Camilla Giuliani, Massimo Marzorati, Matteo Daghio et al.

Molecules • 2019

Two by-products containing phenols and polysaccharides, a "pâté" (OP) from the extra virgin olive oil milling process and a decoction of pomegranate mesocarp (PM), were investigated for their effects on human microbiota using the SHIME ® system. The ability of these products to modulate the microbial community was studied simulating a daily intake for nine days. Microbial functionality, investigated in terms of short chain fatty acids (SCFA) and NH 4 + , was stable during the treatment. A significant increase in Lactobacillaceae and Bifidobacteriaceae at nine days was induced by OP mainly in the proximal tract. Polyphenol metabolism indicated the formation of tyrosol from OP mainly in the distal tract, while urolithins C and A were produced from PM, identifying the human donor as a metabotype A. The results confirm the SHIME ® system as a suitable in vitro tool to preliminarily investigate interactions between complex botanicals and human microbiota before undertaking more challenging human studies.

Francisca L. Aranda, Bernabé L. Rivas

Journal of the Chilean Chemical Society • 2022

Although pharmaceutical compounds such as antibiotics have been of great help to animals and humans, the excessive use of them have become a global problem due to the resistance of pathogens to these drugs, for this reason a series of methods have been reported that we will see below that allow to remove efficiently, economically, and environmentally friendly compounds such as antibiotics.

Martyna Marynowska, David Sillam‐Dussès, Boris Untereiner et al.

BMC Genomics • 2023

Our study provides interesting insights into the distribution of the hydrolytic potential of the highly compartmentalised higher termite gut. The large number of expressed enzymes targeting the different lignocellulose components make the Labiotermes worker gut a relevant lignocellulose-valorising model to mimic by biomass conversion industries.

Franciene Rabiço, Matheus Pedrino, Julia Pereira Narcizo et al.

Microorganisms • 2023

Microbial fuel cells (MFCs) offer sustainable solutions for various biotechnological applications and are a crucial area of research in biotechnology. MFCs can effectively treat various refuse, such as wastewater and biodiesel waste by decomposing organic matter and generating electricity. Certain Pseudomonas species possess extracellular electron transfer (EET) pathways, enabling them to transfer electrons from organic compounds to the MFC's anode. Moreover, Pseudomonas species can grow under low-oxygen conditions, which is advantageous considering that the electron transfer process in an MFC typically leads to reduced oxygen levels at the anode. This study focuses on evaluating MFCs inoculated with a new Pseudomonas species grown with 1 g.L -1 glycerol, a common byproduct of biodiesel production. Pseudomonas sp. BJa5 exhibited a maximum power density of 39 mW.m -2 . Also, the observed voltammograms and genome analysis indicate the potential production of novel redox mediators by BJa5. Additionally, we investigated the bacterium's potential as a synthetic biology non-model chassis. Through testing various genetic parts, including constitutive promoters, replication origins and cargos using pSEVA vectors as a scaffold, we assessed the bacterium's suitability. Overall, our findings offer valuable insights into utilizing Pseudomonas spp. BJa5 as a novel chassis for MFCs. Synthetic biology approaches can further enhance the performance of this bacterium in MFCs, providing avenues for improvement.

Xu-Yan Zhu, Feng Lin, Ji Sun et al.

Microorganisms • 2024

Enhanced denitrification has been reported under weak electric fields. However, it is difficult to investigate the mechanism of enhanced denitrification due to the complex interspecific interactions of mixed-culture systems. In this study, Pseudomonas stutzeri , capable of denitrification under anaerobic conditions, was selected for treating low COD/N (2.0, ratio between concentration of chemical oxygen demand and NO 3 - -N) artificial wastewater under constant external voltages of 0.2, 0.4, and 0.6 V. The results revealed that P. stutzeri exhibited the highest efficiency in nitrate reduction at 0.2 V. Moreover, the maximum nitrate removal rate was 15.96 mg/(L·h) among the closed-circuit groups, 19.39% higher than that under the open-circuit group. Additionally, a notable reduction in nitrite accumulation was observed under weak electric fields. Enzyme activity analysis showed that the nitrate reductase activities were significantly increased among the closed-circuit groups, while nitrite reductase activities were inhibited. Transcriptomic analysis indicated that amino acid metabolism, carbohydrate metabolism, and energy metabolism were increased, enhancing the resistance of P. stutzeri to environmental stress and the efficiency of carbon source utilization for denitrification. The current study examined the impacts of weak electric fields on enzyme activities and microbial metabolic pathways and offers valuable insights into the mechanism by which denitrification is enhanced by weak electric fields.

Rusen Zou, Wenqiang Yang, Babak Rezaei et al.

Water Research • 2024

Peracetic acid (PAA) has received increasing attention as an alternative oxidant for wastewater treatment. However, existing processes for PAA activation to generate reactive species typically require external energy input (e.g., electrically and UV-mediated activation) or catalysts (e.g., Co 2+ ), inevitably increasing treatment costs or introducing potential new contaminants that necessitate additional removal. In this work, we developed a catalyst-free, self-sustaining bioelectrochemical approach within a two-chamber bioelectrochemical system (BES), where a cathode electrode in-situ activates PAA using renewable biogenic electrons generated by anodic exoelectrogens (e.g., Geobacter) degrading biodegradable organic matter (e.g., acetic acid) in wastewater at the anode. This innovative BES-PAA technique achieved 98 % and 81 % removal of 2 µM sulfamethoxazole (SMX) in two hours at pH 2 (cation exchange membrane) and pH 6 (bipolar membrane) using 100 μM PAA without external voltage. Mechanistic studies, including radical quenching, molecular probe validation, electron spin resonance (ESR) experiments, and density functional theory (DFT) calculations, revealed that SMX degradation was driven by reactive species generated via biogenic electron-mediated OO cleavage of PAA, with CH 3 C(O)OO• contributing 68.1 %, •OH of 18.4 %, and CH 3 C(O)O• of 9.4 %, where initial formation of •OH and CH 3 C(O)O• rapidly reacts with PAA to produce CH 3 C(O)OO•. The presence of common water constituents such as anions (e.g., Cl - , NO 3 - , and H 2 PO 4 - ) and humic acid (HA) significantly hinders SMX removal via the BES-PAA technique, whereas CO 3 2- and HCO 3 - ions have a comparatively minor impact. Additionally, the study investigated the removal of various pharmaceuticals present in secondary treated municipal wastewater, attributing differences in removal efficiency to the selective action of CH 3 C(O)OO•. This research demonstrates a novel PAA activation method that is ecologically benign, inexpensive, and capable of overcoming catalyst deactivation and secondary pollution issues.

