Gwyn A. Beattie

Soil salinization and sodicity are accelerating worldwide, reducing crop productivity across more than 160 million hectares of farmland and causing production losses approaching USD 27 billion annually. Despite decades of research documenting these impacts, the extent of salt‐affected soils continues to expand. Salt‐affected soil degradation emerges from feedbacks among physical, biological, and socioeconomic processes that operate across scales and resist intervention when addressed in isolation. This review synthesizes current understanding of these coupled feedbacks. We trace how ion accumulation, soil structural decline, microbial community disruption, and plant stress interact with irrigation practices, land use decisions, and governance systems. These interactions create threshold dynamics in which degradation can appear stable for years before rapid decline. Evidence from diverse regions reveals that effective restoration depends on coordinated interventions matched to the complexity of the system itself. Four research priorities emerge for advancing prediction and prevention. First, quantifying the thresholds that separate reversible from recalcitrant degradation across soil types and climates. Second, expanding predictive capacity through integrated sensor networks and data platforms that enable early warning. Third, improving understanding of how institutional structures influence adoption of restoration practices. Fourth, integrating biophysical and governance models to enable scaling from field trials to basin‐wide implementation. By coupling mechanistic understanding with monitoring infrastructure and adaptive governance, reactive remediation can give way to proactive prevention.

SUMMARY: Cucurbit yellow vine disease (CYVD) is a phloem disease caused by a group of Serratia ureilytica bacteria within the S. marcescens complex. The CYVD pathogen is distinct from other phloem pathogens in two fundamental ways: i) unlike other bacterial phloem pathogens, the CYVD pathogen readily grows on standard laboratory media; and ii) whereas most bacterial phloem diseases are transmitted solely by hemipteran insects, CYVD can be transmitted by both hemipteran (squash bug) and non-hemipteran (cucumber beetle) vectors. The phloem of cucurbits is also distinct, with cucurbits having a unique secondary phloem system, the extrafascicular phloem (EFP), for which a role in CYVD has not been investigated. The distinctive features of this pathosystem prompted a re-evaluation of pathogen localization in planta using a green fluorescent protein-tagged CYVD strain during infection of squash ( Cucurbita pepo ). In epifluorescence and confocal microscopy images of transverse and longitudinal sections of stem and petiole tissues, the fluorescence patterns of the CYVD pathogen were consistent with pathogen colonization of all four known EFP tissues, namely the peripheral, entocyclic, ectocyclic, and commissural sieve tubes. The CYVD pathogen may enter the EFP during herbivory by pathogen-infected vectors that cause mechanical damage, as the EFP exhibits much slower blockage following injury than the conventional fascicular (bundle) phloem. Moreover, although EFP has been proposed to have an antimicrobial function, EFP exudate collected from the stem and petioles of C. pepo supported rapid pathogen growth. These results provide evidence for a unique tissue tropism of the newly emerged plant pathogen S. ureilytica . SIGNIFICANCE STATEMENT: Bacterial phloem pathogens generally colonize the conventional fascicular (bundle) phloem of their host plant. We demonstrate that the bacterial pathogen causing cucurbit yellow vine disease is atypical in that it colonizes the extrafascicular phloem, a unique secondary phloem system of cucurbits that is thought to function beyond photosynthate transport. These findings reshape our understanding of phloem pathogenicity and indicate that the extrafascicular phloem is more physiologically accessible and biologically consequential than previously recognized.

Characterizing community composition is fundamental to understanding microbial community function. Recent advances in Oxford Nanopore Technology (ONT) long-read sequencing now allow community profiling using full-length gene amplicons, affording better taxonomic resolution than standard short-amplicon Illumina sequencing. However, robust ONT-compatible profiling workflows are lacking. To address this, we have created the Amplicon Consensus Taxonomy (ACT) pipeline for classifying long-read amplicons. ACT combines output from three existing pipelines – Emu, Sintax, and LACA – to leverage the strengths of each while offsetting their individual limitations. We also developed the ACT database (ACT-DB), a sequence-similarity-aware reference database that clusters highly similar sequences into multi-taxa groups to reduce overclassification. We benchmarked ACT performance against Emu and Sintax using a defined simple mock community, simulated datasets, and a complex rhizosphere community supplemented with novel species. While ACT exhibited generally comparable or superior performance across datasets, ACT demonstrated a marked advantage over Emu and Sintax in identifying novel and low-abundance taxa in both simple and complex communities, resulting in significantly higher species-richness estimates that better reflected those observed in prior Illumina amplicon studies. Furthermore, by clustering ambiguous reference sequences, ACT-DB allowed ACT to resolve reads to meaningful multi-species groups, improving resolution without coercing artificial precision. Together, ACT and ACT-DB form a robust long-read amplicon profiling workflow that confidently identifies known species while reducing overclassification and preserving low-abundance and unknown taxa. IMPORTANCE: Microbial communities are frequently characterized by amplicon sequencing of marker genes, such as the bacterial 16S rRNA gene and fungal ITS region. Historically, the standard profiling method has been Illumina sequencing of 200-300 bp amplicons, but improved accuracy of ONT long-read sequencing means it is now possible to sequence amplicons spanning full genes of any size, prompting the need for tools optimized for long amplicons. Here, we describe the ACT bioinformatic pipeline for assigning taxonomy to amplicons of any length. We evaluated ACT performance using full-length 16S amplicon data relative to that of two commonly used pipelines. Additionally, we developed a sequence ambiguity-aware ACT database (ACT-DB) of 16S rRNA sequences to further improve classification accuracy and resolution.

