Leilei Xiao, Jiajia Li, Éric Lichtfouse et al.

Journal of Hazardous Materials • 2020

Xiaohong Li, Jizhou Duan, Hui Xiao et al.

Frontiers in Microbiology • 2017

Metal corrosion is of worldwide concern because it is the cause of major economic losses, and because it creates significant safety issues. The mechanism of the corrosion process, as influenced by bacteria, has been studied extensively. However, the bacterial communities that create the biofilms that form on metals are complicated, and have not been well studied. This is why we sought to analyze the composition of bacterial communities living on steel structures, together with the influence of ecological factors on these communities. The corrosion samples were collected from rust layers on steel plates that were immersed in seawater for two different periods at Sanya and Xiamen, China. We analyzed the bacterial communities on the samples by targeted 16S rRNA gene (V3-V4 region) sequencing using the Illumina MiSeq. Phylogenetic analysis revealed that the bacteria fell into 13 phylotypes (similarity level = 97%). Proteobacteria , Firmicutes and Bacteroidetes were the dominant phyla, accounting for 88.84% of the total. Deltaproteobacteria , Clostridia and Gammaproteobacteria were the dominant classes, and accounted for 70.90% of the total. Desulfovibrio spp., Desulfobacter spp. and Desulfotomaculum spp. were the dominant genera and accounted for 45.87% of the total. These genera are sulfate-reducing bacteria that are known to corrode steel. Bacterial diversity on the 6 months immersion samples was much higher than that of the samples that had been immersed for 8 years ( P < 0.001, Student's t -test). The average complexity of the biofilms from the 8-years immersion samples from Sanya was greater than those from Xiamen, but not significantly so ( P > 0.05, Student's t -test). Overall, the data showed that the rust layers on the steel plates carried many bacterial species. The bacterial community composition was influenced by the immersion time. The results of our study will be of benefit to the further studies of bacterial corrosion mechanisms and corrosion resistance.

Zhifeng Zhang, Lirui Liu, Yue-Ping Pan et al.

Microbiome • 2023

The study not only highlights the advantages of HiSeq-PacBio Hybrid assembly for a more complete profiling of environmental microbiomes but also expands our understanding of the microbial diversity and potential roles of distinct microbial groups in biogeochemical cycling in mangrove sediment. Video Abstract.

Byung Hee Chun, Kyung Hyun Kim, Hye Hee Jeon et al.

Scientific Reports • 2017

The genomic and metabolic features of Leuconostoc (Leu) mesenteroides were investigated through pan-genomic and transcriptomic analyses. Relatedness analysis of 17 Leu. mesenteroides strains available in GenBank based on 16S rRNA gene sequence, average nucleotide identity, in silico DNA-DNA hybridization, molecular phenotype, and core-genome indicated that Leu. mesenteroides has been separated into different phylogenetic lineages. Pan-genome of Leu. mesenteroides strains, consisting of 999 genes in core-genome, 1,432 genes in accessory-genome, and 754 genes in unique genome, and their COG and KEGG analyses showed that Leu. mesenteroides harbors strain-specifically diverse metabolisms, probably representing high evolutionary genome changes. The reconstruction of fermentative metabolic pathways for Leu. mesenteroides strains showed that Leu. mesenteroides produces various metabolites such as lactate, ethanol, acetate, CO 2 , mannitol, diacetyl, acetoin, and 2,3-butanediol through an obligate heterolactic fermentation from various carbohydrates. Fermentative metabolic features of Leu. mesenteroides during kimchi fermentation were investigated through transcriptional analyses for the KEGG pathways and reconstructed metabolic pathways of Leu. mesenteroides using kimchi metatranscriptomic data. This was the first study to investigate the genomic and metabolic features of Leu. mesenteroides through pan-genomic and metatranscriptomic analyses, and may provide insights into its genomic and metabolic features and a better understanding of kimchi fermentations by Leu. mesenteroides.

Isabel Douterelo, Bas E. Dutilh, Ksenia Arkhipova et al.

Water Research • 2020

Weiming Tu, Jiabao Xu, Ian P. Thompson et al.

Nature Communications • 2023

Microbial rhodopsin, a significant contributor to sustaining life through light harvesting, holds untapped potential for carbon fixation. Here, we construct an artificial photosynthesis system which combines the proton-pumping ability of rhodopsin with an extracellular electron uptake mechanism, establishing a pathway to drive photoelectrosynthetic CO 2 fixation by Ralstonia eutropha (also known as Cupriavidus necator) H16, a facultatively chemolithoautotrophic soil bacterium. R. eutropha is engineered to heterologously express an extracellular electron transfer pathway of Shewanella oneidensis MR-1 and Gloeobacter rhodopsin (GR). Employing GR and the outer-membrane conduit MtrCAB from S. oneidensis, extracellular electrons and GR-driven proton motive force are integrated into R. eutropha's native electron transport chain (ETC). Inspired by natural photosynthesis, the photoelectrochemical system splits water to supply electrons to R. eutropha via the Mtr outer-membrane route. The light-activated proton pump - GR, supported by canthaxanthin as an antenna, powers ATP synthesis and reverses the ETC to regenerate NADH/NADPH, facilitating R. eutropha's biomass synthesis from CO 2 . Overexpression of a carbonic anhydrase further enhances CO 2 fixation. This artificial photosynthesis system has the potential to advance the development of efficient photosynthesis, redefining our understanding of the ecological role of microbial rhodopsins in nature.

