Benchmarking of shotgun sequencing depth reveals the potential and limitations of shallow metagenomics and strain-level analysis - Nature Microbiology A comparison of sequencing of complex mock communities performed at multiple depths and analysed using different methods establishes minimum standards that can ensure the accuracy of metagenomic analy...

Benchmarking of shotgun sequencing depth reveals the potential and limitations of shallow metagenomics and strain-level analysis
www.nature.com/articles/s41...

A global metagenomic atlas uncovers ubiquitous biosynthetic potential linked to adaptation in extreme environments
doi.org/10.64898/202...

Direct benefits are not necessary for the evolution of multicellularity - Nature Ecology & Evolution A model for the evolution of multicellularity in a spatially heterogeneous environment shows that indirect mechanisms such as escape from competition and increased environmental exploitation can drive the evolution of multicellularity in the absence of direct benefits.

Direct benefits are not necessary for the evolution of multicellularity | Nature Ecology & Evolution https://www.nature.com/articles/s41559-026-03044-y

Identification of hot spring Obelisk-like RNA replicons and expanded diversity of the Obelisk superfamily - Nature Communications In this study, the authors identify circular RNAs replicating in high-temperature hot spring environments and demonstrate that ccc RNA replicons belonging to the Obelisk superfamily are more diverse and widespread than previously recognized, revealing hidden RNA systems in natural environments.

Identification of hot spring Obelisk-like RNA replicons and expanded diversity of the Obelisk superfamily | Nature Communications https://www.nature.com/articles/s41467-026-71096-6

Phage homing endonuclease amplifies anti-defense genes to evade bacterial immunity - Nature Communications Phages employ diverse counter-defense strategies to overcome bacterial immune systems. Here, the authors reveal that the phage homing nuclease SegB facilitates immune evasion by promoting the segmental amplification of antidefense loci.

Phage homing endonuclease amplifies anti-defense genes to evade bacterial immunity | Nature Communications https://www.nature.com/articles/s41467-026-71036-4

Structural basis of QueC-family protein function in qatABCD anti-phage defense | Nature Communications https://www.nature.com/articles/s41467-026-72155-8

Horizontal gene transfer drives the emergence of nitrogen fixation in a unicellular Synechocystis lineage Nitrogen fixation plays a central role in primary productivity and nitrogen cycling in aquatic ecosystems, yet its distribution among cyanobacterial lineages remains incompletely understood. Biological nitrogen fixation is energetically costly and highly oxygen-sensitive, imposing constraints in oxygenic phototrophs. The unicellular cyanobacterial genus Synechocystis has long been regarded as strictly non-diazotrophic. Here, we report that Synechocystis sp. LKSZ1 possesses a functional nitrogen fixation system. Comparative genomics revealed that LKSZ1 is distinct from other Synechocystis strains and uniquely harbors a complete nif gene. Phylogenetic and structural analyses indicate acquisition via horizontal gene transfer from filamentous cyanobacteria. Physiological assays demonstrated photoautotrophic growth under nitrogen-depleted conditions and nitrogenase activity under microoxic to anaerobic conditions. Disruption of nifK abolished both growth and activity. These findings show that ecological nitrogen limitation and host compatibility can enable functional integration of horizontally acquired nitrogen fixation. ### Competing Interest Statement The authors have declared no competing interest. MEXT/JSPS KAKENHI, 22K06276 COI-NEXT, JPMJPF2102

Horizontal gene transfer drives the emergence of nitrogen fixation in a unicellular Synechocystis lineage | bioRxiv www.biorxiv.org/content/10.64898/2026.04...

