Effect of carbonic anhydrase on silicate weathering and carbonate formation at present day CO₂ concentrations compared to primordial values

Harnessing Microbes to Weather Native Silicates in Agricultural Soils for Scalable Carbon Dioxide Removal

Anthropogenic carbon emissions contribute significantly to the greenhouse effect, resulting in global warming and climate change. Thus, addressing this critical issue requires innovative and comprehensive solutions. Silicate weathering moderates atmospheric CO2 levels over geological time, but it occurs too slowly to counteract anthropogenic emissions effectively. Here, we show that the microorganism Bacillus subtilis strain MP1 promotes silicate weathering across different experimental setups with various levels of complexity. First, we found that MP1 was able to form a robust biofilm in the presence of feldspar and significantly increased (p < 0.05) silicate dissolution rates, pH, and calcium carbonate formation in culture experiments. Second, in mesocosm experiments, we found that MP1 enhanced the silicate weathering rate in soil by more than six times compared to the untreated control. In addition, soil inorganic carbon increased by 20%, and the concentrations of ions, including calcium, magnesium, and iron, were also elevated under the MP1 treatment. More importantly, when applied as a seed treatment on eight soybean fields, we found that MP1 significantly (p < 0.05) boosted soil inorganic carbon, leading to a gross accrual of 2.02 tonnes of inorganic carbon per hectare annually. Our findings highlight the potential of enhancing native silicate weathering with microorganisms in agricultural fields to increase soil inorganic carbon, contributing to climate change mitigation.

In-field carbon dioxide removal via weathering of crushed basalt applied to acidic tropical agricultural soil

Enhanced weathering (EW) of silicate rocks such as basalt provides a potential carbon dioxide removal (CDR) technology for combatting climate change. Modelling and mesocosm studies suggest significant CDR via EW but there are few field studies. This study aimed to directly measure in-field CDR via EW of basalt applied to sugarcane on acidic (pH 5.8, 0-0.25 m) Ultisol in tropical northeastern Australia, where weathering potential is high. Coarsely crushed basalt produced as a byproduct of gravel manufacture (<5 mm) was applied annually from 2018 to 2022 at 0 or 50 t ha-1 a-1, incorporated into the soil in 2018 but not in subsequent years. Measurements in 2022 show increased soil pH and extractable Mg and Si at 0-0.25 m depth, indicating significant weathering of the basalt, but showed no increase in crop yield. Soil inorganic carbon content and bicarbonate (HCO3-) flux to deep drainage (1.25 m depth) were measured to quantify CDR in the 2022-2023 wet season (i.e. one year). Soil inorganic carbon was below detection limits. Mean HCO3- flux was 3.15 kmol ha-1 a-1 (±0.40) in the basalt-treated plots and 2.56 kmol ha-1 a-1 (±0.18) in the untreated plots but the difference (0.59 kmol ha-1 a-1 or 0.026 t CO2 ha-1 a-1) was not significant (p = 0.082). Most weathering of the basalt was attributed to acids stronger than carbonic acid. These were, in decreasing order of contribution, surface-bound protons (inherent soil acidity), nitric acid (from nitrification), organic acids, and acids associated with cation uptake by plants. These results indicate in-field CDR via EW of basalt is low where soil and regolith pH is well below the pKa1 of 6.4 for H2CO3. However, increased soil pH, and the consumption of strong acids by weathering will eventually lead to reduced CO2 emission from soil or evasion from rivers, with continued basalt addition.

Enzyme-accelerated CO2 capture and storage (CCS) using paper and pulp residues as co-sequestrating agents

In the present work, four CaCO3-rich solid residues from the pulp and paper industry (lime mud, green liquor sludge, electrostatic precipitator dust, and lime dregs) were assessed for their potential as co-sequestrating agents in carbon capture. Carbonic anhydrase (CA) was added to promote both CO2 hydration and residue mineral dissolution, offering an enhancement in CO2-capture yield under atmospheric (up to 4-fold) and industrial-gas mimic conditions (up to 2.2-fold). Geological CO2 storage using olivine as a reference material was employed in two stages: one involving mineral dissolution, with leaching of Mg2+ and SiO2 from olivine; and the second involving mineral carbonation, converting Mg2+ and bicarbonate to MgCO3 as a permanent storage form of CO2. The results showed an enhanced carbonation yield up to 6.9%, when CA was added in the prior CO2-capture step. The proposed route underlines the importance of the valorization of industrial residues toward achieving neutral, or even negative emissions in the case of bioenergy-based plants, without the need for energy-intensive compression and long-distance transport of the captured CO2. This is a proof of concept for an integrated strategy in which a biocatalyst is applied as a CO2-capture promoter while CO2 storage can be done near industrial sites with adequate geological characteristics.

