7 days after the device was kept open, the anode potential of each device continuously decreased and stabilized. During this process, microorganisms were enriched in the soil and continuously adapted to the soil environment. After connecting the resistance, the electricity generation performance of different group devices during the experiment was shown in Fig. 2. From Fig. 2(b)–(c), within the first 5 days, microorganisms need to adapt to the internal environment and reproduce, leading to a sustained increase in output voltage. After 5 days, the voltage of different devices fluctuated within a certain range (48.44 mV) in six weeks. The average voltages (42 d) were in the order of C-DHem (384.74 ± 48.44 mV) > C-Hem (324.38 ± 28.91 mV) > C-0 (278.61 ± 29.73 mV). At the same time, C-DHem had the maximum power density (324.97 mW/m²), 1.06 times that of C-Hem (305.54 mW/m²) and 1.22 times that of C-0 (266.22 mW/m²) (Fig. S4). Compared with other MFCs systems (Table. S1), C-DHem demonstrated a relatively reasonable power density through interconversion factors [49]. These results suggested that the addition of hematite significantly enhanced the output voltage of the Soil-MFCs (p < 0.05). Moreover, the introduction of defects further amplified this enhancement effect of hematite on the output voltage of the Soil-MFCs (p < 0.05), aligning with the observed increase in dissolved Fe(II) content as mentioned earlier. Building defects in hematite could increase the content of dissolved Fe(II), which may promote more extracellular electron transfer to the anode, thereby improving the electricity generation performance of the device.

Given the semiconductive inherent of iron minerals, it is speculated that the addition of oxide minerals may affect the internal structure of soil layer in Soil-MFCs, including internal resistance [47], organic matter [50], and pH to improve its electrical properties. Therefore, the polarization curves of different groups were measured to determine the change of the internal resistance. The results showed that the internal resistance of C-0 was the highest (292.12 Ω), approximately 1.26 times that of C-Hem (231.21 Ω), and 1.33 times that of C-DHem (219.83 Ω). This indicated that the addition of hematite can reduce the inherent internal resistance of the soil, thereby increasing conductivity and improving the electricity generation performance of the system. The introduction of defects alters the surface structure of hematite, enhancing the mineral’s electrical properties, which may be one of the reasons why DHem can better reduce the internal resistance of the soil compared to Hem.

Fig. 3 in the study depicted the overall efficiency of phenanthrene removal in Soil-MFCs during the operation. It demonstrated that even in the open-circuit group, a certain level of phenanthrene degradation was observed, with rates ranging from 38.23%–48.22%. This degradation likely results from natural degradation pathways, including adsorption hydrolysis of electrodes and soil and degradation of soil microorganisms. Among them, microorganisms play a major role in the degradation of the phenanthrene in the soil [51]. O-Hem (42.20%) and O-DHem (47.52%) resulted in a more effective degradation of phenanthrene compared to the control group O-0 (38.23%) (p < 0.05). This improvement is likely due to the adsorption degradation and facilitation of microbial degradation by the added iron minerals. Studies have shown that the defects site in iron minerals may affect the adsorption of organic pollutants [52], which may explain the better phenanthrene degradation effect in the O-DHem group than in the O-Hem. In closed-circuit groups, the degradation rates of phenanthrene were higher than in open-circuit groups, with C-DHem achieving the highest rate (61.42%), followed by C-Hem (53.94%) and C-0 (44.32%). This pattern suggested that Soil-MFCs promoted the degradation of polycyclic aromatic hydrocarbons like phenanthrene. In the Soil-MFCs, the degradation rates of phenanthrene exhibited significant increases in both the C-Hem and C-DHem groups compared to the open-circuit group, with enhancements of 21.76% and 22.62%, respectively. This enhancement surpassed the control group’s improvement of 13.74%. The addition of hematite likely facilitates this increased degradation, and the enhancement could be further improved by the construction of defects on hematite, possibly due to DHem’s ability to release more Fe(II). Dissolved Fe(II) had a significant effect on electron output from the anode, and promoted electron transfer rate and electron transfer flux in soil [47]. This observation aligned with the experimental findings previously discussed.

Besides overpotential losses in the electrodes, electrode materials and Ohmic losses [53], due to the low mass transfer capacity of the soil, the extracellular electrons can only be transmitted in a limited space near the anode, resulting in a poor degradation effect of pollutants in the soil near the cathode [54]. The addition of electron mediators can improve the strength and distance of electron transport. Thus, we further explored the phenanthrene removal of the three soil areas of the device, within sampling points delineated in Fig. S1(b). It was found that the degradation effect of the phenanthrene in the near anode area was better than that in the middle and near cathode areas, which was related to the properties of the soil. In the closed-circuit group, the soil phenanthrene degradation rate was the highest in the C-DHem group and the lowest in the C-0 group during the experiment in each area. At the end of the experiment, the degradation rates of phenanthrene in near cathode areas were shown in Fig. 3(a) and 3(b), with C-DHem achieving the highest rate (60.71%), followed by C-Hem (50.96%), O-DHem (43.15%), C-0 (40.62%), O-Hem (40.49%), and O-0 (36.88%). It can be seen that the construction of defects on hematite can enhance pollutant removal in the near cathode area of Soil-MFCs. Due to changes in surface active sites and electrochemical properties, the defective area of DHem is more prone to dissolution [55]. Therefore, it can facilitate stronger and farther electron transfer, leading to more electrons being transferred to contaminants for their reduction and degradation. In the Soil-MFCs, the degradation rates of phenanthrene in near cathode areas were notably higher in the C-DHem groups compared to the open circuit group, with increases of 40.70%. This enhancement surpassed the improvements seen in the C-0 and C-Hem groups, which were 13.74% and 25.86%, respectively. This enhancement can be attributed to the degradation of microorganisms under the electrochemical system. In the Soil-MFCs system, the addition of hematite can enhance the capacity of the system for long-distance electron transport, while the construction of defects on hematite promoted the dissolution of iron minerals in the soil, making the better EET ability mediated by Fe(II) / Fe(III) redox cycles. Compared to C-0 and C-Hem, the phenanthrene far from the anode of C-Dem can better obtain the extracellular electrons produced by microorganisms near the anode by long-distance electron transport [56], realizing pollution reductive degradation.

