Dawn Holmes - Academia.edu (original) (raw)

Papers by Dawn Holmes

bioRxiv (Cold Spring Harbor Laboratory), Jul 26, 2023

Anaerobic microbial corrosion of iron-containing metals causes extensive economic damage. Some mi... more Anaerobic microbial corrosion of iron-containing metals causes extensive economic damage. Some microbes are capable of direct metal-to-microbe electron transfer (electrobiocorrosion), but the prevalence of electrobiocorrosion among diverse methanogens and acetogens is poorly understood because of a lack of tools for their genetic manipulation. Previous studies have suggested that respiration with 316L stainless steel as the electron donor is indicative of electrobiocorrosion because, unlike pure Fe 0 , 316L stainless steel does not abiotically generate H 2 as an intermediary electron carrier. Here we report that all of the methanogens

bioRxiv (Cold Spring Harbor Laboratory), Mar 2, 2023

Direct interspecies electron transfer (DIET) is important in anaerobic communities of environment... more Direct interspecies electron transfer (DIET) is important in anaerobic communities of environmental and practical significance. Other than the need for close physical contact for electrical connections, the interactions of DIET partners are poorly understood. Type VI secretion systems (T6SSs) typically kill competitive microbes. Surprisingly, Geobacter metallireducens highly expressed T6SS genes when DIET-based co-cultures were initiated with Geobacter sulfurreducens. T6SS gene expression was lower when the electron shuttle anthraquinone-2,6-disulfonate was added to alleviate the need for interspecies contact. Disruption of hcp, the G. metallireducens gene for the main T6SS needle-tube protein subunit, and the most highly upregulated gene in DIET-grown cells, eliminated the long lag periods required for the initiation of DIET. The mutation did not aid DIET in the presence of granular activated carbon, consistent with the fact that DIET partners do not make physical contact when electrically connected through conductive materials. The hcp-deficient mutant also established DIET quicker with Methanosarcina barkeri. However, the mutant also reduced Fe(III) oxide faster than the wild-type strain, a phenotype not expected from the loss of the T6SS. Quantitative PCR revealed greater gene transcript abundance for key components of extracellular electron transfer in the hcp-deficient mutant versus the wild-type strain, potentially accounting for the faster Fe(III) oxide reduction and impact on DIET. The results highlight that interspecies interactions beyond electrical connections may influence DIET effectiveness. The unexpected increase in the expression of genes for extracellular electron transport components when hcp was deleted emphasize the complexities in evaluating the electromicrobiology of highly adaptable Geobacter species.

RSC Advances, 2019

Geobacter anodireducensis unique in that it can generate high current densities in bioelectrochem... more Geobacter anodireducensis unique in that it can generate high current densities in bioelectrochemical systems (BES) operating under high salt conditions.

The Wilson Bulletin, 2005

Abstract We studied the breeding ecology of the critically endangered Puaiohi (Myadestes palmeri)... more Abstract We studied the breeding ecology of the critically endangered Puaiohi (Myadestes palmeri), a poorly known Hawaiian thrush endemic to the island of Kauai. From 1996 through 1998, we monitored 96 active nests over the course of three breeding seasons. Mean clutch size was 2.0, and pairs produced an average of 1.5 fledglings/successful nest. Pairs renested after failure and some raised multiple broods. The mean annual reproductive effort was 2.1 nesting attempts/territory, and pairs produced a mean 1.1 fledglings/attempt. Large differences in nesting effort and productivity occurred among years, with mean number of fledglings/territory ranging from 0.4 to 4.9. Predation by owls (probably Short-eared Owls, Asio flammeus) and introduced rats (probably black rats, Rattus rattus) accounted for most nest failures. The presence of non-breeding floaters in the population and their largely unsuccessful attempts to gain territories in the study area suggest that the population is near carrying capacity. The high reproductive potential of the Puaiohi may help explain its persistence despite the species' historical rarity.

