Comparative genomics of Ascetosporea gives new insight into the evolutionary basis for animal parasitism in Rhizaria.

BACKGROUND: Ascetosporea (Endomyxa, Rhizaria) is a group of unicellular parasites infecting aquatic invertebrates. They are increasingly being recognized as widespread and important in marine environments, causing large annual losses in invertebrate aquaculture. Despite their importance, little molecular data of Ascetosporea exist, with only two genome assemblies published to date. Accordingly, the evolutionary origin of these parasites is unclear, including their phylogenetic position and the genomic adaptations that accompanied the transition from a free-living lifestyle to parasitism. Here, we sequenced and assembled three new ascetosporean genomes, as well as the genome of a closely related amphizoic species, to investigate the phylogeny, origin, and genomic adaptations to parasitism in Ascetosporea. RESULTS: Using a phylogenomic approach, we confirm the monophyly of Ascetosporea and show that Paramyxida group with Mikrocytida, with Haplosporida being sister to both groups. We report that the genomes of these parasites are relatively small (12-36 Mb) and gene-sparse (~ 2300-5200 genes), while containing surprisingly high amounts of non-coding sequence (~ 70-90% of the genomes). Performing gene-tree aware ancestral reconstruction of gene families, we demonstrate extensive gene losses at the origin of parasitism in Ascetosporea, primarily of metabolic functions, and little gene gain except on terminal branches. Finally, we highlight some functional gene classes that have undergone expansions during evolution of the group. CONCLUSIONS: We present important new genomic information from a lineage of enigmatic but important parasites of invertebrates and illuminate some of the genomic innovations accompanying the evolutionary transition to parasitism in this lineage. Our results and data provide a genetic basis for the development of control measures against these parasites.

Molecular characterization of the evolution of premalignant lesions in the upper aerodigestive tract.

Introduction: Early relapse and development of metastatic disease are some of the primary reasons for the poor prognosis of patients with head and neck squamous cell carcinoma (HNSCC). HNSCC is a heterogeneous disease which may develop in large premalignant fields of genetically altered cells. Yet knowing which individuals will progress and develop clinically significant cancers during their lifetimes remains one of the most important challenges of reducing HNSCC morbidity and mortality. To further elucidate the molecular mechanisms, we performed a focused analysis of the genome and immune microenvironment from multiple, matched normal squamous tissue, premalignant lesions, as well as primary and recurrent tumors from seven patients with p16-negative HNSCC. Methods: We performed targeted panel Next Generation Sequencing (161 genes) to analyze somatic variants from sequentially collected, matched formalin-fixed paraffin-embedded tissue (normal, premalignant, HNSCC) from two patients. These samples plus samples from five additional patients were analyzed with the Nanostring PanCancer Immune Panel. In addition, we performed shallow whole genome sequencing (0.5x coverage on average) on samples from three of these patients. Patients were, apart from one case, primarily treated with curative-intent surgery, and received subsequent adjuvant treatment, if indicated. Results: The most frequently mutated genes were TP53 and NOTCH1. Other mutated genes included NOTCH3 and CDKN2A, among others. A significant number of mutations were private to dysplasia and invasive carcinoma, respectively, however, almost 20% were shared between them. Increasing genomic instability was observed when comparing histologically normal squamous mucosa with higher levels of dysplasia. High-grade dysplasia showed similarly rearranged genomes as invasive carcinoma. Pathways related to interferon alpha and gamma response were upregulated even in moderate dysplastic lesions with increasing expression in higher grades of dysplasia and carcinoma. SPINK5, a known tumor suppressor gene in HNSCC, was already downregulated in low-grade dysplastic lesions, indicating an early deactivation in the evolution of the disease. Conclusion: Genomic alterations as well as aberrant immune gene expression can be observed early in the evolution of tumors of the upper aerodigestive tract, highlighting the potential for targeting early mechanisms of disease progression.

OlCHR, encoding a chromatin remodeling factor, is a killer causing hybrid sterility between rice species Oryza sativa and O. longistaminata.