An analysis of the microbial communities in soil samples from various devices (within 1 cm of the anode) was conducted to investigate the overall improvement of Soil-MFCs performance by the construction of hematite defects at the microbial level. Fig. 4(a) illustrated the dominant microbial community composition at the phylum level (top 10 in abundance) at the end of operation, with a high proportion of Proteobacteria, Firmicutes, Desulfobacterota, Bacteroidota, and Chloroflex in each group. These phyl are typical of microbial communities that are highly enriched in Soil-MFCs [57–59]. Firmicutes and Proteobacteria, rich in electrogens, can enhance the system’s electricity generation capabilities. The addition of iron minerals to MFCs increased the relative abundance of Firmicutes. Research showed Firmicutes was the common dominant phylum in MFCs [60]. Results suggested that iron minerals promoted their attachment to the anode and improved the electricity-generating performance of Soil-MFCs.

A comparison of microbial abundance at the genus level (top 30 in abundance) in different groups (Fig. 4(b)) showed increased abundance of Trichloromonas, Trichococcus, Thauera, Pseudomonas, Desulfobulbus, and Petrimonasin groups with added minerals compared to the control group. To investigate the response of various functional microbes in Soil-MFCs to different mineral additions, the dominant microbes were categorized into two types: 1) the dominant microorganisms that produce electricity and degrade PAHs, such as Pseudomonas, Trichococcusm, Azoarcus, and Trichloromonas; 2) dissimilating iron-reducing bacterium, such as Petrimonas and Thermincola. The relative abundance of dissimilating iron-reducing bacterium in the C-DHem group (0.056) was much higher than that in the C-Hem group (0.020). Thermincola has been reported to participate in the microbial reduction process of Fe(III) [61–63]. Petrimonas was also involved in the reduction process of iron. It indicated that hematite with defects can stimulate the enrichment of more dissimilating iron-reducing bacterium in Soil-MFCs, further explaining the better dissolution ability of DHem in soil in bioelectrochemical systems at the microbial level. Trichloromonas was proved to be an important electroproducing microorganism on the anode membrane [64]. Pseudomonas is an important electroproducing bacterium, and Pseudomonas inoculation has a good purification effect on the soil contaminated with PAHs [65–66]. Thauera is important for the aromatic compound-degrading bacteria [67]. Azoarcus was also reported to be an anaerobic biodegradome of aromatic compounds and a facultative endophyte [68]. The relative abundance of dominant microorganisms responsible for electricity generation and PAHs degradation in the closed groups adding iron minerals (0.789, 0.33) was higher compared to the C-0 group (0.293). This suggested that the addition of iron minerals can enhance the enrichment of electroactive microbes, consequently improving the electricity generation and pollutant degradation performance of Soil-MFCs. In the C-0 group, Trichloromonas was the main electroactive microorganism. After the addition of hematite, the relative abundance of Trichococcus and Pseudomonas increased. The relative abundance of Azoarcus increased after introducing the defects into hematite, showing that hematite affected the overall performance of Soil-MFCs by affecting different functional microorganisms.

Correlation analysis was performed to analyze the diversity of microbial communities, the state of dissolved iron, the electricity-generating performance of the system, and the degradation rate of phenanthrene during the reaction process (Table S3). The possible pathway for the construction of defects on hematite to promote the Soil-MFCs can be obtained. It can be seen that the introduction of defects in hematite can promote mineral dissolution through changes in its own structure, as well as affecting the abundance of dissimilating iron-reducing bacterium in the soil (0.478). More dissolved Fe(II) can significantly promote the electrical production (0.867) and the removal of phenanthrene (0.796) by strengthening EET. The extracellular electrons produced by microbial degradation of substrates can be accepted by iron minerals. Dissolved Fe(II) accepts electrons, which are then transferred to the anode for electricity generation in the system, or transferred to contaminants for their reduction and degradation. Simultaneously, Fe(II) is oxidized to solid Fe(III), completing the cycle of oxidation-reduction. Through this cyclic process, electron transfer is continuously mediated, enabling long-distance electron transfer. Additionally, the relevant functional microorganisms play important roles in this process.