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Amend, J.

Publications and source records attributed to Amend, J..

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Methane-linked mechanisms of electron uptake from cathodes by Methanosarcina barkeri

The Methanosarcinales, a lineage of cytochrome-containing methanogens, have recently been proposed to participate in direct extracellular electron transfer interactions within syntrophic communities. To shed light on this phenomenon, we applied electrochemical techniques to measure electron uptake from cathodes by Methanosarcina barkeri, which is an important model organism that is genetically tractable and utilizes a wide range of substrates for methanogenesis. Here we confirm the ability of M. barkeri to perform electron uptake from cathodes and show that this cathodic current is linked to quantitative increases in methane production. The underlying mechanisms we identified include, but are not limited to, a recently proposed association between cathodes and methanogen-derived extracellular enzymes (e.g. hydrogenases) that can facilitate current generation through the formation of reduced and diffusible methanogenic substrates (e.g. hydrogen). However, after minimizing the contributions of such extracellular enzymes and using a mutant lacking hydrogenases, we observe a lower potential hydrogen-independent pathway that facilitates cathodic activity coupled to methane production in M. barkeri. Our electrochemical measurements of wild-type and mutant strains point to a novel and extracellular-enzyme-free mode of electron uptake able to take up electrons at potentials lower than - 498 mV vs. SHE (over 100 mV more reduced than the observed hydrogenase midpoint potential under these conditions). These results suggest that M. barkeri can perform multiple modes (hydrogenase-mediated and free extracellular enzyme-independent) of electrode interactions on cathodes including a mechanism pointing to a direct interaction, which has significant applied and ecological implications.\n\nImportanceMethanogenic Archaea are of fundamental applied and environmental relevance. This is largely due to their activities in a wide range of anaerobic environments, generating gaseous reduced carbon that can be utilized as a fuel source. While the bioenergetics of a wide variety of methanogens has been well studied with respect to soluble substrates, mechanistic understanding of their interaction with solid phase redox active compounds is limited. This work provides insight into solid phase redox interactions in Methanosarcina using electrochemical methods. We highlight a previously undescribed mode of electron uptake from cathodes, that is potentially informative of direct interspecies electron transfer interactions in the Methanosarcinales.

microbiology

A genus definition for Bacteria and Archaea based on genome relatedness and taxonomic affiliation.

Genus assignment is fundamental in the characterization of microbes, yet there is currently no unambiguous way to demarcate genera solely using standard genomic relatedness indices. Here, we propose an approach to demarcate genera that relies on the combined use of the average nucleotide identity, genome alignment fraction, and the distinction between type species and non-type species. More than 750 genomes representing type strains of species from 10 different phyla, and 19 different taxonomic orders/families in Gram-positive/negative, bacterial and archaeal lineages were tested. Overall, all 19 analyzed taxa conserved significant genomic differences between members of a genus and type species of other genera in the same taxonomic family. Bacillus, Flavobacterium, Hydrogenovibrio, Lactococcus, Methanosarcina, Thiomicrorhabdus, Thiomicrospira, Shewanella, and Vibrio are discussed in detail. Less than 1% of the type strains analyzed need reclassification, highlighting that the adoption of the 16S rRNA gene as a taxonomic marker has provided consistency to the classification of microorganisms in recent decades. One exception to this is the genus Bacillus with 61% of type strains needing reclassification, including the human pathogens B. cereus and B. anthracis. The results provide a first line of evidence that the combination of genomic indices provides appropriate resolution to effectively demarcate genera within the current taxonomic framework that is based on the 16S rRNA gene. We also identify the emergence of natural breakpoints at the genome level that can further help in the circumscription of genera. Altogether, these results show that a distinct difference between distant relatives and close relatives at the genome level (i.e., genomic coherence) is an emergent property of genera in Bacteria and Archaea.

microbiology

Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi

The methyl-coenzyme M reductase (MCR) complex is a key enzyme in archaeal methane generation and has recently been proposed to also be involved in the oxidation of short-chain hydrocarbons including methane, butane and potentially propane. The number of archaeal clades encoding the MCR complex continues to grow, suggesting that this complex was inherited from an ancient ancestor, or has undergone extensive horizontal gene transfer. Expanding the representation of MCR-encoding lineages through metagenomic approaches will help resolve the evolutionary history of this complex. Here, a near-complete Archaeoglobi metagenome-assembled genome (MAG; rG16) was recovered from the deep subseafloor along the Juan de Fuca Ridge flank that encodes two divergent McrABG operons similar to those found in Candidatus Bathyarchaeota and Candidatus Syntrophoarchaeum MAGs. rG16 is basal to members of the class Archaeoglobi, and encodes the genes for {beta}-oxidation, potentially allowing an alkanotrophic metabolism similar to that proposed for Ca. Syntrophoarchaeum. rG16 also encodes a respiratory electron transport chain that can potentially utilize nitrate, iron, and sulfur compounds as electron acceptors. As the first Archaeoglobi with the MCR complex, rG16 extends our understanding of the evolution and distribution of novel MCR encoding lineages among the Archaea.

microbiology