The genetic mechanisms of reproductive isolation have been widely investigated within Asian cultivated rice (Oryza sativa); however, relevant genes between diverged species have been in sighted rather less. Herein, a gene showing selfish behavior was discovered in hybrids between the distantly related rice species Oryza longistaminata and O. sativa. The selfish allele S13l in the S13 locus impaired male fertility, discriminately eliminating pollens containing the allele S13s from O. sativa in heterozygotes (S13s/S13l). Genetic analysis revealed that a gene encoding a chromatin-remodeling factor (CHR) is involved in this phenomenon and a variety of O. sativa owns the truncated gene OsCHR745, whereas its homologue OlCHR has a complete structure in O. longistaminata. CRISPR-Cas9-mediated loss of function mutants restored fertility in hybrids. African cultivated rice, which naturally lacks the OlCHR homologue, is compatible with both S13s and S13l carriers. These results suggest that OlCHR is a Killer gene, which leads to reproductive isolation.

Exceptional Early Jurassic fossils with leathery eggs shed light on dinosaur reproductive biology.

Our understanding of pre-Cretaceous dinosaur reproduction is hindered by a scarcity of evidence within fossil records. Here we report three adult skeletons and five clutches of embryo-containing eggs of a new sauropodomorph from the Lower Jurassic of southwestern China, displaying several significant reproductive features that are either unknown or unlike other early-diverging sauropodomorphs, such as relatively large eggs with a relatively thick calcareous shell formed by prominent mammillary cones, synchronous hatching and a transitional prehatching posture between the crocodilians and living birds. Most significantly, these Early Jurassic fossils provide strong evidence for the earliest known leathery eggs. Our comprehensive quantitative analyses demonstrate that the first dinosaur eggs were probably leathery, elliptical and relatively small, but with relatively long eggshell units, and that along the line to living birds, the most significant change in reptilian egg morphology occurred early in theropod evolution rather than near the origin of Aves.

Research on the Evolution Trend of Group Psychological Security Risks Under Public Health Emergencies: Mining and Analysis Based on Social Media Data.

Background: In the digital age, people's attitudes and psychological security towards public health emergencies will be shared. Similar or identical psychological security states are prone to clustering and differentiation, while differentiated group psychological security is more prone to polarization, leading to group psychological security risks and then posing a threat to social stability and national security. However, existing studies mostly use qualitative analysis methods to study group emotional risks. There are still limitations in the study of dynamics of group psychological security risks through mining real data of social media. Purpose: The study aims to use intelligent analysis methods to understand how group psychological security risks dynamically change. Methods: The study draws on text sentiment analysis, Markov chains and time series analysis to construct a framework for the evolution of group psychological security risks. Based on this framework, text data was crawled on Sina Weibo platform, mainly consisting of posts during public health emergencies (March 1st to June 30th, 2022) in Shanghai, and a psychological security lexicon in the field of public health emergencies was constructed. This laid the foundation for identifying the tendencies, intensity, and transitions of individual text psychological security, and then exploring the evolution trend of group psychological security risks. Results: Compared with the generation and reduction periods, group psychological security risks are more likely to occur during the outbreak and recovery periods, and the intensity level is also higher. The overall intensity of group psychological security risks shows an evolution trend of first increasing, then decreasing, and then increasing again. Conclusion: The paper provides an opportunity to explore the dynamics of psychological security in the digital space. Meanwhile, we call on the government and relevant management departments to pay more attention to the group psychological security risks formed during the outbreak and recovery periods of public health emergencies, and take corresponding measures in a timely manner to guide the public to transform the extreme psychological security state into the normal psychological security state, in order to prevent and resolve group psychological security risks, promote social stability and national security.

A seven-step guide to spatial, agent-based modelling of tumour evolution.

