We performed 50 DOM biodegradation experiments along with microbial community profiling to test whether bacterioplankton taxonomic and functional composition could account for oxygen consumption. Tax...

Dihydrodichlorofluorescein derivatives have been employed as reporters of intracellular reactive oxygen species (ROS) in innumerable studies. Their...

Acquisition of chloroplasts by an early eukaryote and their subsequent spread across eukaryotes is well understood. However, evolution can be undone, …

Mathematical modelling and experimental tests reveal principles that govern displacement of a resident strain by an invader in microbial communities.

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 with multiple evolutionary origins, and lack of a universal barcode gene. While virus ecogenomics has expanded access to and understanding of the virosphere, available classification tools poorly scale to modern discovery-based datasets, lack taxonomic resolution, and/or are unable to classify novel sequence space. Here we develop, benchmark, and release vConTACT3, a machine learning-based tool that improves scalability and accuracy, adds extensive user-requested features, expands classification to both eukaryote and prokaryote viruses for 4/6 officially recognized realms, and establishes accurate hierarchical taxonomy from genus to order. Application to 48,069 public virus genomes provided new taxonomy assignments for thousands of taxa, revealed support for fewer taxonomic ranks than currently available, and systematically identified taxonomically problematic areas across the virosphere. ### Competing Interest Statement The authors have declared no competing interest. U.S. National Science Foundation, https://ror.org/021nxhr62, DBI-2149506, DBI-2022070 Ohio Supercomputer Center, https://ror.org/01apna436 Deutsche Forschungsgemeinschaft, https://ror.org/018mejw64, EXC 2051 – Project-ID 390713860 European Research Council, https://ror.org/0472cxd90, Consolidator grant 865694 Alexander von Humboldt Foundation Biotechnology and Biological Sciences Research Council, BBS/E/F/000PR13631, BBS/E/F/000PR13633, BB/X011011/1, BBS/E/F/000PR13634, BBS/E/F/000PR13635, BBS/E/F/000PR13636

Abstract. Labile dissolved organic carbon in the surface oceans accounts for about one-fourth of carbon produced through photosynthesis and turns over on a

Abstract. The functions of microbial communities, including substrate conversion and pathogen suppression, arise not as a simple sum of individual species’

Abstract. Bioconversion of ammonium to dinitrogen (N2) is an essential process in the nitrogen cycle, primarily driven by O2-dependent nitrification and fo

Abstract. Polyethylene terephthalate (PET)-hydrolyzing enzymes (PETases) are a recently discovered enzyme class capable of plastic degradation. PETases are

Eukaryotic intracellular compartmentalization is a key innovation in the evolution of complex cellular life. While microcompartments enable metabolic specialization in many bacteria, to our knowledge, no analogous systems have been identified in Archaea. Here, we report the discovery of archaeal microcompartments (AMCs) in Hodarchaeales, an order within the phylum Promethearchaeati (Asgard archaea) that includes the closest known archaeal relatives of eukaryotes. Phylogenetic and structural analyses indicate that these catabolic AMCs, which are specialized for sugar-phosphate metabolism, were acquired by horizontal gene transfer from deep-rooted bacteria of the phylum Myxococcota. The shell pentamers of AMCs are fused to lysine/arginine-rich intrinsically disordered regions that capture cytosolic DNA, facilitating nutrient scavenging. Reaction-diffusion modelling predicted that enzyme colocalization and substrate channelling within AMCs, can drive an approximately 100-fold increase in NADH flux. Thus, the AMCs substantially boost energy production in the cell and might have primed the archaeal host for eukaryogenesis. ### Competing Interest Statement The authors have declared no competing interest. National Natural Science Foundation of China, 32370055, 32393970, 32225003, 32200099, 92051102 Shenzhen Natural Science Foundation, JCYJ20230808105711023 Guangdong Basic and Applied Basic Research, 2025A1515012817 Project of Department of Education of Guangdong Province, 2025KCXTD039 Shenzhen University 2035 Program for Excellent Research, 2022B002 Synthetic Biology Research Center of Shenzhen University Moore–Simons Project on the Origin of the Eukaryotic Cell Simons and Moore Foundation, 73592LPI Simons Foundation Investigator in Aquatic Microbial Ecology Award, LI-SIAME-00002001 Intramural Research Program of the National Institutes of Health of the USA

Deep-sea mining in the Clarion-Clipperton Zone may release waste into midwaters that support diverse marine life. This study finds such discharges could dilute key food particles and disrupt trophic links from zooplankton to large marine predators.

