A novel ecological role of the Firmicutes identified in thermophilic microbial fuel cells

Wrighton, Kelly; Agbo, Peter; Warnecke, Falk; Weber, Karrie A.; Brodie, Eoin L.; DeSantis, Todd Z.; Hugenholtz, Philip; Andersen, Gary L.; Coates, John D.

doi:10.1038/ismej.2008.48

Cited by 313 publications

(172 citation statements)

References 50 publications

(67 reference statements)

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“…Viruses were probably obtained on filters by flocculation with iron, which precipitated during the filtering process when the samples were first exposed to oxygen 34 . Total nucleic acids were extracted from the filter using the PowerSoil DNA Isolation kit (MoBio) for Marcellus fluids and a modified phenol chloroform nucleic extraction 35 for Utica fluids and enrichment cultures. Total cells with intact membranes were enumerated from unfiltered fluid samples for calibrated gate ranges on a Guava EasyCyte flow cytometer (EMD Millipore).…”

Section: Methodsmentioning

confidence: 99%

Microbial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales

et al. 2016

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Hydraulic fracturing is the industry standard for extracting hydrocarbons from shale formations. Attention has been paid to the economic benefits and environmental impacts of this process, yet the biogeochemical changes induced in the deep subsurface are poorly understood. Recent single-gene investigations revealed that halotolerant microbial communities were enriched after hydraulic fracturing. Here, the reconstruction of 31 unique genomes coupled to metabolite data from the Marcellus and Utica shales revealed that many of the persisting organisms play roles in methylamine cycling, ultimately supporting methanogenesis in the deep biosphere. Fermentation of injected chemical additives also sustains long-term microbial persistence, while thiosulfate reduction could produce sulfide, contributing to reservoir souring and infrastructure corrosion. Extensive links between viruses and microbial hosts demonstrate active viral predation, which may contribute to the release of labile cellular constituents into the extracellular environment. Our analyses show that hydraulic fracturing provides the organismal and chemical inputs for colonization and persistence in the deep terrestrial subsurface. S hale gas accounts for one-third of natural gas energy resources worldwide. It has been estimated that shale gas will provide half of the natural gas in the USA, annually, by 2040, with the Marcellus shale in the Appalachian Basin projected to produce three times more than any other formation 1 . Recovery of these hydrocarbons is dependent on hydraulic fracturing technologies, where the high-pressure injection of water and chemical additives generates extensive fractures in the shale matrix. Hydrocarbons trapped in tiny pore spaces are subsequently released and collected at the wellpad surface, together with a portion of the injected fluids that have reacted with the shale formation. The mixture of injected fluids and hydrocarbons collected is referred to as 'produced fluids'.Microbial metabolism and growth in hydrocarbon reservoirs has both positive and negative impacts on energy recovery. Whereas stimulation of methanogens in coal beds enhances energy recovery 2 , bacterial hydrogen sulfide production ('reservoir souring') decreases profits and contributes to corrosion and the risk of environmental contamination 3 . Additionally, biomass accumulation within newly generated fractures may reduce their permeability, decreasing natural gas recovery. Despite these potential microbial impacts, little is known about the function and activity of microorganisms in hydraulically fractured shale.Initial work by our group and others 4-9 used single marker gene analyses to identify microorganisms from several geographically distinct shale formations. These analyses showed similar halotolerant taxa in produced fluids several months after hydraulic fracturing. To assign functional roles to these organisms, we conducted metagenomic and metabolite analyses on input and produced fluids up to a year after hydraulic fracturing (HF) from two Appala...

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Section: Methodsmentioning

confidence: 99%

Microbial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales

et al. 2016

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“…Application of the PhyloChip (Affymetrix, Santa Clara, CA, USA) to cathode biofilm communities offered a higherresolution analysis of the microbial community composition than previously reported methods Wrighton et al, 2008), and thus the possibility of uncovering more diversity than was previously observed in these systems. We restricted our analysis to the active members of the communities by monitoring 16S rRNA (rather than the 16S rRNA gene), which is a more responsive biomarker and a better surrogate for microbial activity in bacterial communities (Lueders et al, 2004).…”

