Cell

Ancient proteins provide a direct window into past diets by enabling the identification of consumed foods through the analysis of dental calculus. While previous studies have reliably detected animal-derived proteins such as milk, plant-derived proteins remain markedly underrepresented, leaving a significant gap in our understanding of the role of plants in past human diets. Here, we show how the reanalysis of open-access paleoproteomics datasets can reveal previously overlooked plant proteins by revisiting two archaeological dental calculus datasets spanning the Eneolithic to Iron Age from the Pontic-Caspian region and the Levantine coast (n = 63 individuals). We identify 60 unique peptides derived from 60 distinct proteins of broomcorn millet (Panicum miliaceum) in 39 individuals. All peptides are unique to Panicum miliaceum and their taxonomic assignment was confirmed using a stringent multi-tier validation strategy, providing the first paleoproteomics evidence of its consumption preserved in dental calculus and extending beyond current protein database annotations. Combined with existing radiocarbon chronologies, these findings represent the earliest paleoproteomics evidence of broomcorn millet consumption, substantially revising its chronology and geographic pathways of dispersal across Eurasia. More broadly, this study demonstrates the untapped potential of dental calculus proteomics and open-access data to directly trace plant consumption, opening new avenues for investigating crops that remain underrepresented in archaeological and proteomics research.

Upon infection, arteriviruses, coronaviruses, and other nidoviruses transform endoplasmic reticulum membranes into viral replication organelles. These include large numbers of double-membrane vesicles (DMVs) whose interior is considered the primary site of viral RNA synthesis. Early studies characterized nidovirus DMVs as sealed compartments, leaving it unclear how newly synthesized viral RNA could be exported to the cytosol. The discovery of DMV-spanning pore complexes in coronavirus-infected cells provided a plausible solution for this topological challenge. However, their structural organization, functional features, and evolutionary conservation across the nidovirus order, have remained unclear. Here, we investigated the macromolecular architecture of DMVs induced by two prototypic arteriviruses using cellular cryo-electron tomography. Despite the substantial evolutionary distance separating arteriviruses and coronaviruses, we observed DMV-spanning pore complexes with striking structural similarities to those previously described in coronaviruses. These pores appear to facilitate both export and encapsidation of viral RNA. In the absence of viral RNA synthesis, ectopic expression of the arterivirus transmembrane nonstructural proteins nsp2 and nsp3 sufficed to induce the formation of pore-containing DMVs. Together, our findings reveal the conservation of key structural features of DMV pores across two distantly related nidovirus families and support a central role for these pores in nidovirus replication.

The ascidian Ciona provides a key model for understanding the evolutionary origin of the vertebrate brain. While the larval nervous system has been extensively characterized, the molecular and cellular organization of the adult neural complex remains poorly defined. Here, we generated spatial transcriptomic maps of the adult Ciona neural complex from three individuals, with four serial sections per donor, using the 10x Visium platform. Clustering-based analysis identified five major tissue domains, including the cerebral ganglion, neural gland, ciliated funnel, neural gland duct/dorsal strand, and body wall muscle. To further refine spatial resolution, we computationally reconstructed approximately 980 super-resolution gene expression maps by integrating transcriptomic measurements with histological image features. The super-resolution maps enabled precise delineation of molecular territories within the neural complex. In the cerebral ganglion, high-resolution reconstruction revealed clear molecular zonation, distinguishing the cortex and medulla. Within the cortex, the central region facing the neural gland and anteroposterior distal regions showed distinct molecular properties. In the neural gland, we identified coordinated enrichment of cell-cell interaction- and extracellular matrix-related genes, suggesting specialized structural and physiological properties. We propose that the neural gland play a pivotal role for the cerebral ganglion in maintaining homeostasis, supporting development, and providing a signaling interface, which is reminiscent of a primitive form of the choroid plexus and meninges found in vertebrates. Together, this study provides the first spatially resolved transcriptomic atlas of the adult Ciona neural complex and establishes a molecular framework for investigating functional regionalization and brain evolution in chordates.

