scholarly journals Disentangling the syntrophic electron transfer mechanisms of Candidatus geobacter eutrophica through electrochemical stimulation and machine learning

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Heyang Yuan ◽  
Xuehao Wang ◽  
Tzu-Yu Lin ◽  
Jinha Kim ◽  
Wen-Tso Liu
Keyword(s):  
Machine Learning ◽  
Electron Transfer ◽  
Hydrogen Transfer ◽  
Draft Genome ◽  
Extracellular Electron Transfer ◽  
Hydrogen Metabolism ◽  
Genetic Potential ◽  
Fermentative Bacteria ◽  
Genes Encoding ◽  
Transfer Mechanisms

AbstractInterspecies hydrogen transfer (IHT) and direct interspecies electron transfer (DIET) are two syntrophy models for methanogenesis. Their relative importance in methanogenic environments is still unclear. Our recent discovery of a novel species Candidatus Geobacter eutrophica with the genetic potential of IHT and DIET may serve as a model species to address this knowledge gap. To experimentally demonstrate its DIET ability, we performed electrochemical enrichment of Ca. G. eutrophica-dominating communities under 0 and 0.4 V vs. Ag/AgCl based on the presumption that DIET and extracellular electron transfer (EET) share similar metabolic pathways. After three batches of enrichment, Geobacter OTU650, which was phylogenetically close to Ca. G. eutrophica, was outcompeted in the control but remained abundant and active under electrochemical stimulation, indicating Ca. G. eutrophica’s EET ability. The high-quality draft genome further showed high phylogenomic similarity with Ca. G. eutrophica, and the genes encoding outer membrane cytochromes and enzymes for hydrogen metabolism were actively expressed. A Bayesian network was trained with the genes encoding enzymes for alcohol metabolism, hydrogen metabolism, EET, and methanogenesis from dominant fermentative bacteria, Geobacter, and Methanobacterium. Methane production could not be accurately predicted when the genes for IHT were in silico knocked out, inferring its more important role in methanogenesis. The genomics-enabled machine learning modeling approach can provide predictive insights into the importance of IHT and DIET.

scholarly journals Disentangling Syntrophic Electron Transfer Mechanisms in Methanogenesis Through Electrochemical Stimulation, Omics, and Machine Learning

2021 ◽  
Author(s):  
Heyang Yuan ◽  
Xuehao Wang ◽  
Tzu-Yu Lin ◽  
Jinha Kim ◽  
Wen-Tso Liu
Keyword(s):  
Machine Learning ◽  
Electron Transfer ◽  
Bayesian Network ◽  
Methane Production ◽  
Extracellular Electron Transfer ◽  
Hydrogen Metabolism ◽  
Electrochemical Reactors ◽  
The Core ◽  
Modeling Approach ◽  
Genes Encoding

Abstract Background: Interspecies hydrogen transfer (IHT) and direct interspecies electron transfer (DIET) are two syntrophy models for methanogenesis. Their relative importance in methanogenic environments is still unclear. Our recent discovery of a novel species Candidatus Geobacter eutrophica with the genetic potential of IHT and DIET may serve as a model species to address this knowledge gap. Results: To experimentally demonstrate its DIET ability, we performed electrochemical enrichment of Ca. G. eutrophica-dominating communities under 0 and 0.4 V vs. Ag/AgCl based on the presumption that DIET and extracellular electron transfer (EET) share similar metabolic pathways. After three batches of enrichment, acetate accumulated in all reactors, while propionate was detected only in the electrochemical reactors. Four dominant fermentative bacteria were identified in the core population, and metatranscriptomics analysis suggested that they were responsible for the degradation of fructose and ethanol to propionate, propanol, acetate, and H2. Geobacter OTU650, which was phylogenetically close to Ca. G. eutrophica, was outcompeted in the control but remained abundant and active under electrochemical stimulation. The results thus confirmed Ca. G. eutrophica’s EET ability. The high-quality draft genome (completeness 99.4%, contamination 0.6%) further showed high phylogenomic similarity with Ca. G. eutrophica, and the genes encoding outer membrane cytochromes and enzymes for hydrogen metabolism were actively expressed. Redundancy analysis and a Bayesian network constructed with the core population predicted the importance of Ca. G. eutrophica-related OTU650 to methane production. The Bayesian network modeling approach was also applied to the genes encoding enzymes for alcohol metabolism, hydrogen metabolism, EET, and methanogenesis. Methane production could not be accurately predicted when the genes for IHT were in silico knocked out, inferring its more important role in methanogenesis.Conclusions: Ca. G. eutrophica is electroactive and simultaneously performs IHT and DIET. The results from the metatranscriptomic analysis have provided valuable information for enrichment and isolation of Ca. G. eutrophica. IHT is predicted to have a stronger impact on methane production than DIET in the electrochemical reactors. The genomics-enabled machine learning modeling approach can provide predictive insights into the importance of IHT and DIET.

