Microbial CO2 Research Articles

Longitudinal distributions of CO2-fixing bacteria in forest soils and their potential associations with soil multifunctionality

Autotrophic microorganisms can fix carbon dioxide (CO2) into organic carbon (C), potentially offering a natural mechanism to mitigate global climate change. Forest soils, recognized as vast and critical C repositories with significant microbial CO2 fixation rates, remain understudied, particularly regarding the spatial variations of autotrophic bacteria and their relationship to soil functions in arid regions. In this study, we systematically investigated soil multifunctionality, along with the spatial distribution of autotrophic bacterial communities identified by the RubisCO cbbL and cbbM genes, and the driving factors across a longitudinal gradient in the Loess Plateau forest soils. The investigation spanned an ∼850 km west-east transect with precipitation below 600 mm. The alpha diversity of cbbL-containing bacteria, as measured by the Chao1 index, was correlated with climatic variables such as precipitation and elevation instead of local soil characteristics. In contrast, the alpha diversity of cbbM-containing bacteria was associated with soil properties. The community composition of autotrophic bacteria, based on cbbL and cbbM genes, showed greater similarity in soils from the eastern Loess Plateau and was distinct from those in the western region. The cbbL- and cbbM-containing generalist taxa were subject to differential selection and promotion between the eastern and western regions. Temperature, soil pH and spatial variables were key drivers influencing the community composition of cbbL- and cbbM-containing bacteria. The diversity and communities of soil autotrophic bacteria significantly affected soil multifunctionality. The study demonstrates that soil autotrophic bacteria in forest soils are intricately connected to climatic conditions, soil pH and spatial factors, significantly impacting soil multifunctionality. These insights provide evidence that can be instrumental in predicting and potentially enhancing the functional capacity of forest ecosystems in the Loess Plateau.

Effects of Various Herbicide Types and Doses, Tillage Systems, and Nitrogen Rates on CO2 Emissions from Agricultural Land: A Literature Review

Although herbicides are essential for global agriculture and controlling weeds, they impact soil microbial communities and CO2 emissions. However, the effects of herbicides, tillage systems, and nitrogen fertilisation on CO2 emissions under different environmental conditions are poorly understood. This review explores how various agricultural practices and inputs affect CO2 emissions and addresses the impact of pest-management strategies, tillage systems, and nitrogen fertiliser usage on CO2 emissions using multiple databases. Key findings indicate that both increased and decreased tendencies in greenhouse gas (GHG) emissions were observed, depending on the herbicide type, dose, soil properties, and application methods. Several studies reported a positive correlation between CO2 emissions and increased agricultural production. Combining herbicides with other methods effectively controls emissions with minimal chemical inputs. Conservation practices like no-tillage were more effective than conventional tillage in mitigating carbon emissions. Integrated pest management, conservation tillage, and nitrogen fertiliser rate optimisation were shown to reduce herbicide use and soil greenhouse gas emissions. Fertilisers are similarly important; depending on the dosage, they may support yield or harm the soil. Fertiliser benefits are contingent on appropriate management practices for specific soil and field conditions. This review highlights the significance of adaptable management strategies that consider local environmental conditions and can guide future studies and inform policies to promote sustainable agriculture practices worldwide.

Boosting Microbial CO2 Electroreduction by the Biocompatible and Electroactive Bimetallic Fe–Mn Oxide Cathode for Acetate Production

Boosting Microbial CO₂ Electroreduction by the Biocompatible and Electroactive Bimetallic Fe–Mn Oxide Cathode for Acetate Production

Understanding the Flexibility Challenges of a Plant for Microbial CO2 Electroreduction with Hexanoic Acid Recovery

Understanding the Flexibility Challenges of a Plant for Microbial CO₂ Electroreduction with Hexanoic Acid Recovery

Development of membrane bioreactor for conversion of flue Gas-CO2 to C1 and C2 biomolecules

