James Kosmopoulos

Metabolic capacity is maintained despite shifts in microbial diversity in estuary sediments Abstract. Estuaries are highly productive ecosystems where microbial communities drive nutrient and carbon cycling, supporting complex food webs. With inte

So happy this is finally out! We reconstructed the 1st large-scale spatiotemporal dataset of 600+ MAGs from San Francisco Bay and show they have functional redundancy in key N and S pathways. These functions may better recover from disturbance in this highly urban estuary 💧

@natmicrobiol.nature.com

Taken together, our results show that viruses don't just track host populations but actively respond to environmental conditions with degradation and restoration. Integrating viruses into restoration monitoring will strengthen our ability to assess and enhance peatland ecosystem recovery.

We then show that virus-host abundance trends across several host phyla change with ecosystem health. And, the proportion of temperate viruses increase in damaged soils, which have greater microbial growth rates than natural ones, suggesting piggyback-the-winner dynamics prevail in damaged peatlands

Protein clusters largely contained proteins encoded by viruses from soils of the same ecosystem health. And, specific protein families and auxiliary metabolic genes differed across natural, restored, and damaged soils, showing that viral protein functions are finely tuned to ecosystem health.

Differential abundance analysis across ecosystem health showed more damaged-enriched viruses than restored or natural. And, viral trends often diverged from their hosts, especially for certain C and S cyclers, showing that viral responses to degradation and restoration don't just mirror host shifts.

Most viral species appeared at multiple sites, but 54% were endemic to a single ecosystem health status (natural, damaged, or restored). Many genomes also clustered with viruses from other soil databases, suggesting a shared soil viral "backbone" plus strong local adaptation to ecosystem health.

a, Map of the seven peatland sites. Natural, restored and damaged sampling blocks of EHS are coloured by their average EHI. The map shading indicates peatland cover. No natural blocks were sampled at Stean. b, PCoA of viral community Bray–Curtis dissimilarities (n = 60 soil samples). ANOSIM (999 permutations) shows significant separation by site (R = 0.656, P = 1.0 × 10−3, unadjusted). c, Site-specific PCoAs with ANOSIM statistics for separation of communities by EHS (999 permutations; exact R and P values shown on plots). d, The PCoA from b coloured by EHI. PerMANOVA (two-sided, 999 permutations) reports the marginal R2 for variance in community dissimilarity explained by EHI (R2index = 0.029, P = 4.5 × 10−3 BH-adjusted) and EHS (R2status = 0.051, P = 1.0 × 10−4, BH-adjusted). e, Linear regression of PCoA axis 1 against EHI, where the black line represents the fitted regression mean and the shaded band indicates the 95% confidence interval around the fitted line. Regression statistics from a linear model of the two axes are provided (R2 = 0.30, P = 5.28 × 10−6).

There were several interesting findings! First, PCoA of viral communities showed geography as the main driver of community composition. But ecosystem health also significantly shaped peatland viral communities across the UK.

But the roles of viruses in peatland ecology and recovery were still not understood. @karthik-a.bsky.social and I collaborated with Ashish and Will to examine the relationships between viral communities, their microbial hosts, and environmental factors in natural, damaged, and restored peatlands.

Recovery of microbial ecophysiology and carbon accrual functions in peatlands under restoration Peatlands are water-logged ecosystems that limit microbial decomposition making them effective carbon sinks. However, drainage or erosion removes these constraints on decomposition, switching them to ...

@ashish-malik.bsky.social and his student Will Pallier sampled peatlands spanning a gradient of ecosystem health. They asked how microbial ecophysiology influences carbon fluxes and responds to peatland degradation and restoration. You can read their pre-print here www.biorxiv.org/content/10.1...

Peatlands store 1/3 of Earth’s soil carbon, but drainage can turn them from carbon sinks to sources and accelerate climate change. Restoration aims to reverse that. Since soil microbiomes regulate carbon cycling, understanding how they respond to recovery is crucial for monitoring restoration.

Ecosystem health shapes viral ecology in peatland soils - Nature Microbiology Metagenomics shows that viral diversity and community structure are shaped by geography and ecosystem health status, positioning viruses as unexpected players in peatland restoration.

Soil viruses are important regulators of ecosystem function, but what are their roles in environments that face long-term degradation and restoration? In our paper published today in Nature Micro, we asked how soil viruses influence peatland recovery, and vice versa. www.nature.com/articles/s41...

Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomes Abstract. Viruses are ubiquitous in all environments and impact host metabolism, evolution, and ecology, although our knowledge of their biodiversity is st

🦠🧪🧬🚨 New paper and database alert: the new IMG/VR release is now MetaVR ! We have a new website - meta-virome.org - with quick search capabilities for the >24M viruses, >12M vOTUs, and >42M protein clusters (including >790k with predicted structures !). academic.oup.com/nar/advance-...

