Carbon Source Research Articles

Differences on carboxylic acids bioproduction from soluble carbohydrates or proteins in a sequencing batch reactor: Deciphering the influence of the volumetric and specific organic loading rate

Acidogenic fermentation (AF) has been extensively explored. However, the impact of operational parameters on AF has led to inconsistent results. In this work, AF experiments were performed in a sequencing batch reactor (SBR) using simulated wastewaters solely containing soluble carbohydrates or proteins as carbon sources to independently assess the impact of the volumetric organic loading rate (OLRv) and of the specific OLR (OLRs). When only carbohydrates were used, the main effluent components were acetic and butyric acids at OLRv of 6.0 g COD L−1 d−1, while changing OLRv over 11.0 g COD L−1 d−1 gave acetic acid and ethanol as main components. Conversely, if the carbon source consisted solely of proteins, increasing the OLRv or the OLRs had minimal impact on the AF performance and on the effluent composition. Also, in the case of carbohydrates experiments, increasing the OLRs from 2.3 to 3.8 g COD g−1 VSS d−1 promoted chain elongation reactions, as caproic acid formation was also observed. Besides, at the highest OLRv tested in this work for proteins experiments (18.5 g COD L−1 d−1), the maximum isocaproic acid concentration was obtained using mixed microbial cultures and without adding any external electron donor. The SBR configuration proved to be an adequate system, especially when proteins were used as carbon source, since it makes possible to keep low the OLRs and to reduce the hydrolysis limitations. Finally, the bacterial genera detected in the reactors notably changed between both substrates. Future work must be focused on identifying carboxylic acid producing-genera from proteins.

Improved performance and mechanism of the long-term vanadium(V) remediation by immobilization of rice washing waste

There is an urgent need to develop more efficient microbial technologies suitable for vanadium (V) stressed environments. In this study, rice washing waste (RWW) was utilized as both the carbon and microbial sources immobilized together with sludge to treat V-containing wastewater. Continuous flow reactors were operated, and V(V) removal efficiencies (30 d) with polyvinyl alcohol (PVA) and chitosan as embedded carriers achieved 9.0% and 79.4%, respectively. A superior V(V) removal performance (91.45%) was achieved in the continuous flow reactors with chitosan-based immobilized materials (70 d). V was detected on the surface and within the material, and V(IV) was found, indicating that both adsorption and microbes were able to contribute to V(V) remediation. Increase in the fractions of some functional microbes were observed in response to V(V) stress (unclassified_f_Comamonadaceae, unclassified_f_Enterobacteriaceae) and ammonia stress (unclassified_f_Hungateiclostridiacea). RWW could serve as suitable carbon and microbial sources for long-term operation and enhance V(V) removal by immobilized together with sludge, thereby unveiling a new method for both food and V contaminants.

Microalgal-based carbon encapsulated iron nanoparticles for the removal of pharmaceutical compounds from wastewater

This study evaluates the effectiveness of microalgal-based carbon-encapsulated iron nanoparticles (ME-nFe) in the removal of pharmaceutical compounds (PhACs) from water solutions and real municipal effluent at a laboratory scale. The investigated PhACs were chosen to represent different classes of synthetic drugs: antibiotics, anti-inflammatory drugs, antihypertensives, antiepileptics, neuroprotectors, and antidepressants. The adsorbent material was produced through hydrothermal carbonization (225 °C for three hours), using microalgae grown on wastewater as the carbon source. ME-nFe showed heterogeneity in terms of porosity (with both abundance of macro and mesopores), a total pore volume of 0.65 mL·g-1, a specific surface area of 117 m2·g-1 and a total iron content of 40%. Laboratory scale adsorption tests (1 g·L-1 of nanoparticles with 2 minutes contact time) showed high removal for the most hydrophobic compounds. Removal efficiencies were high (over 98%) for Irbesartan, Ofloxacin and Diclofenac, promising (over 65-80%) for Clarithromycin, Fluoxetine, Lamotrigine and Metoprolol, but low for Gabapentin-Lactam and Propyphenazone (<20%). Electrostatic interactions between the drugs and the surface of the nanoparticles may account for the observed data, although additional removal mechanisms cannot be ruled out.