Cucurbit yellow vine disease (CYVD) is an emerging phloem disease in the United States that causes yield losses of up to 100% in squash, pumpkin, and watermelon. CYVD is caused by a group of closely related strains of Serratia ureilytica, a species comprising entomopathogenic, phytopathogenic, clinical, and environmental strains. One genomic trait distinguishing CYVD-causing S. ureilytica strains from non-CYVD S. ureilytica strains is the presence of a specific type I fimbrial locus, which we found to be uniquely plasmid-borne in CYVD strains. We investigated the contribution of this fim locus to CYVD by comparing the virulence of the wild-type CYVD strain Z07 to a deletion mutant Z07Δ fim that lacked the entire seven-gene fim locus. Infection assays with these strains showed that this locus contributes to virulence on squash ( Cucurbita pepo) and does so by contributing to a higher probability of developing large populations in planta. Moreover, the Z07Δ fim mutant formed larger biofilms than the wild type in vitro, suggesting that these type I fimbriae interfere with biofilm formation. These results support a model in which biofilm development following S. ureilytica plant infection negatively impacts virulence, such as by restricting the number of sites accessed in the phloem tissue, thereby impeding spread and limiting colonization.

Cucurbit yellow vine disease (CYVD) is an emerging disease that can cause up to 100% cucurbit crop losses. CYVD is transmitted by squash bugs ( Anasa tristis), but anecdotal reports indicate the presence of CYVD in cucurbit fields in the apparent absence of squash bugs and presence of cucumber beetles. This study tested the vector competence of two cucumber beetle species ( Acalymma vittatum and Diabrotica undecimpunctata howardi) for CYVD and explored the phylogenetic relatedness of CYVD-causing isolates (i.e., CYVD strains) from cucurbits to those from wild cucumber beetles from fields with endemic CYVD. CYVD strains have heretofore been classified as Serratia marcescens; however, pairwise genomic comparisons and phylogenomic analyses using complete genome assemblies of five CYVD strains, including two from wild cucumber beetles, indicate that CYVD strains form a clade in the S. ureilytica species, which is a species within the S. marcescens complex. The S. ureilytica isolates from both cucumber beetle species were pathogenic based on their ability to induce CYVD when injected into squash ( Cucurbita pepo) plants. Moreover, field-collected cucumber beetles of both species harboring the CYVD pathogen induced CYVD in squash plants in laboratory transmission tests, demonstrating that cucumber beetles can transmit S. ureilytica to plants. Our results support a nomenclature change for the causal agent of CYVD to S. ureilytica and demonstrate that cucumber beetles can both harbor and transmit S. ureilytica CYVD strains. S. ureilytica is thus distinct among phytopathogenic bacteria in its ability to use both hemipterans and coleopterans as vectors for transmission to plants.

Cucurbit yellow vine disease (CYVD), which is caused by the gram-negative bacterium Serratia marcescens and transmitted by squash bugs (Anasa tristis DeGeer), is a devastating disease of cucurbit crops that is emerging rapidly in the eastern half of the United States. The lack of a robust pathogenicity assay for CYVD in the laboratory has hampered functional tests using genomic sequences to investigate the biology of this phytopathogen. In this study we developed and validated a bioassay that yielded consistent and quantifiable CYVD symptoms on squash in the laboratory. We compared inoculation by wounding with a multipronged floral pin frog to inoculation by injection in which a needle was moved in and out of the stem multiple times in each of multiple piercings to mimic the feeding behavior of squash bugs. We found that inoculation by needle injection of ≥10⁸ CFU/ml of S. marcescens into the stem of squash (Cucurbita pepo) plants at the cotyledon growth stage reproducibly induced CYVD symptoms, whereas injecting 10⁶ or 10⁷ CFU/ml did not. Additionally, we found that S. marcescens induced symptoms on all of the squash cultivars tested, and induced symptoms that have not been previously reported, including stem elongation and leaf cupping. In short, through our injection approach of mimicking the natural process of S. marcescens transmission by squash bug feeding, we obtained robust and quantifiable CYVD symptoms. This laboratory bioassay provides a crucial tool for investigating the biology and pathology of this emerging pathogen and for plant breeding screens aimed at combatting CYVD.