Takashi Azuma, Michio Murakami, Yuki Sonoda et al.

Antibiotics • 2022

The occurrence of Staphylococcus aureus ( S. aureus ) and methicillin-resistant S. aureus (MRSA) in a sub-catchment of the Yodo River Basin, a representative water system of a drinking water source in Japan, was investigated. The chromogenic enzyme-substrate medium method was used for the detection of S. aureus and MRSA by the presence or absence of antimicrobials in the medium for viable bacteria in a culture-based setting. The contributions of S. aureus and MRSA from wastewater to the rivers were estimated based on mass flux-based analysis, and quantitative microbial risk assessment (QMRA) was further conducted for S. aureus and MRSA in river environments. The mean abundance of S. aureus and MRSA was 31 and 29 CFU/mL in hospital effluent, 124 and 117 CFU/mL in sewage treatment plant (STP) influent, 16 and 13 CFU/mL in STP effluent, and 8 and 9 CFU/mL in river water, respectively. Contribution of the pollution load derived from the target STP effluent to river water ranged from 2% to 25%. The QMRA showed that to achieve the established health benchmarks, the drinking water treatment process would need to yield 1.7 log 10 and 2.9 log 10 inactivation in terms of infection risk and disability-adjusted life year (DALY) indexes, respectively. These findings highlight the link between medical environment and the importance of environmental risk management for antimicrobial-resistant bacteria in aquatic environments.

Lisa Sudek, Greg Wanger, Alexis S. Templeton et al.

Frontiers in Microbiology • 2017

Phylogenetically and metabolically diverse bacterial communities have been found in association with submarine basaltic glass surfaces. The driving forces behind basalt colonization are for the most part unknown. It remains ambiguous if basalt provides ecological advantages beyond representing a substrate for surface colonization, such as supplying nutrients and/or energy. Pseudomonas stutzeri VS-10, a metabolically versatile bacterium isolated from Vailulu'u Seamount, was used as a model organism to investigate the physiological responses observed when biofilms are established on basaltic glasses. In Fe-limited heterotrophic media, P. stutzeri VS-10 exhibited elevated growth in the presence of basaltic glass. Diffusion chamber experiments demonstrated that physical attachment or contact of soluble metabolites such as siderophores with the basaltic glass plays a pivotal role in this process. Electrochemical data indicated that P. stutzeri VS-10 is able to use solid substrates (electrodes) as terminal electron donors and acceptors. Siderophore production and heterotrophic Fe(II) oxidation are discussed as potential mechanisms enhancing growth of P. stutzeri VS-10 on glass surfaces. In correlation with that we discuss the possibility that metabolic versatility could represent a common and beneficial physiological trait in marine microbial communities being subject to oligotrophic and rapidly changing deep-sea conditions.

Mahdi Hassan, Guangcan Zhu, Zhonglian Yang et al.

Sustainability • 2020

Emerging pollutants in the form of pharmaceuticals have drawn international attention during the past few decades. Ciprofloxacin (CIP) is a common drug widely found in effluents from hospitals, industrial and different wastewater treatment plants, as well as rivers. In this work, the lab-scale 3D-BER system was established, and more than 90% of the antibiotic CIP was removed from Low C/N wastewater. The best results were obtained with the current intensity being taken into account, and a different C/N ratio significantly improved the removal of CIP and nitrates when the ideal conditions were C/N = 1.5–3.5, pH = 7.0–7.5 and I = 60 mA. The highest removal efficiency occurred when CIP = 94.2%, NO3−-N = 95.5% and total nitrogen (TN) = 84.3%, respectively. In this novel system, the autotrophic-heterotrophic denitrifying bacteria played a vital role in the removal of CIP and an enhanced denitrification process. Thus, autotrophic denitrifying bacteria uses CO2 and H2 as carbon sources to reduce nitrates to N2. This system has the assortment and prosperous community revealed at the current intensity of 60 mA, and the analysis of bacterial community structure in effluent samples fluctuates under different conditions of C/N ratios. Based on the results of LC-MS/MS analysis, the intermediate products were proposed after efficient biodegradation of CIP. The microbial community on biodegrading was mostly found at phylum, and the class level was dominantly responsible for the NO3−-N and biodegradation of CIP. This work can provide some new insights towards the biodegradation of CIP and the efficient removal of nitrates from low C/N wastewater treatment through the novel 3D-BER system.

Kaihui Liu, Xiaowei Ding, Xiaofei Tang et al.

Frontiers in Microbiology • 2018

Understanding the effects of environmental factors on microbial communities is critical for microbial ecology, but it remains challenging. In this study, we examined the diversity (alpha diversity) and community compositions (beta diversity) of prokaryotes and fungi in hypersaline sediments and salinized soils from northern China. Environmental variables were highly correlated, but they differed significantly between the sediments and saline soils. The compositions of prokaryotic and fungal communities in the hypersaline sediments were different from those in adjacent saline-alkaline soils, indicating a habitat-specific microbial distribution pattern. The macroelements (S, P, K, Mg, and Fe) and Ca were, respectively, correlated closely with the alpha diversity of prokaryotes and fungi, while the macronutrients (e.g., Na, S, P, and Ca) were correlated with the prokaryotic and fungal beta-diversity ( P ≤ 0.05). And, the nine microelements (e.g., Al, Ba, Co, Hg, and Mn) and micronutrients (Ba, Cd, and Sr) individually shaped the alpha diversity of prokaryotes and fungi, while the six microelements (e.g., As, Ba, Cr, and Ge) and only the trace elements (Cr and Cu), respectively, influenced the beta diversity of prokaryotes and fungi ( P < 0.05). Variation-partitioning analysis (VPA) showed that environmental variables jointly explained 55.49% and 32.27% of the total variation for the prokaryotic and fungal communities, respectively. Together, our findings demonstrate that the diversity and community composition of the prokaryotes and fungi were driven by different macro and microelements in saline habitats, and that geochemical elements could more widely regulate the diversity and community composition of prokaryotes than these of fungi.