Engineering EPS in Halomonas bluephagenesis leads to self-flocculation and filamentation for convenient downstream processing

The halophile Halomonas bluephagenesis has established itself as a cost-effective chassis in industrial bioproduction. However, downstream processing (DSP) expense is a persistent challenge. This study uses genetic knockout of exopolysaccharides (EPS-KO) in six industrially relevant H. bluephagenesis strains, each producing distinct polyhydroxyalkanoate (PHA), to evaluate their impact on reducing DSP costs. Remarkably, EPS-KO cells exhibited an unprecedented filamentous morphology, reaching lengths over 50 times (10–75 μm) that of standard cells. This unexpected behavior initially posed a challenge to industrial applicability due to rapid cell lysis under fermentation agitation. Systematic media supplementation of salt, carbon source, nitrogen, and essential minerals significantly influenced morphology, and tailored nutrient schemes that mitigated filamentation while maintaining production levels were designed. Scaled production in a 5000 L bioreactor demonstrated 85 % PHA and 96 g/L cell dry weight after 40 h fermentation, consistent with non-KO cells. During fermentation, EPS-KO enhanced cell-wall penetrability, reducing the need for high-cost γ-butyrolactone by 40 %. Additionally, a new innovative 5000 L FlipFlow bioreactor design cut rotation speed by 50 % and air input by 25 %. During DSP, centrifugation time decreased tenfold due to rapid cell self-flocculation (15–30 min), and the water and enzyme required for PHA purification was reduced by 30 % and 35 %, respectively. This study highlights the use of EPS-KO cells, a controlled media strategy, and low shear force FlipFlow bioreactor to successfully reduce DSP costs without sacrificing productivity. These novel findings represent a notable advancement in cost-saving strategies while presenting the intriguing discovery of media-controlled filamentous cell behavior.

Identification of Indigenous Bacterial Strains from Thai Agricultural Fields for Potential Bioremediation of Carbofuran

This study explored the bioremediation potential of indigenous soil bacteria for carbofuran-contaminated agricultural areas. Twenty soil samples from regions with a history of pesticide use in Pathum Thani and Nakhon Pathom provinces, Thailand, were collected. Five bacterial strains capable of degrading carbofuran were isolated and subjected to cell morphology and biochemical analyses. Phylogenetic analysis of the 16S rRNA gene sequences identified these strains as related to Pseudomonas and Stenotrophomonas species. High-Performance Liquid Chromatography (HPLC) analysis confirmed the complete degradation of carbofuran within 3 days, reducing its concentration from 0.05 mg/mL to below detectable limits. These bacteria could use carbofuran as their sole carbon source, demonstrating their potential for bioremediation of contaminated soils. Given their resilience and ability to thrive in natural environmental conditions, these indigenous strains are well-suited for in-situ degradation of pollutants. The findings indicate that these isolated soil bacteria present a promising method for reducing the environmental risks associated with carbofuran contamination.

Elucidating the salt-tolerant mechanism of Halomonas cupida J9 and unsterile ectoine production from lignocellulosic biomass.

Ectoine as an amino acid derivative is widely applied in many fields, such as the food industry, cosmetic manufacturing, biologics, and therapeutic agent. Large-scale production of ectoine is mainly restricted by the cost of fermentation substrates (e.g., carbon sources) and sterilization. In this study, Halomonas cupida J9 was shown to be capable of synthesizing ectoine using xylose as the sole carbon source. A pathway was proposed in H. cupida J9 that synergistically utilizes both WBG xylose metabolism and EMP glucose metabolism for the synthesis of ectoine. Transcriptome analysis indicated that expression of ectoine biosynthesis module was enhanced under salt stress. Ectoine production by H. cupida J9 was enhanced by improving the expression of ectoine biosynthesis module, increasing the intracellular supply of the precursor oxaloacetate, and utilizing urea as the nitrogen source. The constructed J9U-P8EC achieved a record ectoine production of 4.12g/L after 60h of xylose fermentation. Finally, unsterile production of ectoine by J9U-P8EC from either a glucose-xylose mixture or corn straw hydrolysate was demonstrated, with an output of 8.55g/L and 1.30g/L of ectoine, respectively. This study created a promising H. cupida J9-based cell factory for low-cost production of ectoine. Our results highlight the potential of J9U-P8EC to utilize lignocellulose-rich agriculture waste for open production of ectoine.

Utilization of formic acid by extremely thermoacidophilic archaea species.