Genetic diversity shapes phenotypes, yet even genetically identical individuals differ. In nine-banded armadillo (Dasypus novemcinctus) quadruplets, we previously showed that allele-specific expression (ASE) imbalances provide a stable molecular fingerprint of individuality. Here, we test whether such transcriptomic individuality reflects functional biological differences. We profiled bulk blood RNA from five cohorts of genetically identical quadruplets across three time points, and found persistent gene-expression signatures that predict individual identity. Focusing on a highly variable cohort, we then performed single-cell RNA-seq and ATAC-seq. In this litter, the most stably distinct individual showed an expanded monocyte-lineage compartment and gene-expression programs enriched for inflammatory and differentiation pathways. These cell-type and regulatory differences were stable over time and robust to experimental leprosy infection. Together, our results link transcriptomic individuality to lasting differences in immune-cell composition, illustrating how early stochastic events can produce persistent, biologically meaningful divergence among genetically identical individuals. TeaserGenetically identical armadillo quadruplets are identifiable by transcriptomic signatures shaped by cellular composition variation.

Sustained mammal-to-mammal transmission of high pathogenicity H5N1 avian influenza viruses is reshaping the host range of these pathogens. One of the longest-running mammalian transmission chains involves the B3.13 genotype circulating in U.S. dairy cattle which was detected in early 2024. Genomic analyses revealed selection and rapid fixation of haemagglutinin mutations D104G and V147M. We demonstate, via glycomic profiling, that bovine tissues, including the mammary gland, are enriched in N- and O-linked glycans capped with N-glycolylneuraminic acid (NeuGc), a sialic acid absent in humans and birds, which instead express only N-acetylneuraminic acid (NeuAc). Early cattle H5 viruses poorly recognized NeuGc, but D104G and V147M enabled efficient engagement of both NeuAc- and NeuGc-containing receptors. These mutations enhanced replication in bovine mammary tissue without major attenuation of replication in human lung and primary nasal epithelial cells. NeuGc-driven receptor adaptation therefore promotes viral fitness in cattle while potentially limiting immediate zoonotic risk. Deep mutational scanning further identified alternative haemagglutinin substitutions that confer NeuGc usage and represent surveillance markers for emerging cattle H5 lineages.

Plant pathogens establish colonization through effector secretion to modulate host immune responses. Within bacterial effectors intrinsically disordered regions (IDRs) contribute to diverse functions and pathogenicity, but their role in effectors of phytopathogenic oomycetes remains poorly understood. Here, analysis of oomycete secretomes across lifestyles reveal widespread intrinsic disorder in secreted proteins, particularly in apoplastic elicitin and elicitin-like effectors (ELLs). Combining in vitro and in planta experiments, we show that IDRs in ELLs from the biotrophic pathogen Albugo candida reduce immune recognition, consistent with an IDR-mediated shielding mechanism. This function is transferable, as fusion of an ELL-derived IDR to the immunogenic elicitin INF1 from Phytophthora infestans abolishes its recognition. These findings identify intrinsic disorder as a functional feature of apoplastic effectors that modulates host detection and promotes pathogen fitness. Graphical summary O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/717489v1_ufig1.gif" ALT="Figure 1"> View larger version (59K): org.highwire.dtl.DTLVardef@1363e05org.highwire.dtl.DTLVardef@21f34dorg.highwire.dtl.DTLVardef@ec6e5borg.highwire.dtl.DTLVardef@41327b_HPS_FORMAT_FIGEXP M_FIG C_FIG

Successful pregnancy requires exquisite balance: the placenta must invade just enough to access maternal blood but not so deep it remains attached at birth. Disrupting this balance causes life-threatening pregnancy complications, for which treatments remain limited. Animal models are desperately needed to discover mechanisms underlying balanced uteroplacental development and how pregnancy complications arise, but this is hampered by the view that mouse placentation lacks human characteristics such as extensive trophoblast invasion and targeting of uterine spiral arteries. Here, we utilize 3D imaging, mouse genetics, and pharmacological perturbations to demonstrate that: (1) The mouse placenta invades more extensively than previously recognized with most spiral arteries heavily enveloped by fetal trophoblasts, (2) This process is disrupted without CXCL12-CXCR4 signaling specifically during early pregnancy, and (3) Disrupting early uteroplacental development ultimately results in excessively deep trophoblast invasion, closely mimicking the pregnancy complication placenta accreta. Mechanistically, uterine epithelium, stroma, and arteries activate CXCR4 signaling in early pregnancy, and inhibition causes decidualization failure, followed by dissolution of spiral artery development. Trophoblasts consequently migrate deep into uterine muscle and its arteries, reproducing hallmarks of human accreta. Thus, with 3D imaging, the mouse more effectively models human uteroplacental development and defines an early etiological window for intervention.