Spatial agent-based models are frequently used to investigate the evolution of solid tumours subject to localized cell-cell interactions and microenvironmental heterogeneity. As spatial genomic, transcriptomic and proteomic technologies gain traction, spatial computational models are predicted to become ever more necessary for making sense of complex clinical and experimental data sets, for predicting clinical outcomes, and for optimizing treatment strategies. Here we present a non-technical step by step guide to developing such a model from first principles. Stressing the importance of tailoring the model structure to that of the biological system, we describe methods of increasing complexity, from the basic Eden growth model up to off-lattice simulations with diffusible factors. We examine choices that unavoidably arise in model design, such as implementation, parameterization, visualization and reproducibility. Each topic is illustrated with examples drawn from recent research studies and state of the art modelling platforms. We emphasize the benefits of simpler models that aim to match the complexity of the phenomena of interest, rather than that of the entire biological system. Our guide is aimed at both aspiring modellers and other biologists and oncologists who wish to understand the assumptions and limitations of the models on which major cancer studies now so often depend.

Evolving Tumor Characteristics and Smart Nanodrugs for Tumor Immunotherapy.

Typical physiological characteristics of tumors, such as weak acidity, low oxygen content, and upregulation of certain enzymes in the tumor microenvironment (TME), provide survival advantages when exposed to targeted attacks by drugs and responsive nanomedicines. Consequently, cancer treatment has significantly progressed in recent years. However, the evolution and adaptation of tumor characteristics still pose many challenges for current treatment methods. Therefore, efficient and precise cancer treatments require an understanding of the heterogeneity degree of various factors in cancer cells during tumor evolution to exploit the typical TME characteristics and manage the mutation process. The highly heterogeneous tumor and infiltrating stromal cells, immune cells, and extracellular components collectively form a unique TME, which plays a crucial role in tumor malignancy, including proliferation, invasion, metastasis, and immune escape. Therefore, the development of new treatment methods that can adapt to the evolutionary characteristics of tumors has become an intense focus in current cancer treatment research. This paper explores the latest understanding of cancer evolution, focusing on how tumors use new antigens to shape their "new faces"; how immune system cells, such as cytotoxic T cells, regulatory T cells, macrophages, and natural killer cells, help tumors become "invisible", that is, immune escape; whether the diverse cancer-associated fibroblasts provide support and coordination for tumors; and whether it is possible to attack tumors in reverse. This paper discusses the limitations of targeted therapy driven by tumor evolution factors and explores future strategies and the potential of intelligent nanomedicines, including the systematic coordination of tumor evolution factors and adaptive methods, to meet this therapeutic challenge.

Interactions between chaperone and energy storage networks during the evolution of Legionella pneumophila under heat shock.

Waterborne transmission of the bacterium Legionella pneumophila has emerged as a major cause of severe nosocomial infections of major public health impact. The major route of transmission involves the uptake of aerosolized bacteria, often from the contaminated hot water systems of large buildings. Public health regulations aimed at controlling the mesophilic pathogen are generally concerned with acute pasteurization and maintaining high temperatures at the heating systems and throughout the plumbing of hot water systems, but L. pneumophila is often able to survive these treatments due to both bacterium-intrinsic and environmental factors. Previous work has established an experimental evolution system to model the observations of increased heat resistance in repeatedly but unsuccessfully pasteurized L. pneumophila populations. Here, we show rapid fixation of novel alleles in lineages selected for resistance to heat shock and shifts in mutational profile related to increases in the temperature of selection. Gene-level and nucleotide-level parallelisms between independently-evolving lineages show the centrality of the DnaJ/DnaK chaperone system in the heat resistance of L. pneumophila. Inference of epistatic interactions through reverse genetics shows an unexpected interaction between DnaJ/DnaK and the polyhydroxybutyrate-accumulation energy storage mechanism used by the species to survive long-term starvation in low-nutrient environments.

Ancient hybridization and repetitive element proliferation in the evolutionary history of the monocot genus Amomum (Zingiberaceae).