Antiviral reverse transcriptase-primase synthesizes protein-templated DNA Defense-associated reverse transcriptases (DRTs) are widespread in bacteria, but how multi-domain DRTs containing RT and additional catalytic activities coordinate antiviral defense remains unclear. Here we show that DRT7, which contains both reverse transcriptase (RT) and primase-polymerase (PP) domains, provides broad-spectrum anti-phage immunity through abortive infection and can be activated by a phage-encoded putative transcriptional regulator. Upon activation, DRT7 synthesizes long, protein-primed, palindromic poly(A)/poly(T)-rich duplex-like DNA. Cryo-electron microscopy structures reveal that RT initiates protein-primed, protein-templated, sequence-specific poly(T) synthesis through an arginine-rich recognition pocket without requiring a complementary nucleic acid template, thereby converting DRT7 from an inactive closed dimer to an active open dimer. The RT-produced poly(T) then serves as both primer and template for PP-mediated poly(A) extension, with iterative handoff between RT and PP generating palindromic, alternating poly(A)/poly(T) ssDNA tracts that assemble into fold-back duplex-like DNA. These findings uncover an unexpected antiviral strategy based on protein self-templating, sequence-specific duplex-like DNA synthesis and reveal how coupling RTs with additional catalytic activities expands the functional scope of nucleic acid synthesis pathways. ### Competing Interest Statement The authors have declared no competing interest. Guangdong Major Project of Basic Research, 2025B0303000005

Antiviral reverse transcriptase-primase synthesizes protein-templated DNA | bioRxiv www.biorxiv.org/content/10.64898/2026.04...

Widespread Genomic Islands in Giant Viruses Shape Genome Plasticity and Mosaicism | bioRxiv www.biorxiv.org/content/10.64898/2026.04...

The AI Rewrite Dilemma https://lh3.github.io/2026/04/17/the-ai-rewrite-dilemma

Metatranscriptome data support the existence of two distinct morphotypes in a single parmalean species in natural environments | bioRxiv www.biorxiv.org/content/10.64898/2026.04...

Multi-kingdom profiling reveals altered gut phage-bacteria-metabolite interactions in MASLD | Nature Communications https://www.nature.com/articles/s41467-026-71981-0

Predicting competition and substrate preferences for targeted microbiome alteration Microbiome science has greatly expanded our understanding of microbial life and its roles in the environment and human health. Yet microbiome science …

Predicting competition and substrate preferences for targeted microbiome alteration - ScienceDirect www.sciencedirect.com/science/article/abs/pii/...

2'3'-cGAMP-induced membrane shearing promotes broad antiphage immunity Cyclic-oligonucleotide-based anti-phage signaling system (CBASS), a central prokaryotic antiviral strategy and evolutionary ancestor of the mammalian …

2'3'-cGAMP-induced membrane shearing promotes broad antiphage immunity - ScienceDirect www.sciencedirect.com/science/article/abs/pii/...

Nutrient availability shapes the diversity and structure of microbial communities | bioRxiv www.biorxiv.org/content/10.64898/2026.04...

Cognition without brains? Learning and memory in microorganisms Memory and learning are cognitive abilities typically associated with animals that possess a complex nervous system. Interestingly, recent studies suggest that microorganisms might also display learning-like behaviours. However, a factor limiting progress in this field is the lack of shared, microbe-specific frameworks that allow microbiologists to easily compare discoveries with concepts developed in cognitive sciences. In this review, we aim to bridge this gap by providing a conceptual overview of the definitional requirements for memory and learning to classify microbial behaviours and capabilities. Additionally, we identify and address problems that cause conceptual ambiguity in the microbial cognition literature, thereby facilitating more productive debates on the topic. Finally, we provide a novel perspective on how microbes might ‘learn’ from each other.

Cognition without brains? Learning and memory in microorganisms: Trends in Microbiology www.cell.com/trends/microbiology/full...

Seasonal bromate formation in the Arctic snowpack: Implications for the bromine biogeochemical cycle | Science Advances www.science.org/doi/abs/10.1126/sciadv.a...

Protein-templated synthesis of dinucleotide repeat DNA by an antiphage reverse transcriptase | Science https://www.science.org/doi/10.1126/science.aed1656

Coexistence of Photosynthetic Marine Microorganisms, Viruses and Grazers: Towards Integration in Ocean Ecosystem Models - Frémont - 2026 - Environmental Microbiology - Wiley Online Library enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/1462-2920.70...

