The spatial organization and microbial community structure of an epilithic biofilm.

Microbial biofilms are common on lithic surfaces, including stone buildings. However, the ecology of these communities is poorly understood. Few studies have focused on the spatial characteristics of lithobiontic biofilms, despite the fact that spatial structure has been demonstrated to influence ecosystem function (and hence biodegradation) and community diversity. Furthermore, relatively few studies have utilized molecular techniques to characterize these communities, even though molecular methods have revealed unexpected microbial diversity in other habitats. This study investigated (1) the spatial structure and (2) the taxonomic composition of an epilithic biofilm using molecular techniques, namely amplicon pyrosequencing and terminal restriction fragment length polymorphism. Dispersion indices and Mantel correlograms were used to test for the presence of spatial structure in the biofilm. Diversity metrics and rank-abundance distributions (RADs) were also generated. The study revealed spatial structure on a centimetre scale in eukaryotic microbes (fungi and algae), but not the bacteria. Fungal and bacterial communities were highly diverse; algal communities much less so. The RADs were characterized by a distinctive 'hollow' (concave up) profile and long tails of rare taxa. These findings have implications for understanding the ecology of epilithic biofilms and the spatial heterogeneity of stone biodeterioration.This work was supported by the Engineering and Physical Sciences Research Council (grant no. EP/G011338/1).This is the author accepted manuscript. The final version is available from OUP at http://femsec.oxfordjournals.org/content/91/3/fiu027

Impact of small-scale vegetation structure on tephra layer preservation.

The factors that influence tephra layer taphonomy are poorly understood, but vegetation cover is likely to play a role in the preservation of terrestrial tephra deposits. The impact of vegetation on tephra layer preservation is important because: 1) the morphology of tephra layers could record key characteristics of past land surfaces and 2) vegetation-driven variability in tephra thickness could affect attempts to infer eruption and dispersion parameters. We investigated small- (metre-) scale interactions between vegetation and a thin (<10 cm), recent tephra layer. We conducted surveys of vegetation structure and tephra thickness at two locations which received a similar tephra deposit, but had contrasting vegetation cover (moss vs shrub). The tephra layer was thicker and less variable under shrub cover. Vegetation structure and layer thickness were correlated on the moss site but not under shrub cover, where the canopy reduced the influence of understory vegetation on layer morphology. Our results show that vegetation structure can influence tephra layer thickness on both small and medium (site) scales. These findings suggest that some tephra layers may carry a signal of past vegetation cover. They also have implications for the sampling effort required to reliably estimate the parameters of initial deposits

Variations in tephra stratigraphy created by small-scale surface features in sub-polar landscapes

Financial support for this work was provided by NERC Doctoral Training Partnership Ph.D. studentship NE/L002558/1 to Polly I. J. Thompson.We explore the effect small-scale surface features have on influencing the morphology and grain-size distribution (GSD) of tephra layers within the Quaternary stratigraphy of sub-polar landscapes. Icelandic thúfur, small cryogenic earth mounds, are used to assess how and why the morphology and GSD of tephra layers vary over such formations. Through measurement of tephra layer thickness and GSD, Hekla 1947 and Grímsvötn 2011 tephra layers are analysed. Results indicate that such microtopographic features do indeed alter the form of tephra deposits and therefore the tephra layer that is preserved in the stratigraphy. Tephra thickness is significantly greater in hollows than on the thúfur crests. There is greater variation in tephra thickness measurements from thúfur in comparison to control measurements from a surface where thúfur are absent. Thúfur crests contain larger grain sizes than hollows, for both H1947 and G2011 tephras; however this was only statistically significant for the G2011 tephra. Such morphological patterns are thought to arise from an interplay of tephra characteristics, altered topography from the thúfur formations and earth surface processes operating at the sites. This study provides insight into the potential of tephra layer morphology and internal structures as indicators of Quaternary landforms and processes. Additionally, it provides important context for the appropriate sampling of tephra layers to infer volcanological processes, as the characteristics of preserved layers do not necessarily reflect those of the original fall-out.Publisher PDFPeer reviewe

Tephra transformations: variable preservation of tephra layers from two well-studied eruptions

