Fungal ecologist. Interested in bioinformatics, metagenomics & statistics. PostDoc at the University of Tartu, 🇪🇪
Vladimir Mikryukov
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Fungal communities in faeces, wood, and subsoil were especially distinct, while leaves, mosses, snow, and topsoil were strongly linked. The patterns show how environmental filtering and dispersal shape fungal distributions across forest ecosystems.
@myco-microbio.bsky.social
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.
How specialized are forest fungi 🍄🟫? Very. In our new study of 11 forest substrates, 63% of 2,772 fungal species were found in only a single substrate, and over 70% occurred in fewer than three.
📑 www.sciencedirect.com/science/arti...
#Fungi #Mycology #ForestEcology #Ecology #BiodiversityScience
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...
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 🔥 ]
Nice read on sandboxing with bwrap: sloonz.github.io/posts/sandbo...
Do forest fungi prefer to grow in/on specific substrates?
Two new papers, including one in Fungal Ecology, examine substrate specificity of boreal forest fungi.
doi.org/10.1016/j.fu...
doi.org/10.1111/mec....
@tedersoo.bsky.social @drhyfe.bsky.social @sundymaurice.bsky.social
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!
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
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...
