scholarly journals Electrosynthesis of Commodity Chemicals by an Autotrophic Microbial Community

2012 ◽  
Vol 78 (23) ◽  
pp. 8412-8420 ◽  
Author(s):  
Christopher W. Marshall ◽  
Daniel E. Ross ◽  
Erin B. Fichot ◽  
R. Sean Norman ◽  
Harold D. May
Keyword(s):  
Microbial Community ◽  
Economic Feasibility ◽  
Liquid Volume ◽  
Active Components ◽  
Hydrogen Electrode ◽  
Content Type ◽  
Midpoint Potential ◽  
Redox Active ◽  
Catalytic Wave ◽  
Commodity Chemicals

ABSTRACTA microbial community originating from brewery waste produced methane, acetate, and hydrogen when selected on a granular graphite cathode poised at −590 mV versus the standard hydrogen electrode (SHE) with CO2as the only carbon source. This is the first report on the simultaneous electrosynthesis of these commodity chemicals and the first description of electroacetogenesis by a microbial community. Deep sequencing of the active community 16S rRNA revealed a dynamic microbial community composed of an invariantArchaeapopulation ofMethanobacteriumspp. and a shiftingBacteriapopulation.Acetobacteriumspp. were the most abundantBacteriaon the cathode when acetogenesis dominated. Methane was generally the dominant product with rates increasing from <1 to 7 mM day−1(per cathode liquid volume) and was concomitantly produced with acetate and hydrogen. Acetogenesis increased to >4 mM day−1(accumulated to 28.5 mM over 12 days), and methanogenesis ceased following the addition of 2-bromoethanesulfonic acid. Traces of hydrogen accumulated during initial selection and subsequently accelerated to >11 mM day−1(versus 0.045 mM day−1abiotic production). The hypothesis of electrosynthetic biocatalysis occurring at the microbe-electrode interface was supported by a catalytic wave (midpoint potential of −460 mV versus SHE) in cyclic voltammetry scans of the biocathode, the lack of redox active components in the medium, and the generation of comparatively high amounts of products (even after medium exchange). In addition, the volumetric production rates of these three commodity chemicals are marked improvements for electrosynthesis, advancing the process toward economic feasibility.

scholarly journals Genomic, Proteomic, and Biochemical Analysis of the Organohalide Respiratory Pathway in Desulfitobacterium dehalogenans

2014 ◽  
Vol 197 (5) ◽  
pp. 893-904 ◽  
Author(s):  
Thomas Kruse ◽  
Bram A. van de Pas ◽  
Ariane Atteia ◽  
Klaas Krab ◽  
Wilfred R. Hagen ◽  
...  
Keyword(s):  
Electron Transport ◽  
Electron Acceptor ◽  
Electron Transport Chain ◽  
Biochemical Analysis ◽  
Active Components ◽  
Organohalide Respiration ◽  
Content Type ◽  
Membrane Complex ◽  
Redox Active ◽  
Transport Chain

Desulfitobacterium dehalogenansis able to grow by organohalide respiration using 3-chloro-4-hydroxyphenyl acetate (Cl-OHPA) as an electron acceptor. We used a combination of genome sequencing, biochemical analysis of redox active components, and shotgun proteomics to study elements of the organohalide respiratory electron transport chain. The genome ofDesulfitobacterium dehalogenansJW/IU-DC1Tconsists of a single circular chromosome of 4,321,753 bp with a GC content of 44.97%. The genome contains 4,252 genes, including six rRNA operons and six predicted reductive dehalogenases. One of the reductive dehalogenases, CprA, is encoded by a well-characterizedcprTKZEBACDgene cluster. Redox active components were identified in concentrated suspensions of cells grown on formate and Cl-OHPA or formate and fumarate, using electron paramagnetic resonance (EPR), visible spectroscopy, and high-performance liquid chromatography (HPLC) analysis of membrane extracts. In cell suspensions, these components were reduced upon addition of formate and oxidized after addition of Cl-OHPA, indicating involvement in organohalide respiration. Genome analysis revealed genes that likely encode the identified components of the electron transport chain from formate to fumarate or Cl-OHPA. Data presented here suggest that the first part of the electron transport chain from formate to fumarate or Cl-OHPA is shared. Electrons are channeled from an outward-facing formate dehydrogenase via menaquinones to a fumarate reductase located at the cytoplasmic face of the membrane. When Cl-OHPA is the terminal electron acceptor, electrons are transferred from menaquinones to outward-facing CprA, via an as-yet-unidentified membrane complex, and potentially an extracellular flavoprotein acting as an electron shuttle between the quinol dehydrogenase membrane complex and CprA.

