iiinova — where your digital self keeps evolving

Chris Rinke @chrisrinke.bsky.social · 18h

The goal is to make plates analysis faster, more reproducible, and accessible to any lab. Now we’d love your feedback. 💬 Test it on your plates, open an issue, or share your results - community input will help us improve the tool further. Let’s make colony counting easier for everyone 😊

lnkd.in

This link will take you to a page that’s not on LinkedIn

100

Chris Rinke @chrisrinke.bsky.social · 18h

🚀 Excited to introduce Agar3000 - our open‑source tool for automatic colony counting! Developed by Vadym Sokhan, Agar3000 detects & counts microbial colonies directly from smartphone photos. We’ve validated it across multiple datasets, growth media, and illumination setups: lnkd.in/dAX2qdkB

lnkd.in

This link will take you to a page that’s not on LinkedIn

141

Chris Rinke @chrisrinke.bsky.social · 31/08/2026

By identifying both known degraders and previously uncharacterized genera with strong biodegradation potential, this work offers a targeted foundation for experimental validation and enzyme discovery.

000

Chris Rinke @chrisrinke.bsky.social · 31/08/2026

High hit densities in polluted rivers, deep-sea environments and polar oceans highlight habitats where natural plastic turnover may be most active.

110

Chris Rinke @chrisrinke.bsky.social · 31/08/2026

We reveal that putative plastic-degrading capacity is far more widespread across #GTDB taxa than previously recognized, spanning diverse bacterial groups and, unexpectedly, #archaeal taxa.

210

Chris Rinke @chrisrinke.bsky.social · 31/08/2026

This study provides a broad, data-driven assessment of genes encoding potential plastic-degrading enzymes across major ecosystems and microbial lineages by applying curated Hidden Markov Models to extensive metagenomic and genomic datasets.

100

Chris Rinke @chrisrinke.bsky.social · 31/08/2026

Plastic pollution is a growing global threat, yet the diversity and distribution of microorganisms capable of degrading plastics remain poorly understood.

100

Chris Rinke @chrisrinke.bsky.social · 31/08/2026

Excited to report that our paper 📃 "Predicting the plastic biodegradation potential within microbial lineages and across global ecosystems" by Harmony Douwes, and Zuzanna Dutkiewicz is out! lnkd.in/d2HN2jsj

lnkd.in

This link will take you to a page that’s not on LinkedIn

175

Reposted by Chris Rinke

Zeke Hausfather @zekehausfather.com · 13/07/2026

With all the July model runs now in, it is very likely that 2026 will see the largest El Niño event since records began in the late 1800s – and potentially by a truly mind-blowing margin. The median estimate is now 3.6C, roughly 0.8C hotter than the prior record (2.75C). www.theclimatebrink....

16514344

Chris Rinke @chrisrinke.bsky.social · 20/04/2026

Thanks, we also implemented the Qiime2 pipeline with SILVA reference as wrapper script – it works well :-)

010

Reposted by Chris Rinke

ace-gtdb.bsky.social @ace-gtdb.bsky.social · 15/04/2026

GTDB release 11 based on RefSeq 232 (R11-RS232) is live at gtdb.ecogenomic.org. This release covers 901,341 genomes (23% increase) and has 199,923 species clusters (39% increase). Release notes at: forum.gtdb.ecogenomic.org/t/announcing.... Release statistics at: gtdb.ecogenomic.org/stats/r232.

gtdb.ecogenomic.org

GTDB - Genome Taxonomy Database

The Genome Taxonomy Database (GTDB) is an initiative to establish a standardised microbial taxonomy based on genome phylogeny.