Algae inhabit diverse environments with highly variable light conditions, making light sensing essential for survival and ecological success. This review exp...

The ongoing evolutionary arm race between archaea and their viruses has led to the development of diverse defense systems against viruses. While recent computational approaches have uncovered many bacterial antiviral defense systems, the viral infection strategies and antiviral responses of archaea remain poorly explored. In this study, we identified antiviral defense systems encoded in the genomes of 20 recently sequenced haloarchaeal strains. These systems are representative of the broader repertoire of defense systems present across all 253 complete sequenced Halobacteria (class) genomes in the RefSeq database. Detailed analysis showed that these haloarchaea usually harbor multiple different defense systems, with a particularly high abundance of uncharacterized predicted defense systems against viruses (Phage Defense Candidates (PDCs)). To further explore the impact of anti-viral defense mechanisms on host range, an extensive virus-host pair screening was performed using a panel of known virulent viruses. By correlating the genomic defense profiles with observed viral infectivity and adsorption profiles, a weak correlation between the number of encoded defense systems and viral susceptibility was detected. Specifically, hosts infected by fewer viruses tended to encode a broader repertoire of antiviral defense systems, whereas those with fewer defense systems were frequently infected. It was found that the host range of haloarchaeal viruses is majorly determined by the availability of viral receptors, whereas the presence of anti-viral defense systems plays a smaller but significant role. These findings offer valuable insights into the evolutionary pressure shaping archaeal antiviral strategies and lay the groundwork for future functional studies of archaeal defense systems.

Abstract. The Protein Data Bank (PDB) archives 3D structures of macromolecules determined experimentally using various methods. It is jointly managed by th

Phase separation stabilizes synthetic gene circuits and boosts production under dynamic growth conditions. By locally concentrating transcription factors at promoters, it protects gene expression from growth-driven dilution and provides a broadly applicable strategy for gene circuit engineering.

Phosphorus availability is vital to ocean ecosystem functioning. Analyses of global seawater samples combined with laboratory experiments reveal the Alteromonas bacteria as a surprising regulator of the marine phosphorus cycling.

This study shows that Alteromonas is a key driver of phosphorus recycling in the ocean and that its alkaline phosphatases are multifunctional—with different families coexisting in one genome by adopting distinct functions and secretion strategies.

Abstract. Drying is threatening global river ecosystems due to climate change, altering community composition and function even upon flow resumption. This

Abstract. Cyanobacterial blooms dominated by Microcystis spp. pose significant ecological challenges, including the release of toxins and disruption of aqu

Contractile injection systems (CISs) are derivatives of phage tails and widely distributed in prokaryotes. CISs load cognate effectors and eject them through contractile actions resembling those of phage tails. Ejected effectors play central roles in CIS functionality by acting on target cells and mediating various biological processes. Here, we report a novel group of CIS effectors related to phage tapemeasure protein, the transmembrane component of the phage infection machinery. This group is broadly distributed within the class actinobacteria, one of the bacterial classes in which CIS gene clusters are highly conserved, and is represented by Sle1, a cognate effector of the intracellularly localised Streptomyces lividans phage tail-like nanoparticle (SLP). This effector is associated with Sle2, which contains a CIS effector core domain and interacts with the SLP core component. Sle1 is packaged inside SLP and is translocated to lipid membranes along with SLPs. The functional domain of Sle1, probably through interactions with ribosome-containing subcellular fractions, upregulates the membrane-associated proteome in S. lividans and E. coli . This effect modifies the physiological properties of S. lividans , ultimately enhancing its adaptation to microbial competition. In addition, we revealed that Sle1-type effectors conserved among actinobacterial species are structurally and functionally diverse in their functional domains. One of them from Micromonospora eburnea constitutes a novel toxin-antitoxin system and introducing its functional domain into Sle1 reprogrammes the phenotypic responsiveness of S. lividans to neighbouring bacteria. Our findings illustrate that phage elements can be incorporated into CISs as reconfigurable platforms for bacterial adaptation to various environmental conditions.

An exploration of previously undescribed variants from the long tail of the CRISPR–Cas distribution.

Natural genetic code expansion is a phenomenon wherein an additional amino acid is encoded by a stop codon. These nonstandard amino acids are benef...