scholarly journals Impact of Substratum Surface on Microbial Community Structure and Treatment Performance in Biological Aerated Filters

2013 ◽  
Vol 80 (1) ◽  
pp. 177-183 ◽  
Author(s):  
Lavane Kim ◽  
Eulyn Pagaling ◽  
Yi Y. Zuo ◽  
Tao Yan
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Bacterial Species ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Rrna Gene ◽  
Content Type ◽  
Property Change ◽  
And Control ◽  
Start Ups

ABSTRACTThe impact of substratum surface property change on biofilm community structure was investigated using laboratory biological aerated filter (BAF) reactors and molecular microbial community analysis. Two substratum surfaces that differed in surface properties were created via surface coating and used to develop biofilms in test (modified surface) and control (original surface) BAF reactors. Microbial community analysis by 16S rRNA gene-based PCR-denaturing gradient gel electrophoresis (DGGE) showed that the surface property change consistently resulted in distinct profiles of microbial populations during replicate reactor start-ups. Pyrosequencing of the bar-coded 16S rRNA gene amplicons surveyed more than 90% of the microbial diversity in the microbial communities and identified 72 unique bacterial species within 19 bacterial orders. Among the 19 orders of bacteria detected,BurkholderialesandRhodocyclalesof theBetaproteobacteriaclass were numerically dominant and accounted for 90.5 to 97.4% of the sequence reads, and their relative abundances in the test and control BAF reactors were different in consistent patterns during the two reactor start-ups. Three of the five dominant bacterial species also showed consistent relative abundance changes between the test and control BAF reactors. The different biofilm microbial communities led to different treatment efficiencies, with consistently higher total organic carbon (TOC) removal in the test reactor than in the control reactor. Further understanding of how surface properties affect biofilm microbial communities and functional performance would enable the rational design of new generations of substrata for the improvement of biofilm-based biological treatment processes.

scholarly journals Arabinose-Induced Catabolite Repression as a Mechanism for Pentose Hierarchy Control inClostridium acetobutylicumATCC 824

mSystems ◽  
2018 ◽  
Vol 3 (5) ◽  
Author(s):  
Matthew D. Servinsky ◽  
Rebecca L. Renberg ◽  
Matthew A. Perisin ◽  
Elliot S. Gerlach ◽  
Sanchao Liu ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Genetic Engineering ◽  
Catabolite Repression ◽  
Clostridium Acetobutylicum ◽  
Regulation Mechanism ◽  
Mrna Levels ◽  
Chemical Production ◽  
Content Type ◽  
Commodity Chemicals ◽  
Pentose Utilization

