Enrichment of Marinobacter sp. and Halophilic Homoacetogens at the Biocathode of Microbial Electrosynthesis System Inoculated With Red Sea Brine Pool

Lactate-mediated medium-chain fatty acid production from expired dairy and beverage waste

Fruits, vegetables, and dairy products are typically the primary sources of household food waste. Currently, anaerobic digestion is the most used bioprocess for the treatment of food waste with concomitant generation of biogas. However, to achieve a circular carbon economy, the organics in food waste should be converted to new chemicals with higher value than energy. Here we demonstrate the feasibility of medium-chain carboxylic acid (MCCA) production from expired dairy and beverage waste via a chain elongation platform mediated by lactate. In a two-stage fermentation process, the first stage with optimized operational conditions, including varying temperatures and organic loading rates, transformed expired dairy and beverage waste into lactate at a concentration higher than 900 mM C at 43 °C. This lactate was then used to produce >500 mM C caproate and >300 mM C butyrate via microbial chain elongation. Predominantly, lactate-producing microbes such as Lactobacillus and Lacticaseibacillus were regulated by temperature and could be highly enriched under mesophilic conditions in the first-stage reactor. In the second-stage chain elongation reactor, the dominating microbes were primarily from the genera Megasphaera and Caproiciproducens, shaped by varying feed and inoculum sources. Co-occurrence network analysis revealed positive correlations among species from the genera Caproiciproducens, Ruminococcus, and CAG-352, as well as Megasphaera, Bacteroides, and Solobacterium, indicating strong microbial interactions that enhance caproate production. These findings suggest that producing MCCAs from expired dairy and beverage waste via lactate-mediated chain elongation is a viable method for sustainable waste management and could serve as a chemical production platform in the context of building a circular bioeconomy.

Microbial alchemists: unveiling the hidden potentials of halophilic organisms for soil restoration

Salinity, resulting from various contaminants, is a major concern to global crop cultivation. Soil salinity results in increased osmotic stress, oxidative stress, specific ion toxicity, nutrient deficiency in plants, groundwater contamination, and negative impacts on biogeochemical cycles. Leaching, the prevailing remediation method, is expensive, energy-intensive, demands more fresh water, and also causes nutrient loss which leads to infertile cropland and eutrophication of water bodies. Moreover, in soils co-contaminated with persistent organic pollutants, heavy metals, and textile dyes, leaching techniques may not be effective. It promotes the adoption of microbial remediation as an effective and eco-friendly method. Common microbes such as Pseudomonas, Trichoderma, and Bacillus often struggle to survive in high-saline conditions due to osmotic stress, ion imbalance, and protein denaturation. Halophiles, capable of withstanding high-saline conditions, exhibit a remarkable ability to utilize a broad spectrum of organic pollutants as carbon sources and restore the polluted environment. Furthermore, halophiles can enhance plant growth under stress conditions and produce vital bio-enzymes. Halophilic microorganisms can contribute to increasing soil microbial diversity, pollutant degradation, stabilizing soil structure, participating in nutrient dynamics, bio-geochemical cycles, enhancing soil fertility, and crop growth. This review provides an in-depth analysis of pollutant degradation, salt-tolerating mechanisms, and plant-soil-microbe interaction and offers a holistic perspective on their potential for soil restoration.

Microbial electrosynthesis of acetate from CO2 in three-chamber cells with gas diffusion biocathode under moderate saline conditions

The industrial adoption of microbial electrosynthesis (MES) is hindered by high overpotentials deriving from low electrolyte conductivity and inefficient cell designs. In this study, a mixed microbial consortium originating from an anaerobic digester operated under saline conditions (∼13 g L^-1 NaCl) was adapted for acetate production from bicarbonate in galvanostatic (0.25 mA cm^-2) H-type cells at 5, 10, 15, or 20 g L^-1 NaCl concentration. The acetogenic communities were successfully enriched only at 5 and 10 g L^-1 NaCl, revealing an inhibitory threshold of about 6 g L^-1 Na⁺. The enriched planktonic communities were then used as inoculum for 3D printed, three-chamber cells equipped with a gas diffusion biocathode. The cells were fed with CO₂ gas and operated galvanostatically (0.25 or 1.00 mA cm^-2). The highest production rate of 55.4 g m^-2 d^-1 (0.89 g L^-1 d^-1), with 82.4% Coulombic efficiency, was obtained at 5 g L^-1 NaCl concentration and 1 mA cm^-2 applied current, achieving an average acetate production of 44.7 kg MWh^-1. Scanning electron microscopy and 16S rRNA sequencing analysis confirmed the formation of a cathodic biofilm dominated by Acetobacterium sp. Finally, three 3D printed cells were hydraulically connected in series to simulate an MES stack, achieving three-fold production rates than with the single cell at 0.25 mA cm^-2. This confirms that three-chamber MES cells are an efficient and scalable technology for CO₂ bio-electro recycling to acetate and that moderate saline conditions (5 g L^-1 NaCl) can help reduce their power demand while preserving the activity of acetogens.