Ruofan Wu, Paramsothy Jeyakumar, Nanthi Bolan et al.

Biochar • 2024

Abstract Iron-carbon micro-electrolysis system is a promising method for promoting electron transfer in nitrate removal. However, many traditional approaches involving simple physical mixing inevitably suffered from the confined iron-carbon contact area and short validity period, leading to the overuse of iron. Here, a ceramsite-loaded microscale zero-valent iron (mZVI) and acidified carbon (AC) coupled-galvanic cell (CMC) was designed to support chemical, autotrophic and heterotrophic denitrification. Long-term experiments were conducted to monitor the nitrogen removal performance of denitrification reactors filled with CMC and thus optimized the denitrification performance by improving fabrication parameters and various operating conditions. The denitrification contributions test showed that the chemical denitrification pathway contributed most to nitrate removal (57.3%), followed by autotrophic (24.6%) and heterotrophic denitrification pathways (18.1%). The microbial analysis confirmed the significant aggregation of related denitrifying bacteria in the reactors, while AC promoted the expression of relevant nitrogen metabolism genes because of accelerated uptake and utilization of iron complexes. Meanwhile, the electrochemical analysis revealed a significantly improved electron transfer capacity of AC compared to pristine carbon. Overall, our study demonstrated the application of a novel mZVI-AC coupled material for effective nitrate removal and revealed the potential impact of CMC in the multipathway denitrification process. Graphical Abstract

Gaofeng Ni, Sebastian Canizales, Elias Broman et al.

Frontiers in Microbiology • 2018

Thiocyanate is a toxic compound produced by the mining and metallurgy industries that needs to be remediated prior to its release into the environment. If the industry is situated at high altitudes or near the poles, economic factors require a low temperature treatment process. Microbial fuel cells are a developing technology that have the benefits of both removing such toxic compounds while recovering electrical energy. In this study, simultaneous thiocyanate degradation and electrical current generation was demonstrated and it was suggested that extracellular electron transfer to the anode occurred. Investigation of the microbial community by 16S rRNA metatranscriptome reads supported that the anode attached and planktonic anolyte consortia were dominated by a Thiobacillus -like population. Metatranscriptomic sequencing also suggested thiocyanate degradation primarily occurred via the 'cyanate' degradation pathway. The generated sulfide was metabolized via sulfite and ultimately to sulfate mediated by reverse dissimilatory sulfite reductase, APS reductase, and sulfate adenylyltransferase and the released electrons were potentially transferred to the anode via soluble electron shuttles. Finally, the ammonium from thiocyanate degradation was assimilated to glutamate as nitrogen source and carbon dioxide was fixed as carbon source. This study is one of the first to demonstrate a low temperature inorganic sulfur utilizing microbial fuel cell and the first to provide evidence for pathways of thiocyanate degradation coupled to electron transfer.

Gilda Varliero, Alexandre M. Anesio, Gary Barker

Frontiers in Microbiology • 2021

The Arctic environment is particularly affected by global warming, and a clear trend of the ice retreat is observed worldwide. In proglacial systems, the newly exposed terrain represents different environmental and nutrient conditions compared to later soil stages. Therefore, proglacial systems show several environmental gradients along the soil succession where microorganisms are active protagonists of the soil and carbon pool formation through nitrogen fixation and rock weathering. We studied the microbial succession of three Arctic proglacial systems located in Svalbard (Midtre Lovénbreen), Sweden (Storglaciären), and Greenland (foreland close to Kangerlussuaq). We analyzed 65 whole shotgun metagenomic soil samples for a total of more than 400 Gb of sequencing data. Microbial succession showed common trends typical of proglacial systems with increasing diversity observed along the forefield chronosequence. Microbial trends were explained by the distance from the ice edge in the Midtre Lovénbreen and Storglaciären forefields and by total nitrogen (TN) and total organic carbon (TOC) in the Greenland proglacial system. Furthermore, we focused specifically on genes associated with nitrogen fixation and biotic rock weathering processes, such as nitrogenase genes, obcA genes, and genes involved in cyanide and siderophore synthesis and transport. Whereas we confirmed the presence of these genes in known nitrogen-fixing and/or rock weathering organisms (e.g., Nostoc , Burkholderia ), in this study, we also detected organisms that, even if often found in soil and proglacial systems, have never been related to nitrogen-fixing or rock weathering processes before (e.g., Fimbriiglobus , Streptomyces ). The different genera showed different gene trends within and among the studied systems, indicating a community constituted by a plurality of organisms involved in nitrogen fixation and biotic rock weathering, and where the latter were driven by different organisms at different soil succession stages.

Mao Ye, Jian‐Qiang Su, Xin‐Li An et al.

Science China Life Sciences • 2022

Daisuke Sasaki, Kengo Sasaki, Yota Tsuge et al.

Biotechnology for Biofuels • 2019

Microbial growth on the anode and intracellular glutamate levels negatively affect electricity generation by MFCs. Reduced formation of anodic biofilm, in which intracellular glutamate concentration is 33.9 μmol g-cell -1 or less, favors the growth of acetate-utilizing Geobacter sp. on the anode and improves current generation.

Masahiro Yamamoto, Yoshihiro Takaki, Hiroyuki Kashima et al.