Antonio Vassallo, Maria Francesca Silletti, Immacolata Faraone et al.

Journal of Nanomaterials • 2020

Today’s human society, product of decades of progress in all fields of knowledge, would have been unimaginable without the discovery of antibiotics and more generally of antimicrobials. However, from the beginning, the scientific community was aware that microorganisms through various strategies were able to hinder and render vain antibiotic action. Common examples are the phenomena of persistence, tolerance, and resistance, up to the creation of the feared bacterial biofilms. Antibiotics are a precious but equally labile resource that must be preserved but at the same time reinforced to safeguard their effectiveness. Nanoparticulate systems such as nanobactericides, with their inherent antibacterial activity, and nanocarriers, which operate as drug delivery systems for conventional antibiotics, are innovative therapies made available by nanotechnology. Inorganic nanoparticles are effective both as nanobactericides (AgNPs, ZnONPs, and TiO 2 NPs) and as nanocarriers (AgNPs, AuNPs, ZnONPs, and TiO 2 NPs) against sensitive and multi-drug-resistant bacterial strains. Liposomes are among the most studied and flexible antibiotic delivery platforms: conventional liposomes allow passive targeting at the mononuclear phagocytic system (MPS); “stealth” liposomes prevent macrophage uptake so as to eradicate infections in tissues and organs outside MPS; thanks to their positive charge, cationic liposomes interact preferentially with bacterial and biofilm surfaces, acting as innate antibacterials as well as drug delivery systems (DDS); fusogenic liposomes have fluid bilayers that promote fusion with microbial membranes; and finally, ligand-targeted liposomes provide active targeting at infection sites. Dendrimers are among the most recent and attractive nanoparticulate systems, thanks to their multibranched nanoarchitecture, which equipped them with multiple active sites for loading antibiotics and also interacting with bacteria. Finally, nanoantibiotics represent a new hopeful generation of antibiotic candidates capable of increasing or even restoring the clinical efficacy of “old” antibiotics rendered useless by the resistance phenomena.

Michael J. Lacasse, Deborah B. Zamble

Biochemistry • 2016

[NiFe]-hydrogenases catalyze the reversible conversion of hydrogen gas into protons and electrons and are vital metabolic components of many species of bacteria and archaea. At the core of this enzyme is a sophisticated catalytic center comprising nickel and iron, as well as cyanide and carbon monoxide ligands, which is anchored to the large hydrogenase subunit through cysteine residues. The production of this multicomponent active site is accomplished by a collection of accessory proteins and can be divided into discrete stages. The iron component is fashioned by the proteins HypC, HypD, HypE, and HypF, which functionalize iron with cyanide and carbon monoxide. Insertion of the iron center signals to the metallochaperones HypA, HypB, and SlyD to selectively deliver the nickel to the active site. A specific protease recognizes the completed metal cluster and then cleaves the C-terminus of the large subunit, resulting in a conformational change that locks the active site in place. Finally, the large subunit associates with the small subunit, and the complete holoenzyme translocates to its final cellular position. Beyond this broad overview of the [NiFe]-hydrogenase maturation process, biochemical and structural studies are revealing the fundamental underlying molecular mechanisms. Here, we review recent work illuminating how the accessory proteins contribute to the maturation of [NiFe]-hydrogenase and discuss some of the outstanding questions that remain to be resolved.

Samrena Jabeen, Subha Malik, Soha Khan et al.

International Journal of Energy Economics and Policy • 2020

The rapid growth of the human population of the planet has led to mounting energy demands; conventional sources of energies are not enough to fulfil the energy demand. Therefore, the search for alternative sources has become the most profuse challenge. Presently, many alternatives are being studied and implemented in literature—the renewable sources which are less harmful and environmentally acceptable for future generations. The current study aims to review the renewable resources which are highly examined in the last decade by the researcher. For this purpose, two databases, web of science and Scopus, are selected to extract the data. The data selection and rejection process are following the PRISMA statement that is an authentic eligibility criterion using by researchers. After a detailed function, the final fifty-two studies are selecting for the current review. The classification of data is mainly discussing biofuels, solar energy, wind energy, and renewable electricity. Literature is also showing that fossil fuels are environmentally very harmful, and developed countries are significantly replacing the renewable energies source. Bibliometric results are showing that research collaborations are exceptionally done in U.S. and European countries. The findings of the current study are a novel concept to evaluate and review the published literature on renewable energies in the last decade. Keywords: Bibliometric Analysis, Sustainability, Renewable Energy Sources JEL Classifications : P28, Q42, Q47 DOI: https://doi.org/10.32479/ijeep.10759

Lei Chen, Zhi Zhou, Chaofeng Shen et al.

Water Science & Technology • 2020

Antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in the environment are of great concern due to their potential risk to human health. The effluents from wastewater treatment plants and livestock production are major sources of ARB and ARGs. Chlorination, UV irradiation, and ozone disinfection cannot remove ARGs completely. In this study, the potential of electrochemical oxidation and electro-Fenton processes as alternative treatment technologies for inactivation of ARB and ARGs in both intracellular and extracellular forms was evaluated. Results showed that the electrochemical oxidation process was effective for the inactivation of selected ARB but not for the removal of intracellular ARGs or extracellular ARGs. The electro-Fenton process was more effective for the removal of both intracellular and extracellular ARGs. The removal efficiency after 120 min of electro-Fenton treatment under 21.42 mA/cm 2 was 3.8 logs for intracellular tetA, 4.1 logs for intracellular ampC, 5.2 logs for extracellular tetA, and 4.8 logs for extracellular ampC, respectively in the presence of 1.0 mmol/L Fe 2+ . It is suggested that electrochemical oxidation is an effective disinfection method for ARB and the electro-Fenton process is a promising technology for the removal of both intracellular and extracellular ARGs in wastewater.

on behalf of MAMI team, Izaskun García‐Mantrana, Cristina Alcántara et al.