ABSTRACTBacterial fermentation of carbohydrates from sustainable lignocellulosic biomass into commodity chemicals by the anaerobic bacteriumClostridium acetobutylicumis a promising alternative source to fossil fuel-derived chemicals. Recently, it was demonstrated that xylose is not appreciably fermented in the presence of arabinose, revealing a hierarchy of pentose utilization in this organism (L. Aristilde, I. A. Lewis, J. O. Park, and J. D. Rabinowitz, Appl Environ Microbiol 81:1452–1462, 2015,https://doi.org/10.1128/AEM.03199-14). The goal of the current study is to characterize the transcriptional regulation that occurs and perhaps drives this pentose hierarchy. Carbohydrate consumption rates showed that arabinose, like glucose, actively represses xylose utilization in cultures fermenting xylose. Further, arabinose addition to xylose cultures led to increased acetate-to-butyrate ratios, which indicated a transition of pentose catabolism from the pentose phosphate pathway to the phosphoketolase pathway. Transcriptome sequencing (RNA-Seq) confirmed that arabinose addition to cells actively growing on xylose resulted in increased phosphoketolase (CA_C1343) mRNA levels, providing additional evidence that arabinose induces this metabolic switch. A significant overlap in differentially regulated genes after addition of arabinose or glucose suggested a common regulation mechanism. A putative open reading frame (ORF) encoding a potential catabolite repression phosphocarrier histidine protein (Crh) was identified that likely participates in the observed transcriptional regulation. These results substantiate the claim that arabinose is utilized preferentially over xylose inC. acetobutylicumand suggest that arabinose can activate carbon catabolite repression via Crh. Furthermore, they provide valuable insights into potential mechanisms for altering pentose utilization to modulate fermentation products for chemical production.IMPORTANCEClostridium acetobutylicumcan ferment a wide variety of carbohydrates to the commodity chemicals acetone, butanol, and ethanol. Recent advances in genetic engineering have expanded the chemical production repertoire ofC. acetobutylicumusing synthetic biology. Due to its natural properties and genetic engineering potential, this organism is a promising candidate for converting biomass-derived feedstocks containing carbohydrate mixtures to commodity chemicals via natural or engineered pathways. Understanding how this organism regulates its metabolism during growth on carbohydrate mixtures is imperative to enable control of synthetic gene circuits in order to optimize chemical production. The work presented here unveils a novel mechanism via transcriptional regulation by a predicted Crh that controls the hierarchy of carbohydrate utilization and is essential for guiding robust genetic engineering strategies for chemical production.

scholarly journals Streptomycin-Induced Inflammation Enhances Escherichia coli Gut Colonization Through Nitrate Respiration

mBio ◽  
2013 ◽  
Vol 4 (4) ◽  
Author(s):  
Alanna M. Spees ◽  
Tamding Wangdi ◽  
Christopher A. Lopez ◽  
Dawn D. Kingsbury ◽  
Mariana N. Xavier ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Microbial Community ◽  
Intestinal Inflammation ◽  
Anaerobic Bacteria ◽  
Nitrate Respiration ◽  
Colonization Resistance ◽  
Content Type ◽  
E Coli ◽  
Gut Colonization ◽  
Facultative Anaerobic Bacteria

ABSTRACTTreatment with streptomycin enhances the growth of human commensalEscherichia coliisolates in the mouse intestine, suggesting that the resident microbial community (microbiota) can inhibit the growth of invading microbes, a phenomenon known as “colonization resistance.” However, the precise mechanisms by which streptomycin treatment lowers colonization resistance remain obscure. Here we show that streptomycin treatment rendered mice more susceptible to the development of chemically induced colitis, raising the possibility that the antibiotic might lower colonization resistance by changing mucosal immune responses rather than by preventing microbe-microbe interactions. Investigation of the underlying mechanism revealed a mild inflammatory infiltrate in the cecal mucosa of streptomycin-treated mice, which was accompanied by elevated expression ofNos2, the gene that encodes inducible nitric oxide synthase. In turn, this inflammatory response enhanced the luminal growth ofE. coliby nitrate respiration in aNos2-dependent fashion. These data identify low-level intestinal inflammation as one of the factors responsible for the loss of resistance toE. colicolonization after streptomycin treatment.IMPORTANCEOur intestine is host to a complex microbial community that confers benefits by educating the immune system and providing niche protection. Perturbation of intestinal communities by streptomycin treatment lowers “colonization resistance” through unknown mechanisms. Here we show that streptomycin increases the inflammatory tone of the intestinal mucosa, thereby making the bowel more susceptible to dextran sulfate sodium treatment and boosting theNos2-dependent growth of commensalEscherichia coliby nitrate respiration. These data point to the generation of alternative electron acceptors as a by-product of the inflammatory host response as an important factor responsible for lowering resistance to colonization by facultative anaerobic bacteria such asE. coli.

scholarly journals The Chthonomonas calidirosea Genome Is Highly Conserved across Geographic Locations and Distinct Chemical and Microbial Environments in New Zealand's Taupō Volcanic Zone

