Comment

Glacier-Rock Boundaries can feed Methanogenic Communities

Not all important science requires fancy multi-million dollar instruments - sometimes, all you need is a sledgehammer. The deceptively simple experiment described in this paper shows that by merely grinding away on silicate rocks, glaciers can produce enough hydrogen to support methanogenic microbes. By extending the biosphere to ice-rock interfaces, we can envision a sustainable microbial community even when glaciations last for millions of years. Presumably, the hydrogen production requires a minimal degree of friction, and a certain chemical environment - the degree to which these may be maintained over extended time periods needed to maintain long-term communities is unclear. Here's the abstract:

Substantial parts of the beds of glaciers, ice sheets and ice caps are at the pressure melting point1. The resulting water harbours diverse subglacial microbial ecosystems2, 3 capable of affecting global biogeochemical cycles4, 5. Such subglacial habitats may have acted as refugia during Neoproterozoic glaciations6. However, it is unclear how life in subglacial environments could be supported during glaciations lasting millions of years because energy from overridden organic carbon would become increasingly depleted7, 8. Here we investigate the potential for abiogenic H2 produced during rock comminution to provide a continual source of energy to support subglacial life. We collected a range of silicate rocks representative of subglacial environments in Greenland, Canada, Norway and Antarctica and crushed them with a sledgehammer and ball mill to varying surface areas. Under an inert atmosphere in the laboratory, we added water, and measured H2 production with time. H2 was produced at 0 °C in all silicate–water experiments, probably through the reaction of water with mineral surface silica radicals formed during rock comminution. H2 production increased with increasing temperature or decreasing silicate rock grain size. Sufficient H2 was produced to support previously measured rates of methanogenesis under a Greenland glacier. We conclude that abiogenic H2 generation from glacial bedrock comminution could have supported life and biodiversity in subglacial refugia during past extended global glaciations.

Comment

Comment

Protein Scaffolds to Bolster Metabolic Pathway Rates

This one falls under the "news to me" category: the physical arrangement of pathway-specific enzymes in order to increase metabolic productivity. The Dueber lab at UC Berkeley has been generating enzyme platforms for the last several years to circumvent rate-limiting issues such as diffusion and intermediate build-ups that suppress upstream reactions. The idea is to construct a molecular scaffold that displays tags, recruiting specific enzymes to the same subcellular location. This way, a metabolic intermediate is shuttled quickly to the next enzyme, removing some of the random walk serendipity that typically governs non-networked pathways. The initial 2007 paper can be found [here] (abstract below), and a more recent iteration builds similar scaffolds within a larger proteinaceous shell.

Engineered metabolic pathways constructed from enzymes heterologous to the production host often suffer from flux imbalances, as they typically lack the regulatory mechanisms characteristic of natural metabolism. In an attempt to increase the effective concentration of each component of a pathway of interest, we built synthetic protein scaffolds that spatially recruit metabolic enzymes in a designable manner. Scaffolds bearing interaction domains from metazoan signaling proteins specifically accrue pathway enzymes tagged with their cognate peptide ligands. The natural modularity of these domains enabled us to optimize the stoichiometry of three mevalonate biosynthetic enzymes recruited to a synthetic complex and thereby achieve 77-fold improvement in product titer with low enzyme expression and reduced metabolic load. One of the same scaffolds was used to triple the yield of glucaric acid, despite high titers (0.5 g/l) without the synthetic complex. These strategies should prove generalizeable to other metabolic pathways and programmable for fine-tuning pathway flux.

Comment

Comment

Direct Electron Transfer in Methanotrophic Consortia?

Ever since the symbiosis between anaerobic methanotrophic (ANME) archaea and sulfate reducing bacteria (SRB) was discovered a couple of decades ago, the inner workings of this close partnership has remained a mystery. What became clear relatively quickly was that the ANME appeared to oxidize methane in an energetically anemic process, and the SRB generated an energetic windfall by reducing sulfate, presumably with the electrons from their ANME neighbors. However, the precise nature of that electron-rich go-between remained unclear - diffusable molecules like hydrogen, formate, or acetate were all ruled out. A recent study out of the Orphan lab at Caltech (COI alert: my PhD home) suggests that ANME release reducing power through direct electron transfer - it's a compelling marriage of anabolic nanoSIMS data, modeling, and metagenomics analysis.