Antibody-secreting cells (ASCs) provide humoral immunity that can mediate lifelong protection against pathogens. Current classifications cannot delineate the heterogenous functionalities, tissue residencies, and lifespans of human ASC subsets, impeding clinical translation. We applied multi-omic sequencing, spatial proteomics, and functional assays to discover and characterize human bone marrow (BM) ASC subsets. We identified two peripheral subsets (ASCp) also present in blood and three BM-resident subsets (ASCr), comprising a maturation continuum associated with increased mitochondrial networking, diminished antibody secretion, differential transcription factor motif accessibility, and preferential co-localization in homotypic niches. CD19+9+ASCr and CD19-ASCr exhibited poor recovery years after BM transplantation, indicating a strong dependence on supportive niches. Childhood vaccine antigens were recognized by long-lived ASCr subsets in adults and by immature HLA-DR+ASCp, implying ASCs can differentiate without recent antigen exposure. Our results provide new insights into ASC identity, maturation, and longevity and a generalizable framework for study and manipulation of human ASCs.

Root exudation mediates the delivery of plant primary and secondary metabolites into soil, where they regulate plant-microbe interactions and terrestrial carbon cycling. Conventional exudate analyses quantify total root-released carbon yet obscure the spatial origin and rhizosphere influence of individual compounds. Here, we develop a rhizobacterial biosensor platform, named Suc-MAPP, to map local exudate profiles along the surface of colonized root tissues. Focusing on sucrose, we engineered sfGFP-based, sucrose-responsive gene circuits in Pseudomonas putida KT2440 for live imaging of exudate concentrations in the micromolar range. These biosensors reveal spatially structured sucrose exudation patterns across eudicots and monocots and implicate photoassimilated source-sink dynamics as a major determinant. We further apply this platform to phenotype exudation modulated by synthetic gene circuitry in Arabidopsis thaliana, identifying genetic design rules for graded sucrose release and quantifying how engineered export sculpts rhizosphere assembly of a defined bacterial community. Together, these results establish programmable rhizobacterial biosensors as tools to spatially resolve plant-environment carbon exchange in situ and provide a framework for extending this approach to diverse exudate targets.

Disruptions in purine metabolism contribute to a range of human diseases, from rare genetic disorders such as Lesch-Nyhan syndrome and xanthinuria to common conditions including gout and cancer. To better understand the metabolic networks that regulate purine homeostasis, we developed a Caenorhabditis elegans model of xanthine dehydrogenase (xdh-1) deficiency. Remarkably, xdh-1 mutant animals form rare xanthine stones, recapitulating a hallmark of human xanthinuria. To uncover genetic regulators of purine homeostasis, we performed a forward genetic screen for mutations that exacerbate xanthine stone formation in xdh-1 mutants. This approach identified multiple loss-of-function alleles in a previously uncharacterized gene, which we named gda-1. We show that gda-1 encodes an intestinal guanine deaminase that mediates a key enzymatic step in purine catabolism. The C. elegans genome also encodes a paralog, gda-2, which shares guanine deaminase activity but is expressed in distinct tissues. While gda-2 can compensate for gda-1 loss in guanine metabolism, the two genes exhibit non-redundant roles in regulating xanthine accumulation and stone formation. Interestingly, our evolutionary analyses suggest that gda-2 was acquired by nematodes via horizontal gene transfer from bacteria. These findings reveal a spatially regulated purine catabolism pathway in C. elegans and suggest that acquisition of bacterial genes has shaped a core nematode metabolic network.

