Yi Yang

Viruses in marine sediments: a review of their effect on biogeochemistry and microbial interactions | Applied and Environmental Microbiology In the ocean, viruses are known to mediate the carbon cycle, keeping dissolved organic carbon (DOC) in the microbial loop and preventing its movement into secondary consumers (1). However, few direct measurements of this carbon flux exist, and recent considerations of the ocean system consider that viruses can not only loop carbon in the dissolved pool but also participate in a carbon shuttle through the creation of aggregates that pellet or can be part of a viral vent that releases carbon into the atmosphere (2). While the pelagic ocean has been well reviewed for viral contributions to microbial diversity and biogeochemical cycling, less attention has been paid in recent years to the sedimentary portion of the ocean, where carbon is potentially stored over geological time, but viral influence can still be felt. Here, we review the literature on viruses in sedimentary ecosystems and their potential role in biogeochemistry and microbial diversity.

Viruses in marine sediments: a review of their effect on biogeochemistry and microbial interactions | Applied and Environmental Microbiology journals.asm.org/doi/full/10....

Complete genome sequences of Acetobacterium wieringae strains Y and N, capable of conjugated diene biohydrogenation | Microbiology Resource Announcements Acetobacterium wieringae is a strictly anaerobic bacterium in the order Eubacteriales (1). Here, A. wieringae strains Y and N, capable of metabolizing isoprene and 1,3-butadiene—pollutants linked to o...

Complete genome sequences of Acetobacterium wieringae strains Y and N, capable of conjugated diene biohydrogenation | Microbiology Resource Announcements journals.asm.org/doi/10.1128/...

Comparative Analysis of Phage Profiles in Environmental Samples: Metagenomic Sequencing Versus Culture-Bas... Culture-based isolation of bacteriophages from wastewater relies on a limited set of laboratory‐cultivable host strains, causing it to recover only a small fraction of the tru...

Comparative Analysis of Phage Profiles in Environmental Samples: Metagenomic Sequencing Versus Culture-Based Isolation www.protocols.io/view/compara...

Complete genome sequence of Rhodococcus qingshengii strain R isolated from Antarctic soil | Microbiology Resource Announcements Rhodococcus qingshengii strain R was isolated from a microcosm established with a sample of 5 g soil collected in 2010 from Beaufort Island in Antarctica (166° 58' 23.6" E, 76° 58' 23.6" S, depth 20.5...

Complete genome sequence of Rhodococcus qingshengii strain R isolated from Antarctic soil | Microbiology Resource Announcements journals.asm.org/doi/full/10....

Comparative proteogenomics reveals ecological and evolutionary insights into the organohalide-respiring Dehalobacter restrictus strain T | Applied and Environmental Microbiology Organohalide-respiring bacteria (OHRB) are essential for breaking down harmful pollutants in the environment. This study investigates a newly discovered OHRB capable of degrading multiple contaminants...

Comparative proteogenomics reveals ecological and evolutionary insights into the organohalide-respiring Dehalobacter restrictus strain T | Applied and Environmental Microbiology journals.asm.org/doi/10.1128/...

Dehalogenimonas Strain W from Estuarine Sediments Dechlorinates 1,2-Dichloroethane under Elevated Salinity Organohalide-respiring bacteria (OHRB) have been found in various environments and play an indispensable role in the biogeochemical cycling and detoxification of halogenated organic compounds (HOCs). Currently, few ORHB have been reported to perform reductive dechlorination under high salinity conditions, indicating a knowledge gap on the diversity of OHRB and the survival strategy of OHRB in saline environments (e.g., estuarine, marine). This study reports the characterization of an enrichment culture dominated by a new Dehalogenimonas population strain W derived from estuarine sediments, which demonstrates the capability to dechlorinate 1,2-dichloroethane (1,2-DCA) to ethene under elevated salinity (≥5.1% NaCl, w/v). Metagenomic and proteomic analyses revealed that the distinctive high-salinity dechlorination of strain W is primarily attributed to a putative reductive dehalogenase (RDase) DdeA, which shares >91.4% amino acid identity with the dihaloeliminating RDase DcpA from other Dehalogenimonas strains. Additionally, ectoine biosynthesis enzymes (EctABC) contribute to the strain’s salt tolerance. These findings underscore the potential of OHRB, particularly Dehalogenimonas, to detoxify HOCs in high-salinity environments, such as estuarine and marine ecosystems, by employing compatible solutes as an adaptive mechanism.