Multifarious Responses of Forest Soil Microbial Community Toward Climate Change

Forest soils are a pressing subject of worldwide research owing to the several roles of forests such as carbon sinks. Currently, the living soil ecosystem has become dreadful as a consequence of several anthropogenic activities including climate change. Climate change continues to transform the living soil ecosystem as well as the soil microbiome of planet Earth. The majority of studies have aimed to decipher the role of forest soil bacteria and fungi to understand and predict the impact of climate change on soil microbiome community structure and their ecosystem in the environment. In forest soils, microorganisms live in diverse habitats with specific behavior, comprising bulk soil, rhizosphere, litter, and deadwood habitats, where their communities are influenced by biotic interactions and nutrient accessibility. Soil microbiome also drives multiple crucial steps in the nutrient biogeochemical cycles (carbon, nitrogen, phosphorous, and sulfur cycles). Soil microbes help in the nitrogen cycle through nitrogen fixation during the nitrogen cycle and maintain the concentration of nitrogen in the atmosphere. Soil microorganisms in forest soils respond to various effects of climate change, for instance, global warming, elevated level of CO2, drought, anthropogenic nitrogen deposition, increased precipitation, and flood. As the major burning issue of the globe, researchers are facing the major challenges to study soil microbiome. This review sheds light on the current scenario of knowledge about the effect of climate change on living soil ecosystems in various climate-sensitive soil ecosystems and the consequences for vegetation-soil-climate feedbacks.

Is the climate change mitigation effect of enhanced silicate weathering governed by biological processes?

A number of negative emission technologies (NETs) have been proposed to actively remove CO₂ from the atmosphere, with enhanced silicate weathering (ESW) as a relatively new NET with considerable climate change mitigation potential. Models calibrated to ESW rates in lab experiments estimate the global potential for inorganic carbon sequestration by ESW at about 0.5-5 Gt CO₂  year^-1 , suggesting ESW could be an important component of the future NETs mix. In real soils, however, weathering rates may differ strongly from lab conditions. Research on natural weathering has shown that biota such as plants, microbes, and macro-invertebrates can strongly affect weathering rates, but biotic effects were excluded from most ESW lab assessments. Moreover, ESW may alter soil organic carbon sequestration and greenhouse gas emissions by influencing physicochemical and biological processes, which holds the potential to perpetuate even larger negative emissions. Here, we argue that it is likely that the climate change mitigation effect of ESW will be governed by biological processes, emphasizing the need to put these processes on the agenda of this emerging research field.

Enhanced diversity and rock-weathering potential of bacterial communities inhabiting potash trachyte surface beneath mosses and lichens - A case study in Nanjing, China

Mosses and lichens have been shown to play an important role in enhancing global chemical weathering of the surface rock. However, there are no studies concerning the effects of mosses and lichens on the microbial communities inhabiting rock surfaces. In this study, culture-dependent and culture-independent analyses were employed to compare the diversity, composition, and rock-weathering activity of bacterial communities inhabiting potash trachyte surfaces covered by mosses (MR) and lichens (LR) with those inhabiting surrounding bare rock surfaces (BR). Analyses of 16S rRNA gene Miseq sequencing revealed that the order of alpha (α) diversity indices, in terms of the number of unique operational taxonomic units (OTUs) and Faith's index of phylogenetic diversity, was MR > LR > BR. Moreover, α-diveristy indices were positively correlated with the content of available phosphorus (AP) in rock samples (r = 0.87-0.92), and this explained 70% of the variation in bacterial community structure. The culture-dependent analyses revealed that 100% of the culturable bacterial strains could enhance potash trachyte weathering, and the order of rock-weathering acitivity of bacterial strains was MR > LR > BR. Acidolysis was found to be the major mechanism involved in the bacteria-mediated weathering of potash trachyte. Moreover, bacterial strians related to the genera Dyella and Ralstonia showed the highest rock-weatheirng activity, and both Dyella and Ralstonia were enriched in MR. The results of this study enhance our understanding of the roles of bacteria facilitated by mosses and lichens in rock weathering, element cycling, and soil formation, and provide new insights into the interaction between non-vascular plants and the bacteria on rock surfaces.