The capture and utilization of CO2 (CCU) from flue gases constitute a novel carbon feedstock for producing renewable chemicals and fuels. To lower the energy demand of CCU, Bio-Integrated Carbon Capture and Utilization (BICCU) was recently presented, where CO2-consuming microorganisms simultaneously desorb and convert CO2 captured from flue gas by methyl diethanolamine (MDEA) with H2 from water-electrolysis as the electron donor. The limiting factor is the microbial toxicity of MDEA, which restricts the capacity of the process. Furthermore, producing soluble molecules like the C2 platform molecule acetate is not possible without contaminating the product with capture agent. To resolve both challenges, we here propose a three-phase membrane system, where the MDEA and microorganisms are separated by a CO2-permeable membrane. Biological batch experiments with a mixed mesophilic culture confirmed the increased capacity of the BICCU-process for producing both methane and acetate when introducing a CO2-permeable membrane to the system to alleviate microbial inhibition by the capture agent and avoid contamination of soluble bioproducts. When using O2-rich flue gas from a biogas combustion engine, the CO2 conversion rate decreased by 18.0 % compared to a clean 20:80 CO2:N2 gas mixture, yet anaerobic metabolisms were still active in the mixed inoculum. Abiotic experiments furthermore showed that the microbial CO2 consumption maintained the gradient across the membrane and enhanced the CO2-flux by a factor of 3.1 ± 0.3. The membrane-based BICCU concept is expected to hold great promise particularly for producing acetate from flue gas-CO2, as the in situ separation eliminates the need for costly downstream separation.

Nitrogen-doped carbon dots boost microbial electrosynthesis via efficient extracellular electron uptake of acetogens

This study investigated the molecular mechanism behind the highly efficient performance of nitrogen-doped carbon dots (NCDs)-assisted microbial electrosynthesis systems (MESs). The impact of NCDs (C:N precursor = 1:0.5–1:3) on acetogens was examined in the biocathode. The highest electrocatalytic performance was observed with NCDs1:1. The maximum acetate production rate of 1.9 ± 0.1 mM d−1 was achieved in NCDs1:1-modified MESs, which was 26.7–216.7 % higher than other MESs (0.6–1.5 mM d−1). With NCDs1:1 modified, the biocathode exhibited a 129.3–186.8 % increase in the abundance of Sporomusa, and 38.5–104.6 % increase in cytochrome expression (cydAB, cybH). Transcriptome confirmed that cytochromes played a crucial role in the extracellular electron uptake (EEU) of NCDs1:1-modified Sporomusa. NCDs1:1 enhanced EEU efficiency, thereby increasing the two H+-pumping steps and accelerating microbial CO2 fixation. These results provide valuable insights into increasing CO2 fixation by maximizing EEU efficiency in acetogens.

Abiotic and Biotic Processes Controlling Deposition of Calcite and Hydrotalcite Calcretes on Niue Island, Southwest Pacific

Calcretes are indurated terrestrial carbonates that are widespread in arid and semi-arid settings and serve as important archives of present and past environments. Here, we use geochemical tools to explore the nature and origin of calcretes documented from tropical Niue Island in the Southwest Pacific. The study recognizes two types of calcretes that differ in their mineral assemblage, microfabrics, elemental chemistry, and carbon and oxygen isotopes. The calcretes common in the paleo-lagoon soils consist of 90% low-Mg calcite and ~10% highly weathered Mg-Al silicates. These pedogenic calcretes formed in the soil profiles within the vadose zone bear the following distinctions: (i) Fe/Al ratio of 0.75, identical to the ratio in soils (Fe/Al = 0.76 ± 0.5), substantiating the link between the calcretes and soils; (ii) presence of rhizoliths, root voids, micritic nodules, and clasts, which are consistent with a pedogenic calcrete fabric; and (iii) 13C and 18O depletions of −10.6‰ and −5.3‰, respectively, which are compatible with carbon sources from microbial and root respiration, as well as formation in oxygen isotope equilibrium with vadose waters. Unlike the pedogenic calcrete, a rare calcrete from the coastal terrace contains an exceptionally rare hydrotalcite [Mg6Al2(CO3)(OH)16(H2O)4] mineral (65%) coated by microbial films. We contend that the hydrotalcite-rich calcrete was deposited through interaction of dolomite with seawater, similar to the method of producing hydrotalcite in the laboratory. 13C and 18O enrichments of 0.8 to 1.7‰ and −1.0 to −1.6‰, respectively, are in agreement with (i) mixed carbon sources consisting of microbial CO2 degassing, seawater HCO3, and dolomite dissolution, and (ii) oxygen isotope equilibration with seawater-derived fluid.