Genome size variation is a crucial aspect of plant evolution, influenced by a complex interplay of factors. Repetitive elements, which are fundamental components of genomic architecture, often play a role in genome expansion by selectively amplifying specific repeat motifs. This study focuses on Amomum, a genus in the ginger family (Zingiberaceae), known for its 4.4-fold variation in genome size. Using a robust methodology involving PhyloNet reconstruction, RepeatExplorer clustering, and repeat similarity-based phylogenetic network construction, we investigated the repeatome composition, analyzed repeat dynamics, and identified potential hybridization events within the genus. Our analysis confirmed the presence of four major infrageneric clades (A-D) within Amomum, with clades A-C exclusively comprising diploid species (2n = 48) and clade D encompassing both diploid and tetraploid species (2n = 48 and 96). We observed an increase in the repeat content within the genus, ranging from 84% to 89%, compared to outgroup species with 75% of the repeatome. The SIRE lineage of the Ty1-Copia repeat superfamily was prevalent in most analyzed ingroup genomes. We identified significant difference in repeatome structure between the basal Amomum clades (A, B, C) and the most diverged clade D. Our investigation revealed evidence of ancient hybridization events within Amomum, coinciding with a substantial proliferation of multiple repeat groups. This finding supports the hypothesis that ancient hybridization is a driving force in the genomic evolution of Amomum. Furthermore, we contextualize our findings within the broader context of genome size variations and repeatome dynamics observed across major monocot lineages. This study enhances our understanding of evolutionary processes within monocots by highlighting the crucial roles of repetitive elements in shaping genome size and suggesting the mechanisms that drive these changes.

Physiology evolves convergently but lags behind warming in cities.

Cities, through the generation of urban heat islands, provide a venue for exploring contemporary convergent evolution to climatic warming. We quantified how repeatable the evolution of heat tolerance, cold tolerance, and body size were among diverse lineages in response to urban heat islands. Our study revealed significant shifts towards higher heat tolerance and diminished cold tolerance among urban populations. We further found that the magnitude of trait divergence was significantly and positively associated with the magnitude of the urban heat island, suggesting that temperature played a major role in the observed divergence in thermal tolerance. Despite these trends, the magnitude of trait responses lagged behind environmental warming. Heat tolerance responses exhibited a deficit of 0.84°C for every 1°C increase in warming, suggesting limits on adaptive evolution and consequent adaptational lags. Other moderators were predictive of greater divergence in heat tolerance, including lower baseline tolerance and greater divergence in body size. Although terrestrial species did not exhibit systematic shifts towards larger or smaller body size, aquatic species exhibited significant shifts towards smaller body size in urban habitats. Our study demonstrates how cities can be used to address long-standing questions in evolutionary biology regarding the repeatability of evolution. Importantly, this work also shows how cities can be used as forecasting tools by quantifying adaptational lags and by developing trait-based associations with responses to contemporary warming.

Buoyancy control and air breathing in royal knifefish (Chitala blanci) and a new hypothesis for the early evolution of vertebrate air-breathing behaviors.

We present the first description of inspiration-first air breaths in royal knifefish, Chitala blanci, a ray-finned fish known to use four-stroke air breaths. Four-stroke breaths are used by nearly all ray-finned fish species that use their gas bladder to breathe air and are the ancestral breath type of ray-finned fishes. Interestingly, one such species, Amia calva, is known to perform two distinct breath types. Amia use four-stroke breaths when they need more oxygen and performs inspiration-first breaths to restore buoyancy. We observed that C. blanci also performs inspiration-first breaths and tested whether the two breath types are performed for the same functions in C. blanci as they are in Amia. We recorded the frequency of each breath type when exposed to aquatic hypoxia and two conditions of oxygen availability. We found that C. blanci performed more four-stroke breaths (81% ± 15% of total breaths) than inspiration-first breaths when exposed to aerial normoxia but performed more inspiration-first breaths (72% ± 40%) than four-stroke breaths when exposed to aerial hyperoxia. These patterns match those described for Amia and indicate that C. blanci performs four-stroke breaths in response to oxygen depletion and performs inspiration-first breaths to maintain buoyancy. Few studies have examined the role of air-breathing in buoyancy regulation. Decreasing buoyancy, rather than oxygen availability, to stimulate air breaths may reveal that inspiration-first breaths are more common among fishes than we are aware. We consider this possibility and present a new hypothesis for the origin and early evolution of air breathing in vertebrates.