Transcriptome Analysis Provides Novel Insights into the Capacity of the Ectomycorrhizal Fungus Amanita pantherina To Weather K-Containing Feldspar and Apatite

Ectomycorrhizal (ECM) fungi, symbiotically associated with woody plants, markedly improve the uptake of mineral nutrients such as potassium (K) and phosphorus (P) by their host trees. Although it is well known that ECM fungi can obtain K and P from soil minerals through biological weathering, the mechanisms regulating this process are still poorly understood at the molecular level. Here, we investigated the transcriptional regulation of the ECM fungus Amanita pantherina in weathering K-containing feldspar and apatite using transcriptome sequencing (RNA-seq) and validated these results for differentially expressed genes using real-time quantitative PCR. The results showed that A. pantherina was able to improve relevant metabolic processes, such as promoting the biosynthesis of unsaturated fatty acids and steroids in the weathering of K-containing feldspar and apatite. The expression of genes encoding ion transporters was markedly enhanced during exposure to solid K-containing feldspar and apatite, and transcripts of the high-affinity K transporter ApHAK1, belonging to the HAK family, were significantly upregulated. The results also demonstrated that there was no upregulation of organic acid biosynthesis, reflecting the weak weathering capacity of the A. pantherina isolate used in this study, especially its inability to utilize P in apatite. Our findings suggest that under natural conditions in forests, some ECM fungi with low weathering potential of their own may instead enhance the uptake of mineral nutrients using their high-affinity ion transporter systems.IMPORTANCE In this study, we revealed the molecular mechanism and possible strategies of A. pantherina with weak weathering potential in the uptake of insoluble mineral nutrients by using transcriptome sequencing (RNA-seq) technology and found that ApHAK1, a K transporter gene of this fungus, plays a very important role in the acquisition of K and P. Ectomycorrhizal (ECM) fungi play critical roles in the uptake of woody plant nutrients in forests that are usually characterized by nutrient limitation and in maintaining the stability of forest ecosystems. However, the regulatory mechanisms of ECM fungi in acquiring nutrients from minerals/rocks are poorly understood. This study investigated the transcriptional regulation of A. pantherina weathering K-containing feldspar and apatite and improves the understanding of fungal-plant interactions in promoting plant nutrition enabling increased productivity in sustainable forestry.

Isolation and Characterization of the High Silicate and Phosphate Solubilizing Novel Strain Enterobacter ludwigii GAK2 that Promotes Growth in Rice Plants

Silicon (Si) and phosphorus (P) are beneficial nutrient elements for plant growth. These elements are widely used in chemical fertilizers despite their abundance in the earth’s crust. Excessive use of chemical fertilizers is a threat to sustainable agriculture. Here, we screened different Si and P solubilizing bacterial strains from the diverse rice fields of Daegu, Korea. The strain with high Si and P solubilizing ability was selected and identified as Enterobacter ludwigii GAK2 through 16S rRNA gene sequence analysis. The isolate GAK2 produced organic acids (citric acid, acetic acid, and lactic acid), indole-3-acetic acid, and gibberellic acid (GA1, GA3) in Luria-Bertani media. In addition, GAK2 inoculation promoted seed germination in a gibberellin deficient rice mutant Waito-C and rice cultivar ‘Hwayoungbyeo’. Overall, the isolate GAK2 increased root length, shoot length, fresh biomass, and chlorophyll content of rice plants. These findings reveal that E. ludwigii GAK2 is a potential silicon and phosphate bio-fertilizer.