Biogas liquid digestate application: influence on soil microbial biomass and CO2 respiration

Biogas liquid digestate application: influence on soil microbial biomass and CO2 respiration

Surprising concentrations of hydrogen and non-geological methane and carbon dioxide in the soil

Due to its potential use as a carbon-free energy resource with minimal environmental and climate impacts, natural hydrogen (H2) produced by subsurface geochemical processes is today the target of intensive research. In H2 exploration practices, bacteria are thought to swiftly consume H2 and, therefore, small near-surface concentrations of H2, even orders of 102 ppmv in soils, are considered a signal of active migration of geological gas, potentially revealing underground resources. Here, we document an extraordinary case of a widespread occurrence of H2 (up to 1 vol%), together with elevated concentrations of CH4 and CO2 (up to 51 and 27 vol%, respectively), in aerated meadow soils along Italian Alps valleys. Based on current literature, this finding would be classified as a discovery of pervasive and massive geological H2 seepage. Nevertheless, an ensemble of gas geochemical and soil microbiological analyses, including bulk and clumped CH4 isotopes, radiocarbon of CH4 and CO2, and DNA and mcrA gene quantitative polymerase chain reaction analyses, revealed that H2 was only coupled to modern microbial gas. The H2-CO2-CH4-H2S association, wet soil proximity, and the absence of other geogenic gases in soils and springs suggest that H2 derives from near-surface fermentation, rather than geological degassing. H2 concentrations up to 1 vol% in soils are not conclusive evidence of deep gas seepage. This study provides a new reference for the potential of microbial H2, CH4 and CO2 in soils, to be considered in H2 exploration guidelines and soil carbon and greenhouse-gas cycle research.

Temperature-Driven Activated Sludge Bacterial Community Assembly and Carbon Transformation Potential: A Case Study of Industrial Plants in the Yangtze River Delta.

Temperature plays a critical role in the efficiency and stability of industrial wastewater treatment plants (WWTPs). This study focuses on the effects of temperature on activated sludge (AS) communities within the A2O process of 19 industrial WWTPs in the Yangtze River Delta, a key industrial region in China. The investigation aims to understand how temperature influences AS community composition, functional assembly, and carbon transformation processes, including CO2 emission potential. Our findings reveal that increased operating temperatures lead to a decrease in alpha diversity, simplifying community structure and increasing modularity. Dominant species become more prevalent, with significant decreases in the relative abundance of Chloroflexi and Actinobacteria, and increases in Bacteroidetes and Firmicutes. Moreover, higher temperatures enhance the overall carbon conversion potential of AS, particularly boosting CO2 absorption in anaerobic conditions as the potential for CO2 emission during glycolysis and TCA cycles grows and diminishes, respectively. The study highlights that temperature is a major factor affecting microbial community characteristics and CO2 fluxes, with more pronounced effects observed in anaerobic sludge. This study provides valuable insights for maintaining stable A2O system operations, understanding carbon footprints, and improving COD removal efficiency in industrial WWTPs.

Picky Eaters: Carbon Isotopic Evidence for the Uniform Bioavailability of Riverine Dissolved Organic Matter to a Model Marine Microorganism

AbstractDissolved organic matter (DOM) is a key component of the global carbon cycle, with rivers delivering significant amounts of DOM to oceans. Urbanization and agricultural land‐use alter the age and chemical composition of riverine DOM, which likely impact the downstream bioavailability of riverine DOM. Here, we use bioreactor incubations of a marine bacterium (Pseudoalteromonas sp. 3D05) to investigate DOM bioavailability from two distinct rivers: the Suwannee River (natural, non‐urbanized), and the Upper Mississippi River Basin (anthropogenically influenced). We measured rates of microbial CO2 production and radiocarbon ages (as Δ14C) to assess DOM remineralization. We observed nearly identical cell densities and degradation patterns for both riverine DOM incubations. Respired DOM Δ14C values were also similar and decreased over time indicative of preferential utilization of recently synthesized “modern” substrates. These findings reveal unexpected similarities in riverine DOM bioavailability, indicating similar short term biological reactivity despite large DOM compositional differences.