Stable Zinc Electrode Reaction Enabled by Combined Cationic and Anionic Electrolyte Additives for Non-Flow Aqueous Zn─Br2 Batteries.

Aqueous zinc-bromine batteries hold immense promise for large-scale energy storage systems due to their inherent safety and high energy density. However, achieving a reliable zinc metal electrode reaction is challenging because zinc metal in the aqueous electrolyte inevitably leads to dendrite growth and related side reactions, resulting in rapid capacity fading. Here, it is reported that combined cationic and anionic additives in the electrolytes using CeCl3 can simultaneously address the multiple chronic issues of the zinc metal electrode. Trivalent Ce3+ forms an electrostatic shielding layer to prevent Zn2+ from concentrating at zinc metal protrusions, while the high electron-donating nature of Cl- mitigates H2O decomposition on the zinc metal surface by reducing the interaction between Zn2+ and H2O. These combined cationic and anionic effects significantly enhance the reversibility of the zinc metal reaction, allowing the non-flow aqueous Zn─Br2 full-cell to reliably cycle with exceptionally high capacity (>400 mAh after 5000 cycles) even in a large-scale battery configuration of 15 × 15 cm2.

The untapped potential of comparative biology in aging research; insights from the extraordinary-long-lived naked mole-rat.

The search for solutions to the vagaries of aging have, historically, been akin to searching at night in the bright light under street lamps by utilizing the few preexisting and well-established animal model systems. Throughout my career as a comparative biologist, I have ventured into the darkness across four continents and studied over 150 different animal species, many of which have evolved remarkable adaptations to survive on the harsh and rugged fitness landscape that exists outside of the laboratory setting. In this Fellows Forum, I will discuss the main focus of my research for the last 25 years and dig deeply into the biology of the preternaturally long -lived naked mole-rat that makes it an ideal model system for the characterization of successful strategies to combat aging.

Comparative analysis of the molecular starvation response of Southern Ocean copepods.

Large lipid-storing copepods dominate mesozooplankton biomass in the polar oceans and form a critical link between primary production and higher trophic levels. The ecological success of these species depends on their ability to survive periods of food deprivation in a highly seasonal environment, but the molecular changes that mediate starvation tolerance in these taxa are unknown. We conducted starvation experiments for two dominant Southern Ocean copepods, Calanoides acutus and Calanus propinquus, allowing us to compare the molecular starvation response between species. These species differ in life history, diet and metabolic traits, and expressed overlapping but distinct transcriptomic responses to starvation. Most starvation-response genes were species-specific, but we identified a conserved core set of starvation-response genes related to RNA and protein metabolism. We used phylotranscriptomics to place these results in the context of copepod evolution and found that starvation-response genes are under strong purifying selection at the sequence level and stabilizing selection at the expression level, consistent with their role in mediating essential biological functions. Selection on starvation-response genes was especially strong in our focal lipid-storing lineage relative to other copepod taxa, underscoring the significance of starvation tolerance for these species. We also found that certain key lipid enzymes (elongases and desaturases) have experienced diversification and positive selection in lipid-storing lineages, reflecting the unique lipid storage needs of these animals. Our results shed light on the molecular adaptations of high-latitude zooplankton to variable food conditions and suggest that starvation-response genes are under particularly strong sequence and expression constraints.

Charge Redistribution of Lattice-Mismatched Co─Cu3P Boosting pH-Universal Water/Seawater Hydrogen Evolution.