Enrichment of halotolerant hydrogen-oxidizing bacteria and production of high-value-added chemical hydroxyectoine using a hybrid biological-inorganic system

Hybrid biological-inorganic (HBI) systems show great promise as CO2 conversion platforms combining CO2 fixation by hydrogen-oxidizing bacteria (HOB) with water splitting. Herein, halotolerant HOB were enriched using an HBI system with a high-ionic-strength medium containing 180 mM phosphate buffer to identify new biocatalysts. The reactors were inoculated with samples from saline environments and applied with a voltage of 2.0 V. Once an increase in biomass was observed with CO2 consumption, an aliquot of the medium was transferred to a new reactor. After two successive subcultures, Achromobacter xylosoxidans strain H1_3_1 and Mycolicibacterium mageritense strain H4_3_1 were isolated from the reactor media. Genome sequencing indicated the presence of genes for aerobic hydrogen-oxidizing chemolithoautotrophy and synthesis of the compatible solute hydroxyectoine in both strains. Furthermore, both strains produced hydroxyectoine in the reactors under the high-ionic-strength condition, suggesting the potential for new HBI systems using halotolerant HOB to produce high-value-added chemicals.

Halophilic CO2-fixing microbial community as biocatalyst improves the energy efficiency of the microbial electrosynthesis process

Using saline electrolytes in combination with halophilic CO₂-fixing lithotrophic microbial catalysts has been envisioned as a promising strategy to develop an energy-efficient microbial electrosynthesis (MES) process for CO₂ utilization. Here, an enriched marine CO₂-fixing lithotrophic microbial community dominated by Vibrio and Clostridium spp. was tested for MES of organic acids from CO₂. At an applied E_cathode of -1V (vs Ag/AgCl) with 3.5 % salinity (78 mScm^-1), it produced 379 ± 53 mg/L (6.31 ± 0.89 mM) acetic acid and 187 ± 43 mg/L (4.05 ± 0.94 mM) formic acid at 2.1 ± 0.30 and 1.35 ± 0.31 mM day^-1, respectively production rates. Most electrons were recovered in acetate (68.3 ± 3 %), formate (9.6 ± 1.2 %) besides hydrogen (11 ± 1.4 %) and biomass (8.9 ± 1.65 %). Notably, the bioproduction of organic acids occurred at a high energetic efficiency (EE) of ∼ 46 % and low E_cell of 2.3 V in saline conditions compared to the commonly used non-saline electrolytes (0.5-1 mScm^-1) in the reported MES studies with CO₂ (E_cell: >2.5 V and EE: <34 %).

Enrichment of hydrogen-oxidizing bacteria using a hybrid biological-inorganic system

Hybrid biological-inorganic (HBI) systems comprising inorganic water-splitting catalysts and aerobic hydrogen-oxidizing bacteria (HOB) have previously been used for CO₂ conversion. In order to identify new biocatalysts for CO₂ conversion, the present study used an HBI system to enrich HOB directly from environmental samples. Three sediment samples (from a brackish water pond, a beach, and a tide pool) and two activated sludge samples (from two separate sewage plants) were inoculated into HBI systems using a cobalt phosphorus (Co-P) alloy and cobalt phosphate (CoPi) as inorganic catalysts with a fixed voltage of 2.0 V. The gas composition of the reactor headspaces and electric current were monitored. An aliquot of the reactor medium was transferred to a new reactor when significant consumption of H₂ and CO₂ was detected. This process was repeated twice (with three reactors in operation for each sample) to enrich HOB. Increased biomass concomitant with increased H₂ and CO₂ consumption was observed in the third reactor, indicating enrichment of HOB. 16S rRNA gene amplicon sequencing demonstrated enrichment of sequences related to HOB (including bacteria from Mycobacterium, Hydrogenophaga, and Xanthobacter genera) over successive sub-cultures. Finally, four different HOB belonging to the Mycobacterium, Hydrogenophaga, Xanthobacter, and Acidovorax genera were isolated from reactor media, representing potential candidates as HBI system biocatalysts.

