Prokaryote evolution is driven in large part by the incessant arms race with viruses. Genomic investments in antivirus defense can be coarsely classified into two categories, immune systems that abrogate virus reproduction resulting in clearance, and programmed cell death (PCD) systems. Prokaryotic defense systems are enormously diverse, as revealed by an avalanche of recent discoveries, but the basic ecological determinants of defense strategy remain poorly understood. Through mathematical modeling of defense against lytic virus infection, we identify two principal determinants of optimal defense strategy and, through comparative genomics, we test this model by measuring the genomic investment into immunity vs. PCD among diverse bacteria and archaea. First, as viral pressure grows, immunity becomes the preferred defense strategy. Second, as host population size grows, PCD becomes the preferred strategy. We additionally predict that, although optimal strategy typically involves investment in both PCD and immunity, investment in immunity can also result in antagonism, increasing the likelihood that a PCD-competent cell will lyse due to infection. Together, these findings indicate that, generally, PCD is preferred at low multiplicity of infection (MOI) and immunity is preferred at high MOI. Finally, we demonstrate that PCD, which is typically considered to be an altruistic trait, is in some cases neutral and can be maintained in an unstructured population over an evolutionary timescale. Our work shows that the landscape of prokaryotic antivirus defense is substantially more complex than previously suspected.

Microalgae induce a CO2-concentrating mechanism (CCM) to maintain photosynthesis when CO2 is limited. Because this system consumes a substantial po...

An antiphage defence system has an activation mechanism that relies on the sensing of phage-encoded proteins that enforce geometry crucial to activation and are not typically present in non-infected cells.

Bacteria use diverse defence systems against phages, including a 164-residue prophage-encoded protein, Rip1, which senses conserved phage assembly rings to form membrane pores that block virion maturation and trigger premature host cell death.

PlasMAAG uses cross-sample information to improve plasmid reconstruction from metagenomic samples.

PlasMAAG uses cross-sample information to improve plasmid reconstruction from metagenomic samples.

Soils harbour immense biosynthetic gene cluster (BGC) diversity that can mediate microbial interactions, yet this potential is still mapped unevenly across the tree of life. Ktedonobacteria , a class of actinomycete-like bacteria within phylum Chloroflexota , are widespread in terrestrial environments and repeatedly dominate pioneer communities in extremely oligotrophic volcanic bare-ground soils; however, their secondary metabolism and genome architecture remain poorly characterised. Here, we integrate targeted cultivation using volcanic soils from Mount Zao with genome-resolved metagenomics and public genomes to analyse 183 ktedonobacterial genomes. Using antiSMASH and BiG-SLiCE, we identified 1,546 BGCs comprising 1,162 non-redundant gene-cluster families (GCFs). In our dataset, nearly one quarter of genomes encode >10 distinct GCFs, and several family-level clades show mean GCF counts comparable to those in genus Streptomyces. Most ktedonobacterial BGCs are highly divergent from reference collections and exhibit unusually low intra-genomic redundancy, suggesting broad, underexplored chemotypes. Long-read assemblies from ten strains reveal recurrent 1.6 - 3.5 Mb chromid-like secondary replicons with chromosome-like composition but distinct maintenance signatures. These replicons are consistently enriched in BGCs and mobility-associated genes, with mobility loci concentrated near BGC boundaries. Collectively, our results expand the current knowledge of the phylogenetic landscape of soil biosynthetic diversity and highlight chromid-like secondary replicons as major genomic reservoirs for specialised metabolism in Ktedonobacteria . ### Competing Interest Statement The authors have declared no competing interest. JSPS KAKENHI, JP25K22374, JP25K01112 The Institute for Fermentation, G-2024-1-019

Chmielowska et al. reveal how arbitrium phages coordinate host stress and viral communication to control induction. An SOS-regulated antirepressor disables an unusual phage repressor by DNA mimicry, while quorum sensing prevents prophage activation when related lysogens are abundant.

The authors leverage experimental and phylogenetic data to propose that anammox bacteria during the Archaean period could have harvested photoholes from cyanobacterial mats for use as an electron acceptor prior to the availability of nitrite.

