Sampling Design and Sample Processing Affect Soil Biodiversity Assessments Biodiversity surveys require an appropriate sampling design for optimal performance and comparability across space and time and across studies. Based on PacBio and Illumina amplicon sequencing of ani...

Manuscript link: onlinelibrary.wiley.com/doi/10.1111/... #soil #eDNA #metabarcoding @myco-microbio.bsky.social

Heatmap comparing richness ranks across soil sampling designs for three organism groups: animals, bacteria, and fungi. Three side-by-side panels, with various sampling designs by rows, and habitats (marked by tree icons) by columns.

How much does sampling design matter in soil biodiversity surveys? A lot. Our new manuscript shows how diversity changes with sampling design, depth, subsample number, and pooling. I'm especially happy this is the first manuscript from Meirong Chen's PhD work, and very proud of her progress.

Nice read on sandboxing with bwrap: sloonz.github.io/posts/sandbo...

Run shell commands in a lightweight sandbox (using `bubblewrap`) Run shell commands in a lightweight sandbox (using `bubblewrap`) - sbx.sh

Safeguard yourself: do backups (yes, now!), don't run random code on production systems. If you must run untrusted pipelines, you can bubblewrap them in a bwrap sandbox - here is an example (works transparently with conda envs & system tools): gist.github.com/vmikk/08212e...

Terminal screenshot showing a minimal bash loop demo: starting in $HOME/project, a for loop runs cd subdir (which fails if missing), then rm * in the current directory, followed by cd .., so on the next iteration it climbs to $HOME and rm * risks deleting files there.

20+ years on #Linux, 🧬🖥️ #bioinformatics pipelines daily - and one relaxed moment running a colleague's script nearly wiped my $HOME 😅 Here's how a silent cd+rm combo escaped my project dir, the original script was quite tangled, but it hid this construct [ ⚠️ danger zone, don't run 🔥 ]

New fungal phylum-level system, with red font indicating novel taxa and size taxonomic diversity.

Fungal phylum-level classification update now available! Used "innovative taxonomy" to describe >100 taxa, from species to phylum, based on long reads, characteristic nucleotides and env-samples.
mycokeys.pensoft.net/article/1616...

#fungi #taxonomy #PacBio #classification #eDNA

New article on equitable reuse of public sequencing data, published in @natmicrobiol.nature.com!
Led by the Data reuse core team @lhug.bsky.social @environmicrobio.bsky.social Cristina Moraru, @geomicrosoares.bsky.social, @folker.bsky.social and with Anke Heyer and The Data Reuse Consotrium!

Who lives underground?

Find out now in our new paper published in @nature.com.

Key finding: 90% of predicted mycorrhizal biodiversity hotspots lie outside protected areas.

Read here: buff.ly/WmDqAP3 🧵

Post-Doc position for 3 years available jointly between University of Tartu (Estonia) and University of Aarhus (Denmark) on soil microbiome and biogeography. Skills required: bioinformatics, metagenome analysis, microbiology
Contact: leho.tedersoo@ut.ee

AM fungi are vital for plants but their global richness remains underexplored. In our latest study, out in Fungal Ecology, we analyzed 4,733 sites, revealing 8,517 G-AMF OTUs (5–15x previous estimates) & 600 E-AMF OTUs, the first global count. Read it for free authors.elsevier.com/c/1kJ7y6ExPy...

A newly discovered fungal species emerges from the open pages of a scientific book, surrounded by various lab journals and books, with research tools scattered around. The image highlights the connection between scientific discovery and publishing.

🍄📖 Do high-impact journals lead to more fungal species discoveries? Think again! Low or even no-impact factor journals contribute significantly! Let's value research quality over impact metrics in funding and hiring decisions! Read more @MycoKeys: mycokeys.pensoft.net/article/136048