The exploration of novel hosts with the ability to assimilate formic acid, a C1 substrate that can be produced from renewable electrons and CO2, is of great relevance for developing novel and sustainable biomanufacturing platforms. Formatotrophs can use formic acid or formate as a carbon and/or reducing power source. Formatotrophy has typically been studied in neutrophilic microorganisms because formic acid toxicity increases in acidic environments below the pKa of 3.75 (25°C). Because of this toxicity challenge, utilization of formic acid as either a carbon or energy source has been largely unexplored in thermoacidophiles, species that possess the ability to produce a variety of metabolites and enzymes of high biotechnological relevance. Here we investigate the capacity of several thermoacidophilic archaea species from the Sulfolobales order to tolerate and metabolize formic acid. Metallosphaera prunae, Sulfolobus metallicus and Sulfolobus acidocaldarium were found to metabolize and grow with 1-2 mM of formic acid in batch cultivations. Formic acid was co-utilized by this species alongside physiological electron donors, including ferrous iron. To enhance formic acid utilization while maintaining aqueous concentrations below the toxicity threshold, we developed a bioreactor culturing method based on a sequential formic acid feeding strategy. By dosing small amounts of formic acid sequentially and feeding H2 as co-substrate, M. prunae could utilize a total of 16.3 mM of formic acid and grow to higher cell densities than when H2 was supplied as a sole electron donor. These results demonstrate the viability of culturing thermoacidophilic species with formic acid as an auxiliary substrate in bioreactors to obtain higher cell densities than those yielded by conventional autotrophic conditions. Our work underscores the significance of formic acid metabolism in extreme habitats and holds promise for biotechnological applications in the realm of sustainable energy production and environmental remediation.

The aquaculture waste as the carbon source for nanocellulose production by Komagataeibacter europaeus

The aquaculture waste as the carbon source for nanocellulose production by <i>Komagataeibacter europaeus</i>

Characterization of the Conversion System of Natural Rubber to Poly(3-Hydroxyalkanoate) in Piscinibacter gummiphilus Strain NS21T.

Poly(3-hydroxyalkanoate) (PHA), a bacteria-synthesized biodegradable polyester, is a useful alternative to fossil resources, and current systems for its production rely predominantly on edible resources, raising concerns about microbial competition for nutrients. Therefore, we investigated mechanisms underlying PHA production from non-edible resources by Piscinibacter gummiphilus strain NS21T. Strain NS21T can utilize natural rubber as a carbon source on solid media and potentially produces PHA. Gas chromatography and nuclear magnetic resonance analyses of NS21T cell extracts revealed the production of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) and poly(3-hydroxybutyrate) from natural rubber and glucose, respectively. Transcriptional analysis suggested that phaC is involved in PHA production. An increased PHBV accumulation rate under nitrogen-limiting conditions indicates the potential of this strain to be used as a PHBV production enhancement strategy. Furthermore, the disruption of PHA depolymerase genes resulted in enhanced PHA production, indicating the involvement of these genes in PHA degradation. These findings highlight the potential of NS21T for PHBV production from natural rubber, a non-edible resource.

Functional and Microbiological Responses of Iron–Carbon Galvanic Cell-Supported Autotrophic Denitrification to Organic Carbon Variation and Dissolved Oxygen Shaking

Iron–carbon galvanic-cell-supported autotrophic denitrification (IC-ADN) is a burgeoning efficient and cost-effective process for low-carbon wastewater treatment. This study revealed the influence of organic carbon (OC) and dissolved oxygen (DO) on IC-ADN in terms of functional and microbiological characteristics. The nitrogen removal efficiency increased to 91.6% and 94.7% with partial organic carbon source addition to COD/TN of 1 and 3, respectively. The results of 16S rRNA high-throughput sequencing with nirS and cbbL clone libraries showed that Thiobacillus was the predominant autotrophic denitrifying bacteria (ADB) in the micro-electrolysis-based autotrophic denitrification, which obtained nitrogen removal efficiency of 80.9% after 96 h. The ADBs shifted gradually to heterotrophic denitrifying bacteria Thauera with increasing COD/TN ratio. DO concentration of 0.8 rarely affected the denitrification efficiency and the denitrifying communities. When the DO concentration increased to 2.8 mg/L, the nitrogen removal efficiency decreased to 69.1%. These results demonstrated that autotrophic denitrification was notably affected by COD/TN and high DO concentration, which could be used to acquire optimum conditions for nitrogen removal. These results provided an in-depth understanding of the influential factors for galvanic-cell-based denitrification and helped us construct a stable and highly efficient treatment process for insufficient carbon source wastewater.

