Novel Alphaproteobacteria transcribe genes for nitric oxide transformation at high levels in a marine oxygen-deficient zone.

Marine oxygen-deficient zones (ODZs) are portions of the ocean where intense nitrogen loss occurs primarily via denitrification and anammox. Despite many decades of study, the identity of the microbes that catalyze nitrogen loss in ODZs is still being elucidated. Intriguingly, high transcription of genes in the same family as the nitric oxide dismutase () gene from Methylomirabilota has been reported in the anoxic core of ODZs.

Single-cell analysis in hypersaline brines predicts a water-activity limit of microbial anabolic activity.

Hypersaline brines provide excellent opportunities to study extreme microbial life. Here, we investigated anabolic activity in nearly 6000 individual cells from solar saltern sites with water activities () ranging from 0.982 to 0.

Climate drivers alter nitrogen availability in surface peat and decouple N fixation from CH oxidation in the Sphagnum moss microbiome.

Peat mosses (Sphagnum spp.) are keystone species in boreal peatlands, where they dominate net primary productivity and facilitate the accumulation of carbon in thick peat deposits. Sphagnum mosses harbor a diverse assemblage of microbial partners, including N -fixing (diazotrophic) and CH -oxidizing (methanotrophic) taxa that support ecosystem function by regulating transformations of carbon and nitrogen.

Goldilocks and RNA: where Mg2+ concentration is just right.

Magnesium, the most abundant divalent cation in cells, catalyzes RNA cleavage but also promotes RNA folding. Because folding can protect RNA from cleavage, we predicted a 'Goldilocks landscape', with local maximum in RNA lifetime at Mg2+ concentrations required for folding. Here, we use simulation and experiment to discover an innate and sophisticated mechanism of control of RNA lifetime.

Something old, something new, something borrowed, something blue: the anaerobic microbial ancestry of aerobic respiration.

Aerobic respiration evolved by bricolage, with modules cobbled together as microbial biochemistry coevolved with Earth's geochemistry. The mitochondrial electron transport chain represents a patchwork of respiratory modules inherited from microbial methanogenesis, iron oxidation, anoxygenic photosynthesis, and denitrification pathways, and preserves a biochemical record of Earth's redox environment over its four-billion-year history. Imprints of the anoxic early Earth are recognizable in Complex I's numerous iron-sulfur cofactors and vestigial binding sites for ferredoxin, nickel-iron, and molybdopterin, whereas the more recent advent of oxygen as a terminal electron acceptor necessitated use of heme and copper cofactors by Complex IV.

The Bioburden and Ionic Composition of Hypersaline Lake Ices: Novel Habitats on Earth and Their Astrobiological Implications.

We present thermophysical, biological, and chemical observations of ice and brine samples from five compositionally diverse hypersaline lakes in British Columbia's interior plateau. Possessing a spectrum of magnesium, sodium, sulfate, carbonate, and chloride salts, these low-temperature high-salinity lakes are analogs for planetary ice-brine environments, including the ice shells of Europa and Enceladus and ice-brine systems on Mars. As such, understanding the thermodynamics and biogeochemistry of these systems can provide insights into the evolution, habitability, and detectability of high-priority astrobiology targets.

Adaptation and Exaptation: From Small Molecules to Feathers.

Evolution works by adaptation and exaptation. At an organismal level, exaptation and adaptation are seen in the formation of organelles and the advent of multicellularity. At the sub-organismal level, molecular systems such as proteins and RNAs readily undergo adaptation and exaptation.

Microbial metabolism and adaptations in Atribacteria-dominated methane hydrate sediments.

Gas hydrates harbour gigatons of natural gas, yet their microbiomes remain understudied. We bioprospected 16S rRNA amplicons, metagenomes, and metaproteomes from methane hydrate-bearing sediments under Hydrate Ridge (offshore Oregon, USA, ODP Site 1244, 2-69 mbsf) for novel microbial metabolic and biosynthetic potential. Atribacteria sequences generally increased in relative sequence abundance with increasing sediment depth.

Methane Hydrate Crystallization on Sessile Water Droplets.

This paper describes a method to form methane hydrate shells on water droplets. In addition, it provides blueprints for a pressure cell rated to 10 MPa working pressure, containing a stage for sessile droplets, a sapphire window for visualization, and temperature and pressure transducers. A pressure pump connected to a methane gas cylinder is used to pressurize the cell to 5 MPa.

Microbial helpers allow cyanobacteria to thrive in ferruginous waters.

