Assessment of Capacity to Capture DNA Aerosols by Clean Filters for Molecular Biology Experiments

Multiplexed food-borne pathogen detection using an argonaute-mediated digital sensor based on a magnetic-bead-assisted imaging transcoding system

Accurate, sensitive and multiplexed detection of food-borne pathogens is crucial for assessing food safety risks. Here we present a digital DNA-amplification-free nucleic acid detection assay to achieve multiplexed and ultrasensitive detection of three food-borne pathogens. We used mesophilic Clostridium butyricum argonaute and magnetic beads in a digital carrier system (d-MAGIC). Clostridium butyricum argonaute, with its two-guide accurate cleavage activity, precisely targets and cleaves fluorescence-quencher reporters corresponding to different bacteria through a two-step process. The system uses fluorescence-encoded magnetic beads as programmable multi-probes, allowing the simultaneous detection of multiple pathogens and easy data interpretation via artificial intelligence. The method showed a wide detection range (101 to 107 CFU ml-1) and a low limit of detection of 6 CFU ml-1 for food-borne pathogens without DNA amplification. Digital nucleic acid testing using d-MAGIC can become a next-generation strategy for accurate and convenient pathogen detection.

Temperature limits to deep subseafloor life in the Nankai Trough subduction zone

Microorganisms in marine subsurface sediments substantially contribute to global biomass. Sediments warmer than 40°C account for roughly half the marine sediment volume, but the processes mediated by microbial populations in these hard-to-access environments are poorly understood. We investigated microbial life in up to 1.2-kilometer-deep and up to 120°C hot sediments in the Nankai Trough subduction zone. Above 45°C, concentrations of vegetative cells drop two orders of magnitude and endospores become more than 6000 times more abundant than vegetative cells. Methane is biologically produced and oxidized until sediments reach 80° to 85°C. In 100° to 120°C sediments, isotopic evidence and increased cell concentrations demonstrate the activity of acetate-degrading hyperthermophiles. Above 45°C, populated zones alternate with zones up to 192 meters thick where microbes were undetectable.

Assessment and mitigation of aerosol airborne SARS-CoV-2 transmission in laboratory and office environments

Bioaerosols are known to be an important transmission pathway for SARS-CoV-2. We report a framework for estimating the risk of transmitting SARS-CoV-2 via aerosols in laboratory and office settings, based on an exponential dose-response model and analysis of air flow and purification in typical heating, ventilation, and air conditioning (HVAC) systems. High-circulation HVAC systems with high-efficiency particulate air (HEPA) filtration dramatically reduce exposure to the virus in indoor settings, and surgical masks or N95 respirators further reduce exposure. As an example of our risk assessment model, we consider the precautions needed for a typical experimental physical science group to maintain a low risk of transmission over six months of operation. We recommend that, for environments where fewer than five individuals significantly overlap, work spaces should remain vacant for between one (high-circulation HVAC with HEPA filtration) to six (low-circulation HVAC with no filtration) air exchange times before a new worker enters in order to maintain no more than 1% chance of infection over six months of operation in the workplace. Our model is readily applied to similar settings that are not explicitly given here. We also provide a framework for evaluating infection mitigation through ventilation in multiple occupancy spaces.

Aerobic microbial life persists in oxic marine sediment as old as 101.5 million years

Sparse microbial populations persist from seafloor to basement in the slowly accumulating oxic sediment of the oligotrophic South Pacific Gyre (SPG). The physiological status of these communities, including their substrate metabolism, is previously unconstrained. Here we show that diverse aerobic members of communities in SPG sediments (4.3‒101.5 Ma) are capable of readily incorporating carbon and nitrogen substrates and dividing. Most of the 6986 individual cells analyzed with nanometer-scale secondary ion mass spectrometry (NanoSIMS) actively incorporated isotope-labeled substrates. Many cells responded rapidly to incubation conditions, increasing total numbers by 4 orders of magnitude and taking up labeled carbon and nitrogen within 68 days after incubation. The response was generally faster (on average, 3.09 times) for nitrogen incorporation than for carbon incorporation. In contrast, anaerobic microbes were only minimally revived from this oxic sediment. Our results suggest that microbial communities widely distributed in organic-poor abyssal sediment consist mainly of aerobes that retain their metabolic potential under extremely low-energy conditions for up to 101.5 Ma.

The discovery of aerobic microbial communities in nutrient-poor sediments below the seafloor begs the question of the mechanisms for their persistence. Here the authors investigate subseafloor sediment in the South Pacific Gyre abyssal plain, showing that aerobic microbial life can be revived and retain metabolic potential even from 101.5 Ma-old sediment.

