A machine-learning framework called symclatron uses genome sequencing content to predict whether uncultivated bacteria and archaea live independently or in close association with hosts. Applied to a g...

Analyzing how giant viruses—and interns—respond to environmental change.

Symbiotic relationships of microorganisms are predicted and cataloged with a machine learning tool.

The publicly available Symbiont Genomes catalog is one of the most comprehensive guides to bacteria and archaea living in partnership with other organisms.

Symbiotic relationships of microorganisms are predicted and cataloged with a machine learning tool.

Identification of CprV during bacterial sporulation reveals insight into how developing cells monitor compartmental integrity during cellular remodelling and differentiation.

Cultivation-dependent techniques, computational analyses and genome-scale metabolic models show widespread amino acid auxotrophies, suggesting that soil microorganisms exist within integrated ecologic...

Biological communities are complex, dynamic systems that underpin ecosystem functionality, yet their long-term dynamics and predictability remain p...

AbstractMotivation. Data-enabled studies of microbial ecology and evolution depend on high-quality descriptions of microbial habitats, based on curated and

AbstractSummary. Phylogenetic trees are ubiquitous and central to biology, but most published trees are available only as visual diagrams and not in the ma

The use of the online tool BSocial can be used to decipher microbial social behaviour and select highly functional plant growth-promoting consortia. Positive correlations are observed between species...

Migration of microbial communities is poorly understood. Here, the authors use a meso-tube assay to show that hundreds of microbial species co-migrate over metre scales via chemotaxis, which restructu...

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 learni...

The Genome Taxonomy Database (GTDB) is an initiative to establish a standardised microbial taxonomy based on genome phylogeny.

Antiphage defense systems protect bacteria from viral infection and have inspired important biotechnologies such as CRISPR-Cas9 while also revealing the evolutionary roots of eukaryotic innate immunit...

This study reveals how plant-associated bacteria dynamically reprogram gene expression during root colonization, using a new high-throughput approach that overcomes low bacterial biomass and interfere...

Novel study looks at microbiomes in aerial surfaces of plants, and their roles in plant health and environmental processes

Upcycling urine in wastewater for nitrogen and phosphorus production has gained attention, but their low market values hamper the application. Here, the authors develop a yeast platform that mimics os...

This study examined the impact of methanotrophic bacteria (MOB) and methanogenic archaea (mGen) on CH4 emissions from oxbow lakes at various successional stages, analysing their interactions with phy....

Microbial symbiosis drives the functional and phylogenomic diversification of life on Earth, yet remains underexplored due to culturing challenges. This study employed machine learning (ML) to predict...

Microbial symbiosis drives the functional and phylogenomic diversification of life on Earth, yet remains underexplored due to culturing challenges. This study employed machine learning (ML) to predict...

Photosynthetic organelles in eukaryotes originated through primary endosymbiosis with a cyanobacterium, an event that profoundly shaped the evolutionary landscape of the eukaryotic tree of life. Primary plastids in Archaeplastida, especially in cultivable plants and algae, contribute most to known plastid diversity. Secondary and higher-order endosymbiosis, involving eukaryotic hosts and algal endosymbionts, further spread photosynthesis among protists within the CASH lineages (Cryptophyta, Alveolata, Stramenopila, and Haptophyta). Despite various hypotheses explaining secondary plastid evolution and distribution, empirical support remains limited. Here, we employ cultivation-independent global metagenomics to expand plastid diversity and investigate plastid origins. We captured 1,027 plastid sequences, including 300 novel sequences belonging to previously unsequenced plastids and representing yet-to-be described microeukaryotes. This includes a new lineage that offers insights into plastid evolution in haptophytes and cryptophytes. Our results confirm that Archaeplastida plastids originated from an early-branching cyanobacterial lineage closely related to Gloeomargaritales and identify the closest extant relative of Paulinella plastids. Additionally, our findings suggest two independent origins of secondary red algal plastids, contributing to plastid diversity in CASH lineages and challenging the prevailing model of single secondary plastid origin. Our study highlights the importance of metagenomic data in uncovering biological diversity and advancing understanding of plastid relationships across photosynthetic eukaryotes. ### Competing Interest Statement The authors have declared no competing interest.

Nigel Mouncey and Phillip Messersmith were among those awarded this lifetime honor.

Three scientists with Berkeley Lab were among the nearly 400 scientists and engineers awarded by President Biden to receive the Presidential Early Career Award for Scientists and Engineers (PECASE).