Optimization of Fermentation Conditions of Cordyceps militaris and In Silico Analysis of Antifungal Property of Cordycepin Against Plant Pathogens.

Cordyceps militaris, a medicinal fungus, has gained considerable attention owing to its potential health benefits, notably the production of bioactive compounds such as cordycepin. Cordycepin possesses significant antifungal, antibacterial, and antiviral properties. The present study focused on optimizing the fermentation conditions for C.militaris to boost the production of mycelia and cordycepin, alongside investigating its antifungal properties using in silico and in vitro approaches. The optimal conditions, yielding the highest cordycepin and mycelial biomass, were a temperature of 20°C and a pH range of 4-6, with glucose and sucrose as carbon sources and yeast extract and casein hydrolysate as nitrogen sources. Under these conditions, cordycepin production peaked at low pH (600-1000 mg/L) and with carbon and maltose (400-500 mg/L). The low temperature favored cordycepin production (400 mg/L), whereas casein hydrolysate as a nitrogen source boosted cordycepin yield (600 mg/L). The docking analysis indicated that cordycepin had the highest binding affinity for the tubulin beta chain 2 (-10.4 kcal/mol) compared to the fungicide tebuconazole (-7.9 kcal/mol for both targets). The in silico results were corroborated by in vitro studies, where the mycelial extract of C.militaris inhibited approximately 75% of fungal growth at a concentration of 6000 ppm. These findings suggest that optimizing fermentation conditions significantly enhances cordycepin production, and cordycepin shows antifungal solid activity, making it a promising agent for biocontrol in agriculture.

Draft genome of the caprolactam-degrading Paenarthrobacter sp. CAP02 isolated from a landfill.

Here, we report the draft genome sequence of Paenarthrobacter sp. CAP02, which metabolizes caprolactam as a sole source of carbon and nitrogen. This bacterium was isolated from Dane County Landfill Site No. 2 in Madison, WI, USA.

Engineering high production of fatty alcohols from methanol by constructing coordinated dual biosynthetic pathways.

Microbial cell factories provide an efficient approach for the green manufacturing of chemicals. However, the excessive use of sugars increases the potential risk of food crisis. Methanol, an abundant feedstock, holds promise in facilitating low-carbon production processes. However, the current methanol bioconversion is hindered by limited regulatory strategies and relatively low conversion efficiency. Here, a yeast biocatalyst was extensively engineered for efficient biosynthesis of fatty alcohols through reinforcement of precursor supply and methanol assimilation in Pichia pastoris. Furthermore, the dual cytoplasmic and peroxisomal biosynthetic pathways were constructed by mating and exhibited robust production of 5.6 g/L fatty alcohols by using methanol as the sole carbon source. This study provides a heterozygous diploid P. pastoris strain with dual cytoplasmic and peroxisomal biosynthetic pathways, which achieved the highest fatty alcohol production from one-carbon feedstocks to date.

Effectiveness of Anaerobic Soil Disinfestation for Weed and Nematode Management in Organic Sweetpotato Production

Weeds and nematodes are particularly problematic in organic sweetpotato production due to a lack of effective pesticides. Anaerobic soil disinfestation (ASD) has the potential to fit into current pest management practices as an alternative to pesticide application. Greenhouse studies were conducted at the Clemson Coastal Research and Education Center (CREC) in Charleston, SC, to investigate the impact of carbon source amendment and a no carbon source treatment, and soil type on cumulative anaerobicity, weed control, nematode population, and sweetpotato vigor. Microcosms were filled with one of three different soil types (Charleston—loamy/native; Blackville—high coarse sand content; and Clemson—high clay content) and were mixed with cottonseed meal (CSM) or no carbon amendment. The pots were then sealed with plastic totally impenetrable film (Tif) for 6 weeks, followed by the transplanting of sweetpotato (cv Bayou Belle) slips. The results suggested that the CSM-treated microcosms spent more time under anaerobic conditions than those treated with the no carbon amendment. The microcosms that experienced a longer duration of anaerobicity had a lower percent weed cover (49%), fewer nematode egg masses, and a lower gall index when compared to microcosms which experienced a shorter duration of anaerobicity. Significantly higher instances of leaf necrosis were observed in the sweetpotato slips sown in the CSM-treated microcosms. The addition of CSM as a carbon source to facilitate ASD resulted in similar above-ground biomasses of the sweetpotato plants compared to the treatments containing no carbon amendment. However, a significantly lower below-ground biomass of the sweetpotato plants was observed in the CSM-treated microcosms.