Section: Introductionmentioning

confidence: 99%

“…The graphite biofilms were extracted as described with the exception that Trizol was used in the place of CTAB extraction buffer (Wrighton et al, 2008). RNA samples were treated using Ambion's Turbo DNase (Ambion, Austin, TX, USA).…”

Section: Analysis and Electrochemical Calculationsmentioning

confidence: 99%

“…Only samples showing negative results (no amplification) were reverse transcribed to cDNA using Superscript II reverse transcriptase per the manufacturer's protocol (Invitrogen, Carlsbad, CA, USA). Bacterial 16S rRNA genes were amplified from cDNA using universal primers 27F (5 0 -AGAGTTTGATCCTGGCT CAG-3 0 ) and 1492R (5 0 -GGTTACCTTGTTACGACTT-3 0 )n. PCR amplifications and PhyloChip hybridization, staining and detection were performed as described previously (Wrighton et al, 2008).…”

Section: Analysis and Electrochemical Calculationsmentioning

confidence: 99%

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Bacterial community structure corresponds to performance during cathodic nitrate reduction

et al. 2010

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Microbial fuel cells (MFCs) have applications other than electricity production, including the capacity to power desirable reactions in the cathode chamber. However, current knowledge of the microbial ecology and physiology of biocathodes is minimal, and as a result more research dedicated to understanding the microbial communities active in cathode biofilms is required. Here we characterize the microbiology of denitrifying bacterial communities stimulated by reducing equivalents generated from the anodic oxidation of acetate. We analyzed biofilms isolated from two types of cathodic denitrification systems: (1) a loop format where the effluent from the carbon oxidation step in the anode is subjected to a nitrifying reactor which is fed to the cathode chamber and (2) an alternative non-loop format where anodic and cathodic feed streams are separated. The results of our study indicate the superior performance of the loop reactor in terms of enhanced current production and nitrate removal rates. We hypothesized that phylogenetic or structural features of the microbial communities could explain the increased performance of the loop reactor. We used PhyloChip with 16S rRNA (cDNA) and fluorescent in situ hybridization to characterize the active bacterial communities. Our study results reveal a greater richness, as well as an increased phylogenetic diversity, active in denitrifying biofilms than was previously identified in cathodic systems. Specifically, we identified Proteobacteria, Firmicutes and Chloroflexi members that were dominant in denitrifying cathodes. In addition, our study results indicate that it is the structural component, in terms of bacterial richness and evenness, rather than the phylogenetic affiliation of dominant bacteria, that best corresponds to cathode performance.

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“…A hemi-transverse incision of the P3 hindgut compartment was made using a needle, and 2 ml of 100 mM phosphate-buffered saline was mixed with luminal contents squeezed out of the P3 compartment. The samples were pooled, maintained on ice, and DNA was isolated using aluminum ammonium sulfate added to cetyl trimethylammonium bromide, followed by a polyethylene glycol precipitation (Wrighton et al, 2008).…”

Section: Dna Extractionmentioning

confidence: 99%

Experimental factors affecting PCR-based estimates of microbial species richness and evenness

Engelbrektson¹,

Kunin²,

et al. 2010

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Pyrosequencing of 16S rRNA gene amplicons for microbial community profiling can, for equivalent costs, yield more than two orders of magnitude more sensitivity than traditional PCR cloning and Sanger sequencing. With this increased sensitivity and the ability to analyze multiple samples in parallel, it has become possible to evaluate several technical aspects of PCR-based community structure profiling methods. We tested the effect of amplicon length and primer pair on estimates of species richness (number of species) and evenness (relative abundance of species) by assessing the potentially tractable microbial community residing in the termite hindgut. Two regions of the 16S rRNA gene were sequenced from one of two common priming sites, spanning the V1-V2 or V8 regions, using amplicons ranging in length from 352 to 1443 bp. Our results show that both amplicon length and primer pair markedly influence estimates of richness and evenness. However, estimates of species evenness are consistent among different primer pairs targeting the same region. These results highlight the importance of experimental methodology when comparing diversity estimates across communities.

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A novel ecological role of the Firmicutes identified in thermophilic microbial fuel cells

Cited by 313 publications

References 50 publications

Microbial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales

Microbial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales

Bacterial community structure corresponds to performance during cathodic nitrate reduction

Experimental factors affecting PCR-based estimates of microbial species richness and evenness

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