BMC Pediatrics • 2019

The study is registered on the ClinicalTrial.gov platform NCT03552939. (June 12, 2018).

Alessandra Fontana, Panagiotis Kougias, Laura Treu et al.

Microbiome • 2018

This is the first study investigating biogas reactor metatranscriptome dynamics following hydrogen injection for biomethanation and carbon fixation to short-chain fatty acids purposes. The same microbes showed different patterns of metabolic regulation in the two reactor configurations. It was observed an effect of the specialized acidogenic reactor on the overall microbial consortium composition and activity in the two-stage digester. There were also suggested the main species responsible for methanation, short-chain fatty acids production, and electron transport chain mechanisms, in both reactor configurations.

Blanca Vera‐Gargallo, António Ventosa

Genes • 2018

Hypersaline environments encompass aquatic and terrestrial habitats. While only a limited number of studies on the microbial diversity of saline soils have been carried out, hypersaline lakes and marine salterns have been thoroughly investigated, resulting in an aquatic-biased knowledge about life in hypersaline environments. To improve our understanding of the assemblage of microbes thriving in saline soils, we assessed the phylogenetic diversity and metabolic potential of the prokaryotic community of two hypersaline soils (with electrical conductivities of ~24 and 55 dS/m) from the Odiel saltmarshes (Spain) by metagenomics. Comparative analysis of these soil databases with available datasets from salterns ponds allowed further identification of unique and shared traits of microbial communities dwelling in these habitats. Saline soils harbored a more diverse prokaryotic community and, in contrast to their aquatic counterparts, contained sequences related to both known halophiles and groups without known halophilic or halotolerant representatives, which reflects the physical heterogeneity of the soil matrix. Our results suggest that Haloquadratum and certain Balneolaeota members may preferentially thrive in aquatic or terrestrial habitats, respectively, while haloarchaea, nanohaloarchaea and Salinibacter may be similarly adapted to both environments. We reconstructed 4 draft genomes related to Bacteroidetes, Balneolaeota and Halobacteria and appraised their metabolism, osmoadaptation strategies and ecology. This study greatly improves the current understanding of saline soils microbiota.

Oskar Modin, Federico Aulenta

Environmental Science Water Research & Technology • 2017

The potential applications of microbial electrochemistry are many; three promising ones are sensors, in situ bioremediation, and metal recovery.

Rafaela Garrido Godoy, Marta Ângela Marcondes, Rodrigo Pessôa et al.

Scientific Reports • 2020

The Pinheiros River in São Paulo, Brazil, crosses through the capital city and has its confluence with the River Tiete, which comprises several reservoirs along its course. Although Pinheiros River is considered one of the heaviest polluted rivers in Brazil, little is known about its bacterial composition, their metabolic functions or how these communities are affected by the physicochemical parameters of the river. In this study, we used the 16S rRNA gene Illumina MiSeq sequencing to profile the bacterial community from the water surface at 11 points along the course of the River. Taxonomical composition revealed an abundance of Proteobacteria phyla, followed by Firmicutes and Bacteroidetes, with a total of 233 classified bacterial families and 558 known bacterial genera. Among the 35 potentially pathogenic bacteria identified, Arcobacter was the most predominant genus. The disrupted physicochemical parameters detected in this study may possibly contribute to the composition and distribution of the bacterial community in the Pinheiros River. Predictive functional analysis suggests the River is abundant in motility genes, including bacterial chemotaxis and flagellar assembly. These results provide novel and detailed insights into the bacterial communities and putative function of the surface water in the Pinheiros River.

Fereidoon Shahidi, Han Peng

Journal of Food Bioactives • 2018

Modern epidemiological and interventional studies have demonstrated that various bioactivities including antioxidant, antiproliferative, immune-regulatory, hormonal-regulation abilities and neuro-/hepato-/cardioprotective effects result from consumption of a phenolic-rich diet. The health benefits of ingesting phenolics are greatly dependent on their bioaccessibility and bioavailability in the digestive tract and circulatory system. This contribution attempts to review the bioaccessibility and bioavailability of phenolic compounds by focusing on the body’s internal mechanism including digestion, absorption, transport, modification, excretion, and colonic fermentation. The bioaccessibility and bioavailability of different phenolics vary depending on the physical condition of an individual, including digestive/absorptive/metabolic/response capability and effective dose. External factors such as processing methods and interaction with various food matrices also play a vital role on the bioavailability of dietary phenolic compounds. On the other hand, some novel phenolics have been synthesized to enable them rendering new bioactivities. The key internal factors influencing the bioaccessibility and bioavailability are also reviewed in this contribution. In addition, suggestions have been made for future measurement and assessment of bioavailability, together with prospects for food/nutraceutical/pharmaceutical application of novel phenolics.