A Microbial Phenomics Approach to Determine Metabolic Signatures to Enhance Seabream Sparus aurata Traceability, Differentiating between Wild-Caught and Farmed

Background: The need for efficient and simplified techniques for seafood traceability is growing. This study proposes the Biolog EcoPlate assay as an innovative method for assessing wild and farmed Sparus aurata traceability, offering advantages over other molecular techniques in terms of technical simplicity. Methods: The Biolog EcoPlate assay, known for its high-throughput capabilities in microbial ecology, was utilized to evaluate the functional diversity of microbial communities from various organs of S. aurata (seabream) from the Mediterranean area. Samples were taken from the anterior and posterior gut, cloaca swabs and gills to distinguish between farmed and wild-caught individuals. The analysis focused on color development in OmniLog Units for specific carbon sources at 48 h. Results: Gills provided the most accurate clusterization of sample origin. The assay monitored the development of color for carbon sources such as α-cyclodextrin, D-cellobiose, glycogen, α-D-lactose, L-threonine and L-phenylalanine. A mock experiment using principal component analysis (PCA) successfully identified the origin of a blind sample. Shannon and Simpson indexes were used to statistically assess the diversity, reflecting the clusterization of different organ samples; Conclusions: The Biolog EcoPlate assay proves to be a quick, cost-effective method for discriminate S. aurata traceability (wild vs. farmed), demonstrating reliable reproducibility and effective differentiation between farmed and wild-caught seabream.

Climate neutrality of the French energy system: overview and impacts of sustainable aviation fuel production

CO2 emission reduction of sectors such as aviation, maritime shipping, road haulage, and chemical production is challenging but necessary. Although these sectors will most likely continue to rely on carbonaceous energy carriers, they are expected to gradually shift away from fossil fuels. In order to do so, the prominent option is to utilize alternative carbon sources—like biomass and CO2 originating from carbon capture—for the production of non-fossil carbonaceous vectors (biofuels and e-fuels). However, the limited availability of biomass and the varying nature of other carbon sources necessitate a comprehensive evaluation of trade-offs between potential carbon uses and existing sources. Then, it is primordial to understand the origin of carbon used in sustainable aviation fuel (SAF) to understand the implications of defossilizing aviation for the energy system. Moreover, the production of SAF implies deep changes to the energy system that are quantified in this work. This study utilizes the linear programming cost optimization tool EnergyScope TD to analyze the holistic French energy system, encompassing transport, industry, electricity, and heat sectors while ensuring net greenhouse gas neutrality. A novel method to model and quantify carbon flows within the system is introduced, enabling a comprehensive assessment of greenhouse gas neutrality. This study highlights the significance of fulfilling clean energy requirements and implementing carbon dioxide removal measures as crucial steps toward achieving climate neutrality. Indeed, to reach climate neutrality, a production of 1,046 TWh of electricity by non-fossil sources is needed. Furthermore, the findings underscore the critical role of efficient carbon and energy valorization from biomass, providing evidence that producing fuels by combining biomass and hydrogen is optimal. The study also offers valuable insights into the future cost and impact of SAF production for air travel originating from France. That is, the European law ReFuelEU would increase the price of plane tickets by +33% and would require 126 TWh of hydrogen and 50 TWh of biomass to produce the necessary 91 TWh of jet fuel. Finally, the implications of the assumption behind the production of SAF are discussed.