“Candidatus Dehalogenimonas loeffleri” pubs.acs.org/doi/10.1021/...

Adaption mechanism and ecological role of CPR bacteria in brackish-saline groundwater - npj Biofilms and Microbiomes npj Biofilms and Microbiomes - Adaption mechanism and ecological role of CPR bacteria in brackish-saline groundwater

www.nature.com/articles/s41...

The Pyramids of Giza, Egypt.

SCARAP: scalable cross-species comparative genomics of prokaryotes https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btae735/7921419 🧬🖥️🧪 https://github.com/swittouck/scarap

piqtree: IQ-TREE2 meets Python via cogent3 · iqtree piqtree · Discussion #145 The developers of IQ-TREE2 and cogent3 have joined forces to bring the power of IQ-TREE2 to Python users as piqtree. piqtree exposes selected IQ-TREE2 capabilities within Python, using the cogent3 ...

🐍🌲 piqtree: IQ-TREE2 meets Python via cogent3! 🤝⚡️

The developers of IQ-TREE2 and cogent3 have joined forces to bring the power of IQ-TREE2 to Python users as piqtree.

piqtree exposes selected IQ-TREE2 capabilities within Python, using the cogent3 library as the interface...

Genomics, evolution, and more starter pack!

Help build community with this starter pack.

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Release Canu v2.3 · marbl/canu These are release notes for Canu version 2.3, which was released on December 17th, 2024. Canu is specialized for assembly of single-molecule sequences. Full documentation can be found at http://can...

New release of Canu - first one in over 3 years!
github.com/marbl/canu/r...

The notes say this will be the very last release. Many thanks to its devs Brian Walenz and @sergek.bsky.social. Canu may be a bit old and it's certainly not fast, but it makes good assemblies and so I still use it!

GitHub - jwohlwend/boltz: Official repository for the Boltz-1 biomolecular interaction model Official repository for the Boltz-1 biomolecular interaction model - jwohlwend/boltz

New Title Alert: Boltz-1- an open-source model which predicts the 3D structure of proteins, rna, dna and small molecules; it handles modified residues, covalent ligands & glycans.

Learn more here: https://buff.ly/3ZAPowA

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The 2025 EMBL Annual Poster, listing all of the courses and conferences taking place in 2025 at EMBL

Hi Bluesky community! 👋

Are you looking forward to 2025 as much as we are? 👀

We just updated our 2025 Annual Poster to include even more events for you to join, so go and have a look!

➡️ s.embl.org/poster-bl

#EMBLEvents #molecularbiology #lifesciencetraining

You want to learn about microbiology from a fantastic lineup of speakers on a beautiful Greek island? PhD students apply now for the @EMBO | @FEBSnews Lecture Course The New Microbiology!
Registration: 1 Apr 2025
Course: 03 – 11 Sep 2025 | Spetses, Greece
meetings.embo.org/event/25-new...

Frontiers | Organohalide Respiration: Retrospective and Perspective through Bibliometrics Organohalide-respiring bacteria (OHRB) play a pivotal role in the transformation of organohalogens in diverse environments. This bibliometric analysis provid...

Organohalide Respiration: Retrospective and Perspective through Bibliometrics www.frontiersin.org/journals/mic... #OHRB

CO-driven electron and carbon flux fuels synergistic microbial reductive dechlorination - Microbiome Background Carbon monoxide (CO), hypothetically linked to prebiotic biosynthesis and possibly the origin of the life, emerges as a substantive growth substrate for numerous microorganisms. In anoxic e...

CO-driven electron and carbon flux fuels synergistic microbial reductive dechlorination microbiomejournal.biomedcentral.com/articles/10....

Complete genome sequence of “Candidatus Dehalogenimonas loeffleri” strain W, a highly salt-tolerant chlorinated alkane-dechlorinating bacterium isolated from estuarine sediments | Microbiology Resourc... Bioremediation of chlorinated contaminants in saline environments is challenging due to the inability of most organohalide-respiring bacteria (OHRB) to thrive under elevated salinity conditions (1–4),...

Complete genome sequence of “Candidatus Dehalogenimonas loeffleri” strain W, a highly salt-tolerant chlorinated alkane-dechlorinating bacterium isolated from estuarine sediments journals.asm.org/doi/10.1128/...