Financial support was provided by the National Science Foundation of America through grant 1202692 ‘Comparative Island Ecodynamics in the North Atlantic’, and grant 1249313 ‘Tephra layers and early warning signals for critical transitions’ (both to AJD).Volcanologists often use terrestrial tephra layers to reconstruct volcanic eruptions. However, the conversion of fresh tephra deposits into tephra layers is poorly understood. To address this knowledge gap, we surveyed tephra layers emplaced by the 1980 eruption of Mount St Helens, USA (MSH1980) and the 1947 eruption of Hekla, Iceland (H1947). We compared our measurements with observations made shortly after the 1947 and 1980 eruptions, to calibrate the subsequent transformation of the tephra deposit. We expected the tephra layers to retain the broad characteristics of the original deposits, but hypothesized a) changes in thickness and mass loading due to re-working, and b) positive correlations between thickness and vegetation density. We observed some systematic changes in tephra layer properties with distance from the vent and the main plume axis. However, the preservation of the layers varied both between and within our survey locations. Closed coniferous forest appeared to provide good conditions for the preservation of the MSH1980 tephra, as expected; preservation of the H1947 deposit in sparsely vegetated parts of Iceland was much more variable. However, preservation of the MSH1980 deposit in sparsely vegetated areas of eastern Washington State was also excellent, possibly due to biocrust formation. We concluded that the preservation of tephra layers is sensitive to surface conditions at the time of the eruption. These findings have implications for the reconstruction of past eruptions where eruption plumes span regions of variable surface cover.PostprintPeer reviewe

Global ecological predictors of the soil priming effect.

Identifying the global drivers of soil priming is essential to understanding C cycling in terrestrial ecosystems. We conducted a survey of soils across 86 globally-distributed locations, spanning a wide range of climates, biotic communities, and soil conditions, and evaluated the apparent soil priming effect using 13C-glucose labeling. Here we show that the magnitude of the positive apparent priming effect (increase in CO2 release through accelerated microbial biomass turnover) was negatively associated with SOC content and microbial respiration rates. Our statistical modeling suggests that apparent priming effects tend to be negative in more mesic sites associated with higher SOC contents. In contrast, a single-input of labile C causes positive apparent priming effects in more arid locations with low SOC contents. Our results provide solid evidence that SOC content plays a critical role in regulating apparent priming effects, with important implications for the improvement of C cycling models under global change scenarios

Long-Term Recovery of Microbial Communities in the Boreal Bryosphere Following Fire Disturbance.

Our study used a ∼360-year fire chronosequence in northern Sweden to investigate post-fire microbial community dynamics in the boreal bryosphere (the living and dead parts of the feather moss layer on the forest floor, along with the associated biota). We anticipated systematic changes in microbial community structure and growth strategy with increasing time since fire (TSF) and used amplicon pyrosequencing to establish microbial community structure. We also recorded edaphic factors (relating to pH, C and N accumulation) and the physical characteristics of the feather moss layer. The molecular analyses revealed an unexpectedly diverse microbial community. The structure of the community could be largely explained by just two factors, TSF and pH, although the importance of TSF diminished as the forest recovered from disturbance. The microbial communities on the youngest site (TSF = 14 years) were clearly different from older locations (>100 years), suggesting relatively rapid post-fire recovery. A shift towards Proteobacterial taxa on older sites, coupled with a decline in the relative abundance of Acidobacteria, suggested an increase in resource availability with TSF. Saprotrophs dominated the fungal community. Mycorrhizal fungi appeared to decline in abundance with TSF, possibly due to changing N status. Our study provided evidence for the decadal-scale legacy of burning, with implications for boreal forests that are expected to experience more frequent burns over the course of the next century.Natural Environment Research Council (Grant ID: NE/ I027150/1), Royal Geographical Society (Grant ID: SRG 13:13), Trinity College Cambridg

'Instead of "closing down" at our ages… we’re thinking of exciting and challenging things to do': older people’s microadventures outdoors on (e-)bikes