Standards in Genomic Sciences, 2015

Geoglobus ahangari" strain 234 T is an obligate Fe(III)-reducing member of the Archaeoglobales, w... more Geoglobus ahangari" strain 234 T is an obligate Fe(III)-reducing member of the Archaeoglobales, within the archaeal phylum Euryarchaeota, isolated from the Guaymas Basin hydrothermal system. It grows optimally at 88°C by coupling the reduction of Fe(III) oxides to the oxidation of a wide range of compounds, including long-chain fatty acids, and also grows autotrophically with hydrogen and Fe(III). It is the first archaeon reported to use a direct contact mechanism for Fe(III) oxide reduction, relying on a single archaellum for locomotion, numerous curled extracellular appendages for attachment, and outer-surface heme-containing proteins for electron transfer to the insoluble Fe(III) oxides. Here we describe the annotation of the genome of "G. ahangari" strain 234 T and identify components critical to its versatility in electron donor utilization and obligate Fe(III) respiratory metabolism at high temperatures. The genome comprises a single, circular chromosome of 1,770,093 base pairs containing 2034 protein-coding genes and 52 RNA genes. In addition, emended descriptions of the genus "Geoglobus" and species "G. ahangari" are described.

FEMS microbiology letters, 2015

Two pathways for para-cresol (p-cresol) degradation by anaerobic bacteria have been elucidated; o... more Two pathways for para-cresol (p-cresol) degradation by anaerobic bacteria have been elucidated; one involves fumarate addition at the methyl group of p-cresol by a hydroxylbenzylsuccinate synthase protein while the other utilizes a methylhydroxylase protein (PCMH) to catalyze hydroxylation of the methyl group of p-cresol. In Geobacter metallireducens, in vitro enzymatic assays showed that p-cresol is degraded via the methylhydroxylation pathway. However, prior to this study these results had not been confirmed by genetic analyses. In this work, the gene coding for benzylsuccinate-CoA dehydrogenase (bbsG), an enzyme required for toluene degradation by G. metallireducens that is homologous to the p-hydroxybenzylsuccinyl-CoA dehydrogenase involved in p-cresol degradation by Desulfobacula toluolica Tol2 via fumarate addition, and the gene encoding the alpha prime subunit of PCMH (pcmI), were deleted to investigate the possibility of co-existing p-cresol degradation pathways in G. metall...

Advances in microbial physiology, 2004

Dissimilatory Fe(III) and Mn(IV) reduction has an important influence on the geochemistry of mode... more Dissimilatory Fe(III) and Mn(IV) reduction has an important influence on the geochemistry of modern environments, and Fe(III)-reducing microorganisms, most notably those in the Geobacteraceae family, can play an important role in the bioremediation of subsurface environments contaminated with organic or metal contaminants. Microorganisms with the capacity to conserve energy from Fe(III) and Mn(IV) reduction are phylogenetically dispersed throughout the Bacteria and Archaea. The ability to oxidize hydrogen with the reduction of Fe(III) is a highly conserved characteristic of hyperthermophilic microorganisms and one Fe(III)-reducing Archaea grows at the highest temperature yet recorded for any organism. Fe(III)- and Mn(IV)-reducing microorganisms have the ability to oxidize a wide variety of organic compounds, often completely to carbon dioxide. Typical alternative electron acceptors for Fe(III) reducers include oxygen, nitrate, U(VI) and electrodes. Unlike other commonly considered e...

Standards in Genomic Sciences, 2011

Ferroglobus placidus belongs to the order Archaeoglobales within the archaeal phylum Euryarchaeot... more Ferroglobus placidus belongs to the order Archaeoglobales within the archaeal phylum Euryarchaeota. Strain AEDII12DO is the type strain of the species and was isolated from a shallow marine hydrothermal system at Vulcano, Italy. It is a hyperthermophilic, anaerobic chemolithoautotroph, but it can also use a variety of aromatic compounds as electron donors. Here we describe the features of this organism together with the complete genome sequence and annotation. The 2,196,266 bp genome with its 2,567 protein-coding and 55 RNA genes was sequenced as part of a DOE Joint Genome Institute Laboratory Sequencing Program (LSP) project.

