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Chris Rinke @chrisrinke.bsky.social · Apr 27

- 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.

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Chris Rinke @chrisrinke.bsky.social · Apr 27

... 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:

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Chris Rinke @chrisrinke.bsky.social · Apr 27

- 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 ...

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Chris Rinke @chrisrinke.bsky.social · Apr 27

Led by @Jiauri Sun & in collab with @Takuro Nunoura and team - we analysed shallow coastal & deep subseafloor sediment cores (0.01 to 600m below the seafloor) in the Western Pacific:

www.microbiologyresearch.org/content/jour...

We found that:

Metagenomic insights into taxonomic and functional patterns in shallow coastal and deep subseafloor sediments in the Western Pacific

Marine sediments are vast, underexplored habitats and represent one of the largest carbon deposits on our planet. Microbial communities drive nutrient cycling in these sediments, but the full extent o...

www.microbiologyresearch.org

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Chris Rinke @chrisrinke.bsky.social · Apr 17

GTDB Release 10-RS226 (16th April 2025) has been published
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.

gtdb.ecogenomic.org

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Reposted by Chris Rinke

Matthew Hahn @3rdreviewer.bsky.social · Apr 10

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...

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

ecoevorxiv.org

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Chris Rinke @chrisrinke.bsky.social · Apr 3

... 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"

Chris Rinke @chrisrinke.bsky.social · Apr 3

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 ...

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Chris Rinke @chrisrinke.bsky.social · Mar 13

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.

Chris Rinke @chrisrinke.bsky.social · Mar 13

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.

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Chris Rinke @chrisrinke.bsky.social · Mar 13

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

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Reposted by Chris Rinke

SeqCode @seqcode.bsky.social · Feb 11

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

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

doi.org

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Chris Rinke @chrisrinke.bsky.social · Feb 8

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

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Chris Rinke @chrisrinke.bsky.social · Feb 8

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

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Chris Rinke @chrisrinke.bsky.social · Feb 8

Great collaboration with Phil Hugenholz @xrefugee13.bsky.social, Tanja Woyke, Per Halkjær Nielsen, and many more:

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

doi.org/10.1093/isme...

Proposal of Patescibacterium danicum gen. Nov., sp. nov. in the ubiquitous ultrasmall 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

doi.org

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Chris Rinke @chrisrinke.bsky.social · Feb 8

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

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Chris Rinke @chrisrinke.bsky.social · Feb 4

#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

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Chris Rinke @chrisrinke.bsky.social · Jan 29

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/...

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Reposted by Chris Rinke

Nature @nature.com · Jan 24

Roughly 6,000 readers answered our poll, with many declaring that Bluesky was nicer, kinder and less antagonistic to science than X

https://go.nature.com/42tH8Ai

Bluesky’s science takeover: 70% of Nature poll respondents use platform

Roughly 6,000 readers answered our poll, with many declaring that Bluesky was nicer, kinder and less antagonistic to science than X.

go.nature.com

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Chris Rinke @chrisrinke.bsky.social · Jan 8

Big congrats to aprabhu90.bsky.social - this is the 2nd paper from her PhD project! 👏

Apoorva Prabhu (@aprabhu90.bsky.social)

Postdoctoral Research Associate - Sydney Institute of Marine Science Honorary Postdoc- University of Technology, Sydney PhD at the Australian Centre for Ecogenomics, The University of Queensland, Bri...

aprabhu90.bsky.social

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Chris Rinke @chrisrinke.bsky.social · Jan 8

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...

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...

doi.org

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Chris Rinke @chrisrinke.bsky.social · Nov 19

Have you tried it?

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Chris Rinke @chrisrinke.bsky.social · Nov 18

Great 👍

Chris Rinke @chrisrinke.bsky.social · Nov 17

Please add me as well:
scholar.google.com.au/citations?us...

Christian Rinke

‪Prof in Environmental Microbiology, University of Innsbruck, AUT & Honorary Associate Prof, UQ, AUS‬ - ‪‪Cited by 16,361‬‬ - ‪microbial evolution & ecology‬ - ‪multi-omics‬ - ‪microbial plastic degra...

scholar.google.com.au

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Chris Rinke @chrisrinke.bsky.social · Nov 17

The #microbial #climate #feedback hypothesis is already becoming reality ...

"shift in methane carbon isotopes suggests microbial emissions drove record high atmospheric methane growth"
#science 🧪
www.pnas.org/doi/10.1073/...

PNAS

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...

www.pnas.org

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