The Carbonation of Wollastonite: A Model Reaction to Test Natural and Biomimetic Catalysts for Enhanced CO2 Sequestration

One of the most promising strategies for the safe and permanent disposal of anthropogenic CO2 is its conversion into carbonate minerals via the carbonation of calcium and magnesium silicates. However, the mechanism of such a reaction is not well constrained, and its slow kinetics is a handicap for the implementation of silicate mineral carbonation as an effective method for CO2 capture and storage (CCS). Here, we studied the different steps of wollastonite (CaSiO3) carbonation (silicate dissolution → carbonate precipitation) as a model CCS system for the screening of natural and biomimetic catalysts for this reaction. Tested catalysts included carbonic anhydrase (CA), a natural enzyme that catalyzes the reversible hydration of CO2(aq), and biomimetic metal-organic frameworks (MOFs). Our results show that dissolution is the rate-limiting step for wollastonite carbonation. The overall reaction progresses anisotropically along different [hkl] directions via a pseudomorphic interface-coupled dissolution–precipitation mechanism, leading to partial passivation via secondary surface precipitation of amorphous silica and calcite, which in both cases is anisotropic (i.e., (hkl)-specific). CA accelerates the final carbonate precipitation step but hinders the overall carbonation of wollastonite. Remarkably, one of the tested Zr-based MOFs accelerates the dissolution of the silicate. The use of MOFs for enhanced silicate dissolution alone or in combination with other natural or biomimetic catalysts for accelerated carbonation could represent a potentially effective strategy for enhanced mineral CCS.

Adsorption and Desorption Characteristics of Cd2+ and Pb2+ by Micro and Nano-sized Biogenic CaCO3

The purpose of this study was to elucidate the characteristics and mechanisms of adsorption and desorption for heavy metals by micro and nano-sized biogenic CaCO3 induced by Bacillus subtilis, and the pH effect on adsorption was investigated. The results showed that the adsorption characteristics of Cd2+ and Pb2+ are well described by the Langmuir adsorption isothermal equation, and the maximum adsorption amounts for Cd2+ and Pb2+ were 94.340 and 416.667 mg/g, respectively. The maximum removal efficiencies were 97% for Cd2+, 100% for Pb2+, and the desorption rate was smaller than 3%. Further experiments revealed that the biogenic CaCO3 could maintain its high adsorption capability for heavy metals within wide pH ranges (3-8). The FTIR and XRD results showed that, after the biogenic CaCO3 adsorbed Cd2+ or Pb2+, it did not produce a new phase, which indicated that biogenic CaCO3 and heavy metal ions were governed by a physical adsorption process, and the high adsorptive capacity of biogenic CaCO3 for Cd2+ and Pb2+ were mainly attributed to its large total specific surface area. The findings could improve the state of knowledge about biogenic CaCO3 formation in the environment and its potential roles in the biogeochemical cycles of heavy metals.

Genomic and Transcriptomic Insights into Calcium Carbonate Biomineralization by Marine Actinobacterium Brevibacterium linens BS258

Calcium carbonate (CaCO3) biomineralization has been investigated due to its wide range of scientific and technological implications, however, the molecular mechanisms of this important geomicrobiological process are largely unknown. Here, a urease-positive marine actinobacterium Brevibacterium linens BS258 was demonstrated to effectively form CaCO3 precipitates. Surprisingly, this bacterium could also dissolve the formed CaCO3 with the increase of the Ca2+ concentration. To disclose the mechanisms of biomineralization, the genome of B. linens BS258 was further completely sequenced. Interestingly, the expression of three carbonic anhydrases was significantly up-regulated along with the increase of Ca2+ concentration and the extent of calcite dissolution. Moreover, transcriptome analyses revealed that increasing concentration of Ca2+ induced KEGG pathways including quorum sensing (QS) in B. linens BS258. Notably, most up-regulated genes related to QS were found to encode peptide/nickel ABC transporters, which suggested that nickel uptake and its associated urease stimulation were essential to boost CaCO3 biomineralization. Within the genome of B. linens BS258, there are both cadmium and lead resistance gene clusters. Therefore, the sequestration abilities of Cd2+ and Pb2+ by B. linens BS258 were checked. Consistently, Pb2+ and Cd2+ could be effectively sequestered with the precipitation of calcite by B. linens BS258. To our knowledge, this is the first study investigating the microbial CaCO3 biomineralization from both genomic and transcriptomic insights, which paves the way to disclose the relationships among bacterial metabolisms and the biomineralization.