Eric Capo, Marie‐Eve Monchamp, Marco J. L. Coolen et al.

Environmental Microbiology • 2022

In-depth knowledge about spatial and temporal variation in microbial diversity and function is needed for a better understanding of ecological and evolutionary responses to global change. In particular, the study of microbial ancient DNA preserved in sediment archives from lakes and oceans can help us to evaluate the responses of aquatic microbes in the past and make predictions about future biodiversity change in those ecosystems. Recent advances in molecular genetic methods applied to the analysis of historically deposited DNA in sediments have not only allowed the taxonomic identification of past aquatic microbial communities but also enabled tracing their evolution and adaptation to episodic disturbances and gradual environmental change. Nevertheless, some challenges remain for scientists to take full advantage of the rapidly developing field of paleo-genetics, including the limited ability to detect rare taxa and reconstruct complete genomes for evolutionary studies. Here, we provide a brief review of some of the recent advances in the field of environmental paleomicrobiology and discuss remaining challenges related to the application of molecular genetic methods to study microbial diversity, ecology, and evolution in sediment archives. We anticipate that, in the near future, environmental paleomicrobiology will shed new light on the processes of microbial genome evolution and microbial ecosystem responses to quaternary environmental changes at an unprecedented level of detail. This information can, for example, aid geological reconstructions of biogeochemical cycles and predict ecosystem responses to environmental perturbations, including in the context of human-induced global changes.

Pauliina Rajala, Dong-Qiang Cheng, Stuart A. Rice et al.

Microbiome • 2022

The corrosion rate observed was higher than what could be expected from abiotic corrosion mechanisms under these environmental conditions. High corrosion rate and the form of corrosion (deep pitting) suggest that the corrosion of the chain links was driven by both abiotic and biotic processes. We posit that the corrosion is driven by deep-sea sulfur-cycling microorganisms which may gain energy by accelerating the reaction between metallic iron and elemental sulfur. The results of this field study provide important new insights on the ecophysiology of the corrosion process in the deep sea.

Lingjun Xu, Adnan Khan, Sarah Al-Aqeel et al.

Petroleum Science • 2025

Microbiologically influenced corrosion (MIC) is caused by microbial biofilms. In this work, an oilfield produced water sample was analyzed using a newly developed disposable electrochemical biofilm/MIC test kit consisting of two solid-state electrodes in a 10 mL standard serum vial for assessing biofilm growth, biocorrosivity and biocide treatment efficacy. The produced water sample was found to be low in microbial cell counts and nutrients. To simulate a possible worst-case scenario, the produced water sample was subcultured at 37 °C using enriched artificial seawater (EASW) for 3 rounds before being used as the seed culture for further MIC and biocide tests. The electrochemical test results from the 10 mL biofilm/MIC test kit including polarization resistance ( R p ) from linear polarization resistance scans and corrosion current density ( i corr ) from Tafel scans indicated a corrosion rate sequence of no biocide treatment >20 ppm ( w / w ) tetrakis hydroxymethyl phosphonium sulfate (THPS) > 50 ppm THPS. R p was able to predict biofilm maturity time using the incubation time when R p leveled off (i.e., time to reach maximum corrosivity). Two common electron transfer promotors were found to accelerate MIC in the test kit vial injection tests, pointing to extracellular electron transfer-MIC as the main mechanism. This observation was consistent with the 30% corrosive sulfate reducers among all microbes in the mixed culture sample found by metagenomics. In the coupon incubation tests in 125 mL anaerobic vials, the 7-d X60 carbon steel weight loss was 1.1 ± 0.2 mg/cm 2 (2.9 mpy uniform corrosion rate) without biocide treatment. With 20 ppm THPS biocide in EASW, it dropped to 0.5 ± 0.2 mg/cm 2 (1.3 mpy), and with 50 ppm THPS, it became negligible. The corresponding MIC pit depths were 10.5, 8.9 μm, and no well-defined pits, respectively for the three biocide treatment conditions. The weight loss data confirmed the corrosion rate sequence from the biofilm/MIC test kit. This work presents a new MIC monitoring and biocide treatment assessment system for oilfield applications using the new biofilm/MIC test kit.

Keiichi Inoue, Shota Ito, Yoshitaka Kato et al.

Nature Communications • 2016

Light-driven outward H + pumps are widely distributed in nature, converting sunlight energy into proton motive force. Here we report the characterization of an oppositely directed H + pump with a similar architecture to outward pumps. A deep-ocean marine bacterium, Parvularcula oceani, contains three rhodopsins, one of which functions as a light-driven inward H + pump when expressed in Escherichia coli and mouse neural cells. Detailed mechanistic analyses of the purified proteins reveal that small differences in the interactions established at the active centre determine the direction of primary H + transfer. Outward H + pumps establish strong electrostatic interactions between the primary H + donor and the extracellular acceptor. In the inward H + pump these electrostatic interactions are weaker, inducing a more relaxed chromophore structure that leads to the long-distance transfer of H + to the cytoplasmic side. These results demonstrate an elaborate molecular design to control the direction of H + transfers in proteins.

Cassandre Sara Lazar, Bill J. Baker, Kaitlyn E. Seitz et al.

