Searching for bacteria in sticky situations:Methods for investigating bacterial survival at solid-air interfaces involving Wyoming MX-80 bentonite

Effective removal of prokaryotic cells from clay interfaces such as bentonite is essential for quantitative assessment of microbial communities, considering that strong bentonite clay-DNA and –RNA complexes challenge the use of molecular-based techniques. In this study, aerobic bacteria were isolated from Wyoming MX-80 bentonite and sequenced for identification (16S rRNA). A glass-bentonite substrate and sterile bentonite powder were inoculated with Arthrobacter sp. (isolated from bentonite) to test cell removal efficiency using sonication and vortexing. Manipulation of pH (pH 7 versus pH 9) did not affect cell removal efficiency, while changes in temperature within limits (15–37 °C) did affect cell removal efficiency. To evaluate microbial survival during desiccation, bacterial isolates were inoculated onto glass and bentonite-covered glass coverslip substrates, and particulate bentonite. Substrates were desiccated, and cells were removed by vortexing at different time points over 31 days. Abundance of viable cells followed a first-order rate of decrease. Vegetative desiccation-tolerant Arthrobacter sp. isolates from bentonite clay had lower loss of viable, culturable cells (0.07 d−1 to 0.89 d−1) than did a Bacillus sp. isolate (&gt;1 d−1) or a Pseudomonas stutzeri isolate (0.79 to &gt;1 d−1), suggesting Arthrobacter sp. may be more tolerant of these prolonged periods of desiccation on the bentonite-air interface. Tolerance to matric stress by microorganisms varies depending on the cellular adaptation of the target species, the physical and chemical properties of the given solid-air environment, as well as the employed population and community-based survival mechanisms.</p

The effect of dietary nitrate supplementation on physiology and performance in trained cyclists

Purpose: To determine the effect of dietary nitrate (NO₃⁻) supplementation on physiology and performance in well-trained cyclists following six to eight-days of NO₃⁻ supplementation. Methods: Eight competitive male cyclists (mean ± SD; age = 26 ± 8 y; body mass = 76.7 ± 6.9 kg; VO2peak = 63 ± 4 ml.kg⁻¹.min⁻¹) participated in a double-blind, placebo-controlled, crossover-design study in which participants ingested 70 ml beetroot juice containing ~4 mmol NO₃⁻ (NIT) or a NO₃⁻ depleted placebo (PLA) , each for 8-days. Replicating pre-treatment measures, participants undertook an incremental ramp assessment to determine VO₂peak, first (VT₁), and second (VT₂) ventilatory thresholds on day 6 (NIT6 and PLA6), moderate-intensity cycling economy on day 7 (NIT7 and PLA7), and a 4-km time-trial on day 8 (NIT8 and PLA8). Results: Relative to PLA, 6 days of NIT supplementation produced unclear effects for VO2peak (mean ±95%CL: 1.8 ±5.5%) and VT1 (3.7 ±12.3%) and trivial effects for both VT2 (-1.0 ±3.0%) and exercise economy on day 7 (-1.0 ±1.6%). However, effects for time-trial performance time (0.7 ±0.9%), and power (2.4 ±2.5%), on day 8 were likely beneficial. Conclusions: Despite mostly unclear outcomes for standard physiological determinants of performance, 8-days of NO₃⁻ supplementation resulted in likely beneficial improvements to 4-km time-trial performance in well trained male endurance cyclists

Scaling the gas transfer velocity and hydraulic geometry in streams and small rivers

Scaling is an integral component of ecology and earth science. To date, the ability to determine the importance of air–water gas exchange across large spatial scales is hampered partly by our ability to scale the gas transfer velocity and stream hydraulics. Here we report on a metadata analysis of 563 direct gas tracer release experiments that examines scaling laws for the gas transfer velocity. We found that the gas transfer velocity scales with the product of stream slope and velocity, which is in alignment with theory on stream energy dissipation. In addition to providing equations that predict the gas transfer velocity based on stream hydraulics, we used our hydraulic data set to report a new set of hydraulic exponents and coefficients that allow the prediction of stream width, depth, and velocity based on discharge. Finally, we report a new table of gas Schmidt number dependencies to allow researchers to estimate a gas transfer velocity using our equation for many gasses of interest

The Effect of Nitrate Supplementation on Cycling Performance in the Heat in Well-Trained Cyclists