15331

Reposted by Chris Rinke

Cheong Xin (CX) Chan @chancx.bsky.social · 30/09/2025

Don't miss out on the 3rd West Pacific Marine Biology Symposium @ UQ Brisbane, 25–28 Nov. Reg & abstracts open: tinyurl.com/wpmbs2025 Early-bird regos now extended to 14 Oct, so you can still secure discounted registration rates! @cnrs.fr @cnrsbiologie.bsky.social UQ Centre for Marine Science

014

Chris Rinke @chrisrinke.bsky.social · 27/04/2025

- Tangaroaeota phyl. nov. (former RBG-13-66-14) - Ryujiniota phyl. nov. (former UBA6262) and - Spongiamicota phyl. nov. (former UBA8248) In summary, we contributed to the understanding of taxonomic and functional diversity in benthic prokaryotic communities across Western Pacific sediments.

030

Chris Rinke @chrisrinke.bsky.social · 27/04/2025

... aerobic respiration and photosynthesis in the shallowest sediment layers to heterotrophic carbon utilization, sulphate reduction and methanogenesis in deeper anoxic sediments. We recovered high-quality metagenome-assembled genomes for all main prokaryotic lineages & proposed names for 3 phyla:

110

Chris Rinke @chrisrinke.bsky.social · 27/04/2025

- metagenomics based taxonomy revealed clusters across all samples, that mainly aligned with depth & sediment type - Thermoproteota & Asgardarchaeota were the most abundant archaeal phyla; Archaea relative abundances > 50% in some samples - Metabolic capabilities ranged from ...

110

Reposted by Chris Rinke

Matthew Hahn @3rdreviewer.bsky.social · 10/04/2025

Not really my announcement to make--I am but a lesser co-author--but IQ-TREE 3 has just been released! (Most credit to Minh Bui and @roblanfear.bsky.social and their labs) ecoevorxiv.org/repository/v...

ecoevorxiv.org

IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models

217896

Chris Rinke @chrisrinke.bsky.social · 03/04/2025

... there is now (2025) a new rule 72 in the ICNP that says "if ... the proposed name is a synonym of a pro-validly published and pro-legitimate Candidatus name of the same rank, then that Candidatus name must be reused"

000

Chris Rinke @chrisrinke.bsky.social · 03/04/2025

Yes, it will be interesting to see how this all plays out - SeqCode vs ICNP. Using previously introduced names is beneficial indeed, and supports taxonomic stability. It seems that the ICSP has realised that as well ...

100

Chris Rinke @chrisrinke.bsky.social · 13/03/2025

Re Minisyncoccota paper #1: Besides the Code controversy, it is a good and longstanding practice to consider previous names, when proposing a new name for a lineage. Unfortunately, these authors did not consider this.

000

Chris Rinke @chrisrinke.bsky.social · 13/03/2025

But, there is obviously a controversy brewing when it comes to authors publishing names under the ICNP that are in conflict with #SeqCode validated names. This is possible since the ICSP does not (yet) recognize SeqCode names. Hopefully that will change soon.

100

Chris Rinke @chrisrinke.bsky.social · 13/03/2025

Not so fast 😊 , #Patescibacteriota is a validly published phylum name under the #SeqCode and is here to stay ;-)

200

Reposted by Chris Rinke

SeqCode @seqcode.bsky.social · 11/02/2025

Originally defined by Rinke et al. (2013) as Candidatus Patescibacteria, the phylum #Patescibacteriota now has a validly published name and an official type! Explore the lifestyle, biogeography, and metabolic capabilities of its type genus, #Patescibacterium, here: doi.org/10.1093/isme... #SeqCode

doi.org

Proposal of Patescibacterium danicum gen. nov., sp. nov. in the ubiquitous bacterial phylum Patescibacteriota phyl. nov.

Abstract. Candidatus Patescibacteria is a diverse bacterial phylum that is notable for members with ultrasmall cell size, reduced genomes, limited metaboli

1104

Chris Rinke @chrisrinke.bsky.social · 08/02/2025

Btw based on phylogenetic diversity, #Patescibacteriota is the fourth-largest phylum in the bacterial domain 😀

030

Chris Rinke @chrisrinke.bsky.social · 08/02/2025

The paper: - covers nomenclatural types for higher ranks including the phylum Patescibacteriota - includes genomic characterization, metabolic reconstruction, and biogeographical analysis of Patescibacterium - explores the occurrence of long gene coding insertions in the 23S rRNA sequences

