SummaryEnvironments that are hostile to life are characterized by reduced microbial activity which results in poor soil-and plant-health, low biomass and biodiversity, and feeble ecosystem development. Whereas the functional biosphere may primarily be constrained by water activity (a w) the mechanism(s) by which this occurs have not been fully elucidated. Remarkably we found that, for diverse species of xerophilic fungi at a w values of Յ 0.72, water activity per se did not limit cellular function. We provide evidence that chaotropic activity determined their biotic window, and obtained mycelial growth at water activities as low as 0.647 (below that recorded for any microbial species) by addition of compounds that reduced the net chaotropicity. Unexpectedly we found that some fungi grew optimally under chaotropic conditions, providing evidence for a previously uncharacterized class of extremophilic microbes. Further studies to elucidate the way in which solute activities interact to determine the limits of life may lead to enhanced biotechnological processes, and increased productivity of agricultural and natural ecosystems in arid and semiarid regions.

In HIV-1 infection, a population of latently infected cells facilitates viral persistence despite antiretroviral therapy (ART). With the aim of identifying individuals in whom ART might induce a period of viraemic control on stopping therapy, we hypothesised that quantification of the pool of latently infected cells in primary HIV-1 infection (PHI) would predict clinical progression and viral replication following ART. We measured HIV-1 DNA in a highly characterised randomised population of individuals with PHI. We explored associations between HIV-1 DNA and immunological and virological markers of clinical progression, including viral rebound in those interrupting therapy. In multivariable analyses, HIV-1 DNA was more predictive of disease progression than plasma viral load and, at treatment interruption, predicted time to plasma virus rebound. HIV-1 DNA may help identify individuals who could safely interrupt ART in future HIV-1 eradication trials.Clinical trial registration: ISRCTN76742797 and EudraCT2004-000446-20DOI: http://dx.doi.org/10.7554/eLife.03821.001

Microbial cells, and ultimately the Earth's biosphere, function within a narrow range of physicochemical conditions. For the majority of ecosystems, productivity is cold-limited, and it is microbes that represent the failure point. This study was carried out to determine if naturally occurring solutes can extend the temperature windows for activity of microorganisms. We found that substances known to disorder cellular macromolecules (chaotropes) did expand microbial growth windows, fungi preferentially accumulated chaotropic metabolites at low temperature, and chemical activities of solutes determined microbial survival at extremes of temperature as well as pressure. This information can enhance the precision of models used to predict if extraterrestrial and other hostile environments are able to support life; furthermore, chaotropes may be used to extend the growth windows for key microbes, such as saprotrophs, in cold ecosystems and manmade biomes.

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Treatment of HIV-1 infection with antiretroviral therapy (ART) in the weeks following transmission may induce a state of ‘post-treatment control' (PTC) in some patients, in whom viraemia remains undetectable when ART is stopped. Explaining PTC could help our understanding of the processes that maintain viral persistence. Here we show that immunological biomarkers can predict time to viral rebound after stopping ART by analysing data from a randomized study of primary HIV-1 infection incorporating a treatment interruption (TI) after 48 weeks of ART (the SPARTAC trial). T-cell exhaustion markers PD-1, Tim-3 and Lag-3 measured prior to ART strongly predict time to the return of viraemia. These data indicate that T-cell exhaustion markers may identify those latently infected cells with a higher proclivity to viral transcription. Our results may open new avenues for understanding the mechanisms underlying PTC, and eventually HIV-1 eradication.

HighlightsThe requirement for protocol adaptation from qPCR to ddPCR is characterised.A potential loss of sensitivity for ddPCR at low target numbers is reported.A new bioinformatic tool ‘definetherain’ to improve droplet calling at low input target numbers is devised and applied.‘Definetherain’ is made available free of charge and open access at www.definetherain.org.uk.

Macrophage infection is considered to play an important role in HIV-

Abstract. North American leaders recently committed to reducing methane emissions from the oil and gas sector, but information on current emissions from upstream oil and gas developments in Canada are lacking. This study examined the occurrence of methane plumes in an area of unconventional natural gas development in northwestern Canada. In August to September 2015 we completed almost 8000 km of vehicle-based survey campaigns on public roads dissecting oil and gas infrastructure, such as well pads and processing facilities. We surveyed six routes 3-6 times each, which brought us past over 1600 unique well pads and facilities managed by more than 50 different operators. To attribute onroad plumes to oil-and gas-related sources we used gas signatures of residual excess concentrations (anomalies above background) less than 500 m downwind from potential oil and gas emission sources. All results represent emissions greater than our minimum detection limit of 0.59 g s −1 at our average detection distance (319 m). Unlike many other oil and gas developments in the US for which methane measurements have been reported recently, the methane concentrations we measured were close to normal atmospheric levels, except inside natural gas plumes. Roughly 47 % of active wells emitted methane-rich plumes above our minimum detection limit. Multiple sites that pre-date the recent unconventional natural gas development were found to be emitting, and we observed that the majority of these older wells were associated with emissions on all survey repeats. We also observed emissions from gas processing facilities that were highly repeatable. Emission patterns in this area were best explained by infrastructure age and type. Extrapolating our results across all oil and gas infrastructure in the Montney area, we estimate that the emission sources we located (emitting at a rate > 0.59 g s −1 ) contribute more than 111 800 t of methane annually to the atmosphere. This value exceeds reported bottom-up estimates of 78 000 t of methane for all oil and gas sector sources in British Columbia. Current bottomup methods for estimating methane emissions do not normally calculate the fraction of emitting oil and gas infrastructure with thorough on-ground measurements. However, this study demonstrates that mobile surveys could provide a more accurate representation of the number of emission sources in an oil and gas development. This study presents the first mobile collection of methane emissions from oil and gas infrastructure in British Columbia, and these results can be used to inform policy development in an era of methane emission reduction efforts.