Many insects manipulate plants by injecting effector proteins. In one extreme example of this molecular "hijacking", Hormaphis cornu aphids inject bicycle proteins into Hamamelis virginiana (Witch Hazel), contributing to the development of novel organs called galls. Bicycle proteins share no amino acid sequence similarity with proteins of known function. Here, we report the crystal structures of two divergent bicycle proteins. Both proteins contain saposin-like folds: one with multiple disulfide bonds exhibits a helix swap; the other has no disulfide bonds and possesses two tandem domains. To explore the structural evolution of bicycle proteins, we predicted bicycle protein structures with Alphafold2 (AF2). While AF2 did not recover the two experimental structures using existing databases, it succeeded after we provided multiple sequence alignments (MSAs) containing protein sequences encoded in new genome sequences from closely related aphid species. Using this customized approach at scale, we generated 2400 high-confidence predictions for bicycle proteins from seven aphid species. This dataset revealed that bicycle proteins without cysteines are outliers in fold space and appear to have evolved from ancestral proteins with disulfide-bonded saposin-like folds. While all bicycle proteins contain predicted saposin-like folds, they display a vast diversity of structural and physicochemical properties. While this diversity thwarts prediction of conserved functions encoded in structure, it suggests that bicycle proteins have evolved to target diverse plant processes and/or to evade plant immune surveillance. Significance statementParasites introduce specialized "effector" proteins into hosts, both to suppress host immunity and to release nutrients. The molecular functions and structures of most effector proteins are unknown. Effector proteins often evolve rapidly and share no similarity with proteins of known function. Here, we demonstrate that machine learning algorithms can accurately predict the structures of aphid "bicycle" effector proteins when supplemented with data from closely related species. We exploit this finding to generate predictions of 2400 bicycle protein structures. These proteins exploit a common motif, yet exhibit diverse structures that form distinct structural clusters. Despite the clustering of these proteins in structure space, they occupy a nearly uniformly physicochemical space, suggesting that they encode a large diversity of molecular functions.

We analyzed 399 shotgun genomes from the Royal Basilica of Szekesfehervar, representing the elite of the Medieval Hungarian Kingdom. Our results reveal that the Carpathian Basin population underwent a marked homogenization during the Middle Ages, driven largely by admixture with eastern immigrant groups, especially the conquering Hungarians, resulting in a genomic landscape distinct from that of the surrounding European populations. The European ancestry component also shifted: the Avar-period Balkan element disappeared, while northern and northwestern European ancestry increased, likely reflecting changing political connections. We identified a previously unrecognized Conquest-period stratum at the site, including two individuals closely related to the Arpad dynasty. No large, continuous kinship networks were detected, indicating a dynamic and continuously renewed elite. At the population level, the strongest affinities were observed with the Conq_Asia_Core group and its ancestor, the Karayakupovo horizon, as well as with medieval populations from neighboring regions (present-day Croatia, Serbia, Slovakia, Poland, and Montenegro), reflecting the diverse sources of the medieval Hungarians.

Animal venoms represent a major source of chemical novelty, yet how venom compounds originate, diversify, and are maintained across deep evolutionary timescales remains poorly understood. This gap is especially pronounced in cephalopods, which evolved venom systems used in predation, defense, and sexual competition, but whose venom genetic architectures, secretory cell types, and venom-producing glands remain largely unexplored. To date, only a single cephalopod venom compound with confirmed paralytic activity and a known primary sequence, SE-CTX from the golden cuttlefish Acanthosepion esculentum, has been described. Here, we reconstruct the evolutionary history, molecular diversity, and glandular localization of SE-CTX-like proteins using a multimodal approach. We identify 29 homologs across 20 squid and cuttlefish species and define a previously unrecognized venom gene family, which we name deca-ctx, specific to decapodiform cephalopods (squids and cuttlefish). Phylogenetic analyses reveal a single origin of deca-ctx followed by gene duplication and lineage-specific diversification, indicating long-term retention of this venom gene. Predicted DECA-CTX protein structures were separated into two clusters and 20 singletons highlighting potentially extensive structural diversity within a single cephalopod venom gene family. Proteomic analysis confirms expression of five DECA-CTX proteins across three species. Our imaging and histological analyses localize deca-ctx expression to specialized secretory cells within squid and cuttlefish venom glands. Together, these findings reposition SE-CTX as part of an evolutionarily and chemically diverse venom system, rather than an isolated venom protein, and establish cephalopods as a key lineage for investigating how new venom genes arise, diversify, and are integrated into functional venom arsenals.

Infective endocarditis (IE) is a life-threatening disease most often caused by blood-borne bacteria that infect previously damaged cardiac tissue. Despite the importance of this disease, the genetic basis for IE virulence remains poorly defined. Here, we present the first genome-wide in vivo analysis of bacterial fitness in a vertebrate model of IE. We identified 146 genes in Streptococcus sanguinis required for IE fitness, the majority of which had not previously been linked to endocarditis. These determinants cluster into conserved metabolic, cell envelope, transport, and regulatory pathways, representing a vast reservoir of potential targets for novel antimicrobial intervention. A subset of these genes was examined in Streptococcus mutans; all were found to be essential for IE fitness in this distantly related oral species as well, suggesting broad conservation. Using experimental evolution, we further show that disruption of key fitness pathways triggers reproducible compensatory "bypass" mechanisms that reveal the inherent physiological constraints of the IE fitness landscape and identify vulnerable nodes for multi-target drug strategies. Together, these findings redefine streptococcal infective endocarditis as a disease shaped by conserved bacterial fitness networks that may be exploited for therapeutic development. HighlightsO_LIA genome-wide in vivo screen identified 146 Streptococcus sanguinis genes required for infective endocarditis fitness. C_LIO_LI94% of these genes represent previously unrecognized determinants of endocarditis. C_LIO_LIMultiple pathways--including CoA biosynthesis, the shikimate pathway, and rhamnan synthesis--are required for cardiac colonization. C_LIO_LIA subset of infective endocarditis fitness factors are conserved between S. sanguinis and S. mutans, with species-specific adaptations. C_LIO_LIExperimental evolution revealed compensatory metabolic networks that buffer IE fitness defects. C_LI

