GPS mapping and fitness tracking

GPS mapping makes exploring new routes really easy and has certainly helped me get out more due to ease of finding routes. I also recently started using Strava to track my performance when running and cycling, providing additional motivation to get out. This post is about how I use Viewranger for mapping …

3D printing for research

We have just received funding from MMU to allow us to buy a 3D printer for research. I am exploring the use of this disruptive technology in my own environmental microbiology research, and am collaborating with other researchers who are interested in applying it in other projects including bryophyte photosynthesis …

Diverse mycorrhizal representation and bacterial-fungal interactions in an upland peatland vegetation mosaic undergoing restoration

Peatlands are under threat from land management, anthropogenic pollution and climate change. These factors are implicated in severe degradation of peatlands in the southern Pennines of northern England. Significant areas of unconsolidated bare peat are both highly vulnerable to peat erosion and resistant to natural re-vegetation. Restoration efforts during the …

Networks of Power and Influence

This week I am attending the 33rd New Phytologist symposium (Networks of Power and Influence) with Robin Sen and Francis Brearley from MMU. I will present a poster of work supported by MMU and Moors for the Future. The poster shows a preliminary network analysis of bacterial and fungal microbial …

Reproducible research

The statistical analyses for our recent paper on the bacterial communities of biological soil crusts in the Kalahari can be fully examined and reproduced via code and data I have deposited on GitHub. The analysis relies heavily on the phyloseq package for R. The phyloseq paper and associated documentation were really an inspiration, and …

Override autocorrect in Excel cells

As a microbial ecologist I often work with spreadsheets where I want to use the header “OTU” which means operational taxonomic unit. We use this acronym instead of saying species because the species concept for microbes is not very clear. Anyway, in Excel you can’t write “OTU” in a cell …

Transparency in PDF output from MS publisher

When using Microsoft Publisher you will likely want to export to PDF for circulation or printing. At this stage I found that all my transparent layers got spoilt and I found some tricky ways to work around it like printing to a PDF printer, but this is not very satisfactory. …

Niche partitioning of bacterial communities in biological crusts and soils under grasses, shrubs and trees in the Kalahari

The Kalahari of southern Africa is characterised by sparse vegetation interspersed with microbe-dominated biological soil crusts (BSC) which deliver a range of ecosystem services including soil stabilisation and carbon fixation. We characterised the bacterial communities of BSCs (0–1 cm depth) and the subsurface soil (1–2 cm depth) in an area typical of …