Biochar promotes microbial CO2 fixation by regulating feedback inhibition of metabolites

Chemoautotrophs, the crucial contributors to biological carbon fixation, derive energy from reducing specific inorganic substances and utilize CO2 for growth. However, the release of extracellular free organic carbon (EFOC) by chemoautotrophic microorganisms can inhibit their own growth and metabolism. To reduce the feedback inhibition effect, a low-release biochar (BC-LR) was applied to adsorb EFOC. BC-LR not only adsorbed EFOC, but also selectively adsorbed the main inhibitory component, low molecular weight organics, in EFOC. In contrast, ordinary biochar could not effectively adsorb EFOC and its addition inhibited microbial growth and CO2 fixation. In Transwell culture, BC-LR promoted microbial growth by 190% and CO2 fixation by 29%, and exhibited better economic advantage, when compared with granular activated carbon. These findings provide a novel insight into the interaction between biochar and autotrophic microbial metabolism, offering an economically feasible approach to mitigate feedback inhibition of metabolites and promoting biological CO2 fixation.

Geochemical tracers associated with methane in aquifers overlying a coal seam gas reservoir

Understanding inter-aquifer connectivity or leakage of greenhouse gases and groundwater to aquifers overlying gas reservoirs is important for environmental protection and social licence to operate. Australia's Great Artesian Basin (GAB) is the largest artesian groundwater system in the world with groundwater extracted for agriculture, livestock, mines, energy, private or town water supply. Microbial coal seam gas (CSG) and production water are also extracted from the GAB. Here a range of groundwater tracers is used to investigate the potential for gas and groundwater connectivity between the CSG reservoir and aquifers.The GAB aquifer and alluvium contained a range of methane concentrations (0.001 to 2100 mg/L) that exhibit an increase with depth and δ13C-CH4. Aquifer and alluvium groundwater 87Sr/86Sr were in the range 0.7042 to 0.7082. CSG production waters however had non-radiogenic, distinctive 87Sr/86Sr signatures <0.7036, indicating a lack of significant groundwater leakage. One gassy aquifer bore with 160 mg/L methane conversely has 87Sr/86Sr, δ13C-CH4, δ2H-CH4 and δ13C-DIC values overlapping the CSG waters. In several aquifers δ34S-SO4 and δ18O-SO4 are sourced from windblown surface salts of inland Australian playa lakes in recharge waters. Bacterial sulphate reduction is additionally occurring in a regional aquifer. Cosmogenic isotopes and tritium show recent recharge and mixing with older groundwaters in several shallow aquifers.Groundwater and gas signatures indicate that leakage of groundwater and methane from the CSG reservoir was not occurring in the majority of areas investigated here. Methane was consistent with in situ generation in shallow GAB aquifers by primary microbial CO2 reduction or acetate fermentation. Connectivity of one alluvial bore and the underlying GAB aquifer could not be completely ruled out. Separately, one gassy Springbok GAB aquifer bore is either connected to the underlying CSG gas reservoir, or has in situ secondary microbial CO2 reduction producing methane from interbedded coal within the aquifer. This study is relevant to other basins in Australia and internationally where gas is observed in aquifers that overly conventional, unconventional or coal seam gas reservoirs.

Unequal impacts of unidirectional freeze-thaw on different soil layers and aggregate sizes: Evidenced by microbial communities and CO2 emissions

Currently available investigations often fail to adequately recognize that soil does not freeze or thaw instantly nor uniformly, but unidirectionally and progressively. Unidirectional freeze-thaw can re-organize soil physio-, chemical- and biological-properties across layers as well among aggregates, thus posing far-reaching yet undervalued impacts on soil carbon biogeochemical cycling, especially in eroding settings. In this study, a Mollisol was refilled into soil columns, and respectively experienced complete freeze-thaw (i.e., no layer distinguished), and progressive freeze-thaw (i.e., from outer layer T1, to inner core T3). After thawing, all soils were fractionated into six size classes, and each size class was then incubated at 10℃ over 7 days to measure daily CO2 emission rate. Our results show that: (1) The soil microbial biomass carbon (SMBC) was generally reduced by 25 % after freeze-thaw, but only the finest aggregates ≤ 32 μm maintained comparable CO2 emission rates. (2) The inner core T3 thawed last and survived with significantly more SMBC and CO2, but lower respiratory quotient (qCO2), than the outer layer T1 thawed first. (3) The fine aggregates survived with more SMBC and total CO2 emissions, but significantly lower qCO2 and smaller ratios of fungal to bacterial biomass carbon, than the coarse aggregates. The disproportionally less respiratory carbon losses (i.e., lower qCO2) in T3 was probably because the lagged freezing and thus weakened water-ice phase changes in the inner core helped to better preserve the soil microbes. The fungal-dominant coarse aggregates were very responsive to freezing and evidently more respiratory active, whereas the fine aggregates were more resilient as the enhanced freezing point depression and the thus prolonged unfrozen state, fostering a better microbial survival with bacteria-dominant communities and robust basal respiration. Although limited to controlled simulation, this study may help to disentangle the role of unidirectional freeze-thaw in perturbing slope-scale soil carbon biogeochemical cycling.

