The deep sea is home to a vast and largely unexplored microbial biosphere, along with significant amounts of complex organic matter (COM). However, the ability of deep-sea microbes to metabolize complex organic matter across diverse regions remains poorly understood. Here, we combine 16S rRNA gene amplicon sequencing, metagenomics, and metatranscriptomics to comprehensively characterize prokaryotic communities across different years and habitats (cold seeps, hydrothermal vents, and seamounts). Our results reveal spatio-temporal community heterogeneity driven by geochemical gradients, alongside widespread genomic and transcriptomic potential for COM metabolism. Notably, the PVC (Planctomycetota-Verrucomicrobiota-Chlamydiota) superphylum exhibits extensive polysaccharide degradation capabilities, with Planctomycetota strain WC338 and Lentisphaerota strain WC36 isolated via laminarin enrichment. Growth and transcriptome data confirm their obligate laminarin dependence and robust degradation capacity, employing distinct enzymes (GH16 and GH2), whose broad distribution across diverse PVC superphylum lineages underscores their prevalence. Furthermore, we demonstrate that laminarin acts as a highly effective selective substrate for enriching and isolating the deep-sea PVC superphylum bacteria. Collectively, these findings delineate specialized adaptations within the PVC superphylum for polysaccharide degradation, significantly expanding our understanding of deep-sea microbial roles in global carbon cycling. ### Competing Interest Statement The authors have declared no competing interest. National Natural Science Foundation of China, 42406104 and 42530409

Abstract. Microorganisms, including bacteria, archaea, fungi, and viruses, are the most taxonomically diverse and ecologically dominant life forms on Earth

Abstract. PROSITE (https://prosite.expasy.org/) is a database of entries documenting protein domains, families, and functional sites, along with the associ

Abstract. The AlphaFold Protein Structure Database (AFDB; https://alphafold.ebi.ac.uk), developed by EMBL–EBI and Google DeepMind, provides open access to

Metabolic strategies of cave microorganisms are poorly studied. Here, the authors show that cave microbes use atmospheric trace gases hydrogen, carbon monoxide and methane as energy and carbon sources, sustaining primary production and revealing how life can thrive in oligotrophic and dark ecosystems.

Abstract. Transformation occurs when bacteria import exogenous DNA via the competence machinery and integrate it into their genome through homologous recom

micov computes coverage breadth across genomes and samples. Its application in metagenomics highlights strain heterogeneity, uncovers associations linking genetic elements to phenotypic traits, and aids taxonomic filtering in low-biomass settings.

Mathematical representations of overflow metabolism, mixotrophy, exoenzymes and reactive oxygen species detoxification recapitulate dynamics in co-cultures of Prochlorococcus and eight heterotrophic bacteria.

DNA replication requires precise coordination between DNA unwinding and DNA synthesis. In all domains of life, protein–protein interactions at the ...

Abstract. Several recent deep learning methods for metagenome binning claim improvements in the recovery of high-quality metagenome-assembled genomes. Thes

micov computes coverage breadth across genomes and samples. Its application in metagenomics highlights strain heterogeneity, uncovers associations linking genetic elements to phenotypic traits, and aids taxonomic filtering in low-biomass settings.

Mobile genetic elements (MGEs) are diverse, self-replicating DNA molecules that can reside within cellular hosts and integrate into one another. This co-occurrence imposes distinct evolutionary pressures. Plasmids often contain insertion sequences (ISs). However, the multi-copy nature of plasmids should hinder IS introduction and spread, disfavoring inheritance of nascent plasmid variants through genetic drift. Mechanisms by which ISs overcome these barriers remain unidentified. Here we find that the RNA-guided nuclease TnpB enables such a mechanism to bias its inheritance in plasmids. We show that TnpB, the likely ancestor to Cas12, enables a gene drive to spread the IS within multicopy plasmids and functions as a primitive anti-self defense system in conjugative plasmids. The gene drive between TnpB-bearing ISs and plasmids promotes the spread of both MGEs beyond the ability of either individually. The nested existence between MGEs is not an incidental result of selfish spread, but a driver of it. ### Competing Interest Statement The authors have declared no competing interest. National Institute of General Medical Sciences, https://ror.org/04q48ey07, R35GM133700, R35GM156320 U.S. National Science Foundation, MCB2426105 Pew Charitable Trusts, https://ror.org/02xhk2825 United States Army Research Office, https://ror.org/05epdh915

Multiple genetic codes developed during the evolution of eukaryotes and bacteria, yet no alternative genetic code is known for archaea. We used proteomics to confirm our prediction that certain archaea consistently incorporate pyrrolysine (Pyl) at TAG ...