120

Chris Rinke @chrisrinke.bsky.social · 08/02/2025

Hmm seems like bsky is not like Twitter/X once was, not much of a discussion here ... or nobody does amplicon sequencing any more 🤣😱🤔

100

Chris Rinke @chrisrinke.bsky.social · 04/02/2025

#Amplicon #16S pipeline in 2025 Hi all, since my lab has moved (from ⛱️ to ⛰️), we now need to establish a new #Amplicon pipeline, mostly 16S but also ITS (fungi). So my question is, is QIIME 2 still state of the art, or are there other/ better tools/workflows out there now? Thanks ☺️

Futuristic visionbof a rRNA gene analysis pipeline, illustrated by AI

362

Chris Rinke @chrisrinke.bsky.social · 29/01/2025

Best #paper #acknowledgements ever 😀 So honest. "Thanks finally to five anonymous reviewers .... and to R.N. whose editorial generosity bears no small responsibility for this paper's rescue from an early grave. .... I've supplied all errors myself." doi.org/10.1093/jos/...

130

Chris Rinke @chrisrinke.bsky.social · 08/01/2025

New #marine #virus paper out 😀 "Insights Into Phylogeny, Diversity and Functional Potential of Poseidoniales Viruses" > we proposed 2 new Magrovirales families: - Apasviridae (magrovirus group A) - Krittikaviridae (magrovirus group E) > and 1 new order: - Adrikavirales doi.org/10.1111/1462...

doi.org

Insights Into Phylogeny, Diversity and Functional Potential of Poseidoniales Viruses

Our spatio-temporal metagenomic study of a subtropical estuary successfully identified viruses and their potential hosts. Viral contigs were detected using a consensus approach comprising geNOMAD and...

175

Chris Rinke @chrisrinke.bsky.social · 17/11/2024

If archaeal viruses count, please add me as well- cheers

100

Chris Rinke @chrisrinke.bsky.social · 03/11/2024

Convincing article about flame retardants in recycled black plastic utensils. We have replaced ours already www.theatlantic.com/health/archi...

theatlantic.com

Throw Out Your Black Plastic Spatula

It’s probably leaching chemicals into your cooking oil.

000

Chris Rinke @chrisrinke.bsky.social · 25/10/2024

A great day for a short after-work hike and a hut visit with the lab 😀

020

Reposted by Chris Rinke

Botany One @botany.one · 25/10/2024

Assistant Professor in Fungal Biology botany.fyi/8uuuga University of California Riverside invites applicants for an Assistant Professor in Fungal Biology position with a focus on molecular plant-fungal interactions in agriculture or natural ecosystems. #PlantSciJobs

botany.fyi

Assistant Professor in Fungal Biology

University of California, Riverside is hiring. Apply now!

0817

Chris Rinke @chrisrinke.bsky.social · 22/10/2024

Would love to be on the list as well- cheers

000

Reposted by Chris Rinke

Roland Hatzenpichler @environmicrobio.bsky.social · 11/10/2024

My department at Montana State University is starting a faculty search for the position of Assistant Professor of Biochemistry: jobs.montana.edu/postings/43522 Feel free to contact me with questions. #Ilivewhereyouwannagoonvacation

0814

Reposted by Chris Rinke

Jonathan Eisen @phylogenomics.bsky.social · 17/09/2024

Assistant Professor of Teaching in the Dept. of Evolution and Ecology at UC Davis Open position in the Department of Evolution and Ecology at UC Davis (my home department). See recruit.ucdavis.edu/JPF06690

recruit.ucdavis.edu

Professor of Teaching (PoT)

University of California, Davis is hiring. Apply now!

03053

Chris Rinke @chrisrinke.bsky.social · 15/12/2023

Currently, we have the following open positions in the Rinke Group for Microbial MultiOmics and Biorecycling (MMOB) @ the University of Innsbruck, Austria: 1x postdoc 3x PhD 1x RA More info @ rinkelab.org/index.php/op...

02528