The Great Oxidation Event (GOE) was a rapid accumulation of oxygen in the atmosphere as a result of the photosynthetic activity of cyanobacteria. This accumulation reflected the pervasiveness of O on the planet's surface, indicating that cyanobacteria had become ecologically successful in Archean oceans. Micromolar concentrations of Fe in Archean oceans would have reacted with hydrogen peroxide, a byproduct of oxygenic photosynthesis, to produce hydroxyl radicals, which cause cellular damage.

Microbial diversity and activity in Southern California salterns and bitterns: analogues for remnant ocean worlds.

Concurrent osmotic and chaotropic stress make MgCl -rich brines extremely inhospitable environments. Understanding the limits of life in these brines is essential to the search for extraterrestrial life on contemporary and relict ocean worlds, like Mars, which could host similar environments. We sequenced environmental 16S rRNA genes and quantified microbial activity across a broad range of salinity and chaotropicity at a Mars-analogue salt harvesting facility in Southern California, where seawater is evaporated in a series of ponds ranging from kosmotropic NaCl brines to highly chaotropic MgCl brines.

Transition metals enhance prebiotic depsipeptide oligomerization reactions involving histidine.

Biochemistry exhibits an intense dependence on metals. Here we show that during dry-down reactions, zinc and a few other transition metals increase the yield of long histidine-containing depsipeptides, which contain both ester and amide linkages. Our results suggest that interactions of proto-peptides with metal ions influenced early chemical evolution.

Water and Life: The Medium is the Message.

Water, the most abundant compound on the surface of the Earth and probably in the universe, is the medium of biology, but is much more than that. Water is the most frequent actor in the chemistry of metabolism. Our quantitation here reveals that water accounts for 99.

Corrigendum: Meta-omic signatures of microbial metal and nitrogen cycling in marine oxygen minimum zones.

[This corrects the article DOI: 10.3389/fmicb.2015.

Mainly on the Plane: Deep Subsurface Bacterial Proteins Bind and Alter Clathrate Structure.

Gas clathrates are both a resource and a hindrance. They store massive quantities of natural gas but also can clog natural gas pipelines, with disastrous consequences. Eco-friendly technologies for controlling and modulating gas clathrate growth are needed.

Lanthanide rarity in natural waters: implications for microbial C1 metabolism.

Research in the last decade has illuminated the important role that lanthanides play in microbial carbon metabolism, particularly methylotrophy. Environmental omics studies have revealed that lanthoenzymes are dominant in some environments, and laboratory studies have shown that lanthoenzymes are favored over their calcium-containing counterparts even when calcium is far more abundant. Lanthanide elements are common in rocks but occur at exceedingly low levels in most natural waters (picomolar to nanomolar range) with the exception of volcanic hot springs, which can reach micromolar concentrations.

Archaeal roots of intramembrane aspartyl protease siblings signal peptide peptidase and presenilin.

Signal peptides help newly synthesized proteins reach the cell membrane or be secreted. As part of a biological process key to immune response and surveillance in humans, and associated with diseases, for example, Alzheimer, remnant signal peptides and other transmembrane segments are proteolyzed by the intramembrane aspartyl protease (IAP) enzyme family. Here, we identified IAP orthologs throughout the tree of life.

A blueprint for academic laboratories to produce SARS-CoV-2 quantitative RT-PCR test kits.

Widespread testing for the presence of the novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in individuals remains vital for controlling the COVID-19 pandemic prior to the advent of an effective treatment. Challenges in testing can be traced to an initial shortage of supplies, expertise, and/or instrumentation necessary to detect the virus by quantitative RT-PCR (RT-qPCR), the most robust, sensitive, and specific assay currently available. Here we show that academic biochemistry and molecular biology laboratories equipped with appropriate expertise and infrastructure can replicate commercially available SARS-CoV-2 RT-qPCR test kits and backfill pipeline shortages.

A blueprint for academic labs to produce SARS-CoV-2 RT-qPCR test kits.

Widespread testing for the presence of the novel coronavirus SARS-CoV-2 in individuals remains vital for controlling the COVID-19 pandemic prior to the advent of an effective treatment. Challenges in testing can be traced to an initial shortage of supplies, expertise and/or instrumentation necessary to detect the virus by quantitative reverse transcription polymerase chain reaction (RT-qPCR), the most robust, sensitive, and specific assay currently available. Here we show that academic biochemistry and molecular biology laboratories equipped with appropriate expertise and infrastructure can replicate commercially available SARS-CoV-2 RT-qPCR test kits and backfill pipeline shortages.