2016 ◽  
Vol 82 (12) ◽  
pp. 3572-3581 ◽  
Author(s):  
Kevin C. Lee ◽  
Matthew B. Stott ◽  
Peter F. Dunfield ◽  
Curtis Huttenhower ◽  
Ian R. McDonald ◽  
...  
Keyword(s):  
Microbial Community ◽  
Genomic Sequence ◽  
Geographic Distance ◽  
Taupo Volcanic Zone ◽  
Rrna Gene ◽  
Volcanic Zone ◽  
Carbohydrate Utilization ◽  
Content Type ◽  
Local Selection ◽  
Stochastic Dispersal

ABSTRACTChthonomonas calidiroseaT49Tis a low-abundance, carbohydrate-scavenging, and thermophilic soil bacterium with a seemingly disorganized genome. We hypothesized that theC. calidiroseagenome would be highly responsive to local selection pressure, resulting in the divergence of its genomic content, genome organization, and carbohydrate utilization phenotype across environments. We tested this hypothesis by sequencing the genomes of fourC. calidiroseaisolates obtained from four separate geothermal fields in the Taupō Volcanic Zone, New Zealand. For each isolation site, we measured physicochemical attributes and defined the associated microbial community by 16S rRNA gene sequencing. Despite their ecological and geographical isolation, the genome sequences showed low divergence (maximum, 1.17%). Isolate-specific variations included single-nucleotide polymorphisms (SNPs), restriction-modification systems, and mobile elements but few major deletions and no major rearrangements. The 50-fold variation inC. calidirosearelative abundance among the four sites correlated with site environmental characteristics but not with differences in genomic content. Conversely, the carbohydrate utilization profiles of theC. calidiroseaisolates corresponded to the inferred isolate phylogenies, which only partially paralleled the geographical relationships among the sample sites. Genomic sequence conservation does not entirely parallel geographic distance, suggesting that stochastic dispersal and localized extinction, which allow for rapid population homogenization with little restriction by geographical barriers, are possible mechanisms ofC. calidiroseadistribution. This dispersal and extinction mechanism is likely not limited toC. calidiroseabut may shape the populations and genomes of many other low-abundance free-living taxa.IMPORTANCEThis study compares the genomic sequence variations and metabolisms of four strains ofChthonomonas calidirosea, a rare thermophilic bacterium from the phylumArmatimonadetes. It additionally compares the microbial communities and chemistry of each of the geographically distinct sites from which the fourC. calidiroseastrains were isolated.C. calidiroseawas previously reported to possess a highly disorganized genome, but it was unclear whether this reflected rapid evolution. Here, we show that each isolation site has a distinct chemistry and microbial community, but despite this, theC. calidiroseagenome is highly conserved across all isolation sites. Furthermore, genomic sequence differences only partially paralleled geographic distance, suggesting thatC. calidiroseagenotypes are not primarily determined by adaptive evolution. Instead, the presence ofC. calidiroseamay be driven by stochastic dispersal and localized extinction. This ecological mechanism may apply to many other low-abundance taxa.

scholarly journals Prospects of applying 3-D printing to economics of remote communities

2018 ◽  
Vol 12 (4) ◽  
pp. 488-509 ◽  
Author(s):  
Svetlana Obydenkova ◽  
Nicholas C. Anzalone ◽  
Joshua M. Pearce
Keyword(s):  
Open Source ◽  
Case Studies ◽  
Raw Materials ◽  
Economic Feasibility ◽  
Environmental Benefits ◽  
Remote Communities ◽  
Fused Filament Fabrication ◽  
Content Type ◽  
Climate Conditions ◽  
Reindeer Herder