Comparison of virus-host prediction from Hi-C and in silico tools. Top: Eular plot showing the overlap of viruses with host predictions obtained from the experimental Hi-C linkage approach, or one of two in silico tools (iPHoP and VirMatcher) that use different probabilistic models to aggregate output of various sequence-based features to create host prediction scores. Bottom: Comparison of virus-host predictions across all samples between Hi-C and iPHoP, shown with and without applying a Z-score filter for the Hi-C linkages. Black bars indicate congruent predictions identified from both tools and gray bars indicate non-congruent predictions. Note: Although many viruses had multiple predicted hosts from each tool, only the top-scoring prediction for each virus was considered in this comparison.

#Virus discovery has accelerated but linking viruses to hosts is hard. @sullivan-lab.bsky.social use synthetic #microbiomes to optimize & benchmark #Hi-C for virus-host linkage inference, applying this to existing #soil data to reveal 100s of novel linkages @plosbiology.org 🧪 plos.io/3MlAENO

Surely SOMEBODY mourns the wicked

Thank you Ashish! That means a lot, coming from you 🙂

Viral Dark Matter: Illuminating Protein Function, Ecology, and Biotechnological Promises Viruses are the most abundant biological entities on Earth and play central roles in shaping microbiomes and influencing ecosystem functions. Yet, most viral genes remain uncharacterized, comprising w...

Viral "dark matter" dominates the virosphere. In this review by me & @karthik-a.bsky.social, we synthesize what's known, highlight major gaps, and outline paths forward for illuminating viral protein functions in diverse ecosystems.

Scalable and systematic hierarchical virus taxonomy with vConTACT3 Viruses are key players in diverse ecosystems, but studying their impacts is technically and taxonomically challenging. Taxonomic complexities derive from undersampling, diverse DNA and RNA genomes wi...

🚨vConTACT3 preprint live!🚨(Peer Review soon...!)

vConTACT3 delivers a unified, scalable, and transparent framework for genome-based virus taxonomy — helping translate big viral data into systematic classification.

🔗 Read the preprint: doi.org/10.1101/2025...

Improvements details below 👇

Beautiful!!!

I also really like the feature that links publications to the annotations obtained for each gene. Really useful. Nice work!

Hi Yunha. Just tried this with a MAG from one of my datasets. I'm super impressed by how fast it annotated the whole genome. How does SeqHub obtain its HMM and embedding-based annotations so quickly? Just curious, because it blew me away!

Poster showing the following text: PhD in microbial mechanisms of soil carbon cycling. Soil microbes shape the global carbon cycle in life and death. We study the effect of aboveground land management on belowground soil carbon cycling processes. We aim create a scalable understanding of microbial processes from single cells to populations to communities to ecosystems. Pictures with text: peatland restoration, sustainable agriculture and woodland regeneration.

📢 Funded PhD opportunities for UK candidates in beautiful Edinburgh. Get in touch if you're interested in a PhD on understanding the mechanisms of soil carbon cycling and the role of microbes. We work in different ecosystems: peatlands, forests and agricultural soils. Please repost/spread the word.

You might still... but probably to ask you "Have you tried the Nug-ee's?"

@urineri.bsky.social Have you seen this new sequence aligner? I wonder if its approach would help mitigate some of the alignment issues you pointed out in your preprint on spacer-protospacer alignments.

Your support means the world to us. Thank you for helping my family take these steps together!

Parkinson's Foundation: Keep on Moving! The Parkinson's Foundation Moving Day Walk is a fun, inspiring fundraising event that unites families, friends and communities in the fight against Parkinson's disease. Held in cities across the Unite...

Please donate whatever you can to our team (Team Kosmo!) to stand with us and my dad in our effort to build a better future for people with Parkinson's. Here's the link to donate: secure.parkinson.org/site/TR/Movi...

My goal is to raise $500 by October 5th. Every dollar raised goes directly to the Parkinson's Foundation, funding research, improving care, and providing resources that make a real difference for families like ours.

I'm so proud of how he's faced it by staying active, raising awareness, and by doing what he does best: (1) being a great dad, and (2) being a very talented DJ who brings people together, making them dance, and showing that you don't have to let life's hurdles stop you from doing what you love.

This past year, my dad was diagnosed with Parkinson's disease. On October 5th, our family will walk together as Team Kosmo at Moving Day Chicago to celebrate his strength and support everyone living with Parkinson's.

An updated view of metabolic handoffs in microbiomes From the human gut to the deep ocean, diverse microbial communities underpin essential ecosystem processes. Limited understanding of the dynamics and …

New review paper on metabolic handoffs in microbiomes led by PhD student Katie Klier.

We define major types of metabolic handoffs, examine their drivers and benefits, & describe their importance in different complex microbial systems and environments.

www.sciencedirect.com/science/arti...