The ISME Journal • 2017

Genomic bins belonging to multiple archaeal lineages were recovered from distinct redox regimes in sediments of the White Oak River estuary. The reconstructed archaeal genomes were identified as belonging to the rice cluster subgroups III and V (RC-III, RC-V), the Marine Benthic Group D (MBG-D), and a newly described archaeal class, the Theionarchaea. The metabolic capabilities of these uncultured archaea were inferred and indicated a common capability for extracellular protein degradation, supplemented by other pathways. The multiple genomic bins within the MBG-D archaea shared a nearly complete reductive acetyl-CoA pathway suggesting acetogenic capabilities. In contrast, the RC-III metabolism appeared centered on the degradation of detrital proteins and production of H 2 , whereas the RC-V archaea lacked capabilities for protein degradation and uptake, and appeared to be specialized on carbohydrate fermentation. The Theionarchaea appeared as complex metabolic hybrids; encoding a complete tricarboxylic acid cycle permitting carbon (acetyl-CoA) oxidation, together with a complete reductive acetyl-CoA pathway and sulfur reduction by a sulfhydrogenase. The differentiated inferred capabilities of these uncultured archaeal lineages indicated lineage-specific linkages with the nitrogen, carbon and sulfur cycles. The predicted metabolisms of these archaea suggest preferences for distinct geochemical niches within the estuarine sedimentary environment.

Blair Ney, F. Hafna Ahmed, Carlo R. Carere et al.

The ISME Journal • 2016

F 420 is a low-potential redox cofactor that mediates the transformations of a wide range of complex organic compounds. Considered one of the rarest cofactors in biology, F 420 is best known for its role in methanogenesis and has only been chemically identified in two phyla to date, the Euryarchaeota and Actinobacteria. In this work, we show that this cofactor is more widely distributed than previously reported. We detected the genes encoding all five known F 420 biosynthesis enzymes (cofC, cofD, cofE, cofG and cofH) in at least 653 bacterial and 173 archaeal species, including members of the dominant soil phyla Proteobacteria, Chloroflexi and Firmicutes. Metagenome datamining validated that these genes were disproportionately abundant in aerated soils compared with other ecosystems. We confirmed through high-performance liquid chromatography analysis that aerobically grown stationary-phase cultures of three bacterial species, Paracoccus denitrificans, Oligotropha carboxidovorans and Thermomicrobium roseum, synthesized F 420 , with oligoglutamate sidechains of different lengths. To understand the evolution of F 420 biosynthesis, we also analyzed the distribution, phylogeny and genetic organization of the cof genes. Our data suggest that although the F o precursor to F 420 originated in methanogens, F 420 itself was first synthesized in an ancestral actinobacterium. F 420 biosynthesis genes were then disseminated horizontally to archaea and other bacteria. Together, our findings suggest that the cofactor is more significant in aerobic bacterial metabolism and soil ecosystem composition than previously thought. The cofactor may confer several competitive advantages for aerobic soil bacteria by mediating their central metabolic processes and broadening the range of organic compounds they can synthesize, detoxify and mineralize.

Tingbei Bo, Xueying Zhang, Kevin D. Kohl et al.

The ISME Journal • 2020

Many small mammals engage in coprophagy, or the behavior of consuming feces, as a means to meet nutritional requirements when feeding on low-quality foods. In addition to nutritional benefits, coprophagy may also help herbivores retain necessary gut microbial diversity and function, which may have downstream physiological effects, such as maintaining energy balance and cognitive function. Here, we used collars to prevent Brandt's vole (Lasiopodomys brandtii) from engaging in coprophagy and monitored changes in microbial community structure, energy metabolism, and cognitive performance. In this research, we found that coprophagy prevention decreased alpha diversity of the gut microbiota, and altered proportions of microbial taxa such as Bacteroidetes, Firmicutes, and Oscillospira. Preventing coprophagy resulted in a reduced body mass, and increased food intake. Importantly, coprophagy prevention decreased vole cognitive behavior and altered levels of neurotransmitters in brain. Daily acetate administration was able to reverse some of the coprophagy prevention-induced changes in microbiota composition, metabolism, neurochemistry, and cognitive behavior. These findings identify the functional importance of coprophagy behavior and interactions between the gut microbiota, energy metabolism, and neurological function. Our results suggest that coprophagy contributes to stabilizing the gut microbiota, promoting microbial metabolism, maintaining host energy balance and, consequently, altering cognitive performance.

Naomi M. de Almeida, Hans J. C. T. Wessels, Rob M. de Graaf et al.

Biochimica et Biophysica Acta (BBA) - Bioenergetics • 2016

Anastasia Zerva, Stefan Simić, Evangelos Topakas et al.

Catalysts • 2019

There is a high number of well characterized, commercially available laccases with different redox potentials and low substrate specificity, which in turn makes them attractive for a vast array of biotechnological applications. Laccases operate as batteries, storing electrons from individual substrate oxidation reactions to reduce molecular oxygen, releasing water as the only by-product. Due to society’s increasing environmental awareness and the global intensification of bio-based economies, the biotechnological industry is also expanding. Enzymes such as laccases are seen as a better alternative for use in the wood, paper, textile, and food industries, and they are being applied as biocatalysts, biosensors, and biofuel cells. Almost 140 years from the first description of laccase, industrial implementations of these enzymes still remain scarce in comparison to their potential, which is mostly due to high production costs and the limited control of the enzymatic reaction side product(s). This review summarizes the laccase applications in the last decade, focusing on the published patents during this period.

Zaisheng Yan, Yu-Hong He, Haiyuan Cai et al.