The ISME Journal • 2022

Electroautotrophic microorganisms have attracted great attention since they exhibit a new type of primary production. Here, in situ electrochemical cultivation was conducted using the naturally occurring electromotive forces at a deep-sea hydrothermal vent. The voltage and current generation originating from the resulting microbial activity was observed for 12 days of deployment, with fluctuation in response to tidal cycles. A novel bacterium belonging to the genus Thiomicrorhabdus dominated the microbial community specifically enriched on the cathode. Metagenomic analysis provided the draft genome of the bacterium and the gene repertoire indicated that the bacterium has the potential for thio-autotrophic growth, which is a typical physiological feature of the members of the genus, while the bacterium had a unique gene cluster encoding multi-heme cytochrome c proteins responsible for extracellular electron transfer. Herein, we propose this bacterium as a new species, specifically enriched during electricity generation, as 'Candidatus Thiomicrorhabdus electrophagus'. This finding suggests the natural occurrence of electrosynthetic microbial populations using the geoelectricity in deep-sea hydrothermal environments.

Leyden Fernández, Stefan Bertilsson, Sari Peura

Limnology and Oceanography • 2019

Abstract There is a growing concern about the implications of accelerated thawing of permafrost for regional biogeochemical cycling of carbon and other bioreactive elements. One such element of concern is nitrogen, and in this study, we investigated the diversity and biogeography of potential diazotrophs within a series of thaw ponds representing different ontogenetic stages in pond development. Using metagenomic sequence data from subarctic thaw ponds, we identified an array of nitrogenase genes across the ponds. The iron‐only nitrogenase gene ( anfH ) was positively correlated with sulfate, while there was no correlation with methane despite previous findings that organisms carrying anfH can simultaneously participate in nitrogen fixation and methanogenesis. Sulfate is known to inhibit microbial uptake of molybdate, an element essential for the activity of the nifH (molybdenum‐iron) nitrogenase and this may explain the high potential for nitrogen fixation utilizing anfH in sulfate‐rich ponds. NifH was particularly abundant in the hypolimnion of the deeper and older ponds, with Deltaproteobacteria and Chlorobi as the putative dominant diazotrophs. In the epilimnetic waters, nifH composition was more variable, with various Gammaproteobacteria as abundant representatives, while cyanobacterial diazotrophs were scarce. Interestingly, nifH gene abundance was significantly positively correlated with in situ methane concentration. Based on genome‐resolved metagenomics, we hypothesize that diazotrophs and methanogens engage in syntrophic interactions in anoxic waters, possibly via propionate oxidation or (in Geobacter) by interspecies electron transfer. Our results also suggest that nitrogen fixers may supply bioreactive nitrogen compounds to the thaw pond communities, thereby enhancing growth and activity of methanogens.

Sandhya Nanjani, Dhiraj Paul, Haresh Keharia

BMC Microbiology • 2021

This exploratory study is the first-ever attempt to divulge the genetic basis of azo-dye co-metabolism by cross-genome comparisons and can be harnessed as an example for demonstrating microbial syntrophy.

Brandon Kieft, Niko Finke, Ryan J. McLaughlin et al.

Nature Communications • 2023

Anaerobic digestion of municipal mixed sludge produces methane that can be converted into renewable natural gas. To improve economics of this microbial mediated process, metabolic interactions catalyzing biomass conversion to energy need to be identified. Here, we present a two-year time series associating microbial metabolism and physicochemistry in a full-scale wastewater treatment plant. By creating a co-occurrence network with thousands of time-resolved microbial populations from over 100 samples spanning four operating configurations, known and novel microbial consortia with potential to drive methane production were identified. Interactions between these populations were further resolved in relation to specific process configurations by mapping metagenome assembled genomes and cognate gene expression data onto the network. Prominent interactions included transcriptionally active Methanolinea methanogens and syntrophic benzoate oxidizing Syntrophorhabdus, as well as a Methanoregulaceae population and putative syntrophic acetate oxidizing bacteria affiliated with Bateroidetes (Tenuifilaceae) expressing the glycine cleavage bypass of the Wood-Ljungdahl pathway.

Milena Marycz, Anna Brillowska‐Dąbrowska, Raúl Muñoz et al.

Reviews in Environmental Science and Bio/Technology • 2022

Abstract The physical/chemical abatement of gas pollutants creates many technical problems, is costly and entails significant environmental impacts. Biological purification of off-gases is a cheap and ecologically safe way of neutralization of gas pollutants. Despite the recent advances, the main technological challenge nowadays is the purification of volatile organic compounds (VOCs) of hydrophobic character due to their low solubility in water. Among all known biological methods of air purification, the most cost-effective biodegradation of hydrophobic VOCs is conducted by biotrickling filters. In this context, fungi have gained an increasing interest in this field based on their ability to biodegrade hydrophobic VOCs. In addition, biotrickling filtration using fungi can support a superior hydrophobic VOC abatement when compared to the bacterial biofilters. This paper aims at reviewing the latest research results concerning biocatalytic activity of fungi and evaluating the possibilities of their practical application in biofiltration systems to remove hydrophobic VOCs.

Djamel Ghernaout

OALib • 2020

Taking into account its merits in terms of high efficiency and low energy consumption, electrochemical (EC) technology especially bioelectrochemical system (BES) has been applied largely in reducing different antibiotics from wastewater. BES averts the spread of antibiotic resistance genes (ARGs) via forming less quantity of sludge compared with wastewater treatment plants. Nevertheless, transmembrane permeability and membrane potential could be influenced by the electrical stimulation, conducting to augmentations in the antibiotic-resistant bacteria (ARB) and ARGs in BES. This work discusses the utilization of EC technology especially BES for antibiotic reduction and the fate of ARB and ARGs in such systems. BES can effectively remove antibiotics. Nevertheless, low electric current promotes vertical and horizontal ARGs transfer during the treatment of antibiotics in BES. ARB and ARGs could be inhibited by a higher electric current. Questions regarding the potential role of BES in antibiotic removal and the consequent fate of ARGs and ARB in wastewater are presented. Further research is needed to elucidate the primary ARG transfer mechanism and to fully understand the advantages of BESs.