Most Ralstonia solanacearum species complex strains cause bacterial wilts in tropical or subtropical zones, but the group known as race 3 biovar 2 (R3bv2) is cool virulent and causes potato brown rot at lower temperatures. R3bv2 has invaded potato-growing regions around the world but is not established in the United States. Phylogenetically, R3bv2 corresponds to a subset of the R. solanacearum phylotype IIB clade, but little is known about the distribution of the cool virulence phenotype within phylotype IIB. Therefore, genomes of 76 potentially cool virulent phylotype IIB strains and 30 public genomes were phylogenetically analyzed. A single clonal lineage within the sequevar 1 subclade of phylotype IIB that originated in South America has caused nearly all brown rot outbreaks worldwide. To correlate genotypes with relevant phenotypes, we quantified virulence of 10 Ralstonia strains on tomato and potato at both 22 and 28°C. Cool virulence on tomato did not predict cool virulence on potato. We found that cool virulence is a quantitative trait. Strains in the sequevar 1 pandemic clonal lineage caused the most disease, whereas other R3bv2 strains were only moderately cool virulent. However, some non-R3bv2 strains were highly cool virulent and aggressively colonized potato tubers. Thus, cool virulence is not consistently correlated with strains historically classified as the R3bv2 group. To aid in the detection of sequevar 1 strains, this group was genomically delimited in the LINbase web server, and a sequevar 1 diagnostic primer pair was developed and validated. We discuss implications of these results for the R3bv2 definition.

The choline–glycine betaine pathway plays an important role in bacterial survival in hyperosmotic environments. Osmotic activation of the choline transporter BetT promotes the uptake of external choline for synthesizing the osmoprotective glycine betaine. Here, we report the cryo–electron microscopy structures of Pseudomonas syringae BetT in the apo and choline-bound states. Our structure shows that BetT forms a domain-swapped trimer with the C-terminal domain (CTD) of one protomer interacting with the transmembrane domain (TMD) of a neighboring protomer. The substrate choline is bound within a tryptophan prism at the central part of TMD. Together with functional characterization, our results suggest that in Pseudomonas species, including the plant pathogen P. syringae and the human pathogen Pseudomonas aeruginosa , BetT is locked at a low-activity state through CTD-mediated autoinhibition in the absence of osmotic stress, and its hyperosmotic activation involves the release of this autoinhibition.

Plant−microbe interaction research has had a transformative trajectory, from individual microbial isolate studies to comprehensive analyses of plant microbiomes within the broader phytobiome framework. Acknowledging the indispensable role of plant microbiomes in shaping plant health, agriculture, and ecosystem resilience, we underscore the urgent need for sustainable crop production strategies in the face of contemporary challenges. We discuss how the synergies between advancements in ‘omics technologies and artificial intelligence can help advance the profound potential of plant microbiomes. Furthermore, we propose a multifaceted approach encompassing translational considerations, transdisciplinary research initiatives, public-private partnerships, regulatory policy development, and pragmatic expectations for the practical application of plant microbiome knowledge across diverse agricultural landscapes. We advocate for strategic collaboration and intentional transdisciplinary efforts to unlock the benefits offered by plant microbiomes and address pressing global issues in food security. By emphasizing a nuanced understanding of plant microbiome complexities and fostering realistic expectations, we encourage the scientific community to navigate the transformative journey from discoveries in the laboratory to field applications. As companies specializing in agricultural microbes and microbiomes undergo shifts, we highlight the necessity of understanding how to approach sustainable agriculture with site-specific management solutions. While cautioning against overpromising, we underscore the excitement of exploring the many impacts of microbiome−plant interactions. We emphasize the importance of collaborative endeavors with societal partners to accelerate our collective capacity to harness the diverse and yet-to-be-discovered beneficial activities of plant microbiomes.

Most Ralstonia solanacearum species complex strains cause bacterial wilts in tropical or subtropical zones, but the group known as Race 3 biovar 2 (R3bv2) is cool virulent and causes potato brown rot at lower temperatures. R3bv2 has invaded potato-growing regions around the world but is not established in the United States. Phylogenetically, R3bv2 corresponds to a subset of the R. solanacearum phylotype IIB clade, but little is known about the distribution of the cool virulence phenotype within phylotype IIB. Therefore, genomes of 76 potentially cool virulent phylotype IIB strains and 30 public genomes were phylogenetically analyzed. A single clonal lineage within the sequevar 1 subclade of phylotype IIB that originated in South America has caused nearly all brown rot outbreaks worldwide. To correlate genotypes with relevant phenotypes, we quantified virulence of ten Ralstonia strains on tomato and potato at both 22°C and 28°C. Cool virulence on tomato did not predict cool virulence on potato. We found that cool virulence is a quantitative trait. Strains in the sequevar 1 pandemic clonal lineage caused the most disease, while other R3bv2 strains were only moderately cool virulent. However, some non-R3bv2 strains were highly cool virulent and aggressively colonized potato tubers. Thus, cool virulence is not consistently correlated with strains historically classified as R3bv2 group. To aid detection of sequevar 1 strains, this group was genomically delimited in the LINbase web server and a sequevar 1 diagnostic primer pair was developed and validated. We discuss implications of these results for the R3bv2 definition.