Environmental Science & Technology • 2017

Sediment microbial fuel cells (SMFCs) can stimulate the degradation of polycyclic aromatic hydrocarbons in sediments, but the mechanism of this process is poorly understood at the microbial functional gene level. Here, the use of SMFC resulted in 92% benzo[a]pyrene (BaP) removal over 970 days relative to 54% in the controls. Sediment functions, microbial community structure, and network interactions were dramatically altered by the SMFC employment. Functional gene analysis showed that c-type cytochrome genes for electron transfer, aromatic degradation genes, and extracellular ligninolytic enzymes involved in lignin degradation were significantly enriched in bulk sediments during SMFC operation. Correspondingly, chemical analysis of the system showed that these genetic changes resulted in increases in the levels of easily oxidizable organic carbon and humic acids which may have resulted in increased BaP bioavailability and increased degradation rates. Tracking microbial functional genes and corresponding organic matter responses should aid mechanistic understanding of BaP enhanced biodegradation by microbial electrochemistry and development of sustainable bioremediation strategies.

Hassan Ahmadi, A.A. Jalil, Sohail Khan et al.

Energy Nexus • 2025

• The implementation of pre-treatments enhanced protein and carbohydrate accumulation by 90–95%. • CCPH-Pre-treatment yielded 1,962 mg/L TVFA post-dark fermentation (11.4-fold× untreated sludge) Acetic/propionic acids comprised 80% of TVFAs as dominant electron-donor metabolites. • CCPH-Pre-treatment achieved 172.5 A/m³ current density with 133.071 ml/g VS bio-H₂ in MECs. • Firmicutes dominated the genus in all pre-treated substrates (60–88% vs. 10.5% untreated). • CCPH-Pre-treatment integrates into the DF and MEC for efficient bio-H₂ production, optimizing substrate solubilization and microbial activity in sewage sludge energy recovery. The production of biohydrogen from sewage sludge presents a promising avenue for sustainable energy conversion and pollution control. This study systematically evaluates biohydrogen (bio-H₂) production through dark fermentation (DF) and single-chamber microbial electrolysis cells (MECs), employing diverse substrate pretreatment methods, including acidic, ultrasonic, heat, alkaline, and a novel combined CalciumCarbonate-2Potassiumhydroxide (CCPH) pretreatment. The findings reveal that these pretreatments significantly enhance the accumulation of proteins, carbohydrates, and volatile fatty acids (VFAs), with the DF phase further augmenting the solubilization of these critical components. Notably, 90–95% of carbohydrate and protein accumulation occurs during the pretreatment phase, which concurrently suppresses methanogenesis in sewage sludge, thereby optimizing conditions for bio-H₂ production in subsequent MEC processes. Among the pretreatments, CCPH-P demonstrates exceptional performance, achieving a total volatile fatty acid (TVFAs) concentration of 1,962 ± 124 mg/L post-dark fermentation, representing an 11.4-fold increase compared to untreated sludge. In MEC experiments, CCPH-P sludge attains a maximum current density of 172.5 A/m³ and an average bio-H₂ yield of 133.071 ml/g VS, underscoring its efficiency in electrochemical hydrogen recovery. Acetic and propionic acids, derived from sludge fermentation, emerge as the predominant electron donors, constituting approximately 80% of the total VFAs content across all pretreated substrates. Metagenomic analysis further reveals that Firmicutes exhibit the highest relative abundance, ranging from 60% to 88% in pretreated substrates, compared to merely 10.5% in untreated sewage sludge. These results collectively indicate that CCPH-pre-treatment serves as a viable and efficient method for enhancing biohydrogen recovery from sewage sludge through DF and MEC systems, thereby advancing the potential for waste-to-energy applications.

Lovisa Heyman‐Lindén, Dorota Kotowska, Elin Sand et al.

Food & Nutrition Research • 2016

Our results show that supplementation with lingonberries to an HF diet prevents low-grade inflammation and is associated with significant changes of the microbiota composition. Notably, the anti-inflammatory properties of lingonberries seem to be independent of effects on body weight gain.

Song Wang, Danfei Zeng, Biao Jin et al.

Chemical Engineering Journal • 2022

The retention of microplastics in sewage sludge, a reservoir of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), has attracted increasing attention. However, the impact of polyethylene microplastics (PE-MP) on the fate of ARGs and MGEs is far from fully understood in sewage sludge's thermophilic anaerobic digestion process (AD). The present study demonstrated that PE-MP with the size of 40–48 µm at concentrations of 50, 100, and 200 particles/g-TS could enlarge total ARGs abundance. Meanwhile, a significant positive (r = 0.96, p < 0.05) correlation was observed between PE-MP concentration and total MGEs content. Microbial analysis revealed the enrichment of some functional genus under the stress of PE-MP, which might be the potential host of ARGs and MGEs. The relative abundance of acetogens Thermoanaerobacter increased from 27.60 % to 32.80 % and hydrolytic bacteria Caldicoprobacter enriched by 28.03 % when PE-MP content increased from zero to 200 particles/g-TS. The potential hosts were subsequently identified through co-occurrence networks, some of which were identified as pathogens. Strong positive correlations between PE-MP, ARGs, and MGEs were observed using redundancy analysis and correlation analysis. Additionally, the structural equation model indicated the direct and indirect influence of PE-MP on the abundance of ARGs and MGEs. MGEs could enhance the acquisition and dissemination of ARGs directly. Taking together, our findings deciphered the contribution of PE-MP to the spread of ARGs and MGEs in the sludge AD process, which might pose risks to human health and should be considered during sewage sludge disposal.