scholarly journals Modeling biofilms with dual extracellular electron transfer mechanisms

2013 ◽  
Vol 15 (44) ◽  
pp. 19262 ◽  
Author(s):  
Ryan Renslow ◽  
Jerome Babauta ◽  
Andrew Kuprat ◽  
Jim Schenk ◽  
Cornelius Ivory ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Extracellular Electron Transfer ◽  
Transfer Mechanisms

scholarly journals A Hybrid Extracellular Electron Transfer Pathway Enhances the Survival of Vibrio natriegens

2020 ◽  
Vol 86 (19) ◽  
Author(s):  
Bridget E. Conley ◽  
Matthew T. Weinstock ◽  
Daniel R. Bond ◽  
Jeffrey A. Gralnick
Keyword(s):  
Electron Transfer ◽  
Shewanella Oneidensis ◽  
Anaerobic Respiration ◽  
Basic Research ◽  
Extracellular Electron Transfer ◽  
Content Type ◽  
Electron Transfer Pathway ◽  
Sedimentary Environments ◽  
Genetic Potential ◽  
Iron And Manganese

ABSTRACT Vibrio natriegens is the fastest-growing microorganism discovered to date, making it a useful model for biotechnology and basic research. While it is recognized for its rapid aerobic metabolism, less is known about anaerobic adaptations in V. natriegens or how the organism survives when oxygen is limited. Here, we describe and characterize extracellular electron transfer (EET) in V. natriegens, a metabolism that requires movement of electrons across protective cellular barriers to reach the extracellular space. V. natriegens performs extracellular electron transfer under fermentative conditions with gluconate, glucosamine, and pyruvate. We characterized a pathway in V. natriegens that requires CymA, PdsA, and MtrCAB for Fe(III) citrate and Fe(III) oxide reduction, which represents a hybrid of strategies previously discovered in Shewanella and Aeromonas. Expression of these V. natriegens genes functionally complemented Shewanella oneidensis mutants. Phylogenetic analysis of the inner membrane quinol dehydrogenases CymA and NapC in gammaproteobacteria suggests that CymA from Shewanella diverged from Vibrionaceae CymA and NapC. Analysis of sequenced Vibrionaceae revealed that the genetic potential to perform EET is conserved in some members of the Harveyi and Vulnificus clades but is more variable in other clades. We provide evidence that EET enhances anaerobic survival of V. natriegens, which may be the primary physiological function for EET in Vibrionaceae. IMPORTANCE Bacteria from the genus Vibrio occupy a variety of marine and brackish niches with fluctuating nutrient and energy sources. When oxygen is limited, fermentation or alternative respiration pathways must be used to conserve energy. In sedimentary environments, insoluble oxide minerals (primarily iron and manganese) are able to serve as electron acceptors for anaerobic respiration by microorganisms capable of extracellular electron transfer, a metabolism that enables the use of these insoluble substrates. Here, we identify the mechanism for extracellular electron transfer in Vibrio natriegens, which uses a combination of strategies previously identified in Shewanella and Aeromonas. We show that extracellular electron transfer enhanced survival of V. natriegens under fermentative conditions, which may be a generalized strategy among Vibrio spp. predicted to have this metabolism.