Purpose: The aim of this study was to determine the effect of NO₃⁻ consumption on measures of perception, thermoregulation and cycling performance in hot conditions. Methods: Using a randomised, double-blind, crossover-design, 8 well-trained cyclists (mean ± SD: age: 25 ± 8 y, V̇O2peak: 64 ± 5 ml·kg⁻¹·min⁻¹) performed 2 separate trials, in hot (35°C, 60% relative humidity) environments, having ingested either 140 ml NO3--rich beetroot juice ~8 mmol NO₃⁻ (NIT), or placebo (PLA), daily for 3-days with a 7-day washout period separating trials. Trials consisted of 2 × 10 min bouts at 40 and 60% peak power output (PPO) to determine physiological and perceptual responses in the heat, followed by a 4 km cycling time-trial. Results: Basal [nitrite] was substantially elevated in NIT (2.70 ± 0.98 μM) vs PLA (1.10 ± 0.61 μM) resulting in a most likely (ES = 1.58 ± 0.93) increase after 3-days. There was a very likely trivial increase in rectal temperature [Tᵣₑ] in NIT at 40% (PLA;37.4 ± 0.2°C vs NIT;37.5 ± 0.3°C, 0.1 ± 0.2°C) and 60% (PLA;37.8 ± 0.2°C vs NIT;37.9 ± 0.3°C, 0.1 ± 0.2°C) PPO. Cycling performance was similar between trials (PLA;336 ± 45 W vs NIT;337 ± 50 W, CV±95%CL; 0.2 ± 2.5%). Outcomes for heart rate, and perceptual measures were unclear across the majority of time-points. Conclusions: Three days of NO₃⁻ supplementation, resulted in small increases in Tᵣₑ during low- to moderate-intensity exercise, however this did not appear to influence 4 km cycling time-trial performance in hot climates

Metal-macrofauna interactions determine microbial community structure and function in copper contaminated sediments

Peer reviewedPublisher PD

Fine-Scale in Situ Measurement of Riverbed Nitrate Production and Consumption in an Armored Permeable Riverbed

Alteration of the global nitrogen cycle by man has increased nitrogen loading in waterways considerably, often with harmful consequences for aquatic ecosystems. Dynamic redox conditions within riverbeds support a variety of nitrogen transformations, some of which can attenuate this burden. In reality, however, assessing the importance of processes besides perhaps denitrification is difficult, due to a sparseness of data, especially in situ, where sediment structure and hydrologic pathways are intact. Here we show in situ within a permeable riverbed, through injections of 15N-labeled substrates, that nitrate can be either consumed through denitrification or produced through nitrification, at a previously unresolved fine (centimeter) scale. Nitrification and denitrification occupy different niches in the riverbed, with denitrification occurring across a broad chemical gradient while nitrification is restricted to more oxic sediments. The narrow niche width for nitrification is in effect a break point, with the switch from activity “on” to activity “off” regulated by interactions between subsurface chemistry and hydrology. Although maxima for denitrification and nitrification occur at opposing ends of a chemical gradient, high potentials for both nitrate production and consumption can overlap when groundwater upwelling is strong

Retinoid X receptor gamma signaling accelerates CNS remyelination

The molecular basis of CNS myelin regeneration (remyelination) is poorly understood. We generated a comprehensive transcriptional profile of the separate stages of spontaneous remyelination that follow focal demyelination in the rat CNS and found that transcripts that encode the retinoid acid receptor RXR-γ were differentially expressed during remyelination. Cells of the oligodendrocyte lineage expressed RXR-γ in rat tissues that were undergoing remyelination and in active and remyelinated multiple sclerosis lesions. Knockdown of RXR-γ by RNA interference or RXR-specific antagonists severely inhibited oligodendrocyte differentiation in culture. In mice that lacked RXR-γ, adult oligodendrocyte precursor cells efficiently repopulated lesions after demyelination, but showed delayed differentiation into mature oligodendrocytes. Administration of the RXR agonist 9-cis-retinoic acid to demyelinated cerebellar slice cultures and to aged rats after demyelination caused an increase in remyelinated axons. Our results indicate that RXR-γ is a positive regulator of endogenous oligodendrocyte precursor cell differentiation and remyelination and might be a pharmacological target for regenerative therapy in the CNS

A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data

MicrobeMASST, a taxonomically-informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbial-derived metabolites and relative producers, without a priori knowledge, will vastly enhance the understanding of microorganisms’ role in ecology and human health