Carol Robinson

Frontiers in Marine Science • 2019

Microbial plankton respiration is the key determinant in the balance between the storage of organic carbon in the oceans or its conversion to carbon dioxide with accompanying consumption of dissolved oxygen. Over the past fifty years, dissolved oxygen concentrations have decreased in many parts of the world’s oceans, and this trend of ocean deoxygenation is predicted to continue. Yet despite its pivotal role in ocean deoxygenation, microbial respiration remains one of the least constrained microbial metabolic processes. Improved understanding of the magnitude and variability of respiration, including attribution to component plankton groups, and quantification of the respiratory quotient, would enable better predictions and projections of the intensity and extent of ocean deoxygenation and of the integrative impact of ocean deoxygenation, ocean acidification, warming, and changes in nutrient concentration and stoichiometry on marine carbon storage. This study will synthesize current knowledge of respiration in relation to deoxygenation, including the drivers of its variability, identify key unknowns in our ability to project future scenarios and suggest methodological approaches to move the field forward.

Geoffrey Michael Gadd

Environmental Microbiology Reports • 2016

Geomycology can be simply defined as the roles and significance of fungi in processes of relevance to geology, and as such is part of the more general area of geomicrobiology (Gadd, 2010). Rock and mineral bioweathering, metal transformations, mineral formation and cycling of the elements, all of which are involved in mineral soil formation, are the most obvious geomicrobial processes under this heading. In the case of fungi, their additional significance as major decomposers of organic material underlines their important role in the cycling of major elements such as C, H, N, O, P, S, as well all other elements that may be associated with organic matter. The majority of stable elements can be found in living organisms, including metal pollutants, and the release of these in decomposition can result in further interaction with environmental components resulting in mineral formation for example. There are therefore clear connections between organic and inorganic components of geomicrobial processes, and between the aerobic and anaerobic domains of life. This is not always appreciated in geomicrobiology where to some the ‘geo’ prefix is equated with chemolithotrophy and anaerobiosis in certain prokaryotes. While environmental microbiologists are generally aware of the global significance of fungi in organic matter decomposition, plant productivity, food spoilage and biodeterioration, there is rather less awareness of their significance in a geomycological context. The problem is exacerbated in geomicrobiology where the preponderant attention given to prokaryotes has led to neglect of major eukaryotic groups such as fungi and algae. A recent example of such a narrow appreciation of microbial roles in major biosphere processes is found in a special edition of Elements dedicated to geomicrobiology where microbes were even defined as solely comprising bacteria and archaea (Druschel and Kappler, 2015), and with the entire perspective solely concentrating on these organisms. While some of this problem is undoubtedly due to the fragmentation and diversity of the different scientific communities that study prokaryotic and fungal processes, it is about time that geomycology received proper attention within geomicrobiology and Earth sciences as a vital and integral component. It is also clear that further integration is necessary between the different relevant disciplines. Geomicrobiology is by definition interdisciplinary requiring interaction between microbiologists, geologists, geochemists, mineralogists, etc., yet there are still some obvious barriers that remain in some quarters. Witness the pejorative comments about Life Sciences in a section of the Elements editorial, for example, [“Microbiology (or biology) may not be your favourite subject. Or maybe you dreaded taking “life science” courses while at the university. Even if life science is not your preferred area of interest……”]. Thankfully, there is a growing realisation in intelligent geological circles that microbes are important and this is bound to increase as knowledge and integration between disciplines develops. Another important point is that prokaryotes and eukaryotes are generally studied separately yet in the natural environment fungi rarely are found without bacteria, and vice versa in aerobic habitats. Even the obvious demarcation between aerobiosis and anaerobiosis is now rather blurred. It is abundantly clear that fungi are major geoactive agents in their own rite, but it is also clear that fungal–prokaryotic interactions are also of great significance. It is also evident that the extent of the biosphere influenced by fungi stretches into anaerobic domains and even to the deep subsurface where again interactions with prokaryotes appear highly significant. Environmentally significant fungi are traditionally regarded as aerobic organisms (notwithstanding the anaerobic alcoholic fermentation found in certain yeasts) and often dominant inhabitants of rock and mineral su

Tomokazu Hata, Noriyuki Miyata, Shu Takakura et al.

Endocrinology • 2019

Anorexia nervosa (AN) results in gut dysbiosis, but whether the dysbiosis contributes to AN-specific pathologies such as poor weight gain and neuropsychiatric abnormalities remains unclear. To address this, germ-free mice were reconstituted with the microbiota of four patients with restricting-type AN (gAN mice) and four healthy control individuals (gHC mice). The effects of gut microbes on weight gain and behavioral characteristics were examined. Fecal microbial profiles in recipient gnotobiotic mice were clustered with those of the human donors. Compared with gHC mice, gAN mice showed a decrease in body weight gain, concomitant with reduced food intake. Food efficiency ratio (body weight gain/food intake) was also significantly lower in gAN mice than in gHC mice, suggesting that decreased appetite as well as the capacity to convert ingested food to unit of body substance may contribute to poor weight gain. Both anxiety-related behavior measured by open-field tests and compulsive behavior measured by a marble-burying test were increased only in gAN mice but not in gHC mice. Serotonin levels in the brain stem of gAN mice were lower than those in the brain stem of gHC mice. Moreover, the genus Bacteroides showed the highest correlation with the number of buried marbles among all genera identified. Administration of Bacteroides vulgatus reversed compulsive behavior but failed to exert any substantial effect on body weight. Collectively, these results indicate that AN-specific dysbiosis may contribute to both poor weight gain and mental disorders in patients with AN.