This paper explores how people aged 50 and over, who were returning to cycling as part of an eight-week health and wellbeing trial, created their own cycling microadventures. Applying a stage model of the process of adventure to qualitative data generated from personal diaries and focus groups, we examine how older people anticipated and prepared for their microadventures, the challenges and discoveries they experienced, the benefits they gained and how electrically assisted ‘e-bikes’ can provide further opportunities for adventure. We conclude that cycles are a mode uniquely placed to facilitate microadventures and that e-bikes, in particular, offer further potential to enable older people to (re-)connect with place and other people. But, while this type of activity can provide benefits in terms of health and wellbeing, we argue that more supportive physical and social infrastructure is required to provide opportunities for more people to undertake microadventures close to their homes

Integration of Global Signaling Pathways, cAMP-PKA, MAPK and TOR in the Regulation of FLO11

The budding yeast, Saccharomyces cerevisiae, responds to various environmental cues by invoking specific adaptive mechanisms for their survival. Under nitrogen limitation, S. cerevisiae undergoes a dimorphic filamentous transition called pseudohyphae, which helps the cell to forage for nutrients and reach an environment conducive for growth. This transition is governed by a complex network of signaling pathways, namely cAMP-PKA, MAPK and TOR, which controls the transcriptional activation of FLO11, a flocculin gene that encodes a cell wall protein. However, little is known about how these pathways co-ordinate to govern the conversion of nutritional availability into gene expression. Here, we have analyzed an integrative network comprised of cAMP-PKA, MAPK and TOR pathways with respect to the availability of nitrogen source using experimental and steady state modeling approach. Our experiments demonstrate that the steady state expression of FLO11 was bistable over a range of inducing ammonium sulphate concentration based on the preculturing condition. We also show that yeast switched from FLO11 expression to accumulation of trehalose, a STRE response controlled by a transcriptional activator Msn2/4, with decrease in the inducing concentration to complete starvation. Steady state analysis of the integrative network revealed the relationship between the environment, signaling cascades and the expression of FLO11. We demonstrate that the double negative feedback loop in TOR pathway can elicit a bistable response, to differentiate between vegetative growth, filamentous growth and STRE response. Negative feedback on TOR pathway function to restrict the expression of FLO11 under nitrogen starved condition and also with re-addition of nitrogen to starved cells. In general, we show that these global signaling pathways respond with specific sensitivity to regulate the expression of FLO11 under nitrogen limitation. The holistic steady state modeling approach of the integrative network revealed how the global signaling pathways could differentiate between multiple phenotypes

Genetic mechanisms of critical illness in COVID-19.

Host-mediated lung inflammation is present1, and drives mortality2, in the critical illness caused by coronavirus disease 2019 (COVID-19). Host genetic variants associated with critical illness may identify mechanistic targets for therapeutic development3. Here we report the results of the GenOMICC (Genetics Of Mortality In Critical Care) genome-wide association study in 2,244 critically ill patients with COVID-19 from 208 UK intensive care units. We have identified and replicated the following new genome-wide significant associations: on chromosome 12q24.13 (rs10735079, P = 1.65 × 10-8) in a gene cluster that encodes antiviral restriction enzyme activators (OAS1, OAS2 and OAS3); on chromosome 19p13.2 (rs74956615, P = 2.3 × 10-8) near the gene that encodes tyrosine kinase 2 (TYK2); on chromosome 19p13.3 (rs2109069, P = 3.98 ×  10-12) within the gene that encodes dipeptidyl peptidase 9 (DPP9); and on chromosome 21q22.1 (rs2236757, P = 4.99 × 10-8) in the interferon receptor gene IFNAR2. We identified potential targets for repurposing of licensed medications: using Mendelian randomization, we found evidence that low expression of IFNAR2, or high expression of TYK2, are associated with life-threatening disease; and transcriptome-wide association in lung tissue revealed that high expression of the monocyte-macrophage chemotactic receptor CCR2 is associated with severe COVID-19. Our results identify robust genetic signals relating to key host antiviral defence mechanisms and mediators of inflammatory organ damage in COVID-19. Both mechanisms may be amenable to targeted treatment with existing drugs. However, large-scale randomized clinical trials will be essential before any change to clinical practice