Jinha Kim, Myung Hwangbo, Chih-Hsuan Shih et al.

Water Research X • 2023

Stable isotope probing (SIP) is a powerful tool to study microbial community structure and function in both nature and engineered environments. Coupling with advanced genomics and other techniques, SIP studies have generated substantial information to allow researchers to draw a clearer picture of what is occurring in complex microbial ecosystems. This review provides an overview of the advances of SIP-based technologies over time, summarizes the status of SIP applications to contaminant biodegradation, provides critical perspectives on ecological interactions within the community, and important factors (controllable and non-controllable) to be considered in SIP experimental designs and data interpretation. Current trend and perspectives of adapting SIP techniques for environmental applications are also discussed.

Junqi Zhang, Zheng Chen, Changjiang Liu et al.

Frontiers in Bioengineering and Biotechnology • 2021

Background: Microbial fuel cells (MFCs) are a novel bioelectrochemical devices that can use exoelectrogens as biocatalyst to convert various organic wastes into electricity. Among them, acetate, a major component of industrial biological wastewater and by-product of lignocellulose degradation, could release eight electrons per mole when completely degraded into CO 2 and H 2 O, which has been identified as a promising carbon source and electron donor. However, Shewanella oneidensis MR-1, a famous facultative anaerobic exoelectrogens, only preferentially uses lactate as carbon source and electron donor and could hardly metabolize acetate in MFCs, which greatly limited Coulombic efficiency of MFCs and the capacity of bio-catalysis. Results: Here, to enable acetate as the sole carbon source and electron donor for electricity production in S. oneidensis , we successfully constructed three engineered S. oneidensis (named AceU1, AceU2, and AceU3) by assembling the succinyl-CoA:acetate CoA-transferase (SCACT) metabolism pathways, including acetate coenzyme A transferase encoded by ato1 and ato2 gene from G. sulfurreducens and citrate synthase encoded by the gltA gene from S. oneidensis , which could successfully utilize acetate as carbon source under anaerobic and aerobic conditions. Then, biochemical characterizations showed the engineered strain AceU3 generated a maximum power density of 8.3 ± 1.2 mW/m 2 with acetate as the sole electron donor in MFCs. In addition, when further using lactate as the electron donor, the maximum power density obtained by AceU3 was 51.1 ± 3.1 mW/m 2 , which approximately 2.4-fold higher than that of wild type (WT). Besides, the Coulombic efficiency of AceU3 strain could reach 12.4% increased by 2.0-fold compared that of WT, which demonstrated that the engineered strain AceU3 can further utilize acetate as an electron donor to continuously generate electricity. Conclusion: In the present study, we first rationally designed S. oneidensis for enhancing the electron generation by using acetate as sole carbon source and electron donor. Based on synthetic biology strategies, modular assembly of acetate metabolic pathways could be further extended to other exoelectrogens to improve the Coulombic efficiency and broaden the spectrum of available carbon sources in MFCs for bioelectricity production.

Mohamed Hemida Abd‐Alla, Fify Alfy Gabra, Amal W. Danial et al.

International Journal of Energy Research • 2018

Five facultative anaerobic bacterial isolates were recovered from domestic wastewater. These isolates were identified based on the 16S rRNA as Enterobacter aerogenes (one isolate), Enterobacter cloacae (two isolates), and Cronobacter sakazakii (three isolates). These isolates were examined for their potential to evolve hydrogen on a glucose medium. The most potent hydrogen-producing isolates, E aerogenes (KY549389) and E cloacae (KY524293), were examined for their capacity to generate hydrogen, acetone, butanol, and ethanol using orange peel (OP) hydrolysate. OP powder was pretreated with n-hexane to remove the toxicity of d-limonene. Different concentrations (4%, 6%, and 8% w/v) of limonene-free OP were subjected to the boiling water (temperature of 100°C) or acid (HCl) treatments. The maximum fermentative H2 production of 1700 and 1620 mL/L was obtained from 6% OP hydrolysate extracted with boiling water using facultative anaerobic E aerogenes (KY549389) and E cloacae (KY524293), respectively. Hydrogen production efficiency was 0.99 and 1.19 mol H2/mol glucose for E aerogenes and E cloacae, respectively. The total fermentative acetone, butanol, and ethanol (ABE) generated by E aerogenes and E cloacae were 0.78 and 0.38 g/L including acetone (0.05 and 0.04 g/L), butanol (0.011 and 0.013 g/L), and ethanol (0.71 and 0.32 g/L), respectively. The maximum ABE productivity was 0.01 and 0.005 g/L/h generated at 60 g/L OP hydrolysate by E aerogenes and E cloacae, respectively. These strains were positive for nitrogen fixation (nitrogenase) capability estimated by the acetylene reduction assay. Application of OP hydrolysate without the addition of any nutritional components or reducing agent is considered an eco-friendly, economical, and commercial substrate for desired biofuel production.

Kai Cui, Zhiyong Zhang, Zhongzhi Zhang et al.

Scientific Reports • 2019

Low permeability oil reservoirs are a widespread petroleum reservoir type all over the world. Therefore, methods to recover these reservoirs efficiently are of importance to guarantee energy supply. Here we report our novel stimulation of indigenous microbes by optimizing the water cut in low permeability reservoirs for green and enhanced oil recovery. We aimed to investigate the characteristics of indigenous bacterial communities with changes in water cut in reservoirs by high-throughput sequencing technology, and reveal the mechanism and characteristics of the crude oil biotreatment under different crude oil-water ratio conditions and the optimum activation time of indigenous functional microbial groups in reservoirs. The indigenous microbial metabolism products were characterized by gas chromatography mass spectrometry. Results showed that Acinetobacter (47.1%) and Pseudomones (19.8%) were the main functional genus of crude oil degradation at the optimal activation time, and can reduce the viscosity of crude oil from 8.33 to 5.75 mPa·s. The dominant bacteria genus for oil recovery after activation of the production fluids was similar to those in the reservoirs with water cut of 60-80%. Furthermore seven mechanism pathways of enhancing oil recovery by the synergistic of functional microbial groups and their metabolites under different water cut conditions in low permeability reservoirs have been established.