Purpose Isolated communities face a variety of inconveniences including severe remoteness, poor roads and extreme climate conditions, resulting in the lack of security of supply chains and exorbitant prices for cargo delivery. This paper aims to investigate the present advantages and prospects of applying 3-D printing to improve economics and everyday life of remote communities, reindeer herder case taken as an example. Design/methodology/approach This study covers the use of a low-cost open-source 3-D printer (RepRap) capable of fused filament fabrication to reduce operating costs for nomadic reindeer herder groups. Three case studies are provided for reindeer-specific applications to probe economic and technical viability of the technology, namely, ear-tags, electric fence components and lasso accessories. Findings 3-D printed objects feature technical characteristics similar to those of analogues available on the market while reducing the price by 63 per cent. Distributed 3-D printing reduces the cost of raw materials by 68 per cent and shipping costs by 50 because of lower trip frequency. If all reindeer herders globally were to adopt distributed manufacturing of the three aforementioned sample items only, their annual savings from such solution would amount to US$2m. The paper discovers other economic, entrepreneurial, technical and environmental opportunities offered by 3-D printing put to service the needs of remote communities. Research limitations As the paper is the first-ever study of 3-D printing potential applied to the reindeer husbandry case, it is based on a more thorough analysis of the techno-economic feasibility of the technology, while cultural and entrepreneurial factors have been discussed as preconditions only. Practical implications The paper might serve as a valuable source of information for entrepreneurs, as well as for students and academics for further case studies in this area. Originality/value In remote conditions, 3-D printing offers a more sustainable way of good manufacturing. Numerous open source designs already available for specialists, financial effectiveness, environmental benefits and vast opportunities for entrepreneurs are among the most promising advantages of the technology.

scholarly journals A Previously Uncharacterized, Nonphotosynthetic Member of the Chromatiaceae Is the Primary CO2-Fixing Constituent in a Self-Regenerating Biocathode

2014 ◽  
Vol 81 (2) ◽  
pp. 699-712 ◽  
Author(s):  
Zheng Wang ◽  
Dagmar H. Leary ◽  
Anthony P. Malanoski ◽  
Robert W. Li ◽  
W. Judson Hervey ◽  
...  
Keyword(s):  
Microbial Fuel Cells ◽  
Iron Oxidation ◽  
Extracellular Electron Transfer ◽  
Hydrogen Electrode ◽  
Content Type ◽  
Iron Oxidizing Bacteria ◽  
Distinct Cluster ◽  
The Family

ABSTRACTBiocathode extracellular electron transfer (EET) may be exploited for biotechnology applications, including microbially mediated O2reduction in microbial fuel cells and microbial electrosynthesis. However, biocathode mechanistic studies needed to improve or engineer functionality have been limited to a few select species that form sparse, homogeneous biofilms characterized by little or no growth. Attempts to cultivate isolates from biocathode environmental enrichments often fail due to a lack of some advantage provided by life in a consortium, highlighting the need to study and understand biocathode consortiain situ. Here, we present metagenomic and metaproteomic characterization of a previously described biocathode biofilm (+310 mV versus a standard hydrogen electrode [SHE]) enriched from seawater, reducing O2, and presumably fixing CO2for biomass generation. Metagenomics identified 16 distinct cluster genomes, 15 of which could be assigned at the family or genus level and whose abundance was roughly divided betweenAlpha- andGammaproteobacteria. A total of 644 proteins were identified from shotgun metaproteomics and have been deposited in the the ProteomeXchange with identifier PXD001045. Cluster genomes were used to assign the taxonomic identities of 599 proteins, withMarinobacter,Chromatiaceae, andLabrenziathe most represented. RubisCO and phosphoribulokinase, along with 9 other Calvin-Benson-Bassham cycle proteins, were identified fromChromatiaceae. In addition, proteins similar to those predicted for iron oxidation pathways of known iron-oxidizing bacteria were observed forChromatiaceae. These findings represent the first description of putative EET and CO2fixation mechanisms for a self-regenerating, self-sustaining multispecies biocathode, providing potential targets for functional engineering, as well as new insights into biocathode EET pathways using proteomics.

scholarly journals A thylakoid membrane-bound and redox-active rubredoxin (RBD1) functions in de novo assembly and repair of photosystem II