Physicochemical and Fungal Analysis of a Hydrocarbon-Polluted Soil at Amadi-Ama Creek of Bonny River Port Harcourt, Rivers State, Nigeria

Numerous hydrocarbon-utilizing fungal species have been implicated with the ability to utilize/degrade hydrocarbon as carbon source, which indicate their potential for environmental cleanup in hydrocarbon-contaminated sites. In this study, five (5) indigenous fungal species were isolated from a petroleum-hydrocarbon polluted soil at Amadi-ama Creek, Bonny river shoreline, Port Harcourt, Rivers State. These fungal species may have high potential to biodegrade petroleum hydrocarbon pollutants. Samples were collected randomly from the hydrocarbon impacted soil at Amadi-ama Creek, Bonny river shoreline. Sabouraud’s Dextrose Agar (SDA) and Czapek Agar were used as growth media. Samples were examined to assess the physical and chemical characteristics such as conductivity, pH, temperature, nitrate, iron, copper, zinc, chromium, phosphate, sulphate, total hydrocarbon content, total petroleum hydrocarbon, and polycyclic aromatic hydrocarbon. These parameters are known to influence the occurrence, diversity and distribution of microorganisms in an ecological niche. Soil pH showed to be acidic (6.21), result also showed that Total hydrocarbon content, Total petroleum hydrocarbon and Polycyclic aromatic hydrocarbon values were at 306.55mg/kg, 112.134mg/kg, 44.227mg/kg respectively establishing the incidence of hydrocarbon pollution. Electrical conductivity and Temperature were at 1250 Us/cm, and 29.580C respectively while Nitrate, Phosphate, Sulphate, Iron, Copper, Zinc, and Chromium values were at 1.228mg/kg, 0.751mg/kg, 20.214mg/kg, 18.431mg/kg, 0.113mg/kg, 0.121mg/kg, and 0.042mg/kg respectively. Monitoring of the soil quality established the incidence of hydrocarbon pollution as well the incidence of anthropogenic influence on the soil putting into cognizance human activities at the shoreline. Morphological identification of obtained fungal species led to their assignment into four (4) genera and five (5) species; Aspergillus niger (28%), Aspergillus flavus (22%), Cladosporium herbarum (20%), Penicillium notatum (17%), Fusarium spp (11%). The predominance of Aspergillus isolates (28% and 22%) in this study could be a pointer to their potential to utilize hydrocarbon as their sole source of nutrient. The isolation of these indigenous fungal species could serve as a baseline study on which further analysis such as hydrocarbon degradation screening test could determine their individual hydrocarbon degradation potentials and subsequent consideration as hydrocarbon degrading microbes in subsequent bioremediation study.

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.

Reconstruction and Analysis of a Genome-Scale Metabolic Model of Acinetobacter lwoffii

Acinetobacter lwoffii is widely considered to be a harmful bacterium that is resistant to medicines and disinfectants. A. lwoffii NL1 degrades phenols efficiently and shows promise as an aromatic compound degrader in antibiotic-contaminated environments. To gain a comprehensive understanding of A. lwoffii, the first genome-scale metabolic model of A. lwoffii was constructed using semi-automated and manual methods. The iNX811 model, which includes 811 genes, 1071 metabolites, and 1155 reactions, was validated using 39 unique carbon and nitrogen sources. Genes and metabolites critical for cell growth were analyzed, and 12 essential metabolites (mainly in the biosynthesis and metabolism of glycan, lysine, and cofactors) were identified as antibacterial drug targets. Moreover, to explore the metabolic response to phenols, metabolic flux was simulated by integrating transcriptomics, and the significantly changed metabolism mainly included central carbon metabolism, along with some transport reactions. In addition, the addition of substances that effectively improved phenol degradation was predicted and validated using the model. Overall, the reconstruction and analysis of model iNX811 helped to study the antimicrobial systems and biodegradation behavior of A. lwoffii.

Microbial Metabolism and Environmental Controls of Acetate Cycling in the Northwest Pacific Ocean

AbstractMicrobial acetate metabolism is an important part of marine carbon cycling. We present a comprehensive study to constrain microbial acetate metabolism and its regulation in surface seawater of the northwest Pacific Ocean. We found that acetate oxidation (rate constant k: 0.016–0.506 day−1) accounted for 77.6%–99.4% of the total microbial acetate uptake, suggesting that acetate was predominantly used as a microbial energy source. Acetate also served as a significant biomass carbon source, as reflected by the elevated contribution of acetate assimilation to bacterial carbon production. Acetate turnover was largely influenced by water mass mixing and nutrient conditions. Atmospheric deposition was a source of acetate in surface water and this process can also impact the microbial acetate uptake. Microbial utilization of acetate could account for up to 25.9% of the bacterial carbon demand, suggesting the significant role of acetate metabolism in microbial carbon cycling in the open ocean.