Trait biases in microbial reference genomes

Common culturing techniques and priorities bias our discovery towards specific traits that may not be representative of microbial diversity in nature. So far, these biases have not been systematically examined. To address this gap, here we use 116,884 publicly available metagenome-assembled genomes (MAGs, completeness ≥80%) from 203 surveys worldwide as a culture-independent sample of bacterial and archaeal diversity, and compare these MAGs to the popular RefSeq genome database, which heavily relies on cultures. We compare the distribution of 12,454 KEGG gene orthologs (used as trait proxies) in the MAGs and RefSeq genomes, while controlling for environment type (ocean, soil, lake, bioreactor, human, and other animals). Using statistical modeling, we then determine the conditional probabilities that a species is represented in RefSeq depending on its genetic repertoire. We find that the majority of examined genes are significantly biased for or against in RefSeq. Our systematic estimates of gene prevalences across bacteria and archaea in nature and gene-specific biases in reference genomes constitutes a resource for addressing these issues in the future.

Microbial electrosynthesis of acetate from CO2 under hypersaline conditions

Microbial electrosynthesis (MES) enables the bioproduction of multicarbon compounds from CO₂ using electricity as the driver. Although high salinity can improve the energetic performance of bioelectrochemical systems, acetogenic processes under elevated salinity are poorly known. Here MES under 35-60 g L^-1 salinity was evaluated. Acetate production in two-chamber MES systems at 35 g L^-1 salinity (seawater composition) gradually decreased within 60 days, both under -1.2 V cathode potential (vs. Ag/AgCl) and -1.56 A m^-2 reductive current. Carbonate precipitation on cathodes (mostly CaCO₃) likely declined the production through inhibiting CO₂ supply, the direct electrode contact for acetogens and H₂ production. Upon decreasing Ca²⁺ and Mg²⁺ levels in three-chamber reactors, acetate was stably produced over 137 days along with a low cathode apparent resistance at 1.9 ± 0.6 mΩ m² and an average production rate at 3.80 ± 0.21 g m^-2 d^-1. Increasing the salinity step-wise from 35 to 60 g L^-1 gave the most efficient acetate production at 40 g L^-1 salinity with average rates of acetate production and CO₂ consumption at 4.56 ± 3.09 and 7.02 ± 4.75 g m^-2 d^-1, respectively. The instantaneous coulombic efficiency for VFA averaged 55.1 ± 31.4%. Acetate production dropped at higher salinity likely due to the inhibited CO₂ dissolution and acetogenic metabolism. Acetobacterium up to 78% was enriched on cathodes as the main acetogen at 35 g L^-1. Under high-salinity selection, 96.5% Acetobacterium dominated on the cathode along with 34.0% Sphaerochaeta in catholyte. This research provides a first proof of concept that MES starting from CO₂ reduction can be achieved at elevated salinity.

A meta-analysis of acetogenic and methanogenic microbiomes in microbial electrosynthesis

A meta-analysis approach was used, to study the microbiomes of biofilms and planktonic communities underpinning microbial electrosynthesis (MES) cells. High-throughput DNA sequencing of 16S rRNA gene amplicons has been increasingly applied to understand MES systems. In this meta-analysis of 22 studies, we find that acetogenic and methanogenic MES cells share 80% of a cathodic core microbiome, and that different inoculum pre-treatments strongly affect community composition. Oxygen scavengers were more abundant in planktonic communities, and several key organisms were associated with operating parameters and good cell performance. We suggest Desulfovibrio sp. play a role in initiating early biofilm development and shaping microbial communities by catalysing H₂ production, to sustain either Acetobacterium sp. or Methanobacterium sp. Microbial community assembly became more stochastic over time, causing diversification of the biofilm (cathodic) community in acetogenic cells and leading to re-establishment of methanogens, despite inoculum pre-treatments. This suggests that repeated interventions may be required to suppress methanogenesis.

Microbial community and functional prediction during the processing of salt production in a 1000-year-old marine solar saltern of South China