Bacteria of the phylum Bacteroidota move by gliding and export proteins using a type-9 secretion system. Here, Liu et al. show that these two processes use a shared mechanism in which outer membrane proteins are covalently attached by disulfide bonds to a moving track structure inside the cell.

Virus discovery has accelerated but linking viruses to hosts remains challenging. This study uses synthetic microbiomes to optimize and benchmark Hi-C for virus-host linkage inference, and applies this to previously studied soil data to reveal hundreds of novel linkages.

Abstract. The pervasive availability of publicly available microbial genomes has opened many new avenues for microbiology research, yet it also demands rob

Abstract. Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) systems of bacteria and archaea provide immunities

Recent advances in metaviromics have revealed vast viral diversity across aquatic environments, yet coastal marine viromes remain underexplored compared to their open-ocean counterparts. In this study, we analyzed 49 surface water samples from 16 coastal sites around Korea, generating 265 gigabases of metagenomic sequence data. Following quality control, 754 DNA viral contigs of ≥10 kb (medium quality or higher) were recovered, with bacteriophages comprising 95% and nucleocytoplasmic large DNA viruses (NCLDVs) 5% of the total. Among these, Puniceispirillum phage HMO-2011 and Micromonas pusilla virus 12 T exhibited the highest relative abundance within their respective groups. In addition, we provided the dataset of environmental parameters such as water temperature, salinity, etc., as well as viral taxonomic profiling of contig-level metadata. This dataset provides a resource for the investigation of coastal DNA viral communities and supports comparative studies across marine environments.

The discovery of an unusual protist named Solarion arienae, which has a mitochondrial genome with some intriguing features, provides insight into the early radiation of eukaryotic groups.

The discovery of an unusual protist named Solarion arienae, which has a mitochondrial genome with some intriguing features, provides insight into the early radiation of eukaryotic groups.

AbstractMotivation. Taxonomic classification in biodiversity studies is the process of assigning the anonymous sequences of a marker gene (barcode) or whol

Bacterial immune systems have evolved in response to diverse molecular "parasites", yet their ecological roles remain poorly understood. This Essay explores how interactions between mobile genetic elements and bacterial defences shape microbiome structure and function.

Marine phytoplankton need to regulate their vertical position in the ocean to access light and nutrients. This study of the effects of nutrient availability on gravitational sinking in nine species reveals that phytoplankton physiology has evolved multiple mechanisms that impact sinking in response to starvation.

Delivery of recombinant DNA is foundational for understanding and engineering a target organism. Electroporation can be applied to any cell type, yet identification of a working protocol for new organisms remains bespoke and laborious because no systematic framework exists, and appropriate instrumentation is lacking. Here, we describe an automated high-throughput platform which uses active learning to discover electroporation protocols for non-model microbes. We first devised a 24-condition electroporation screen, based on systematic evaluation and selection of key parameters, that can be applied to any microbe. Facilitated by a custom-built fully-programmable electroporator, we successfully identified electroporation protocols for eight non-model bacteria using this screen alone. We then combined this electroporation screen with our pooled POSSUM plasmid library to simultaneously evaluate 408 experimental conditions per organism and identified both a protocol and a replicating plasmid for five non-model Proteobacteria spanning three major classes (alpha-, beta-, and gamma-). We report the first electroporation protocols for Shewanella indica , Shewanella putrefaciens 200, Shewanella putrefaciens 95, Halomonas elongata , Piscinibacter sakaiensis , and Duganella zoogloeoides , as well as multiple alternative protocols for Shewanella amazonensis , Shewanella oneidensis , Azospirillum brasilense , Cupriavidus necator , Pseudomonas alcaliphila , and Escherichia coli . Finally, we developed an active learning pipeline to guide the selection of parameters based on gathered experimental data. Using our robotic platform, we iteratively tested 538 conditions over three iterations to improve electroporation for the emerging industrial chassis C. necator , achieving 8.6-fold higher transformation efficiency than state of the art. This work establishes a discovery platform for DNA delivery to diverse and recalcitrant microbes that can be extended broadly to non-model organisms in our biosphere. ### Competing Interest Statement A.C.C., S.L.B., N.O., and H.H.L. have filed a patent application based on this work.