2019 ◽  
Vol 116 (33) ◽  
pp. 16631-16640 ◽  
Author(s):  
José G. García-Cerdán ◽  
Ariel L. Furst ◽  
Kent L. McDonald ◽  
Danja Schünemann ◽  
Matthew B. Francis ◽  
...  
Keyword(s):  
Photosystem Ii ◽  
Thylakoid Membrane ◽  
De Novo Assembly ◽  
Biochemical Characterization ◽  
De Novo ◽  
Midpoint Potential ◽  
Photosynthetic Organisms ◽  
Redox Active ◽  
Photooxidative Damage

Photosystem II (PSII) undergoes frequent photooxidative damage that, if not repaired, impairs photosynthetic activity and growth. How photosynthetic organisms protect vulnerable PSII intermediate complexes during de novo assembly and repair remains poorly understood. Here, we report the genetic and biochemical characterization of chloroplast-located rubredoxin 1 (RBD1), a PSII assembly factor containing a redox-active rubredoxin domain and a single C-terminal transmembrane α-helix (TMH) domain. RBD1 is an integral thylakoid membrane protein that is enriched in stroma lamellae fractions with the rubredoxin domain exposed on the stromal side. RBD1 also interacts with PSII intermediate complexes containing cytochrome b559. Complementation of the Chlamydomonas reinhardtii (hereafter Chlamydomonas) RBD1-deficient 2pac mutant with constructs encoding RBD1 protein truncations and site-directed mutations demonstrated that the TMH domain is essential for de novo PSII assembly, whereas the rubredoxin domain is involved in PSII repair. The rubredoxin domain exhibits a redox midpoint potential of +114 mV and is proficient in 1-electron transfers to a surrogate cytochrome c in vitro. Reduction of oxidized RBD1 is NADPH dependent and can be mediated by ferredoxin-NADP+ reductase (FNR) in vitro. We propose that RBD1 participates, together with the cytochrome b559, in the protection of PSII intermediate complexes from photooxidative damage during de novo assembly and repair. This role of RBD1 is consistent with its evolutionary conservation among photosynthetic organisms and the fact that it is essential in photosynthetic eukaryotes.

scholarly journals Electrochemical, Spectroscopic, and Computational Investigations on Redox Reactions of Selenium Species on Galena Surfaces

Minerals ◽  
2019 ◽  
Vol 9 (7) ◽  
pp. 437 ◽  
Author(s):  
Peter Cook ◽  
YoungJae Kim ◽  
Ke Yuan ◽  
Maria C. Marcano ◽  
Udo Becker
Keyword(s):  
Photoelectron Spectroscopy ◽  
Redox Reactions ◽  
Redox Potentials ◽  
Free Energies ◽  
Cathodic Peak ◽  
Redox Transformation ◽  
Hydrogen Electrode ◽  
Midpoint Potential ◽  
Ph Conditions ◽  
Cv Measurements

Despite previous studies investigating selenium (Se) redox reactions in the presence of semiconducting minerals, Se redox reactions mediated by galena (PbS) are poorly understood. In this study, the redox chemistry of Se on galena is investigated over a range of environmentally relevant Eh and pH conditions (+0.3 to −0.6 V vs. standard hydrogen electrode, SHE; pH 4.6) using a combination of electrochemical, spectroscopic, and computational approaches. Cyclic voltammetry (CV) measurements reveal one anodic/cathodic peak pair at a midpoint potential of +30 mV (vs. SHE) that represents reduction and oxidation between HSeO3− and H2Se/HSe−. Two peak pairs with midpoint potentials of −400 and −520 mV represent the redox transformation from Se(0) to HSe− and H2Se species, respectively. The changes in Gibbs free energies of adsorption of Se species on galena surfaces as a function of Se oxidation state were modeled using quantum-mechanical calculations and the resulting electrochemical peak shifts are (−0.17 eV for HSeO3−/H2Se, −0.07 eV for HSeO3−/HSe−, 0.15 eV for Se(0)/HSe−, and −0.15 eV for Se(0)/H2Se). These shifts explain deviation between Nernstian equilibrium redox potentials and observed midpoint potentials. X-ray photoelectron spectroscopy (XPS) analysis reveals the formation of Se(0) potentials below −100 mV and Se(0) and Se(−II) species at potentials below −400 mV.

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