Shanyun Wang, Bangrui Lan, Longbin Yu et al.

Nature Communications • 2024

Global riverine nitrous oxide (N 2 O) emissions have increased more than 4-fold in the last century. It has been estimated that the hyporheic zones in small streams alone may contribute approximately 85% of these N 2 O emissions. However, the mechanisms and pathways controlling hyporheic N 2 O production in stream ecosystems remain unknown. Here, we report that ammonia-derived pathways, rather than the nitrate-derived pathways, are the dominant hyporheic N 2 O sources (69.6 ± 2.1%) in agricultural streams around the world. The N 2 O fluxes are mainly in positive correlation with ammonia. The potential N 2 O metabolic pathways of metagenome-assembled genomes (MAGs) provides evidence that nitrifying bacteria contain greater abundances of N 2 O production-related genes than denitrifying bacteria. Taken together, this study highlights the importance of mitigating agriculturally derived ammonium in low-order agricultural streams in controlling N 2 O emissions. Global models of riverine ecosystems need to better represent ammonia-derived pathways for accurately estimating and predicting riverine N 2 O emissions.

Wu Qu, Dan Lin, Zhouhao Zhang et al.

Frontiers in Microbiology • 2018

Monosaccharides and oligosaccharides produced by agarose degradation exhibit potential in the fields of bioenergy, medicine, and cosmetics. Mangrove sediments (MGSs) provide a special environment to enrich enzymes for agarose degradation. However, representative investigations of the agarlytic genes in MGSs have been rarely reported. In this study, agarlytic genes in MGSs were researched in detail from the aspects of diversity, abundance, activity, and location through deep metagenomics sequencing. Functional genes in MGSs were usually incomplete but were shown as results, which could cause virtually high number of results in previous studies because multiple fragmented sequences could originate from the same genes. In our work, only complete and nonredundant (CNR) genes were analyzed to avoid virtually high amount of the results. The number of CNR agarlytic genes in our datasets was significantly higher than that in the datasets of previous studies. Twenty-one recombinant agarases with agarose-degrading activity were detected using heterologous expression based on numerous complete open-reading frames, which are rarely obtained in metagenomics sequencing of samples with complex microbial communities, such as MGSs. Aga2, which had the highest crude enzyme activity among the 21 recombinant agarases, was further purified and subjected to enzymatic characterization. With its high agarose-degrading activity, resistance to temperature changes and chemical agents, Aga2 could be a suitable option for industrial production. The agarase ratio with signal peptides to that without signal peptides in our MGS datasets was lower than that of other reported agarases. Six draft genomes, namely, Clusters 1-6, were recovered from the datasets. The taxonomic annotation of these genomes revealed that Clusters 1, 3, 5, and 6 were annotated as Desulfuromonas sp., Treponema sp., Ignavibacteriales spp., and Polyangiaceae spp., respectively. Meanwhile, Clusters 2 and 4 were potential new species. All these genomes were first reported and found to have abilities of degrading various important polysaccharides. The metabolic pathway of agarose in Cluster 4 was also speculated. Our results showed the capacity and activity of agarases in the MGS microbiome, and MGSs exert potential as a repertory for mining not only agarlytic genes but also almost all genes of the carbohydrate-active enzyme family.

Sanne M. T. Raes, Ludovic Jourdin, C.J.N. Buisman et al.

ChemistrySelect • 2020

Abstract Valorization of organic residual streams that produce short‐chain fatty acids (SCFA) require an energetic electron donor to form more valuable elongated products. By microbial electrosynthesis such electrons donor is supplied by an electrode. Here we show that bioelectrochemical chain elongation (BCE) of SCFA was steered to high selective product formation efficiencies depending on the supplied fatty acid. n‐ Butyrate, n‐ valerate, n‐ caproate were in different experimental conditions formed at respectively 94.1, 95.4 and 83.4% carbon‐based selectivity. The reactor microbiomes adapted to the new feeding conditions within a few days. Remarkably, propionate elongation appeared to be preferred over acetate elongation. Propionate elongation resulted in highly selective formation of the odd‐chain fatty acid n‐ valerate; this seems contradictory to ethanol chain elongation studies in which acetate is concurrently formed leading to straight fatty acids as by products.

Mei Zhuang, Edmond Sanganyado, Liang Xu et al.

Microorganisms • 2020

Estuaries and coastal environments are often regarded as a critical resource for the bioremediation of organic pollutants such as azo dyes due to their high abundance and diversity of extremophiles. Bioremediation through the activities of azoreductase, laccase, and other associated enzymes plays a critical role in the removal of azo dyes in built and natural environments. However, little is known about the biodegradation genes and azo dye degradation genes residing in sediments from coastal and estuarine environments. In this study, high-throughput sequencing (16S rRNA) of sediment DNA was used to explore the distribution of azo-dye degrading bacteria and their functional genes in estuaries and coastal environments. Unlike laccase genes, azoreductase ( azoR ), and naphthalene degrading genes were ubiquitous in the coastal and estuarine environments. The relative abundances of most functional genes were higher in the summer compared to winter at locations proximal to the mouths of the Hanjiang River and its distributaries. These results suggested inland river discharges influenced the occurrence and abundance of azo dye degrading genes in the nearshore environments. Furthermore, the azoR genes had a significant negative relationship with total organic carbon, Hg, and Cr ( p < 0.05). This study provides critical insights into the biodegradation potential of indigenous microbial communities in nearshore environments and the influence of environmental factors on microbial structure, composition, and function which is essential for the development of technologies for bioremediation in azo dye contaminated sites.

José L. Garcı́a, Beatriz Galán

Microbial Biotechnology • 2021

State of the art on the valorisation of C1 carbon sources obtained either from natural or anthropogenic origins as a key challenge for the circular economy.

