Iron Chelation in Soil: Scalable Biotechnology for Accelerating Carbon Dioxide Removal by Enhanced Rock Weathering

Abstract

Enhanced rock weathering (EW) is an emerging atmospheric carbon dioxide removal (CDR) strategy being scaled up by the commercial sector. Here, we combine multiomics analyses of belowground microbiomes, laboratory-based dissolution studies, and incubation investigations of soils from field EW trials to build the case for manipulating iron chelators in soil to increase EW efficiency and lower costs. Microbial siderophores are high-affinity, highly selective iron (Fe) chelators that enhance the uptake of Fe from soil minerals into cells. Applying RNA-seq metatranscriptomics and shotgun metagenomics to soils and basalt grains from EW field trials revealed that microbial communities on basalt grains significantly upregulate siderophore biosynthesis gene expression relative to microbiomes of the surrounding soil. Separate in vitro laboratory incubation studies showed that micromolar solutions of siderophores and high-affinity synthetic chelator (ethylenediamine-N,N'-bis-2-hydroxyphenylacetic acid, EDDHA) accelerate EW to increase CDR rates. Building on these findings, we develop a potential biotechnology pathway for accelerating EW using the synthetic Fe-chelator EDDHA that is commonly used in agronomy to alleviate the Fe deficiency in high pH soils. Incubation of EW field trial soils with potassium-EDDHA solutions increased potential CDR rates by up to 2.5-fold by promoting the abiotic dissolution of basalt and upregulating microbial siderophore production to further accelerate weathering reactions. Moreover, EDDHA may alleviate potential Fe limitation of crops due to rising soil pH with EW over time. Initial cost-benefit analysis suggests potassium-EDDHA could lower EW-CDR costs by up to U.S. $77 t CO₂ ha^-1 to improve EW's competitiveness relative to other CDR strategies.

Keywords: EDDHA; basalt; biotechnology; carbon capture; carbon dioxide removal; chelating agent; chelator; enhanced weathering; siderophore.

Figure 1

Omics analyses of microbial siderophore production during enhanced rock weathering (EW) trials in the U.S. Corn Belt agroecosystems. (A) Metatranscriptomic RNA-seq analyses show greater expression of siderophore biosynthesis genes in the in situ basalt microbiome than in the surrounding soil microbiome (two-tailed t test, *P < 0.05). (B) Hot water-soluble iron (Fe) levels are significantly lower in basalt than in the surrounding soil matrix (two-tailed t test, **P < 0.01). (C) Siderophore biosynthesis gene classification reveals significantly greater expression of genes involved in the production of hydroxamates and catecholates than other groups (two-tailed t test, **P < 0.01, * < 0.05). (D) Breakdown of hydroxamate biosynthesis genes into separate siderophore types shows that desferrioxamines and arthrobactin are among the most upregulated in the basalt microbiome. Green and red asterisks indicate significant increases or decreases, respectively, in basalt over control microbiomes (two-tailed t test, ***P < 0.001, ** < 0.01, * < 0.05). (E) Greater genus-specific ratios of desB to rpoA (a gene present as a single copy in microbial genomes) in the metagenomes of in situ basalt relative to soil indicate positive selection for microbes producing desferrioxamines/arthrobactin. This pattern is robust across key genera. rpoA = DNA-directed RNA polymerase subunit α. Error bars show the standard error of the mean (SEM). Replication for each substrate was as follows: n = 15 (metatranscriptomics) and n = 16 (metagenomics) replicates for soil-weathered basalt rock microbiomes, n = 4 replicates (both types of omics) for the surrounding soil microbiomes.

Figure 2

Diverse siderophores increase in vitro iron and basalt dissolution. (A) Weathering rate of iron (Fe) release (R_Fe) from basalt in response to desferrioxamine B mesylate (DF) dissolved in a microbial medium (1–40 μM). (B) Release rate of Fe from basalt by weathering in response to cell-free supernatant from Fe-deficient B. thailandensis E264 culture containing malleobactin and pyochelin (1–40 μM DF equivalents). (C) Release rate of Fe from basalt by weathering in response cell-free supernatant from Fe-deficient P. fluorescens ATCC 13525 culture containing pyoverdine and pyochelin (1–20 μM DF equivalents). (D) Release rate of Fe from basalt by weathering in response to citrate dissolved in the microbial medium (40–300 μM citrate). (E–H) Rates of basalt weathering in response to the same conditions described in (A)–(D) R_basalt is calculated as the sum of R_Mg, R_Ca, R_Na, R_Si, R_Al, R_Ti, and R_Fe. Error bars show SEM. Akaike’s Information Criterion (AICs) was used to compare quadratic vs linear model and the higher-ranking best-fit model was used. Replication for each concentration and each chelator in replicates of four, n = 4. The non-SI units “μM DF equivalents” are used since the concentration of unpurified siderophores is measured based on their activity in the CAS assay (see Materials and Methods) relative to a standard curve based on known amounts of desferrioxamine B mesylate (DF).