Uncovering alternate charge transfer mechanisms in Escherichia coli chemically functionalized with conjugated oligoelectrolytes

2014 ◽  
Vol 50 (60) ◽  
pp. 8223-8226 ◽  
Author(s):  
Victor Bochuan Wang ◽  
Natalia Yantara ◽  
Teck Ming Koh ◽  
Staffan Kjelleberg ◽  
Qichun Zhang ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Electron Transfer ◽  
Charge Transfer ◽  
Extracellular Electron Transfer ◽  
Transfer Mechanisms

Conjugated oligoelectrolytes integrated in Escherichia coli have been proposed to induce release of electroactive cytosolic components, which contributes to extracellular electron transfer.

Extracellular electron transfer mechanisms between microorganisms and minerals

2016 ◽  
Vol 14 (10) ◽  
pp. 651-662 ◽  
Author(s):  
Liang Shi ◽  
Hailiang Dong ◽  
Gemma Reguera ◽  
Haluk Beyenal ◽  
Anhuai Lu ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Extracellular Electron Transfer ◽  
Transfer Mechanisms

scholarly journals Syntrophic interspecies electron transfer drives carbon fixation and growth by Rhodopseudomonas palustris under dark, anoxic conditions

2021 ◽  
Vol 7 (27) ◽  
pp. eabh1852
Author(s):  
Xing Liu ◽  
Lingyan Huang ◽  
Christopher Rensing ◽  
Jie Ye ◽  
Kenneth H. Nealson ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Carbon Fixation ◽  
Rhodopseudomonas Palustris ◽  
Reducing Power ◽  
Extracellular Electron Transfer ◽  
Geobacter Metallireducens ◽  
Electron Transfer Pathway ◽  
Anoxygenic Phototrophs ◽  
Anoxic Environments ◽  
Genes Encoding

In natural anoxic environments, anoxygenic photosynthetic bacteria fix CO2 by photoheterotrophy, photoautotrophy, or syntrophic anaerobic photosynthesis. Here, we describe electroautotrophy, a previously unidentified dark CO2 fixation mode enabled by the electrosyntrophic interaction between Geobacter metallireducens and Rhodopseudomonas palustris. After an electrosyntrophic coculture is formed, electrons are transferred either directly or indirectly (via electron shuttles) from G. metallireducens to R. palustris, thereby providing reducing power and energy for the dark CO2 fixation. Transcriptomic analyses demonstrated the high expression of genes encoding for the extracellular electron transfer pathway in G. metallireducens and the Calvin-Benson-Bassham carbon fixation cycle in R. palustris. Given that sediments constitute one of the most ubiquitous and abundant niches on Earth and that, at depth, most of the sedimentary niche is both anoxic and dark, dark carbon fixation provides a metabolic window for the survival of anoxygenic phototrophs, as well as an as-yet unappreciated contribution to the global carbon cycle.

Hydrogen vs. electron transfer mechanisms in the chain decomposition of phenacyl bromides. Use of isotopic labeling as a mechanistic probe

1996 ◽  
Vol 74 (9) ◽  
pp. 1724-1730 ◽  
Author(s):  
Jocelyn Renaud ◽  
J. C. Scaiano
Keyword(s):  
Electron Transfer ◽  
Charge Transfer ◽  
Key Words ◽  
Hydrogen Transfer ◽  
Isotopic Labeling ◽  
Chain Reaction ◽  
Phenacyl Bromides ◽  
Mechanistic Probe ◽  
A Chain ◽  
Transfer Mechanisms

Ring-substituted α-bromoacetophenones react with alcohols in a chain reaction leading to the corresponding acetophenone, HBr, and the carbonyl compound from oxidation of the alcohol. Two different mechanisms, involving hydrogen or electron transfer by ketyl radicals, have been proposed in order to accommodate the unusual selectivities of these reactions. By studying the efficiency of isotope incorporation from deuterated alcohols, it has been possible to determine the relative contributions from both mechanisms. For example, electron transfer dominates in the case of 2-propanol, while hydrogen transfer is more important for methanol. The results demonstrate that ring substitution in the starting ketone is not a main contributing factor in the discrimination between the two mechanisms. The only parameter that seems to be playing a major role is the nature (reducing strength) of the ketyl radicals. Key words: dehydrobromination, charge transfer, isotope effect, ketyl radicals.

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