Kengo Sasaki, Daisuke Sasaki, Yota Tsuge et al.

Biotechnology for Biofuels • 2018

The altered redox potential in the BES likely transformed the structure of the microbial consortium and metabolic pattern to increase methane production and decrease carbon dioxide production in the two-stage process. This study showed the utility of the BES to act on the microbial consortium, resulting in improved gas production from carbohydrate compounds.

Cristiane Angélica Ottoni, Marta Filipa Simões, J. G. dos Santos et al.

Biotechnology Letters • 2018

Taking our preliminary results into consideration, we concluded that the MFC technology presents itself as highly promising for the treatment of vinasse.

Mingyi Xu, Dan Zhao, Xinyu Zhu et al.

Chemical Engineering Journal • 2021

Valorization of crude biogas to value-added products is the key step toward techno-economic biogas business. Besides, the increasing world population puts heavy pressure on food supply and will double protein demand in the coming decades. In this context, we propose a bioinorganic electrosynthesis process for the integration of biogas upgrading and edible single-cell protein production, which could be an alternative solution to address these challenges. With a biogas inflow of 70%CH4/30%CO2 at 50 mL·d−1 and an applied voltage of 3.0 V, the protein concentration of 472.04 ± 22.05 mg·L−1 was achieved with the “CO2-to-CH4” bioconversion efficiency of 92.97 ± 5.61%. Higher CO2 content in the biogas resulted in a comparatively lower protein concentration. The system was tested resilient to the toxic H2S in biogas (up to 5000 ppm). It was possible to improve the protein yield three times by scaling up the fermenter from 100 mL to 1 L, with a “CH4-to-SCP” fermentation efficiency of 70.67 ± 2.37%. The methanotrophic biomass produced in the system was found rich in protein with a total amino acids mass-content of over 62.8%. The outcomes of this study will offer a new solution for sustainable protein production, biogas upgrading and valorization, which are perfectly in line with the United Nations Sustainable Development Goals.

Léa Laguillaumie, Yan Rafrafi, Elisabeth Moya-Leclair et al.

Bioresource Technology • 2022

Zhongqing Yan, Enze Kang, Kerou Zhang et al.

ISME Communications • 2022

Peatlands act as an important sink of carbon dioxide (CO 2 ). Yet, they are highly sensitive to climate change, especially to extreme drought. The changes in the net ecosystem CO 2 exchange (NEE) under extreme drought events, and the driving function of microbial enzymatic genes involved in soil organic matter (SOM) decomposition, are still unclear. Herein we investigated the effects of extreme drought events in different periods of plant growth season at Zoige peatland on NEE and microbial enzymatic genes of SOM decomposition after 5 years. The results showed that the NEE of peatland decreased significantly by 48% and 26% on average (n = 12, P < 0.05) under the early and midterm extreme drought, respectively. The microbial enzymatic genes abundance of SOM decomposition showed the same decreasing trend under early and midterm extreme drought, but an increasing trend under late extreme drought. The microbial community that contributes to these degradation genes mainly derives from Proteobacteria and Actinobacteria. NEE was mainly affected by soil hydrothermal factors and gross primary productivity but weakly correlated with SOM enzymatic decomposition genes. Soil microbial respiration showed a positive correlation with microbial enzymatic genes involved in the decomposition of labile carbon (n = 18, P < 0.05). This study provided new insights into the responses of the microbial decomposition potential of SOM and ecosystem CO 2 sink function to extreme drought events in the alpine peatland.

Xiaolin Zhang, Wendan Xue, Guoliang Wang et al.

Communications Earth & Environment • 2025

Oil contamination in coastal wetlands jeopardizes these ecosystems and worsens climate warming. Here we analyze 87 metagenomic samples from representative Chinese wetland oilfields and find that genes associated with dissimilatory iron reduction respond to hydrocarbon levels. These genes were closely linked to the breakdown of organic matter into carbon dioxide and methane, highlighting the potential of dissimilatory iron reduction for degrading stubborn hydrocarbons and altering electron transfer pathways. Notably, Geobacter, a key genus for dissimilatory iron reduction, showed strong correlation with iron(II) production and hydrocarbon degradation. To validate these findings, a targeted enhancement of dissimilatory iron reduction with external iron oxide and Geobacter maximized carbon removal, transforming organic-bound fraction of iron into carbonate-bound fraction. The intensified iron reduction process reduced methane emissions by 38–40% and strengthened microbial interactions by redirecting electron transfer in carbon flow. Our study innovatively mitigates pollution and reduces methane emissions in oil-contaminated wetlands. Microorganisms play an important role in the degradation of petroleum-hydrocarbon in oil-polluted coastal wetlands through bio-geo-coupling of carbon and Fe(II), according to metagenomic analysis of 87 samples from Chinese wetland oilfields.