The lateral patch epitope of the H1 hemagglutinin (HA) was a dominant target of antibodies following exposure to the 2009 pandemic H1N1 virus. However, the conservation and potential for antigenic drift in the lateral patch remain unresolved. Here, we used lateral patch-specific monoclonal antibodies (mAbs) to understand the antigenicity of the lateral patch of human, avian, and swine H1Nx viruses spanning from 1918 to 2022. We identified discrete mutations that evaded lateral patch-targeting mAbs in pre- and post-2009 H1N1 viruses, leading to genetic differences in lateral patch-targeting antibodies in individuals across birth years. We observed that the lateral patch remains well conserved across zoonotic sources, suggesting existing lateral patch antibodies could protect against a future H1Nx pandemic. Together, these data support that lateral patch antigenic drift has shaped the human B cell repertoire against influenza viruses and that the lateral patch remains an attractive target for pandemic preparedness.

The Norman Conquest of 1066 CE reshaped the political and cultural landscape of England, yet its demographic consequences remain poorly understood, particularly outside elite and urban contexts where historical evidence is concentrated. Here, we investigate the population history of a rural English community spanning the Conquest using genome-wide ancient DNA from the Priory Orchard site, a cemetery in Godalming (Surrey) in use between the 9th and early 13th centuries CE. We generated genomic data from 78 individuals and established radiocarbon dates for 98 individuals from the site. Population genetic analyses place Priory Orchard individuals within the genetic continuum of early medieval populations from the North Sea region. Ancestry modelling indicates that this rural community carried substantial Scandinavian/Viking-related ancestry alongside a persistent Saxon-related component and a smaller French-related contribution. However, stratifying individuals by date, before and after 1066 CE, reveals no clear genome-wide discontinuity across the Conquest horizon, suggesting demographic continuity through this crucial political and social transition. This pattern is consistent with historical and archaeological evidence indicating that many of the most visible transformations following the Conquest occurred primarily among the elite. Our results provide the first genomic perspective on communities living through the Norman Conquest and indicate that rural southern England saw persistent migration links with other areas facing the North Sea rather than abrupt population replacement.

Three-dimensional (3D) genome architecture is the foundation of gene regulation, and plays a critical role in normal physiology and disease. However, our understanding of its biochemical determinants has long been limited by technology: imaging-based screens only profile a small number of loci, while sequencing-based studies rarely exceed 100 samples or conditions. Here we present "in-plate chromosome conformation capture" (Plate-C), a high-throughput, cost-effective platform that profiles thousands of whole-genome architectures in a day. Plate-C enabled the first chemical screen for whole-genome structural changes--profiling 2,956 samples from 834 conditions across 5 neuronal and glial types, accompanied by 6,081 single cells using "easy diploid chromosome conformation capture" (Easy Dip-C) and 200,893 single-cell transcriptomes. We discovered that diverse, dose/time-dependent, and cell type/species-specific modes of DNA structural changes can be rapidly induced by manipulating epigenetic (HDAC, BET), metabolic (mTOR), proteostatic (UPR), developmental (GSK3/Wnt, Hedgehog), immune (cGAS/STING), and neurotransmission pathways. To validate our finding in vivo, we demonstrated in newborn mice that HDAC inhibition drives brain-wide genome rewiring within hours, highly correlated with changes in vitro and inducing a latent structural and transcriptional state orthogonal to normal differentiation. By enabling massively parallel profiling of whole-genome structures, Plate-C paves the way for systematic discovery of DNA folding principles to better understand and engineer the human genome in 3D.