Engineering a solar formic acid/pentose (SFAP) pathway in Escherichia coli for lactic acid production

Microbial CO2 fixation into lactic acid (LA) is an important approach for low-carbon biomanufacturing. Engineering microbes to utilize CO2 and sugar as co-substrates can create efficient pathways through input of moderate reducing power to drive CO2 fixation into product. However, to achieve complete conservation of organic carbon, how to engineer the CO2-fixing modules compatible with native central metabolism and merge the processes for improving bioproduction of LA is a big challenge. In this study, we designed and constructed a solar formic acid/pentose (SFAP) pathway in Escherichia coli, which enabled CO2 fixation merging into sugar catabolism to produce LA. In the SFAP pathway, adequate reducing equivalents from formate oxidation drive glucose metabolism shifting from glycolysis to the pentose phosphate pathway. The Rubisco-based CO2 fixation and sequential reduction of C3 intermediates are conducted to produce LA stoichiometrically. CO2 fixation theoretically can bring a 20% increase of LA production compared with sole glucose feedstock. This SFAP pathway in the integration of photoelectrochemical cell and an engineered Escherichia coli opens an efficient way for fixing CO2 into value-added bioproducts.

Coupling use of stable isotopes and functional genes as indicators for the impacts of artificial restoration on the carbon storage of a coastal wetland invaded by Spartina alterniflora, southeastern China

Coastal wetlands are characterized by high production and thus play an important role in global climate change. In past decades, the invasion of Spartina alterniflora has caused many problems of coastal wetlands in southeastern China, and the restoration of such areas was mainly conducted by replacing Spartina alterniflora with mangrove plants. This may impact the carbon storage dynamics in such areas. In this study, stable isotopes (δ13C and δ15N) and molecular analysis were used to reveal the impact of artificial restoration on the carbon storage of Quanzhou Bay Estuary Wetland Natural Reserve. The major results are as follows: (1) the change in dominant plants results in a changing major source of soil organic matter, from external sources to mangrove plants; (2) the decrease in soil organic matter following the removal of Spartina alterniflora may be primarily caused by the loss of external organic matter, while the production of mangroves may offset such loss and enhance the content and stability of carbon storage over the long term; (3) microbial CO2 assimilation may serve as an alternative source of bioavailable carbon and thus support the activity of benthic community. Our results revealed the long-term benefits of such restoration on the carbon storage function of wetlands invaded by Spartina alterniflora. Furthermore, the integrating of isotopic tracers and molecular technology may provide new insights in understanding the response of the carbon storage in coastal areas to human activity.

Biochar facilitated Biological CO2 conversion to C2-C6 alcohols and fatty acids

Microbial CO2 utilization reduces the carbon footprint, providing economic potential. Biochar, rich in minerals and trace metals, can enhance microbial activity. This study investigates poultry litter and switchgrass biochars produced at 350 and 700 °C (PLB350, PLB700, SGB350 and SGB700, respectively) affect CO2 conversion to C2–C6 alcohols and acids by Clostridium muellerianum P21, C. ragsdalei P11 and C. carboxidivorans P7. Fermentations were in 250-mL bottles containing H2:CO2:N2 (60:20:20) shaken at 125 rpm and 37 °C. SGB350 increased alcohol titers by 1.1–2.1 fold, and PLB350 enhanced acid concentrations by 1.2–1.7 fold compared to the control without biochar. About 2.0–3.3 fold more ethanol was formed by strain P11 compared to strains P7 and P21 with SGB350. However, strain P21 produced 2.4-fold more butanol than strain P7 with SGB350, including unique hexanol production. These results highlight the potential of biochar in enhancing C2–C6 alcohol production from CO2, thereby boosting process feasibility.