Bradley G. Lusk

Frontiers in Microbiology • 2019

Approximately four billion years ago, the first microorganisms to thrive on earth were anaerobic chemoautotrophic thermophiles, a specific group of extremophiles that survive and operate at temperatures ∼50 - 125°C and do not use molecular oxygen (O 2 ) for respiration. Instead, these microorganisms performed respiration via dissimilatory metal reduction by transferring their electrons extracellularly to insoluble electron acceptors. Genetic evidence suggests that Gram-positive thermophilic bacteria capable of extracellular electron transfer (EET) are positioned close to the root of the Bacteria kingdom on the tree of life. On the contrary, EET in Gram-negative mesophilic bacteria is a relatively new phenomenon that is evolutionarily distinct from Gram-positive bacteria. This suggests that EET evolved separately in Gram-positive thermophiles and Gram-negative mesophiles, and that EET in these bacterial types is a result of a convergent evolutionary process leading to homoplasy. Thus, the study of dissimilatory metal reducing thermophiles provides a glimpse into some of Earth's earliest forms of respiration. This will provide new insights for understanding biogeochemistry and the development of early Earth in addition to providing unique avenues for exploration and discovery in astrobiology. Lastly, the physiological composition of Gram-positive thermophiles, coupled with the kinetic and thermodynamic consequences of surviving at elevated temperatures, makes them ideal candidates for developing new mathematical models and designing innovative next-generation biotechnologies. KEY CONCEPTS Anaerobe: organism that does not require oxygen for growth. Chemoautotroph: organism that obtains energy by oxidizing inorganic electron donors. Convergent Evolution: process in which organisms which are not closely related independently evolve similar traits due to adapting to similar ecological niches and/or environments. Dissimilatory Metal Reduction: reduction of a metal or metalloid that uses electrons from oxidized organic or inorganic electron donors. Exoelectrogen: microorganism that performs dissimilatory metal reduction via extracellular electron transfer. Extremophiles: organisms that thrive in physical or geochemical conditions that are considered detrimental to most life on Earth. Homoplasy: a character shared by a set of species that is not shared by a common ancestor Non-synonymous Substitutions (K a ): a substitution of a nucleotide that changes a codon sequence resulting in a change in the amino acid sequence of a protein. Synonymous Substitutions (K s ): a substitution of a nucleotide that may change a codon sequence, but results in no change in the amino acid sequence of a protein. Thermophiles: a specific group of extremophiles that survive and operate at temperatures ∼50-125°C.

Luz Bretón‐Deval, Ayixón Sánchez‐Reyes, Alejandro Sánchez‐Flores et al.

Microorganisms • 2020

The objective of this study is to understand the functional and metabolic potential of the microbial communities along the Apatlaco River and highlight activities related to bioremediation and its relationship with the Apatlaco's pollutants, to enhance future design of more accurate bioremediation processes. Water samples were collected at four sampling sites along the Apatlaco River (S1-S4) and a whole metagenome shotgun sequencing was performed to survey and understand the microbial metabolic functions with potential for bioremediation. A HMMER search was used to detect sequence homologs related to polyethylene terephthalate (PET) and polystyrene biodegradation, along with bacterial metal tolerance in Apatlaco River metagenomes. Our results suggest that pollution is a selective pressure which enriches microorganisms at polluted sites, displaying metabolic capacities to tolerate and transform the contamination. According to KEGG annotation, all sites along the river have bacteria with genes related to xenobiotic biodegradation. In particular, functions such as environmental processing, xenobiotic biodegradation and glycan biosynthesis are over-represented in polluted samples, in comparison to those in the clean water site. This suggests a functional specialization in the communities that inhabit each perturbated point. Our results can contribute to the determination of the partition in a metabolic niche among different Apatlaco River prokaryotic communities, that help to contend with and understand the effect of anthropogenic contamination.

Tian Zhang, Xiaochen Shi, Ran Ding et al.

The ISME Journal • 2020

Multiple Fe(III)-reducing Geobacter species including the model Geobacter sulfurreducens are thought to be incapable of carbon dioxide fixation. The discovery of the reversed oxidative tricarboxylic acid cycle (roTCA) for CO 2 reduction with citrate synthase as key enzyme raises the possibility that G. sulfurreducens harbors the metabolic potential for chemolithoautotrophic growth. We investigate this hypothesis by transferring G. sulfurreducens PCA serially with Fe(III) as electron acceptor and formate as electron donor and carbon source. The evolved strain T17-3 grew chemolithoautotrophically with a 2.7-fold population increase over 48 h and a Fe(III) reduction rate of 417.5 μM h -1 . T17-3 also grew with CO 2 as carbon source. Mutations in T17-3 and enzymatic assays point to an adaptation process where the succinyl-CoA synthetase, which is inactive in the wild-type, became active to complete the roTCA cycle. Deletion of the genes coding for the succinyl-CoA synthetase in T17-3 prevented growth with formate as substrate. Enzymatic assays also showed that the citrate synthase can perform the necessary cleavage of citrate for the functional roTCA cycle. These results demonstrate that G. sulfurreducens after adaptation reduced CO 2 via the roTCA cycle. This previously hidden metabolism can be harnessed for biotechnological applications and suggests hidden ecological functions for Geobacter.

Alastair W. Tait, Emma J. Gagen, Sasha Wilson et al.

Frontiers in Microbiology • 2017

Finding fresh, sterilized rocks provides ecologists with a clean slate to test ideas about first colonization and the evolution of soils de novo. Lava has been used previously in first colonizer studies due to the sterilizing heat required for its formation. However, fresh lava typically falls upon older volcanic successions of similar chemistry and modal mineral abundance. Given enough time, this results in the development of similar microbial communities in the newly erupted lava due to a lack of contrast between the new and old substrates. Meteorites, which are sterile when they fall to Earth, provide such contrast because their reduced and mafic chemistry commonly differs to the surfaces on which they land; thus allowing investigation of how community membership and structure respond to this new substrate over time. We conducted 16S rRNA gene analysis on meteorites and soil from the Nullarbor Plain, Australia. We found that the meteorites have low species richness and evenness compared to soil sampled from directly beneath each meteorite. Despite the meteorites being found kilometers apart, the community structure of each meteorite bore more similarity to those of other meteorites (of similar composition) than to the community structure of the soil on which it resided. Meteorites were dominated by sequences that affiliated with the Actinobacteria with the major Operational Taxonomic Unit (OTU) classified as Rubrobacter radiotolerans. Proteobacteria and Bacteroidetes were the next most abundant phyla. The soils were also dominated by Actinobacteria but to a lesser extent than the meteorites. We also found OTUs affiliated with iron/sulfur cycling organisms Geobacter spp. and Desulfovibrio spp. This is an important finding as meteorites contain abundant metal and sulfur for use as energy sources. These ecological findings demonstrate that the structure of the microbial community in these meteorites is controlled by the substrate, and will not reach homeostasis with the Nullarbor community, even after ca. 35,000 years. Our findings show that meteorites provide a unique, sterile substrate with which to test ideas relating to first-colonizers. Although meteorites are colonized by microorganisms, the microbial population is unlikely to match the community of the surrounding soil on which they fall.