Nature Biotechnology, 2002

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 2002

A novel, regular to irregular, coccoid-shaped, anaerobic, Fe(III)-reducing microorganism was isol... more A novel, regular to irregular, coccoid-shaped, anaerobic, Fe(III)-reducing microorganism was isolated from the Guaymas Basin hydrothermal system at a depth of 2000 m. Isolation was carried out with a new technique using Fe(III) oxide as the electron acceptor for the recovery of colonies on solid medium. The isolate, designated strain 234 T , was strictly anaerobic and exhibited a tumbling motility. The cells had a single flagellum. Strain 234 T grew at temperatures between 65 and 90 SC, with an optimum at about 88 SC. The optimal salt concentration for growth was around 19 g l N1. The isolate was capable of growth with H 2 as the sole electron donor coupled to the reduction of Fe(III) without the need for an organic carbon source. This is the first example of a dissimilatory Fe(III)-reducing microorganism capable of growing autotrophically on hydrogen. In addition to molecular hydrogen, strain 234 T oxidizes pyruvate, acetate, malate, succinate, peptone, formate, fumarate, yeast extract, glycerol, isoleucine, arginine, serine, glutamine, asparagine, stearate, palmitate, valerate, butyrate and propionate with the reduction of Fe(III). This isolate is the first example of a hyperthermophile capable of oxidizing long-chain fatty acids anaerobically. Isolate 234 T grew exclusively with Fe(III) as the sole electron acceptor. The GMC content was 587 mol %. Based on detailed analysis of its 16S rDNA sequence, GMC content, distinguishing physiological features and metabolism, strain 234 T is proposed to represent a novel genus within the Archaeoglobales. The name proposed for strain 234 T is Geoglobus ahangari gen. nov., sp. nov.

Environmental Microbiology Reports, 2013

Removal of selenium from groundwater was documented during injection of acetate into a uranium-co... more Removal of selenium from groundwater was documented during injection of acetate into a uranium-contaminated aquifer near Rifle, Colorado (USA). Bioreduction of aqueous selenium to its elemental form (Se0) concentrated it within mineralized biofilms affixed to tubing used to circulate acetate-amended groundwater. Scanning and transmission electron microscopy revealed close association between Se0 precipitates and cell surfaces, with Se0 aggregates having a diameter of 50-60 nm. Accumulation of Se0 within biofilms occurred over a three-week interval at a rate of c. 9 mg Se0 m(-2) tubing day(-1). Removal was inferred to result from the activity of a mixed microbial community within the biofilms capable of coupling acetate oxidation to the reduction of oxygen, nitrate and selenate. Phylogenetic analysis of the biofilm revealed a community dominated by strains of Dechloromonas sp. and Thauera sp., with isolates exhibiting genetic similarity to the latter known to reduce selenate to Se0. Enrichment cultures of selenate-respiring microorganisms were readily established using Rifle site groundwater and acetate, with cultures dominated by strains closely related to D. aromatica (96-99% similarity). Predominance of Dechloromonas sp. in recovered biofilms and enrichments suggests this microorganism may play a role in the removal of selenium oxyanions present in Se-impacted groundwaters and sediments.

The genome of Geobacter bemidjiensis, exemplar for the subsurface clade of Geobacter species that... more The genome of Geobacter bemidjiensis, exemplar for the subsurface clade of Geobacter species that predominate in Fe(III)-reducing subsurface environments

Applied and Environmental Microbiology, 2002

It has recently been recognized that the ability to use Fe(III) as a terminal electron acceptor i... more It has recently been recognized that the ability to use Fe(III) as a terminal electron acceptor is a highly conserved characteristic in hyperthermophilic microorganisms. This suggests that it may be possible to recover as-yet-uncultured hyperthermophiles in pure culture if Fe(III) is used as an electron acceptor. As part of a study of the microbial diversity of the Obsidian Pool area in Yellowstone National Park, Wyo., hot sediment samples were used as the inoculum for enrichment cultures in media containing hydrogen as the sole electron donor and poorly crystalline Fe(III) oxide as the electron acceptor. A pure culture was recovered on solidified, Fe(III) oxide medium. The isolate, designated FW-1a, is a hyperthermophilic anaerobe that grows exclusively by coupling hydrogen oxidation to the reduction of poorly crystalline Fe(III) oxide. Organic carbon is not required for growth. Magnetite is the end product of Fe(III) oxide reduction under the culture conditions evaluated. The cell...

chromes mediate electron transfer to electrodesD. E. Holmes et al.

mBio, 2021

The conversion of organic matter to methane plays an important role in the global carbon cycle an... more The conversion of organic matter to methane plays an important role in the global carbon cycle and is an effective strategy for converting wastes to a useful biofuel. The reduction of carbon dioxide to methane accounts for approximately a third of the methane produced in anaerobic soils and sediments as well as waste digesters.