Practical applications of the hydrogen evolution reaction (HER) rely on the development of highly efficient, stable, and low-cost catalysts. Tuning the electronic structure, morphology, and architecture of catalysts is an important way to realize efficient and stable HER electrocatalysts. Herein, Co-doped Cu3P-based sugar-gourd structures (Co─Cu3P/CF) are prepared on copper foam as active electrocatalysts for hydrogen evolution. This hierarchical structure facilitates fast mass transport during electrocatalysis. Notably, the introduction of Co not only induces a charge redistribution but also leads to lattice-mismatch on the atomic scale, which creates defects and performs as additional active sites. Therefore, Co─Cu3P/CF requires an overpotential of only 81, 111, 185, and 230 mV to reach currents of 50, 100, 500, and 1000 mA cm-2 in alkaline media and remains stable after 10 000 CV cycles in a row and up to 110 h i-t stability tests. In addition, it also shows excellent HER performance in water/seawater electrolytes of different pH values. Experimental and DFT show that the introduction of Co modulates the electronic and energy level structures of the catalyst, optimizes the adsorption and desorption behavior of the intermediate, reduces the water dissociation energy barrier during the reaction, accelerates the Volmer step reaction, and thus improves the HER performance.

Design and Synthesis of Electrocatalysts Base on Catalysis-Unit Engineering.

It is a pressing need to develop new energy materials to address the existing energy crisis. However, screening optimal targets out of thousands of materials candidates remains a great challenge. Herein, we propose and validate an alternative concept for highly effective materials screening based on dual-atom salphen catalysis units. Such an approach simplifies the design of catalytic materials and reforms the trial-and-error experimental model into a building-blocks-assembly like process. Firstly, density functional theory (DFT) calculations were performed on a series of potential catalysis units which were possible to synthesize. Then, machine learning (ML) was employed to define the structure-performance relationship and acquire chemical insights. Afterwards, the projected catalysis units were integrated into covalent organic frameworks (COFs) to validate the concept Electrochemical tests confirm that Ni-SalphenCOF and Co-SalphenCOF are promising conductive agent-free oxygen evolution reaction (OER) catalysts. This work provides a fast-tracked strategy for design and development of functional materials, which serves as a potentially workable framework for seamlessly integrating DFT calculations, ML, and experimental approaches. This article is protected by copyright. All rights reserved.

Identification of RNF213 as a potential suppressor of local invasion in intrahepatic cholangiocarcinoma.

Intrahepatic cholangiocarcinoma (ICC) is a lethal cancer with poor survival especially when it spreads. The histopathology of its rare intraductal papillary neoplasm of the bile duct type (IPNB) characteristically shows cancer cells originating within the confined bile duct space. These cells eventually invade and infiltrate the nearby liver tissues, making it a good model to study the mechanism of local invasion, which is the earliest step of metastasis. To discover potential suppressor genes of local invasion in ICC, we analyzed the somatic mutation profiles and performed clonal evolution analyses of the 11 pairs of macrodissected IPNB tissues with local invasion (LI-IPNB) and IPNB tissues without local invasion from the same patients. We identified a protein-truncating variant (PTV) in an E3 ubiquitin ligase, RNF213 (c.6967C>T; p.Gln2323X; chr17: 78,319,102 [hg19], exon 29), as the most common PTV event in LI-IPNB samples (4/11 patients). Knockdown of RNF213 in HuCCT1 and YSCCC cells showed increased migration and invasion, and reduced vasculogenic mimicry, but maintained normal proliferation. Transcriptomic analysis of the RNF213-knockdown versus control cells was then performed in the HuCCT1, YSCCC, and KKU-100 cells. Gene Ontology (GO) enrichment analysis of the common differentially expressed genes revealed significantly altered cytokine and oxidoreductase-oxidizing metal ions activities, as confirmed by western blotting. Gene Set Enrichment Analysis (GSEA) identified the most enriched pathways being oxidative phosphorylation, fatty acid metabolism, reactive oxygen species, adipogenesis, and angiogenesis. In sum, loss of function of RNF213 is a common genetic alteration in LI-IPNB tissues. RNF213 knockdown leads to increased migration and invasion of ICC cells, potentially through malfunctions of the pathways related inflammation, and energy metabolisms.