Enhancing microbial CO2 electrocatalysis for multicarbon reduction in a wet amine-based catholyte.

Microbial CO2 electroreduction (mCO2ER) offers a promising approach for producing high-value multicarbon reductants from CO2 by combining CO2 fixing microorganisms with conducting materials (i. e., cathodes). However, the solubility and availability of CO2 in an aqueous electrolyte pose significant limitations in this system. This study demonstrates the efficient production of long-chain multicarbon reductants, specifically carotenoids (~C40 ), within a wet amine-based catholyte medium during mCO2ER. Optimizing the concentration of the biocompatible CO2 absorbent, monoethanolamine (MEA), led to enhanced CO2 fixation in the electroautotroph bacteria. Molecular biological analyses revealed that MEA in the catholyte medium redirected the carbon flux towards carotenoid biosynthesis during mCO2ER. The faradaic efficiency of mCO2ER with MEA for carotenoid production was 4.5-fold higher than that of the control condition. These results suggest the mass transport bottleneck in bioelectrochemical systems could be effectively addressed by MEA-assissted mCO2ER, enabling highly efficient production of valuable products from CO2 .

Probing efficient microbial CO2 utilisation through metabolic and process modelling.

Acetogenic gas fermentation is increasingly studied as a promising technology to upcycle carbon-rich waste gasses. Currently the product range is limited, and production yields, rates and titres for a number of interesting products do not allow for economically viable processes. By pairing process modelling and host-agnostic metabolic modelling, we compare fermentation conditions and various products to optimise the processes. The models were then used in a simulation of an industrial-scale bubble column reactor. We find that increased temperatures favour gas transfer rates, particularly for the valuable and limiting H2 , while furthermore predicting an optimal feed composition of 9:1 mol H2 to mol CO2 . Metabolically, the increased non-growth associated maintenance requirements of thermophiles favours the formation of catabolic products. To assess the expansion of the product portfolio beyond acetate, both a product volatility analysis and a metabolic pathway model were implemented. In-situ recovery of volatile products is shown to be within range for acetone but challenging due to the extensive evaporation of water, while the direct production of more valuable compounds by acetogens is metabolically unfavourable compared to acetate and ethanol. We discuss alternative approaches to overcome these challenges to utilise acetogenic CO2 fixation to produce a wider range of carbon negative chemicals.

Novel electrochemical strategies for the microbial conversion of CO2 into biomass and volatile fatty acids using a fluid-like bed electrode in a three-phase reactor.

Microbial electrosynthesis (MES) constitutes a bioelectrochemical process where bacteria uptake electrons extracellularly from a polarized electrode to incorporate them into their anabolic metabolism. However, the efficiency of current MES reactor designs can be lower than expected due to limitations regarding electron transfer and mass transport. One of the most promising bioreactor configurations to overcome these bottlenecks is the Microbial Electrochemical Fluidized Bed Reactor (ME-FBR). In this study, microbial CO2 fixation is investigated for the first time in a ME-FBR operated as a 3-phase reactor (solid-liquid-gas). An electroconductive carbon bed, acting as a working electrode, was fluidized with gas and polarized at different potentials (-0.6, -0.8 and -1 V vs. Ag/AgCl) so it could act as an electron donor (biocathode). Under these potentials, CO2 fixation and electron transfer were evaluated. Autotrophic electroactive microorganisms from anaerobic wastewater were enriched in a ME-FBR in the presence of 2-bromoethanosulfonic acid (BES) to inhibit the growth of methanogens. Cyclic voltammetry analysis revealed interaction between the microorganisms and the cathode. Furthermore, volatile fatty acids like propionate, formate and acetate were detected in the culture supernatant. Acetate production had a maximum rate of ca. 1 g L-1 day-1 . Planktonic cell biomass was produced under continuous culture at values as high as ca. 0.7 g L-1 dry weight. Overall, this study demonstrates the feasibility of employing a fluidized electrode with gaseous substrates and electricity as the energy source for generating biomass and carboxylic acids.