Applied and Environmental Microbiology, 2021

Biogenic methane is a significant greenhouse gas, and the conversion of organic wastes to methane... more Biogenic methane is a significant greenhouse gas, and the conversion of organic wastes to methane is an important bioenergy process. Methanosarcina species play an important role in methane production in many methanogenic soils and sediments as well as anaerobic waste digesters. The studies reported here emphasize that the genus Methanosarcina is composed of two physiologically distinct groups.

mBio, 2019

The anaerobic corrosion of iron structures is expensive to repair and can be a safety and environ... more The anaerobic corrosion of iron structures is expensive to repair and can be a safety and environmental concern. It has been known for over 100 years that the presence of anaerobic respiratory microorganisms can accelerate iron corrosion. Multiple studies have suggested that there are sulfate reducers, methanogens, and acetogens that can directly accept electrons from Fe(0) to support sulfate or carbon dioxide reduction. However, all of the strains studied can also use H 2 as an electron donor for growth, which is known to be abiotically produced from Fe(0). Furthermore, no proteins definitely shown to function as extracellular electrical contacts with Fe(0) were identified. The studies described here demonstrate that direct electron transfer from Fe(0) can support anaerobic respiration. They also map out a simple genetic approach to the study of iron corrosion mechanisms in other microorganisms. A better understanding of how microorganisms promote iron corrosion is expected to lead...

Conservation of energy to support growth solely from extracellular electron transfer was demonstr... more Conservation of energy to support growth solely from extracellular electron transfer was demonstrated for the first time in a methanogen. Methanosarcina acetivorans grew with methanol as the sole electron donor and the extracellular electron acceptor anthraquione-2,6-disulfonate (AQDS) as the sole electron acceptor when methane production was inhibited with bromoethanesulfonate. Transcriptomics revealed that transcripts for the gene for the transmembrane, multi-heme, c-type cytochrome MmcA were 4-fold higher in AQDS-respiring cells versus methanogenic cells. A strain in which the gene for MmcA was deleted failed to grow via AQDS reduction whereas strains in which other cytochrome genes were deleted grew as well as the wild-type strain. The MmcA-deficient strain grew with the conversion of methanol or acetate to methane, suggesting that MmcA has a specialized role as a conduit for extracellular electron transfer. Enhanced expression of genes for methanol conversion to methyl-coenzyme...

Frontiers in Microbiology, 2018

Direct interspecies electron transfer (DIET) is important in diverse methanogenic environments, b... more Direct interspecies electron transfer (DIET) is important in diverse methanogenic environments, but how methanogens participate in DIET is poorly understood. Therefore, the transcriptome of Methanosarcina barkeri grown via DIET in co-culture with Geobacter metallireducens was compared with its transcriptome when grown via H 2 interspecies transfer (HIT) with Pelobacter carbinolicus. Notably, transcripts for the F 420 H 2 dehydrogenase, Fpo, and the heterodisulfide reductase, HdrABC, were more abundant during growth on DIET. A model for CO 2 reduction was developed from these results in which electrons delivered to methanophenazine in the cell membrane are transferred to Fpo. The external proton gradient necessary to drive the otherwise thermodynamically unfavorable reverse electron transport for Fpo-catalyzed F 420 reduction is derived from protons released from G. metallireducens metabolism. Reduced F 420 is a direct electron donor in the carbon dioxide reduction pathway and also serves as the electron donor for the proposed HdrABC-catalyzed electron bifurcation reaction in which reduced ferredoxin (also required for carbon dioxide reduction) is generated with simultaneous reduction of CoM-S-S-CoB. Expression of genes for putative redox-active proteins predicted to be localized on the outer cell surface was higher during growth on DIET, but further analysis will be required to identify the electron transfer route to methanophenazine. The results indicate that the pathways for electron and proton flux for CO 2 reduction during DIET are substantially different than for HIT and suggest that gene expression patterns may also be useful for determining whether Methanosarcina are directly accepting electrons from other extracellular electron donors, such as corroding metals or electrodes.