Electronic Structure Engineering of Pt-Ni Alloy NPs by Coupling of Gold Single Atoms on N-Doped Carbon for Highly Efficient Oxygen Reduction Reaction and Hydrogen Evolution Reaction.

Improving the catalytic activity and durability of platinum-based alloy catalysts remains a formidable challenge in the context of renewable energy electrolysis applications. Herein, a facile and rapid photochemical deposition strategy for the synthesis of gold single atoms (Au SAs) anchored on N-doped carbon is presented. These Au SAs serve as a charge redistribution support for Pt-Ni alloy nanoparticles (PtNiNPs/AuSA-NDC), creating an extended electron-donating interface with Pt-Ni alloy sites. Consequently, the PtNiNPs/AuSA-NDC hybrid catalyst manifests exceptional catalytic performance and durability in both the oxygen reduction reaction (ORR) and hydrogen evolution reaction (HER) under acidic conditions. Specifically, in ORR, it exhibits a half-wave potential (0.92 V vs RHE), with a mass activity 20.4 times superior to Pt/C at 0.9 V. In HER, PtNiNPs/AuSA-NDC demonstrates a notably reduced overpotential of 19.1 mV vs RHE at 10 mA cm-2 and a mass activity 38 times higher than Pt/C (at 0.25 mV). Furthermore, this hybrid catalyst displays outstanding durability, with only an 8.0 mV decay observed for ORR and a 6.9 mV decay for HER after 10 000 cycles. Theoretical calculations provide insight into the mechanism, demonstrating that isolated Au sites effectively modulate the electronic structure of Pt-Ni alloy sites, facilitating intermediate adsorption and enhancing reaction kinetics.

What makes a temperate phage an effective bacterial weapon?

Temperate bacteriophages (phages) are common features of bacterial genomes and can act as self-amplifying biological weapons, killing susceptible competitors and thus increasing the fitness of their bacterial hosts (lysogens). Despite their prevalence, however, the key characteristics of an effective temperate phage weapon remain unclear. Here, we use systematic mathematical analyses coupled with experimental tests to understand what makes an effective temperate phage weapon. We find that effectiveness is controlled by phage life history traits-in particular, the probability of lysis and induction rate-but that the optimal combination of traits varies with the initial frequency of a lysogen within a population. As a consequence, certain phage weapons can be detrimental when their hosts are rare yet beneficial when their hosts are common, while subtle changes in individual life history traits can completely reverse the impact of an individual phage weapon on lysogen fitness. We confirm key predictions of our model experimentally, using temperate phages isolated from the clinically relevant Liverpool epidemic strain of Pseudomonas aeruginosa. Through these experiments, we further demonstrate that nutrient availability can also play a critical role in driving frequency-dependent patterns in phage-mediated competition. Together, these findings highlight the complex and context-dependent nature of temperate phage weapons and the importance of both ecological and evolutionary processes in shaping microbial community dynamics more broadly. IMPORTANCE: Temperate bacteriophages-viruses that integrate within bacterial DNA-are incredibly common within bacterial genomes and can act as powerful self-amplifying weapons. Bacterial hosts that carry temperate bacteriophages can thus gain a fitness advantage within a given niche by killing competitors. But what makes an effective phage weapon? Here, we first use a simple mathematical model to explore the factors determining bacteriophage weapon utility. Our models suggest that bacteriophage weapons are nuanced and context-dependent; an individual bacteriophage may be beneficial or costly depending upon tiny changes to how it behaves or the bacterial community it inhabits. We then confirm these mathematical predictions experimentally, using phages isolated from cystic fibrosis patients. But, in doing so, we also find that another factor-nutrient availability-plays a key role in shaping bacteriophage-mediated competition. Together, our results provide new insights into how temperate bacteriophages modulate bacterial communities.