Full paper [here], and abstract below:

Multicellular assemblages of microorganisms are ubiquitous in nature, and the proximity afforded by aggregation is thought to permit intercellular metabolic coupling that can accommodate otherwise unfavourable reactions. Consortia of methane-oxidizing archaea and sulphate-reducing bacteria are a well-known environmental example of microbial co-aggregation; however, the coupling mechanisms between these paired organisms is not well understood, despite the attention given them because of the global significance of anaerobic methane oxidation. Here we examined the influence of interspecies spatial positioning as it relates to biosynthetic activity within structurally diverse uncultured methane-oxidizing consortia by measuring stable isotope incorporation for individual archaeal and bacterial cells to constrain their potential metabolic interactions. In contrast to conventional models of syntrophy based on the passage of molecular intermediates, cellular activities were found to be independent of both species intermixing and distance between syntrophic partners within consortia. A generalized model of electric conductivity between co-associated archaea and bacteria best fit the empirical data. Combined with the detection of large multi-haem cytochromes in the genomes of methanotrophic archaea and the demonstration of redox-dependent staining of the matrix between cells in consortia, these results provide evidence for syntrophic coupling through direct electron transfer.

Comment

Comment

Protein Interactions via Microfluidics

Understanding how proteins interact with each other is a growing challenge in microbiology - it seems pretty important, but the analytical resolution on how such interactions happen and exactly how they modulate activity isn't quite up to the task yet. This work out of Steve Quake's lab uses microfluidic chambers to test binary protein-protein interactions and assign potential functions to partner proteins with unknown function. Abstract below, full paper [here].

Despite the enormous proliferation of bacterial genome data, surprisingly persistent collections of bacterial proteins have resisted functional annotation. In a typical genome, roughly 30% of genes have no assigned function. Many of these proteins are conserved across a large number of bacterial genomes. To assign a putative function to these conserved proteins of unknown function, we created a physical interaction map by measuring biophysical interaction of these proteins. Binary protein-–protein interactions in the model organism Streptococcus pneumoniae (TIGR4) are measured with a microfluidic high-throughput assay technology. In some cases, informatic analysis was used to restrict the space of potential binding partners. In other cases, we performed in vitro proteome-wide interaction screens. We were able to assign putative functions to 50 conserved proteins of unknown function that we studied with this approach.

Comment

Comment

Metallo- Meta-omics!

New work out of the Glass group at Georgia Tech, looking at the Fe:Cu ratios in OMZs. Looks like genomes and transcriptomes are pretty finely attuned not only to metal abundances but also electron acceptors.

Abstract below, paper site [here].

Iron (Fe) and copper (Cu) are essential cofactors for microbial metalloenzymes, but little is known about the metalloenyzme inventory of anaerobic marine microbial communities despite their importance to the nitrogen cycle. We compared dissolved O2, NO3-, NO2-, Fe and Cu concentrations with nucleic acid sequences encoding Fe and Cu-binding proteins in 21 metagenomes and 9 metatranscriptomes from Eastern Tropical North and South Pacific oxygen minimum zones and 7 metagenomes from the Bermuda Atlantic Time-series Station. Dissolved Fe concentrations increased sharply at upper oxic-anoxic transition zones, with the highest Fe:Cu molar ratio (1.8) occurring at the anoxic core of the Eastern Tropical North Pacific oxygen minimum zone and matching the predicted maximum ratio based on data from diverse ocean sites. The relative abundance of genes encoding Fe-binding proteins was negatively correlated with O2, driven by significant increases in genes encoding Fe-proteins involved in dissimilatory nitrogen metabolisms under anoxia. Transcripts encoding cytochrome c oxidase, the Fe- and Cu-containing terminal reductase in aerobic respiration, were positively correlated with O2 content. A comparison of the taxonomy of genes encoding Fe- and Cu-binding vs. bulk proteins in OMZs revealed that Planctomycetes represented a higher percentage of Fe genes while Thaumarchaeota represented a higher percentage of Cu genes, particularly at oxyclines. These results are broadly consistent with higher relative abundance of genes encoding Fe-proteins in the genome of a marine planctomycete vs. higher relative abundance of genes encoding Cu-proteins in the genome of a marine thaumarchaeote. These findings highlight the importance of metalloenzymes for microbial processes in oxygen minimum zones and suggest preferential Cu use in oxic habitats with Cu > Fe vs. preferential Fe use in anoxic niches with Fe > Cu.

Comment