Andrew Bell, Jason Brunt, Emmanuelle H. Crost et al.

Nature Microbiology • 2019

Henan Li, Yan Tian, Youpeng Qu et al.

Scientific Reports • 2017

A benthic microbial electrochemical systems (BMES) of 195 L (120 cm long, 25 cm wide and 65 cm height) was constructed for sediment organic removal. Sediment from a natural river (Ashi River) was used as test sediments in the present research. Three-dimensional anode (Tri-DSA) with honeycomb structure composed of carbon cloth and supporting skeleton was employed in this research for the first time. The results demonstrated that BMES performed good in organic-matter degradation and energy generation from sediment and could be considered for river sediments in situ restoration as novel method. Community analysis from the soil and anode using 16S rDNA gene sequencing showed that more electrogenic functional bacteria was accumulated in anode area when circuit connected than control system.

Thomas Franke, Uwe Deppenmeier

Molecular Microbiology • 2018

The human gut microbiota is a crucial factor for the host's physiology with respect to health and disease. Metagenomic shotgun sequencing of microbial gut communities revealed that Prevotella copri is one of the most important players in the gastrointestinal tract of many individuals. Because of the importance of this bacterium we analyzed the growth behavior and the central metabolic pathways of P. copri. Bioinformatic data, transcriptome profiling and enzyme activity measurements indicated that the major pathways are based on glycolysis and succinate production from fumarate. In addition, pyruvate can be degraded to acetate and formate. Electron transport phosphorylation depends on fumarate respiration with NADH and reduced ferredoxin as electron donors. In contrast to Bacteroides vulgatus, P. copri showed a more pronounced dependency on the addition of CO 2 or bicarbonate for biomass formation, which is a remarkable difference between P. copri and Bacteroides spp. with important implication in the context of gut microbial competition. The analysis of substrate consumption and product concentrations from many P. copri cultures with different optical densities allowed a prediction of the carbon and electron flow in the central metabolism and a detailed calculation of growth yields as well as carbon and redox balances.

Libu Manjakkal, Srinjoy Mitra, Yvan Pétillot et al.

IEEE Internet of Things Journal • 2021

The sensor technology for water quality monitoring (WQM) has improved during recent years. The cost-effective sensorised tools that can autonomously measure the essential physical-chemical-biological (PCB) variables are now readily available and are being deployed on buoys, boats, and ships. Yet, there is a disconnect between the data quality, data gathering, and data analysis due to the lack of standardized approaches for data collection and processing, spatiotemporal variation of key parameters in water bodies and new contaminants. Such gaps can be bridged with a network of multiparametric sensor systems deployed in water bodies using autonomous vehicles, such as marine robots and aerial vehicles to broaden the data coverage in space and time. Furthermore, intelligent algorithms [e.g., artificial intelligence (AI)] could be employed for standardized data analysis and forecasting. This article presents a comprehensive review of the sensors, deployment, and analysis technologies for WQM. A network of networked water bodies could enhance the global data intercomparability and enable WQM at a global scale to address global challenges related to food (e.g., aqua/agriculture), drinking water, and health (e.g., water-borne diseases).

Mengzhi Ji, Zichen Liu, Kaili Sun et al.

Frontiers of Environmental Science & Engineering • 2020

Pedro J. Cabello‐Yeves, Francisco Rodríguez‐Valera

Microbiome • 2019

The marked changes at the level of protein amino acid composition and pI provide a tool to predict the preferred habitat of a culture or a metagenome-assembled genome (MAG). The exact physiological explanation for such variations in the pIs and electrostatic surface potentials is not known yet. However, these changes might reflect differences in membrane bioenergetics derived from the absence of significant Na + concentrations in most freshwater habitats. In any case, the changes in amino acid composition in most proteins imply that a long evolutionary time is required to adapt from one type of habitat to the other.

Xiaobo Guo, Chihe Sun, Richen Lin et al.

Journal of Hazardous Materials • 2020

Xueqin Zhang, Georgina Helen Joyce, Andy O Leu et al.

Nature Communications • 2023

Anaerobic methanotrophic archaea (ANME) carry out anaerobic oxidation of methane, thus playing a crucial role in the methane cycle. Previous genomic evidence indicates that multi-heme c-type cytochromes (MHCs) may facilitate the extracellular electron transfer (EET) from ANME to different electron sinks. Here, we provide experimental evidence supporting cytochrome-mediated EET for the reduction of metals and electrodes by 'Candidatus Methanoperedens nitroreducens', an ANME acclimated to nitrate reduction. Ferrous iron-targeted fluorescent assays, metatranscriptomics, and single-cell imaging suggest that 'Ca. M. nitroreducens' uses surface-localized redox-active cytochromes for metal reduction. Electrochemical and Raman spectroscopic analyses also support the involvement of c-type cytochrome-mediated EET for electrode reduction. Furthermore, several genes encoding menaquinone cytochrome type-c oxidoreductases and extracellular MHCs are differentially expressed when different electron acceptors are used.