Caste identity in Harpegnathos saltator ants remains plastic beyond development and throughout adulthood. Adult Harpegnathos workers can become dominant reproductives, known as "gamergates," through a social caste transition that involves extensive transcriptional and cellular remodeling of the brain. To gain insight into the epigenetic regulation of this process, we generated comprehensive, caste-specific epigenomic atlases of the Harpegnathos brain, including chromatin accessibility, histone modifications, and 3D genome architecture. Using these data we refined the genome assembly, annotated enhancers, and linked them to target genes. We then identified candidate 3D-architectural factors, many of which were specifically upregulated in gamergate brains. Promoters of genes upregulated during the worker-gamergate transition formed an unusually high number of 3D chromatin contacts with their regulatory regions, and most of these contacts were already present in workers. We propose that the pre-existing hyper-connectivity of socially regulated genes is essential to adult brain plasticity and behavioral reprogramming.

Prostate cancer encompasses a spectrum of disease states driven by complex cellular heterogeneity. To delineate the transcriptional programs underlying lineage plasticity and metastasis, we constructed a comprehensive single-cell atlas of 128 patients, spanning localized, castration-resistant, and metastatic disease. Lineage plasticity was prevalent in localized disease, with subsets of tumor cells adopting distinct basal-like and club-like states. Luminal-like cancer cells also displayed extensive lineage infidelity, defined not by a binary loss of identity but by the combinatorial erosion of luminal gene modules associated with higher grade and stage. In the metastatic setting, gene program association analysis (GPAS) identified a broad induction of cell-cycle gene modules across organ sites as well as an induction of organ-specific gene modules, including osteomimetic signaling in bone, neuro-migratory genes in brain, and erythroid-like transitions in liver. Neuroendocrine prostate cancers (NEPCs) were not monolithic but defined by combinations of NE-associated gene modules including a novel HES6 program. Notably, these modules were detected at intermediate levels in localized samples, suggesting molecular plasticity precedes histological transformation. We also developed a refined NE signature that could distinguish NEPC tumors more accurately than previously published signatures. Within the tumor microenvironment (TME), we observed an elevation of pro-inflammatory Th17 T-cells in African American patients and identified a rare Schwann cell population. Finally, we present PCformer, a transformer-based foundation model trained on >500,000 cells to automate cell-state classification. Together, this comprehensive atlas demonstrates the complex nature of gene modules underlying lineage infidelity and plasticity in cancer cells and highlights distinct immune and stromal populations within the tumor ecosystem.

Plants host complex communities of microbes that are attached to root surfaces. While many studies have sampled mutant populations after prolonged incubation on roots to identify bacterial genes that enable long-term colonization, the molecular mechanisms governing the early stages root attachment remain less understood. Here, we developed an in vitro root culture system that enables controlled and scalable investigation of bacterial attachment to root tissue. We used this platform to perform a genome-wide screen for root attachment determinants in the plant-associated bacterium Pseudomonas protegens Pf-5. Our results reveal that the gacSA two-component system functions as a sensory integration hub for coordinating early root attachment. Mutations that disrupt gacS or gacA cause severe root attachment defects despite having no effect on abiotic surface attachment in standard biofilm assays. Mutation of flagellar assembly genes enhances root attachment by mimicking surface contact and activating the gac system. In parallel, chemical cues released by roots stimulate surface attachment in a gac dependent manner. By integrating these signals, the gac system activates cyclic di-GMP-mediated attachment programs that drive the transition from planktonic to sessile behavior required for root association. We build on this model to show that manipulating flagellar surface sensing enhances the competitive fitness of Pf-5 in the presence of a synthetic bacterial community, suggesting a strategy to improve the competitive fitness of beneficial microbes on crops. These findings establish a mechanistic framework linking surface sensing, global regulation, and root attachment in a beneficial rhizobacterium. ImportancePlant roots are covered with diverse microbes that strongly influence plant health. Growing in association with roots has many benefits, but how bacteria attach to root tissue remains poorly understood. We developed a system to study how a bacterium that improves plant growth called Pseudomonas protegens Pf-5 attaches to root tissue. We found that physical contact with the root surface and chemical cues released by roots both enhance attachment to root tissue. A sensory system called gacSA is responsible for integrating physical and chemical cues to activate a root attachment program. Variant bacteria that prematurely activate the gac system compete more effectively with other bacteria on roots, suggesting that the root attachment pathway we characterized could serve as a strategy to use beneficial bacteria in agriculture.