Figure 3

Effects of the high-affinity chelators potassium desferrioxamine B mesylate (K-DF) and potassium-EDDHA (K-EDDHA) on basalt dissolution, alkalinity, and CDR in vitro. (A) Dissolved concentration of elements from basalt over 90 h incubation at atmospheric pCO₂ in response to varied K-DF concentrations. (B) Summed dissolved divalent base cations (Ca²⁺ + Mg²⁺) in response to varied K-DF concentrations. (C) Correlation between the sum of dissolved (Ca²⁺ + Mg²⁺) concentration and measured HCO₃^– concentration in K-DF treatment. (D) Dissolved concentration of elements from basalt over 90 h incubation at atmospheric pCO₂ in response to varied K-EDDHA concentrations. (E) Sum of the dissolved divalent base cations (Ca²⁺ + Mg²⁺) from basalt in response to varied K-EDDHA concentrations. (F) Correlation between dissolved the sum of dissolved (Ca²⁺ + Mg²⁺) and measured HCO₃^– concentration in K-EDDHA treatment. (G) Tabulated measurements of solution DIC, pH, and HCO₃^– over the basalt-free solution compared to solution with Hillhouse basalt dust added at varied chelator concentrations. Statistical tests performed include the Pearson correlation test and analysis of variance (ANOVA) tests with Benjamini–Hochberg multiple comparison correction. Different letters signify significantly different means. Values in the table show mean ± SEM. Replication for each concentration for each chelator in replicates of four, n = 4.

Figure 4

Effects of the chelating agent EDDHA on basalt weathering and carbon dioxide removal potential in soil. (A) Bioassay-based estimates of total hydroxamate concentrations in soil and soil + basalt incubated substrates after 10 days in response to EDDHA (Pearson correlation test, P < 0.05, r = 0.41). (B) Hot water-extractable Fe concentrations respond to EDDHA supporting the proposed role of EDDHA as a Fe-sequestering agent (measured 20 days after the start of incubation; Pearson correlation test, P < 0.001, r = 0.91). (C) Hot water-extractable Fe measured 20 days after the start of incubation is significantly lower in substrate incubations by prebound Fe-desferrioxamine siderophores. These results indicate a significant role of siderophores produced by the native community in dissolving Fe from soil and basalt. Difference in the exchangeable pools (1 M ammonium acetate extracts, pH 7.0) of (D) calcium (Ca), (E) magnesium (Mg), (F) sodium (Na), (G) potassium (K), and (H) silicon (Si) in substrate extracts after 20 days as a function of different levels of applied EDDHA. The differences between soil + basalt and soil for each EDDHA treatment show the effect of EDDHA on basalt weathering; two-tailed t tests were performed for each concentration (***P < 0.001, ** < 0.01, * < 0.05, ∧ < 0.10, ns > 0.10). (I) Potential enhanced weathering carbon dioxide removal (CDR) gain in response to EDDHA shows a significant linear relationship (Pearson correlation test, P < 0.05, r = 0.63) with the concentration of free EDDHA applied. CDR calculations are based on the following equation: Δcation_{exch. soil+basalt} – Δcation_exch. soil for the major divalent [Ca, Mg] and monovalent [Na, K] ions. Replication for each concentration and each soil treatment (soil vs soil + basalt) in replicates of three, n = 3. The non-SI units “mg kg^–1 20 days^–1” are here preferred over the SI unit expression “mg kg^–1 day^–1” as to make clear that the delta values for soil nutrients are derived based on the difference in their values from day 20 to day 0 as per our incubation protocol. In this way, we also do not assume uniformity in the rate of change throughout the 20-day period.

Figure 5

Cost-benefit analysis of EDDHA-driven enhanced weathering. (A) Rates of EDDHA application and costs for achieving target molar soil concentrations at different soil moisture levels. (B) Amount of K added by soil amendment with K-EDDHA. (C) Life-cycle assessment (LCA) emission of EDDHA. (D) CDR increase as a function of EDDHA and varied basalt application rates [experimental uncertainty and variability due to soil moisture (e.g., 10–25 wt %) are propagated; error bars show SEM]. (E) Cost per t CO₂ year^–1 captured by EW with or without chelating EDDHA; error bars show 1 standard deviation (SD) and are associated with the uncertainty of different soil moistures (propagation as specified in (D)). (F) Conceptual diagram illustrating how the application of Fe-free K-EDDHA increases EW and CDR through direct (EDDHA attack on basalt) and indirect effects (Fe-EDDHA effects on the microbiome and siderophore biosynthesis gene expression). The proposed treatment can increase crop yields and crop nutritional value for human consumption by improving the availability of Fe, adding additional K and increasing the supply of basalt-derived nutrients (e.g., Ca, Mg, Si, P).