Horizontal gene transfer (HGT) is a promising avenue for microbiome engineering that enables DNA delivery to microbes in their native environment. Integrative and conjugative elements (ICEs), a class of genomically-integrated mobile elements, are ideal vectors for this purpose. Developing targeted ICE transfer for controlled microbiome engineering requires a better understanding of ICE mobility in complex communities. However, current methods for tracking horizontal gene transfer are not high throughput. To improve upon current methods, we developed a sequencing-based strategy to track and quantify ICE transfer in complex mixtures that we refer to as ‘ICE-seq.’ This method was able to assess ICE transfer in a synthetic community of 150 recipients simultaneously and in combination with phenotypic assays demonstrated that restriction-modification (RM) systems in the donor and recipient alter ICE transfer rate with subspecies resolution by up to 10,000-fold. We propose that manipulating RM systems can be a strategy to engineer targeted ICE transfer for directed microbiome engineering.

Radiolaria are unicellular marine organisms (protists) that have been drifting in oceanic plankton for hundreds of millions of years. These mineral architects can build extraordinarily complex skelet...

Methanogenic archaea affect the climate through their production of the greenhouse gas, methane. However, it is unclear how a changing climate and other anthropogenic influences impact methanogen physiology and consequent methane flux. The Great Salt Lake (GSL) is an environment that has been heavily impacted by human activity; more than doubling its salt concentration since the last methanogen was cultured from it in 1985. In this study, we enriched a novel methanogen, for which we propose the name Candidatus Methanohalophilus hillemani, from the GSL at a time when its salinity reached a historical high. Interestingly, Ca. M. hillemani does not increase expression of energy-conservation or osmo-tolerance proteins when challenged with salinity or oxygen. In contrast, Ca. M. hillemani prioritizes trace metal uptake and immune functions in response to the presence of the sulfate-reducing bacterium Desulfovermiculus . 16S rRNA gene amplicon data from GSL shore soils with extremely high and variable methane flux indicated the presence of Ca. M. hillemani. Our results show that Ca. M. hillemani is active when challenged with environmental stressors and contributes to the methane flux emanating from the GSL.

The in situ relevance of biosynthetic gene clusters (BGCs) remains poorly understood. We applied meta-omics to characterize BGC diversity and activity along a peatland redox gradient. From seven metagenomes, we recovered 9,694 BGCs spanning diverse taxa, most lacking close relatives in reference databases, indicating extensive novelty. Only 9-27% of this potential was expressed in situ, with Acidobacteriota, despite moderate repertoires, accounting for over half of all BGC transcription. “Talented producers” with up to 24 clusters were largely silent, and expression was inversely related to BGCs per genome. Acidobacteriota and other oligotrophic taxa expressed most of their BGCs, whereas copiotrophic Pseudomonadota expressed a few, suggesting that life-history and stress-responsive regulation govern activation. PKS and terpene BGCs expression was enriched in genomes expressing markers of aerobic respiration and stress, whereas RiPPs were associated with antimicrobial resistance, stationary phase and stress. Thus, although BGCs are widespread, environmental constraints determine which are realized. ### Competing Interest Statement The authors have declared no competing interest.

Microorganisms colonize all environments on Earth, yet it remains unclear which taxa merely broadly persist and which consistently outperform others across environments. Here we introduce the Baas-Becking score (BB-score), a performance metric to rank taxa across communities that integrates occupancy, relative abundance, and penalized absences. Applying BB-scores to 576,531 microbial communities spanning 24 biomes (categorized as either host-associated or free-living), we found that most species-level operational taxonomic units (OTUs) were widespread, but their success was substantially more restricted. Although 64% of OTUs were detected in at least one host-associated and one free-living biome, only six taxa ranked within the top 1% of performers in >50% of biomes: Aerococcus viridans, Faucicola (previously: Moraxella) osloensis, Lawsonella clevelandensis, Methylorubrum populi, Sphingobium yanoikuyae, and Pseudomonas fluorescens complex. These globally successful taxa were present in a quarter of all airborne communities, consistent with the atmosphere acting as a dispersal corridor. Network analysis of shared top 5% performers identified the phyllosphere and freshwaters as hubs linking animal-associated, plant-associated, and soil biomes. BB-score provides a scalable framework to map microbial success across Earth's biomes and to put new focus on globally successful yet woefully understudied taxa. ### Competing Interest Statement The authors have declared no competing interest. Swiss National Science Foundation, 10000877