Continental-scale multi-omics reveals a distinct microbial-viral biome in sandy beach ecosystems structured by tidal zonation | bioRxiv www.biorxiv.org/content/10.64898/2026.04...

Beyond metabolic dormancy: metabolic rewiring in bacterial persistence - Nature Communications Bacterial persister cells exhibit a transient state of antibiotic tolerance and are commonly assumed to be metabolically ‘dormant’. In this Perspective, Orman et al. re-examine common assumptions and emphasize that persisters represent a range of metabolic states, driven by internal and external factors, which may explain the inconsistent expression of classic persister hallmarks.

Beyond metabolic dormancy: metabolic rewiring in bacterial persistence | Nature Communications https://www.nature.com/articles/s41467-026-71427-7

Beyond metabolic dormancy: metabolic rewiring in bacterial persistence - Nature Communications Bacterial persister cells exhibit a transient state of antibiotic tolerance and are commonly assumed to be metabolically ‘dormant’. In this Perspective, Orman et al. re-examine common assumptions and emphasize that persisters represent a range of metabolic states, driven by internal and external factors, which may explain the inconsistent expression of classic persister hallmarks.

Beyond metabolic dormancy: metabolic rewiring in bacterial persistence | Nature Communications https://www.nature.com/articles/s41467-026-71427-7

Beyond metabolic dormancy: metabolic rewiring in bacterial persistence - Nature Communications Bacterial persister cells exhibit a transient state of antibiotic tolerance and are commonly assumed to be metabolically ‘dormant’. In this Perspective, Orman et al. re-examine common assumptions and emphasize that persisters represent a range of metabolic states, driven by internal and external factors, which may explain the inconsistent expression of classic persister hallmarks.

Beyond metabolic dormancy: metabolic rewiring in bacterial persistence | Nature Communications https://www.nature.com/articles/s41467-026-71427-7

Diversity-generating retroelements for programmable targeted hypermutagenesis - Nature Biotechnology Diversity-generating retroelements are engineered for directed evolution in E.coli.

Diversity-generating retroelements for programmable targeted hypermutagenesis | Nature Biotechnology https://www.nature.com/articles/s41587-026-03078-4

Fast prediction of protein flexibility | Bioinformatics | Oxford Academic academic.oup.com/bioinformatics/advance-a...

High-throughput characterization of Mycobacterium tuberculosis gene function across diverse conditions Limited-throughput genetics has slowed discovery of gene functions in Mycobacterium tuberculosis. This study develops a genome-wide barcoded transposon library and tests it across 95 environmental conditions, providing a rich resource of new gene functions, including metabolic and drug-resistance pathways.

High-throughput characterization of Mycobacterium tuberculosis gene function across diverse conditions | PLOS Biology journals.plos.org/plosbiology/article

Structure-centric searching enables global mapping of the public metabolome - Nature Biotechnology StructureMASST enables pan-repository MS/MS searches using a chemical name or structure.

Structure-centric searching enables global mapping of the public metabolome | Nature Biotechnology https://www.nature.com/articles/s41587-026-03082-8

Microbiome assembly statistics toward ecosystem-scale insights, forecasting, and management Abstract. Microbiomes are increasingly recognized as key to addressing global challenges in health and sustainability, as they can provide emergent biologi

Microbiome assembly statistics toward ecosystem-scale insights, forecasting, and management | The ISME Journal | Oxford Academic academic.oup.com/ismej/advance-article/do...

Light-activated cAMP signaling controls sodium-driven motility in Vibrio cholerae | PNAS https://www.pnas.org/doi/10.1073/pnas.2530860123

Quinones operate as proton-collecting antennas in energy-transducing membranes | PNAS www.pnas.org/doi/abs/10.1073/pnas.253...