In Hainan Island, South China, a 1000-year-old marine saltern has been identified as an intangible cultural heritage due to its historical complicated salt-making techniques, whereas the knowledge about this saltern is extremely limited. Herein, DNA sequencing and biochemical technologies were applied to determine bacterial and fungal communities of this saltern and their possible functions during four stages of salt-making, i.e. seawater storage, mud solarization, brine concentrating, and solar crystallization. The results showed that both of bacterial and fungal communities were suffered from significant changes during processing of salt-making in Danzhou Ancient Saltern, whereas the richness and diversity of bacterial community dominated by Proteobacteria, Bacteroidota and Cyanobacteria was considerably greater than that of fungal community dominated by Ascomycota, Basidiomycota and Mortierellomycota. Additionally, the succession of bacterial community was closely associated with both of salt physicochemical properties (Na⁺, Cl^-, total phosphorus, total nitrogen, Ca²⁺ and Mg²⁺) and bacteria themselves, whereas fungal community was more closely associated with physicochemical properties than fungi themselves. Importantly, Cyanobium_PCC-6307, Synechococcus_CC9902, Marinobacter, Prevotella and Halomonas as dominant bacterial genera respectively related to the metabolisms of amino acid, carbohydrate, terpenoids/polyketides, lipid and nucleotide were correlated with salt flavors. Saprophytic and saprotroph-symbiotroph fungi dominated by Aspergillus, Mortierella, Amanita, Neocucurbitaria and Tausonia also played core roles in the formation of salt flavors including umami and sweet smells. These findings revealed the highly specified microbiome community in this 1000-year-old saltern that mainly selected by brine solarization on basalt platforms, which is helpful to explore the underlying mechanisms of traditional salt-making techniques and to explore the useful microbes for nowadays food, medicine and chemical industries.

Microbial electrochemical approaches of carbon dioxide utilization for biogas upgrading

Microbial electrochemical approach is an emerging technology for biogas upgrading through carbon dioxide (CO₂) reduction and biomethane (or value-added products) production. There is limited literature critically reviewing the latest scientific developments on the bioelectrochemical system (BES) based biogas upgrading technologies, including CO₂ reduction efficiency, methane (CH₄) yields, reactor operating conditions, and electrode materials tested in the BES reactor. This review analyzes the reported performance and identifies crucial parameters considered for future optimization, which is currently missing. Further, the performances of BES approach of biogas upgrading under various operating settings in particular fed-batch, continuous mode in connection to the microbial dynamics and cathode materials have been thoroughly scrutinized and discussed. Additionally, other versatile application options associated with BES based biogas upgrading, such as resource recovery, are presented. Three-dimensional electrode materials have shown superior performance in supplying the electrons for the reduction of CO₂ to CH₄. Most of the studies on the biogas upgrading process conclude hydrogen (H₂) mediated electron transfer mechanism in BES biogas upgrading.

Enrichment of salt-tolerant CO2-fixing communities in microbial electrosynthesis systems using porous ceramic hollow tube wrapped with carbon cloth as cathode and for CO2 supply

Microbial inocula from marine origins are less explored for CO₂ reduction in microbial electrosynthesis (MES) system, although effective CO₂-fixing communities in marine environments are well-documented. We explored natural saline habitats, mainly salt marsh (SM) and mangrove (M) sediments, as potential inoculum sources for enriching salt-tolerant CO₂ reducing community using two enrichment strategies: H₂:CO₂ (80:20) enrichment in serum vials and enrichment in cathode chamber of MES reactors operated at -1.0 V vs. Ag/AgCl. Porous ceramic hollow tube wrapped with carbon cloth was used as cathode and for direct CO₂ delivery to CO₂ reducing communities growing on the cathode surface. Methanogenesis was dominant in both the M- and SM-seeded MES and the methanogenic Archaea Methanococcus was the most dominant genus. Methane production was slightly higher in the SM-seeded MES (4.9 ± 1.7 mmol) compared to the M-seeded MES (3.8 ± 1.1 mmol). In contrast, acetate production was almost two times higher in the M-seeded MES (3.1 ± 0.9 mmol) than SM-seeded MES (1.5 ± 1.3 mmol). The high relative abundance of the genus Acetobacterium in the M-seeded serum vials correlates with the high acetate production obtained. The different enrichment strategies affected the community composition, though the communities in MES reactors and serum vials were performing similar functions (methanogenesis and acetogenesis). Despite similar operating conditions, the microbial community composition of M-seeded serum vials and MES reactors differed from the SM-seeded serum vials and MES reactors, supporting the importance of inoculum source in the evolution of CO₂-reducing microbial communities.

Resistance assessment of microbial electrosynthesis for biochemical production to changes in delivery methods and CO2 flow rates

Microbial electrosynthesis (MES) for CO₂ valorization could be influenced by fluctuations in CO₂ mass transfer and flow rates. In this study, we developed an efficient method for CO₂ delivery to cathodic biofilm by directly sparging CO₂ through the pores of ceramic hollow fiber wrapped with Ni-foam/carbon nanotube electrode, and obtained 45% and 77% higher acetate and methane production, respectively. This was followed by the MES stability test in response to fluctuations in CO₂ flow rates varying from 0.3 ml/min to 10 ml/min. The biochemical production exhibited an increasing trend with CO₂ flow rates, achieving higher acetate (47.0 ± 18.4 mmol/m²/day) and methane (240.0 ± 32.2 mmol/m²/day) generation at 10 ml/min with over 90% coulombic efficiency. The biofilm and suspended biomass, however, showed high resistance to CO₂ flow fluctuations with Methanobacterium and Acetobacterium accounting for 80% of the total microbial community, which suggests the robustness of MES for onsite carbon conversion.