Variation of airborne DNA mass ratio and fungal diversity in fine particles with day-night difference during an entire winter haze evolution process of Central China

Airborne fungi are a primary component of bioaerosols and proved to impact human health and climatic change. Deoxyribonucleic acid (DNA) is the essential component of most living organisms with relatively stable physicochemical properties. Little is known about day-night and pollution-episode differences of DNA mass ratio and fungal community in fine particles (PM_2.5) during serious winter haze events in China. Here we collected twenty-nine PM_2.5 samples every day and night during an entire winter haze evolution process in a megacity of Central China, Wuhan. DNA extraction and high-throughput sequencing methods were adopted to analyze fungal community. Results showed that mass ratio of DNA in PM_2.5 (R_D/P %) changed with pollution process and showed significant negative correlations with PM_2.5 concentration (r = -0.72, P < 0.05) and temperature (r = -0.74, P < 0.05). R_D/P became lower (4.40 × 10^-4%) after haze episodes than before (7.16 × 10^-4%). R_D/P of night-samples (1.98 × 10^-4-4.97 × 10^-4%) were all lower than those for day-samples (3.05 × 10^-4-9.99 × 10^-4%) for the same period. The fungal species richness became much lower (76 operational taxonomic units (OTUs)) after haze episodes than before (198 OTUs). The species richness of night-samples (119-537 OTUs) were all higher than those of day-samples (71-198 OTUs) for the same period. The OTUs specially owned by night-samples were also more than those by day-samples. Fungal community diversity showed random variations. The fungal community composition of each sample was classified from phylum to genus level. Pathogenic fungi accounted for 8.60% of the entire fungal community. The significantly enriched fungal taxa in the night-sample group (29 taxa) were also much more than that in the day-sample group (9 taxa), which could explain the higher species richness of airborne fungi community in the night during the haze evolution episodes. These findings may serve as an important reference or inspiration to other aerosol studies focusing on human health and behavior of aerosols in the atmosphere.

A cautionary tale of cross-contamination among plasmids from commercial suppliers

Many researchers have switched to purchasing their desired plasmids from commercial suppliers to save time and resources, as we did for 17 high-risk human papillomavirus plasmids. To our surprise, they were shown to be cross-contaminated with one another. Comparison between the production schedule and the pattern of contaminations proved that this contamination occurred during the production process, which was also shown for another two sets of commercial plasmids. Our experience indicates that the absolute purity of plasmids obtained from external sources cannot be guaranteed. Extreme caution should be exercised, especially when such plasmids are used for human gene therapies and DNA vaccines, where even a minute amount of contamination may pose significant risks to patients.

Origin of Short-Chain Organic Acids in Serpentinite Mud Volcanoes of the Mariana Convergent Margin

Serpentinitic systems are potential habitats for microbial life due to frequently high concentrations of microbial energy substrates, such as hydrogen (H₂), methane (CH₄), and short-chain organic acids (SCOAs). Yet, many serpentinitic systems are also physiologically challenging environments due to highly alkaline conditions (pH > 10) and elevated temperatures (>80°C). To elucidate the possibility of microbial life in deep serpentinitic crustal environments, International Ocean Discovery Program (IODP) Expedition 366 drilled into the Yinazao, Fantangisña, and Asùt Tesoru serpentinite mud volcanoes on the Mariana Forearc. These mud volcanoes differ in temperature (80, 150, 250°C, respectively) of the underlying subducting slab, and in the porewater pH (11.0, 11.2, 12.5, respectively) of the serpentinite mud. Increases in formate and acetate concentrations across the three mud volcanoes, which are positively correlated with temperature in the subducting slab and coincide with strong increases in H₂ concentrations, indicate a serpentinization-related origin. Thermodynamic calculations suggest that formate is produced by equilibrium reactions with dissolved inorganic carbon (DIC) + H₂, and that equilibration continues during fluid ascent at temperatures below 80°C. By contrast, the mechanism(s) of acetate production are not clear. Besides formate, acetate, and H₂ data, we present concentrations of other SCOAs, methane, carbon monoxide, and sulfate, δ¹³C-data on bulk carbon pools, and microbial cell counts. Even though calculations indicate a wide range of microbial catabolic reactions to be thermodynamically favorable, concentration profiles of potential energy substrates, and very low cell numbers suggest that microbial life is scarce or absent. We discuss the potential roles of temperature, pH, pressure, and dispersal in limiting the occurrence of microbial life in deep serpentinitic environments.