Carbonate Mineral Formation under the Influence of Limestone-Colonizing Actinobacteria: Morphology and Polymorphism

Microorganisms and their biomineralization processes are widespread in almost every environment on earth. In this work, Streptomyces luteogriseus DHS C014, a dominant lithophilous actinobacteria isolated from microbial mats on limestone rocks, was used to investigate its potential biomineralization to allow a better understanding of bacterial contributions to carbonate mineralization in nature. The ammonium carbonate free-drift method was used with mycelium pellets, culture supernatant, and spent culture of the strain. Mineralogical analyses showed that hexagonal prism calcite was only observed in the sub-surfaces of the mycelium pellets, which is a novel morphology mediated by microbes. Hemispheroidal vaterite appeared in the presence of spent culture, mainly because of the effects of soluble microbial products (SMP) during mineralization. When using the culture supernatant, doughnut-like vaterite was favored by actinobacterial mycelia, which has not yet been captured in previous studies. Our analyses suggested that the effects of mycelium pellets as a molecular template almost gained an advantage over SMP both in crystal nucleation and growth, having nothing to do with biological activity. It is thereby convinced that lithophilous actinobacteria, S. luteogriseus DHS C014, owing to its advantageous genetic metabolism and filamentous structure, showed good biomineralization abilities, maybe it would have geoactive potential for biogenic carbonate in local microenvironments.

The selective expression of carbonic anhydrase genes of Aspergillus nidulans in response to changes in mineral nutrition and CO2 concentration

Carbonic anhydrase (CA) plays an important role in the formation and evolution of life. However, to our knowledge, there has been no report on CA isoenzyme function differentiation in fungi. Two different CA gene sequences in Aspergillus nidulans with clear genetic background provide us a favorable basis for studying function differentiation of CA isoenzymes. Heterologously expressed CA1 was used to test its weathering ability on silicate minerals and real-time quantitative PCR was used to detect expression of the CA1 and CA2 genes at different CO2 concentrations and in the presence of different potassium sources. The northern blot method was applied to confirm the result of CA1 gene expression. Heterologously expressed CA1 significantly promoted dissolution of biotite and wollastonite, and CA1 gene expression increased significantly in response to soluble K-deficiency. The northern blot test further showed that CA1 participated in K-feldspar weathering. In addition, the results showed that CA2 was primary involved in adapting to CO2 concentration change. Taken together, A. nidulans can choose different CA to meet their survival needs, which imply that some environmental microbes have evolved different CAs to adapt to changes in CO2 concentration and acquire mineral nutrition so that they can better adapt to environmental changes. Inversely, their adaption may impact mineral weathering and/or CO2 concentration, and even global change.

A Global View of Gene Expression of Aspergillus nidulans on Responding to the Deficiency in Soluble Potassium

Many researchers have suggested that microbes can accelerate the weathering of silicate minerals. However, many genes and metabolic pathways related to microorganisms obtaining potassium (K) from silicate remain undiscovered. It is feasible to detect the gene expression within the scope of the whole genome through high-throughput sequencing. Surprisingly, only a few reports have shown fungal weathering of silicate using this technology. This study explored differences in gene expression of Aspergillus nidulans, which was cultured with different K sources, KCl, and K-feldspar. A. nidulans RNA was extracted by the construction of a cDNA library. Identification of K-acquisition-related genes with GO and KEGG pathway analysis revealed that primarily differentially expressed genes were related to the biosynthesis of amino acids. When these genes were grouped in accordance with the physiological functions, the genes involved in the synthesis of protease, ribosome, and mitochondria, trans-membrane transport, and oxidative phosphorylation were significantly different. Moreover, 20 genes selected were further tested using RT-qPCR. One half (10 genes) exhibited differential expression, which was consistent with the results of RNA-seq. Combining the results of RNA-seq and RT-qPCR, we summarised a possible way to obtain mineral K in A. nidulans as well. The differentially expressed genes and their associated metabolic pathways revealed will improve the understanding of the molecular mechanisms of microbial weathering of silicate minerals.