Microbial Electrosynthesis: Where Do We Go from Here?

The valorization of CO₂ to valuable products via microbial electrosynthesis (MES) is a technology transcending the disciplines of microbiology, (electro)chemistry, and engineering, bringing opportunities and challenges. As the field looks to the future, further emphasis is expected to be placed on engineering efficient reactors for biocatalysts, to thrive and overcome factors which may be limiting performance. Meanwhile, ample opportunities exist to take the lessons learned in traditional and adjacent electrochemical fields to shortcut learning curves. As the technology transitions into the next decade, research into robust and adaptable biocatalysts will then be necessary as reactors shape into larger and more efficient configurations, as well as presenting more extreme temperature, salinity, and pressure conditions.

Effects of set cathode potentials on microbial electrosynthesis system performance and biocathode methanogen function at a metatranscriptional level

Microbial electrosynthesis exploits the catalytic activity of microorganisms to utilize a cathode as an electron donor for reducing waste CO2 to valuable fuels and chemicals. Electromethanogenesis is the process of CO2 reduction to CH4 catalyzed by methanogens using the cathode directly as a source of electrons or indirectly via H2. Understanding the effects of different set cathode potentials on the functional dynamics of electromethanogenic communities is crucial for the rational design of cathode materials. Replicate enriched electromethanogenic communities were subjected to different potentials (- 1.0 V and - 0.7 V vs. Ag/AgCl) and the potential-induced changes were analyzed using a metagenomic and metatranscriptomic approach. The most abundant and transcriptionally active organism on the biocathodes was a novel species of Methanobacterium sp. strain 34x. The cathode potential-induced changes limited electron donor availability and negatively affected the overall performance of the reactors in terms of CH4 production. Although high expression of key genes within the methane and carbon metabolism pathways was evident, there was no significant difference in transcriptional response to the different set potentials. The acetyl-CoA decarbonylase/synthase (ACDS) complex were the most highly expressed genes, highlighting the significance of carbon assimilation under limited electron donor conditions and its link to the methanogenesis pathway.

Microbial electroactive biofilms dominated by Geoalkalibacter spp. from a highly saline-alkaline environment

Understanding of the extreme microorganisms that possess extracellular electron transfer (EET) capabilities is pivotal to advance electromicrobiology discipline and to develop niche-specific microbial electrochemistry-driven biotechnologies. Here, we report on the microbial electroactive biofilms (EABs) possessing the outward EET capabilities from a haloalkaline environment of the Lonar lake. We used the electrochemical cultivation approach to enrich haloalkaliphilic EABs under 9.5 pH and 20 g/L salinity conditions. The electrodes controlled at 0.2 V vs. Ag/AgCl yielded the best-performing biofilms in terms of maximum bioelectrocatalytic current densities of 548 ± 23 and 437 ± 17 µA/cm² with acetate and lactate substrates, respectively. Electrochemical characterization of biofilms revealed the presence of two putative redox-active moieties with the mean formal potentials of 0.183 and 0.333 V vs. Ag/AgCl, which represent the highest values reported to date for the EABs. 16S-rRNA amplicon sequencing of EABs revealed the dominance of unknown Geoalkalibacter sp. at ~80% abundance. Further investigations on the haloalkaliphilic EABs possessing EET components with high formal potentials might offer interesting research prospects in electromicrobiology.

Microbial electrosynthesis from CO2: Challenges, opportunities and perspectives in the context of circular bioeconomy

Recycling CO₂ into organic products through microbial electrosynthesis (MES) is attractive from the perspective of circular bioeconomy. However, several challenges need to be addressed before scaling-up MES systems. In this review, recent advances in electrode materials, microbe-catalyzed CO₂ reduction and MES energy consumption are discussed in detail. Anode materials are briefly reviewed first, with several strategies proposed to reduce the energy input for electron generation and enhance MES bioeconomy. This was followed by discussions on MES cathode materials and configurations for enhanced chemolithoautotroph growth and CO₂ reduction. Various chemolithoautotrophs, effective for CO₂ reduction and diverse bioproduct formation, on MES cathode were also discussed. Finally, research efforts on developing cost-effective process for bioproduct extraction from MES are presented. Future perspectives to improve product formation and reduce energy cost are discussed to realize the application of the MES as a chemical production platform in the context of building a circular economy.